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Unexpected high levels of genetic variability and the population structure of an island endemic rodent (Oryzomys couesi cozumelae)
Abstract
Oryzomys couesi cozumelae is an endemic, threatened rodent from Cozumel Island, Mexico. We estimated its genetic diversity and structure by analyzing microsatellite loci in 228 samples from 12 sampling sites widely distributed throughout the island. Unexpected high levels of genetic and allelic diversity were found: a total of 54 alleles, an average of 10.8 alleles per locus, and high heterozygosity values (mean HO = 0.624, HE = 0.690 and HNei = 0.689). These values are higher than those reported for small sized insular mammals, higher than that found in 37 individuals of the mainland O. couesi from southern Mexico (HO = 0.578) that we analyzed for comparative purposes, and similar to those of other mainland small mammal populations. Despite factors that affect Cozumel’s biota, such as exotic predators and competitors, hurricanes, seasonal population fluctuations and anthropogenic activities, no evidence of genetic bottlenecks was found. A significant population structure was observed and a model of isolation-by-distance was supported. Our findings render O. c. cozumelae a high conservation value, not only for its high genetic diversity and structure, but because available data suggests that its population has declined significantly in recent years. Further habitat fragmentation and population isolation could result in a higher genetic structure and loss of genetic diversity. The protection of habitat, the maintenance of habitat connectivity and the removal of introduced competitors and predators are a conservation priority. Acknowledging that the genetic structure of populations has crucial conservation implications, the present genetic information should be taken into account in management plans for the conservation of O. c. cozumelae.
... Despite the fact that the Couesi's rice rat, O. couesi, has a wide distribution and has abundant populations at some sites, it has been little studied ecologically and genetically (Vega et al. 2007;Vázquez-Domínguez et al. 2009;Gutiérrez-García 2013). Hence, this is the first study evaluating the rangewide microsatellite phylogeography of O. couesi, identifying geographic differentiated genetic clusters, together with a novel ecological niche modeling approach to evaluate the potential current and future distribution of the species' distinct genetic clusters. ...
... It is notable that although we had a relatively small sample size-considering the wide distribution evaluated-the genetic variability found is within that reported for other populations, which suggests that populations throughout the species range have maintained adequate levels of genetic diversity. The AMOVA results corroborate the latter, where the majority of the genetic variability is significantly distributed within individuals (80.7%), while when smaller, localized distributions have been evaluated, the distribution of the genetic variability has been identified within populations (Vega et al. 2007;Vázquez-Domínguez et al. 2009). Our findings also demonstrate that O. couesi is genetically structured as four distinct genetic clusters, distributed along both the Pacific (Pacific north and Pacific south) and the Atlantic (Gulf and Cozumel) coasts (Fig. 2), and with significant high differentiation levels among them. ...
... Notably, the Gulf cluster is the widest distributed one, encompassing several provinces from northern Mexico throughout Central America to the southern limit distribution of the species in Colombia. The Cozumel group is highly differentiated, which is not surprising considering that this island population has previously been shown to have significant levels of genetic differentiation from the adjacent mainland populations (Vega et al. 2007). ...
The different life forms on Earth are distributed in a non-random fashion, resulting from a diverse array of events during the Earth’s history that has governed the spatial and temporal distribution of species. Anthropogenic activities have produced changes in global climate and land use that have affected, and will continue to impact, the distribution of biodiversity. Here, we aimed to estimate the genetic diversity and structure of the Couesi’s rice rat Oryzomys couesi, a rodent with a distribution that extends across the Neartic and the Neotropical biogeographic zones in Mexico and Central America, to evaluate the species rangewide microsatellite phylogeography and identify geographic differentiated genetic clusters. We also determined both the current and the potential (under different climate change scenarios) distribution of the identified clusters. Our findings show that O. couesi is genetically structured as four distinct genetic clusters, distributed along both the Pacific and the Atlantic coasts, with high levels of genetic diversity. The Sierra Madre Oriental, Sierra Madre Occidental and Trans-Mexican Volcanic belt are key features associated with the historic dispersal and differentiation of these groups. O. couesi is negatively affected by the climate change projections of its potential future distribution, where the identified clusters lose 7.5–45.1% of their original distribution area. Furthermore, when based on land cover corrections, results show more drastic reductions in which genetic clusters are projected to maintain only a fraction of the area with suitable land cover conditions. In reality, under such scenarios, with extremely reduced and fragmented distributions, these clusters would undoubtedly go extinct. We recommend that suitable potential areas should be conserved and those not currently suitable should be considered as priority areas for restoration, while significantly reducing climate change emissions needs to be of the highest priority.
... Although the island retains much of its natural vegetation, in recent years serious threats such as exotic species, hurricanes and habitat fragmentation have jeopardized its native biota (Walton 2004;Cuarón et al. 2009). Three endemic rodent species inhabit Cozumel, Oryzomys couesi cozumelae, Reithrodontomys spectabilis and Peromyscus cozumelae, although the latter is probably extinct (Vega et al. 2007;Fuentes-Montemayor et al. 2009). We have gathered, through the long-term study of their populations, detailed information about the ecology and demography of the former two species (Fortes-Corona 2004;Fuentes-Montemayor et al. 2009;Vázquez-Domínguez et al. 2012), although the population genetics has only been studied for O. c. cozumelae (Vega et al. 2007;Sunny 2010). ...
... Three endemic rodent species inhabit Cozumel, Oryzomys couesi cozumelae, Reithrodontomys spectabilis and Peromyscus cozumelae, although the latter is probably extinct (Vega et al. 2007;Fuentes-Montemayor et al. 2009). We have gathered, through the long-term study of their populations, detailed information about the ecology and demography of the former two species (Fortes-Corona 2004;Fuentes-Montemayor et al. 2009;Vázquez-Domínguez et al. 2012), although the population genetics has only been studied for O. c. cozumelae (Vega et al. 2007;Sunny 2010). ...
... Intensive fieldwork was done throughout the island between September 2001 and January 2005, during which we systematically performed trapping sessions with Sherman and other kinds of traps, as a part of an ongoing study on the ecology, evolution, genetics and conservation of the Cozumel biota (e.g. Cuarón et al. 2004Cuarón et al. , 2009Romero-Nájera et al. 2007;Vega et al. 2007;Vázquez-Domínguez et al. 2012). In each site, we placed two quadrants, each with 49 Sherman live traps separated by approximately 8.5 m from each other in a 7 9 7 trap-grid arrangement. ...
We assessed the genetic structure and diversity of Reithrodontomys spectabilis, a critically endangered, endemic rodent from Cozumel Island, México. A total of 90 individuals were trapped from September 2001 to January 2005. Microsatellite data analysis revealed high genetic diversity values: a total of 113 alleles (average 12.5 per locus), H
o
= 0.78, H
e
= 0.80. These high values can be related to Cozumel’s size (478 km2) and extensive native vegetation cover, factors that could be promoting a suitable population size, high heterozygosity and the persistence of rare alleles in the species, as well as some long-term movement of individuals between sampling localities. A strong genetic structure was also observed, with at least four genetic groups, associated with a pattern of isolation by distance. We found a strong allelic and genetic differentiation shown between localities, with negligible recent gene flow and low inbreeding coefficients. The species life history and ecological characteristics—being nocturnal, semi-terrestrial, a good tree climber, having lunar phobia and significant edge effect—are likely affecting its genetic structure and differentiation. The high genetic diversity and population structure award R. spectabilis a significant conservation value. Our results can serve as a basis for future research and conservation of the species, particularly considering the problems the island is facing from habitat perturbation, urbanization and introduction of exotic species. In view of the structure and genetic variability observed, it is essential to establish and reinforce protected areas and management programs for the conservation of the endemic and endangered Cozumel Harvest mice.
... La variación genética se genera, básicamente, a través de la mutación y del flujo génico, y se pierde debido a la deriva génica o a la selección natural (Frankham 1997; Amos y Harwood 1998). Las islas son de importancia prioritaria para la conservación de la biodiversidad, ya que constituyen ecosistemas con altos niveles de endemismos (MacArthur y Wilson 1967; Grant 1998; Vega et al. 2007) y, en general, los organismos que habitan islas presentan poca variabilidad genética (Frankham 1997). Las islas se consideran un laboratorio para estudiar procesos evolutivos (Mayr 1963;) ya que, al existir poco o nulo flujo génico, los organismos evolucionan rápidamente a través de deriva génica y selección natural (Barton 1998; Abdelkrim et al. 2005). ...
... Las islas se consideran un laboratorio para estudiar procesos evolutivos (Mayr 1963;) ya que, al existir poco o nulo flujo génico, los organismos evolucionan rápidamente a través de deriva génica y selección natural (Barton 1998; Abdelkrim et al. 2005). Dadas las condiciones particulares de limitación de área, aislamiento, bajo número de especies, extinciones locales, dispersión y colonización, las islas presentan diversos problemas de conservación (Eldridge et al. 2004; Vega et al. 2007). Como resultado de dichas condiciones, las poblaciones isleñas tienen mayores tasas de extinción en comparación con sus contrapartes continentales (Vitousek 1988; Case et al. 1992; Smith et al. 1993; Frankham 1997 Frankham , 1998). ...
... La descripción de resultados que se presenta en esta segunda parte implica la comparación de los datos genéticos de la población posthuracanes (85 individuos analizados en el presente trabajo) y aquellos de la población prehuracanes (Vega et al. 2007), pero considerando sólo los cinco alelos evaluados por Vega y colaboradores. Así, y para fines de poder hacer análisis comparativos, es que se repiten los análisis descritos en la primera parte, aunque aquí sólo con cinco loci. ...
Se evaluó la estructura y diversidad genética de Oryzomys couesi cozumelae para determinar si existían cambios en sus niveles de variabilidad genética y diferenciación entre poblaciones, resultado de la disminución de las poblaciones consecuencia de los huracanes Emily y Wilma del 2005 en isla Cozumel, Quintana Roo. Su calidad de especie isleña favorece la pérdida de diversidad genética y con ello el potencial incremento de la endogamia, en particular asociado a fenómenos naturales como huracanes. Se analizaron 85 individuos con nueve loci de microsatélites (población posthuracanes); para la comparación con los datos previos a los huracanes (población prehuracanes), se analizaron 228 individuos y se consideraron sólo los cinco loci reportados por Vega et al. (2007). Ambas poblaciones presentan altos niveles de diversidad genética y alélica, aunque la población posthuracanes muestra una tendencia a disminuir, no se encontró una diferencia significativa, posiblemente porque no ha pasado el suficiente tiempo para que los cambios sean evidentes y detectables genéticamente.
El éxito de captura posthuracanes fue mucho menor que el que se tenía en muestreos equivalentes antes de los huracanes, y también en una ubicación distinta de los organismos, además la población prehuracanes estaba estructurada y la posthuracanes se homogenizó perdiendo la estructura previamente detectada, posiblemente con el paso del tiempo y el aumento del número de individuos, la estructuración podría reflejarse de nuevo.
The present study was performed to evaluate the genetic structure of the population of an endemic rodent Oryzomys couesi cozumelae to determinate a possible change in their diversity and genetic structure as a result of a reduction in their populations after the Impact of the hurricanes Emily and Wilma in Cozumel Island. The island populations are much more prone to loss of genetic diversity and a potential increase inbreeding than their mainland populations, and a natural phenomena such as hurricanes increases this risk. The DNA was obtained from 85 individuals and the analysis was conducted using nine microsatellite loci (prehurricane population); for the comparison analysis with the previous prehurricane data we used 5 microsatellite loci and 228 DNA samples reported for Vega et al. (2007). The post and pre hurricane populations have a high level of genetic and allelic diversity, although the data of the posthurricane population are showing a reducing tendency; the no significant difference between the two populations is possibly because not enough time has passed to detect a genetic differences.
The capture success was lower and in a different location after the hurricanes, the pre-hurricane population was clearly structured, the post-hurricane population losses the structure and now are homogenized, maybe with the passage of time and a increase number of individuals, the structure could be reflected again.
... At the same time, insular populations and species are extremely vulnerable and have, in comparison with their continental counterparts, a high susceptibility of extinction (Frankham, 1998;Vázquez-Domínguez et al., 2004;Fleming and Murray, 2009). Oceanic islands, which have never been in contact with the mainland, are characterized by high levels of endemism of fauna and flora, generally associated with the genetic differentiation of populations after their establishment from a reduced number of mainland migrants (Frankham, 1997;Grant, 1998;Vega et al., 2007). A variety of genetic factors affect island populations: as isolated populations, they experience loss of genetic and allelic variability, genetic bottlenecks, inbreeding, changes in selective pressures or a combination of these. ...
... Cozumel's size (478 km 2 ) and extensive native vegetation cover are factors that could be promoting a suitable population size in A. jamaicensis. Also, the species' dispersal abilities result in high movement of individuals across the island and, potentially, between the mainland and the island as documented for other Artibeus species (Pumo et al., 1988), factors that could be promoting high heterozygosity and the persistence of rare alleles, as observed for the Cozumel endemic rodent Oryzomys couesi cozumelae (Vega et al., 2007). High levels of structure and significant correlation between geographic and genetic distances have been identified in a variety of bat species, in continental (Burland et al., 1999;Worthington Wilmer et al., 1999;Maharadatunkamsi et al., 2000) and island populations (Juste et al., 2000). ...
... In addition, with genetic information based on mitochondrial DNA we could evaluate historical diversity changes, levels of gene flow between island and continent and the origin of migrants. The present genetic information is of great value and can serve as the basis for future research and conservation of this species, particularly considering the evolutionary forces at play on Cozumel and the conservation problems the island is facing from habitat perturbation, urbanization and introduction of exotic species (for examples see Vega et al., 2007;Cuarón et al., 2009;Fuentes-Montemayor et al., 2009;Vázquez-Domínguez et al., 2012). Bat species that form small groups and have temporal roosting sites, like A. jamaicensis on Cozumel, are highly susceptible to landscape-scale perturbations (Rossiter et al., 2012). ...
Islands and insular biotas have been recognized as ideal models for studying adaptive radiations and evolutionary processes. In the present study we investigated the Jamaican fruit-eating bat, Artibeus jamaicensis from Cozumel Island, to evaluate the effect of ecological features on genetic diversity and structure across three different environments, semi-evergreen tropical forest, mangrove, and cenotes, using six microsatellite loci in 105 individuals. Genetic diversity was relatively high (forest HO = 0.693, HNei = 0.825; mangrove HO = 0.702, HNei = 0.710; cenotes HO = 0.695, HNei = 0.847). Pairwise genetic differentiation measures between localities were not significant and the overall level of differentiation was markedly low (FST = 0.009, G’ST = 0.088). Likewise, results showed that A. jamaicensis consists of one genetic group and relatedness among individuals was low. Results are concordant with our predictions that the island population will show high genetic diversity and null structure at the fine spatial scale examined. We conclude that ecological features like dispersal and generalist habits are the factors influencing population structure and genetic diversity of A. jamaicensis on the island, and that factors like the species polygynous mating system, female philopatry and male differential dispersal do not prevail in the island population. Cozumel Island is facing severe conservation problems, mainly from habitat perturbation, urbanization and introduction of exotic species, hence the present genetic information is of great value as a basis for future research and protection of the species.
... This is particularly relevant for endemic insular biotas, which have naturally depauperate communities . On islands, species are vulnerable to extinction due to geographical isolation, reduced population size and reduced genetic diversity (Frankham 1998; MacPhee & Flemming 1999; Vega et al. 2007), and greater exposure to natural (e.g. hurricanes) and anthropogenic (e.g. ...
... O. c. cozumelae is mainly terrestrial, but it is also a good swimmer and climber. It has low population numbers ( ca. 14·5 ind ha –1 ; Fortes-Corona 2004) and high genetic and allelic diversity (Vega et al. 2007). It is currently classified as 'Threatened' by Mexican legislation (Semarnat 2002 ). ...
... We live-trapped rodents from July 2001 to March 2003, monthly or bimonthly (except April–July 2002), during three nights per site, as part of an ongoing study on the ecology, evolution, genetics and of the Cozumel biota (Martínez-Morales & Cuarón 1999; Cuarón et al. 2004; Romero-Nájera et al . 2006; Vega et al. 2007). We used 16 sampling plots (eight plots each in axes 6 and 8;Fig. ...
Roads may affect wildlife populations through habitat loss and disturbances, as they create an abrupt linear edge, increasing the proportion of edge exposed to a different habitat. Three types of edge effects have been recognized: abiotic, direct biotic, and indirect biotic.
We explored the direct biotic edge effects of 3‐ to 4‐m wide roads, and also a previously unrecognized type of edge effect: social. We live‐trapped two threatened endemic rodents from Cozumel Island ( Oryzomys couesi cozumelae and Reithrodontomys spectabilis ) in 16 plots delimited by roads on two sides, to compare edge effects between two adjacent edges (corners), single‐edge and interior forest, on life history and social variables.
No significant edge effects were observed on the life‐history variables, with the exception of differences in body condition between males and females of O. c. cozumelae near edges. Both species showed significant and contrasting effects on their social variables.
O. c. cozumelae was distributed according to its age and sex: the proportion of adults and males was higher in interior than near edges, while juveniles and females were more abundant near edges. More nonreproductive females were present in corners than in single‐edge and interior, while the opposite distribution was observed for nonreproductive males.
The distribution of R. spectabilis was related to its age and reproductive condition, but not to its sex. The proportion of adults was significantly higher in corners, while juveniles were only caught in single‐edge and interior quadrants. The proportion of reproductive individuals was higher in edge than interior quadrants, while reproductive females were only present in edge quadrants.
We found significant differences between the quadrants with the greatest edge exposure in comparison with other quadrants. The social edge effects we identified complement the typology of edge effects recognized in ecological literature. Our study provides insight into the effects that sharp road edges have on biological and social characteristics of small mammal populations, highlighting how such effects vary among species. Our findings have important conservation implications for these threatened species, but are also applicable in a broader context wherever there are abrupt edges caused by linear landscape features.
... Cozumel is the largest of the Mexican Caribbean islands and has the highest number of endemics (31 taxa), including among mammals two carnivores (Procyon pygmaeus and Nasua nelsoni) and three rodents (Oryzomys couesi cozumelae, Reithrodontomys spectabilis, and Peromyscus leucopus cozumelae; the latter potentially extinct) (Vega et al. 2007;Cuarón 2009;Fuentes-Montemayor et al. 2009;Espindola et al. 2014;Flores-Manzanero et al. 2022). Nearly 75% of the island's surface is covered with native vegetation (Cuarón 2009). ...
... Importantly, the significant association we identified of the house mouse with impervious surfaces likely limits the chances of a secondary invasion to natural environments. We highlight that in our studies of rodent population ecology and genetics on Cozumel, performed in natural vegetation and conserved areas over many years, we have not trapped black rats nor house mice (see Vega et al. 2007;Fuentes-Montemayor et al. 2009;Espindola et al. 2014). Whether these invasive rodents are indeed absent from natural areas or present in low abundance is not clear. ...
Humans and wildlife experience complex interactions in urban ecosystems, favoring the presence of commensal species, among which invasive species are particularly successful. Rodents are the main vertebrate group introduced to oceanic islands, where the invasion process and dispersal patterns strongly influence their evolutionary and genetic patterns. We evaluated the house mouse Mus musculus and the black rat Rattus rattus on Cozumel Island, Mexico. We assessed genetic diversity and structure, connectivity, gene flow, relatedness and bottleneck signals based on microsatellite loci. Our genetic findings suggest that introduction of individuals of different geographic sources to the island promotes high allelic diversity and the effective establishment of migrants. We identified a clear genetic structure and low connectivity for the two species, tightly linked with anthropogenic and urban features. Notably, we found that the genetic structure of the house mouse sampled within the city of San Miguel Cozumel is associated with the historical human population growth pulses accompanying the urbanization of the city. At the fine-scale genetic level, the main urban drivers of connectivity of the house mouse were both the impervious land surfaces, i.e. the urban landscape, and the informal commerce across the city (a proxy of resources availability). Chances of a secondary invasion to natural environments have been relatively low, which is crucial for the endemic taxa of the island. Nonetheless, improving urban planning to regulate future expansions of San Miguel Cozumel is of the outmost importance to prevent these invasive species to disperse further.
... Islands are ideal natural systems in which to address questions about population genetics and evolution (Robertson et al. 2014), mainly due to their particular features like geographic isolation and small area, where species commonly have low population sizes and exhibit unique dispersal and colonization processes (Allendorf and Luikart 2007;Hinten et al. 2003). Oceanic islands in particular harbor a unique biota and high endemism, associated with genetic differentiation of populations after their establishment from a reduced number of mainland migrants (Eldridge et al. 2004;Grant 1998;Vega et al. 2007). In consequence, island populations frequently face detrimental genetic processes like bottlenecks, drift and inbreeding (Frankham 1997(Frankham , 1998Hinten et al. 2003), which makes them highly susceptible to extinction in comparison with their mainland counterparts. ...
... Such pattern has been observed in island mammal species like rodents (Almeida et al. 2005;Hinten et al. 2003), carnivores (Kurose et al. 2001;Moncrief et al. 2017) and endemic marsupials (Eldridge et al. 2004). This is also true for both the pygmy raccoon Procyon pygmaeus and the dwarf coati Nasua nelsoni, which exhibited moderate levels of nuclear genetic diversity (H o = 0.485; H E = 0.513 and H o = 0.478; H E = 0.535, respectively), similar to other mammals from the island like the rodents Oryzomys couesi cozumelae (Vega et al. 2007) and Reithrodontomys spectabilis (Espindola et al. 2014). As expected for island populations, they have lower genetic variability in comparison with their mainland congeneric species. ...
Genetic diversity is crucial for conservation biology and for understanding evolutionary processes. Oceanic islands harbor a unique biota and high endemism, with populations frequently facing detrimental genetic processes (e.g. drift, bottlenecks). Human activities like habitat transformation further increase extinction risk of insular biota. Mammals comprise the most endangered group among insular fauna. Our aim was to evaluate the genetic and evolutionary patterns of two critically endangered dwarf carnivores from Cozumel Island, the pygmy raccoon (Procyon pygmaeus) and the dwarf coati (Nasua nelsoni), at both historical and contemporary evolutionary scales. We also reviewed their genetic relationships with their mainland counterparts (P. lotor, N. narica), not intended to describe their phylogeny but to ascertain their endemism. Our mitochondrial results support that both Cozumel carnivores are divergent from continental populations, strengthening their endemic status. Both species showed moderate levels of nuclear genetic diversity that were, as expected for island populations, lower in comparison with their mainland congeneric species; they also exhibited significantly low population sizes. We documented historical and contemporary bottleneck signals for P. pygmaeus, whereas N. nelsoni may be suffering the initial stages of a bottleneck not yet fully manifested. The pygmy raccoon is structured into two isolated genetic clusters likely due to interactions with humans on the north of the island, where most potential for disease transmission and health problems exist. We also add evidence about the introduction of the mainland species into the island, risking genetic introgression and hybridization. We discuss specific conservation measures that should include our genetic information, directed to the long-term viability of these endemic carnivores.
... Studies focusing on the intra-island genetic structures of small islands (<500 km 2 ) have been rare. A genetic structure analysis of endemic rodents on Cozumel Island, Mexico (Vega et al. 2007, Espindola et al. 2014) and phylogenetic studies among islands (Hinten et al. 2003, Salgueiro et al. 2004) have suggested that population subdivisions (e.g., Wahlund effect) and discontinuity of haplotype distributions may occur within an island, though intra-island genetic structures have not been well studied. ...
... among populations 1.17-26.19 km apart; Vega et al. 2007). Such small-scale differentiation was not detected in other genetic studies in Leporidae species with nuclear microsatellite data, including the snowshoe hare (Lepus americanus; F ST ¼ 0.000-0.243 ...
Population fragmentation can reduce genetic diversity and increase the extinction risk of island endemic mammals, especially those with low dispersal ability. However, the intra‐island genetic structure and demographic history of mammals have not yet been well evaluated, especially on small geographic scales. We performed a genetic analysis of isolated island populations of the Amami rabbit (Pentalagus furnessi) on Tokunoshima Island using mitochondrial D‐loop region sequences and 8 nuclear microsatellite markers. Using data from fecal samples, we detected 2 genetic groups that corresponded with the northern and southern forested areas of the island based on the mitochondrial and nuclear genomes. We detected some admixture between the 2 groups in the nuclear genomes but did not detect gene flow between the 2 groups in the mitochondrial genomes. Although genetic diversity was higher in the southern population than in the northern population, the fixation index showed higher levels of inbreeding in the southern area with a signal of a recent bottleneck. We inferred the divergence time between the northern and southern groups (∼4,320 years ago) using approximate Bayesian computations. These genetic structure patterns may have been generated by a combination of the demographic history of the species in relation to the geology of the island, human activities in the stone age, deforestation due to sugar plantations (beginning approximately 300 years ago), and recent human activities. This study highlights the importance of considering genetic structure in relation to complex factors within a single‐island habitat for appropriate genetic management of endemic mammals on islands. © 2018 The Wildlife Society.
... With no natural enemies, B.c. imperator has become a keystone generalist predator (Romero-Nájera et al. 2007), and its presence has been directly linked to the collapse of populations of diverse native species, many of them endemic to Cozumel (e.g. Cuarón et al. 2004Cuarón et al. , 2009Fuentes-Montemayor et al. 2009;Martínez-Morales and Cuarón 1999;Martínez-Morales et al. 2009;Vega et al. 2007). Although the ecology (e.g. ...
... approximately eight generations), it has become a successful top predator with no natural enemies other than humans (Romero-Nájera et al. 2007). It is important to highlight that the time frame over which the sharp population decline and, in some cases virtual extinction of endemic taxa, like the rodent Peromyscus leucopus cozumelae and the Cozumel Thrasher Toxostoma guttatum, has occurred (Cuarón 2009;Cuarón et al. 2004Cuarón et al. , 2009Cuarón et al. unpublished data;Fuentes-Montemayor et al. 2009;Martínez-Morales et al. 2009;McFadden et al. 2010;Perdomo 2006;Vega et al. 2007), is directly correlated with the introduction of the boa onto Cozumel. During this time however, substantial feral populations of non-native predator species and potential competitors have also established on Cozumel, namely cats (Felis catus) and dogs (Canis familiaris) (Cuarón et al. 2004Martínez-Morales et al. 2009;Mena 2007;Torres Villegas 2006), as well as house rats (Rattus rattus) and mice (Mus musculus) (Sotomayor 2009), which also have contributed to the collapse of endemic species populations. ...
Only one study has described the population genetic structure of Boa constrictor imperator and only in a single naturally colonized island. B.c. imperator, a snake with a naturally wide distribution across the Neotropics, was introduced to Cozumel Island, Mexico, in 1971. At present, it is one of the most abundant, widely distributed, terrestrial vertebrate on the island. We analysed the genetic diversity and structure, based on seven microsatellite loci, of 76 individuals of B.c. imperator from Cozumel. We also included 96 samples from different localities across mainland Mexico, to review the potential origin of the founder individuals. We identified two genetically differentiated populations on Cozumel that showed moderate levels of genetic diversity (H
o
= 0.590–0.620), with a low but significant level of genetic structure (F
ST
= 0.032). Individuals were highly unrelated (71 %) and the majority of genetic variation was distributed within individuals (84 %). We detected a signal of reduction in population size and evidence of genetic bottleneck. The genetically closest mainland populations, indicating potential source of island founders, are localities from the Gulf of Mexico and Yucatan peninsula. Results are in agreement with a recently introduced population, founded by a few individuals originating from several sources, which has been successful. B.c. imperator is jeopardizing a highly vulnerable insular ecosystem, hence its eradication from Cozumel is urgently needed. Our information is also valuable for other introduced-boa cases or as a basis for its conservation elsewhere given its classification as a threatened species.
... However, counter-examples exist such as of Oryzomys couesi cozumelae or Reithrodontomys spectabilis, both endemic rodents on the island of Cozumel, the largest island of the Mexican Caribbean (with an area of c. 486 km 2 ). These species exhibited unexpectedly high levels of genetic diversity (Vega et al. 2007;Espindola et al. 2014). Indeed, genetic diversity is known to be influenced by island size, with larger islands able to harbour a larger number of individuals (Frankham 1997). ...
Mus cypriacus is one of three small palaeoendemic mammals that have survived the Mediterranean islands' anthropization. This species, endemic to Cyprus, was described in 2006 and stands out as one of the last mammal species to have been discovered in Europe. Despite scarce data on its genetics, ecology, and life-history traits, Mus cypriacus is assessed as Least Concern LC in the IUCN Red List, partly due to its morphological similarity with the sympatric house mouse that prevented earlier identification. Our study uses mitochondrial and microsatellite markers to investigate this small rodent's population genetic structure and diversity. Our analysis did not identify any population genetic structure and suggested a high genetic diversity across Cyprus. When inferring habitat preference using sample locations, it appeared that M. cypriacus utilizes a diverse variety of habitats, covering more than 80% of the island. Although these results are encouraging for the conservation status of the species, they still need to be cautiously applied as potential threats may arise due to increasing habitat destruction and changes in land use. Consequently, our encouraging results should be applied judiciously. Additional ecological data are urgently needed to gain a more comprehensive understanding of this inconspicuous endemic species.
... However, this structure was too weak to be detected with our sampling strategy (spatially dispersed individuals) and the clustering analysis. Several other genetic studies in rodents also find low population structure even in the presence of major landscape barriers or considerable landscape heterogeneity (Gauffre et al., 2008;Vega et al., 2007). This is likely because irruptive boom-bust population dynamics obscure any signals of population structure. ...
Landscape genetics is increasingly transitioning away from microsatellites, with Single Nucleotide Polymorphisms (SNPs) providing increased resolution for detecting patterns of spatial-genetic structure. This is particularly pertinent for research in arid-zone mammals due to challenges associated with unique life history traits, boom-bust population dynamics and long-distance dispersal capacities. Here, we provide a case study assessing the performance of SNPs versus microsatellites in evaluating three explicit landscape genetic hypotheses (isolation-by-distance, isolation-by-barrier, and isolation-by-resistance) in a suite of small, arid-zone mammals in the Pilbara region of Western Australia. Using clustering algorithms, Mantel tests, and linear mixed effects models, we compare functional connectivity between genetic marker types and across species, including one marsupial, Ningaui timealeyi, and two native rodents, Pseudomys chapmani and P. hermannsburgensis. SNPs resolved subtle genetic structuring not detected by microsatellites, particularly for N. timealeyi where two genetic clusters were identified. Furthermore, stronger signatures of isolation-by-distance and isolation-by-resistance were detected when using SNPs, and model selection based on SNPs tended to identify more complex resistance surfaces (i.e., composite surfaces of multiple environmental layers) in the best-performing models. While we found limited evidence for physical barriers to dispersal across the Pilbara for all species, we found that topography, substrate, and soil moisture were the main environmental drivers shaping functional connectivity. Our study demonstrates that new analytical and genetic tools can provide novel ecological insights into arid landscapes, with potential application to conservation management through identifying dispersal corridors to mediate the impacts of ongoing habitat fragmentation in the region.
... However, this structure was too weak to be detected with our sampling strategy (spatially dispersed individuals) and the clustering analysis. Several other genetic studies in rodents also find low population structure even in the presence of major landscape barriers or considerable landscape heterogeneity (Gauffre, Estoup, Bretagnolle, & Cosson, 2008;Vega, Vázquez-Domínguez, Mejía-Puente, & Cuarón, 2007). This is likely because irruptive boom-bust population dynamics obscure any signals of population structure. ...
Landscape genetics is increasingly transitioning away from microsatellites, with Single Nucleotide Polymorphisms (SNPs) providing increased resolution for detecting patterns of spatial-genetic structure. This is particularly pertinent for research in arid-zone mammals due to challenges associated with unique life history traits, boom-bust population dynamics and long-distance dispersal capacities. Here, we provide a case study assessing the performance of SNPs versus microsatellites in evaluating three explicit landscape genetic hypotheses (isolation-by-distance, isolation-by-barrier, and isolation-by-resistance) in a suite of small, arid-zone mammals in the Pilbara region of Western Australia. Using clustering algorithms, Mantel tests, and linear mixed effects models, we compare functional connectivity between genetic marker types and across species, including one marsupial, Ningaui timealeyi , and two native rodents, Pseudomys chapmani and P. hermannsburgensis . SNPs resolved subtle genetic structuring not detected by microsatellites, particularly for N. timealeyi where two genetic clusters were identified. Furthermore, stronger signatures of isolation-by-distance and isolation-by-resistance were detected when using SNPs, and model selection based on SNPs tended to identify more complex resistance surfaces (i.e., composite surfaces of multiple environmental layers) in the best-performing models. While we found limited evidence for physical barriers to dispersal across the Pilbara for all species, we found that topography, substrate, and soil moisture were the main environmental drivers shaping functional connectivity. Our study demonstrates that new analytical and genetic tools can provide novel ecological insights into arid landscapes, with potential application to conservation management through identifying dispersal corridors to mediate the impacts of ongoing habitat fragmentation in the region.
... One potential reason for differing results among systems-and for empirical deviations from theoretical expectations-is that insular populations can differ drastically from each other in a variety of factors influencing GD. These factors can include different evolutionary histories, effective population size, selection pressures, and demographic histories, which can lead to vastly different contemporary genetic structures (Frankham, 1995(Frankham, , 1996Kuo & Janzen, 2004;Luna et al., 2007;Vega et al., 2007). Another important consideration is the extent to which populations are at or near demographic equilibrium. ...
We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Using populations from within the same studies, we were able to control for between‐study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen—particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non‐insular populations of the same study system—suggesting an important role for the “scope” of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices. We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Contradictory to typical expectations, we found that insularity had relatively minor effects on GD within and among populations, which points to the more important roles of other factors in shaping evolutionary processes. Our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.
... On the American continent, particularly in Mexico, phylogeography has been used to study populations of wild fauna, especially endemic mammals, or those sought by hunters, or those included in some category of risk, leading to important implications for their conservation (Vázquez-Domínguez 2005;Vega et al. 2007;Vázquez-Domínguez et al. 2009;Escobedo-Morales et al. 2016). There is evidence that phylogeographic studies have had a considerable impact on species management (Vázquez-Domínguez and Vega 2002), especially in the ungulates, describing cervid lineages in order to define particular strategies of management (Serna-Lagunes et al. 2021), identifying bottlenecks and low gene flow in species of interest to hunters (Castillo-Rodríguez et al. 2020) and evidence of genetic divergence among lineages of the same species (Fuentes-Hurtado et al. 2011). ...
Anthropogenic threats have increasingly isolated the populations of Mazama temama (Erxleben, 1777) and limited the gene flow in this species. Knowledge of the phylogeographic structure of this species is therefore essential for its conservation. Thus, in this study, we describe the phylogeographic structure of two M. temama populations of Veracruz and Oaxaca, Mexico. We sequenced the D-Loop region of the mitochondrial DNA of 16 individuals, in order to estimate the diversity and genetic differentiation ( F ST ), Tajima’s D index, "Mismatch distribution" test; a phylogram and a haplotype network was constructed and we performed multidimensional scaling analysis to test the hypothesis of association between geographic distance and genetic diversity. The haplotypic and nucleotide diversity was high, indicating divergent populations ( F ST = 0.223), while the Tajima’s D index (-1,03300; P > 0.10) determined disequilibrium in the D-Loop region, derived from a population expansion that was evidenced in the "Mismatch distribution" test and confirmed with the haplotype network in the form of a star. Four lineages were identified in the phylogram (Veracruz n = 3, Oaxaca n = 1), evidencing geographic and reproductive isolation between the two populations. This was confirmed by the multidimensional scaling analysis, which evidenced recent evolutionary divergence between the populations analyzed, which are considered evolutionary units of conservation.
... On the American continent, particularly in Mexico, phylogeography has been used to study populations of wild fauna, especially endemic mammals, or those sought by hunters, or those included in some category of risk, leading to important implications for their conservation (Vázquez-Domínguez 2005;Vega et al. 2007;Vázquez-Domínguez et al. 2009;Escobedo-Morales et al. 2016). There is evidence that phylogeographic studies have had a considerable impact on species management (Vázquez-Domínguez and Vega 2002), especially in the ungulates, describing cervid lineages in order to define particular strategies of management (Serna-Lagunes et al. 2021), identifying bottlenecks and low gene flow in species of interest to hunters (Castillo-Rodríguez et al. 2020) and evidence of genetic divergence among lineages of the same species (Fuentes-Hurtado et al. 2011). ...
Citation: Serna-Lagunes R, Romero-Ramos DK, Delfín-Alfonso CA, Salazar-Ortiz J (2021) Phylogeography of the Central American red brocket, Mazama temama (Artiodactyla, Cervidae) in southeastern Mexico. Neotropical Biology and Conservation @(@): 1-@. https://doi.
Abstract
Anthropogenic threats have increasingly isolated the populations of Mazama temama (Erxleben 1777) and limited the gene flow in this species. Knowledge of the phylogeographic structure of this species is therefore essential for its conservation. Thus, in this study, we describe the phylogeographic structure of two M. temama populations of Veracruz and Oaxaca, Mexico. We sequenced the D-Loop region of the mitochondrial DNA of 16 individuals, in order to estimate the diversity and genetic differentiation (F ST), Tajima's D index, Mismatch distribution test; a phylogram and a haplotype network was constructed and we performed multidimensional scaling analysis to test the hypothesis of association between geographic distance and genetic diversity. The haplotypic and nucleotide diversity was high, indicating divergent populations (F ST = 0.223), while the Tajima's D index (-1,03300; P > 0.10) determined disequilibrium in the D-Loop region, derived from a population expansion that was evidenced in the Mismatch distribution test and confirmed with the haplotype network in the form of a star. Four lineages were identified in the phylogram (Veracruz n = 3, Oaxaca n = 1), evidencing geographic Neotropical Biology and Conservation @(@): 1-@ (2021) Ricardo Serna-Lagunes et al. 2 and reproductive isolation between the two populations. This was confirmed by the multidimensional scaling analysis, which evidenced recent evolutionary divergence between the populations analyzed, which are considered evolutionary units of conservation.
... However, since rodents were the order of mammals most represented in this review, highlighting the studies conducted in Mexico, we believe landscape genetics studies with rodents will likely increase in the near future. This is based on the diversity of studies conducted with rodents in different environments in Mexico focused on aspects of genetic structure and diversity Castañeda-Rico et al. 2011;Espindola et al. 2014), taxonomy and systematics (Arellano et al. 2006;Álvarez-Castañeda et al. 2009;Fernández et al. 2012), phylogeography (Espinoza-Medinilla et al. 2006;Gutiérrez-García and Vázquez-Domínguez 2012;Álvarez-Castañeda and Murphy 2014), diversification and speciation (Castañeda- Rico et al. 2013;Pérez-Consuegra and Vázquez-Domínguez 2015), and even the development of molecular markers (Munguía- Vega et al. 2007;Vázquez-Domínguez and Espindola 2013), to mention a few. In addition, the development of environmental and climatic layers with better resolution for Mexico (Téllez-Valdés et al. 2010;Cuervo-Robayo et al. 2014) will be key for the development of these studies in the country, in combination with remote sensing data that are currently freely accessible (Landsat 8; http://landsat.usgs.gov/). ...
Since the term was coined in 2003, landscape genetics (LG) is a field that integrates population genetics, landscape ecology, and spatial analytical techniques to quantify the effects of landscape on microevolutionary processes. Despite the growing interest in LG, there is little knowledge about the trends in LG research for America in general and regarding mammals in particular, as well as about which ecosystems are being most studied. Deserts represent nearly one-third of the Earth’s surface and are characterized by high heterogeneity and species richness. However, they are underrepresented in the LG literature. Hence, we performed a thorough review of published scientific articles addressing LG of mammals in America, with emphasis on deserts. The objectives were to 1) determine the mammal groups that have been most studied; 2) establish the representation of desert ecosystems; 3) describe the research questions and analytical methods most frequently used; and 4) summarize the key landscape factors and environmental variables associated with genetic diversity and structure patterns of mammals in America. We conducted a comprehensive literature search of published articles between 2003 and 2019 in the Web of Science (http://apps.webofknowledge.com) based on search words specific to the revision subject. We verified and screened the articles recovered, and gathered basic information (species, authors, publication year), together with the research questions addressed and the genetic and statistical methods used. We recovered 36 publications on LG involving mammals in America; of these, only eight were conducted on desert ecosystems (Table 1). Rodentia was the most represented order in all American ecosystems (n = 20), while Artiodactyla (n = 4) was specifically represented in deserts. Of all studies, the most common research questions focused on estimating ‘connectivity’ (n = 14) and ‘genetic structure’ (n = 12), and the most frequent analytical methods were Mantel and partial Mantel tests. Dispersal capabilities and vegetation cover were the most important variables regarding the genetic structure of desert populations. Most studies evaluated connectivity with simple and partial Mantel tests, but the use of novel methodologies (i. e., genomics) was also identified. Ecological traits of species, particularly for rodents, and vegetation cover were the main factors related to genetic patterns in deserts. Notably, we identified that North America is the most studied region, while LG studies with mammals are scarce in Mexico and South America (one study encompassed North and Central America), as well as in desert ecosystems, hence the urgency to conduct studies in those regions and in deserts.
... Albinism in the population might have resulted from inbreeding, which is more common in insular 4 populations (Frankham 1998). However, while some of Cozumel's vertebrate populations exhibit low levels of genetic diversity (Váquez-Domínguez et al. 2012) and presumably high levels of inbreeding, others exhibit similar levels of genetic diversity to their mainland counterparts (Vega et al. 2007). ...
I observed a group of four albino Dasypus novemcinctus (nine-banded armadillos) foraging in close proximity to one another on Isla Cozumel, México, in July 2009. To my knowledge, this observation represents the first directly documented account of albinism in the species and only the fourth incidence of albinism in the Xenarthra. Given this armadillo's mode of reproduction (i.e., birthing identical quadruplets) and the relative rarity of xenarthran albinism, I hypothesize that this group comprised close kin (perhaps clonal siblings) and encourage further work on the Cozumel population of nine-banded armadillos and the species more generally.
accompanying video: https://www.youtube.com/watch?v=bblQfhoR2ng
Published in The Caribbean Naturalist (ISSN 2326-7119).
... A possible explanation for the observed decrease in heterozygosity could be associated to the effects of genetic drift (Hedrick 2011), which are more prominent in small populations and lead to both short-and long-term losses of genetic diversity. Furthermore, small population size may also increase levels of inbreeding, one of the main genetic factors threatening the short-term survival of populations (Frankham et al. 2005;Vega et al. 2007;Heredia-Bobadilla et al. 2016. In addition to these genetic factors, other ecological or behavioral factors such as habitat loss, fragmentation, or changes in social structure, may affect movement, levels of isolation, and ultimately reproductive success, increasing the probability of extinction of this species. ...
Land use changes are threatening the maintenance of biodiversity. Genetic diversity is one of the main indicators of biological diversity and is highly important as it shapes the capability of populations to respond to environmental changes. We studied eleven populations of Pseudoeurycea robertsi, a micro-endemic and critically endangered species from the Nevado de Toluca Volcano, a mountain that is part of the Trans-Mexican Volcanic Belt, Mexico. We sequenced the mitochondrial cytochrome b gene from 71 individuals and genotyped 9 microsatellites from 150 individuals. Our results based on the cytochrome b showed two divergent lineages, with moderate levels of genetic diversity and a recently historical demographic expansion. Microsatellite-based results indicated low levels of heterozygosity for all populations and few alleles per locus, as compared with other mole salamander species. We identified two genetically differentiated subpopulations with a significant level of genetic structure. These results provide fundamental data for the development of management plans and conservation efforts for this critically endangered species.
... These species have different habitat preferences and ecological characteristics (Lawlor 1982, Reid 1997. Few studies about these species exist, their genetics having been used mainly to describe the phylogenetic relationships of major rodent groups (i.e., Steppan et al. 2004, Reeder et al. 2006, Weksler 2006 and population genetics at local scales (for O. couesi only; i.e., Vega et al. 2007). Accordingly, the main objectives of this work were to evaluate the intraspecific and comparative phylogeographic patterns of the two rodent species and assess if they have a concordant phylogeographic response to their shared geologic and climatic history. ...
... These species have different habitat preferences and ecological characteristics (Lawlor 1982, Reid 1997. Few studies about these species exist, their genetics having been used mainly to describe the phylogenetic relationships of major rodent groups (i.e., Steppan et al. 2004, Reeder et al. 2006, Weksler 2006 and population genetics at local scales (for O. couesi only; i.e., Vega et al. 2007). Accordingly, the main objectives of this work were to evaluate the intraspecific and comparative phylogeographic patterns of the two rodent species and assess if they have a concordant phylogeographic response to their shared geologic and climatic history. ...
... Genetic diversity is the most basic component of biological diversity, which determines the potential of populations to adapt to changing environments and the vulnerability of species to extinction (Frankham 2005). However, the genetic diversity of Mexican rodents is mostly unknown, although a few studies have found it can show high levels (Vega et al. 2007;Castañeda-Rico et al. 2011;Vargas et al. 2012;Vázquez-Domínguez et al. 2013;Espindola et al. 2014). To the best of our knowledge, our work represents the first population genomic study using high-throughput sequencing in a Mexican endemic rodent, and highlights the importance of developing genomic markers for non-model organisms in conservation studies (Kettle 2014;Shafer et al. 2015). ...
Recent advances in genomic sequencing have opened new horizons in the study of population genetics and evolution in non-model organisms. However, very few population genomic studies have been performed on wild mammals to understand how the landscape affects the genetic structure of populations, useful information for the conservation of biodiversity. Here, we applied a genomic approach to evaluate the relationship between habitat features and genetic patterns at spatial and temporal scales in an endangered ecosystem, the Tropical Dry Forest (TDF). We studied populations of the Plateau deer mouse Peromyscus melanophrys to analyse its genomic diversity and structure in a TDF protected area in the Huautla Mountain Range (HMR), Mexico based on 8209 SNPs obtained through Genotyping-by-Sequencing. At a spatial scale, we found a significant signature of isolation-by-distance, few significant differences in genetic diversity indices among study sites, and no significant differences between habitats with different levels of human perturbation. At a temporal scale, while genetic diversity levels fluctuated significantly over time, neither seasonality nor disturbance levels had a significant effect. Also, outlier analysis revealed loci potentially under selection. Our results suggest that the population genetics of P. melanophrys may be little impacted by anthropogenic disturbances, or by natural spatial and temporal habitat heterogeneity in our study area. The genome-wide approach adopted here provides data of value for conservation planning, and a baseline to be used as a reference for future studies on the effects of habitat fragmentation and seasonality in the HMR and in TDF.
... So, the observed deviation from HWE could be the result of Weir and Cockerham (1984), G ST_est -nearly unbiased estimator of relative differentiation (Nei et al. 1983), G0 ST_est -standardized measure of genetic differentiation (Hedrick 2005), (Hedrick 2005). Genetic drift is considered to be the main cause of long-term loss of genetic variation and it leads to an increased chance of inbreeding, the foremost genetic factor threatening short-term survival of populations (Frankham et al. 2005;Vega et al. 2007;Sunny et al. 2014b). The genetic variability found in this study was slightly higher than the figure reported for A. rivulare from the SRMB (Parra-Olea et al. 2012). ...
Human activities are affecting the distribution of species worldwide by causing fragmentation and isolation of populations. Isolation and fragmentation lead to populations with lower genetic variability and an increased chance of inbreeding and genetic drift, which results in a loss of biological fitness over time. Studies of the genetic structure of small and isolated populations are critically important for management and conservation decisions. Ambystoma rivulare is a micro-endemic Mexican mole salamander from central Mexico. It is found in the most ecologically disturbed region in Mexico, the Trans-Mexican Volcanic Belt. The goal of this study of the population genetics of the micro-endemic mole salamander was to provide information to be used as a basis for future research and conservation planning of this species and other species of the Ambystoma genus in Mexico. The structural analysis found two subpopulations, one for each river sampled, with no signs of admixture and very high levels of genetic differentiation. Medium to high levels of heterozygosity and few alleles and genotypes were observed. Evidence of an ancestral genetic bottleneck, low values of effective population size, small inbreeding coefficients, and low gene flow were also found.
... Actualmente también existe un serio problema con las especies que han sido introducidas, particularmente en la Isla Cozumel, entre las que se encuentran roedores exóticos, gatos y perros ferales, además de la liberación de boas (Boa constrictor) en 1971, que en conjunto están impactando negativamente a los vertebrados de la isla (Martínez-Morales y Cuarón 1999; Harper y Bunbury 2015). Esto aumenta el riesgo de peligro para las especies amenazadas en la zona como los roedores O. couesi cozumelae (Vega et al. 2007), R. spectabilis y P. leucopus cozumelae cuyas poblaciones hoy día son desconocidas en términos de su hábitos alimenticios, anatomía, morfología y aspectos reproductivos para la península. El hecho de que algunos de los pequeños roedores de la Península de Yucatán estén bajo alguna categoría de riesgo, debiera motivar la generación de conocimiento con el fin de proponer estrategias efectivas para su conservación. ...
Studies conducted on small mammals, such as tropical rodents, have generated great interest since they can easily provide information concerning to their populations. The present article presents an analysis of the bibliography and sampling locations of small rodents of the Yucatán Peninsula in Mexico. In addition, the information contamine within the literature is revised in order to identify the geographic and thematic coverage of the species records for the purpose of analyzing perspectives in the study of small rodents and in order to contribute to the efforts being made towards their protection and conservation. Publications of periodical journals, books and book chapters published between 1901 and 2015 were reviewed and analyzed. The literature covered research of the 15 small rodent species that are distribuye on the Yucatán Peninsula. The studies were grouped into 10 themes, an accumulation curve was prepared by decade for each state of the Yucatan Peninsula and a map of distribution was generated detailing the locations of the records of each species. A total of 212 references were obtained, of which 162 corresponded to articles in periodical publications and 50 to books and book chapters. The most studied species were Peromyscus yucatanicus, Heteromys gaumeri and Ototylomys phyllotis; in contrast, those for which practically no information exists were Tylomys nudicaudus, Reithrodontomys spectabilis and Heteromys desmarestianus. The State of Yucatán has been the most explored and has the greatest number of sites and records of small rodents, followed by Quintana Roo and finally Campeche. The most commonly addressed themes were distribution, taxonomy, phylogeny, diseases and parasitism. Gaps in the information were detected for the majority of the species in the different themes such as feeding, reproduction, anatomy and morphology. For this reason, it is important to carry out studies in these themes in order to further the knowledge of the small rodents of the Yucatán Peninsula. These studies could provide information with the aim to propose changes to their conservation status in both Mexican and international legislation, or take appropriate decisions regarding protection of their specific habitats.
... The genetic distance (F ST ) between the bank vole population in 2008 and previous years was very low, which demonstrates the relative stability of genetic structure of the local population of this species. Other investigations on rodents have shown that their populations may maintain unexpectedly high levels of genetic variability over a long period of time, unless the populations are too small (Vega et al. 2007). ...
We examined changes in genetic diversity in populations of two small mammal species inhabiting islands on a lake. We hypothesized that a less mobile species, such as the bank vole, would lose genetic diversity quicker than the yellow-necked mouse, which can more easily cross habitat barriers. In contrast to this we found that the effects of isolation were much more prominent in the case of the mouse than the vole. In the vole population, on the larger island, genetic diversity remained constant over subsequent years in spite of marked isolation. On the smaller island, we noted an increase in genetic diversity which was probably caused by immigration of a small group of individuals. Genetic diversity in the mouse population decreased markedly over the course of the study. In the bank vole, the preservation of genetic diversity, especially on the larger island, may have been possible due to the specific spatial and social organization of this species, which allows the maintenance of a relatively stable number of individuals. In contrast to the bank vole, the lack of territorial behavior in adult females of yellow-necked mice may lead to frequent dramatic seasonal ’booms and busts' in population size and genetic diversity. This can lead to extremely low numbers of mice, which are likely to lead to the extinction of some island populations.
... In Isla Mujeres (7 km from the Yucatán Peninsula in Mexico), the arrival of the moth was associated with the occurrence of hurricane Stan in 2005 (Zimmermann and Pérez-Sandi 2006). Parallel to their devastating environmental consequences (Lugo et al. 2000;Chazdon 2003), hurricanes in the Caribbean are known to reduce population size in several species exposing them to genetic bottlenecks (Hurtado et al. 2012;Szczys et al. 2012; but see Vega et al. 2007), and to promote dispersal among isolated islands (Fleming and Murray 2009). Within the Caribbean region, the historical records of winds and hurricanes indicate a consistent spatio-temporal pattern (Landsea 1993;Landsea et al. 1996;Lugo et al. 2000;Muscarella et al. 2011) characterized by two major east-west trajectories (Fig. 1). ...
The cactus moth, Cactoblastis cactorum mainly distributed throughout central and northeastern Argentina was intentionally introduced in the Caribbean region in 1957 as a biological control agent of cacti species of the genus Opuntia. This moth invaded during the last 20–30 years the North American continent, threatening the major center of biodiversity of native Opuntia species. Although human induced and natural dispersal have been invocated to explain its expansion in the non-native distribution range, there is still no evidence to support natural dispersal. In particular, hurricanes are one of the major environmental factors affecting species dispersal in the region. In this study we used mitochondrial DNA to examine whether the spatial distribution of haplotype variation of C. cactorum is at least partially explained by hurricane trajectories within the Caribbean region. DNA sequences for the mitochondrial gene cytochrome oxidase I were obtained for a sample of 110 individuals from the Antillean islands. This information was combined with existing sequences in the GenBank for the same gene for the Caribbean and Florida (N = 132 sequences). Genetic diversity descriptors, a haplotypic network, a spatial analyses of molecular variance and a landscape genetic analysis of migration conditioned by hurricane tracks were conducted to test our hypothesis. Our results revealed a significant spatial grouping of haplotypes consistent with the more frequent hurricane trajectories in the Caribbean region. Significant isolation by distance conditioned by hurricane tracks was detected. Populations of Florida were genetically closer to those of Cuba than to the rest of the population sampled. Within the region, Cuba appears as a reservoir of genetic diversity increasing the risk of invasion to Mexico and the US. Despite commercial transportation of Opuntia promoted dispersal to Florida, our results support the hypothesis that natural disturbances such as hurricanes played a role dispersing this invasive insect. Future conservation programs of North American Opuntia species requires taking into account hurricane mediated dispersal events and permanent whole regional monitoring and international control policies to prevent future range expansions of C. cactorum.
... Thus, we test the assumption of the genetic diversity hypothesis by comparing nucleotide diversity and heterozygosity of the two populations. The size and proximity to the mainland of our island population (Isla Cozumel) may have prevented genetic impoverishment of its catbirds, as has been documented for some other components of the island's fauna (Vega et al. 2007). ...
The Black Catbird (Melanoptila glabrirostris ) is a poorly known endemic resident of the Yucatán Peninsula and a member of the passerine family Mimidae. I studied the social breeding system and the social and genetic mating systems of Black Catbirds in 2008 and 2009 at two sites in Quintana Roo, México: on the mainland, the Sian Ka'an Biosphere Reserve, and on Isla Cozumel. Field results yielded the first definitive report of bi-parental care without cooperative breeding in both populations, larger samples of clutch size compared to previous studies, more accurate estimates of nesting phenology, and different patterns of breeding density between populations. Genetic analyses revealed genetic monogamy in the high-density mainland population and moderate levels of extra-pair paternity in the low-density island population. This research underscores the need for more complete data sets in comparative studies of social evolution and further research on the genetic mating systems of Neotropical birds.
... These species have different habitat preferences and ecological characteristics (Lawlor 1982, Reid 1997. Few studies about these species exist, their genetics having been used mainly to describe the phylogenetic relationships of major rodent groups (i.e., Steppan et al. 2004, Reeder et al. 2006, Weksler 2006 and population genetics at local scales (for O. couesi only; i.e., Vega et al. 2007). Accordingly, the main objectives of this work were to evaluate the intraspecific and comparative phylogeographic patterns of the two rodent species and assess if they have a concordant phylogeographic response to their shared geologic and climatic history. ...
scholarly publishing services to the University of California and delivers a dynamic research platform to scholars worldwide. Title: Comparative phylogeography of Oryzomys couesi and Ototylomys phyllotis; historic and geographic implications for the Central America conformation Journal Issue: Frontiers of Biogeography, 5(4) Acknowledgements: I would like to give special thanks to my advisor Dr. Ella Vázquez-Domínguez, who directed and advised this work with professionalism and enthusiasm. I also thank my PhD committee members, Dr. Daniel Piñero and Dr. Enrique Martínez-Meyer, for their support and valuable contributions. The PhD scholarship and financial support were provided by the National Council of Science and Technology (CONACyT) and the National Autonomous University of México (UNAM). This work was financed by the following projects: PAPIIT IN215205-2, IX238004, IN21907 and CONACyT 101861. Abstract: Central America is an ideal region for comparative phylogeographic studies because of its intricate geologic and biogeographic history, diversity of habitats and dynamic climatic and tectonic history. The aim of this work was to assess the phylogeography of two rodents codistributed throughout Central America, in order to identify if they show concordant genetic and phylogeographic patterns. The synopsis includes four parts: (1) an overview of the field of comparative phylogeography;
... We analysed 129 O. phyllotis museum and field samples, together with three O. phyllotis sequences 594 T. A. GUTIÉRREZ-GARCÍA and E. VÁZQUEZ-DOMÍNGUEZ from GenBank (AY009788, AY009789, DK179814), from 47 localities covering most of the species' range of distribution (Supporting Information, Table S1 and Fig. S1). Forty individuals were live-trapped during different field trips between 2003 and 2004, as part of an ongoing study on the ecology, phylogeography, and conservation of vertebrate fauna from southern Mexico (Zambrano et al., 2006;Vega et al., 2007;Vázquez-Domínguez et al., 2009). Tissue samples for molecular analyses were ethically obtained, with the corresponding collecting permits, and stored in labelled Eppendorf tubes with ethanol 97% until DNA extraction. ...
Central America is an ideal region in which to study patterns of historical divergence and population genetic differentiation, because of its extraordinarily dynamic biogeographical, tectonic, and climatic history. The rodent Ototylomys phyllotis is the only extant species of the genus Ototylomys and is distributed within this region from the Isthmus of Tehuantepec, Mexico, to central Costa Rica, offering an excellent opportunity to study spatial and temporal patterns of population structure of the species and to explain the ecological and evolutionary processes responsible for those patterns. We estimated the genetic diversity and structure within and between populations of O. phyllotis, times of divergence, and migration patterns using mitochondrial DNA and a comprehensive combination of phylogenetic and phylogeographical computational analyses. Our results support monophyly of the genus Ototylomys. We identified three major phylogeographical lineages within O. phyllotis that are linked to its diversification and coincide with the main geological features that shaped Middle America. The origin of the genus was before 3.35 Mya, prior to the Great American Biotic Interchange (GABI), and its initial occurrence was near the centre of its current distribution (Honduras/El Salvador), from which it later spread (3.20–2.84 Mya) following a series of GABI pulses. The species showed an initial northward dispersal to the Chiapas and Guatemala highlands (2.27 Mya) followed by diversification. A later dispersal (1.82 Mya) occurred toward both the south (Nicaragua, Costa Rica) and the north (Belize). The Yucatan peninsula was colonized (0.8 Mya) by individuals from Belize. Extremely high radiation and range expansion occurred throughout the entire range, the highest of which was in the Yucatan peninsula (0.125 Mya). © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.
... et al. 2007); the giant kangaroo rat (Dipodomys ingens), whose fragmented habitat has been reduced to 3% of its historical distribution (H E 5 0.690-0.720, n o 5 14.5- Loew et al. 2005); the island-endemic Oryzomys couesi cozumelae (H E 5 0.689, n o 5 10.8- Vega et al. 2007); and the banner-tailed kangaroo rat (Dipodomys spectabilis), a species that has passed through several genetic bottlenecks but has maintained high levels of genetic diversity (H O 5 0.630-0.730, n o 5 6.5-7.4- ...
The Jico crested-tailed mouse (Habromys simulatus) is an arboreal rodent endemic to Mexico, with only 2 known extant populations restricted to montane cloud forests in the states of Hidalgo and Oaxaca. The habitat of this species has been reduced and fragmented as a result of anthropogenic activities, isolating populations and likely decreasing their sizes. We evaluated the effects of such isolation by analyzing the genetic diversity and structure of H. simulatus using 10 microsatellite loci. DNA was obtained from 52 samples from both populations. Despite the isolated and fragmented nature of the species, we found high levels of genetic diversity (H(Nei) = 0.732), similar to those reported in other endangered species with fragmented distributions. Genetic differentiation was significant (F(ST) = 0.178) and number of migrants was negligible (NmF(ST) = 0.196), a result supported by an assignment test and a factorial correspondence test. Molecular analysis of variance showed that 82% of genetic variation was distributed within populations, not unexpected given that each of the individuals' genotypes was distinct. Individuals within each population were mostly unrelated. The smallest population showed evidence of genetic bottleneck. We found evidence of detrimental genetic processes such as allelic fixation, genetic drift, and inbreeding. Our results strongly suggest that each of the 2 populations is a unique genetic entity that must be considered a distinct evolutionary unit. Unfortunately, both populations are at high risk of extinction, primarily due to habitat loss and population decline.
... Dispersal may affect the genetic structure of small terrestrial mammals on a smaller geographic scale than larger mammals, because small mammals typically disperse over shorter distances and thus have reduced dispersal ability. Large scale geographic structuring has been found in small mammals primarily due to isolation by distance (Boone et al. 1999, Vega et al. 2007. Populations that are farther apart geographically are more genetically divergent because individuals mate with others that are in close proximity. ...
The marsh rice rat (Oryzomys palustris) is a semi-aquatic rodent endemic to the southeastern United States. Unlike most terrestrial small mammals, the marsh rice rat can easily disperse over water and has a close association with wetlands. These specialized traits have likely greatly shaped the genetic structure and diversity within this species. I studied genetic patterns within the marsh rice rat to understand how this species' specialized ecology, as well as the geologic and climatic history of the southeastern United States, affected the genetic structuring within this species. The phylogeography of many species in the southeastern United States has been studied and concordant geographic patterns of genetic variation exist among many of these species. Researchers have hypothesized that the biogeography of the southeastern United States has been influenced by the Pleistocene glacial cycles, producing similar genetic patterns within unrelated species. I first examined genetic patterns within the marsh rice rat at the macro scale of phylogenetics. This nominal species actually represents two cryptic species; populations in the eastern and western regions of its range are genetically divergent. I also identified three subspecies, in contrast to the six morphological subspecies historically recognized. The silver rice rat in the Lower Florida Keys and the Sanibel Island rice rat from Sanibel Island Florida are both subspecific taxa. Only one mainland marsh rice rat subspecies exists. I then studied the phylogeographic patterns within the marsh rice rat and determined that geographic patterns of genetic variation in this species are not concordant with the phylogeographic patterns uncovered in most other species of the southeastern United States. The genetic structuring within the marsh rice rat has been influenced not only by the geologic and climatic history of this region, but also by the species' semi-aquatic adaptation. I also studied genetic patterns at a micro scale by estimating present levels of gene flow and genetic diversity within populations. Gene flow is a contemporary factor in maintaining levels of genetic diversity within populations of the marsh rice rat. From the macro scale of phylogenetics to the micro scale of population genetics, the genetic structure of the marsh rice rat has been shaped by past climatic history and by this species' specialized ecology.
... Although the implementation of species-specific studies has let to recognize the effect of social organization, phylopatry, limited-dispersal, temporal variation in population density and sex-biased dispersal on the genetic structure of small mammals (Koenig et al. 1996;Patton et al. 1996;Gerlach and Musolf 2000;Vázquez-Domínguez et al. 2002;Peakall et al. 2003;Schweizer et al. 2007;Zhou et al. 2011), interestingly, a common pattern is that genetic structure of the rodent species seems to depend on the geographical separation of populations. Populations separated at a local scale (5-10 km) tend to exhibit low genetic differentiation as indicated by an F ST of less than 0.05 (Peakall et al. 2003;Vignieri 2005;Schweizer et al. 2007;Vega et al. 2007). Then in comparison, populations separated by higher distances typically exhibit greater genetic differentiation (100-1,000 km; Trizio et al. 2005;Bogdanov et al. 2009). ...
Tropical dry forests are biologically important biomes sustaining a high rate of endemic species. However, these forests are highly threatened by human activities that negatively impact them on distinct levels, including the genetic diversity. Within the framework of landscape genetics (that seeks to evaluate the relation of characteristics of the environmental matrix with population genetics), we used ISSR markers to evaluate the relationship between the alteration of tropical dry forest by human-induced activities (conserved vs. disturbed) with the genetic structure of four breeding sites of the southern pygmy mouse Baiomys musculus. Averaging among the 105 loci used, the unbiased heterozygosis per population (0.247–0.305) was statistically similar among the four sites, as well as between conserved and disturbed conditions (2-way ANOVA F
(3,16) = 1.47, P = 0.1984). The genetic differentiation among the four breeding sites was high (F
ST = 0.1122; 95 % CI 0.082–0.146) considering the geographical scale evaluated (ca. 4 km). Both, a factorial correspondence analysis and a model-based clustering analysis showed the existence of four genetic groups (one per breeding site). However, no association of genetic structure with disturbance conditions was revealed by these analyses. The absence of differences in mean genetic diversity and the lack of association of genetic structure with habitat transformation suggest that B. musculus has enough behavioral plasticity and enough genetic diversity to respond to environmental heterogeneity caused by human activities. We discussed conditions in which habitat transformation could indeed favor B. musculus.
... White-footed mice achieve their highest population densities in small habitat fragments (); if the populations are large enough, then loss of genetic variation owing to drift may be slowed or prevented altogether. Insular, endemic small mammals can maintain genetic variation at levels similar to mainland populations (Degner et al. 2007; Vega et al. 2007 ), possibly attributable to low density or absence of native predators and competitors that would otherwise regulate small mammal density. Another possible explanation is that detectable genetic structure may develop more rapidly than loss of genetic diversity in fragmented populations (reviewed in Keyghobadi 2007). ...
We investigated genetic diversity and structure of urban white-footed mouse, Peromyscus leucopus, populations in New York City (NYC) using variation at 18 microsatellite loci. White-footed mice are 'urban adapters' that occur at higher population densities as habitat fragments are reduced in area but have a limited ability to disperse through urbanized areas. We hypothesized that this combination of traits has produced substantial genetic structure but minimal loss of genetic variation over the last century in NYC. Allelic diversity and heterozygosity in 14 NYC populations were high, and nearly all of our NYC study sites contained genetically distinct populations of white-footed mice as measured by pairwise F(ST) , assignment tests, and Bayesian clustering analyses performed by Structure and baps. Analysis of molecular variance revealed that genetic differences between populations separated by a few kilometres are more significant than differences between prehistorically isolated landmasses (i.e. Bronx, Queens, and Manhattan). Allele size permutation tests and lack of isolation by distance indicated that mutation and migration are less important than drift as explanations for structure in urban, fragmented P. leucopus populations. Peromyscus often exhibit little genetic structure over even regional scales, prompting us to conclude that urbanization is a particularly potent driver of genetic differentiation compared to natural fragmentation.
Genomic tools are now commonly used to assess the genetic diversity and genetic structure of species and populations, and they provide the ability to describe and address the negative effects of population declines and fragmentation. However, such studies are lacking for arboreal mammals despite their contribution to various ecosystem services, especially in uncommon and critically endangered ecosystems such as cloud forests. The aim of this work was to evaluate and compare the genetic diversity and population structure of two endemic arboreal mice from Mexican cloud forests that are associated with areas with different levels of impacts from human activities. We performed genotyping-by-sequencing in 47 Habromys schmidlyi and 17 Reithrodontomys wagneri individuals to evaluate genetic diversity and differentiation. In both species, the genetic diversity was low compared to other cricetid species, and we observed different population structure patterns, potentially linked to the different ecological associations. We detected two genetic groups in H. schmidlyi , that is a territorial species present in areas of low incline, while a single genetic group was found in R. wagneri , which forms family groups in areas with steep slopes. Overall, these results highlight how species’ genetic diversity can be differentially impacted depending on differential ecological associations within the same ecosystem. This information is essential for the development of the adequate conservation and management of these species.
San Bernardino kangaroo rat (Dipodomys merriami parvus; SBKR), an endangered subspecies, faces ongoing anthropogenic threats such as habitat loss. Their habitat has undergone strong human-mediated fragmentation, resulting in extinction of some local populations and dramatic size reduction of the remaining populations. We examined the genetic diversity, population structure, and phylogeography of this subspecies using partial mitochrondrial DNA sequencing and microsatellite genotyping. Our study indicates that currently, the three remaining populations seem to be highly fragmented. Clear population structure and low level of haplotype sharing suggests that there has been no recent gene flow among populations, except in the case of human mediated gene flow as a result of a single translocation event. Diversity levels are on par with other species with fragmented distributions. Further, shallow phylogenetic divergence suggests the populations have not been diverged long enough to detect phylogenetic structure and separation is likely recent. Given the limited gene flow, low numbers of SBKR as evident by low return on trapping efforts, and low effective population size, habitat restoration and translocations may be warranted to maintain levels of diversity in a declining metapopulation.
Relevance and goals. The study of population polymorphism is an important task of modern biology
both from the perspective of theoretical ideas about the variability of biological items and biological diversity, and
from the practical side of studying the laws of species existence within the historical area. Russet ground squirrel
(Spermophilus major Pall.) is a proper model species for exploring individual and population variability due to
changes in the structure of the range. The study was aimed at examining the individual and population variability
of the morphological indicators of russet ground squirrel in the Volga Region and in adjacent territories, taking into
account the fragmentation of their range. Materials and methods. The material for the study comprises the collections
and data on the lifetime certification of individuals (n = 412) obtained in the course of research (2011–2018)
of 55 populations of russet ground squirrel in the Volga Region and adjacent territories. The study of features of
the body external morphology covered body length (L), metatarsus (PL) and tail (C) (in mm). Statistical processing
of the results was based on standard statistical parameters, as well as cycle-by-cycle discriminant and cluster analyses.
Statistical data processing was conducted in Microsoft Office Excel 2010 and STATISTICA 10.0. Results.
The morphological analysis of populations and metapopulations of russet ground squirrel using the methods of
descriptive statistics and variance analysis prevents reliable recognition of the existence of the fragmented structure
of the range for this species in the study region. The cycle-by-cycle discriminant analysis of morphological indicators
samples characterizing populations of russet ground squirrel in the study region revealed their good differentiation
in the space of discriminant functions and enabled determining some features of the morphological
variability of russet ground squirrel in the study region. Due to the wide range of variability compared with the
Volga populations, the Ural populations of russet ground squirrel occupy an extreme position in a series of morphological
changes. At that, right-bank populations are characterized by a more balanced composition and absence
of sharp changes in morphological indicators. Findings. The statistical analysis of samples of russet ground
squirrel morphological indicators revealed a heterogeneous population polymorphism associated with a strong
fragmentation of the habitat, and confirmed the existence of the metapopulation structure of its range.
En el segundo capítulo se examina el impacto de las actividades humanas en la biodiversidad y los ecosistemas
de México, con un análisis de los principales factores de cambio de estos, incluidos los efectos de
la fragmentación y pérdida del hábitat, del cambio de uso del suelo, de las enfermedades y zoonosis emergentes, así como los de la contaminación.
The type collection of Recent mammals in the Division of Mammals, National Museum of Natural History, Smithsonian Institution, contains 945 specimens bearing names of 931 species-group taxa of Rodentia (Myomorpha, Anomaluromorpha, and Hystricomorpha) as of August 2013. This catalog presents an annotated list of these holdings comprised of 905 holotypes, 16 lectotypes, 8 syntypes (48 specimens), and 2 neotypes. In addition, we include 44 specimens that are part of syntype series that should be in the collection but cannot be found or are now known to be in other collections. One hundred and ten of the names are new since the last type catalog covering these suborders A lectotype for Mus peruvianus Peale, 1848, is newly designated herein. Nine specimens previously reported were subsequently sent to the vertebrate paleontology collection and are not included here. Suborders and families are ordered as in Carleton and Musser; within families, currently recognized genera are arranged alphabetically; within each currently recognized genus, accounts are arranged alphabetically by original published name. Information in each account includes original name and abbreviated citation thereto, current name if other than original, citation for first use of current name combination for the taxon (or new name combination if used herein for the first time), type designation, U.S. National Museum catalog number(s), preparation, age and sex, date of collection and collector, original collector number, type locality, and remarks as appropriate. Digital photographs of each specimen will serve as a condition report and will be attached to each electronic specimen record.
Reithrodontomys spectabilis is an endemic rodent inhabiting Cozumel island in the Mexican Caribbean. This species is categorized as Threatened by Mexican law and as Critically Endangered by the IUCN. We report 10 polymorphic microsatellite loci, which were tested in 30 individuals trapped on the island. Results show a number of alleles ranging from 3 to 14, an observed heterozygosity of 0.200–0.967 and expected heterozygosities from 0.396 to 0.899. Two loci showed deviation from Hardy–Weinberg equilibrium. None of the loci showed linkage disequilibrium. These new microsatellite loci for R. spectabilis are vital to investigate different aspects of genetic diversity and help conservation of this endemic, threatened species.
The endangered twoline skiffia Neotoca bilineata, a viviparous fish of the subfamily Goodeinae, endemic to central Mexico (inhabiting two basins, Cuitzeo and Lerma-Santiago) was evaluated using genetic and habitat information. The genetic variation of all remaining populations of the species was analysed using both mitochondrial and microsatellite markers and their habitat conditions were assessed using a water quality index (I(WQ) ). An 80% local extinction was found across the distribution of N. bilineata. The species was found in three of the 16 historical localities plus one previously unreported site. Most areas inhabited by the remaining populations had I(WQ) scores unsuitable for the conservation of freshwater biodiversity. Populations showed low but significant genetic differentiation with both markers (mtDNA φ(ST) = 0·076, P < 0·001; microsatellite F(ST) = 0·314, P < 0·001). Borbollon, in the Cuitzeo Basin, showed the highest level of differentiation and was identified as a single genetic unit by Bayesian assignment methods. Rio Grande de Morelia and Salamanca populations showed the highest genetic diversity and also a high migration rate facilitated by an artificial channel that connected the two basins. Overall, high genetic diversity values were observed compared with other freshwater fishes (average N(a) = 16 alleles and loci and mean ±s.d. H(o) = 0·63 ± 0·10 and nucleotide diversity π = 0·006). This suggests that the observed genetic diversity has not diminished as rapidly as the species' habitat destruction. No evidence of correlation between habitat conditions and genetic diversity was found. The current pattern of genetic diversity may be the result of both historical factors and recent modifications of the hydrological system. The main threat to the species may be the rapid habitat deterioration and associated demographic stochasticity rather than genetic factors.
The vlei rat Otomys irroratus has a wide distribution in southern Africa with several datasets indicating the presence of two putative species (O.irroratus and O.auratus). In the present study we use mitochrondrial cyt b data (∼950bp) from 98 specimens (including museum material) collected throughout the range of the species to determine the geographical limits of the two recognized species, and we link this to niche modelling to validate these species. Phylogenetic analysis of the DNA sequence data, using maximum parsimony, neighbour joining and Bayesian inference, retrieved two divergent statistically well-supported clades. Clade A occurs in the Western and Eastern Cape while Clade B occurs in the Free State, KwaZulu-Natal, Northern Cape and Mpumalanga provinces of South Africa and Zimbabwe. Mean sequence divergence between the two clades (A and B) was 7.0% and between sub-clades comprising clade B it was 4.8%; the two clades diverged during the Pleistocene. Within Clade A the mean sequence divergence among specimens was 1.91%. Niche modelling revealed that the incipient species occupy distinct bioclimatic niches associated with seasonality of precipitation. Our data allow insightful analysis into the factors that could have led to cladogenesis within this rodent. More significantly, the new data enable us to pinpoint the Eastern Cape province as a contact zone for the divergent species.
Resources are produced in pulses in many terrestrial environments, and have important effects on the population dynamics and assemblage structure of animals that consume them. Resource-pulsing is particularly dramatic in Australian desert environments owing to marked spatial and temporal variability in rainfall, and thus primary productivity. Here, we first review how Australia's desert mammals respond to fluctuations in resource production, and evaluate the merits of three currently accepted models (the ecological refuge, predator refuge and fire-mosaic models) as explanations of the observed dynamics. We then integrate elements of these models into a novel state-and-transition model and apply it to well-studied small mammal assemblages that inhabit the vast hummock grassland, or spinifex, landscapes of the continental inland. The model has four states that are defined by differences in species composition and abundance, and eight transitions or processes that prompt shifts from one state to another. Using this model as a template, we construct three further models to explain mammalian dynamics in cracking soil habitats of the Lake Eyre Basin, gibber plains of the Channel Country, and the chenopod shrublands of arid southern Australia. As non-equilibrium concepts that recognise the strongly intermittent nature of resource pulsing in arid Australia, state-and-transition models provide useful descriptors of both spatial and temporal patterns in mammal assemblages. The models should help managers to identify when and where to implement interventions to conserve native mammals, such as control burns, reduced grazing or predator management. The models also should improve understanding of the potential effects of future climate change on mammal assemblages in arid environments in general. We conclude by proposing several tests that could be used to refine the models and guide further research.
Detecting bottlenecks or population declines
The relationship between heterozygosity and spatial and temporal changes in population density, and between heterozygosity and body weight, were studied in four populations of the spiny pocket mouse, Liomys pictus, from tropical dry forests in Chamela, Jalisco, Mexico. Individuals of L. pictus experience profound fluctuations in populations mainly due to the strong environmental seasonality of their habitat. Nineteen presumptive gene loci were assayed with starch-gel electophoresis to estimate heterozygosity, and mean body weight was analyzed as a fitness-correlated character. Observed average heterozygosity values were high (H = 0.188-0.198), whereas average fixation values (F = 0.350-0.429) were positive, indicating a significant deficiency of heterozygotes. Changes in numbers of individuals and heterozygous loci per individual were associated with different phases of fluctuations in density of L. pictus. During the increase phase, persistence of individuals was higher and average heterozygosity values declined, probably due to inbreeding. During the decline of the population when food and water were scarce, heterozygosity increased, and adults, which overall showed less deficiency of heterozygotes, were significantly more abundant. Average number of heterozygous loci and body weight also showed a positive and significant correlation. These results agree with the hypothesis that changes in genetic variability may be a consequence of demographic changes, and that, consequently, traits associated with fitness could show correlations with heterozygosity.
The identification of areas of high priority for conservation is becoming a major endeavor for conservation biologists. Regions of high species richness and high concentrations of endemic and endangered species have been considered a priority for conservation. In this paper we use information about the species richness, composition, and distribution of mammals from Mexico for selecting priority areas for conservation. All species of terrestrial mammals were characterized by geographic range size, body mass, and conservation status, and their distributions were overlaid on a 2 degrees X 2 degrees grid to detect areas of high concentrations of species richness, endemicity, and endangered species. We focused our analyses at both species and biogeographic levels. At the species level we examined differences among endangered, endemic, and nonendemic species in ecological characteristics correlated with vulnerability to extinction. There were significant differences between endangered and non-endangered species, and between endemic and non-endemic mammals in body size and geographic range size. At the biogeographic level simple correlation analyses were carried out to determine the relation between latitude, total species richness, number of endemic species, and number of endangered species. We found a very low correspondence among areas of high diversity, high endemicity, or high number of endangered species. The distribution of many species with restricted geographic ranges, including endemic and non-endemic species, did not coincide with areas of high species richness, endemicity, or endangerment. We suggest a conservation strategy that gives priority to areas of high concentration of endangered species and of non-endangered species with restricted distributions. Among endangered species a higher priority should be given to endemic taxa vs. non-endemic species, and to restricted species over widespread taxa in these two groups.
I assessed the population status and habitat preferences of the Cozumel Cu- rassow, Crax rubra griscomi, in the forests of Cozumel Island, Mexico, from October 1994 to June 1995. The estimated density was 0.9 curassows km-* with a population size of about 300 birds. These numbers and the fact that the Cozumel Curassow is restricted to the island, place this endemic cracid within the conservation status of Critically Endangered. Hunting is likely the main cause of its present conservation status. This curassow showed a greater preference for the tropical semi-deciduous forest than for the low tropical deciduous forest. Likewise, older stands of forest have a positive influence on its distribution. Freshwater sources within the forests have a positive influence on the Cozumel Curassow distribution within a radius of about 2 km. Human settlements and human accesses to the forest interior
Species introductions are among the most pervasive types of disturbance, seriously affecting island biota and ecosystem dynamics. The management of introduced generalist species, which may live in a wide range of environmental conditions, can be particularly difficult and is a major challenge for the conservation of native insular species. Boa constrictor was introduced onto Cozumel Island, Mexico, in 1971. The introduction of this generalist predator has affected negatively the native species (many of them endemic to the island) on which the boa feed. It is important to determine temporal variation in boa abundance, the areas of the island in which boas live, and the vegetation types they use in order to develop management strategies to reduce boa pressure on the native biota. We used nocturnal road transect sampling and occasional boa encounters during field work, to estimate boa distribution, abundance and habitat use, taking into account its spatiotemporal patterns on Cozumel Island. This study confirms that Boa constrictor is well established, widespread, and abundant on the island. Our results show that boas are distributed throughout Cozumel, in all vegetation types and geographical regions. Overall, there were 0.11 ± 0.03 boa/10 km road transect. There were no significant spatiotemporal differences in boa activity (time of day) and abundance (monthly, seasonally, by vegetation types or regions of the island). According to the habitat use analysis, there were, however, fewer boas than expected in the subdeciduous tropical forest we sampled and in the central-northern region of the island, which coincide with areas inhabited by humans. There were more boas in areas uninhabited by humans, and there was a tendency towards a greater proportion of dead boas in inhabited areas and live boas in uninhabited areas. Cozumel boas are habitat generalists, which are affected by human induced mortality in inhabited areas. There is a vast area uninhabited by humans, with natural vegetation, on the island where boas have suitable habitats available for their continuous existence on Cozumel. This situation, and the adaptability of the boa, makes the control or eradication of this introduced species a critical conservation challenge.
Species introductions are among the most pervasive types of disturbance, seriously affecting island biota and ecosystem dynamics. The management of introduced generalist species, which may live in a wide range of environmental conditions, can be particularly difficult and is a major challenge for the conservation of native insular species. Boa constrictor was introduced onto Cozumel Island, Mexico, in 1971. The introduction of this generalist predator has affected negatively the native species (many of them endemic to the island) on which the boa feed. It is important to determine temporal variation in boa abundance, the areas of the island in which boas live, and the vegetation types they use in order to develop management strategies to reduce boa pressure on the native biota. We used nocturnal road transect sampling and occasional boa encounters during field work, to estimate boa distribution, abundance and habitat use, taking into account its spatiotemporal patterns on Cozumel Island. This study confirms that Boa constrictor is well established, widespread, and abundant on the island. Our results show that boas are distributed throughout Cozumel, in all vegetation types and geographical regions. Overall, there were 0.11 ± 0.03 boa/10 km road transect. There were no significant spatiotemporal differences in boa activity (time of day) and abundance (monthly, seasonally, by vegetation types or regions of the island). According to the habitat use analysis, there were, however, fewer boas than expected in the subdeciduous tropical forest we sampled and in the central-northern region of the island, which coincide with areas inhabited by humans. There were more boas in areas uninhabited by humans, and there was a tendency towards a greater proportion of dead boas in inhabited areas and live boas in uninhabited areas. Cozumel boas are habitat generalists, which are affected by human induced mortality in inhabited areas. There is a vast area uninhabited by humans, with natural vegetation, on the island where boas have suitable habitats available for their continuous existence on Cozumel. This situation, and the adaptability of the boa, makes the control or eradication of this introduced species a critical conservation challenge.
The Angel de la Guarda deer mouse Peromyscus
guardia on Estanque Island, in the Angel de la Guarda archipelago of the Gulf of California, was probably driven to extinction by a single introduced domestic cat. P.
guardia was trapped on the island in October 1995, at which time the species was still relatively abundant. In 1998 a domestic cat was spotted on the island; no deer mice were found at that time nor during subsequent field work in 1999 and 2001. In 1998, c. 100 cat scats were collected, 2% of which contained P.
guardia bone remains and 90% P.
guardia hair. The cat, which was eradicated in 1999, was the only introduced predator on the island. Our results confirm the extreme vulnerability of island rodent populations to the introduction of alien mammalian predators. To our knowledge, apart from the extermination of Stephens Island wren Xenicus
lyalli in New Zealand in 1894 by the lighthouse keeper's cat, this is the first report of the destruction of the total population of an insular species by a single cat. With two of the three subspecies of P.
guardia now extinct the only potentially extant population is on the larger Angel de la Guarda Island, where the species was last seen in 1991. A comprehensive survey of the island is required, with subsequent action for the species recovery and conservation if it is found to be extant.
Pest eradication is an important facet of conservation and ecological restoration and has been applied successfully to invasive rat species on offshore and oceanic islands. Successful eradication requires the definition of a target population that is of manageable size, with low recolonization risk. We applied a molecular genetic approach to the identification of populations suitable for eradication (eradication units) to provide a new tool to assist the management of brown rats Rattus norvegicus on South Georgia (Southern Ocean).
A single eradication attempt on South Georgia (4000 km ² ) would be an order of magnitude larger than any previously successful rat eradication programme (110 km ² ). However, rats are demarcated into glacially isolated populations, which could allow sequential eradication. We examined genetic variation at 18 nuclear microsatellite loci to identify gene flow between two glacially isolated rat populations. One population, Greene Peninsula (30 km ² ), was earmarked for an eradication trial.
Genetic diversity in 40 rats sampled from each population showed a pronounced level of genetic population differentiation, allowing individuals to be assigned to the correct population of origin.
Our study suggests limited or negligible gene flow between the populations and that glaciers, permanent ice and icy waters restrict rat dispersal on South Georgia. Such barriers define eradication units that, with due care, could be eradicated with low risk of recolonization, hence facilitating the removal of brown rats from South Georgia.
Synthesis and applications . We propose that the molecular definition of eradication units is a valuable approach to management as it (i) provides a temporal perspective to gene flow, which is important if dispersal events are rare; (ii) allows an eradication failure (i.e. surviving individuals) to be distinguished from a recolonization event, opening the way for adaptive management in the face of failure; and (iii) can aid the management of pest species in habitat continua by resolving meta‐population dynamics, so guiding pest eradication/control strategies. This study further illustrates the developing array of applied ecological issues in which molecular techniques can help guide management.
To understand the impact of various factors on the maintenance of genetic variation in natural populations, we need to focus on situations where at least some of these factors are removed or controlled. In this study, we used highly variable, presumably neutral, microsatellite and mtDNA markers to assess the nature of genetic variation in 14 island and two mainland populations of the Australian bush rat, where there is no migration between islands. Thus we are controlling for selection and gene flow. Both marker sets revealed low levels of diversity within the small island populations and extreme differentiation between populations. For six microsatellite loci, all of the small island populations had less genetic variation than the mainland populations; reduction in allelic diversity was more pronounced than loss of heterozygosity. Kangaroo Island, the large island population, had similar levels of diversity to the mainland populations. A 442 base pair (bp) section of the mtDNA control region was screened for variation by outgroup heteroduplex analysis/temperature gradient gel electrophoresis (OHA/TGGE). Only three of the 13 small island populations showed haplotypic diversity: Gambier (2), Waldegrave (2), and Eyere (3). The level of haplotypic diversity in the small island populations was similar to that on the mainland, most likely reflecting a recent population bottleneck on the mainland. In contrast, Kangaroo Island had 9 mtDNA haplotypes. The dominant factor influencing genetic diversity on the islands was island size. No correlation was detected between genetic diversity and the time since isolation or distance form the mainland. The combination of genetic drift within and complete isolation among the small island populations has resulted in rapid and extreme population divergence. Population pair-wise comparisons of allele frequency distributions showed significant differences for all populations for all loci (F
st = 0.11–0.84, R
st = 0.07–0.99). For the mtDNA control region, 92.6% of variation was apportioned between populations; only the Pearson islands shared a haplotype. Mantel tests of pair-wise genetic distance with pair-wise geographic distance showed no significant geographical clustering of haplotypes. However, population substructuring was detected within populations where sampling was conducted over a broader geographical range, as indicated by departures from Hardy-Weinberg equilibrium. Thus substructuring in the ancestral population cannot be ruled out. The dominant evolutionary forces on the islands, after the initial founder event, are stochastic population processes such as genetic drift and mutation.
Since European settlement, mainland Australia has experienced a wave of mammal extinctions and population declines. However, some species have persisted on off-shore islands, which are now viewed as important wildlife refuges. In this study, we assessed the level of genetic diversity, at 7–11 microsatellite loci, in island and remnant mainland populations of three endemic species of macropodid marsupial; the tammar wallaby Macropus eugenii(n = 92); rufous hare-wallaby Lagorchestes hirsutus(n = 40) and black-footed rock-wallaby Petrogale lateralis(n = 164). There was a consistent pattern of significantly higher levels of microsatellite diversity in the remnant mainland population (A= 4.9–13.9; He= 0.61–0.86) of each species compared to conspecific pristine island populations (A= 1.2–3.7; He= 0.05–0.44). These marked differences are even apparent where island populations currently have a substantially larger census size. In addition, island populations were substantially inbred (Fe= 0.49–0.91). Although island populations have been insulated from the relatively recent threatening processes operating on the mainland, they have nevertheless been significantly impacted by increased inbreeding and the substantial erosion of genetic diversity. Despite the difficulties of ensuring the survival of remnant mainland populations, they appear to retain substantially more genetic diversity than their island counterparts and therefore are more likely to contribute to the long-term persistence of their species. These data also demonstrate that small remnant mainland populations (n < 10–20)="" are="" often="" capable="" of="" rapid="" recovery="" and="" are="" not="" necessarily="" genetically="">
Low levels of genetic variation are thought to contribute significantly to the higher extinction rates of endemic island populations compared to their mainland counterparts. We used six microsatellite loci to compare the genetic structure of the endangered silver rice rat (Oryzomys argentatus) population in Saddlebunch Key, Florida to the mainland population of the closely related marsh rice rat (Oryzomys palustris natator) in Everglades National Park. Allelic richness and gene diversity are significantly lower in Saddlebunch Key than in the larger mainland population, and the two populations are significantly differentiated as measured by both F-statistics and Bayesian clustering methods. These findings support the classification of the Keys population as a “distinct vertebrate population” by the U.S. Fish and Wildlife Service. Current gene diversity (H
E) is higher than expected under mutation-drift equilibrium in Saddlebunch Key, indicating a genetic bottleneck. The Keys population also exhibits a mode shift in its allele frequency distribution which suggests a very recent bottleneck has occurred and is consistent with reports of recent population declines. Although habitat loss and exotic species pose a more immediate and serious threat to silver rice rats, the continued loss of genetic variation may contribute to their long-term extinction risk due to inbreeding or by lowering the population’s ability to adapt to future environmental changes. The protection of habitat and the removal of introduced predators and competitors may help increase the population size of silver rice rats and lower their risk of extinction, both from a demographic and a genetic perspective.
Cozumel Island in the Mexican Caribbean is inhabited by four carnivores, of which two, the Cozumel coati Nasua nelsoni and pygmy raccoon Procyon pygmaeus, are endemic species. The taxonomic status of a third carnivore, a dwarf gray fox Urocyon cinereoargenteus, is undetermined, but may deserve subspecific or species-level recognition. The fourth species, the kinkajou (Potos flavus), may be a recent introduction. We review the status of these carnivores, report our field observations and results of line transect and trapping efforts, discuss current threats to these taxa, and make recommendations for their conservation. A population density of 0.43 0.27 coatis/km2, and a total island population size of 150 95 individuals, was estimated from 386 km of line transects in 1994–1995. Intensive trapping efforts (1479 trap-nights) in 2001 at multiple localities were unsuccessful. Pygmy raccoons were observed in the mangrove and coastal wetland areas of the island and in 2001 we captured 11 individuals with the same sampling efforts as for coatis (8.8 raccoons/1000 trap-nights). The gray fox is also apparently very rare on the island. While a few observations of the animals have been made (1984, 1994 and 2001), no animals were seen along transects and none were trapped. The primary threats to the persistence of these taxa include introduced congeners, introduced predators, parasite and disease spill-over from exotic animals, habitat fragmentation, hunting and collection as pets, and hurricanes. We suggest that the Cozumel coati, pygmy raccoon, and the Cozumel population of the gray fox be considered as Critically Endangered according to the IUCN classification system. Current conservation actions focusing on Cozumel carnivores are extremely limited. We recommend eradication of introduced species, maintenance of habitat connectivity, ex situ conservation programs, explicit public policies on land-use and sustainable development, public awareness campaigns, and continuous scientific research and monitoring.
We present evidence indicating that the boa (Boa constrictor) was introduced onto Cozumel Island, Quintana Roo, Mexico, in 1971. This snake is now firmly established and has a wide distribution on Cozumel. We recorded an encounter rate of 1.8 boas per 100 km of forest surveyed. The introduction of the boa onto Cozumel, where it has few predators, is a threat to the existence of endemic and other native terrestrial vertebrates of the island. We recommend the following immediate actions: (1) undertake research to confirm the origin of the boa on Cozumel; (2) assess the effect of the boa on the biota of Cozumel; and, (3) if an anthropogenic origin is confirmed, an eradication programme for the boa on Cozumel should be undertaken, obtaining information on the biology and ecology of the species. Options for the destiny of the eradicated boas are discussed.
We analyze the status of the Angel de la Guarda deer mouse (Peromyscus guardia), a species endemic to Mexico, based on our own fieldwork, bibliographic records and information from colleagues. This species, with different subspecies on three islands and a population of an undetermined subspecies on a fourth, was apparently common until the mid-1960s. Currently the species is critically endangered, if not already extinct. One of the subspecies and the undetermined population are presumed extinct. Of the two other subspecies, one is at least in critical condition, and the other at least reduced. The demise of the species can be attributed to the introduction of domestic cats. The case of P. guardia is a good example of the vulnerability of other taxa of endemic rodents on islands in the Gulf of California.
Formulae are given for estimators for the parameters F, θ, f (FIT, FST, FIS) of population structure. As with all such estimators, ratios are used so that their properties are not known exactly, but they have been found to perform satisfactorily in simulations. Unlike the estimators in general use, the formulae do not make assumptions concerning numbers of populations, sample sizes, or heterozygote frequencies. As such, they are suited to small data sets and will aid the comparisons of results of different investigators. A simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure.
Note that an updated reference for Genepop is Rousset (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux (DOI: 10.1111/j.1471-8286.2007.01931.x)
We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.
A new measure of the extent of population subdivision as inferred from allele frequencies at microsatellite loci is proposed and tested with computer simulations. This measure, called R(ST), is analogous to Wright's F(ST) in representing the proportion of variation between populations. It differs in taking explicit account of the mutation process at microsatellite loci, for which a generalized stepwise mutation model appears appropriate. Simulations of subdivided populations were carried out to test the performance of R(ST) and F(ST). It was found that, under the generalized stepwise mutation model, R(ST) provides relatively unbiased estimates of migration rates and times of population divergence while F(ST) tends to show too much population similarity, particularly when migration rates are low or divergence times are long [corrected].
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
The "cozumela complex" of parthenogenetic teiid lizards is currently identified by three taxa: Cnemidophorus cozumela cozumela from Isla Cozumel, Quintana Roo, Mexico; C. c. maslini from scattered localities in Campeche and Quintana Roo, Mexico, Guatemala, and Belize; and C. rodecki from Islas Contoy and Mujeres and the adjacent mainland of Quintana Roo, Mexico. We used 59 individuals of C. c. cozumela, 126 individuals of C. c. maslini, and 48 individuals of C. rodecki and principal components and canonical variate analyses of meristic characters to resolve patterns of morphological variation within and among the three taxa. The principal components analysis identified three primary groups of individuals corresponding to the three taxa presently recognized. Collectively, each taxon exhibits approximately the same level of morphological distinctiveness; 92% of C. cozumela, 98% of C. maslini, and 100% of C. rodecki were assigned to the correct a priori group by a jackknifed classification in canonical variate analysis. We propose species level status for C. c. maslini to reflect a level of morphological divergence commensurate with that
seen between C. c. cozumela and C. rodecki. Cnemidophorus maslini is comprised of a minimum of three meristically distinctive groups: MC-A from coastal Campeche, Mexico, MC-B from coastal Campeche, approximately 13 km southwest of MC-A, and MG from northern Guatemala. A small sample from southern Quintana Roo and a single specimen from Belize may represent a fourth group. In the absence of evidence for polyphyly, these four subsidiary groups of C. maslini can be referred to as the Cnemidophorus maslini complex.
A method is presented by which the gene diversity (heterozygosity) of a subdivided population can be analyzed into its components, i.e., the gene diversities within and between subpopulations. This method is applicable to any population without regard to the number of alleles per locus, the pattern of evolutionary forces such as mutation, selection, and migration, and the reproductive method of the organism used. Measures of the absolute and relative magnitudes of gene differentiation among subpopulations are also proposed.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
It has been argued that demographic and environmental factors will cause small, isolated populations to become extinct before genetic factors have a significant negative impact. Islands provide an ideal opportunity to test this hypothesis because they often support small, isolated populations that are highly vulnerable to extinction. To assess the potential negative impact of isolation and small population size, we compared levels of genetic variation and fitness in island and mainland populations of the black-footed rock-wallaby (Petrogale lateralis[Marsupialia: Macropodidae]). Our results indicate that the Barrow Island population of P. lateralis has unprecedented low levels of genetic variation ( He= 0.053, from 10 microsatellite loci) and suffers from inbreeding depression (reduced female fecundity, skewed sex ratio, increased levels of fluctuating asymmetry). Despite a long period of isolation (∼1600 generations) and small effective population size ( Ne∼15), demographic and environmental factors have not yet driven this population to extinction. Nevertheless, it has been affected significantly by genetic factors. It has lost most of its genetic variation and become highly inbred ( Fe= 0.91), and it exhibits reduced fitness. Because several other island populations of P. lateralis also exhibit exceptionally low levels of genetic variation, this phenomenon may be widespread. Inbreeding in these populations is at a level associated with high rates of extinction in populations of domestic and laboratory species. Genetic factors cannot then be excluded as contributing to the extinction proneness of small, isolated populations.
Along a narrow, unsealed road through rainforest in north-eastern Queensland,
movements of small mammals were examined to determine whether the road would
inhibit road crossings, thereby causing linear barrier effects. Crossings of a
12- or 20-m-wide road clearing by Melomys cervinipes
were severely inhibited, crossing inhibition of Rattus
sp. was less severe, while crossings by
Uromys caudimaculatus were unaffected. This differential
effect was attributed to species differences in size, mobility and behaviour.
Baiting on only one side of the road increased crossing rates for all species.
During the breeding season, crossings of 20-m clearings by
Rattus sp. were almost completely inhibited and were
significantly fewer than crossings of 12-m clearings. Clearing width had
little effect on crossing rate outside the breeding season. Seasonal dispersal
of juvenile and breeding animals appeared to explain this discrepancy in
clearing-width effects. Rattus sp. were significantly
less likely to cross a road where there was no vegetative cover at the
entrance to a road culvert than where there was cover at both culvert
entrances. Linear barrier effects for small mammals may be mitigated by
narrower road-clearing widths, by replanting of grassy road verges resulting
in increased cover at culvert entrances and canopy closure above the road, and
by providing more faunal underpasses.
The fixation of new deleterious mutations is analyzed for a randomly mating population of constant size with no environmental or demographic stochasticity. Mildly deleterious mutations are far more important in causing loss of fitness and eventual extinction than are lethal and semilethal mutations in populations with effective sizes, N-e, larger than a few individuals. If all mildly deleterious mutations have the same selection coefficient, s against heterozygotes and 2s against homozygotes, the mean time to extinction, (t) over bar, is asympototically proportional to e(4Nes)/N-e for 4N(e)s > 1. Nearly neutral mutations pose the greatest risk of extinction for stable populations, because the magnitude of selection coefficient that minimizes (t) over bar is about (s) over cap = 0.4/N-e. The influence of variance in selection coefficients among mutations is analyzed assuming a gamma distribution of s, with mean (s) over bar and variance sigma(s)(2). The mean time to extinction increases with variance in selection coefficients if (s) over bar is near (s) over cap, but can decrease greatly if (s) over bar is much larger than (s) over cap. For a given coefficient of variation of s, c = sigma(s)/(s) over bar, the mean time to extinction is asymptotically proportional to N-e(1+/c2) for 4N(e) (s) over bar > 1. When s is exponentially distributed, (c = 1) (t) over bar is asymptotically proportional to N-e(2). These results in conjunction with data on the rate and magnitude of mildly deleterious mutations in Drosophila melanogaster indicate that even moderately large populations, with effective sizes on the order of N-e = 10(3), may incur a substantial risk of extinction from the fixation of new mutations.
Current research in interorganizational information systems (IOS) for B2B eCommerce tends to focus on the factors that lead to the intention to adopt these systems. One important factor is the IT capability of a network member in the supply chain, but the extant literature is silent on the nature of the link between this factor and the intention to adopt. This paper contributes to the research literature by a critical approach that examines in detail the structure, dynamics and complexity of the link between them. Based on the literature review we suggest six mediating factors between IT capability and its intention to increase the sophistication of its business-to-business integration (B2Bi). We develop a relational model of network atmosphere and network structure, which between them, encompass these factors. Based on the model and previous research findings, we justify 12 propositions grouped into three sets which has the following contributions. First, it has proposed an integrated model which allows us to understand the interaction between factors in a firm's environment and factors inside a firm. Second, the structural model has firstly posited external factors as the mediating variables interacting with each other along the proposed links. Third, the study suggests that the state can play a significant role in enhancing the capability of channel stakeholders in the new economy associated with B2Bi.
Many of the world's oceanic and oceanic-like islands possessed endemic mammal faunas before they were colonized by humans. These faunas, unbalanced and impoverished compared to continental faunas, usually lacked large mammalian carnivores. In virtually all cases, the arrival of humans and their domesticants and commensals on these islands is related to the extirpation of large numbers of endemic insular mammals. These extinction events affected at least 27% of autochthonous mammal species on the world's oceanic and oceanic-like islands. This percentage rises the 35% when volant mammals are excluded. This reduction in the natural biodiversity brought about the disappearance of several unique biological types that apparently never existed on the continents.
Small populations lose genetic variability because of genetic drift, and inbreeding within populations can further decrease individual variability. Lower variation depresses individual fitness, resistance to disease and parasites, and flexibility in coping with environmental challenges. Lower variation decreases mean fitness of populations (population growth rates), resilience. and long-term adaptability. Genetic drift can threaten viability of populations not just by depleting variation, but also by replacing natural selection as the predominant force driving evolutionary change. Although most genetic studies use laboratory or domesticated populations, evidence is accumulating that the effects of inbreeding are at least as severe on wild animals in natural habitats. Natural selection is expected to reduce the frequency of deleterious alleles in populations that persist through bottlenecks, but as yet there is little evidence for such purging of the genetic load in mammalian populations. No species of mammal has been shown to be unaffected by inbreeding. Genetic problems are contributing to the decline and vulnerability of at least several mammalian ta,va. Genetic threats to population viability will be expressed through their effects on and interactions with demographic and ecological processes. Theoretical analyses. experimental tests, field studies, and conservation actions should recognize the fundamental interdependency of generic and non-genetic processes affecting viability of populations.
Island populations are more prone to extinction than mainland populations, with island endemic species having higher extinction rates than nonendemic species. Inbreeding depression is one possible explanation for this. Insular populations are expected to suffer increased inbreeding relative to mainland populations due to bottlenecks at foundation and to lower subsequent population sizes. Inbreeding coefficients for 182 nonendemic and 28 endemic island populations were estimated from allozyme and microsatellite heterozygosities in island and related mainland populations. Island populations were significantly inbred, with inbreeding coefficients significantly higher in endemic than nonendemic island populations. Many island populations showed levels of inbreeding associated with elevated extinction rates in domestic and laboratory species. Inbreeding depression cannot be excluded as a factor in the extinction proneness of island populations.
Intracruza y Extinción: Poblaciones Isleñas
Poblaciones Isleñas presentan una mayor tendencia a la extinció que las poblaciones continentales, teniendo las especies endémicas una mayor tasa de extinción que las especies no endémicas. La depresión por intracruza es una explicación posible a esto. Es de esperarse que poblaciones insulares sufran una intracruza relativemente mas alta que las poblaciones continentales debido a cuellos de botella a nivel de tamaño poblacional de fundación y subsecuentes tamaños poblacionales menores. Los coeficientes de intracruza para 182 poblaciones no endémicas y 28 poblaciones endémicas se estimaron mediante heterozigocidades de alozimas y microsatélites de poblaciones de islas y especies continentales relacionadas. Las poblaciones isleñas estuvieron significativamente intracruzadas, con coeficientes de intracruza signifiativamente mayores en poblaciones endémicas que en las poblaciones no endémicas. Muchas poblaciones isleñas mostraron niveles de intracruza asocidos con elevadas tasas de extinción en especies domesticas y de laboratorio. La depresión por intracruza no puede ser excluída como un factor en la tendencia a la extinción de especies isleñas.
On islands in the Gulf of California, many species and subspecies of rodents are relict species, restricted to the islands, and now considered extinct or verging on extinction. From 1991 to 1999, each island was surveyed and an average of 15 work-nights were spent on each island, for a total of 15,000 trap-nights. A Fourier series was used to estimate population density. Five native taxa are now considered extinct (Chaetodipus baileyi fornicatus, Peromyscus guardia mejiae, P. g. harbinsoni, P. pembertoni, and Neotoma bunkeri). Two species are at risk of extinction (Dipodomys insularis and Neotoma albigula varia). The most probable cause for extinction is the introduction of nonnative species, specifically cats. We believe that the most vulnerable rodent populations of the islands in the Gulf of California to non-native species are Neotoma lepida latirostra on Danzante island and Neotoma lepida abbreviata on San Francisco island, both in the state of Baja California Sur.
The Nova Scotia population of Blanding’s turtle (Emydoidea blandingii) is small and disjunct but surprisingly contains spatial structure. In this paper we explore the nature of that structure and attempt to identify the processes underlying it. Recent studies of the species in Nova Scotia have identified three discrete groups in what was previously thought to be a single panmictic population. There is no evidence of current movement between these groups. One group, at Kejimkujik National Park and National Historic Site, is restricted to the Mersey watershed; the other two groups are on the adjacent Medway watershed. The lack of current movement led to the prediction that there might be measurable genetic structure among these groups. Microsatellite analysis of five loci revealed significant genetic structure (FST = 0.042–0.124; p < 0.05) in pairwise comparisons between groups. Distance rather than watershed appears to be the principal determinant of spatial structure. Two separate analyses reveal no evidence of recent population bottlenecks. Population simulations suggest that this differentiation likely pre-dated human influence on the local landscape. In the face of rapid environmental change, understanding spatial structure in this population complex is essential so that we can match management scale to ecological scale in this long-lived, late maturing species.
: In this comprehensive review, a range of factors is considered that may influence the significance of genetic diversity for the survival of a population. Genetic variation is essential for the adaptability of a population in which quantitatively inherited, fitness-related traits are crucial. Therefore, the relationship between genetic diversity and fitness should be studied in order to make predictions on the importance of genetic diversity for a specific population. The level of genetic diversity found in a population highly depends on the mating system, the evolutionary history of a species and the population history (the latter is usually unknown), and on the level of environmental heterogeneity. An accurate estimation of fitness remains complex, despite the availability of a range of direct and indirect fitness parameters. There is no general relationship between genetic diversity and various fitness components. However, if a lower level of heterozygosity represents an increased level of inbreeding, a reduction in fitness can be expected. Molecular markers can be used to study adaptability or fitness, provided that they represent a quantitative trait locus (QTL) or are themselves functional genes involved in these processes. Next to a genetic response of a population to environmental change, phenotypic plasticity in a genotype can affect fitness. The relative importance of plasticity to genetic diversity depends on the species and population under study and on the environmental conditions. The possibilities for application of current knowledge on genetic diversity and population survival for the management of natural populations are discussed.
A statistic useful for detecting deviations from the Hardy-Weinberg equilibrium in population genetics is discussed. Both exact and asymptotic distributions are given and a special case where there is misclassification is discussed. The distribution obtained also arises from a certain card matching problem.