No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Genetic diversity, but not hatching success, is jointly affected by postglacial colonization and isolation in the threatened frog (vol 16, pg 1787, 2007)
Abstract
Both postglacial colonization and habitat fragmentation can reduce the genetic diversity of populations, which in turn can affect fitness. However, since these processes occur at different spatial and temporal scales, the consequences of either process may differ. To disentangle the relative role of isolation and postglacial colonization in determining genetic diversity and fitness, we studied microsatellite diversity of 295 individuals from 10 populations and measured the hatch rate of 218 clutches from eight populations of a threatened frog, R. latastei. The populations that were affected by fragmentation to a greater extent suffered higher embryo mortality and reduced hatch rate, while no effects of distance from glacial refugium on hatch rate were detected. Altogether, distance from glacial refugium and isolation explained > 90% of variation in genetic diversity. We found that the genetic diversity was lowest in populations both isolated and far from the glacial refugium, and that distance from refugium seems to have the primary role in determining genetic diversity. The relationship between genetic diversity and hatch rate was not significant. However, the proportion of genetic diversity lost through recent isolation had a significant, negative effect on fitness. It is possible that selection at least partially purged the negative effects of the ancestral loss of genetic diversity.
... In anuran amphibians, typically 80–95% of mortality occurs between hatch and metamorphosis (Vonesh and De la Cruz 2002) and inbreeding depression may be most readily detected through the measurement of relevant population genetics parameters during these periods of heavy mortality (Rowe and Beebee 2003; Halverson et al. 2006; Chapman et al. 2009). In this study, we used microsatellite DNA polymorphisms to study temporal variation of genetic features in small, isolated population of a threatened frog suffering strong inbreeding depression (Ficetola et al. 2007 ). We analyzed the genetic features of the same cohort at two subsequent life-history stages, immediately after hatch and at metamorphosis; our sampling protocol was therefore designed to compare the genetic features of a cohort before and after the effects of potentially strong natural selection. ...
... In particular, the western part of the distribution of R. latastei is broken into a limited number of small and isolated forest fragments. Many breeding sites are characterized by small census size and geographic isolation (Ficetola et al. 2007 ) and this combination of isolation and small population size has increased the risk of extinction of populations (Ficetola and De Bernardi 2004). Further, the part of the species range from which our study population comes from is characterized by a 3· reduction in genetic variability when compared to the eastern part of the range (Garner et al. 2004 ) and experiments have shown that reductions in genetic variability correlate well with reduced fitness (Pearman and Garner 2005; Ficetola et al. 2007). ...
... Many breeding sites are characterized by small census size and geographic isolation (Ficetola et al. 2007 ) and this combination of isolation and small population size has increased the risk of extinction of populations (Ficetola and De Bernardi 2004). Further, the part of the species range from which our study population comes from is characterized by a 3· reduction in genetic variability when compared to the eastern part of the range (Garner et al. 2004 ) and experiments have shown that reductions in genetic variability correlate well with reduced fitness (Pearman and Garner 2005; Ficetola et al. 2007). Breeding occurs in late winter; females lay a single egg mass per year (Barbieri and Mazzotti 2006 ), therefore the number of clutches represents both annual population reproductive output and the number of breeding females in a population. ...
Populations that are small and isolated can be threatened through loss of fitness due to inbreeding. Nevertheless, an increased frequency of recessive homozygotes could increase the efficiency of selection against deleterious mutants, thus reducing inbreeding depression. In wild populations, observations of evolutionary changes determined by selection against inbreeding are few. We used microsatellite DNA markers to compare the genetic features of tadpoles immediately after hatch with those of metamorphosing froglets belonging to the same cohort in a small, isolated population of the threatened frog Rana latastei. Within a generation, the inbreeding coefficient (FIS) decreased: at hatch, FIS was significantly >0, whereas FIS was <0 after metamorphosis. Furthermore, heterozygosity increased and allelic frequencies changed over time, resulting in the loss of genotypes at metamorphosis that were present in hatchlings. One microsatellite locus exhibited atypically large FST values, suggesting it might be linked to a locus under selection. These results support the hypothesis that strong selection against the most inbred genotypes occurred among early life-history stages in our population. Selective forces can promote changes that can affect population dynamics and should be considered in conservation planning.
... In real populations, however, deviations from this ideal situation may result in a reduction in N e and thus, an increased loss of genetic variation (Frankham, Ballou & Briscoe, 2002). Assuming a negative relationship between genetic erosion and the probability of population persistence , decreasing values for N e or the ratio N e /N should increase the risk of loss of population-averaged fitness and possible population extinction through inbreeding (Frankham et al., 2002; Spielman, Brook & Frankham, 2004; O'Grady et al., 2006; Ficetola, Garner & De Bernardi, 2007; Palstra & Ruzzante, 2008). As such, small N e or N e /N values are considered to be indications of the potential for loss of genetic variability within a population; the assessment of N e in wild populations, in conjunction with population size estimates, is an extremely valuable tool for the conservation management of populations. ...
... Metapopulation dynamics and concurrent gene flow can maintain N e (Matocq, 2004; Schmeller & Meriïa, 2007) and amphibian populations often exhibit metapopulation dynamics or are maintained through post-metamorphic dispersal (see Smith & Green, 2005). Thus, anthropogenic habitat alteration and landscape fragmentation that reduces connectivity among populations and associated gene flow may directly and negatively affect N e (Hitchings & Beebee, 1997; Johansson et al., 2005; Cushman, 2006; Ficetola et al., 2007). At the population level, several factors can influence the N e /N ratio: periodic fluctuations in census size, an unequal sex ratio and high variance in reproductive success (Frankham, 1995). ...
... Rana latastei exists in small, isolated populations threatened through increasing fragmentation and exploitation of terrestrial habitat (Ficetola & De Bernardi, 2004, 2005). Previous work has shown that population genetic variability can be severely depleted in this species (Garner, Angelone & Pearman, 2004), and that population isolation as well as historical processes contribute to the pattern observed (Ficetola et al., 2007). To date, the role population size and mating system have played in determining population genetic structure has not been assessed; research suggests mating system should influence genetic structure (Hettyey & Pearman, 2003). ...
Effective population size (N(e)) is a key determinant of genetic diversity of populations. In amphibians, the ratio effective population size/census size (N(e)/N) is often very low, raising concerns for the long-term persistence of genetic diversity in isolated populations. It has been proposed that the phenomenon of 'genetic compensation' increases the ratio N(e)/N in small populations, but the underlying mechanisms are poorly understood. Polygyny can decrease N(e)/N because of the negative relationship between polygyny and N(e). We used genetic information (microsatellites) to evaluate the relationship between census size, polygyny and N(e) in populations of the threatened Italian agile frog Rana latastei. We reconstructed parentage in tadpoles from nine populations with eight to 32 breeding females, using a likelihood-based method; we analysed simulated datasets with known properties to confirm the reliability of this approach in reconstructing polygyny. Furthermore, we estimated N(e) using approximate Bayesian computation. The level of polygyny differed strongly among populations (average number of mates per breeding male: 2-6.4). Polygyny was greater in populations with larger census sizes. Moreover, variance in male mating success was larger in large populations. Effective population size increased with population size, but was negatively related to polygyny; as polygyny increased in large populations, this was associated with reduced N(e)/N. In polygynous species, increasing levels of polygyny in large populations may explain the low N(e)/N values, with important implications for the conservation of genetic diversity and for long-term population persistence.
... One of the primary challenges facing contemporary ecological and evolutionary research is predicting the potential effects of global climate change on populations across broad latitudinal ranges. Of recent concern has been the theoretical prediction that populations expanding into northern climates will experience a rapid loss of genetic diversity [1][2][3][4][5][6], which may in turn restrict the ability of populations to adapt to new selection regimes and novel stressors [7][8][9][10]. The current global warming event is comparable to past episodes of glacial retreat [11]. ...
... The primary hypothesis for how genetic diversity is patterned across the postglacial landscape states that populations founded after a postglacial expansion should have less genetic diversity as a result of population bottlenecks and/or new selection pressures, resulting in reduced effective population sizes and thus less genetic diversity relative to their historical populations outside the glacial barrier [16,17]. Many studies have evaluated this hypothesis by comparing genetic diversity along latitudinal gradients spanning the glacial boundaries for various species using neutral genetic markers, including allozymes [18,4,7,19,20], mitochondrial markers [19,21,22], and microsatellite loci [10,22,23]. Overall, these neutral marker studies have supported the hypothesis that a loss of genetic diversity is associated with the expansion of populations in a postglacial landscape. ...
... Under this scenario, populations that show low heritabilities as a result of stabilizing selection in the source population become subject to drift and founder effects in the colonial population, which in turn reduces epistasis, increases dominance effects, and ultimately exposes variability that was masked in the source population. The founder effects combined with novel selection regimes can also increase genetic variability in the short term by favoring new allelic combinations [10,20] and thus inflating heritable variation. ...
Global climate change is expected to trigger northward shifts in the ranges of natural populations of plants and animals, with subsequent effects on intraspecific genetic diversity. Investigating how genetic diversity is patterned among populations that arose following the last Ice Age is a promising method for understanding the potential future effects of climate change. Theoretical and empirical work has suggested that overall genetic diversity can decrease in colonial populations following rapid expansion into postglacial landscapes, with potential negative effects on the ability of populations to adapt to new environmental regimes. The crucial measure of this genetic variation and a population's overall adaptability is the heritable variation in phenotypic traits, as it is this variation that mediates the rate and direction of a population's multigenerational response to selection. Using two large full-sib quantitative genetic studies (N(Manitoba) = 144; N(South Dakota) = 653) and a smaller phenotypic analysis from Kansas (N(Kansas) = 44), we compared mean levels of pigmentation, genetic variation and heritability in three pigmentation traits among populations of the common garter snake, Thamnophis sirtalis, along a north-south gradient, including a postglacial northern population and a putative southern refuge population. Counter to our expectations, we found that genetic variance and heritability for the three pigmentation traits were the same or higher in the postglacial population than in the southern population.
... Furthermore, the landscape surrounding breeding wetlands is extremely important for dispersal. Habitat split and fragmentation impede dispersal, disrupting the dynamics of extinction/colonization associated with metapopulations ( Ficetola and De Bernardi 2004;Willson and Hopkins 2013), cause genetic drift and loss of genetic diversity Beebee 1997, 1998;Rowe et al. 1999;Ficetola et al. 2007;Johansson et al. 2007), and may ultimately result in loss of fitness (Hitchings and Beebee 1998;Rowe et al. 1999;Rowe and Beebee 2003;Ficetola et al. 2007;Johansson et al. 2007) and population extinctions ( Saccheri et al. 1998;Ficetola and De Bernardi 2004;Becker et al. 2007;Willson and Hopkins 2013). Actually, the presence of terrestrial habitat nearby breeding wetlands has been proposed as a major parameter to assess threat status of species ( Almeida-Gomes et al. 2014). ...
... Furthermore, the landscape surrounding breeding wetlands is extremely important for dispersal. Habitat split and fragmentation impede dispersal, disrupting the dynamics of extinction/colonization associated with metapopulations ( Ficetola and De Bernardi 2004;Willson and Hopkins 2013), cause genetic drift and loss of genetic diversity Beebee 1997, 1998;Rowe et al. 1999;Ficetola et al. 2007;Johansson et al. 2007), and may ultimately result in loss of fitness (Hitchings and Beebee 1998;Rowe et al. 1999;Rowe and Beebee 2003;Ficetola et al. 2007;Johansson et al. 2007) and population extinctions ( Saccheri et al. 1998;Ficetola and De Bernardi 2004;Becker et al. 2007;Willson and Hopkins 2013). Actually, the presence of terrestrial habitat nearby breeding wetlands has been proposed as a major parameter to assess threat status of species ( Almeida-Gomes et al. 2014). ...
Amphibian conservation is a central theme of biodiversity research, as demonstrated by the growing number of studies on this theme. I combined a review of the literature with a quantitative analysis of papers published from 1992 to 2013, to evaluate whether methodological and thematic shifts occurred during the last two decades, and to identify major lines along which amphibian biodiversity research may be developed and improved. Spatial autocorrelation and imperfect detection are major issues of the analysis of data from amphibian populations. During the last decade, technical developments allowed to take into account these statistical issues in a growing number of studies. Nevertheless, the use of these approaches may be more widespread, particularly for the analysis of spatially-autocorrelated data. It is widely recognized that amphibian decline is often determined by the joint effect of multiple processes. However, the majority of recent studies focused on one potential threat only, and research rarely integrated analyses on terrestrial and aquatic environments. Finally, tropical areas remain insufficiently represented in amphibian conservation studies, despite they harbour most of biodiversity and threatened species. A better incorporation of technical advancements, and an expansion of themes and geographical scope can improve our understanding of processes determining the amphibian biodiversity crisis, and to improve the linkages between conservation research and practical actions.
... For instance, within the Ontario contact zone, the Eastern lineage is the furthest from its presumed glacial refugium in the southern Appalachians (Austin et al. 2002Austin et al. , 2004) and protracted northerly migration after glacial retreat probably involved sequential founder events and genetic drift in populations with small effective size. Erosion of genetic variability through sequential founder effects during range expansion from glacial refugia and contemporary range fragmentation can combine to diminish population genetic diversity (Garner et al. 2004; Ficetola et al. 2007). In fact, the highest level of genetic diversity for spring peepers was found in populations closest to the posited refugia (Austin et al. 2002 ). ...
... Moreover, such genetic erosion is accentuated by inbreeding with consequent fitness reductions in other anurans (Hitchings and Beebee 1998). For example, genetic diversity affects hatching success and tadpole fitness in Rana latastei (Ficetola et al. 2007), and premetamorphic survival in Bufo bufo (Hitchings and Beebee 1998). Alternatively, differential hatching success and tadpole survival among different environments may be a consequence of past selection. ...
Phenotypically cryptic lineages appear common in nature, yet little is known about the mechanisms that initiate and/or maintain barriers to gene flow, or how secondary contact between them might influence evolutionary trajectories. The consequences of such contact between diverging lineages depend on hybrid fitness, highlighting the potential for postzygotic isolating barriers to play a role in the origins of biological species. Previous research shows that two cryptic, deeply diverged intraspecific mitochondrial lineages of a North American chorus frog, the spring peeper (Pseudacris crucifer), meet in secondary contact in Southwestern Ontario, Canada. Our study quantified hatching success, tadpole survival, size at metamorphosis, and development time for experimentally generated pure lineage and hybrid tadpoles. Results suggest that lineages differ in tadpole survival and that F1 hybrids may have equal fitness and higher than average mass at metamorphosis compared with pure parental crosses. These findings imply hybrid early life viability may not be the pivotal reproductive isolation barrier helping to maintain lineage boundaries. However, we observed instances of tadpole gigantism, failure to metamorphose, and bent tails in some tadpoles from hybrid families. We also speculate and provide some evidence that apparent advantages or similarities of hybrids compared with pure lineage tadpoles may disappear when tadpoles are raised with competitors of different genetic makeup. This pilot study implies that ecological context and consideration of extrinsic factors may be a key to revealing mechanisms causing negative hybrid fitness during early life stages, a provocative avenue for future investigations on barriers to gene flow among these intraspecific lineages.
... Similarly, a study of the Natterjack toad (Bufo calamita) across Europe revealed a remarkable decrease in genetic diversity with increasing northern latitude that could not be easily attributed to anthropogenic effects [77]. In an elegant study, Ficetola et al. [78] were able to show that the genetic signal in Rana latastei was jointly shaped by postglacial colonization patterns and recent fragmentation, but that fitness, in this case hatching success, was only affected by the latter. It can be a difficult task to discriminate between low genetic diversity as a result of recent fragmentation or as a remnant of the phylogeographic history (e.g., [62]), but from a conservation perspective, an attempt to make the distinction is important. ...
... In this context, any adaptations conferring local advantage on the small inbred population appear to be largely over-ruled by much greater general fitness among individuals from the genetically diverse population. Clutch size [117] and hatching success [78] have both shown a significant GFC. The latter study is especially interesting in that it effectively manages to isolate the effects of long term genetic loss due to long term dispersal patterns from more recent habitat fragmentation, with fitness only negatively affected by the recent genetic loss, again providing a compelling argument for the direct link between human-mediated landscape changes and reduced amphibian viability because of genetic effects. ...
It is well established that a decrease in genetic variation can lead to reduced fitness and lack of adaptability to a changing environment. Amphibians are declining on a global scale, and we present a four-point argument as to why this taxonomic group seems especially prone to such genetic processes. We elaborate on the extent of recent fragmentation of amphibian gene pools and we propose the term dissociated populations to describe the residual population structure. To put their well-documented loss of genetic diversity into context, we provide an overview of 34 studies (covering 17 amphibian species) that address a link between genetic variation and >20 different fitness traits in amphibians. Although not all results are unequivocal, clear genetic-fitness-correlations (GFCs) are documented in the majority of the published investigations. In light of the threats faced by amphibians, it is of particular concern that the negative effects of various pollutants, pathogens and increased UV-B radiation are magnified in individuals with little genetic variability. Indeed, ongoing loss of genetic variation might be an important underlying factor in global amphibian declines.
... Though recent fragmentation of wetlands in the KV may have contributed to the reduced genetic variation, other factors have also contributed. For example, genetic variation is generally lower in areas that have been colonized by a species since the last period of wide-spread glaciation (10,000-15,000 years ago; Beebee and Rowe 2000; Newman and Squire 2001; Ficetola et al. 2007;Allentoft et al. 2009). Ficetola et al. (2007) found that genetic variation within populations of the frog, R. latastei, was affected by patterns of postglacial colonization, as well as contemporary isolation. ...
... For example, genetic variation is generally lower in areas that have been colonized by a species since the last period of wide-spread glaciation (10,000-15,000 years ago; Beebee and Rowe 2000; Newman and Squire 2001; Ficetola et al. 2007;Allentoft et al. 2009). Ficetola et al. (2007) found that genetic variation within populations of the frog, R. latastei, was affected by patterns of postglacial colonization, as well as contemporary isolation. Wood frog populations in Colorado occur in a few isolated mountain valleys (Hammerson 1999) and appear to be the result of colonization from populations in present-day Wisconsin following the last glaciation (Lee Yaw et al. 2008). ...
Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and this result was further supported by factorial component analysis. In addition, an estimate of F
ST (F
ST = 0.0675, P value <0.0001) supported the genetic differentiation of the two clusters. Estimates of migration rates among the two subpopulations were low, as were estimates of genetic variability. Conservation of the population of wood frogs may be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.
... Frog species in the genus Rana often show low genetic diversity within populations (Garner et al. 2003Garner et al. , 2004 Martínez-Solano et al. 2005; Ficetola et al. 2007) and high genetic differentiation among populations (Monsen and Blouin 2003; Palo et al. 2004a; Funk et al. 2005). This population structuring is usually attributed to behavioral philopatry and to a limited ability to disperse long distances between aquatic habitats (Seppa and Laurila 1999; Palo et al. 2004b). ...
... The few pairs of loci showing significant genotypic disequilibrium were not consistent across populations. The average expected heterozygosity (H e ), allelic richness (AR), and allelic richness rarified to n = 15 (AR 15 ) of each population are listed inTable 1. Genetic diversity measures for the R. cascadae populations are given in Online Resource 4. Levels of genetic variation in populations of R. pretiosa are low for a frog (Ficetola et al. 2007), with mean H e = 0.31 (range 0.14–0.50) versus mean H e = 0.54 in R. cascadae (range 0.33–0.74). ...
The Oregon spotted frog (Rana pretiosa) is one of the most threatened amphibians in the Pacific Northwest. Here we analyzed data from 13 microsatellite loci and 298 bp of mitochondrial DNA in frogs collected from 23 of the remaining R. pretiosa populations in order to (1) assess levels of genetic diversity within populations of R. pretiosa, (2) identify the major genetic groups in the species, (3) estimate levels of genetic differentiation and gene flow among populations within each major group, and (4) compare the pattern of differentiation among R. pretiosa populations with that among populations of R. cascadae, a non-endangered congener that also occurs in Oregon and Washington. There is a strong, hierarchical genetic structure in R. pretiosa. That structure includes six major genetic groups, one of which is represented by a single remaining population. R. pretiosa populations have low genetic diversity (average H
e = 0.31) compared to R. cascadae (average H
e = 0.54) and to other ranid frogs. Genetic subdivision among populations is much higher in R. pretiosa than in R. cascadae, particularly over the largest geographic distances (hundreds of kilometers). A joint analysis of migration rates among populations and of effective sizes within populations (using MIGRATE) suggests that both species have extremely low migration rates, and that R. pretiosa have slightly smaller effective sizes. However, the slight difference in effective sizes between species appears insufficient to explain the large difference in genetic diversity and in large-scale genetic structure. We therefore hypothesize that low connectivity among the more widely-spaced R. pretiosa populations (owing to their patchier habitat), is the main cause of their lower genetic diversity and higher among-population differentiation. Conservation recommendations for R. pretiosa include maintaining habitat connectivity to facilitate gene flow among populations that are still potentially connected, and either expanding habitat or founding additional ‘backup’ populations to maintain diversity in the isolated populations. We recommend that special consideration be given to conservation of the Camas Prairie population in Northern Oregon. It is the most geographically isolated population, has the lowest genetic diversity (H
e = 0.14) and appears to be the only remaining representative of a major genetic group that is now almost extinct. Finally, because the six major groups within R. pretiosa are strongly differentiated, occupy different habitat types, and are geographically separate, they should be recognized as evolutionarily significant units for purposes of conservation planning.
... Conservation studies in general and conservation genetics in particular are almost invariably concerned with the problems of small populations, where the rate at which genetic variation is lost (strength of genetic drift) is negatively correlated with the effective population size (Falconer and Mackay 1996; Gillespie 1998). Small and isolated populations will thus harbour little genetic variation and drift is likely to unveil the effects of genetic load that may build up in larger populations. ...
... Since fragmentation of natural habitats is likely to result in higher environmental stress and increased loss of genetic diversity (Willi et al. 2007), environment-dependent fitness costs associated with low genetic variation have considerable conservation implications . Moreover, if purging of deleterious alleles is important in reducing inbreeding depression under stressful conditions, the interaction between inbreeding depression and stress may be more detrimental in recently fragmented habitats where purging has not had the opportunity to act (Swindell and Bouzat 2006; Ficetola et al. 2007). Clearly, more research on the role of interaction between inbreeding and environmental stress is needed in order to evaluate the consequences of habitat fragmentation and environmental stress on natural populations. ...
A basic premise of conservation geneticists is that low levels of genetic variation are associated with fitness costs in terms
of reduced survival and fecundity. These fitness costs may frequently vary with environmental factors and should increase
under more stressful conditions. However, there is no consensus on how fitness costs associated with low genetic variation
change under natural conditions in relation to the stressfulness of the environment. On the Swedish west coast, natterjack
toad Bufo calamita populations show a strong population genetic structure and large variation in the amount of within-population genetic variation.
We experimentally examined the survival of natterjack larvae from six populations with different genetic variation in three
thermal environments corresponding to (a) the mean temperature of natural ponds (stable, laboratory), (b) a high temperature
environment occurring in desiccating ponds (stable, laboratory) and (c) an outdoor treatment mimicking the natural, variable
thermal conditions (fluctuating, semi-natural). We found that larvae in the outdoor treatment had poorer survival than larvae
in the stable environments suggesting that the outdoor treatment was more stressful. Overall, populations with higher genetic
variation had higher larval survival. However, a significant interaction between treatments and genetic variation indicated
that fitness costs associated with low genetic variation were less severe in the outdoor treatment. Thus, we found no support
for the hypothesis that fitness costs associated with low genetic variation increase under more stressful conditions. Our
results suggest that natural thermal stress may mask fitness losses associated with low genetic variation in these populations.
KeywordsConservation genetics-Genetic structure-Peripheral populations-Genetic diversity-Amphibians-Environmental stress
... From a genetic perspective, resulting loss of genetic diversity can lead to inbreeding and/or loss of evolutionary potential in changing environments (Reed and Frankham 2003; Andersen et al. 2004). While landscape change due to recent human activity is known to shape the genetic structure of populations, these effects are overlaid on biogeographical processes that have acted over a longer period of time (Beebee and Rowe 2000; Hoffman and Blouin 2004b; Ficetola et al. 2007). Such older changes in the landscape may complicate interpretation of patterns of genetic variation found among current habitat patches. ...
... Because amphibian populations are often difficult to monitor using traditional field based techniques, molecular markers are viewed as a more practical way to infer features of metapopulation structure and demographic history for use in management decisions (Jehle and Arntzen 2002; Cushman 2006). While this perspective is generally apt, our results suggest that inferences made without consideration of presettlement history of demographic change could be misleading (Hoffman and Blouin 2004b; Ficetola et al. 2007). The relationship between salamander occurrence and patch size (results above; Kolozsvary and Swihart 1999) clearly suggests that recent fragmentation is a threat to red-backed salamanders. ...
Forest loss and fragmentation is expected to shape the genetic structure of amphibian populations and reduce genetic variation. Another factor widely understood to have impacted these same parameters in North America is the range expansion that occurred following glacial retreat at the end of the Pleistocene. The Eastern Red-Backed Salamander (Plethodon cinereus) has been sub-jected to both processes. In this context, we investigated the historical events that are likely to have shaped genetic variation in this species using a panel of six microsatellite markers screened on individuals sampled across ten localities in northeastern Indiana, USA. We found low genetic diversity across forest patches and minimal dif-ferentiation. We expected population structure associated with forest fragmentation to result from genetic drift in isolation but instead found that a balance between gene flow and drift was *50 times more likely. Ratios of allele number and range (M), and coalescent modeling of popu-lation demography suggested the occurrence of marked historic decline in effective population size across the region. Taken together, the data point to a loss of genetic variation which preceded deforestation over the past 200 years. This result indicates an important role for ancient demographic processes in shaping current genetic variation that may make it difficult to detect the effect of recent habitat fragmentation.
... This poses a general problem in conservation biology, which can, at least in part, be attributed to overgeneralizations across spatial and temporal scales. Peripheral populations, for example, might be characterized by lower amounts of genetic variation for reasons other than habitat fragmentation, and low allelic diversity is not necessarily linked to fitness reductions (Ficetola et al. 2007; Eckert et al. 2008; but see also Dufresnes and Perrin 2015). A population genetic signature of habitat fragmentation also needs time to accumulate after human-induced fragmentation occurred, leading to a genetic structure which does not necessarily match with current landscape features (Zellmer and Knowles 2009; Anderson et al. 2010; Chiucchi and Gibbs 2010; Safner et al. 2011). ...
The last decades have shown a surge in studies focusing on the interplay between fragmented habitats, genetic variation, and conservation. In the present study, we consider the case of a temperate pond-breeding anuran (the common toad Bufo bufo) inhabiting a naturally strongly fragmented habitat at the Northern fringe of the species’ range: islands offshore the Norwegian coast. A total of 475 individuals from 19 populations (three mainland populations and 16 populations on seven adjacent islands) were genetically characterized using nine microsatellite markers. As expected for a highly fragmented habitat, genetic distances between populations were high (pairwise Fst values ranging between 0.06 and 0.33), with however little differences between populations separated by ocean and populations separated by terrestrial habitat (mainland and on islands). Despite a distinct cline in genetic variation from mainland populations to peripheral islands, the study populations were characterized by overall high genetic variation, in line with effective population sizes derived from single-sample estimators which were on average about 20 individuals. Taken together, our results reinforce the notion that spatial and temporal scales of fragmentation need to be considered when studying the interplay between landscape fragmentation and genetic erosion.
... Similarly, for the last two decades, Western pig breeds have been imported into the Korean peninsula and crossed with the Korean native pig (KNP) to improve its growth and carcass-related traits, which has led to a dramatic drop in the KNP population (Yeo et al., 2000;Kim et al., 2005). Small effective population sizes can result in the loss of genetic diversity, which can in turn lead to reduced individual fitness and response to selection (Ficetola et al., 2007). Although commercial pig breeds are superior in terms of growth and feed efficiency traits, the KNP is known for its better meat quality (high redness and intramuscular fat), and greater ability to thrive under lowmanagement conditions (Yeo et al., 2000;Park et al., 2007;Kim et al., 2011). ...
Comprehensive information on genetic diversity and introgression is desirable for the design of rational breed improvement and conservation programs. Despite the concerns regarding the genetic introgression of Western pig breeds into the gene pool of the Korean native pig (KNP), the level of this admixture has not yet been quantified. In the present study, we genotyped 93 animals, representing four Western pig breeds and KNP, using the porcine SNP 60K BeadChip to assess their genetic diversity and to estimate the level of admixture among the breeds. Expected heterozygosity was the lowest in Berkshire (0.31) and highest in Landrace (0.42). Population differentiation (FST) estimates were significantly different (p<0.000), accounting for 27% of the variability among the breeds. The evidence of inbreeding observed in KNP (0.029) and Yorkshire (0.031) may result in deficient heterozygosity. Principal components one (PC1) and two (PC2) explained approximately 35.06% and 25.20% of the variation, respectively, and placed KNP somewhat proximal to the Western pig breeds (Berkshire and Landrace). When K = 2, KNP shared a substantial proportion of ancestry with Western breeds. Similarly, when K = 3, over 86% of the KNP individuals were in the same cluster with Berkshire and Landrace. The linkage disquilbrium (LD) values at r2
0.3, the physical distance at which LD decays below a threshold of 0.3, ranged from 72.40 kb in Landrace to 85.86 kb in Yorkshire. Based on our structure analysis, a substantial level of admixture between Western and Korean native pig breeds was observed.
... P. multijuga is expected to have a similar mating system and so the small, isolated fragments that we found could be vulnerable to inbreeding depression. The severity of inbreeding depression may depend on the timescale over which fragmentation and isolation has occurred ( Ficetola et al. 2007). If fragmentation and loss of genetic diversity is due primarily to historical processes, then selection may have had sufficient time to at least partially purge delete- rious variants thereby lowering the strength of inbreeding depression relative to more recent fragmentation effects. ...
Fragmentation is predicted to increase inbreeding depression and lower the evolutionary potential of organisms by disrupting dispersal. Trees may be more resilient to fragmentation effects due to potential long-distance dispersal mechanisms that genetically connect fragments. Polylepis woodlands in the high Andes are highly fragmented and are currently the focus of reforestation and conservation efforts. Polylepis multijuga Plige (Rosaceae) is a threatened, endemic tree species in the northern Andes of Peru. Samples were collected from 371 adult trees in nine forest fragments separated by 0.5–80 km and genotyped at amplified fragment length polymorphism loci (AFLP) and chloroplast intergenic regions to determine the connectedness of fragments and their suitability for collecting seed for restoration efforts. P. multijuga is wind-pollinated and dispersed; however, genetic diversity in P. multijuga was about half that reported for other wind-pollinated species. Genetic spatial autocorrelation and patterns of chloroplast and AFLP diversity suggest seed dispersal is very limited and that wind dispersed pollen does not effectively connect all fragments. Conservation of this species will require reforestation efforts and possibly augmentation of some fragments to increase their genetic diversity. Collecting seed from multiple large fragments and from individuals separated by at least 25 m within fragments would maximize the genetic diversity of seed collections for reforestation or augmentation. Future studies of this and other Polylepis species should determine how complex topography may affect wind mediated dispersal between fragments and patterns of genetic diversity.
... Genetic studies are essential to infer gene flow between populations and the potential for re-colonization, which are two critical parameters in metapopulation models (Marsh and Trenham 2001). Besides, it is recognised that the amount of genetic variation can be correlated with fitness traits (Reed and Frankham 2003; Hitchings and Beebee 1997; Rowe et al. 1999; Ficetola et al. 2007). All these aspects are important for population conservation and for a better understanding of the ''global amphibian population decline'' (Stuart et al. 2004). ...
The increasing fragmentation of natural habitats may strongly affect patterns of dispersal and gene flow among populations, and thus alter evolutionary dynamics. We examined genetic variation at twelve microsatellite loci in the Agile frog (Rana dalmatina) from 22 breeding ponds in the Iberian Peninsula, the southwest limit of its range, where populations of this species are severely fragmented and are of conservation concern. We investigated genetic diversity, structure and gene flow within and among populations. Diversity as observed heterozygosities ranged from 0.257 to 0.586. The mean number of alleles was 3.6. Just one population showed a significant F
IS value. Four populations show evidence of recent bottlenecks. Strong pattern of structure was observed due to isolation by distance and to landscape structure. The average degree of genetic differentiation among populations was F
ST = 0.185. Three operational conservation units with metapopulation structure were identified. Additionally, there are some other isolated populations. The results reinforce the view that amphibian populations are highly structured even in small geographic areas. The knowledge of genetic structure pattern and gene flow is fundamental information for developing programmes for the preservation of R. dalmatina at the limits of its geographic distribution.
... Analyzing the genetic patterns that result from this exchange allows researchers to identify landscape features that enhance or diminish species movement, which in turn affects gene flow (Manel et al. 2003; Holderegger and Wagner 2008; Storfer et al. 2010 ). Landscape genetic studies have demonstrated how topographic and environmental gradients, habitat fragmentation, and barriers such as roads, streams and mountains create genetic structure within and among populations (e.g., Jacquemyn et al. 2004; Sork and Smouse 2004; McRae et al. 2005; Cushman et al. 2006; Ficetola et al. 2007; Dixo et al. 2009; Murphy et al. 2010). Results from such studies are increasingly used to inform management and conservation applications, specifically with respect to corridor design (Epps et al. 2007; Braunisch et al. 2010; Segelbacher et al. 2010). ...
A common approach used to estimate landscape resistance involves comparing correlations of ecological and genetic distances calculated among individuals of a species. However, the location of sampled individuals may contain some degree of spatial uncertainty due to the natural variation of animals moving through their home range or measurement error in plant or animal locations. In this study, we evaluate the ways that spatial uncertainty, landscape characteristics, and genetic stochasticity interact to influence the strength and variability of conclusions about landscape-genetics relationships. We used a neutral landscape model to generate 45 landscapes composed of habitat and non-habitat, varying in percent habitat, aggregation, and structural connectivity (patch cohesion). We created true and alternate locations for 500 individuals, calculated ecological distances (least-cost paths), and simulated genetic distances among individuals. We compared correlations between ecological distances for true and alternate locations. We then simulated genotypes at 15 neutral loci and investigated whether the same influences could be detected in simple Mantel tests and while controlling for the effects of isolation-by-distance using the partial Mantel test. Spatial uncertainty interacted with the percentage of habitat in the landscape, but led to only small reductions in correlations. Furthermore, the strongest correlations occurred with low percent habitat, high aggregation, and low to intermediate levels of cohesion. Overall genetic stochasticity was relatively low and was influenced by landscape characteristics.
... However, animal movements are strongly influenced by landscape features (Bélisle, 2005; Fahrig, 2007 ). Amphibians are particularly susceptible to fragmentation and to the presence of barriers (Cushman, 2006): the study area is strongly modified by humans, and elements such as roads and urbanization may have precluded colonization (Ficetola et al., 2007c). Finally, the models developed for the three temporal steps were not identical. ...
Species distribution models often assume a changing climate (dynamic climate variables) but unchanged land use (static land use variables) to estimate future species distribution shifts. However, scenarios of projected land use change are available to calculate dynamic land use variables. Surprisingly, the importance of using dynamic instead of static land use variables when projecting potential future species distributions under climate change remains largely unexplored. We tested whether the joint inclusion of land use and climate change scenarios altered the projection of future species distribution compared with the classical approach assuming unchanged land use.
Europe
We used land use and climate change scenarios to estimate the future distribution of a butterfly species (Lycaena dispar) according to different perspectives of projected environmental change: (1) land use change (dynamic land use and static climate variables), (2) climate change (static land use and dynamic climate variables) and (3) global change (dynamic land use and climate variables). As the importance of land use variables is known to depend on the spatial resolution of the models, we built them across a range of resolutions (50 km, 10 km and 5 km) to examine the resolution-dependent relevance of using dynamic instead of static variables.
For each resolution, the projected distribution changes were unaltered when using dynamic instead of static land use variables in the models. It was mainly due to the low thematic resolution of the land use change scenarios that include only few dynamic variables.
Even at fine spatial resolution (5 km), the available land use change scenarios poorly represent habitat suitability for the species. Hence, they may be of limited support to estimate future species distributions. Instead of supporting the assumption of unchanged future land use, our results plea for an improvement of the thematic resolution of land use change scenarios.
... European common frog contains deep mitochondrial lineages, 167 which partly are given the rank of subspecies (Veith et al., 168 2002Veith et al., 168 , 2003Veith et al., 168 , 2012 Palo et al., 2004; Teacher et al., 2009 Arribas, 2008), R. latastei (Ficetola et al., 2007), and the 178 northernmost populations of R. italica (Canestrelli et al., 2008 the PHASE algorithm (Stephens et al., 2001Templeton et al., 1992) using the software TCS, version 270 1.21 (Clement et al., 2000) The microsatellite data sets were pruned to contain only popu- 319 lations with an initial minimum of 9 individuals, and from these, 320 all individuals with 10% or more missing data were removed. The 321 software msa (Dieringer and Schlötterer, 2003 ) was used to calcu- 322 late the distances between all pairs of populations for the propor- 323 tion of shared alleles (Bowcock et al., 1994). ...
... As a consequence, genetically eroded populations are assumed to show a reduced mean fitness. Numerous studies demonstrated in various taxa a reduction in fitness caused by genetic erosion (for example, Rowe and Beebee, 2003; Reed, 2005; Ficetola et al., 2007; Johansson et al., 2007; Angelone, 2010; Luquet et al., 2011b), but they rarely unraveled the genetic process behind this reduction (but see Luquet et al., 2011a). An approach to measure the detrimental effects of genetic erosion on fitness is to estimate correlations between molecular variation and phenotypic performances within and among populations (see Szulkin et al., 2010; Luquet et al., 2011a ). ...
Assessing in wild populations how fitness is impacted by inbreeding and genetic drift is a major goal for conservation biology. An approach to measure the detrimental effects of inbreeding on fitness is to estimate correlations between molecular variation and phenotypic performances within and among populations. Our study investigated the effect of individual multilocus heterozygosity on body size, body condition and reproductive investment of males (that is, chorus attendance) and females (that is, clutch mass and egg size) in both small fragmented and large non-fragmented populations of European tree frog (Hyla arborea). Because adult size and/or condition and reproductive investment are usually related, genetic erosion may have detrimental effects directly on reproductive investment, and also on individual body size and condition that in turn may affect reproductive investment. We confirmed that the reproductive investment was highly size-dependent for both sexes. Larger females invested more in offspring production, and larger males attended the chorus in the pond more often. Our results did not provide evidence for a decline in body size, condition and reproductive effort with decreased multilocus heterozygosity both within and among populations. We showed that the lack of heterozygosity-fitness correlations within populations probably resulted from low inbreeding levels (inferior to ca. 20% full-sib mating rate), even in the small fragmented populations. The detrimental effects of fixation load were either low in adults or hidden by environmental variation among populations. These findings will be useful to design specific management actions to improve population persistence.Heredity advance online publication, 19 December 2012; doi:10.1038/hdy.2012.110.
... Genetic diversity within these populations, as measured by the mean number of alleles per microsatellite locus and expected heterozygosity , is quite low compared to other montane Rana (Monsen and Blouin, 2004; Zhan et al., 2009; Zhao et al., 2009). While these studies were conducted with different microsatellite loci, it is noteworthy that only a few threatened or endangered ranids show similar low levels of microsatellite variation, including Rana luteiventris (Funk et al., 2005), Rana latastei (Ficetola et al., 2007), and Rana pipiens (Wilson et al., 2008 ). It is not known whether reduced levels of genetic variability will affect fitness, and, currently, inbreeding in R. muscosa is not strong, with the highest inbreeding (F ranges from 0.11 to 0.21 in adults) found in the East Fork City Creek, Little Rock Creek, Dark Canyon and Milestone Basin populations . ...
... In animal breeding, crosses with non-commercial populations are rarely applied and genetically improved animals are often kept in small, closed populations. Small effective population sizes and epistasis can result in loss of genetic diversity, which can lead to reduced individual fitness and reduced response to selec- tion [32,33]. Several studies have assessed genetic diversity in different livestock species [32,34353637383940 using different types of markers. ...
Background
The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome.
Results
Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles.
Conclusion
The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.
... However, animal movements are strongly influenced by landscape features (Bélisle, 2005; Fahrig, 2007 ). Amphibians are particularly susceptible to fragmentation and to the presence of barriers (Cushman, 2006): the study area is strongly modified by humans, and elements such as roads and urbanization may have precluded colonization (Ficetola et al., 2007c). Finally, the models developed for the three temporal steps were not identical. ...
Biological invasions and land-use changes are two major causes of the global modifications of biodiversity. Habitat suitability models are the tools of choice to predict potential distributions of invasive species. Although land-use is a key driver of alien species invasions, it is often assumed that land-use is constant in time. Here we combine historical and present day information, to evaluate whether land-use changes could explain the dynamic of invasion of the American bullfrog Rana catesbeiana (=Lithobathes catesbeianus) in Northern Italy, from the 1950s to present-day. We used maxent to build habitat suitability models, on the basis of past (1960s, 1980s) and present-day data on land-uses and species distribution. For example, we used models built using the 1960s data to predict distribution in the 1980s, and so on. Furthermore, we used land-use scenarios to project suitability in the future. Habitat suitability models predicted well the spread of bullfrogs in the subsequent temporal step. Models considering land-use changes predicted invasion dynamics better than models assuming constant land-use over the last 50 years. Scenarios of future land-use suggest that suitability will remain similar in the next years. Habitat suitability models can help to understand and predict the dynamics of invasions; however, land-use is not constant in time: land-use modifications can strongly affect invasions; furthermore, both land management and the suitability of a given land-use class may vary in time. An integration of land-use changes in studies of biological invasions can help to improve management strategies.
... Santucci et al., 1996). Both historical and contemporary processes are expected to affect the genetic diversity of populations and disentangling the two can be hard, particularly when no clear geographical pattern is expected to be associated with the hypothesized history of populations (Ficetola et al., 2007). This is also the case for the pool frogs from Sicily, where both the prolonged insularity and the more recent human-driven alterations of habitats could account for the observed paucity of genetic diversity. ...
Aim To infer the evolutionary history of Rana ( Pelophylax ) lessonae Camerano within its inferred Quaternary refugial range, and to shed light on the processes that have contributed to shaping the patterns of diversity within the southern European peninsulas.
Location The Italian peninsula south of the Alps and Sicily.
Methods Sequence analysis of a mitochondrial cytochrome b gene fragment in 149 individuals sampled from 25 localities.
Results Three mitochondrial DNA (mtDNA) phylogroups were identified, distributed in northern Italy, the whole Italian peninsula south of the northern Apennines, and Sicily. Syntopy between the northern and peninsular lineages was observed close to the northern Apennines. The northern lineage was the most differentiated, showing a net sequence divergence of 4.8 ± 0.8% with respect to the two others, whereas the net divergence between peninsular and Sicilian lineages was 2.6 ± 0.6%. Analysis of molecular variance ( amova ) revealed that 93% of the overall variation occurred between these three groups. Historical demographic statistics support a recent expansion for both the northern and peninsular groups, but not for the Sicilian group. In both northern and peninsular Italy, such an expansion was likely to have occurred during the last glaciation.
Main conclusions Our results suggest that a number of microevolutionary processes were involved in shaping the present genetic structure of R. lessonae in Italy. These encompass allopatric differentiations in three distinct Pleistocene refugia, recent population expansions and secondary contacts. Our results, together with some previous work, support (1) the existence of a suture zone in the northern Apennines, and (2) the possibility of population expansions during the last glacial phase, when a vast widening of the lowland floodplain habitats followed sea‐level fall, particularly in northern Italy. When compared with previous analyses of allozyme data, it appears that the peninsular mtDNA lineage has recently replaced the Sicilian one in southern Calabria, and we suggest that this event occurred due to selective introgression. The implications of such an occurrence for the study of factors underlying the patterns of diversity within this southern European biodiversity hotspot are discussed. Taxonomic implications of the results are also evaluated.
... If froglet movement is being interrupted by both human disturbance and the presence of trails, this may have a strong effect on overall population dynamics since juvenile dispersal is often the major contributor to amphibian population maintenance (Rothermel 2004; Funk et al. 2005, Sinsch 1997 Joly & Grolet 1996; Berven & Grudzien 1990; but see Smith & Green 2006 ). Significant restriction of juvenile dispersal is presumed to have a strong influence on general demography, genetic structure and population persistence, and the deleterious consequences of isolation on amphibian populations are well documented (Sjö gren-Gulve 1994; Taylor & Scott 1997; Trenham et al. 2000; Carr & Fahrig 2001; Andersen et al. 2004; Funk et al. 2005; Johansson et al. 2005; Marsh et al. 2005; Ficetola et al. 2007). If populations of Arthroleptis spp. in patches of remnant forest of the Eastern Arc mountains are connected through post-hatching dispersal , foot paths and human disturbance may be altering local metapopulation or source–sink processes (Ewers & Didham 2006). ...
Habitat can be rendered less suitable because of numerous factors, including the presence of humans. Human disturbance is implicated as a threat for hundreds of amphibian species, but there is a dearth of peer-reviewed literature addressing this topic, and what little is available focuses on adults. Here we present the results of a study examining the effects human disturbance may have on the distribution and behaviour of juvenile Eastern African leaf litter frogs of the genus Arthroleptis. Our findings show that human activity affects the local density of juveniles and strongly influences escape behaviour. These results indicate that costs of human disturbance to juvenile frogs may be severe and that human disturbance may play a role in fragmenting local frog populations.
... However, animal movements are strongly influenced by landscape features (Bélisle, 2005; Fahrig, 2007 ). Amphibians are particularly susceptible to fragmentation and to the presence of barriers (Cushman, 2006): the study area is strongly modified by humans, and elements such as roads and urbanization may have precluded colonization (Ficetola et al., 2007c). Finally, the models developed for the three temporal steps were not identical. ...
Biological invasions and land-use changes are two major causes of the global modifications of biodiversity. Habitat suitability models are the tools of choice to predict potential distributions of invasive species. Although land-use is a key driver of alien species invasions, it is often assumed that land-use is constant in time. Here we combine historical and present day information, to evaluate whether land-use changes could explain the dynamic of invasion of the American bullfrog Rana catesbeiana (5 Litho-bathes catesbeianus) in Northern Italy, from the 1950s to present-day. We used MAXENT to build habitat suitability models, on the basis of past (1960s, 1980s) and present-day data on land-uses and species distribution. For example, we used models built using the 1960s data to predict distribution in the 1980s, and so on. Furthermore, we used land-use scenarios to project suitability in the future. Habitat suitability models predicted well the spread of bullfrogs in the subsequent temporal step. Models considering land-use changes predicted invasion dynamics better than models assuming constant land-use over the last 50 years. Scenarios of future land-use suggest that suitability will remain similar in the next years. Habitat suitability models can help to understand and predict the dynamics of invasions; however, land-use is not constant in time: land-use modifications can strongly affect invasions; furthermore, both land management and the suit-ability of a given land-use class may vary in time. An integration of land-use changes in studies of biological invasions can help to improve management strategies.
... One recurrent theme in molecular studies of the European common frog has been a relatively high amount of variation found among and within populations of this species. On the contrary, preliminary data suggest low genetic variation in several other European brown frogs, such as the geographically restricted R. pyrenaica (Carranza and Arribas, 2008), R. latastei (Ficetola et al., 2007 ), and the northernmost populations of R. italica (Canestrelli et al., 2008), but also the widespread agile frog, R. dalmatina (e.g., Petraccioli et al., 2010 ). This latter species co-occurs with R. temporaria over much of its range, although its distribution is located more to the south (Grossenbacher, 1997a), and its phylogeography is not well known. ...
Amphibians often show complex histories of intraspecific and interspecific genetic introgression, which might differ in mitochondrial and nuclear genes. In our study of the genetic differentiation of the European common frog, Rana temporaria (159 specimens from 23 populations were analyzed for 24 presumptive allozyme loci; 82 specimens were sequenced for a 540-bp fragment of the mitochondrial 16S rRNA gene), multilocus correspondence analysis (CA) and Bayesian assignment tests of the nuclear data were concordant in identifying 2 population groups corresponding to 1) the Pyrenees in the east and 2) the Galicia and Asturias regions in the west, the latter corresponding to the subspecies R. temporaria parvipalmata. Geographically intermediate populations were genetically intermediate in the allozyme CA and, less clearly in the Bayesian assignment, with mitochondrial haplotypes exclusively belonging to the parvipalmata group. This indicates different degrees of introgression in the mitochondrial and nuclear genomes. Although Pyrenean high-altitude populations are morphologically distinct from low-altitude populations, these 2 groups were not separate clusters in any analysis. This suggests that the morphological differences may be due to fast adaptation to elevational gradients, likely under maintenance of gene flow, and that the underlying genetic changes are not detectable by the analyzed markers. We argue that a parsimonious explanation for the observed pattern along the east-west axis in northern Spain may be competition between invading and resident populations, with no need to invoke selection. However, in order to conclusively rule out selective processes, additional and finer scale data are required to test for asymmetric mating preference/behaviour, sex-biased gene flow, or sex-biased survival of potential hybrids.
... Only a few critically endangered species and very small, isolated populations showed heterozygosity values as low as C. walie (Supporting Information Appendix S1). Only 5% of species of endangered birds reviewed by Jamieson et al. (2006), and only 14% of amphibians reviewed by Ficetola, Garner & De Bernardi (2007) showed values of expected heterozygosity lower than C. walie. These comparisons include only polymorphic loci because most publications use and report results from polymorphic microsatellites (Maudet et al., 2002). ...
Knowledge about the phylogenetic history, genetic variation and ecological requirements of a species is important for its conservation and management. Unfortunately, for many species this information is lacking. Here we use multiple approaches (phylogenetics, population genetics and ecological modelling) to evaluate the evolutionary history and conservation status of Capra walie, an endangered flagship species of wild goat endemic to Ethiopia. The analysis of mitochondrial cytochrome b and Y-chromosome DNA sequences suggests that C. walie forms a monophyletic clade with Capra nubiana, but potentially has been isolated for up to 0.8 million years from this closely related species. Microsatellite DNA analyses show that C. walie has very low genetic variation (mean heterozygosity=0.35) compared with other endangered mammals. This reduced variation likely derives from a prolonged demographic decline and small effective population size. Ecological niche modelling using the bioclimatic features of habitats occupied by C. walie, suggests ecological differences between C. walie and C. nubiana, and identifies the areas most suitable for future reintroductions of C. walie. The genetic and bioclimatic data suggest that C. walie is distinct and requires immediate conservation actions including genetic monitoring and reintroductions to establish independent populations. This study illustrates how combining noninvasive sampling along with genetic and ecological (bioclimatic) approaches can help assess conservation status of poorly known species.
... In a conservation perspective, knowing how populations lose fitness (inbreeding vs. fixed load) is useful to design management actions to improve the persistence of populations (Jaquiéry et al. 2009). Translocation of animals from the genetically divergent populations is often proposed to improve fitness but at the risk of outbreeding depression (Ingvarsson 2001; Tallmon et al. 2004; Ficetola et al. 2007). Some degree of outbreeding depression may be concealed by the heterosis effect (Escobar et al. 2008 ). ...
Quantifying the impacts of inbreeding and genetic drift on fitness traits in fragmented populations is becoming a major goal in conservation biology. Such impacts occur at different levels and involve different sets of loci. Genetic drift randomly fixes slightly deleterious alleles leading to different fixation load among populations. By contrast, inbreeding depression arises from highly deleterious alleles in segregation within a population and creates variation among individuals. A popular approach is to measure correlations between molecular variation and phenotypic performances. This approach has been mainly used at the individual level to detect inbreeding depression within populations and sometimes at the population level but without consideration about the genetic processes measured. For the first time, we used in this study a molecular approach considering both the interpopulation and intrapopulation level to discriminate the relative importance of inbreeding depression vs. fixation load in isolated and non-fragmented populations of European tree frog (Hyla arborea), complemented with interpopulational crosses. We demonstrated that the positive correlations observed between genetic heterozygosity and larval performances on merged data were mainly caused by co-variations in genetic diversity and fixation load among populations rather than by inbreeding depression and segregating deleterious alleles within populations. Such a method is highly relevant in a conservation perspective because, depending on how populations lose fitness (inbreeding vs. fixation load), specific management actions may be designed to improve the persistence of populations.
... Cushman et al. 2006). Also, several studies provide examples for distinguishing influences of historic and recent landscape patterns on observed genetic structures (Holzhauer et al. 2006; Ficetola et al. 2007; Vandergast et al. 2007). Finally, empirical studies also demonstrate that genetic effective population size influences the magnitude and detectability of genetic road effects. ...
Transportation infrastructures such as roads, railroads and canals can have major environmental impacts. Ecological road effects include the destruction and fragmentation of habitat, the interruption of ecological processes and increased erosion and pollution. Growing concern about these ecological road effects has led to the emergence of a new scientific discipline called road ecology. The goal of road ecology is to provide planners with scientific advice on how to avoid, minimize or mitigate negative environmental impacts of transportation. In this review, we explore the potential of molecular genetics to contribute to road ecology. First, we summarize general findings from road ecology and review studies that investigate road effects using genetic data. These studies generally focus only on barrier effects of roads on local genetic diversity and structure and only use a fraction of available molecular approaches. Thus, we propose additional molecular applications that can be used to evaluate road effects across multiple scales and dimensions of the biodiversity hierarchy. Finally, we make recommendations for future research questions and study designs that would advance molecular road ecology. Our review demonstrates that molecular approaches can substantially contribute to road ecology research and that interdisciplinary, long-term collaborations will be particularly important for realizing the full potential of molecular road ecology.
... xamined patterns of genetic diversity across the entire range of a widely distributed species. It is generally recognized that higher levels of genetic diversity usually occur towards the centre of a species' range (e.g. Arnaud-Haond et al. 2006 and Schwartz et al. 2003), a pattern also seen in our data. The reasons for such a pattern are multiple. Ficetola et al. (2007) found that distance from glacial refugia and geographical isolation together explain over 90% of variation in microsatellite diversity in the frog Rana latastei in northern Italy, suggesting a major impact of sequential bottlenecks and/or founder events. Similar patterns are seen even among modern humans, reflecting loss of diversity as ...
Many studies use genetic markers to explore population structure and variability within species. However, only a minority use more than one type of marker and, despite increasing evidence of a link between heterozygosity and individual fitness, few ask whether diversity correlates with population trajectory. To address these issues, we analysed data from the Steller's sea lion, Eumetiopias jubatus, where three stocks are distributed over a vast geographical range and where both genetic samples and detailed demographic data have been collected from many diverse breeding colonies. To previously published mitochondrial DNA (mtDNA) and microsatellite data sets, we have added new data for amplified fragment length polymorphism (AFLP) markers, comprising 238 loci scored in 285 sea lions sampled from 23 natal rookeries. Genotypic diversity was low relative to most vertebrates, with only 37 loci (15.5%) being polymorphic. Moreover, contrasting geographical patterns of genetic diversity were found at the three markers, with Nei's gene diversity tending to be higher for AFLPs and microsatellites in rookeries of the western and Asian stocks, while the highest mtDNA values were found in the eastern stock. Overall, and despite strongly contrasting demographic histories, after applying phylogenetic correction we found little correlation between genetic diversity and either colony size or demography. In contrast, we were able to show a highly significant positive relationship between AFLP diversity and current population size across a range of pinniped species, even though equivalent analyses did not reveal significant trends for either microsatellites or mtDNA.
... Bullfrogs have a very high fertility (average clutch size > 13 000 eggs; Govindarajulu et al. 2005); thus, invasive populations can quickly overcome demographic bottlenecks. Moreover, in species with large fertility and in populations with high growth rate, selection has more potential to purge inbreeding depression (Wang 2000; Miller & Hedrick 2001; Ficetola et al. 2007b). Several non-native populations originated from independent introduction events, as there are strong genetic differences among them (Table 2). ...
Propagule pressure is considered the main determinant of success of biological invasions: when a large number of individuals are introduced into an area, the species is more likely to establish and become invasive. Nevertheless, precise data on propagule pressure exist only for a small sample of invasive species, usually voluntarily introduced. We studied the invasion of the American bullfrog, Rana catesbeiana, into Europe, a species that is considered a major cause of decline for native amphibians. For this major invader with scarce historical data, we used population genetics data (a partial sequence of the mitochondrial cytochrome b gene) to infer the invasion history and to estimate the number of founders of non-native populations. Based on differences between populations, at least six independent introductions from the native range occurred in Europe, followed by secondary translocations. Genetic diversity was strongly reduced in non-native populations, indicating a very strong bottleneck during colonization. We used simulations to estimate the precise number of founders and found that most non-native populations derive from less than six females. This capability of invasion from a very small number of propagules challenges usual management strategies; species with such ability should be identified at an early stage of introduction.
... This involves characterization of present day diversity of critical ecological communities (e.g. Apprill & Gates 2007; Pfenninger et al. 2007; Pommier et al. 2007; Van Oppen 2007), calculation of migration rates for all kinds of organisms (Byrne et al. 2007; Devaux et al. 2007; Fievet et al. 2007; Garcia et al. 2007; Giordano et al. 2007; Jones et al. 2007; Lukoschek et al. 2007; Richards et al. 2007; Underwood et al. 2007; Vignieri 2007; Watts et al. 2007; Werth et al. 2007), identification of traits that are likely to be under selection during climate change (Chapuis et al. 2007), determination of the genetic basis and heritability of these traits (Brock et al. 2007; Kassahn et al. 2007; Norry et al. 2007; Rako et al. 2007), and estimation of the effects of habitat fragmentation on the rate of adaptation (Ficetola et al. 2007; Johansson et al. 2007). Also, analyses of organismal responses to previous bouts of climate change (Brito 2007; Crottini et al. 2007; Hoarau et al. 2007; Naciri & Gaudeul 2007; Parisod & Besnard 2007) provide a means of predicting future responses. ...
A novel method for measuring the diffusion coefficient of liquids is introduced in this paper. A transparency capillary is used as both diffusive pool and imaging element, spatially resolving ability of the capillary in measuring refractive index of liquid is utilized to observe and record diffusive process directly, diffusion coefficient of liquid is calculated based on Fick second law and acquired experimental data. With the new method, the diffusive process of pure glycerol in water at 25 degrees C is investigated, the obtained diffusion coefficient is 0.898 x 10(-5) cm(2)/s, which is of a relative error 4.47% compared with the literature value measured by the holographic interference. The influence of measurement accuracy of refractive index and capillary viscosity on measuring result is also analyzed. The method is characterized by micro-quantity sample required, faster measurement and better stability, which opens a new way to measure diffusion coefficient of liquid medium.
In Africa, the genus Xenopus presents cryptic species and diverse hybrids between species. It has been assumed that the invasive populations of this genus correspond to X. laevis and that they are derived from the subspecies that inhabits the Mediterranean Cape region of South Africa. In part, this is supported by the successful establishment of this species in several Mediterranean regions of the world. In Mediterranean Chile, Xenopus has invaded an area of about 21,000 km2, with scarce attention to genetic aspects underlying its invasion. Using mitochondrial DNA sequences we determined that Xenopus laevis laevis from the Cape region of South Africa is the subspecies that invaded Chile. The analysis indicated that the invaders have low genetic diversity (only two haplotypes, compared to 10 in two localities of their native range), and that probably the invasion in Chile occurred only once. Landscape genetics revealed that factors such as aridity and elevation have determined the spread of the species, both from the ecological and genetic points of view. Our results show that the invasion of the African clawed frog in Chile has been successful for at least 30 years, in spite of low genetic variability, few events of introduction, low propagule pressure, and bottlenecks in the founding population.
The European natterjack toad (Bufo calamita) has declined rapidly in recent years, primarily due to loss of habitat, and in Denmark it is estimated that 50% of the isolated populations are lost each decade. To efficiently manage and conserve this species and its genetic diversity, knowledge of the genetic structure is crucial. Based on nine polymorphic microsatellite loci, the genetic diversity, genetic structure and gene flow were investigated at 12 sites representing 5–10% of the natterjack toad localities presently known in Denmark. The expected heterozygosity (H
E) within each locality was generally low (range: 0.18–0.43). Further analyses failed to significantly correlate genetic diversity with population size, degree of isolation and increasing northern latitude, indicating a more complex combination of factors in determining the present genetic profile. Genetic differentiation was high (overall θ = 0.29) and analyses based on a Bayesian clustering method revealed that the dataset constituted 11 genetic clusters, defining nearly all sampling sites as distinct populations. Contemporary gene flow among populations was undetectable in nearly all cases, and the failure to detect a pattern of isolation by distance within major regions supported this apparent lack of a gene flow continuum. Indications of a genetic bottleneck were found in three populations. The analyses suggest that the remaining Bufo calamita populations in Denmark are genetically isolated, and represent independent units in a highly fragmented gene pool. Future conservation management of this species is discussed in light of these results.
Decreased fitness due to loss of genetic variation is a well recognised issue in conservation biology. Along the Swedish west coast, the endangered natterjack toad (Bufo calamita) occurs on, for the species, highly unusual habitat of rocky islands. Although the toads inhabit a restricted geographical area (maximum distance between the populations is 71 km), the fragmented nature of the landscape makes the genetic properties of the populations of conservation interest. However, lack of genetic variation found using conventional methods (microsatellites) has impeded genetic studies within these peripheral populations so far. In this study we assess population structure and genetic variation among seven of these fringe populations using 105 polymorphic Amplified Fragment Length Polymorphism (AFLP) loci. We found a well-defined population structure without evidence for isolation by distance, implying restricted gene flow between populations. Additionally, the populations differed in their amount of genetic variation, emphasizing the need to monitor genetically impoverished populations for possible declines mediated by inbreeding depression and reduced adaptive potential. Conservation implications for these unique populations are discussed in the light of our results.
A well-designed sampling scheme is critical for obtaining accurate results from population genetic studies. Larval samples contain only the genetic material of successful breeders, often of a single year, and may be biased towards particular families. To quantify the bias of using larval samples to infer population and landscape genetic structure and explore how this bias may be reduced using sibship analysis, we analysed eight microsatellite loci from 484 tissue samples of larvae and adults of Columbia spotted frogs (Rana luteiventris) and long-toed salamanders (Ambystoma macrodactylum) at nine breeding sites in north Idaho. Differences in allele frequencies between adult and larval samples were not detected after full-siblings were removed from the larval data set for Columbia spotted frogs; for long-toed salamanders, these differences remained at two out of four ponds. Data from Columbia spotted frog larvae indicated higher levels of differentiation among populations (median difference in F(ST) = 0.020, P < 0.01), as predicted by population genetic theory, whereas data from larval samples of long-toed salamanders showed some evidence of lower levels of differentiation among populations (median difference in F(ST) = 0.012, P = 0.06). For both species, removing all but one individual from each full-sibling family led to parameter estimates that were closer to those calculated from adult samples for both population and landscape genetic measures. Removal of full-siblings is likely to improve estimates of population genetic parameters; however, knowledge of the species' breeding system is essential for understanding additional sources of bias when inferring population genetic structure from larval samples.
One of the main questions in evolutionary and conservation biology is how geographical and environmental features of the landscape shape neutral and adaptive genetic variation in natural populations. The identification of genomic polymorphisms that account for adaptive variation can aid in finding candidate loci for local adaptation. Consequently, a comparison of spatial patterns in neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection at the landscape scale. Many amphibians breed in wetlands, which differ in environmental conditions and in the degree of isolation, enhancing the potential for local adaptation. We used microsatellite markers to measure genetic differentiation among 17 local populations of Rana arvalis breeding in a network of wetlands. We found that locus RC08604 deviated from neutral expectations, suggesting that it is a good candidate for directional selection. We used a genetic network analysis to show that the allele distribution in this locus is correlated with habitat characteristics, whereas this was not the case at neutral markers that displayed a different allele distribution and population network in the study area. The graph approach illustrated the genomic heterogeneity (neutral loci vs. the candidate locus for directional selection) of gene exchange and genetic divergence among populations under directional selection. Limited gene flow between wetlands was only observed at the candidate genomic region under directional selection. RC08604 is partially located inside an up-regulated thyroid-hormone receptor (TRβ) gene coordinating the expression of other genes during metamorphosis and appears to be linked with variation in larval life-history traits found among R. arvalis populations. We suggest that directional selection on genes coding larval life-history traits is strong enough to maintain the divergence in these genomic regions, reducing the effective recombination of locally adapted alleles but not in other regions of the genome. Integrating this knowledge into conservation plans at the landscape scale will improve the design of management strategies to preserve adaptive genetic diversity in wetland networks.
is alsofound, in limited distributions, in Southern Switzer-land, and parts of Slovenia and Croatia (North-western Yugoslavia in Capula et al. 1991). Morpho-logical and allozymatic variation in this species arelow (Schmidtler 1977; Capula et al. 1991), andSwiss populations are thought to be derived from apostextirpation recolonization event (Grossenbacher1982). Although listed as a lower risk species (‘nearthreatened’, Baillie and Groombridge 1996), rangelimitations, habitat fragmentation, large-scale indus-trialization and urbanization within its range, potentialeffects of bottlenecks and increasing evidence for aglobal decline of amphibian species (Houlahan 2000)all indicate that
Discusses the assertion that effectively states that habitat fragmentation should be innocuous to most species, and therefore need not be a consideration in reserve design. This conclusion runs counter to the prevailing view that habitat fragmentation negatively affects population survival, and thus biological diversity, and therefore should be a prime consideration in conservation strategy. This apparent contradiction arises from 3 sources: 1) the 'single large or several small reserves will protect more species' is not equivalent to, or is at very best a special case of, the problem of habitat fragmentation; 2) the population model Simerloff and Abele (1982) (see 83L/2948) employ is inadequate because it ignores key factors affecting population survival; and 3) Simerloff and Abele's treatment does not consider how the disposition of one species may affect the survival of others, because it is limited to single-species population phenomena and ignores interspecific interactions or community-level phenomena.-from Authors
A ten year census was carried out on Rana dalmatina and R. latastei egg masses deposited in 36 reproductive sites in a 10‐hectare area, subject to periodic flooding, on the banks of the Ticino River. The vegetation type surrounding reproductive sites was noted. There were no signs of decline in the populations of either frog species. The number of egg clutches fluctuated widely from year to year but no correlation between clutch number and either flooding or climate parameters were detected. R. dalmatina preferred partly open areas for reproductive sites, whereas R. latastei selected areas characterized by hygrophilous vegetation and a high tree canopy.
It has been proposed that inbreeding contributes to the decline and
eventual extinction of small and isolated populations,. There is ample
evidence of fitness reduction due to inbreeding (inbreeding depression)
in captivity and from a few experimental, and observational field
studies,, but no field studies on natural populations have been
conducted to test the proposed effect on extinction. It has been argued
that in natural populations the impact of inbreeding depression on
population survival will be insignificant in comparison to that of
demographic and environmental stochasticity,. We have now studied the
effect of inbreeding on local extinction in a large metapopulation of
the Glanville fritillary butterfly (Melitaea cinxia). We found that
extinction risk increased significantly with decreasing heterozygosity,
an indication of inbreeding, even after accounting for the effects of
the relevant ecological factors. Larval survival, adult longevity and
egg-hatching rate were found to be adversely affected by inbreeding and
appear to be the fitness components underlying the relationship between
inbreeding and extinction. To our knowledge, this is the first
demonstration of an effect of inbreeding on the extinction of natural
populations. Our results are particularly relevant to the increasing
number of species with small local populations due to habitat loss and
fragmentation.
Regional variation in spore deposition and viability was studied for two fungi, Fomitopsis rosea (Alb. & Schwein.: Fr.) P. Karst. and Phlebia centrifuga P. Karst., both confined to old-growth spruce forests in the boreal zone. Seven regions in Sweden were studied along a north-south transect in which the historical impact from forestry increases and the amount old forests decreases towards the south. The two southernmost regions were located outside the distribution border of the species. Spore deposition was measured species specifically as heterokaryotisation of homokaryotic mycelia growing on wood discs. There was a significant decline in spore deposition towards the south for both species. F. rosea deposited an average amount of 111 spores m−2 24 h−1 in the northernmost region compared to less than 1 spore in the four southernmost regions. The corresponding values for P. centrifuga were 27 spores m−2 24 h−1 in the north compared to less than 2 spores in the 4 southernmost regions. No deposition was found south of the distribution borders. The viability of spores from local populations within each region was measured as germination success on nutrient media. Individual fruiting bodies from large populations in the north generally produced spores with higher germinability than fruiting bodies from geographically isolated populations in the central and southern regions. However, there was a high variation among the southern populations. Our data suggest that some populations in mid- and south Sweden may suffer from negative genetic effects, possibly associated with fragmentation and loss of habitat. Thus, the combination of low spore deposition and low germinability of spores may be a threat to the long-term persistence of F. rosea and P. centrifuga in southern Sweden. Several other species may experience the same situation, especially when considering the severe decline of dead wood in Swedish forests.
Chloroplast DNA variation was studied in a total of 878 French oak populations from four different species. Three main cpDNA lineages were found, which have well-demarcated distributions in the country. The study of the distribution of haplotypes in each species supports the view that the four species were restricted to different refugia during the last ice-age. This is evident despite the fact that extensive cpDNA introgression occurred during and after postglacial recolonisation. Nevertheless, the individual species have different ecological requirements and also differ in their ability to hybridise, resulting in heterogeneous levels of partitioning of cpDNA diversity and incomplete cpDNA introgression. The first analysis of the effect of the landscape structure on genetic diversity in these oak species is presented here. The only discernible effect of landscape structure on cpDNA diversity was found in Quercus robur, and is very weak and rather counterintuitive. The biology and abundance of these oak species may make them particularly resistant to fragmentation; in addition, artificial seed flow may complicate the picture, and will require more direct investigations. (C) 2002 Elsevier Science B.V. All rights reserved.
The Swedish sand lizard (Lacerta agilis) is a relict species from the post-glacial warmth period. From the geological history of this region, and more recent data on population fragmentation due to disturbance by man, it can be surmised that the Swedish sand lizards passed through at least one population bottleneck in relatively recent times. We tested this hypothesis by investigating the amount and structuring of genetic variability in six microsatellite loci in ten lizard populations from different parts of Sweden. We contrasted these data against those from a Hungarian population which we have reason to assume strongly resembles the founder population for Swedish sand lizards. The average number of alleles per locus in Sweden was 3.3, and these alleles were common in almost all populations, whereas the average number of alleles in the Hungarian population was 8.0. Likewise, the level of expected heterozygosity was lower in the Swedish populations (0.45) compared to the Hungarian population (0.70). The lower variability in Swedish populations is probably a consequence of a common population bottleneck during the immigration subsequent to the latest glacial period. The remaining variability is strongly subdivided between populations (FST=0.30) with the main genetic differences being between rather than within populations. Despite the marked isolation of the populations and the present small population sizes (N= 10–300 adults), the Swedish relict populations show a surprisingly high level of observed heterozygosity, indicating that small population size is probably a recent phenomenon.
Amphibians are frequently characterized as having limited dispersal abilities, strong site fidelity and spatially disjunct breeding habitat. As such, pond-breeding species are often alleged to form metapopulations. Amphibian species worldwide appear to be suffering population level declines caused, at least in part, by the degradation and fragmentation of habitat and the intervening areas between habitat patches. If the simplification of amphibians occupying metapopulations is accurate, then a regionally based conservation strategy, informed by metapopulation theory, is a powerful tool to estimate the isolation and extinction risk of ponds or populations. However, to date no attempt to assess the class-wide generalization of amphibian populations as metapopulations has been made. We reviewed the literature on amphibians as metapopulations (53 journal articles or theses) and amphibian dispersal (166 journal articles or theses for 53 anuran species and 37 salamander species) to evaluate whether the conditions for metapopulation structure had been tested, whether pond isolation was based only on the assumption of limited dispersal, and whether amphibian dispersal was uniformly limited. We found that in the majority of cases (74%) the assumptions of the metapopulation paradigm were not tested. Breeding patch isolation via limited dispersal and/or strong site fidelity was the most frequently implicated or tested metapopulation condition, however we found strong evidence that amphibian dispersal is not as uniformly limited as is often thought. The frequency distribution of maximum movements for anurans and salamanders was well described by an inverse power law. This relationship predicts that distances beneath 11–13 and 8–9 km, respectively, are in a range that they may receive one emigrating individual. Populations isolated by distances approaching this range are perhaps more likely to exhibit metapopulation structure than less isolated populations. Those studies that covered larger areas also tended to report longer maximum movement distances – a pattern with implications for the design of mark-recapture studies. Caution should be exercised in the application of the metapopulation approach to amphibian population conservation. Some amphibian populations are structured as metapopulations – but not all.
Interspecific reproductive interference can affect fitness-related breeding performance, thus influencing fitness and distribution of populations. Laboratory studies demonstrated the social interference of Rana dalmatina males on R. latastei breeding females: the presence of heterospecific males reduced the percentage of viable embryos in R. latastei eggs. Here, we tested if the negative effects of R. dalmatina males on R. latastei reproductive success occur in field conditions. We compared the percentage of viable embryos of eggs laid in field conditions from populations where R. latastei breeds alone with the percentage of viable embryos of populations where R. latastei cohabits with R. dalmatina. We did not find any significant difference in percentage of viable embryos between R. latastei populations syntopic and allotopic with R. dalmatina, nor a relationship between the relative abundance of heterospecifics and reproductive success. In natural conditions, the presence of heterospecific males does not seem to interfere with the reproductive success of R. latastei. The experimental procedure may influence the interaction among individuals. Therefore, we suggest to validate on natural populations the results of experiments dealing with complex interactions.
Development rate early in the ontogeny is believed to correlate positively with fitness. Geographic variation in intrinsic
development rate suggests the existence of trade-offs between development rate and other fitness related traits. We investigated
whether these trade-offs exist between intrinsic larval development rate and post-metamorphic traits in an organism with a
complex life cycle. In laboratory, we measured if the tadpoles of the frog Rana latastei with fast intrinsic development rate have a suboptimal post-metamorphic morphology, by comparing froglets from five populations.
Then, we evaluated the relationship between age at metamorphosis, hindlimb length and jumping performance for frogs grown
in nature in two populations. Under laboratory conditions, froglets with fast intrinsic development had shorter absolute and
shorter size-adjusted tibiofibulas. We observed a strong, positive relationship between tibiofibula length and jumping performance.
In nature, froglets from the last metamorphosing population had longer absolute and size-adjusted tibiofibulas, and were able
to jump further. The cost of fast development could be the shorter legs of early metamorphosing frogs, and their poor jumping
performance. Thus, a fast intrinsic development rate may not always be positively related to lifetime fitness, since delayed
effects of larval development persist also across life history stages.
We studied amphibian populations in a human-dominated landscape, in Northern Italy, to evaluate the effects of patch quality and isolation on each species distribution and community structure. We used logistic and linear multiple regression to relate amphibian presence during the breeding season in 84 wetlands to wetland features and isolation. Jackknife procedure was used to evaluate predictive capability of the models. Again, we tested the response of each species to habitat features related to the richest communities. Amphibian presence depends strongly on habitat quality and isolation: the richest communities live in fish-free, sunny wetlands near to occupied wetlands. The negative effects of isolation do not seem to be biased by spatial autocorrelation of habitat features. The system shows strong nestedness: amphibian persistence depends on the contemporary effects of species adaptability and mobility. The commonest species, the pool frog (Rana synklepton esculenta) and the Italian tree frog (Hyla intermedia), are able to move through the matrix using canals and hedgerows, and can maintain metapopulations across the landscape; the rarest species (newts and toads) are more sensitive to habitat alteration, and they are strongly affected by isolation effects. If human exploitation of the landscape continues, only few species, mobile and opportunistic, will persist in this landscape.
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.
Whether inbreeding affects the demography and persistence of natural populations has been questioned. However, new pedigree data from field populations and molecular and analytical tools for tracing patterns of relationship and inbreeding have now enhanced our ability to detect inbreeding depression within and among wild populations. This work reveals that levels of inbreeding depression vary across taxa, populations and environments, but are usually substantial enough to affect both individual and population performance. Data from bird and mammal populations suggest that inbreeding depression often significantly affects birth weight, survival, reproduction and resistance to disease, predation and environmental stress. Plant studies, based mostly on comparing populations that differ in size or levels of genetic variation, also reveal significant inbreeding effects on seed set, germination, survival and resistance to stress. Data from butterflies, birds and plants demonstrate that populations with reduced genetic diversity often experience reduced growth and increased extinction rates. Crosses between such populations often result in heterosis. Such a genetic rescue effect might reflect the masking of fixed deleterious mutations. Thus, it might be necessary to retain gene flow among increasingly fragmented habitat patches to sustain populations that are sensitive to inbreeding.
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)
When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed.
Natal dispersal is a key life-history component that may be influenced by the fitness consequences of inbreeding. We studied natal dispersal and inbreeding within a large population of cooperatively breeding, endangered Red-cockaded Woodpeckers (Picoides borealis). We assessed the costs of close inbreeding, the spatial distribution of related males and its relationship to dispersal distance of females, and the change in dispersal behavior of females in the presence of closely related males. Close inbreeding resulted in a significant loss of fitness, through two separate effects: closely related pairs (kinship coefficient ≥ 0.125) exhibited lowered hatching rates and lowered survival and recruitment of fledglings relative to unrelated pairs. Despite a highly predictable spatial clustering of closely related males near the female's natal territory, natal dispersal distance of females was not sufficient to avoid these males as mates. Females changed dispersal behavior in the presence of closely related males on the natal territory: female fledglings were significantly more likely to disperse from natal territories if there were closely related males breeding there in the following year. Females did not change dispersal behavior in the presence of related males that were not on the natal territory. We suggest that dispersal behavior is a trade-off between benefits of short-distance dispersal, e.g., an advantage in competing for scarce breeding vacancies, and the substantial cost of close inbreeding.
In many respects, amphibian spatial dynamics resemble classical metapopulation models, in which subpopulations in breeding ponds blink in and out of existence and extinction and colonization rates are functions of pond spatial arrangement. This "ponds-as-patches" view of amphibian spatial dynamics is useful in several respects. First, it highlights the importance of regional and landscape processes in determining local patterns of abundance. Second, it offers a straightforward, pond-based approach to monitoring and managing amphibian populations. For many species, however, the ponds-as-patches view may be an oversimplification and metapopulation structure may be more apparent than real. Changes in distribution may be caused by processes other than extinction and recolonization, and most extinctions probably result from deterministic factors, not stochastic processes. In addition, the effects of pond isolation appear to be important primarily in disturbed environments, and in many cases these isolation effects may be better explained by the distribution of terrestrial habitats than by the distribution of breeding ponds. These complications have important implications for both researchers and managers. For researchers, future efforts need to determine the mechanisms underlying patterns of abundance and distributional change and patterns in amphibian populations. For managers, effective conservation strategies must successfully balance metapopulation considerations with careful attention to local habitat quality. Furthermore, translocations and active management may be indispensable tools for conserving amphibians in landscapes containing multiple breeding ponds.
Although it is widely recognised that spatial subdivision of populations is common in nature, there is no consensus as to how metapopulation dynamics affect genetic diversity. We investigated the genetic differentiation of natterjack toads, Bufo calamita, in three regions of Britain where habitat continuity indicated the likely occurrence of extensive metapopulations. Our intention was to determine whether genetic analysis supported the existence of metapopulation structures, if so of what type, and to identify barriers to migration between subpopulations. Allele frequencies were determined across eight polymorphic microsatellite loci for a total of 24 toad subpopulations at three separate sites. Genetic differentiation was assessed using five measures of genetic distance, notably FST, RST, Nei's standard distance Ds,Δ2 and the Cavalli-Sforza chord distance Dc. B. calamita exhibited small but significant levels of genetic differentiation between subpopulations in all three study areas, and genetic and geographic distance correlations indicated isolation-by-distance effects in all three cases. The effects on correlation strengths of compensation for positive (sea, rivers, urban development) and negative (pond clusters) barriers to toad migration between the subpopulations in each area were also determined. Dc, a measure which assumes that differentiation is caused by drift with negligible mutation effect, yielded the most plausible interpretation of metapopulation structures. Overall the patterns of genetic variation suggested the existence of a mixed metapopulation model for this species, with high levels of gene flow compatible with one version of the classical model but often supported by particularly stable subpopulations as in the mainland-island model.
In order to find out the influence of land use and topographic distance on the genetic structure of populations of the common frog Rana temporaria L. in the Saar-Palatinate lowlands (Federal Republic of Germany), tissue of larvae was examined by means of horizontal starch gel electrophoresis. A total of 24 loci coding for 14 different enzymes were studied. Genotype frequencies, allele frequencies and mean heterozygosity were calculated, and genetic distances using Nei's formula. Strong deviations from the Hardy-Weinberg equilibrium were found; the degree of homozygosity was higher than expected.Separation by highways reduced average heterozygosity as well as genetic polymorphism of local populations.One area surrounded by roads had high genetic distances to other sampling stations. A multiple regression analysis showed that motorways and railways have a significant (p = 0·03) barrier effect on frog populations within 3–4 km. Meadowland apparently enabled individual exchange in a range between 2 and 7 km. Consequences for the design of biotope systems are discussed.
Genetic structure and diversity are studied in two European saltmarsh beetles, Bembidion mini- mum and B. normannum, on a regional as well as a Western European scale. Results are based on allozymes, studied at four polymorphic loci for more than 1600 individuals from all remaining saltmarshes in Belgium and from a selection of European reference sites. Average gene diversity is not related to habitat or population size, but is larger in the more common B. minimum, in comparison to Atlantic samples of B. normannum. One Mediterranean sample of the latter species reveals a much higher diversity and suggests this region as the evo- lutionary centre of origin and/or as a possible glacial refugium of the species. Significant overall genetic struc- ture is observed in the complete data of both species, with 2 to 6 % of the total genetic variation explained by differentiation between populations. Genetic differentiation in both species is significant at different geo- graphic scales, with higher values at a larger scale. A Mantel-test (isolation by distance) between geographic and genetic distance is significant in B. normannum. Our results indicate that habitat fragmentation has not yet resulted in genetic erosion, probably because of the large population sizes of both species, even in very small saltmarshes. The observed genetic differentiation suggests that metapopulations at a relatively large geographic scale are still functional in these highly mobile species. Re-establishment of even small saltmarshes is sug- gested as a positive conservation measure for long term survival of these specialised ground beetles.
Relationships between mean individual fitness and genetic heterozygosity remain controversial because multiple studies over many years have yielded inconsistent results. However, molecular measurements of genetic variation have mostly been based on allozyme markers, which may have substantial limitations due to their relative insensitivity and occasionally also to the effects of natural selection. We investigated variation in the number of tandem dinucleotide repeats at eight polymorphic microsatellite loci in 38 natterjack toad, Bufo
calamita, populations that varied in census size, degree of isolation and distance from the distributional range edge. We also measured fitness attributes, notably larval survival and growth rates, under standardized conditions using samples from six of these populations. The results indicated that larval growth rates were positively and strongly correlated with expected heterozygosity (He) across the microsatellite loci. He was in turn highest in large populations with minimal isolation, but low near the biogeographical range edge irrespective of population size. Larvae from the smallest and most isolated natterjack population exhibited particularly low fitness and heterozygosity. Our results suggest that microsatellite loci may provide a valuable new approach in studies of links between fitness and heterozygosity.
The natterjack toad Bufo calamita is rare in Britain, which is at the northwestern edge of its biogeographical range. We investigated the level of genetic differentiation amongst almost all (34 out of 38) of the surviving British populations of this species, and among six new populations established by translocations during the 1980s. For eight microsatellite loci, allele sizes and frequencies were analysed using samples from each of these populations. The populations clustered into three robustly differentiated groups, each of which corresponded with a geographical region (east/southeast England, Merseyside and Cumbria). The Cumbrian populations showed a further weak geographical substructuring into northern and southern clades. The populations in south Cumbria were genetically more diverse than those in any of the other regions, as judged by the mean numbers of alleles per locus and the mean heterozygosity estimates. The translocated populations clustered close to their founders and, with one exception, did not differ significantly with respect to mean allele numbers, heterozygosity or polymorphism level. However, significant genetic differentiation (as measured by unbiased RST) was found between all but one of the founder-translocation pairs. The implications of this phylogeographic study for the future conservation of B. calamita in Britain are discussed.
Rana iberica is an Iberian endemic with populations mainly distributed in northwestern Iberia, but with scattered populations along the Sistema Central in central Spain. These latter populations inhabit mostly mountain areas and are endangered due to habitat loss and fragmentation. At present, no information about genetic variability and gene flow patterns between populations is available and, consequently, it is unknown to what extent geographical fragmentation might have caused restrictions to gene flow. We used six microsatellite loci to characterise genetic variability in R. iberica populations from the Sistema Central. We analysed samples of 142 specimens from 15 populations in this region and another two from additional locations in the Iberian Peninsula. The number of alleles per locus observed ranged from four to 15. Allelic richness, percentage of private alleles and gene diversity was significantly lower in populations from the Sistema Central, where inbreeding coefficients were relatively high. Analysis of molecular variance (AMOVA) and estimated FST values indicated the existence of genetic substructuring within this region and suggested the existence of restrictions to gene flow in geographically close populations. Low heterozygosities and a trend towards lower values of genetic variability from western to eastern populations within the Sistema Central suggest that R. iberica has colonised this region recently. We hypothesise that the observed pattern is due to the interaction of both historical (reduced genetic variability in peripheral populations) and present-day (anthropogenic habitat loss) factors that confirm the vulnerable status of populations of R. iberica in central Spain and point to the need for adopting measures directed towards the preservation of existing habitat.
Populations of the amphibian Bufo calamita were sampled for genetic analysis in eleven areas distributed across its biogeographical range in Europe. Genetic diversity estimates across eight microsatellite loci showed a decline in polymorphism, numbers of alleles and heterozygosity as a function of distance from the presumed ice-age refugium in Iberia. Trials with a selection of tree-building algorithms indicated mat UPGMA of Cavalli-Sforza chord distances (Dc) generated the tree topology most easily reconciled with other biogeographical information. Genetic distance measures were also calibrated against a postglacial event from which the separation of extant populations could be estimated in real time. Dc again outperformed two other measures (Nei's standard distance, Ds, and δμ2) in producing realistic correlations with minimal variance. The genetic analysis was consistent wim die hypodiesis that B. calamita survived in a single refugium (Iberia) during the Pleistocene glaciation and indicated that it spread north and east from there during the last interstadial which commenced about 14 000 years before present (BP). Microsatellites should provide useful tools for biogeographical investigations of other species, especially with respect to patterns of population dispersal.
Genetic diversity is one of the three forms of biodiversity recognized by the World Conservation Union (IUCN) as deserving conservation. The need to conserve genetic diversity within populations is based on two arguments: the necessity of genetic diversity for evolution to occur, and the expected relation-ship between heterozygosity and population fitness. Because loss of genetic diversity is related to inbreed-ing, and inbreeding reduces reproductive fitness, a correlation is expected between heterozygosity and pop-ulation fitness. Long-term effective population size, which determines rates of inbreeding, should also be correlated with fitness. However, other theoretical considerations and empirical observations suggest that the correlation between fitness and heterozygosity may be weak or nonexistent. We used all the data sets we could locate (34) to perform a meta-analysis and resolve the issue. Data sets were included in the study, provided that fitness, or a component of fitness, was measured for three or more populations along with heterozygosity, heritability, and/or population size. The mean weighted correlation between measures of genetic diversity, at the population level, and population fitness was 0.4323. The correlation was highly sig-nificant and explained 19% of the variation in fitness. Our study strengthens concerns that the loss of het-erozygosity has a deleterious effect on population fitness and supports the IUCN designation of genetic di-versity as worthy of conservation. Correlación entre Adaptabilidad y Diversidad Genética Resumen: La diversidad genética es una de las tres formas de biodiversidad reconocidas por la Unión de Conservación Mundial (IUCN) que merecen ser conservadas.
Measures of genetic diversity (including heterozygosity), survival and developmental homeostasis were found to be significantly lower in small, urban populations of the Common Toad (Bufo bufo) than in larger, rural populations of the same region. The autecology and genetic analysis of this relatively sedentary species suggested that the causal mechanism was genetic drift, arising from barriers to migration created by urban development. The pre-metamorphic survival of larvae cultured in identical conditions increased positively with the mean number of alleles at a locus and the percentage of polymorphic loci. Observed heterozygosity in urban garden and rural populations was correlated inversely with the number of observed physical abnormalities (used as a measure of developmental homeostasis) in the developing tadpoles. Genetic distances between town sites of mean 2.2 km separation were significantly higher than those between rural sites of mean 37 km separation. Genetic data were based on allozyme analysis of 27 loci in 8 urban and 4 rural populations. A subset of these sites (3 urban, 2 rural) were also assessed at 3 minisatellite loci and a positive correlation found between the average number of alleles per locus detected by the two methods. Estimates of Nei's 1972 genetic distance, derived separately from the DNA and protein data, were not, however, correlated. The reduction in genetic diversity and fitness observed in these urban toads provides an example of the effect on population persistence that longer term depletion in numbers and habitat fragmentation can have in the wider environment.
Drastic reductions in population size, or bottlenecks, are thought to significantly erode genetic variability and reduce fitness. However, it has been suggested that a population can be purged of the genetic load responsible for reduced fitness when subjected to bottlenecks. To investigate this phenomenon, we put a number of Drosophila melanogaster isofemale lines known to differ in inbreeding depression through four ‘founder-flush’ bottleneck cycles with flush sizes of 5 or 100 pairs and assayed for relative fitness (single-pair productivity) after each cycle. Following the founder-flush phase, the isofemale lines, with a large flush size and a history of inbreeding depression, recovered most of the fitness lost from early inbreeding, consistent with purging. The same isofemale lines, with a small flush size, did not regain fitness, consistent with the greater effect of genetic drift in these isofemale lines. On the other hand, the isofemale lines that did not show initial inbreeding depression declined in fitness after repeated bottlenecks, independent of the flush size. These results suggest that the nature of genetic variation in fitness may greatly influence the way in which populations respond to bottlenecks and that stochastic processes play an important role. Consequently, an attempt intentionally to purge a population of detrimental variation through inbreeding appears to be a risky strategy, particularly in the genetic management of endangered species.
Population structure is the result of both present processes and past history. Molecular markers are proving of great value in describing the former, and it is important to similarly determine the latter in order to understand their respective contributions. The study of palaeo-climates has also advanced significantly, and in particular that of the Pleistocene ice ages, which modified species ranges considerably. The last ice age and rapid post-glacial colonization of Europe is summarized. Possible population genetic consequences of expansion northward from southern refugia, and those of remaining in these mountainous regions are discussed. A series of recent case studies are detailed where DNA sequence information has been used to describe species genetic variation and subdivision across Europe. These include a grasshopper, the hedgehog, oak trees, the common beech, the black alder, the brown bear, newts, shrews, water vole, silver fir and house mice. These molecular data confirm southern peninsulas of Europe as major ice age refugia, and in most cases demonstrate that genetically distinct taxa emerged from them. They can thus define genomic differences and so gready augment previous fossil data. The refugial genomes contributed differently in various species to die re-colonization of Europe, with three broad patterns described as paradigms–‘grasshopper’, ‘hedgehog’ and ‘bear’. These different expansion patterns produced clusters of hybrid zones where they made contact, and it is argued that many species genomes may be further cryptically subdivided. A reduction in diversity from southern to northern Europe in the extent of allelic variation and species subdivision is seen; this is attributed to rapid expansion northward and the varied topography of southern refugia allowing populations to diverge through several ice ages. The differences in DNA sequence indicate that some species have been diverging in refugial regions for a few ice ages at most, whilst distinct lineages in other species suggest much more ancient separation.
The genetic effects of pleistocene ice ages are approached by deduction from paleoenvironmental information, by induction from the genetic structure of populations and species, and by their combination to infer likely consequences. (1) Recent palaeoclimatic information indicate rapid global reversals and changes in ranges of species which would involve elimination with spreading from the edge. Leading edge colonization during a rapid expansion would be leptokurtic and lead to homozygosity and spatial assortment of genomes. In Europe and North America, ice age contractions were into southern refugia, which would promote genome reorganization. (2) The present day genetic structure of species shows frequent geographic subdivision, with parapatric genomes, hybrid zones and suture zones. A survey of recent DNA phylogeographic information supports and extends earlier work. (3) The grasshopper Chorthippus parallelus is used to illustrate such data and processes. Its range in Europe is divided on DNA sequences into five parapatric races, with southern genomes showing greater haplotype diversity - probably due to southern mountain blocks acting as refugia and northern expansion reducing diversity. (4) Comparison with other recent studies shows a concordance of such phylogeographic data over pleistocene time scales. (5) The role that ice age range changes may have played in changing adaptations is explored, including the limits of range, rapid change in new invasions and refugial differentiation in a variety of organisms. (6) The effects of these events in causing divergence and speciation are explored using Chorthippus as a paradigm. Repeated contraction and expansion would accumulate genome differences and adaptations, protected from mixing by hybrid zones, and such a composite mode of speciation could apply to many organisms.
Human-caused habitat destruction and modification constitute one of the largest threats to population persistence and biodiversity, and are also suspected to be the major cause behind the global decline of amphibian populations. We assessed the potential role of agriculture-related habitat fragmentation on population size and genetic variability in the common frog (Rana temporaria) by recording the occurrence, population density and genetic diversity in three geographically disparate regions in Sweden – each containing landscapes of high and low agricultural activity – and related these to landscape variables extracted from digital maps. We found a highly significant region-by-landscape interaction in occurrence, population density and genetic diversity revealing a reversed response to agriculture from south to north: while the effects of agriculture on R. temporaria populations were negative in the south, there were no effects in the central region, whereas positive effects were observed in the north. Spatial autocorrelation analyses of genetic data revealed that populations in high agricultural activity areas were more isolated than populations in low activity areas both in the southern and central regions of Sweden. Landscape diversity showed a strong positive correlation with both density and occurrence of frogs in Sweden as a whole, as well as in the southern region. Also, negative effects of roads and positive effects of ditches on genetic diversity were found in the south. Overall, these results suggest clear but regionally opposite effects of habitat structure on the population size and genetic diversity of amphibian populations. This means that the management strategy aiming to maximize the size and genetic diversity of local common frog populations, and perhaps also those of other amphibian populations, should account for regional differences in existing land-use patterns.
— The ability of populations to undergo adaptive evolution depends on the presence of quantitative genetic variation for ecologically important traits. Although molecular measures are widely used as surrogates for quantitative genetic variation, there is controversy about the strength of the relationship between the two. To resolve this issue, we carried out a meta-analysis based on 71 datasets. The mean correlation between molecular and quantitative measures of genetic variation was weak (r = 0.217). Furthermore, there was no significant relationship between the two measures for life-history traits (r =−0.11) or for the quantitative measure generally considered as the best indicator of adaptive potential, heritability (r =−0.08). Consequently, molecular measures of genetic diversity have only a very limited ability to predict quantitative genetic variability. When information about a population's short-term evolutionary potential or estimates of local adaptation and population divergence are required, quantitative genetic variation should be measured directly.
Western populations of the Italian agile frog (Rana latastei) experience widespread genetic depletion. Based on population genetic theory, molecular models of immunity and previous empirical studies, population genetic depletion predicts increased susceptibility of populations to emergent pathogens. We experimentally compared susceptibility of R. latastei populations upon exposure to an emerging strain of Ranavirus, frog virus 3 (FV3), using six populations spanning the geographical range and range of population genetic diversity found in nature. Our findings confirm this prediction, suggesting that the loss of genetic diversity accompanying range expansion and population isolation is coincident with increased mortality risk from an emergent pathogen. Loss of heterozygosity and escape from selection imposed by immunologically cross-reactive pathogens may potentially generate range-wide variation in disease resistance.
In many respects, amphibian spatial dynamics resemble classical metapopulation models, in which subpopulations in breeding ponds blink in and out of existence and extinction and colonization rates are functions of pond spatial arrangement. This “ponds-as-patches” view of amphibian spatial dynamics is useful in several respects. First, it highlights the importance of regional and landscape processes in determining local patterns of abundance. Second, it offers a straightforward, pond-based approach to monitoring and managing amphibian populations. For many species, however, the ponds-as-patches view may be an oversimplification and metapopulation structure may be more apparent than real. Changes in distribution may be caused by processes other than extinction and recolonization, and most extinctions probably result from deterministic factors, not stochastic processes. In addition, the effects of pond isolation appear to be important primarily in disturbed environments, and in many cases these isolation effects may be better explained by the distribution of terrestrial habitats than by the distribution of breeding ponds. These complications have important implications for both researchers and managers. For researchers, future efforts need to determine the mechanisms underlying patterns of abundance and distributional change and patterns in amphibian populations. For managers, effective conservation strategies must successfully balance metapopulation considerations with careful attention to local habitat quality. Furthermore, translocations and active management may be indispensable tools for conserving amphibians in landscapes containing multiple breeding ponds.
Given the recent interest in declining amphibian populations, it is surprising that there are so few data on genetic drift and gene flow in anuran species. We used seven microsatellite loci to investigate genetic structure and diversity at both large and small geographic scales, and to estimate gene flow in the Cascades frog, Rana cascadae. We sampled 18 sites in a hierarchical design (inter-population distances ranging from 1–670km) to test for isolation by distance and to determine the geographic scale over which substantial gene flow occurs. Eleven of these sites were sampled as three fine-scale clusters of three, three, and five sites separated by pairwise distances of 1–23km to estimate number of migrants exchanged per generation via F
ST
and by a coalescent approach. We found R. cascadae exhibits a strong pattern of isolation by distance over the entire species range, and that there is a sharp drop in migrants exchanged between sites separated by greater than 10km. These data, in conjunction with results of other recent studies, suggest that montane habitats promote unusually strong genetic isolation among frog populations. We discuss our results in light of future management and conservation of R. cascadae.
Human activities are simultaneously decreasing the size of wildlife populations (causing inbreeding) and increasing the level of stress that wildlife populations must face. Inbreeding reduces population fitness and increases extinction risk. However, very little information on the impact of stressful environments on extinction risk under inbreeding is available. We evaluated the impact of full sib inbreeding on extinction risk, using Drosophila melanogaster, in a benign and three stressful environments. The three stressful environments involved the addition to the medium of copper sulfate, methanol or alternating copper sulfate and methanol. There were 128 replicate populations for each of the four treatments. Under inbreeding, extinction rates were significantly higher in all three stressful environments compared with the benign environment. The percent extinct at generation eight (F = 0.826) for the four treatments were: 62.5% in the benign environment, 75.8%in the copper sulfate environment, 82.8% in the methanol environment, and 83.6% in the variable stress environment. However, the extinction rate in the variable stress environment did not differ significantly from the constant stress environments. Highly significant differences, among lineages, in extinction risk were detected. The results of this study indicate that wild populations are more vulnerable to inbreeding than indicated by extrapolation from captive environments.
Glacial refugia are generally expected to harbor higher levels of genetic diversity than are areas that have been colonized after the retreat of the glaciers because colonization often involves only a few individuals. A new paper by Comps et al. challenges this expectation by demonstrating a more complex situation in the European beech Fagus sylvatica, for which some measures of genetic diversity are higher in newly colonized areas than in refugia. The key to understanding this counter-intuitive result rests both in the estimators used to measure genetic diversity and in the processes affecting these estimators during postglacial recolonization.
Genetic studies in endangered species have become widespread in the past decade, and with new information from various genome projects, new applications and insights are forthcoming. Generally, neutral variants are used for conservation applications, and when combined with highly variable loci and/or many more markers, these approaches should become much more informative. Conservation genetics is also concerned with detrimental and adaptive variation, which are more difficult to identify and characterize; however, the ability to predict the extent of such variation might become more successful and applied in future conservation efforts. Neutral variants might be used to identify adaptive variants, but the overlay of different mutational processes and selective regimes suggests that extreme caution should be used in making such identifications.
Climatic oscillations in the Quaternary have played a major role in changing the geographical distribution of plant species. Recent molecular work has provided new insights into the location of glacial refugia and routes of postglacial expansion. A comparative analysis shows that phylogeographic patterns in Europe appear to be less congruent than in North America. The change of geographical distribution has also provided opportunities for speciation through isolation, and hybridization after secondary contact. However, a complete understanding of the significance of the Quaternary climatic changes for plant speciation requires further research into the estimation of reliable and accurate divergence times.
Relocation of endangered species can be an effective conservation tool if it does not mix populations that represent significant intraspecific variation. The threatened Italian agile frog, Rana latastei, has small populations with low genetic diversity: translocation has been proposed to improve the likelihood of survival of populations. Using a common environment experiment and field surveys, we investigated whether there were differences in larval growth and developmental rate between foothill and lowland R. latastei populations, to evaluate if they are evolutionarily significant units. In nature, the colder climate of the foothills causes delayed metamorphosis. Conversely, in a common environment, larvae from foothill populations show faster growth and development. We did not find a significant egg-size related maternal effect or any differences in size at metamorphosis. We hypothesise that counter-gradient selection promoted fast growing phenotypes in a cold environment, where low temperatures slow down larval development. Foothill populations, despite being only a small geographical distance away from lowland populations, seem to be adapted to a colder climate and represent an evolutionarily significant unit. Different populations should, therefore, be managed independently, avoiding translocation. We suggest that evolutionary divergence between populations should be verified prior to planning relocation programmes, to prevent the risk of genetic homogenisation.
To study genetic effects of habitat fragmentation on plant performance and plant response to biotic interactions, we performed a greenhouse study with plants from 27 populations of the common plant Lychnis flos-cuculi differing in size, isolation, and microsatellite heterozygosity. We germinated seeds of 449 plants and grew up to nine offspring per maternal plant in single pots assigned to a factorial competition-by-pathogen infection treatment. We applied competition by sowing seeds of the grass Anthoxanthum odoratum into half of the pots. Moreover, half of the plants were inoculated with infective sporidia of the anther smut Microbotryum violaceum. Significant variation among populations in most size measures indicated genetic differentiation between populations. Plants from smaller populations developed fewer flowers than plants from larger populations indicating a genetic Allee effect. A decrease in flower number was also observed for populations with decreased microsatellite heterozygosity, suggesting higher inbreeding depression. Competition and pathogen infection reduced plant size independently from one another and independent from the fragmentation of the habitats of plant origin. While pathogen infection increased the total number of flowers per plant, it decreased the number of uninfected flowers per plant. This study demonstrates that even common species are negatively affected by habitat fragmentation. At the same time, it suggests little effect of habitat fragmentation on plant response to experimental competition and pathogen infection.
When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed.