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How large must population be to retain evolutionary potential?
Abstract
Maintaining genetic variation for future evolutionary change is an important issue for conservation biology. However, there is controversy over the effective population size (Ne) required for endangered species to retain their evolutionary potential, with proposed sizes ranging from 500 to 5000. The highest estimate is based on the assumption that 90% of mutations are deleterious. We review the arguments for an effective size of 5000 and conclude that it assumes effective mutation rates that are too low, and heritabilities that are, in general, very high. We conclude that an Ne of 500-1000 is appropriate at this time.
... Inbreeding may eventually lead to reduction in additive genetic variance owing to fixation of alleles (Esfandyari et al., 2017). A high rate of inbreeding affects response to selection for individual traits negatively, and levels beyond 0.1% would not be optimal for evolution (Franklin & Frankham 1998;Tongsiri et al., 2019). Ignoring loss in genetic variance and inbreeding and not accounting for mitigation strategies such as genomic selection against these factors could be detrimental to long-term genetic gain in a breeding programme. ...
... Inbreeding has also been shown to affect negatively traits such as milk production, growth and health in cattle (Mészáros et al., 2014).This could explain the low genetic gain for individual traits and subsequent economic response realized under CSP in the current study. Generally, all three breeding schemes had higher rates of inbreeding than the recommended levels of 0.1% for evolutionary potential (Franklin & Frankham, 1998). This could be explained by the low effective population size of 320, since rate of inbreeding is determined by population size (Wang et al., 2016). ...
... This could be explained by the low effective population size of 320, since rate of inbreeding is determined by population size (Wang et al., 2016). This size was lower than the recommended 500 to 1000 for conservation in animal populations (Frankham & Franklin, 1998;Krupa et al., 2015;Lopes et al., 2019).The highest genetic gains and lowest rates of inbreeding for GSS compared with CSN and CSP implied that this scheme could yield more response to selection in IC breeding. ...
This study tested the hypothesis that the use of pooled genetic and phenotypic parameters and genomic selection would optimize selection response in indigenous chicken breeding programmes. This premise was tested with deterministic simulation in three breeding schemes based on the sources of information used to estimate breeding values. These schemes used a conventional breeding scheme with non-pooled parameters (CSN), pooled parameters (CSP), and genomic information in a genomic selection scheme (GSS). A one-tier closed nucleus breeding programme was considered with a mating ratio of 1 to 5 for males to females, Four traits were used in the breeding goal, namely live weight at twelve weeks (LW), egg number for twelve weeks (EN), age at first egg (AFE), and antibody response (Ab). The genetic gain for CSN was 1.5 times higher than that of CSP. The rate of inbreeding for CSN was 19% lower than in CSP. The accuracy of selection followed the same trend with CSN producing 9% higher accuracy of selection than CSP. The GSS scheme resulted in an additional 59.3% genetic gain and 30% accuracy compared with CSP. The GSS scheme also had a reduced rate of inbreeding by 46% compared with CSP. When compared with CSN, GSS produced 38.7% greater genetic gain, a 27% lower rate of inbreeding and 21.0% higher accuracy of selection. Use of pooled parameter estimates and genomic information optimized response to selection, whereas non-pooled inputs overestimated and underestimated rates of genetic gain and inbreeding.
... The minimum N e for genetically viable natural populations, which prevents inbreeding depression and ensures lasting maintenance of genetic variation and the evolutionary potential, is much debated and proposals vary from 500 to 5000 (Allendorf & Ryman, 2002;Frankham et al., 2014;Franklin, 1980;Franklin & Frankham, 1998;Lande, 1995;Lynch & Lande, 1998). In such evaluations, the longterm genetic viability is often assessed with a time frame of 40 generations, as scaling by generation time allows comparisons between taxa with different demography (Frankham et al., 2014). ...
... In such evaluations, the longterm genetic viability is often assessed with a time frame of 40 generations, as scaling by generation time allows comparisons between taxa with different demography (Frankham et al., 2014). The criteria for minimum N e are based on an assessment of the overall effect of genetic drift and the mutation rate (Franklin & Frankham, 1998;Wang et al., 2016), and should also include the effect of how quickly a population can adapt to changing environmental conditions (natural selection, Lynch & Lande, 1998). Franklin's (1980) well-known proposal of N e ≥ 500 has been criticized as being too low because it does not account for the influence of natural selection on the genetic variation (Lande, 1995;Lynch & Lande, 1998), it overestimates the proportion of new mutations that are neutral (Lande, 1995) and it ignores random effects from demographic, genetic, and environmental sources of stochasticity (Lynch & Lande, 1998). ...
Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long‐term viability. The effective population size (Ne) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate Ne of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The Ne/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14 years period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2% in 2005–2018 and 44.8% in 2021). Increased harvest rates decreased Ne in the simulations, but less sex biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased Ne. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long‐term genetic viability of wildlife populations subject to a disease will also depend on population impacts of the disease and how these interact with management actions.
... Benue ( Benue 3,4,6,7,9,10,12,13,14) and 8 out of the 14 (57.14%) Donga specimens (16,18,21,22,23,24,26,27). The tree in Figure 2 showed the haplotype in clade 1 rooted to C. gariepinus NCBI voucher MF683196.1, ...
... In addition, Donga river populations had lower haplotype diversities than Benue populations, this could be attributed to genetic drift and cannibalism among the fish, which caused a reduction in gene frequencies in the samples and also higher fishing pressure, especially in the Donga population could have reduced its genetic diversity, through fishing mortality [17] . Small and isolated populations also suffer lower genetic diversities due to genetic drift that results from founder effects and lower effective population sizes [18] . This reflects a high divergence of the population, which could be attributed to the possibility of multiple sources of the C. gariepinus. ...
Molecular diagnosis on strains of African catfish, Clarias gariepinus is fundamental step to study genetic diversity, this study was aim to reveal and compare the genetic structure of C. gariepinus from Benue and Donga River population. Thirty (30) matured C. gariepinus; 15 specimens each of Benue and Donga River were utilised for the molecular analytic study, DNA specimens were prepared for sequencing through PCR technique, partial genome sequences of 30 specimens covered 0.998% region of the Clarias gariepinus mitochondrion, total score compared to the whole genome ranged 0.99-1.00%. The Tajima's neutrality test, revealed that the 561 positions in the 29 specimen sequences has 2 segregating sites (S), the nucleotide diversity (π) was 0.000869, and the Tajima test statistic D was-0.087728 while the tree diagram showed 3 clusters/haplotypes within 2 divergent clades. The Tajima's relative rate test showed that 557 identical sites out of the 558 positions in all the three haplotypes. Only one unique nucleotide difference occurred in haplotype 1. Alignment of the nucleotides showed a T-C point mutation/single nucleotide polymorphism at Locus 430 indicating that the genetic distance between the species is distinct. Analysis of the genetic diversity of the population revealed clearly different strains and their respective population structures.
... However, restoration by colonization from adjacent habitats may also impose the risk of genetic diversity loss, because founder groups may consist of just a limited number of individuals and comprise only a part of the source populations genetic diversity (Franklin and Frankham 1998;Vandepitte et al. 2012). Further, the loss of alleles and changes in their frequencies may additionally occur due to random genetic drift in small populations (Franklin 1980). ...
... The broad population genetic diversity is a necessary raw material for the population's adaptability to changing environments. If levels of genetic diversity are reduced, then populations would be at risk in the long term due to the loss of their evolutionary potential (Franklin and Frankham 1998;Bucharova et al. 2022). ...
Species-rich calcareous grasslands in Europe strongly declined during the twentieth century due to drastic land use changes. Many grasslands were converted into more productive pastures or are covered by shrubs or forests today, since they were overgrown after abandonment or afforested. Restoration of calcareous grasslands by shrub or forest clearing and subsequent recolonization of grassland species from adjacent grasslands is, therefore, an important conservation approach. Restored populations of calcareous grassland species may, however, differ from their source populations in genetic diversity and differentiation due to potential founder and bottleneck effects. In our study we analyzed, therefore, the impact of restoration by forest clearing and natural recolonization on the genetic variation of three common calcareous grassland species ( Agrimonia eupatoria , Campanula rotundifolia , and Knautia arvensis ) without a contribution of persistent seed bank, in South Western Germany. We used molecular markers AFLPs (Amplified fragment length polymorphisms) to compare genetic diversity within and differentiation between spontaneously recovered subpopulations with adjacent historically old, natural subpopulations at eight study sites. Restored parts of the grasslands have been re-established during the 1990s. Molecular markers revealed broadly similar levels of genetic diversity in source and restored subpopulations of the study species. Only A. eupatoria exhibited slightly higher diversity in restored subpopulations, which may be explained by higher dispersal potential due to the hooky fruits of the species. Genetic differentiation between source and restored subpopulations was not significant, indicating strong gene flow between the subpopulations. Our study underlines, therefore, that restoration of calcareous grasslands by natural recolonization after forest clearing is an efficient method to re-establish genetically variable subpopulations comparable to their sources.
... Incidentally, the timeframe of interest in conservation biology is also several generations (short-term) to a few hundred generations (medium-term) [50]. In conservation biology, Ne of 500-1000 is required to maintain genetic variation for future evolutionary change, considering the mutation rate, and populations with Ne of over 500 are considered not to be doomed to extinction in the short to medium term and to have the ability to evolve with environmental change in the long term [51,52]. Using EVOLVE, I found that a medium crew size (1,900-2,000 humans) is sufficient for 6300-year interstellar travel to maintain genetic variation for future environmental change, such as living on the exoplanet after reaching it. ...
... However, several studies have reported beneficial and deleterious mutations that relate to fitness and extinction risk, and there is no consensus about the rate and distributions of the effect of new mutations [51]. If we could understand the relationship between mutation of protein-coding genes and phenotypic evolution, the effects of selection could be included in EVOLVE, and more precise estimation would be possible. ...
Designing multigenerational interstellar ships requires defining crew size, which factors into many variables, including food production, air/water control, and propulsion. Previously published computations provided a critical crew number of 98 (Marin, 2018), 150-180 (Moore, 2003) and 14,000 people (Smith, 2014), considering reproductive parameters such as inbreeding and infertility, but not including population genetics parameters such as mutation and genetic drift in computations. Estimating the critical size to maintain genetically healthy crews is difficult without genetic parameters. Marin (2021) included genetic parameters and provided a minimum crew of 100-500 at the beginning of the travel, but the spaceship capacity is equally important as initial crew size. Therefore, I present a Monte Carlo code named EVOLVE to estimate the critical crew size, the spaceship capacity, for multigenerational interstellar travel, including genetic parameters. I show in this paper that a crew of a few hundred people can reach the destination without facing extinction but cannot maintain a genetically healthy crew and that a minimum crew size of 1,900-2,000 people is necessary and sufficient to maintain a genetically healthy crew for a long-duration mission towards the closest exoplanet. Finally, this paper estimates the possibility of human evolution during interstellar travel, which might affect the spaceship design.
... We found small effective population sizes potentially resulting in strong stochastic effects, dependence of the ratio of Ne and Nc on the size of the population, a very recent divergence of the larger populations following deforestation as revealed by ABC models, and a meta-population structure with source and sink subpopulations. The effective meta-population size was under the critical population size limit of 500-5000 individuals often suggested for vertebrate taxa (Franklin and Frankham 1998;Lynch and Lande 1998;Traill et al. 2007; Jamieson and Allendorf 2012; but see Frankham et al. (2014) for critical notes on these numbers), and some populations appear prone to local extinction due to outward migration that is not fully compensated by inward migration. While the overall Ne to Nc ratio of 0.13 for the meta-population size is relatively low in comparison with other bird species, our temporal data suggest that some populations may have slightly increasing, rather than decreasing, census and effective sizes, and both the census and effective metapopulation sizes increased too. ...
... Despite Ne estimates as low as 4 (ND) and 7 (FU) individuals during 1996-2000 (the generation previous to this interval) that are well below the thresholds of 50 and 500 individuals generally assumed to minimize the effects of genetic inbreeding and drift (Lande 1988;Franklin and Frankham 1998;Lynch and Lande 1998), none of the populations showed evidence for a recent population bottleneck (heterozygote excess) in either period, despite a potentially high power to detect it after few generations (Cornuet and Luikart 1996). In contrast, two populations (NG and FU) showed lower levels of heterozygosity than expected under an equilibrium SSM during the second period. ...
... Populations that have suffered genetic bottlenecks or that have low genetic diversity are more vulnerable to extirpation as they have less potential to cope with changes resulting from climate change and habitat fragmentation (Crow and Kimura 1970;Frankham et al. 2017). Smaller populations are more susceptible to the erosion of genetic diversity because genetic drift and inbreeding occur at faster rates (Frankham 1996;Franklin and Frankham 1998;Allendorf et al. 2013). Several empirical studies in plants and animals have shown that population size is positively correlated with genetic diversity (e.g., Soulé 1976;Frankham 1996;Hague and Routman 2016). ...
... N e of Neotropical otter from the three studied basins are therefore too small to maintain the genetic variation of the populations in the short and long term. It is likely that otter populations are subject to the detrimental effects of small population sizes, including inbreeding, genetic drift and mutational meltdown (Franklin 1998;Higgins and Lynch 2001;Frankham et al. 2014). ...
Habitat deterioration and fragmentation increase the risk of wildlife extirpation as they have strong impacts on population size, genetic diversity and gene flow. Small populations are more susceptible to these factors because the loss of genetic diversity by drift and inbreeding occurs at faster rates. Therefore, estimates of genetic diversity and population sizes of threatened and small wildlife populations in deteriorated landscapes are critical for managing and conservation. Here, we used a non-invasive sampling approach in combination with eleven microsatellite loci to evaluate genetic diversity, genetic structure, and demographic parameters of the Neotropical otter (Lontra longicaudis) in three river basins (Actopan, La Antigua and Jamapa), which are priority conservation areas for Veracruz, Mexico. Our results revealed moderate genetic diversity and genetic structure among river basins. However, we detected first-generation migrants among basins, suggesting current gene flow. Effective population size for each basin was considerably lower than the value (Ne < 100) suggested to maintain genetic variation of populations in the short-term. Similarly, census population size was lower than estimates reported for L. longicaudis in a conserved region in Mexico. We did not find evidence of recent genetic bottlenecks for any basin. Our genetic and demographic results suggest that L. longicaudis in the three river basins could be experiencing genetic isolation and erosion, with La Antigua being the most vulnerable basin. Natural fragmentation and habitat deterioration seem to be shaping the observed patterns of genetic variation in the Neotropical otter.
... The LD and EPA point estimates of contemporary Ne for the GKNP were 500-700. These estimates are close to values of Ne that have been proposed as absolute minimum for the long-term maintenance of quantitative genetic variation and evolutionary potential of a population (Ne = 500-1000) [179][180][181][182][183]. Clearly, the current census size of a population, which in the case of the GKNP elephants is estimated at about 21,000 individuals [26], can give a misleadingly optimistic impression of population viability [184]. ...
... For reasons discussed above, such as a rapid population recovery following the demographic bottleneck during the 19th-20th century transition, immigration from neighbouring populations and a long generation time, the Kruger elephant population does not appear to have significantly lower levels of genetic diversity than other Southern African elephant populations and different methods of demographic inference also did not detect consistent signs of a recent reduction in Ne or deviation from mutation-drift equilibrium [28,30]. However, given their recent history the Kruger elephants are likely a nonequilibrium population, the estimates of contemporary Ne are at the lower end of the range of values that have been suggested as the critical minimum for the long-term maintenance of genetic variation and adaptive potential [180,181,183] and the current Ne/N may be quite low (<0.1). Clearly, in the future there is a need for genetic monitoring [195] and analyses including samples from neighbouring populations, particularly from Mozambique and Zimbabwe, for an adequate assessment of changes and trends in Ne and Ne/N, ideally also using genomic data [196]. ...
Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination of rapid post-bottleneck population growth, immigration and long generation time. Point estimates of contemporary effective population size (Ne) for the GKNP were ~ 500-700, that is, at the low end of the range of Ne values that have been proposed for maintaining evolutionary potential and the current ratio of Ne to census population size (Nc) may be quite low (<0.1). This study illustrates the difficulties in assessing the impacts on Ne in populations that have suffered demographic crashes but have recovered rapidly and received gene flow, particularly in species with long generation times in which genetic time lags are longer. This work provides a starting point and baseline information for genetic monitoring of the GKNP elephants.
... Generally, narrowly distributed species often have reduced population sizes, increased inbreeding levels, and restricted dispersal or gene flow, which makes them particularly vulnerable to loss of genetic variation (Frankham, 1996). Compared with natural selection and random genetic drift in large, widespread populations, selection and drift are generally thought to have more impact on smaller populations because more alleles are lost by chance due to the sampling effects in small populations (Franklin & Frankham, 1998;Frankham, 2005). Narrowly distributed species are often threatened and potentially vulnerable to extinction in the near future. ...
... Narrowly distributed species typically have reduced population sizes, increased inbreeding levels, and restricted gene flow, which make them particularly susceptible to loss of genetic variation (Lynch, Conery & Burger, 1995;Frankham, 1996Frankham, , 2005Franklin & Frankham, 1998;Keller & Waller, 2002;Briskie & Mackintosh, 2004). For narrowly distributed endemics amphibians, genetic diversity is directly related species persistence in the future (Green, 2003;Reed & Frankham, 2003;Allentoft & O'Brien, 2010;Collins, 2010). ...
Landscape features (e.g., mountains and rivers) can act as barriers to dispersal and gene flow, and therefore impede population connectivity, increasing genetic differentiation between populations. The concave‐eared torrent frog (Odorrana tormota) is a rare, stream‐associated species in eastern China. In this study, we investigated the genetic structure and population demography of this narrowly distributed frog based on mitochondrial Cyt b gene and seven nuclear microsatellite loci. As a result, we found that the rare frog still preserved a relatively high level of genetic diversity compared to some other amphibia. Population structure analyses distinctly identified three or four tentative genetic clusters for the species in the study area. Additionally, by fine‐scale spatial autocorrelation analysis, significant positive genetic structure was uncovered in the shortest distance classes (0–5 km, 5–10 km). Demographic analyses revealed a population expansion (0.075–0.017 Mya) and 15 times population decline (c. 9000 years ago). In conclusion, we supposed that stable montane environments and associated historical population expansion might provide an opportunity for the species to harbor high genetic diversity. The relatively recent population decline might be correlated with climate change as well as genetic differentiation among populations. In addition, our results showed that, on a small landscape scale, dispersal is closely linked to geographic distance and the presence of river systems may not substantially affect the genetic structure for the narrowly distributed O. tormota.
... However, different levels of genetic diversity were detected between the Jinsha and Yangtze River X. nudicorpa populations. The low level of genetic diversity in Jinsha River populations (PZH and QJ) might have been caused by the founder effect or genetic drift (Franklin & Frankham, 1998). In addition, X. boulengeri was only rarely present in the QJ-PZH section of the Jinsha River. ...
... We surmise that X. nudicorpa, particularly individuals with the most frequent mtDNA haplotype, is better adapted to the local environment. However, low genetic diversity would reduce the capacity to cope with environmental change in the Jinsha River populations of X. nudicorpa (Franklin & Frankham, 1998). Interestingly, the genetic diversity of the Cyt b gene was higher than that of the CR in these two species, except for X. nudicorpa populations in the Jinsha River (Table 2). ...
Background
Xenophysogobio boulengeri and X. nudicorpa are the only two species within the genus Xenophysogobio (Cyprinidae, Cypriniformes), and both are endemic to the upper reaches of the Yangtze River. In recent years, due to human activities, the natural resources available to both species have declined sharply. Sympatric species with overlapping niches inevitably compete for their habitats, and genetic structure and diversity can reflect population history and their potential for adaptation to changing environments, which is useful for management decisions.
Methods
In the present study, microsatellite DNA and mitochondrial DNA (mtDNA) markers were used to investigate the patterns of population genetic structure for X. boulengeri and X. nudicorpa . Microsatellite DNA data, jointly with traditional summary statistics including FST and Fis , were used to assess the population genetic structure by structure analysis. The mtDNA sequences were then used to examine these patterns through time to detect demographic history.
Results
Xenophysogobio boulengeri and X. nudicorpa exhibited high levels of genetic diversity in Yangtze River populations, except for two populations of X. nudicorpa in the Jinsha River, which were low in mtDNA diversity. X. boulengeri showed genetic homogeneity among populations, whereas X. nudicorpa appeared to have significant geographic genetic divergence. Both species experienced a late-Pleistocene sudden population expansion in Yangtze River populations, but not in the Jinsha River populations of X. nudicorpa .
Discussion
The genetic homogeneity of X. boulengeri populations might result from similar population expansion events and environment features. The geographic genetic subdivision for X. nudicorpa between the Jinsha and Yangtze Rivers might be caused by the geographic isolation in the middle Pliocene, as well as climate and environmental heterogeneity.
... Ontario cisco have retained a sufficient level of genetic diversity to maintain their adaptive capacity in the face of future environmental change (Franklin and Frankham 1998). ...
... Lake Ontario cisco present a similar scenario: having once supported the largest freshwater commercial fishery in North America, cisco were overfished with such intensity that the vast majority of spawning populations disappeared and the fishery was defunct by the early 1900's. It is reasonable to predict that this huge demographic decline was followed by a genetic decline: however, we found no evidence for a recent genetic bottleneck, and the lakewide effective population size is likely large enough to maintain future evolutionary potential (Franklin and Frankham 1998). Similarly, fishery-related declines did not reduce genetic diversity in Great Slave Lake whitefish (Chebib et al. 2016) or Lake Constance whitefish (Gum et al. 2014). ...
Cisco Coregonus artedi are an important prey fish for many Great Lakes predators, including lake trout Salvelinus namaycush and Atlantic salmon Salmo salar. Their numbers have declined drastically in the last century due to the impacts of invasive species, overfishing, and habitat degradation. However, rehabilitation efforts for cisco have been increasing as interest in restoring native food webs grows across the Great Lakes. This thesis addresses many research questions facing cisco restoration in Lake Ontario, including larval ecology and distribution, spawning behavior, and population genetics. Lake Ontario cisco larvae cannot be reliably distinguished from lake whitefish larvae using traditional visual methods, which complicates early life history studies. Instead, coregonine larvae in Lake Ontario should be identified via genetic barcoding. Cisco larvae were distributed throughout Chaumont Bay during the spring of 2014, and we found no evidence of predation by alewife Alosa pseudoharengus or rainbow smelt Osmerus mordax. Egg mat surveys in several historical spawning locations in eastern Lake Ontario identified two remnant spawning populations that were previously unknown; one in Henderson Harbor, New York, and another near Fox and Grenadier Islands. Population genetics analyses show no genetic structure among Lake Ontario cisco populations. Additionally, we found no evidence of a genetic bottleneck despite historical population declines due to overfishing, and relatively high genetic diversity measures across all sampling locations. We confirmed the presence of several cisco/lake whitefish hybrids from the Bay of Quinte and Chaumont Bay using a three-marker RFLP panel developed during this study. However, the hybridization rate in 2014 larvae from Chaumont Bay was low. Finally, two major science communication efforts using social media are presented in this thesis. We were able to greatly extend the reach of a small coregonine science conference by live streaming video of presentations and posters on Twitter and Periscope. Additionally, a two year social media campaign on Twitter aimed to educate Great Lakes residents about cisco restoration, share scientific findings, and promote public interest in cisco research. Overall, the results presented in this thesis not only go a long way towards our understanding of cisco ecology in Lake Ontario, but also build a foundation of public support for future restoration efforts.
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Pedigree analysis is a useful tool for the study of structure, genetic diversity and history of populations. This study was conducted to characterize population structure, estimation of inbreeding and effective population size in Markhoz goats using pedigree analysis. Data consisted of pedigree records of 5726 animals, collected between 1987 and 2016 by Markhoz goat Performance Testing Station. Computer programs, including CFC for descriptive statistics of pedigree, ENDOG for estimation of effective population size and generation interval and EVA for inbreeding trend were used in this research. The ratio of inbred animals was 54.3% of total population. The mean of co-ancestry and inbreeding coefficients in the population were 2.61 and 2.68, respectively, indicated that the observed inbreeding level is higher than expectation. Estimated effective number of founders was 85.65, represents unequal founder contributions in population. Undesirable trend for inbreeding could be due to high contribution of few ancestors in reproduction and low migration rate of animals in Markhoz goat station. The mean generation interval for total population and founders were 3.23 and 5.73 years, respectively, emphasizing the replacement of young bucks and does in the recent generations. Effective population size computed via individual increase in inbreeding was equal to 60.41 and was not far from the 50, a critical level proposed for an ideal population. The results indicate that the biodiversity of population has decreased. In conclusion, this research supports the priority for conservation genetic strategy instead of selection programs in Markhoz goat.
... The FAO recommends that a population with Ne less than 50 is insufficient to maintain fitness and results in inbreeding depression. In contrast, the threshold of Ne up to 100 is essential for long-term adaptation potential and for designing successful breeding plans (Franklin and Frankham, 1998). Effective population size estimation in the sampled population demonstrated a declining trend from 625 individuals around 150 generations ago to 74 individuals approximately 13 generations ago (Fig. 2). ...
The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (FHOM, FUNI, FROH, and FGROM), ranged from -0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075-35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population.
... Among these, the effective size of a population plays an essential role in population biology 1 . A population's effective size is defined as the number of individuals in an idealized evolutionary model 2,3 , and the ability to infer it from genomic data has a wide range of applications, including the study of past demographic events 4,5 and cultural practices 6 , the quantification of the effectiveness of natural selection 1,7 , and the prediction of viability in conservation biology 8 . ...
Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2000 years in both modern and ancient DNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe shows improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We apply HapNe to several modern populations from the 1,000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups.
... However, under novel fire regimes, all populations will express some degree of fire naivety [4], and the degree of naivety might depend on historical variation in fire regimes. The key to evolutionary resilience under novel fire regimes will be whether populations are sufficiently large and genetically diverse to contain adequate variation in fitness-relevant trait values to maintain evolutionary potential [92,93], exhibit sufficient phenotypic and behavioral plasticity to endure extreme fire events [94], or whether they have the capacity to recover quickly after fire (i.e., because of high immigration or population growth rates). If conservation practitioners can obtain information on variation in fire response traits in natural populations, conservation actions could be prioritized to facilitate propagation of fire savviness and influence evolutionary resilience. ...
Fire is a pervasive driver of trait evolution in animals and its importance may be magnified as fire regimes rapidly change in the coming decades. This was the thesis of our paper published recently in Trends in Ecology and Evolution [1]. In their response letter, Nimmo et al. [2] reinforce our thesis and suggest expansion of some of our conceptual models.
... Por otro lado, a pesar de los bajos niveles de diversidad genética, los niveles de abundancia en el PNO parecen ser suficientes para mantener el acervo genético de la población. Estudios sobre el tamaño de las poblaciones y su potencial vulnerabilidad ante un cambio ambiental calculan que el número mínimo de individuos adultos suficiente para mantener la variabilidad genética en una población y asegurar su potencial evolutivo oscila entre 500 y 1000 individuos (Franklin 1980, Franklin & Frankham 1998). La abundancia absoluta de la población del PNO fue estimada en un N > 3,000 individuos aproximadamente (Dewar et al. 2013) mientras que un cálculo local en la sub-población Californiana fue estimada aproximadamente N > 2000 (Burgess et al. 2014); la población Australiana se estimó solo para hembras con valores entre N = 2,728 -13,746 (Malcolm et al. 2001), y para ambos sexos se estimó un N e = 1,512 individuos adultos basándose en seis loci microsatelitales (Blower et al. 2012); la población de Sudáfrica se ha estimado entre N = 808 -1008 y un N e = 333 (Towner et al. 2013, Andreotti et al. 2016 El análisis de flujo genético indicó un alto número de migrantes (N m ) entre las localidades muestreadas (Tabla 10), lo cual podría explicar la baja estructura genética nuclear en el PNO, además que estos resultados concuerdan con los patrones de movimiento reportados por marcas satelitales (Weng et al. 2007b(Weng et al. , 2012. ...
... According to the genetic diversity patterns observed in the NEP white shark population, the low nuclear genetic diversity can be attributed to a founder effect (Franklin 1980, Franklin & Frankham 1998. Thus, it is likely that the observed discrepancy between the estimated population size and genetic diversity of NEP white sharks results from an insufficient number of generations following the founder effect needed to increase genetic diversity. ...
The Northeastern Pacific (NEP) population of white sharks (Carcharodon carcharias) is genetically distinct from the rest of the world. This uniqueness results from adult fidelity to central California and Guadalupe Island aggregations sites. The strong mitochondrial genetic structure between the white sharks of central California and Guadalupe Island is also present, which indicates female philopatry. To date, few studies using nuclear DNA have found evidence of genetic patterns in the NEP white shark population, which could indicate that these sharks exhibit sex-biased dispersal. In this study, we evaluated the genetic structure, connectivity, and genetic diversity of NEP white sharks using samples from the southern California Bight (SCB), Baja California (including Sebastian Vizcaino Bay), the Gulf of California, and Guadalupe Island (GI) using nDNA (i.e. microsatellite loci). A total of five loci were successfully genotyped in 54 individuals. The patterns found in this study indicated low levels of genetic diversity among all localities (observed heterozygosity: Ho = 0.47), likely due to a founder effect. A slight genetic structure was present for NEP localities in this study (FST = 0.045, P = 0.0001), mainly identified between the SCB and GI locations. A sibship assignment analysis indicated low and moderate probabilities of full-and half-siblings between white shark juveniles from coastal areas, suggesting a high degree of connectivity between nursery areas in the NEP. Our results suggest that juveniles can mask the genetic structure in coastal zones.
... We refer to these as sites with "recognized biodiversity value." Including them in a conservation network ensures that it is embedded with species and habitats that provide the capacity for adapting to climate change (41,42). In the United States, state agencies and nongovernment organizations (NGOs) have identified over a thousand areas with recognized biodiversity value through comprehensive ecoregional or statebased assessments specifically targeting viable rare species populations, exemplary natural communities, and intact ecosystems. ...
Motivated by declines in biodiversity exacerbated by climate change, we identified a network of conservation sites designed to provide resilient habitat for species, while supporting dynamic shifts in ranges and changes in ecosystem composition. Our 12-y study involved 289 scientists in 14 study regions across the conterminous United States (CONUS), and our intent was to support local-, regional-, and national-scale conservation decisions. To ensure that the network represented all species and ecosystems, we stratified CONUS into 68 ecoregions, and, within each, we comprehensively mapped the geophysical settings associated with current ecosystem and species distributions. To identify sites most resilient to climate change, we identified the portion of each geophysical setting with the most topoclimate variability (high landscape diversity) likely to be accessible to dispersers (high local connectedness). These "resilient sites" were overlaid with conservation priority maps from 104 independent assessments to indicate current value in supporting recognized biodiversity. To identify key connectivity areas for sustaining species movement in response to climate change, we codeveloped a fine-scale representation of human modification and ran a circuit-theory-based analysis that emphasized movement potential along geographic climate gradients. Integrating areas with high values for two or more factors, we identified a representative, resilient, and connected network of biodiverse lands covering 35% of CONUS. Because the network connects climatic gradients across 250,000 biodiversity elements and multiple resilient examples of all geophysical settings in every ecoregion, it could form the spatial foundation for targeted land protection and other conservation strategies to sustain a diverse, dynamic, and adaptive world.
... It is very important to hold relatively large broodstocks for preserving the genetic diversity of stock enhancement programs. From the perspective of conservation genetics, the effective population size should be at least 50 to ensure short-term viability or 500 to ensure long-term viability, to avoid inbreeding depression and retain evolutionary potential (Soulé and Wilcox, 1980;Franklin and Frankham, 1998). For example, studies on genetic variability of a hatchery-reared stock of red sea bream (Pagrus major) showed that even a reduction in the number of alleles per locus was observed, the hatchery-reared stock maintained a high heterozygosity and low inbreeding coefficient. ...
... The N e estimates of a few hundreds are comparable to most other estimates found in anadromous brown trout populations using temporal or LD-based methods [59,[82][83][84], but higher than most estimates from strictly resident populations [85][86][87][88]. Whereas N e in the Guddal population is lower than the 500 or even 1000 assumed to be required for maintaining evolutionary potential [89][90][91][92], it should be noted that it is part of a larger system in the Hardanger Fjord where gene flow occurs among populations [59]. In general, anadromous brown trout populations have been found to exhibit a hierarchical genetic structure shaped by both geographical distance between populations and environmental parameters, with low genetic differentiation among local populations resulting from gene flow [93]. ...
Background: In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps installed in the Guddal River allowed for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers based on biopsy samples of all individuals ascending from 2006-2016, along with all emigrating smolts in 2017. We investigated 1) if there was evidence for declines in census numbers and effective population size during that period, 2) if there was association between kinship and migration timing in smolts and anadromous adults, and 3) to what extent resident trout were parents of outmigrating smolts.
Results: Census counts of anadromous spawners showed no evidence for a decline from 2006-2016, but were lower than in 2000-2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts based on anadromous parents from previous years, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents.
Conclusions: The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.
... Finally, it is important to point out that our viability analyses did not take population genetics' considerations into account, a component that plays a crucial role in species persistence over the long run (Franklin & Frankham, 1998;Sanderson, 2006). But R. muscosa is in such a state of urgency that the current priority is to ensure demographic viability in the short term. ...
The endangered mountain yellow‐legged frog (Rana muscosa) has been reduced to <10 isolated populations in the wild. Due to frequent catastrophic events (floods, droughts, wildfires), the recent dynamics of these populations have been erratic, making the future of the species highly uncertain. In 2018, a recovery plan was developed to improve the species status by reducing the impacts of various threats (predation, disease, habitat destruction), as well as reinforcing wild populations through the reintroduction of captive‐bred frogs. The short‐term goal stated in this plan was to reach a minimum of 20 populations of 50 adults each (hereafter, the 20/50 target), before the species can be considered for downlisting from the U.S. Endangered Species Act. However, there is no guarantee that this 20/50 target will be sufficient to ensure the species persistence in the long run. Using 19 years of mark‐recapture data, we estimated populations' demographic trends and assessed the viability of R. muscosa from a starting state of 20 populations of 50 adults each (i.e., the downlisting criteria). Our results reveal that, from this 20/50 state, the species has high chances of persistence only at a short time horizon (50 years). Moreover, >80% of populations would be extinct 50 years later. Therefore, the species will not be able to persist without implementation of the reintroduction program. We found that it is more important to increase the number of suitable sites occupied by R. muscosa than to simply reinforce or augment existing populations. Expanding the current distribution by establishing new populations at suitable sites, even after the “20 populations” mark has been reached, would increase the likelihood of the species' persistence in the longer term.
... Our confidence interval between 6 and 36 individuals per 100 km 2 indicates a population size from 11 to 63 individuals. A population of at least 50 individuals is proposed to prevent problems caused by inbreeding (Franklin 1980;Shaffer 1981;Franklin & Frankham 1998). In the case of an isolated population, the estimated maximum density is the best scenario for TUSP. ...
Knowledge on population density and activity patterns may help to understand how species with wide geographical distribution survive in different environments. The ocelot (Leopardus pardalis) is one of the neotropical felids with the greatest geographical range. We estimated the density and activity patterns of ocelots in the austral extreme of the species distribution (Southern Brazil), comparing our results with those of previous studies. We obtained ocelot records in three out of six sampled areas, but only two had sufficient records to estimate ocelot density. We estimated 15.5 (±6SE) and 27 (±24SE) individuals/100 km² in two protected areas. These values seem low when compared to ocelots’ density estimates in other areas of the Atlantic Forest. In the most pristine area, density values were similar to those from a study carried out 10 years ago, suggesting that this population remains stable. Our results indicate that austral populations of the ocelot are likely to be dependent on preserved patches of deciduous seasonal forests. As in other areas of the species’ distribution, ocelots were mainly nocturnal, potentially avoiding humans and domestic animals. The preservation of those areas and the connectivity between them is a priority for the long-term conservation of stable ocelot´s populations in the southern Atlantic Forest range.
... The N e estimates of a few hundreds are comparable to most other estimates found in anadromous brown trout populations using temporal or LD-based methods [59,[82][83][84], but higher than most estimates from strictly resident populations [85][86][87][88]. Whereas N e in the Guddal population is lower than the 500 or even 1000 assumed to be required for maintaining evolutionary potential [89][90][91][92], it should be noted that it is part of a larger system in the Hardanger Fjord where gene flow occurs among populations [59]. In general, anadromous brown trout populations have been found to exhibit a hierarchical genetic structure shaped by both geographical distance between populations and environmental parameters, with low genetic differentiation among local populations resulting from gene flow [93]. ...
Background
In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout ( Salmo trutta ) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006–2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts.
Results
Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000–2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents.
Conclusions
The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.
... Basic population genetic theory shows that population size and connectivity play major roles in determining Va, and thus adaptive potential. Isolated populations below a certain size should lose Va due to genetic drift more rapidly than it is replenished via mutation (49,52). ...
The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on the conservation of genome-wide genetic variation, and that this approach should be replaced with another that focuses instead on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that the conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations towards extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide variation on long-term population viability will only worsen the biodiversity crisis.
... Our N e estimates were highly variable and included several wide confidence intervals ( Table 2). The LD approach we used is generally robust (Gilbert & Whitlock, 2015;Luikart et al., 2010) and yielded estimates that are clearly below any recommended threshold for avoiding inbreeding and maintaining evolutionary potential (Franklin & Frankham, 1998;Lynch & Lande, 1998). When taken together, our estimates of genetic diversity and N e both ultimately point to an elevated risk of extinction for R. cascadae in California in the long term, likely through fixation of deleterious alleles and loss of adaptive variation by drift (Hare et al., 2011;Newman & Pilson, 1997;Phifer-rixey et al., 2012). ...
Catastrophic population declines due to disease often lead to fragmented remnant populations and loss of gene flow. Managers are left to determine appropriate conservation actions to recover and maintain population persistence. The recent utilization of genomic data to assist in species recovery now allows us to combine genome‐wide surveys of differentiation and diversity with the identification of potentially adaptive regions to develop conservation plans that incorporate ecological and evolutionary processes. The unprecedented global decline of amphibian populations due to the pathogen Batrachochytrium dendrobatidis has increased the need to apply genomic tools to amphibian conservation practices. We show here how understanding genetic characteristics of remnant frog populations affected by disease can be applied directly to restoration efforts. Cascades frogs (Rana cascadae) occur in the mountainous regions of the Pacific northwestern United States and have declined dramatically at the southern edge of their range in California. We conducted genome‐wide surveys within this region to inform conservation and reintroduction efforts. We found strong north‐south genetic differentiation between Oregon and California and novel spatial structure within California. Genetic diversity was lower in California than Oregon and genetic drift was the most important driver of genetic diversity and population structure in California, making conservation efforts aimed at boosting overall genetic diversity most urgent. Spatial genetic structure of populations within California suggests that reintroductions to Lassen Volcanic National Park, where they were recently extirpated, should use remaining source populations south of the park. Our findings support the treatment of California's R. cascadae populations separately from the rest of their range and highlight the importance of conservation genomics in applied species conservation.
... The use of population genetic data to estimate N e represents a powerful tool to consider the strength of genetic drift as a driver for the loss of genetic diversity, the potential for inbreeding, and to identify potential contemporary population differentiation (Weckworth et al. 2013). The 50/500 rule suggests that an N e of 50 is large enough to prevent short-term problems of inbreeding, but to maintain a genetically diverse population N e should be at least 500-1,000 or higher (Franklin andFrankham 1998, Weckworth et al. 2013). Thus, estimates of N e in the context of the 50/500 rule can help to identify populations of potential conservation concern; particularly because extinction risks are closely tied to stochastic factors like drift (Melbourne andHastings 2008, Robertson et al. 2019). ...
Seaside Sparrows (Ammospiza maritima) are tidal salt marsh endemic passerines found along the Atlantic and Gulf coasts of North America. Currently, there are 7 described subspecies, and “MacGillivray’s” Seaside Sparrow (A. m. macgillivraii) is the name given to the Atlantic coast subspecies breeding from North Carolina to northern Florida. In 2019 the US Fish and Wildlife Service received a petition to list this subspecies under the Endangered Species Act due to shrinking populations and loss of marsh habitat, which necessitated a Species Status Assessment. As part of the Species Status Assessment, we analyzed genetic (microsatellite and mitochondria) data from 464 Seaside Sparrows from Connecticut to Florida, USA, to infer population connectivity (gene flow) among Atlantic coast populations, and to assess the concordance of population genetic data with the putative ranges of the subspecies. Bayesian cluster analysis (program Structure) indicates three genetically distinct population segments: (1) Florida + Georgia, (2) Charleston, South Carolina, and (3) North Carolina to Connecticut. The population in Charleston, South Carolina was the most strongly differentiated based on microsatellite data, and harbored a unique mitochondrial haplotype not shared by other sampling locations, possibly reflecting long-standing isolation. Our results indicate population genetic discordance with currently described ranges of the subspecies of Seaside Sparrow and provide grounds for the consideration of separate management plans for the three populations.
... Asimismo, la diversidad genética se asocia positivamente con el potencial de evolución adaptativa (Ayala 1965, Franklin y Frankham 1998. De esta forma, las especies que son afectadas negativamente por actividades humanas presentan poblaciones con menor diversidad genética, cuya capacidad para adaptarse a nuevas presiones bióticas (patógenos, herbívoros, competidores) o abióticas (cambios de temperatura, humedad, entre otras) es limitada, por lo cual tienen una mayor probabilidad de extinción. ...
... Ten of the nineteen AMUs had a Ne below 100 and another two AMUs were just slightly above this threshold from which decline in fitness can be avoided in short term (Frankham et al. 2014). However, Ne from 500 to 1000 are required to maintain the evolutionary potential and a long-term adaptive potential (Frankham 1995;Franklin and Frankham 1998). These values were not achieved by any of the studied AMUs, even when subpopulations with a still assumed genetic exchange were aggregated. ...
Nineteen red deer areas in a densely populated region with a huge network of fenced motorways and the division into administrative management units (AMUs) with restricted ecological connectivity were investigated. In the season 2018/2019, a total of 1291 red deer samples (on average 68 per area) were collected and genotyped using 16 microsatellite markers. The results show a clear genetic differentiation between most of the AMUs. Fourteen AMUs may be combined into four regions with a considerable internal genetic exchange. Five areas were largely isolated or showed only a limited gene flow with neighbouring areas. Ten of the 19 AMUs had an effective population size below 100. Effective population sizes greater than 500–1000, required to maintain the evolutionary potential and a long-term adaptation potential, were not achieved by any of the studied AMUs, even when AMUs with an appreciable genetic exchange were aggregated. Substantial genetic differentiation between areas can be associated with the presence of landscape barriers hindering gene flow, but also with the maintenance of ‘red deer–free’ areas. Efforts to sustainably preserve the genetic diversity of the entire region should therefore focus on measures ensuring genetic connectivity. Opportunities for this goal arise from the establishment of game bridges over motorways and from the protection of young male stags migrating through the statutory ‘red deer–free’ areas.
... In Malaysia for example, mate allocation strategies employed for sixth generation GIFT families post-introduction in 2001/2002, has resulted in minimised inbreeding rates and a satisfactory effective population size to sustain a selective breeding programme (Ponzoni et al., 2005;Ponzoni et al., 2009). However, Ponzoni et al. (2010) cautioned that while the effective population size of 88 determined for this nucleus is adequate for containing inbreeding and maintaining heritability, it is still below the recommended threshold of 500 for maintaining evolutionary potential (Franklin and Frankham, 1998). Similarly in Sri Lanka, heterozygosity has been maintained and inbreeding minimised in three GIFT lines from generations six and nine, suggesting they are competent for further use (De Silva, 2015). ...
The Genetically Improved Farmed Tilapia (GIFT) strain of Nile tilapia is a valuable global freshwater aquaculture commodity, forming the basis of the Fiji Islands' largest freshwater aquaculture industry. Unfortunately, recent negative stock performance has been reported by farmers, possibly indicating reduced genetic diversity and inbreeding in the primary broodstock nucleus. Using high-resolution genome-wide markers (5208 SNPs), 282 individuals from three Fijian broodstock ponds were analysed and compared against two reference strains of Nile tilapia: 9th generation GIFT fish from the WorldFish Center, Malaysia, and 11th generation fish from the Abbassa Selection Line, Eygpt, (n = 94 respectively). Genetic data were used to evaluate levels of genetic diversity, inbreeding, relatedness and genetic structure; and assess the viability of the Fijian nucleus for future seed production. Results revealed only mild declines in the Fijian GIFT nucleus genetic diversity compared to both reference strains, since introduction 20 years ago. Average observed and expected heterozygosities were largely comparable for all sample groups, except for one Fijian pond which showed a heterozygote deficit (Ho = 0.2025, Hn.b. = 0.2320). One of the three Fijian ponds sampled exhibited reduced effective population size; (NeLD = 3.2 [95% C.I. = 3.2–3.2], cf. 23.3[23.2–23.3] and 31.5[31.4–31.6]), however allelic diversity remained high (A = 1.953, cf. 1.765–1.770). Fish sampled from this pond also showed a loss of rare alleles (Ar = 0.1542, cf. 0.4063–0.4065) and displayed genetic sub-structuring, possibly as a result of wild O. niloticus entering the broodstock nucleus. Analyses of genetic structure and relatedness revealed admixture of founding individuals, likely due to a combination of stock management practices and past pond flooding events. These findings suggest that the Fijian GIFT nucleus has retained much of the genetic diversity from its source population. It is recommended that the nucleus culture performance (fecundity, growth and survival) be evaluated through a phenotypic audit, to determine if valuable high-performing alleles have been lost. Over the longer term, stock management guidelines and genetic monitoring of the broodstock nucleus at regular intervals are proposed, to minimise further erosion of valuable genetic diversity. These results have important implications for stock management practices by demonstrating the importance of monitoring, and undertaking genetic assessments of broodstock nuclei after initial introduction, to ensure that genetic quality and performance is maintained over subsequent generations.
... Effective size should be larger than 50-100 to maintain the critical potential to withstand adverse effects due to inbreeding [31]. In the long-term, a Ne of 500 was proposed for a sustainable development of a population [32]. The decrease in Ne from 1990 to 2014 to a Ne of 95 is the result of an increasing individual rate of inbreeding per generation. ...
Increase of inbreeding and loss of genetic diversity have large impact on farm animal genetic resources. Therefore, the aims of the present study were to analyse measures of genetic diversity as well as recent and ancestral inbreeding using pedigree data of the German Brown population, and to identify causes for loss of genetic diversity. The reference population included 922,333 German Brown animals born from 1990 to 2014. Pedigree depth and completeness reached an average number of complete equivalent generations of 6.24. Estimated effective population size for the German Brown reference population was about 112 with a declining trend from 141 to 95 for the birth years. Individual inbreeding coefficients increased from 0.013 to 0.036. Effective number of founders, ancestors and founder genomes of 63.6, 36.23 and 20.34 indicated unequal contributions to the reference population. Thirteen ancestors explained 50% of the genetic diversity. Higher breed proportions of US Brown Swiss were associated with higher levels of individual inbreeding. Ancestral inbreeding coefficients, which are indicative for exposure of ancestors to identical-by-descent alleles, increased with birth years but recent individual inbreeding was higher than ancestral inbreeding. Given the increase of inbreeding and decline of effective population size, measures to decrease rate of inbreeding and increase effective population size through employment of a larger number of sires are advisable.
... Cumulative impacts of severe deforestation (Webb, Stojanovic, & Heinsohn, 2018) and predation (Heinsohn et al., 2015) likely contributed to a small contemporary N e , which results in loss of evolutionary potential and increased vulnerability to genetic stochasticity (Frankham, Briscoe, & Ballou, 2010). The "50/500 rule" in conservation genetics says that N e should not fall below 50 to minimize short-term problems related to inbreeding and should remain above 500 in the long term to maintain sufficient evolutionary potential (Franklin & Frankham, 1998). With some qualifications, this rule still has a useful place in conservation biology (Jamieson & Allendorf, 2012), while others even recommended that this rule should be changed to 100/1,000 (Frankham, Bradshaw, & Brook, 2014). ...
Understanding the current population size of small, spatially aggregating populations of species is essential for their conservation. Reliable estimates of the effective population size (Ne) can be used to provide an early warning for conservation managers of the risks to genetic viability of small populations. Critically endangered, migratory swift parrots Lathamus discolor exist in a single panmictic population in Australia. In their Tasmanian breeding range, they are at severe risk of predation by introduced sugar gliders, exacerbated by deforestation. We used three genetic approaches to estimate Ne using DNA samples genotyped by microsatellite markers and existing life‐history data of swift parrots. Based on all samples, we revealed small contemporary Ne estimates across methods (range: 44–140), supporting the need to urgently address threatening processes. Using the 0.5 Ne/N ratio calculated from demographic data suggests that the minimum potential contemporary population size is below 300 individual swift parrots. This is considerably lower than the published estimates derived from expert elicitation, and accords with modeled estimates of extinction risk in this species. Our study has important implications for other threatened species with unknown population sizes and demonstrates that by utilizing available genetic data, reasonable estimates of Ne can be derived.
... D'autre part une baisse de la diversité génétique est généralement associée à une augmentation du taux de consanguinité dans la population et à une baisse générale de la survie et de la reproduction. Franklin & Frankham (1998) a ainsi estimé que la taille efficace (Ne) minimale d'une population devait être au minimum de 50 individus pour une conservation optimale à court terme et de 500 individus pour une conservation optimale à long terme. Cette règle des 50/500 a été longtemps appliquée (voir Jamieson & Allendorf 2012), mais a été récemment revue à 100/1000 (Frankham et al. 2014). ...
La génétique de la conservation a pour but de protéger à la fois la diversité génétique et les processus qui l’ont forgée, et nécessite de comprendre ces derniers. Les Procellariiformes (puffins, pétrels et albatros) représentent de nombreuses espèces avec de hautes capacités de dispersion mais un fort comportement philopatrique et avec un fort enjeu de conservation. Nous avons mené une étude multi-locus sur le complexe du puffin d’Audubon, Puffinus lherminieri, du nord de l’Atlantique et ses deux lignées-sœurs en océan Indien. Nous avons d’abord montré que les marqueurs génétiques appliqués ici, et typiquement utilisés pour étudier la phylogéographie des oiseaux marins, étaient probablement soumis à l’introgression, l’hybridation, l’hétéroplasmie, ainsi que la duplication et la pseudogénisation de loci mitochondriaux. Tous ces phénomènes ont un impact sur la qualité et la quantité d’information produite par ces marqueurs. Nous avons réalisé une étude comparative et montré comment gérer au mieux certains de ces problèmes de données et leur traitement. Nous avons également approfondi la composition de la région mitochondriale dupliquée et montré qu’elle avait une évolution complexe au sein des Procellariiformes et pourrait avoir une influence sur leur biologie et leur conservation. Enfin, nous avons montré l’influence des barrières continentales mais surtout de la température de surface de la mer sur la différenciation des oiseaux marins. Nous avons également mis au jour une structuration chez le complexe de puffins qui nécessite de définir des nouvelles priorités de conservation.
... The estimation of the effective population size (N e ) can be used to quantify how a population could be affected by genetic drift or inbreeding (Falconer & Mackay, 1996) and thus help in the monitoring and control of genetic diversity . An N e value ranging from 50 to 200 is recommended to ensure the genetic variability and diversity in breeding programs (Smitherman & Tave, 1987); however, N e values above 500 are suggested to be necessary in order to retain the evolutionary potential of a population (Franklin & Frankham, 1998). In Nile tilapia, the N e calculated based on the rate of increase of coancestry was 88 in the GIFT Nile tilapia population and 95 in the GST strain (Joshi et al., 2018b), whereas using information from a 50K SNP panel, a contemporary N e value, ranging from 78 to 159, was calculated for three commercial Nile tilapia populations from Latin America (Yoshida et al., 2019c). ...
Selective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree information to select for growth traits with reported genetic gains of up to 20% per generation. The involvement of international breeding companies and research institutions has resulted in the rapid development and application of genomic resources in the last few years. GWAS and genomic selection are expected to contribute to uncovering the genetic variants involved in economically relevant traits and increasing the genetic gain in selective breeding programs, respectively. Developments over the next few years will probably focus on achieving a deep understanding of genetic architecture of complex traits, as well as accelerating genetic progress in the selection for growth‐, quality‐ and robustness‐related traits. Novel phenotyping technologies (i.e. phenomics), lower‐cost whole‐genome sequencing approaches, functional genomics and gene editing tools will be crucial in future developments for the improvement of tilapia aquaculture.
... More important, the cNe of farmed catfish in Vietnam (52.2) is in the order of recommendations (Ne ≥ 50) by FAO to maintain inbreeding level below 1% per generation in captive breeding programs for terrestrial and aquatic animal species [67]. However, to retain evolutionary adaptation to environmental changes, a significantly larger cNe is required, e.g., between 500 to 1000 as suggested by Franklin and Frankham [68]. To date, there is no comparative cNe estimates for striped catfish to compare with this study. ...
The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity of striped catfish. Hence, this study aims to conduct a systematic genetic diversity assessment of wild and farmed catfish stocks collected from four major pangasius-farming countries, using a new genotyping by sequencing platform known as DArT-seq technology. Our population genomic analyses using 7263 single-nucleotide polymorphisms (SNPs) after high-quality-control showed that there were two distinct populations of striped catfish in the lower Mekong river: (i) wild catfish from Thailand and (ii) catfish from Cambodia and Vietnam. The genetic diversity was greatest (0.363) in the wild stock from Thailand, but it was lower in farmed and wild stocks in other countries (0.049 to 0.088). The wild stocks were more genetically diverse than the farmed animals (0.103 vs 0.064). The inbreeding coefficient ranged from 0.004 and 0.109, with the lowest value (−0.499) in the wild animals from Thailand. Molecular inference methods revealed high degree of historical effective population size (1043.9–1258.4), but there was considerable decline in the contemporary estimates in all populations (10.8 to 73.6). Our additional analyses calculating divergent times and migration patterns showed that the wild catfish from Thailand stand out as separate lineages, while those from Cambodia and Vietnam are genetically identical. Our results also indicated that the cultured stock in Bangladesh originated from the lower part of the Mekong river. These findings have significant practical implications in the context of genetic selection and conservation of striped catfish in the region. Collectively, they will contribute to the sustainable development of the striped catfish sector in these countries.
... A minimum population size of 500 has been suggested as necessary to maintain evolutionary potential and a genetically secure population (Franklin 1980). Though, there is debate that potentially a minimum of 1000 individuals and even 5000 is necessary for a population to persist (Lande 1995;Franklin and Frankham 1998;Lynch and Lande 1998). According to Franklin, any population with fewer than 500 individuals are at longterm risk of extinction, while 50 individuals represents populations at immediate risk of extinction due to genetic inbreeding. ...
Assessing the effects of flow regime variation on Blue Sucker spawning movements, habitat use, and recruitment in the lower Colorado River, TX
Blue Sucker Cycleptus elongatus is widely distributed throughout the United States. Even though it was once a commercially-harvested species, Blue Sucker is currently listed in 19 of 23 states as a species of greatest conservation need, threatened, presumed extirpated, or endangered. They are associated with riffle-run habitat where flows are generally swifter, rendering them vulnerable to alterations to the natural flow regime. Within Texas they are known to occur in three major watersheds; the Red River, Neches-Sabine, and the Colorado River. The population in the lower Colorado River therefore likely represents the southwestern extent of the species range, as the next nearest neighbor occurs in the Sabine-Neches Rivers approximately 400 km east. The lower Colorado River between Austin, Texas and Garwood Dam near Altair, Texas is the only known population of Blue Sucker in the Colorado River and has been presumed to suffer from a lack of recruitment for the last several years. Unfortunately, the lower Colorado River has experienced drastic changes in hydrology with a significant increase in extreme low flow (< 4.53 m3s-1 or 160 ft3s-1) frequency and decrease in small flood pulse (> 685.3 m3s-1 or 24,201 ft3s-1, and < 2874 m3s-1 or 101,494 ft3s-1) frequency following construction of the highland lakes in the late 1930s and 1940s. These alterations and others may be responsible for the current status of Blue Sucker in the lower Colorado River.
This grant served as the primary funding support for the Doctoral Dissertation of Matthew Acre and his attached dissertation serves as the final report for this project. Relevant results for each primary objective are briefly summarized below with further details provided in the attached dissertation.
Acre, Matthew R. 2019. Assessing demography, habitat use, and flow regime effects on spawning migrations of Blue Sucker in the lower Colorado River, Texas. PhD Dissertation. Texas Tech University, Lubbock. (Attachment 1)
Methods
Habitat use, selection, and movement patterns, including likely spawning migrations were analyzed from data collected on 42 adult Blue Sucker. Fish were tagged in December 2014 and December 2015 with a combined acoustic radio transmitter (CART) tag at Utley (n = 7), Bastrop (n = 12), La Grange (n = 12), Columbus (n = 1), and Altair (n = 10). Fish were then monitored from January 2015-May 2017 which resulted in 1,157 detections during 38 attempts to determine fish locations. These data were used to determine the effects of streamflow, instream temperature, and habitat availability on movements which included spawning migrations. River discharge data was downloaded from USGS gage stations at Austin, Bastrop, Smithville, La Grange, and Wharton. Instream temperature data was collected from nine iButton data loggers mounted throughout the river. Discharge data was assigned to fish depending on the nearest gage station. Submersible ultrasonic receivers were also mounted throughout the river to passively monitor tagged fish. A substrate availability map was created of the 290-rkm study area using side-scan sonar data. The substrate map was used to determine season habitat selection and avoidance, and to determine if locations within the river being used at higher rate could be explained by habitat.
To assess population size and the viability of the population to persist into the future, 30 mark-recapture sites were identified and sampled six times over two years (2016-2017) with standard boat-mounted electrofishing techniques. The 30 sites were split in riffle, run, and pool habitat and sampled separately which resulted in 540 samples over two years and 97 hours of electrofishing. This sampling effort resulted in 152 captures of which 15 were recaptures. These data were used to estimate population size and mesohabitat use. When fish were captured a fin ray clip was taken to be used in age estimation analysis. The age estimation data was used to determine back-calculated hatch years which informed the estimated yearly cohort strength. Discharge data was downloaded from the USGS gage station in Bastrop, Texas and temperature data was downloaded from the NOAA Camp Mabry station. These data were then used to determine the effects of abiotic variables on yearly cohort strength.
Objectives and Primary Findings
1) Describe movement and habitat use under various experimental releases via radio and acoustic telemetry
Greater duration and magnitude of high flows coupled with warmer temperatures likely alter seasonal movement patters and may hinder spawning migrations. Additionally, fish that were in riffle dense areas were less likely to make large movements and more likely to remain in that area. Seasonal movement patterns in the first year of tracking (2015) were typical compared to other Blue Sucker populations across the country. In the winter, most movements were upstream and the mean distance between movements, regardless of direction, was approximately 35 rkm during this time. In the following spring, most movements were downstream, and fish had a mean of 55 rkm between detections. During the summer and fall of 2015 movements were significantly reduced. The next year the pattern begins much the same, but flooding and subsequent duration of high flows during the spring of 2016 may have altered the spawning patterns observed during 2015. In 2017, there was an almost complete cessation of movement that may be partly attributed to increased magnitude and duration of river discharge as 2017 was an exceptionally wet year. River discharge was high leading up to Hurricane Harvey, which brought record high flows below La Grange, Texas in 2017. Throughout this study, fish that were originally tagged in Bastrop, Texas were 2.5x more likely to remain in that location while those tagged both upstream and downstream were more likely to move, particularly during the spawning season. This result further supports the importance of the approximately 15-rkm (9-mi) reach surrounding Bastrop. The timing and to some degree, the magnitude of movements from the manual tracking are supported by the data collected from SUR units. However, SUR data made clear that movement estimates were underestimated as we were missing some movements into tributaries where we did not manually track, particularly in 2015. Additional detail is contained in Chapter 3 (Habitat Use and Selection) of the attached dissertation (Attachment 1).
2) Determine the timing and extent of use of spawning habitats in relation to streamflow and temperature
Migrations to spawning habitat were best predicted by cooler temperatures and discharge between 283-2296 ft3s-1. Variable flows best predicted spawning movements. Additionally, spawning habitat is likely limited to about 34 miles of river near Bastrop, Smithville, and La Grange. Blue Sucker selected boulder habitats more frequently during winter and spring, likely associated with spawning due to this timing. Additionally, Blue Sucker selected cobble and bedrock habitat throughout the year and actively avoided sandy substrates, as well as areas with increased anthropogenic items which included waste material. Spawning movements, which included migrations, were most likely to occur when temperatures were between 13.5-18°C (56-64°F) and river discharge was between 8-65 m3s-1 (283-2296 ft3s-1). When a spawning movement was detected, there was 78% probability the fish moved to riffle or run habitat. Optimized hotspot analysis identified three locations within the lower Colorado River that are likely integral reaches of river for Blue Sucker. These three locations combined represent 55 rkm (34 mi) of the 290-rkm (180-mi) study area and are located around Bastrop, Smithville, and La Grange, Texas. The Bastrop reach was also identified as integral spawning habitat in addition to daily activities. This is further supported by acoustic data which detected 60% of the tagged population utilizing this area and is representative of at least one individual from each tagging location except Columbus where only a single female was tagged. In general, males had a larger linear home range than females. Home ranges increased in size as the percentage of sand and anthropogenic materials increased within their core area. This is an indication that Blue Sucker are moving to specific habitats to complete aspects of their life history and must move further if located in an area with fewer riffle/run habitats available.
Additional detail is contained in Chapter 4 (River Discharge, Temperature, and Habitat Effects on Blue Sucker Movements) of the attached dissertation (Attachment 1).
3) Estimate population size and demographic characteristics
The Blue Sucker population in the lower Colorado River is relatively small and seems to be recruitment-limited. The estimated population size from these data was 679 individuals with a lower boundary (95% confidence interval) of 449 and upper boundary of 1089 individuals. The population has an estimated annual mortality of 15%, therefore, 85% of the population survives annually. However, recruitment in the population has been relatively low or completely lacking from 2009-2017. Multiple gear types sampled from 2015-2017 aimed at capturing young-of-year and sub-adults resulted in zero Blue Sucker captures. In the event recruitment of young individuals back into the adult population does not increase, there is a high probability Blue Sucker will be extirpated from the lower Colorado River. The best models informing what results in a strong recruitment class suggests that greater river discharge in September, lower September and July minimum temperatures, and an increase in high flow pulse frequency best predict strong recruitment years.
More details can be found in Chapter 2 (Blue Sucker Demographics and probability of persistence in the lower Colorado River, Texas) of the attached dissertation (Attachment 1)
4) Evaluate the effects of streamflow on recruitment and age-0 habitat use.
The Blue Sucker population within the lower Colorado River seems to be suffering from reduced recruitment. Limited habitat availability, including spawning grounds, and potentially alteration of environmental cues for migration and spawning may act to limit recruitment. Altered spawning cues may be linked to increased river discharge and an increase in river temperatures, while also correlated with increased duration of high flows. While 2015 had the highest probability of spawning migration and was associated with lower flows than 2016 and 2017, those low flows occurred on the descending leg of flood pulse which were estimated to be approximately 206 m3s-1 (7,274 ft3s-1). The model was built from fish detection that were identified as likely spawning movements or migrations based on peer-reviewed literature. The results from this study identify a lack of flood pulses, increased duration of flood pulses that do occur, an increase in the magnitude of flood pulses, and increased temperatures as likely culprits in the current threatened status of the species within the study area. In addition to alterations of the flow regime from historic standards, there has undoubtedly been a decrease in available habitat post dam construction. The results from this study identify 55 rkm (34 mi) with the 290 rkm (180 mi) between Austin and Altair, Texas (Garwood Dam) that is used at higher rate than the rest of the river. This suggests that habitat may be an additional limiting factor for Blue Sucker in the lower Colorado River.
Further detail can be found in Chapter 2 (Blue Sucker Demographics and probability of persistence in the lower Colorado River, Texas) of the attached dissertation (Attachment 1)
Recommendations:
-Continue monitoring population trends of Blue Sucker population in lower Colorado River o The observed and estimated recruitment from 2009-2017, which is lower than previous years, is a troubling trend. The results from this study suggest that the population may be in trouble and could be declining. The population viability analysis indicated that if he reduced recruitment continues the population may be extirpated from the river. However, without a continuation of the mark-recapture work it will be difficult to determine how the population is responding to various environmental conditions.
-Consider modification timing/duration of flow pulses for Blue Sucker spawning o Migration probabilities related to spawning were most likely to occur in January-March and were best predicted by variable flows on the descending leg of flood pulses. River discharge between 283-2296 ft3s-1 preceded by small flood pulse estimated at 7,274 ft3s-1 were estimated from fish detections assumed to be for spawning. A component that may be missing from the current water management plan is variation in flow regime during spawning windows.
-Consider adjustment of summer minimum flows to benefit YOY Blue Sucker o Estimated yearly cohort strength (recruitment) was best predicted by increased September low flows, increased high pulse frequency (as defined by IHA see Indicators of hydrologic alteration, version 7.1 user’s manual, The Nature Conservancy, 2009), decreased September and July minimum temperatures. This may be an indication that variable hydrology throughout the spawning and the months following hatch date are vital to survival for young-of year Blue Sucker.
-Start a genetic and early life history study on the population
o Determine current levels of bottlenecking, genetic uniqueness within the population, and effective population size. A possible explanation for the reduced recruitment throughout this study may be linked to genetics as opposed to the effects of a small population (𝑁̂=679).
o The other possibility for the reduced recruitment may be linked to some aspect of the larval stage. An early life history study focused on what conditions are optimal for successful hatching may illuminate issues with the current habitat and substrate availability, and current flow regime.
o Dependent on the genetic results actions may include: ▪ Modify habitat in the river to increase spawning habitat which results in successful hatching.
▪ Modify the water management plan to increase success of early life history stages.
▪ Start a captive propagation program to supplement the lack of recruitment. • If this action is taken the genetics will inform where broodstock should be gathered and fish pairings to maximize genetic diversity.
... Guidelines suggest that an Ne of at least 50 is required to prevent inbreeding depression 71 , and an Ne greater than 1,000 is needed to avoid the accumulation of deleterious alleles 72 . In order to retain the long-term evolutionary potential of a species, it has been suggested that an Ne greater than 500 or even 1,000 is necessary [73][74][75] . Although estimates of Ne were derived with relatively large 95% CIs, it can be (which was not certified by peer review) is the author/funder. ...
Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark Carcharias taurus (also known as the sandtiger or grey nurse shark) is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, it was found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.
... Up to 80% of those patches are smaller than half a square kilometre (Ribeiro et al., 2009), which is too small to sustain even a single jaguar individual, partially explaining the very low N e (17-26) estimates for that biome. Indeed, those figures put Atlantic Forest jaguars (even when treating the biome as a single unit) below the N e = 50 threshold proposed by Franklin and Frankham (1998) to avoid short-term risks due to inbreeding (Rutledge et al., 2017). Given the evidence for strong human-induced isolation among remnant Atlantic Forest populations, local effective sizes are actually much lower (Haag et al., 2010;Srbek-Araujo et al., 2018). ...
... Furthermore, the lower bounds for the effective population size estimates suggest that N e is in the 1000s at a minimum. For conservation purposes, N e estimates for horseshoe crabs in South Carolina are more than the minimum value of 50 recommended to prevent significant inbreeding and maintain short-term fitness of a population (Franklin 1980) and are within the minimum numbers suggested to maintain the evolutionary potential (Frankham 1995) and long-term viability of a population (N e ¼ 500-1,000, Franklin & Frankham 1998 or N e ¼ 1,000-5,000, Lynch & Lande 1998). Effective population size can be reduced below the population census size by a variety of factors, including skewed sex ratios, unequal reproductive contribution among individuals, and past fluctuations in population size (Frankham 1995). ...
... This effect may further be intensified by genetic drift, especially when the number of founders is small (Nei et al. 1975;Leberg 1993;Sjoberg 1996). Reduced genetic diversity can impact individual fitness and decreases the viability and the evolutionary potential of the populations (Franklin and Frankham 1998). Understanding the genetic consequences of reintroductions is therefore necessary to evaluate the success of a reintroduction and to inform wildlife managers on best practices. ...
Understanding populations' response to environmental variation is a central issue of ecology, and has become a compelling goal in the last years due to climate change. In this broad context we could expect some species-specific ecological characteristics known to influence life history traits, such as lifestyle, to shape the demography of populations in variable environments as well as structure between-species differences in response to environmental change. Yet, the influence of species' lifestyle on population demographic responses to environmental variation is still poorly understood. During my PhD, I tried to fill this gap primarily through the analysis of an extensive data set of an Alpine marmot (Marmota marmota) population in the Alps. Alpine marmots present a particular lifestyle. 1ndividuals live in family groups of variable size, typically composed of one dominant breeding pair, of sexually mature and immature subordinates and of pups of the year. Half the year, they hibernate together in burrows and practise cooperative breeding with male subordinates acting as helpers for the pups, increasing their survival probability during hibernation. I first investigated how the marmot's lifestyle (hibernation and sociality) mediated the effects of weather fluctuations on age-specific survival variation. I found that juvenile survival strongly decreased over the years because of inter-related effects of harsher winter weather conditions and social factors (i.e., decrease in helpers' presence). In a second step, I studied the adaptive value of cooperative breeding in this Alpine marmot population, and showed that the positive influence of helpers' presence on juvenile survival was vanishing with climate change. The Alpine marmot population is currently decreasing accordingly. However, in parallel to the latter changes, I found a better access to dominance for subordinate individuals over the years, compensating in part this decrease, and highlighting a complex influence of sociality on marmot response to climate change. Finally, I compared the demography of the Alpine marmot population with that of an Alpine chamois (Rupicapra rupicapra) population, subjected to similar weather conditions in the Alps. I was able to show that the difference in lifestyle and reproductive tactic between these species shaped their demographic responses to environmental variation, providing them with differentresistance to current environmental change
... Since there is no report about genetic markers for P. sinensis so far, these polymorphic microsatellite makers and further mining of transcriptomic data may helpful for future research of P. sinensis and its related species. [19]. This may due to the poor swimming ability of P. sinensis. ...
Background:
The Chinese grass shrimp, Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration of germplasm resources and assist in the understanding of P. sinensis aquaculture. Microsatellite markers are widely used in research of genetic backgrounds since it is considered an important molecular marker for the analyses of genetic diversity and structure. Hence, the aim of this study was to evaluate the genetic diversity and structure of wild P. sinensis populations in China using the polymorphic microsatellite makers from the transcriptome.
Results:
Sixteen polymorphic microsatellite markers were developed for P. sinensis from transcriptome, and analyzed for differences in genetic diversity and structure in multiple wild P. sinensis populations in China. Totally of 319 individual shrimps from seven different populations were genotyped to find that allelic polymorphisms varied in two to thirteen alleles seen in the entire loci. Compared to other populations analyzed, the two populations including LD and SJ showed lower genetic diversity. Both the genetic distance (D) and Wrights fixation index (FST) comparing any two populations also indicated that LD and SJ populations differed from the other five populations. An UPGMA tree analysis showed three main clusters containing SJ, LD and other populations which were also confirmed using STRUCTURE analysis.
Conclusion:
This is the first study where polymorphic microsatellite markers from the transcriptome were used to analyze genetic diversity and structures of different wild P. sinensis populations. All the polymorphic microsatellite makers are believed useful for evaluating the extent of the genetic diversity and population structure of P. sinensis. Compared to the other five populations, the LD and SJ populations exhibited lower genetic diversity, and the genetic structure was differed from the other five populations. Therefore, they needed to be protected against further declines in genetic diversity. The other five populations, LP, LA, LSL, LSY and LSH, are all belonging to Liaohe River Drainage with a relatively high genetic diversity, and hence can be considered as hot spots for in-situ conservation of P. sinensis as well as sources of desirable alleles for breeding values.
... Second, the condor population is still small enough that some continuing loss of genetic diversity through genetic drift is unavoidable (Frankham et al. 2002). Genetic diversity will be lost more slowly as population size increases but will continue until the population reaches a size where this loss is balanced by gains in diversity produced through new mutation (N e ϳ 500; Franklin and Frankham 1998). ...
The last wild California Condor (Gymnogyps californianus) was brought into captivity in 1987. Captive breeding was successful and reintroduction efforts began in 1992. The current population is descended from 14 individuals belonging to three genetic “clans.” This population bottleneck led to the loss of genetic variation and changes in allele frequencies, including a probable increase in the frequency of the putative allele for chondrodystrophy, a lethal form of dwarfism. We use studbook data to analyze the current genetic and demographic status of the population and explain how it is managed to meet specific goals. In August 2002 the population consisted of 206 individuals distributed among three captive-breeding facilities and three reintroduction sites. The population is managed to preserve genetic diversity using the concept of mean kinship. Growth of the total population has been between 10% and 15% per year since 1987, but the growth of the captive population has been only about 5% per year since 1992 due to the removal of chicks for reintroduction. Assuming that founding birds within clans were half-siblings, the birds used to found the captive population theoretically contained 92% of the heterozygosity present in the hypothetical wild base population. About 99.5% of this heterozygosity has been retained in the current population. Alleles from most founders are well represented across captive- breeding facilities and reintroduction sites. The genetic status of this population compares favorably with other species that have been rescued from extinction by captive breeding.
Situación Genética y Manejo de Gymnogyps californianus
Resumen. El último cóndor californiano (Gymnogyps californianus) silvestre fue puesto en cautiverio en 1987. La reproducción en cautiverio fue exitosa y las reintroducciones comenzaron en 1992. La población actual desciende de 14 individuos pertenecientes a tres “clanes” genéticos. Este cuello de botella poblacional dió lugar a la pérdida de variabilidad genética y a cambios en la frecuencia de alelos, incluyendo un probable incremento en la frecuencia del alelo para condrodistrofia, una forma letal de enanismo. En este estudio, utilizamos datos del libro genealógico para analizar la situación genética y demográfica actual de la población y para explicar cómo se está manejando la población para cumplir con metas específicas. En agosto del 2002 la población consistía de 206 individuos distribuidos en tres instalaciones de reproducción en cautiverio y tres sitios de reintroducción. La población fue manejada con el propósito de conservar la diversidad genética usando el concepto de parentesco medio. El crecimiento de la población ha sido de entre 10% y 15% por año desde 1987, pero el crecimiento de la población en cautiverio ha sido únicamente de aproximadamente un 5% por año desde 1992 debido a la remoción de los pollos para su reintroducción. Suponiendo que los cóndores fundadores dentro de cada clan eran medio- hermanos, las aves que fueron utilizadas para fundar la población en cautiverio teóricamente contienen un 92% de la heterocigosidad presente en la población silvestre base hipotética. Cerca de un 99.5% de esta heterocigosidad ha sido retenida en la población actual. Alelos de la mayoría de los fundadores están bien representados en las diversas instalaciones de reproducción en cautiverio y sitios de reintroducción. La situación de esta población parece ser mejor que la de otras especies silvestres que han sido rescatadas por medio de la reproducción en cautiverio.
... The relationship between population size and genetic structure is important to conservation strategies (Franklin & Frankham 1998, Waples 2002. Migratory bats with great dispersal abilities tend to show less population structure than non-migratory species (Burns & Broders 2014), yet dispersal can still be affected by barriers created by sexual behavior or physical boundaries (such as oceanic channels). ...
Determining the connections between islands and assessing subpopulations are required to effectively manage an endemic, seasonally migrant bat species with an observed archipelago wide distribution. An innovative technique to characterize the connectivity among populations is to evaluate the genetic similarity between individuals sampled from among and within islands. By combining mitochondrial and nuclear DNA markers (or genetic variants), we can identify how island groups may differ between populations, sexes, and estimate relative abundances. One mitochondrial gene and six nuclear microsatellite loci were used to explore genetic connectivity among and within three islands inhabited by the endangered Hawaiian hoary bat (Lasiurus cinereus semotus). Employing the resources of an existing collection of bat tissue samples (~140) from the four major islands (Kaua`i, Hawai`i, Maui, and O`ahu) and applying classical population genetics analyses, I tested for population structure; quantified levels of genetic variation, genetic distance, and gene flow in bats among and within the Hawaiian Islands; estimated both historical long-term female effective population size, and contemporary effective population size; and examined the data for patterns of past bottleneck events. In order to accurately measure degree of population structure and phenotypic variation with respect to sex, I conducted genetic sex determination tests on bat samples from both live and desiccated specimens. I also examined the morphological characteristics of bat skull and wing size on 23 individuals to determine differences with respect to island, mitochondrial clade, and sex. This project provides the most current data set of population level information, describing the genetic diversity and geographic structure of Hawai`i’s only endemic terrestrial land mammal. This study contributes demographic information, sex determination techniques, and banking of diverse DNA samples available for future genomic sequencing, to support management and recovery of an endangered species. Research results may provide support to state and federal agencies tasked with balancing the demands of sustainable wind generated energy and wildlife conservation in Hawai`i.
... Thus, even large releases can result in small founding populations (Fauvergue et al., 2012), and effective population sizes can be even smaller if the release comes from a large population that was started from a small sample. In conservation biology, the recommended effective population size to preserve evolutionary potential is 500-1 000 individuals (Franklin & Frankham, 1998). Even though there are records of establishment and short-term survival of biocontrol introductions that were founded with very few individuals (Grevstad, 1999b(Grevstad, , 2006Memmott et al., 1998Memmott et al., , 2005, the long-term survival and evolutionary potential of those introductions may be compromised. ...
Novel environmental conditions experienced by introduced species can drive rapid evolution of diverse traits. In turn, rapid evolution, both adaptive and non‐adaptive, can influence population size, growth rate, and other important ecological characteristics of populations. In addition, spatial evolutionary processes that arise from a combination of assortative mating between highly dispersive individuals at the expanding edge of populations and altered reproductive rates of those individuals can accelerate expansion speed. Growing experimental evidence shows that the effects of rapid evolution on ecological dynamics can be quite large, and thus it can affect establishment, persistence, and the distribution of populations. We review the experimental and theoretical literature on such eco‐evolutionary feedbacks and evaluate the implications of these processes for biological control. Experiments show that evolving populations can establish at higher rates and grow larger than non‐evolving populations. However, non‐adaptive processes, such as genetic drift and inbreeding depression can also lead to reduced fitness and declines in population size. Spatial evolutionary processes can increase spread rates and change the fitness of individuals at the expansion front. These examples demonstrate the power of eco‐evolutionary dynamics and indicate that evolution is likely more important in biocontrol programs than previously realized. We discuss how this knowledge can be used to enhance efficacy of biological control. Rapid evolution, both adaptive and non‐adaptive, can drive changes in population size, growth rate, and other important ecological characteristics of populations. As populations disperse, rapid spatial evolutionary processes can increase spread rates and alter growth rates of individuals at the expansion front. We review evidence for these eco‐evolutionary processes and discuss how this knowledge can be used to enhance the efficacy of biological control.
... Ne is an important quantity in that it suggests how resilient a population is to environmental stresses. Franklin (97,98) proposed that an Ne of 500 is associated with the eventual long-term elimination of a population, while Lande (99) proposed that 5,000 was sufficient for predicting extinction. A lower value of 50 has been suggested as predictive of short-term extinction (68,100). ...
Population Structure and Dynamics of Helminthic Infection: Schistosomiasis * , Page 1 of 2
Abstract
While disease and outbreaks are mainly clonal for bacteria and other asexually reproducing organisms, sexual reproduction in schistosomes and other helminths usually results in unique individuals. For sexually reproducing organisms, the traits conserved in clones will instead be conserved in the group of organisms that tends to breed together, the population. While the same tools are applied to characterize DNA, how results are interpreted can be quite different at times (see another article in this collection, http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.AME-0002-2018). It is difficult to know what the real effect any control program has on the parasite population without assessing the health of this population, how they respond to the control measure, and how they recover, if they do. This review, part of the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases, concentrates on one approach using pooled samples to study schistosome populations and shows how this and other approaches have contributed to our understanding of this parasite family’s biology and epidemiology. *This article is part of a curated collection.
... That is, the effective population size of the Mogollon Rim populations of the Western Hercules beetle is equal to or smaller than the sizes of conserved monarch populations. The estimated effective population size, however, is larger than the critical value for maintaining genetic diversity needed for future adaptive potential (Franklin and Frankham 1998;Frankham 2005Frankham , 2010. The lack of genetic structure between geographically distant populations revealed in this study also implies the effective population size could be large enough to counter genetic drift (Figure 2 and Supplementary Figures S2 and S3). ...
The Western Hercules beetle (Dynastes grantii) is endemic to the highland forest habitats of southwestern USA and northern Mexico. The habitats harbor many endemic species, but are being threatened by rapid climate change and urban development. In this study, the genetic structure of D. grantii populations from southwestern USA was investigated. Specifically, genomic data from double-digest RADseq (ddRADseq) libraries were utilized to test whether geographically distant populations from the Mogollon Rim (Arizona [N = 12 individuals] and New Mexico [N = 10 individuals]) are genetically structured. The study also estimated the effective population size of the Mogollon Rim populations based on genetic diversity. The results indicated that the two geographic populations from the Mogollon Rim were not genetically structured. A population size reduction was detected since the end of the last glacial period, which coincided with a reduction of forest habitat in the study area. The results implied that the connectivity and the size of highland forest habitats in the Mogollon Rim could have been the major factors shaping the population genetic structure and demographic history of D. grantii. The Western Hercules beetle could be a useful flagship species for local natural history education and to promote the conservation of highland forest habitats.
... Further, the small N e in extant Cab populations may seriously limit its evolutionary potential to adapt to ongoing and future environmental change (Franklin and Frankham 1998). These challenges may include relatively rapid climate change, competition from invasive plant species, and threats posed by exotic pathogens and phytophagous insects. ...
Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthusampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of Caulanthusampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), in order to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g. > 1 km), possibly via zoochory.
... It is therefore important to maintain an effective population size (N e ) to accommodate drastic changes in the environment. To ensure the long-term sustainability of a genetic improvement programme, the minimum N e is considered to be 50 (Hall 2004), while the minimum N e to retain the evolutionary capacity of a population is considered to be much higher at 500 (Franklin & Frankham 1998). A N e equal or greater than 500 is nearly impossible to achieve in a single aquaculture breeding programme; however, it could be achieved if several breeding programmes with the same aim were genetically linked providing more resilience of these populations to unexpected changes in future environmental conditions (Y añez et al. 2014c). ...
Genetic improvement is key to the development of a more efficient aquaculture industry. By 2010, there were 104 breeding programmes for aquaculture species in the world, most of them for fish species. Usually, the breeding goals include traits such as growth rate, disease resistance, maturation and carcass quality. Resistance to specific pathogens has been one of the main objectives of research and development in the genetic improvement programmes of salmonids in Chile and worldwide. In Chile, trait selection has been conducted through the application of selection indexes. New technologies like next generation sequencing and genotyping have helped disentangle the genetic basis and enhance genetic evaluation methods of economically important traits. This work aims to review the advances in genetic improvement for salmon and trout aquaculture with emphasis on the Chilean experience. We focus on the implementation of breeding programmes in the country, definition of breeding objectives, results on genetic parameters and response to selection and incorporation of genomics. Future challenges
and opportunities regarding genotype-by-environment interactions, climate change and research and development, plus the demonstration of the economic benefit of breeding programmes are also addressed.
Even though cuscus is protected, this species is highly hunted and continues to decline. This is due to the decline in population in its natural habitat due to forest degradation and loss by logging, agricultural expansion, and human settlements, poaching and illegal wildlife trade. Illegal hunting is the basis for trading in its illegal meat, as it is consumed as a protein source and to meet meat needs during traditional ceremonies. In addition to using cuscus meat from hunting, the fur is also used for hat decoration, the teeth are arranged to form a necklace, the skull is a pendant, the tail is dried into a bracelet by local communities, especially in Papua, North Sulawesi, East Nusa Tenggara. According to the International Union for Conservation of Nature (IUCN), several species of cuscus are listed as Endangered Species with a declining population trend, and it was assigned to Appendix II by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES).
Chirostoma humbodtianum (Valenciennes, 1835), es una especie de pez blanco, endémica de México, habita de manera discontinua en sistemas lénticos desde el Estado de México hasta Nayarit, a lo largo de las cuencas del Río Lerma-Santiago. Esta especie tiene importancia biológica, económica y social ya que desde la época precolombina ha sido consumida por los habitantes de la región. Hoy en día, se han observado declives poblacionales aunados a fragmentación del hábitat, sobreexplotación, introducción de especies exóticas y contaminación de los lagos en el Valle de México. El objetivo del presente trabajo fue evaluar dos poblaciones silvestres (Tiacaque, Edo. México (T) y Tepuxtepec, Michoacán (Tx)) y realizar la fertilización in vitro de las mismas poblaciones que se encuentran en cautiverio en la Planta Experimental de Producción Acuícola (PExPA), con la finalidad de determinar la existencia de barreras reproductivas en la F1, su diversidad genética y morfológica, así como comparar la diversidad con las poblaciones silvestres y el lote reproductor; para orientar su manejo acuícola y contrarrestar la sobrexplotación
de la especie.
Se llevaron a cabo fertilizaciones in vitro a través de la extracción de gametos femeninos y
masculinos de organismos presentes de dos poblaciones en cautiverio en PExPA UAM-I.
(Tiacaque y Tepuxtepec). Se le dio seguimiento a la F1 durante el desarrollo temprano desde el momento de la activación del huevo hasta el periodo juvenil. Se cuantificó la sobrevivencia. El análisis morfológico, consistió en el registro del tamaño corporal (LT, LNC) y el peso de los peces (P). Los análisis genéticos consistieron en la evaluación, por medio de análisis de diversidad y estructura genética y análisis de parentesco, de una muestra de cada una de las poblaciones silvestres, los juveniles y reproductores con ocho loci microsatelitales nucleares.
La mayor sobrevivencia se presentó en la cruza de T ♀ X Tx ♂ con 17.47%, mientras que la
cruza de Tx♀ X T♂ fue de solo 3%. La población silvestre de Tepuxtepec presentó mayor número de heterocigotos (Tx; HE= 0.759), mientras que la F1 (PT) obtuvo el menor número de heterocigos en todas las poblaciones analizadas HE= 0.414. Todas las poblaciones mostraron un número significativo, positivo y alto en el coeficiente de endogamia (FIS). Se observó una fuerte estructura genética con tres pozas génicas diferenciadas (K=3), en donde las poblaciones silvestres T y Tx presentan cada una su propia poza génica, mientras que los individuos en cautiverio (reproductores y F1) comparten una misma poza génica con flujo génico entre ellas. La fuerte estructura poblacional y la pérdida de heterocigotos sugiere una tendencia hacia la adaptación al entorno cautivo, un proceso de efecto fundador y por lo tanto una pérdida de diversidad genética; mientras que en las poblaciones silvestres, la pérdida de variación genética puede ser debido a la fragmentación del hábitat, a eventos de cuello de botella, deriva génica y un bajo tamaño efectivo poblacional, relacionado con la historia evolutiva de la especie. Se sugiere, considerar estos resultados para orientar la eficiencia en las prácticas del manejo de la especie tanto en cautiverio como en las poblaciones silvestres.
The objective of this study was to evaluate, through data simulation, the impact of restrictions on the maximum number of full- and half-sibs selected for males and females on the level of inbreeding and genetic gain of the herd. Data came from real populations A and B, composed of Pietrain and Landrace breed pigs, respectively. To generate the simulated populations, a Fortran-language simulator was developed using the (co)variances of the breeding values and the productive and reproductive rates obtained from populations A and B. Two data files were created. The first contained the pedigree of the previous 10 years, with 21,906 and 251,343 animals in populations A and B, respectively. The second included breeding values for age to reach 110 Kg body weight, backfat thickness, and feed conversion, for both populations; longissimus dorsi muscle depth, for population A only; and number of live piglets at the 5th day of life per farrowing, for population B only. Three scenarios were simulated with ten generations by varying the restrictions on the number of full- and half-sibs selected for males and females, with 30 replicates per generation and scenario. Regardless of the mating strategy used in a closed production unit, there is an increase in inbreeding levels. Inbreeding increases are larger in populations of smaller effective size. Restrictions on the number of full- and half-sibs selected are effective in reducing increments in inbreeding. Restriction to a maximum of two full-sibs and three half-sibs for males and three full sisters for females provided the highest genetic gains.
Replicated divergent artificial selection for abdominal and sternopleural bristle number from a highly inbred strain of Drosophila melanogaster resulted in an average divergence after 125 generations of selection of 12.0 abdominal and 8.2 sternopleural bristles from the accumulation of new mutations affecting bristle number. Responses to selection were highly asymmetrical, with greater responses for low abdominal and high sternopleural bristle numbers. Estimates of VM, the mutational variance arising per generation, based on the infinitesimal model and averaged over the responses to the first 25 generations of selection, were 4.32 x 10(-3) VE for abdominal bristle number and 3.66 x 10(-3) VE for sternopleural bristle number, where VE is the environmental variance. Based on 10 generations of divergent selection within lines from generation 93, VM for abdominal bristle number was 6.75 x 10(-3) VE and for sternopleural bristle number was 5.31 x 10(-3) VE. However, estimates of VM using the entire 125 generations of response to selection were lower and generally did not fit the infinitesimal model largely because the observed decelerating responses were not compatible with the predicted increasing genetic variance over time. These decelerating responses, periods of response in the opposite direction to artificial selection, and rapid responses to reverse selection all suggest new mutations affecting bristle number on average have deleterious effects on fitness. Commonly observed periods of accelerated responses followed by long periods of stasis suggest a leptokurtic distribution of mutational effects for bristles.
Experimental data on the rate of response to artificial selection in initially inbred lines or the rate of divergence among inbred sublines can be used to estimate the rate of increase in variance of quantitative traits from new mutations. So far estimates have been based on the infinitesimal model of many genes with small additive effects which imply a rate of increase in heritability for Drosophila melanogaster bristle number traits of about 0.1% per generation. Such estimates are biased because mutants tend to have large effects, to have non-additive gene action, and to be deleterious. Here, recent information on the distribution of effects of new mutations on Drosophila melanogaster bristle number and viability is used to infer the direction and magnitude of this bias. The infinitesimal model tends to underestimate the mutational variance, typically by a factor of about 3, but this factor depends on the experimental design. Averages of revised estimates, accounting for this bias, of the per generation increment in heritability from mutation are 0.36% and 0.21% for abdominal and sternopleural bristle number, respectively, in experiments involving M strains, and 1.4% and 0.7% for abdominals and sternopleurals, respectively, in P strains.
We have reviewed the available data on VM, the amount of genetic variation in phenotypic traits produced each generation by mutation. We use these data to make several qualitative tests of the mutation-selection balance hypothesis for the maintenance of genetic variance (MSB). To compare VM values, we use three dimensionless quantities: mutational heritability, VM/VE, the mutational coefficient of variation, CVM; and the ratio of the standing genetic variance to VM, VC/VM. Since genetic coefficients of variation for life history traits are larger than those for morphological traits, we predict that under MSB, life history traits should also have larger CVM. This is confirmed; life history traits have a median CVM value more than six times higher than that for morphological traits. VC/VM approximates the persistence time of mutations under MSB in an infinite population. In order for MSB to hold, VC/VM must be small, substantially less than 1000, and life history traits should have smaller values than morphological traits. VC/VM averages about 50 generations for life history traits and 100 generations for morphological traits. These observations are all consistent with the predictions of a mutation-selection balance model.
Two new population genetics studies provide sobering news for efforts to protect endangered species. The minimum number of
individuals needed to provide a genetically robust population capable of long-term survival may be as high as 10,000. Previous
estimates had put the figure at 500, and many endangered species are down to just a few dozen individuals.
Mutation can critically affect the viability of small populations by causing inbreeding depression, by maintaining potentially adaptive genetic variation in quantitative characters, and through the erosion of fitness by accumulation of mildly detrimental mutations. I review and integrate recent empirical and theoretical work on spontaneous mutation and its role in population viability and conservation planning. I analyze both the maintenance of potentially adaptive genetic variation in quantitative characters and the role of detrimental mutations in increasing the extinction risk of small populations. Recent experiments indicate that the rate of production of quasineutral, potentially adaptive genetic variance in quantitative characters is an order of magnitude smaller than the total mutational variance because mutations with large phenotypic effects tend to be strongly detrimental. This implies that, to maintain normal adaptive potential in quantitative characters under a balance between mutation and random genetic drift (or among mutation, drift, and stabilizing natural selection), the effective population size should be about 5000 rather than 500 (the Franklin-Soulé number). Recent theoretical results suggest that the risk of extinction due to the fixation of mildly detrimental mutations may be comparable in importance to environmental stochasticity and could substantially decrease the long-term viability of populations with effective sizes as large as a few thousand. These findings suggest that current recovery goals for many threatened and endangered species are inadequate to ensure long-term population viability.
The discussion of a population's minimum viable size provides a focus for the study of ecological and genetic factors that influence the persistence of a threatened population. There are many causes of extinction and the fate of a specific population cannot generally be predicted. This uncertainty has been dealt with in two ways: through stochastic demographic models to determine how to minimize extinction probabilities; and through population genetic theory to determine how best to maintain genetic variation, in the belief that the ability to evolve helps buffer a population against the unknown. Recent work suggests that these two very different approaches lead to very similar conclusions, at least under panmictic conditions. However, defining the ideal spatial distribution for an endangered species remains an important challenge.
Predicting the extinction of single populations or species requires ecological and evolutionary information. Primary demographic
factors affecting population dynamics include social structure, life history variation caused by environmental fluctuation,
dispersal in spatially heterogeneous environments, and local extinction and colonization. In small populations, inbreeding
can greatly reduce the average individual fitness, and loss of genetic variability from random genetic drift can diminish
future adaptability to a changing environment. Theory and empirical examples suggest that demography is usually of more immediate
importance than population genetics in determining the minimum viable sizes of wild populations. The practical need in biological
conservation for understanding the interaction of demographic and genetic factors in extinction may provide a focus for fundamental
advances at the interface of ecology and evolution.