scholarly journals Coalescent models at small effective population sizes and population declines are positively misleading

2019 ◽  
Author(s):  
M. Elise Lauterbur
Keyword(s):  
Genetic Diversity ◽  
Sample Size ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Relationships ◽  
Population Decline ◽  
Population Declines ◽  
Effective Population ◽  
Analytical Approximations ◽  
Population Sizes

AbstractPopulation genetics employs two major models for conceptualizing genetic relationships among individuals – outcome-driven (coalescent) and process-driven (forward). These models are complementary, but the basic Kingman coalescent and its extensions make fundamental assumptions to allow analytical approximations: a constant effective population size much larger than the sample size. These make the probability of multiple coalescent events per generation negligible. Although these assumptions are often violated in species of conservation concern, conservation genetics often uses coalescent models of effective population sizes and trajectories in endangered species. Despite this, the effect of very small effective population sizes, and their interaction with bottlenecks and sample sizes, on such analyses of genetic diversity remains unexplored. Here, I use simulations to analyze the influence of small effective population size, population decline, and their relationship with sample size, on coalescent-based estimates of genetic diversity. Compared to forward process-based estimates, coalescent models significantly overestimate genetic diversity in oversampled populations with very small effective sizes. When sampled soon after a decline, coalescent models overestimate genetic diversity in small populations regardless of sample size. Such overestimates artificially inflate estimates of both bottleneck and population split times. For conservation applications with small effective population sizes, forward simulations that do not make population size assumptions are computationally tractable and should be considered instead of coalescent-based models. These findings underscore the importance of the theoretical basis of analytical techniques as applied to conservation questions.

scholarly journals The paradox of retained genetic diversity of Hippocampus guttulatus in the face of demographic decline

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rupert Stacy ◽  
Jorge Palma ◽  
Miguel Correia ◽  
Anthony B. Wilson ◽  
José Pedro Andrade ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Population Decline ◽  
Genetic Bottleneck ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Hippocampus Guttulatus ◽  
Ria Formosa

AbstractGenetic diversity is the raw foundation for evolutionary potential. When genetic diversity is significantly reduced, the risk of extinction is heightened considerably. The long-snouted seahorse (Hippocampus guttulatus) is one of two seahorse species occurring in the North-East Atlantic. The population living in the Ria Formosa (South Portugal) declined dramatically between 2001 and 2008, prompting fears of greatly reduced genetic diversity and reduced effective population size, hallmarks of a genetic bottleneck. This study tests these hypotheses using samples from eight microsatellite loci taken from 2001 and 2013, on either side of the 2008 decline. The data suggest that the population has not lost its genetic diversity, and a genetic bottleneck was not detectable. However, overall relatedness increased between 2001 to 2013, leading to questions of future inbreeding. The effective population size has seemingly increased close to the threshold necessary for the population to retain its evolutionary potential, but whether these results have been affected by sample size is not clear. Several explanations are discussed for these unexpected results, such as gene flow, local decline due to dispersal to other areas of the Ria Formosa, and the potential that the duration of the demographic decline too short to record changes in the genetic diversity. Given the results presented here and recent evidence of a second population decline, the precise estimation of both gene flow and effective population size via more extensive genetic screening will be critical to effective population management.

scholarly journals Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size

2021 ◽  
Author(s):  
Michaela Halsey ◽  
John Stuhler ◽  
Natalia J Bayona-Vasquez ◽  
Roy N Platt ◽  
Jim R Goetze ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Population Fluctuations ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Single Nucleotide ◽  
Demographic Dynamics ◽  
Population Sizes

Organisms with low effective population sizes are at greater risk of extinction because of reduced genetic diversity.   Dipodomys elator  is a kangaroo rat that is classified as threatened in Texas and field surveys from the past 50 years indicate that the distribution of this species has decreased. This suggests geographic range reductions that could have caused population fluctuations, potentially impacting effective population size. Conversely, the more common and widespread  D. ordii  is thought to exhibit relative geographic and demographic stability. Genetic variation between  D. elator  and  D. ordii  samples was assessed using 3RAD, a modified restriction site associated sequencing approach. It was hypothesized that  D. elator  would show lower levels of nucleotide diversity, observed heterozygosity, and effective population size when compared to  D. ordii . Also of interest was identifying population structure within contemporary samples of  D. elator  and detecting genetic variation between temporal samples that could indicate demographic dynamics. Up to 61,000 single nucleotide polymorphisms were analyzed. It was determined that genetic variability and effective population size in contemporary  D. elator  populations were lower than that of  D. ordii, that there is only slight, if any, structure within contemporary  D. elator  populations, and there is little genetic differentiation between spatial or temporal historical samples suggesting little change in nuclear genetic diversity over 30 years. Results suggest that genetic diversity of  D. elator  has remained stable despite claims of reduced population size and/or abundance, which may indicate a metapopulation-like system, whose fluctuations might counteract any immediate decrease in fitness.

scholarly journals Genetic diversity and structure of two endangered mole salamander species of the Trans-Mexican Volcanic Belt

Herpetozoa ◽  
2019 ◽  
Vol 32 ◽  
pp. 237-248 ◽  
Author(s):  
Octavio Monroy-Vilchis ◽  
Rosa-Laura Heredia-Bobadilla ◽  
Martha M. Zarco-González ◽  
Víctor Ávila-Akerberg ◽  
Armando Sunny
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Size ◽  
Effective Population Size ◽  
Volcanic Belt ◽  
Population Declines ◽  
Effective Population ◽  
Mexican Volcanic Belt ◽  
Genetic Diversity And Structure ◽  
Trans Mexican Volcanic Belt

The most important factor leading to amphibian population declines and extinctions is habitat degradation and destruction. To help prevent further extinctions, studies are needed to make appropriate conservation decisions in small and fragmented populations. The goal of this study was to provide data from the population genetics of two micro-endemic mole salamanders from the Trans-Mexican Volcanic Belt. Nine microsatellite markers were used to study the population genetics of 152 individuals from two Ambystoma species. We sampled 38 individuals in two localities for A. altamirani and A. rivualre. We found medium to high levels of genetic diversity expressed as heterozygosity in the populations. However, all the populations presented few alleles per locus and genotypes. We found strong genetic structure between populations for each species. Effective population size was small but similar to that of the studies from other mole salamanders with restricted distributions or with recently fragmented habitats. Despite the medium to high levels of genetic diversity expressed as heterozygosity, we found few alleles, evidence of a genetic bottleneck and that the effective population size is small in all populations. Therefore, this study is important to propose better management plans and conservation efforts for these species.

scholarly journals Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity

2019 ◽  
Vol 286 (1911) ◽  
pp. 20190304 ◽  
Author(s):  
Balaji Chattopadhyay ◽  
Kritika M. Garg ◽  
Rajasri Ray ◽  
Frank E. Rheindt
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Global Climate ◽  
Future Climate Change ◽  
Effective Population ◽  
Population Sizes ◽  
Earth’S Climate ◽  
The Impact

Over the last approximately 2.6 Myr, Earth's climate has been dominated by cyclical ice ages that have profoundly affected species' population sizes, but the impact of impending anthropogenic climate change on species’ extinction potential remains a worrying problem. We investigated 11 bat species from different taxonomic, ecological and geographical backgrounds using combined information from palaeoclimatic habitat reconstructions and genomes to analyse biotic impacts of historic climate change. We discover tightly correlated fluctuations between species' historic distribution and effective population size, identify frugivores as particularly susceptible to global warming, pinpoint large insectivores as having overall low effective population size and flag the onset of the Holocene (approx. 10–12 000 years ago) as the period with the generally lowest effective population sizes across the last approximately 1 Myr. Our study shows that combining genomic and palaeoclimatological approaches reveals effects of climatic shifts on genetic diversity and may help predict impacts of future climate change.

Effective population size of koala populations under different population management regimes including contraception

2009 ◽  
Vol 36 (7) ◽  
pp. 601 ◽  
Author(s):  
Mark M. Tanaka ◽  
Romane Cristescu ◽  
Desmond W. Cooper
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Equal Opportunity ◽  
Management Strategies ◽  
Effective Population ◽  
Population Sizes ◽  
Wildlife Populations ◽  
Population Genetic Variation

Context. The management of wildlife populations aiming to control population size should also consider the preservation of genetic diversity. Some overabundant koala populations, for example, have low genetic variation. Different management strategies will affect population genetic variation differently. Aims. Here, we compare four strategies with respect to their effects on the effective population size, Ne , and therefore on genetic variation. Methods. The four strategies of interest are: (1) sterilisation or culling (which have the same effect on genetic variation); (2) random contraception of females with replacement; (3) random contraception of females without replacement; and (4) regular contraception, giving every female equal opportunity to reproduce. We develop mathematical models of these alternative schemes to evaluate their impact on Ne . We also consider the effect of changing population sizes by investigating a model with geometric population growth in which females are removed by sterilisation or culling. Key results. We find that sterilisation/culling at sexual maturity has the most detrimental effect on Ne , whereas regular contraception has no impact on Ne . Random contraception lies between these two extremes, leading to a moderate reduction in Ne . Removal of females from a growing population results in a higher Ne than the removal of females from a static population. Conclusions. Different strategies for controlling a population lead to different effective population sizes. Implications. To preserve genetic diversity in a wildlife population under control, the effective population size should be kept as large as possible. We suggest that a suitable approach in managing koala populations may be to prevent reproduction by all females older than a particular age.

scholarly journals Inconsistent effects of urbanization on amphibian genetic diversity

2020 ◽  
Author(s):  
Chloé Schmidt ◽  
Colin J Garroway
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Habitat Loss ◽  
Gene Diversity ◽  
Amphibian Declines ◽  
Population Declines ◽  
Effective Population ◽  
Negative Effects ◽  
Amphibian Species

AbstractHabitat loss and fragmentation are leading causes of vertebrate population declines. These declines are thought to be partly due to decreased connectivity and habitat loss reducing population sizes in human transformed habitats. With time this can lead to reduced effective population size and genetic diversity which restricts the ability of wildlife to cope with environmental change through genetic adaptation. However, it is not well understood whether these effects are generally applicable across taxa. Here, we repurposed and synthesized raw microsatellite data from online repositories from 19 amphibian species sampled at 554 sites in North America. For each site, we estimated gene diversity, allelic richness, effective population size, and population differentiation. Using binary urban-rural census designations, and continuous measures of human population density and the Human Footprint Index, we tested for generalizable effects of human land use on amphibian genetic diversity. We found no consistent relationships for any of our genetic metrics. While we did not detect directional effects for most species, a few generalist species responded positively to urbanization. These results contrast with consistent negative effects of urbanization in mammals and species specific positive and negative effects in birds. In the context of widespread amphibian declines, our results suggest that habitat loss in human transformed habitats is a more immediate concern than declining genetic diversity in populations that persist.

Underwater but not out of sight: genetic monitoring of effective population size in the endangered North Sea houting (Coregonus oxyrhynchus)

2006 ◽  
Vol 63 (4) ◽  
pp. 780-787 ◽  
Author(s):  
Michael M Hansen ◽  
Einar E Nielsen ◽  
Karen-Lise D Mensberg
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
North Sea ◽  
Population Decline ◽  
Genetic Monitoring ◽  
Population Declines ◽  
Effective Population ◽  
The North ◽  
The North Sea ◽  
Temporal Method

We analysed 12 microsatellite DNA loci in temporal samples (1980, 1994, and 2002) from the only remaining indigenous population of the North Sea houting (Coregonus oxyrhynchus) in the Vidaa River, Denmark. Using a novel temporal method, we estimated effective population size (Ne) to be 577.4 (90% highest posterior density limits 297.2–3719.8). The same method was used to estimate Ne at the beginning and end of the sampled time interval, and the results were indicative of a relatively stable population. In contrast, tests for recent bottlenecks suggested population declines in the 1980 and 1994 samples, possibly reflecting declines prior to 1980 in the total North Sea houting population. To evaluate the usefulness of the two methods for routine genetic monitoring, we simulated population declines corresponding to reproduction by only 20 or 50 parents in 2002. For both simulated samples, the temporal method provided evidence for a population decline, whereas the test for bottlenecks did not suggest population decline. We conclude that the North Sea houting in the Vidaa River is not immediately threatened by inbreeding or loss of evolutionary potential, and the applied temporal method appears very useful for genetic monitoring of effective population size in endangered, isolated fish populations.

scholarly journals Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species

2021 ◽  
Author(s):  
Zachariah Gompert ◽  
Amy Springer ◽  
Megan Brady ◽  
Samridhi Chaturvedi ◽  
Lauren K. Lucas
Keyword(s):  
Genetic Diversity ◽  
Time Series ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Time Series Data ◽  
Series Data ◽  
Effective Population ◽  
Population Sizes

AbstractEffective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show thatLycaeidesbutterfly populations maintain low contemporary (variance) effective population sizes (e.g., ∼200 individuals) and thus evolve rapidly by genetic drift. Contemporary effective sizes were consistent with local census populations sizes. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift inLycaeideshas implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.

scholarly journals Low genetic diversity in the endangered Taxus yunnanensis following a population bottleneck, a low effective population size and increased inbreeding

2016 ◽  
Vol 65 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Y. C. Miao ◽  
Z. J. Zhang ◽  
J. R. Su
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Population Bottleneck ◽  
Effective Population ◽  
Taxus Yunnanensis ◽  
Low Genetic Diversity ◽  
Two Populations

Abstract Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

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