scholarly journals Molecular evolutionary consequences of island colonisation

2015 ◽  
Author(s):  
Jennifer James ◽  
Robert Lanfear ◽  
Adam Eyre-Walker
Keyword(s):  
Genetic Diversity ◽  
Population Bottleneck ◽  
Surprising Result ◽  
Population Bottlenecks ◽  
Adaptive Potential ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Evolutionary Consequences ◽  
The Relationship

Island endemics are likely to experience population bottlenecks; they also have restricted ranges. Therefore we expect island species to have small effective population sizes (Ne) and reduced genetic diversity compared to their mainland counterparts. As a consequence, island species may have inefficient selection and reduced adaptive potential. We used both polymorphisms and substitutions to address these predictions, improving on the approach of recent studies that only used substitution data. This allowed us to directly test the assumption that island species have small values of Ne. We found that island species had significantly less genetic diversity than mainland species; however, this pattern could be attributed to a subset of island species that had undergone a recent population bottleneck. When these species were excluded from the analysis, island and mainland species had similar levels of genetic diversity, despite island species occupying considerably smaller areas than their mainland counterparts. We also found no overall difference between island and mainland species in terms of effectiveness of selection or mutation rate. Our evidence suggests that island colonisation has no lasting impact on molecular evolution. This surprising result highlights gaps in our knowledge of the relationship between census and effective population size.

scholarly journals Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

2020 ◽  
Vol 287 (1922) ◽  
pp. 20192613 ◽  
Author(s):  
Elisa G. Dierickx ◽  
Simon Yung Wa Sin ◽  
H. Pieter J. van Veelen ◽  
M. de L. Brooke ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Sex Chromosomes ◽  
Demographic History ◽  
Large Population ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Approaches To Study ◽  
Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

scholarly journals Neo-sex chromosomes, genetic diversity and demographic history in the Critically Endangered Raso lark

2019 ◽  
Author(s):  
Elisa Dierickx ◽  
Simon Sin ◽  
Pieter van Veelen ◽  
M. de L. Brooke ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Sex Chromosomes ◽  
Allelic Variation ◽  
Demographic History ◽  
Large Population ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Genetic Signatures

ABSTRACTSmall effective population sizes could expose island species to inbreeding and loss of genetic variation. Here we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for ~500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. It is plausible that these regions might inadvertently and temporarily preserve pre-existing allelic variation in females that would otherwise be lost through genetic drift. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present day diversity can be shaped by ancient demographic events.

Species traits influence the genetic consequences of river fragmentation on two co-occurring redhorse (Moxostoma) species

2008 ◽  
Vol 65 (9) ◽  
pp. 1892-1904 ◽  
Author(s):  
Scott M. Reid ◽  
Chris C. Wilson ◽  
Leon M. Carl ◽  
Troy G. Zorn
Keyword(s):  
Genetic Diversity ◽  
Allelic Richness ◽  
Species Traits ◽  
Population Bottlenecks ◽  
Effective Population ◽  
Length Effect ◽  
Microsatellite Dna Markers ◽  
Population Sizes ◽  
River Fragmentation ◽  
Movement Differences

We used microsatellite DNA markers to test whether fragmentation of the Trent River (Ontario, Canada) has reduced genetic diversity and increased genetic differentiation among populations of river redhorse ( Moxostoma carinatum ) and shorthead redhorse (Moxostoma macrolepidotum). Allelic richness of both species was significantly greater along the free-flowing Muskegon River (Michigan, USA) than along the fragmented Trent River. Contrary to expectations, there was no evidence of a fragment length effect on genetic diversity, recent population bottlenecks, or increased relatedness among individuals in fragmented populations. High levels of linkage disequilibrium indicate extinction–recolonization population dynamics along the Trent River. For both species, pairwise FST tests identified weak but statistically significant population differentiation. In the Trent River, differentiation was significantly greater for river redhorse than for shorthead redhorse and, for both species, greater than in the Muskegon River. Moderate fragmentation effects likely reflect the permeability of the dam-lock system to redhorse movement. Differences between species indicate that as a result of smaller effective population sizes, habitat specialists and species at the periphery of their geographic range are more sensitive to river fragmentation.

Habitat loss, fragmentation, and the genetic status of Roanoke bass

2020 ◽  
Vol 77 (2) ◽  
pp. 375-387
Author(s):  
Jackman C. Eschenroeder ◽  
James H. Roberts
Keyword(s):  
Genetic Diversity ◽  
Habitat Loss ◽  
Agricultural Development ◽  
Genetic Relationships ◽  
Population Bottlenecks ◽  
Effective Population ◽  
Conservation Genetic ◽  
Population Sizes ◽  
Nuclear Microsatellite

Roanoke bass (Ambloplites cavifrons) persist in five river basins in the eastern US, where they are threatened by invasive species, habitat loss and degradation, and hydrologic fragmentation. We conducted the first conservation genetic study of A. cavifrons, analyzing variation at 19 nuclear microsatellite DNA loci and the cytochrome b mitochondrial DNA gene to estimate population structure and demography, genetic relationships among populations, and the role of landscape features in regulating genetic diversity and differentiation. Most streams harbored genetically distinguishable populations, with high connectivity among reaches within streams but no contemporary dispersal among streams. In contrast, mitochondrial divergence within and among basins was weak, suggesting historically higher range-wide connectivity. Most populations exhibited small effective population sizes and evidence of past population bottlenecks. Genetic diversity correlated positively with patch size but negatively with watershed urban and agricultural development, suggesting that habitat loss, degradation, and fragmentation have acted in concert to reduce population viability. Mitigating these impacts may require a combination of tactics, including restoring habitat, limiting the spread of invasive competitors, and reestablishing historical connectivity.

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.

scholarly journals Challenges to assessing connectivity between massive populations of the Australian plague locust

2011 ◽  
Vol 278 (1721) ◽  
pp. 3152-3160 ◽  
Author(s):  
Marie-Pierre Chapuis ◽  
Julie-Anne M. Popple ◽  
Karine Berthier ◽  
Stephen J. Simpson ◽  
Edward Deveson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Large Population ◽  
Movement Ecology ◽  
Effective Population ◽  
Continental Scale ◽  
Australian Continent ◽  
Population Structuring ◽  
Population Sizes ◽  
Approximate Bayesian ◽  
Australian Plague Locust

Linking demographic and genetic dispersal measures is of fundamental importance for movement ecology and evolution. However, such integration can be difficult, particularly for highly fecund species that are often the target of management decisions guided by an understanding of population movement. Here, we present an example of how the influence of large population sizes can preclude genetic approaches from assessing demographic population structuring, even at a continental scale. The Australian plague locust, Chortoicetes terminifera , is a significant pest, with populations on the eastern and western sides of Australia having been monitored and managed independently to date. We used microsatellites to assess genetic variation in 12 C. terminifera population samples separated by up to 3000 km. Traditional summary statistics indicated high levels of genetic diversity and a surprising lack of population structure across the entire range. An approximate Bayesian computation treatment indicated that levels of genetic diversity in C. terminifera corresponded to effective population sizes conservatively composed of tens of thousands to several million individuals. We used these estimates and computer simulations to estimate the minimum rate of dispersal, m , that could account for the observed range-wide genetic homogeneity. The rate of dispersal between both sides of the Australian continent could be several orders of magnitude lower than that typically considered as required for the demographic connectivity of populations.

scholarly journals Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes

2020 ◽  
Vol 12 (12) ◽  
pp. 2441-2449
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Range Size ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

Abstract What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12–20%, providing one of the first quantifications of the relationship between diversity and the census population size.

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 Continent-wide effects of urbanization on bird and mammal genetic diversity

2019 ◽  
Author(s):  
C. Schmidt ◽  
M. Domaratzki ◽  
R.P. Kinnunen ◽  
J. Bowman ◽  
C.J. Garroway
Keyword(s):  
Genetic Diversity ◽  
Environmental Changes ◽  
Bird Species ◽  
Population Level ◽  
Natural Environments ◽  
Population Declines ◽  
Effective Population ◽  
Human Footprint ◽  
Rate Of Increase ◽  
Population Sizes

AbstractUrbanization and associated environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding, and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalyzed publicly archived genetic data sets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41,023 individuals, sampled from 1,008 locations spanning 41 mammal and 25 bird species. We used census-based urban-rural designations, human population density, and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.

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