scholarly journals Spatio-temporal ecological and evolutionary dynamics in natural butterfly populations

2016 ◽  
Vol 39 ◽  
pp. 32-37
Author(s):  
Zachariah Gompert ◽  
Lauren Lucas
Keyword(s):  
Genetic Diversity ◽  
Host Plant ◽  
Evolutionary Dynamics ◽  
Plant Cover ◽  
Distance Sampling ◽  
Spatial And Temporal Variation ◽  
Effective Population ◽  
Long Term Study ◽  
Population Size Estimates ◽  
Population Sizes

Spatial and temporal variation in the strength and nature of natural selection could help explain genetic diversity in natural populations and data on short term evolutionary responses to fluctuations in temperature and rainfall could facilitate predictions of climate change impacts. In 2012, we began a long term study of genome-wide molecular evolution in populations of Lycaeides idas in the Greater Yellowstone Ecosystem (GYE). In 2016, we used distance sampling to estimate population densities of 10 butterfly populations spread across the GYE in Wyoming and Montana. In parallel, we estimated host plant cover and conducted insect community surveys at each site. We also completed a genotyping-by-sequencing survey for eight populations sampled in 2013 and 2015 to estimate contemporary variance in effective population sizes. Based on 480 samples across sites, we found significant variation in population sizes (as estimated by distance sampling) among sites and years. Host plant abundance, climate, and insect communities varied among sites but were not consistently predictive of population size. Estimates of effective population sizes among sites showed pronounced variation that was uncorrelated with genetic diversity, possibly due to widespread fluctuating selection.   Featured photo from Figure 1 in report.

scholarly journals Forecasting eco-evolutionary dynamics in the Northern Blue butterfly (Lycaeides idas)

2018 ◽  
Vol 41 ◽  
pp. 77-85
Author(s):  
Zachariah Gompert ◽  
Lauren Lucas
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Global Change ◽  
Evolutionary Dynamics ◽  
Distance Sampling ◽  
Effective Population ◽  
Long Term Study ◽  
Greater Yellowstone Area ◽  
Population Sizes ◽  
Highly Correlated

Natural selection can drive rapid evolutionary change, particularly in human-altered habitats. Rapid adaptation to global change requires standing genetic variation for ecologically important traits, but at present little is known about how much relevant genetic variation most populations possess. With this in mind, we began a long term study of genome-wide molecular evolution in a series of natural butterfly populations in the Greater Yellowstone Area (GYA) in 2012 to quantify the contribution of environment-dependent natural selection to evolution in these butterfly populations, and determine whether selection varies enough across space and time to maintain variation that could facilitate adaptation to global change. In 2018, we visited 11 focal populations to collect samples for DNA, estimate population sizes (using distance sampling and mark-release-recapture methods), and survey arthropod communities at the sites. Our analyses are ongoing, and this is a preliminary report, but thus far we have found that census population sizes are much higher than contemporary effective population sizes (though these metrics are highly correlated), and that both are independent of genetic diversity levels. These results are consistent with the hypothesis that selection plays a central role in eco-evolutionary dynamics in this system.   Featured photo from Figure 1 in report.

scholarly journals Spatio-temporal ecological and evolutionary dynamics in natural butterfly populations

2017 ◽  
Vol 40 ◽  
pp. 31-36
Author(s):  
Zachariah Gompert ◽  
Lauren Lucas
Keyword(s):  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Distance Sampling ◽  
Spatial And Temporal Variation ◽  
Insect Community ◽  
Long Term Study ◽  
Greater Yellowstone Area ◽  
Genome Wide ◽  
Spatio Temporal

Long term studies of wild populations indicate that natural selection can cause rapid and dramatic changes in traits, with spatial and temporal variation in the strength of selection a critical driver of genetic variation in natural populations. In 2012, we began a long term study of genome-wide molecular evolution in populations of the butterfly Lycaeides ideas in the Greater Yellowstone Area (GYA). We aimed to quantify the role of environment-dependent selection on evolution in these populations. Building on previous work, in 2017 we collected new samples, incorporated distance sampling, and surveyed the insect community at each site. We also defined the habitat boundary at anew, eleventh site. Our preliminary analyses suggest that both genetic drift and selection are important drivers in this system.   Featured photo from Figure 1 in report.

scholarly journals Forecasting eco-evolutionary dynamics in the Northern Blue butterfly (2019 field season)

2019 ◽  
Vol 42 ◽  
pp. 80-89
Author(s):  
Zachariah Gompert ◽  
Lauren Lucas
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Global Change ◽  
Evolutionary Dynamics ◽  
Effective Population ◽  
Long Term Study ◽  
Greater Yellowstone Area ◽  
Population Sizes ◽  
Field Season ◽  
Highly Correlated

Natural selection can drive rapid evolutionary change, particularly in human-altered habitats. Rapid adaptation to global change requires standing genetic variation for ecologically important traits, but at present little is known about how much relevant genetic variation most populations possess. With this in mind, we began a long term study of genome-wide molecular evolution in a series of natural butterfly populations in the Greater Yellowstone Area in 2012 to quantify the contribution of environment-dependent natural selection to evolution in these butterfly populations, and determine whether selection varies enough across space and time to maintain variation that could facilitate adaptation to global change. In 2019, we visited 11 focal populations to collect samples for DNA and plant chemistry, estimate population sizes (mark-release-recapture methods), and survey arthropod communities at the sites. Our analyses are ongoing, and this is a preliminary report, but thus far we have found that census population sizes are much higher than contemporary effective population sizes (though these metrics are highly correlated), and that both are independent of genetic diversity levels. These results are consistent with the hypothesis that selection plays a central role in eco-evolutionary dynamics in this system.   Featured photo from figure 1 in report. 

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 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 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.

scholarly journals Population diversity and relatedness in Sugarbirds (Promeropidae:Promeropsspp.)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5000
Author(s):  
Evan S. Haworth ◽  
Michael J. Cunningham ◽  
Kathleen M. Calf Tjorve
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Gene ◽  
Conservation Status ◽  
Tail Length ◽  
Population Diversity ◽  
Breeding Systems ◽  
Effective Population ◽  
Socially Monogamous ◽  
Population Sizes ◽  
Polymorphic Microsatellite

Sugarbirds are a family of two socially-monogamous passerine species endemic to southern Africa. Cape and Gurney’s Sugarbird (Promerops caferandP. gurneyi) differ in abundance, dispersion across their range and in the degree of sexual dimorphism in tail length, factors that affect breeding systems and potentially genetic diversity. According to recent data,P. gurneyiare in decline and revision of the species’ IUCN conservation status to a threatened category may be warranted. It is therefore necessary to understand genetic diversity and risk of inbreeding in this species. We used six polymorphic microsatellite markers and one mitochondrial gene (ND2) to compare genetic diversity inP. caferfrom Helderberg Nature Reserve andP. gurneyifrom Golden Gate Highlands National Park, sites at the core of each species distribution. We describe novel universal avian primers which amplify the entire ND2 coding sequence across a broad range of bird orders. We observed high mitochondrial and microsatellite diversity in both sugarbird populations, with no detectable inbreeding and large effective population sizes.

scholarly journals Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico

2017 ◽  
Vol 60 (2) ◽  
pp. 137-143
Author(s):  
José Fernando Vázquez-Armijo ◽  
Gaspar Manuel Parra-Bracamonte ◽  
Miguel Abraham Velazquez ◽  
Ana María Sifuentes-Rincón ◽  
José Luis Tinoco-Jaramillo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
The Other ◽  
Genetic Integrity ◽  
Effective Population ◽  
South Central ◽  
Microsatellite Dna Markers ◽  
Quarter Horse ◽  
Population Sizes

Abstract. The South-Central region of Mexico has experienced a sizeable introduction of purebred horses for recreational aims. A study was designed to assess effective population sizes and genetic diversity and to verify the genetic integrity of four horse breeds. Using a 12-microsatellite panel, Quarter Horse, Azteca, Thoroughbred and Creole (CRL) horses were sampled and analysed for diversity and genetic structure. Genetic diversity parameters showed high numbers of heterozygous horses but small effective population sizes in all breeds. Population structure results suggested some degree of admixture of CRL with the other reference breeds. The highly informative microsatellite panel allowed the verification of diversity in introduced horse populations and the confirmation of small effective population sizes, which suggests a risk for future breed integrity.

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