scholarly journals Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus)

2019 ◽  
Author(s):  
Kyle A. O’Connell ◽  
Jamie R. Oaks ◽  
Amir Hamidy ◽  
Kyle J. Shaney ◽  
Nia Kurniawan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Demographic History ◽  
Volcanic Eruptions ◽  
Population Declines ◽  
Effective Population ◽  
Size Change ◽  
Forest Expansion ◽  
Target Capture ◽  
Full Likelihood

Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target-capture data (∼950 loci and ∼440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (∼80 kya). However, we infer a stronger signal of expansion in southern populations around ∼400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid-Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.

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 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 Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)

2019 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Sequencing Data ◽  
Effective Population ◽  
Genome Wide

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity of P.abies is low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

scholarly journals Conservation priorities in an endangered estuarine seahorse are informed by demographic history

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Thomas Kalama Mkare ◽  
Bettine Jansen van Vuuren ◽  
Peter R. Teske
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Demographic History ◽  
Conservation Status ◽  
Limited Range ◽  
The Other ◽  
Conservation Priorities ◽  
Population Declines ◽  
Term Survival

AbstractHistorical demographic events shape genetic diversity that remains evident in the genomes of contemporary populations. In the case of species that are of conservation concern, this information helps to unravel evolutionary histories that can be critical in guiding conservation efforts. The Knysna seahorse, Hippocampus capensis, is the world’s most endangered seahorse species, and it presently survives in only three estuaries on the South African south coast. Factors that contributed to the species becoming endangered are unclear; additionally, the lack of information on whether the three populations should be managed separately because of potential long-term isolation hampers effective management efforts. In the present study, we reconstructed the seahorses’ demographic history using a suite of microsatellite loci. We found that the largest population (Knysna Estuary) has colonised the other estuaries relatively recently (< 450 years ago), and that its population size is comparatively large and stable. Neither of the other two populations shows signs of long-term reductions in population size. The high conservation status of the species is thus a result of its limited range rather than historical population declines. Our findings indicate that the long-term survival of H. capensis depends primarily on the successful management of the Knysna population, although the other estuaries may serve as reservoirs of genetic diversity.

scholarly journals Population genetic structure of the Natterjack toad (Epidalea calamita) in Ireland: implications for conservation management

2021 ◽  
Author(s):  
Marina Reyne ◽  
Kara Dicks ◽  
Claire McFarlane ◽  
Aurélie Aubry ◽  
Mark Emmerson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Population Genetic ◽  
Species Conservation ◽  
Conservation Strategies ◽  
Population Declines ◽  
Effective Population ◽  
Genetic Structuring ◽  
Genetic Diversity And Structure ◽  
Epidalea Calamita

AbstractMolecular methods can play a crucial role in species management and conservation. Despite the usefulness of genetic approaches, they are often not explicitly included as part of species recovery plans and conservation practises. The Natterjack toad (Epidalea calamita) is regionally Red-Listed as Endangered in Ireland. The species is declining and is now present at just seven sites within a highly restricted range. This study used 13 highly polymorphic microsatellite markers to analyse the population genetic diversity and structure. Genetic diversity was high with expected heterozygosity between 0.55 and 0.61 and allelic richness between 4.77 and 5.92. Effective population sizes were small (Ne < 100 individuals), but not abnormal for pond breeding amphibians. However, there was no evidence of historical or contemporary genetic bottlenecks or high levels of inbreeding. We identified a positive relationship between Ne and breeding pond surface area, suggesting that environmental factors are a key determinant of population size. Significant genetic structuring was detected throughout the species’ range, and we identified four genetic entities that should be considered in the species’ conservation strategies. Management should focus on preventing further population declines and future loss of genetic diversity overall and within genetic entities while maintaining adequate local effective population size through site-specific protection, human-mediated translocations and head-start programs. The apparent high levels of genetic variation give hope for the conservation of Ireland’s rarest amphibian if appropriately protected and managed.

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 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.

scholarly journals Inferring the Demographic History of Japanese Eel (Anguilla japonica) from Genomic Data: Insights for Conservation and Fisheries Management

2021 ◽  
Author(s):  
Leanne Faulks ◽  
Prashant Kaushik ◽  
Shoji Taniguchi ◽  
Masashi Sekino ◽  
Reiichiro Nakamichi ◽  
...  
Keyword(s):  
Population Size ◽  
Environmental Conditions ◽  
Wildlife Conservation ◽  
Demographic History ◽  
Population Decline ◽  
Anguilla Japonica ◽  
Japanese Eel ◽  
Population Declines ◽  
Effective Population ◽  
History Of

Assessing the status or population size of species is a key task for wildlife conservation and the sustainable management of harvested species. In particular, assessing historical changes in population size provides an evolutionary perspective on current population dynamics and can help distinguish between anthropogenic and natural causes for population decline. Japanese eel (Anguilla japonica) is an endangered yet commercially important catadromous fish species. Here we assess the demographic history of Japanese eel using the pairwise and multiple sequentially Markovian coalescent methods. The analyses indicate a reduction in effective population size (Ne) from 38 000 to 10 000 individuals between 4 and 1 Ma, followed by an increase to 80 000 individuals, between 1 Ma and 22-30 kya. Approximately 22-30 kya there is evidence for a reduction in Ne to approximately 60 000 individuals. These events are likely due to changes in environmental conditions, such as sea level and oceanic currents, especially around the last glacial maximum (19-33 kya). The results of this study suggest that Japanese eel has experienced at least two population bottlenecks, interspersed by a period of population growth. This pattern of demographic history may make Japanese eel sensitive to current and future population declines. Conservation management of Japanese eel should focus on practical ways to prevent further population decline and the loss of genetic diversity that is essential for the species to adapt to changing environmental conditions such as climate change.

Elusive does not always equal rare: genetic assessment of a protected Gila monster (Heloderma suspectum) population in Saguaro National Park, Arizona

2017 ◽  
Vol 38 (1) ◽  
pp. 1-14 ◽  
Author(s):  
Victoria Sophia Farrar ◽  
Taylor Edwards ◽  
Kevin Edward Bonine
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
National Parks ◽  
Sonoran Desert ◽  
National Park ◽  
Sequence Data ◽  
Demographic History ◽  
Effective Population ◽  
Heloderma Suspectum

Population genetic baselines for species perceived to be at-risk are crucial for monitoring population trends and making well-informed management decisions. We characterized the genetic status of a population of Gila monsters (Heloderma suspectum), a large venomous lizard native to deserts of the southwestern United States and northern Mexico, by sampling 100 individuals in Sonoran Desert upland habitat at Saguaro National Park, Arizona, USA. We used 18 microsatellite markers, along with 1195 bp of sequence data from the mitochondrial DNA 12S locus, to examine genetic diversity, estimate effective population size, and assess demographic history. Despite suburban development adjacent to the study area, we observed high genetic diversity with uninhibited gene flow within this protected population. We estimated effective population size (Ne) for the total sample area (80 km2) using the linkage disequilibrium method in NeEstimator to be 94 individuals (95% confidence interval: 80.7-111.2). In 2011, we used capture-recapture methods to estimate that 80 adult Gila monsters (95% CI = 37-225) inhabited the area along the 14-km transect that we surveyed most frequently; probability of detecting resident Gila monsters during surveys was <0.01, highlighting the challenges of studying the species. Despite being considered an elusive and thus potentially rare species, these data reveal that in this protected environment the population appears healthy and robust. The results provide an important genetic baseline for future studies and monitoring, and exemplify the success of protective population measures in National Parks and under Arizona state laws.

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