scholarly journals Low diversity, little genetic structure but no inbreeding in a high density island endemic pit-viper Gloydius shedaoensis

2021 ◽  
Author(s):  
Guannan Wen ◽  
Long Jin ◽  
Yayong Wu ◽  
Xiaoping Wang ◽  
Jinzhong Fu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Size ◽  
Demographic History ◽  
Iucn Red List ◽  
Conservation Priorities ◽  
Important Species ◽  
Island Endemic ◽  
Island Species ◽  
Low Genetic Diversity

Abstract Islands species and their ecosystems play an important role in global biodiversity preservation, and many vulnerable island species are conservation priorities. Although insular habitat likely facilitates the species diversification process, it may also aggravate the fragility of these species with high risk of inbreeding. The Shedao pit-viper Gloydius shedaoensis is an island endemic species with an extremely high population density, which has been categorized as vulnerable in the IUCN Red List. We collected 13,148 SNP from across its genome and examined its genetic diversity and demographic history. The Shedao pit-viper has a low genetic diversity but shows no sign of inbreeding. Furthermore, population genetic structure analysis, including the NJ tree, PCoA, clustering, and spatial autocorrelation, revealed a general lack of spatial structure. Only the IBD residues suggested a weak patchiness. Overall, the population is nearly panmictic and gene flow is evenly distributed across the island. The large number of individuals, small size of the island, and the lack of population structure likely all contribute to the lack of inbreeding in this species. We also detected signs of male-biased dispersal, which likely is another inbreeding avoidance strategy. Historical demographic analysis suggested that the historical population size and distribution of the species are much larger than their current ones. The multiple transgressive-regressive events since the Late Pleistocene are likely the main cause of the population size changes. Taken together, our results provide a basic scientific foundation for the conservation of this interesting and important species.

scholarly journals Demographic decline and lineage-specific adaptations characterize New Zealand kiwi

2021 ◽  
Vol 288 (1965) ◽  
Author(s):  
Jordan B. Bemmels ◽  
Else K. Mikkelsen ◽  
Oliver Haddrath ◽  
Rogan M. Colbourne ◽  
Hugh A. Robertson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Size ◽  
Genetic Drift ◽  
Demographic History ◽  
Small Population ◽  
Population Declines ◽  
Demographic Stochasticity ◽  
Fragmented Populations ◽  
Low Genetic Diversity

Small and fragmented populations may become rapidly differentiated due to genetic drift, making it difficult to distinguish whether neutral genetic structure is a signature of recent demographic events, or of long-term evolutionary processes that could have allowed populations to adaptively diverge. We sequenced 52 whole genomes to examine Holocene demographic history and patterns of adaptation in kiwi ( Apteryx ), and recovered 11 strongly differentiated genetic clusters corresponding to previously recognized lineages. Demographic models suggest that all 11 lineages experienced dramatic population crashes relative to early- or mid-Holocene levels. Small population size is associated with low genetic diversity and elevated genetic differentiation ( F ST ), suggesting that population declines have strengthened genetic structure and led to the loss of genetic diversity. However, population size is not correlated with inbreeding rates. Eight lineages show signatures of lineage-specific selective sweeps (284 sweeps total) that are unlikely to have been caused by demographic stochasticity. Overall, these results suggest that despite strong genetic drift associated with recent bottlenecks, most kiwi lineages possess unique adaptations and should be recognized as separate adaptive units in conservation contexts. Our work highlights how whole-genome datasets can address longstanding uncertainty about the evolutionary and conservation significance of small and fragmented populations of threatened species.

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 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 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 Genetic structure of island and mainland populations of a Neotropical bumble bee species

2015 ◽  
Author(s):  
Flavio O Francisco ◽  
Leandro R Santiago ◽  
Yuri M Mizusawa ◽  
Benjamin P Oldroyd ◽  
Maria C Arias
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Biodiversity Loss ◽  
Urban Environments ◽  
Dispersal Ability ◽  
Bumble Bee ◽  
Island Species ◽  
Low Genetic Diversity ◽  
High Dispersal ◽  
Bombus Morio

Biodiversity loss is a global problem and island species/populations are particularly vulnerable to such loss. Low genetic diversity is one of the factors that can lead a population to extinction. Loss of bee populations is of particular concern because of the knock-on consequences for the pollination guilds that the lost bees once serviced. Here we evaluate the genetic structure of the bumble beeBombus moriopopulations on the mainland of South East Brazil and on nearby islands. We analyzed a total of 659 individuals from 24 populations by sequencing two mitochondrial genes (COI and Cytb) and using 14 microsatellite loci. Levels of diversity were high in most of populations and were similar on islands and the mainland. Furthermore, genetic diversity was not significantly correlated with island area, although it was lower in populations from distant islands. Our data suggest that long-term isolation on islands is not affecting the population viability of this species. This may be attributed to the high dispersal ability ofB. morio, its capacity to suvive in urban environments, and the characteristics of the studied islands.

scholarly journals Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies)

2020 ◽  
Vol 12 (2) ◽  
pp. 3803-3817 ◽  
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 ◽  
Neutral Theory ◽  
Effective Population ◽  
Low Genetic Diversity

Abstract Under the neutral theory, species with larger effective population size are expected to harbor 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 resequencing 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 corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring 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 European Colonization, Not Polynesian Arrival, Impacted Population Size and Genetic Diversity in the Critically Endangered New Zealand Kākāpō

2016 ◽  
Vol 107 (7) ◽  
pp. 593-602 ◽  
Author(s):  
Laura M. Bergner ◽  
Nicolas Dussex ◽  
Ian G. Jamieson ◽  
Bruce C. Robertson
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Population Size ◽  
Demographic History ◽  
Critically Endangered ◽  
Museum Specimens ◽  
Human Settlement ◽  
Island Endemic ◽  
Population Size Estimates ◽  
European Colonization

Abstract Island endemic species are often vulnerable to decline and extinction following human settlement, and the genetic study of historical museum specimens can be useful in understanding these processes. The kākāpō (Strigops habroptilus) is a critically endangered New Zealand parrot that was formerly widespread and abundant. It is well established that both Polynesian and European colonization of New Zealand impacted the native avifauna, but the timeframe and severity of impacts have differed depending on species. Here, we investigated the relative importance of the 2 waves of human settlement on kākāpō decline, using microsatellites and mitochondrial DNA (mtDNA) to characterize recent kākāpō genetic and demographic history. We analyzed samples from 49 contemporary individuals and 54 museum specimens dating from 1884 to 1985. Genetic diversity decreased significantly between historical and contemporary kākāpō, with a decline in mean number of microsatellite alleles from 6.15 to 3.08 and in number of mtDNA haplotypes from 17 to 3. Modeling of demographic history indicated a recent population bottleneck linked to the period of European colonization (approximately 5 generations ago) but did not support a major decline linked to Polynesian settlement. Effective population size estimates were also larger for historical than contemporary kākāpō. Our findings inform contemporary kākāpō management by indicating the timeframe and possible cause of the bottleneck, which has implications for the management of extant genetic diversity. We demonstrate the broader utility of a historical perspective in understanding causes of decline and managing extinction risk in contemporary endangered species.

scholarly journals Low effective population size and high spatial genetic structure of black poplar populations from the Oder valley in Poland

2021 ◽  
Vol 78 (2) ◽  
Author(s):  
Błażej Wójkiewicz ◽  
Andrzewj Lewandowski ◽  
Weronika B. Żukowska ◽  
Monika Litkowiec ◽  
Witold Wachowiak
Keyword(s):  
Genetic Structure ◽  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Demographic History ◽  
River Valley ◽  
Ex Situ ◽  
Effective Population ◽  
Black Poplar

Abstract Context Black poplar (Populus nigra L.) is a keystone species of European riparian ecosystems that has been negatively impacted by riverside urbanization for centuries. Consequently, it has become an endangered tree species in many European countries. The establishment of a suitable rescue plan of the remaining black poplar forest stands requires a preliminary knowledge about the distribution of genetic variation among species populations. However, for some parts of the P. nigra distribution in Europe, the genetic resources and demographic history remain poorly recognized. Aims Here, we present the first study on identifying and characterizing the genetic resources of black poplar from the Oder valley in Poland. This study (1) assessed the genetic variability and effective population size of populations and (2) examined whether gene flow is limited by distance or there is a single migrant pool along the studied river system. Methods A total of 582 poplar trees derived from nine black poplar populations were investigated with nuclear microsatellite markers. Results (1) The allelic richness and heterozygosity level were high and comparable between populations. (2) The genetic structure of the studied poplar stands was not homogenous. (3) The signatures of past bottlenecks were detected. Conclusion Our study (1) provides evidence for genetic substructuring of natural black poplar populations from the studied river catchment, which is not a frequent phenomenon reported for this species in Europe, and (2) indicates which poplar stands may serve as new genetic conservation units (GCUs) of this species in Europe. Key message The genetic resources of black poplar in the Oder River valley are still substantial compared to those reported for rivers in Western Europe. On the other hand, clear signals of isolation by distance and genetic erosion reflected in small effective population sizes and high spatial genetic structure of the analyzed populations were detected. Based on these findings, we recommend the in situ and ex situ conservation strategies for conserving and restoring the genetic resources of black poplar populations in this strongly transformed by human river valley ecosystem.

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 Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 361 ◽  
Author(s):  
Shuqi Diao ◽  
Shuwen Huang ◽  
Zhiting Xu ◽  
Shaopan Ye ◽  
Xiaolong Yuan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Conservation Status ◽  
Snp Array ◽  
Size Analysis ◽  
Selection Signatures ◽  
Effective Population ◽  
Low Genetic Diversity ◽  
Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

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