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 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.

Genetic Diversity Within and Among Populations of Shorea Robusta Roxb. Ex Gaertn. In Bangladesh and Its Implications for Conservation

2021 ◽  
Vol 50 (2) ◽  
pp. 405-412
Author(s):  
Pragga Saha Sharmi ◽  
Md Abul Kashem ◽  
Rifat Samad ◽  
Mohammad Zabed Hossain
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Isolation By Distance ◽  
Genetic Erosion ◽  
Mantel Test ◽  
Small Population ◽  
Deciduous Forests ◽  
Shorea Robusta ◽  
Low Genetic Diversity ◽  
Geographical Regions

Fragmentation and reduction of natural population size render threats to the conservation of forest resources through depletion of genetic diversity. Hence, information on genetic structure of Sal (Shorea robusta Roxb. ex Gaertn.) populations is relevant for proper management and conservation of the tropical deciduous forests. The present study focused on assessing the genetic diversity of the populations of Sal which was the dominant tree species of the deciduous forests of Bangladesh. Plant leaf samples were collected from the three populations of Sal distributed in the three geographical regions including Madhupur tract in the districts Tangail and Gazipur and that of the districts of Cumilla and Dinajpur. DNA band profiles were generated using eight ISSR primers for a total of 13 samples taken from the three populations. Statistical analysis was done using PopGen 32 and GenAlEx 6.5 softwares. Principal coordinate analysis done on the DNA band profiles revealed that Sal populations of Madhupur tract and Cumilla positioned nearby while Dinajpur showed maximum genetic distance with that of Cumilla. Mantel test showed significant (p=0.05) correlation between genetic and geographic distances indicating “Isolation by Distance”. Data of the present study indicated higher genetic polymorphism (68.87%) in the Sal population of Madhupur tract compared to other two populations. Small population size of Sal of Dinajpur forest might be related with its low genetic diversity. Data of the present study suggest immediate attention for the conservation of Sal forests in Bangladesh before further genetic erosion occurs. Bangladesh J. Bot. 50(2): 405-412, 2021 (June)

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 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 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.

Genetic signature of disease epizootic and reintroduction history in an endangered carnivore

2020 ◽  
Vol 101 (3) ◽  
pp. 779-789
Author(s):  
Payton Phillips ◽  
Travis M Livieri ◽  
Bradley J Swanson
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Emerging Infectious Diseases ◽  
Allelic Diversity ◽  
Population Declines ◽  
Effective Population ◽  
Mustela Nigripes ◽  
Low Genetic Diversity ◽  
Loss Of Genetic Diversity ◽  
Susceptible Populations

Abstract Emerging infectious diseases have recently increased in wildlife and can result in population declines and the loss of genetic diversity in susceptible populations. As populations of impacted species decline, genetic diversity can be lost, with ramifications including reduced effective population size and increased population structuring. For species of conservation concern, which may already have low genetic diversity, the loss of genetic diversity can be especially important. To investigate the impacts of a novel pathogen on genetic diversity in a genetically depauperate endangered species, we assessed the ramifications of a sylvatic plague-induced bottleneck in black-footed ferrets (Mustela nigripes). Following a plague epizootic, we genotyped 184 ferrets from Conata Basin and Badlands National Park, South Dakota, at seven microsatellite loci. We compared our results to pre-plague studies in the same population. We observed population substructuring into three genetic clusters. These clusters reflect founder effects from ferret reintroduction events followed by genetic drift. Compared to the pre-plague population, we observed losses of allelic diversity in all clusters, as well as significantly reduced heterozygosity in one cluster. These results indicate that disease epizootics may reduce population size and also genetic diversity. Our results suggest the importance of early and sustained management in mitigating disease epizootics in naïve populations for the maintenance of genetic diversity.

Life history and genetic diversity in red pine: implications for gene conservation in forestry

1992 ◽  
Vol 68 (6) ◽  
pp. 701-708 ◽  
Author(s):  
A. Mosseler
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Ecology ◽  
Tree Species ◽  
Small Population ◽  
Red Pine ◽  
Gene Conservation ◽  
Population Declines ◽  
Demographic Stochasticity ◽  
Ecological Stability

Red pine, Pinus resinosa Ait., is a suffusively rare species throughout its geographical range, occurring as small, highly fragmented populations. Such species are particularly vulnerable to the genetic and demographic stochasticity that can lead to local extinction and losses of genetic variation. Red pine illustrates the difficulty that species with long generation times have in recovering genetic diversity once it has been lost. Tree species that lose their genetic diversity may not recover the genetic variation required for effective adaptive responses to environmental challenges. Population declines in rare tree species should be viewed with greater concern by forest managers because the loss of a tree species threatens ecological stability and future economic potential in areas of limited biodiversity. Newfoundland's red pine population provides an example for a broader discussion of concepts in population ecology and genetics useful in developing gene conservation efforts for tree populations characterized by fragmented distributions, small population sizes, and declining population numbers. Key words: population ecology, genetic diversity, gene conservation, metapopulation, reproductive success

Evolutionary genetics of small populations

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Evolutionary Genetics ◽  
Small Population ◽  
Small Populations ◽  
Effective Population ◽  
Genetic Management ◽  
Evolutionary Genetic ◽  
Loss Of Genetic Diversity ◽  
Number Of Individuals

Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift) and gene flow (migration). Large outbreeding, sexually reproducing populations typically contain substantial genetic diversity, while small populations typically contain reduced levels. Genetic impacts of small population size on inbreeding, loss of genetic diversity and population differentiation are determined by the genetically effective population size, which is usually much smaller than the number of individuals.

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.

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