scholarly journals Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across the Indian subcontinent

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8482
Author(s):  
Supriya Bhatt ◽  
Suvankar Biswas ◽  
Krithi Karanth ◽  
Bivash Pandav ◽  
Samrat Mondol
Keyword(s):  
Population Structure ◽  
Indian Subcontinent ◽  
Demographic History ◽  
Regional Scale ◽  
Population Decline ◽  
Local Extinction ◽  
Panthera Pardus ◽  
Anthropogenic Pressures ◽  
Genetic Analyses ◽  
Extinction Probabilities

Background Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, Panthera pardus, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline. Methods We collected faecal samples from the Terai-Arc landscape of northern India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities. Results Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75–90% population decline between ∼120–200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India. Conclusions Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.

scholarly journals Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across Indian subcontinent

2019 ◽  
Author(s):  
Supriya Bhatt ◽  
Suvankar Biswas ◽  
Krithi K. Karanth ◽  
Bivash Pandav ◽  
Samrat Mondol
Keyword(s):  
Population Structure ◽  
Indian Subcontinent ◽  
Regional Scale ◽  
Population Decline ◽  
Ecological Monitoring ◽  
Panthera Pardus ◽  
Anthropogenic Pressures ◽  
Occupancy Modelling ◽  
Genetic Analyses ◽  
Large Carnivore

AbstractLarge carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, Panthera pardus, is probably the most widely distributed and adaptable large carnivore, still persisting in most of its’ historic range. However, we lack subspecies level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline. Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of north Indian landscapes, each with high genetic variation. Coalescent simulations with 13 microsatellite loci revealed a 75-90% population decline in between 120-200 years ago across India, possibly human induced. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in four sub-populations obtained from occupancy modelling of historic and current distribution of leopards in India. Our results confirm population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species, and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.

scholarly journals A globally threatened shark, Carcharias taurus, shows no population decline in South Africa

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Juliana D. Klein ◽  
Aletta E. Bester-van der Merwe ◽  
Matthew L. Dicken ◽  
Arsalan Emami-Khoyi ◽  
Kolobe L. Mmonwa ◽  
...  
Keyword(s):  
South Africa ◽  
Census Data ◽  
Demographic History ◽  
Conservation Status ◽  
Population Decline ◽  
Multilocus Genotype ◽  
Population Declines ◽  
Effective Population ◽  
Anthropogenic Pressures ◽  
Carcharias Taurus

Abstract Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark, Carcharias taurus (also known as the sandtiger or grey nurse shark), is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, we found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.

scholarly journals Insights into platypus population structure and history from whole-genome sequencing

2017 ◽  
Author(s):  
Hilary C. Martin ◽  
Elizabeth M. Batty ◽  
Julie Hussin ◽  
Portia Westall ◽  
Tasman Daish ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
De Novo ◽  
Demographic History ◽  
Population Decline ◽  
Egg Laying ◽  
Whole Genome ◽  
Data Set ◽  
Important Species

AbstractThe platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly-improved reference genome, we called over 6.7M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative amongst other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0×10−9/bp/generation (95% CI 4.1×10−9 − 1.2×10−8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

scholarly journals Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 338 ◽  
Author(s):  
Xue Zhang ◽  
Yuan-Huan Liu ◽  
Yue-Hua Wang ◽  
Shi-Kang Shen
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Population Decline ◽  
Population Expansion ◽  
Distribution Models ◽  
Recent Population Expansion

Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000–100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.

scholarly journals A globally threatened shark, Carcharias taurus, shows no population decline in South Africa

2020 ◽  
Author(s):  
Juliana D. Klein ◽  
Aletta E. Bester-van der Merwe ◽  
Matthew L. Dicken ◽  
Arsalan Emami-Khoyi ◽  
Kolobe L. Mmonwa ◽  
...  
Keyword(s):  
South Africa ◽  
Census Data ◽  
Demographic History ◽  
Conservation Status ◽  
Population Decline ◽  
Multilocus Genotype ◽  
Population Declines ◽  
Effective Population ◽  
Anthropogenic Pressures ◽  
Carcharias Taurus

AbstractKnowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark Carcharias taurus (also known as the sandtiger or grey nurse shark) is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, it was found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. Taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.

scholarly journals Microsatellite analysis reveals low genetic diversity in managed populations of the critically endangered gharial (Gavialis gangeticus) in India

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Surya Prasad Sharma ◽  
Mirza Ghazanfarullah Ghazi ◽  
Suyash Katdare ◽  
Niladri Dasgupta ◽  
Samrat Mondol ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Indian Subcontinent ◽  
Population Decline ◽  
Mitochondrial Control Region ◽  
Critically Endangered ◽  
Term Survival ◽  
Low Level ◽  
Genetic Status ◽  
In The Wild ◽  
Gavialis Gangeticus

AbstractThe gharial (Gavialis gangeticus) is a critically endangered crocodylian, endemic to the Indian subcontinent. The species has experienced severe population decline during the twentieth century owing to habitat loss, poaching, and mortalities in passive fishing. Its extant populations have largely recovered through translocation programmes initiated in 1975. Understanding the genetic status of these populations is crucial for evaluating the effectiveness of the ongoing conservation efforts. This study assessed the genetic diversity, population structure, and evidence of genetic bottlenecks of the two managed populations inhabiting the Chambal and Girwa Rivers, which hold nearly 80% of the global gharial populations. We used seven polymorphic nuclear microsatellite loci and a 520 bp partial fragment of the mitochondrial control region (CR). The overall mean allelic richness (Ar) was 2.80 ± 0.40, and the observed (Ho) and expected (He) heterozygosities were 0.40 ± 0.05 and 0.39 ± 0.05, respectively. We observed low levels of genetic differentiation between populations (FST = 0.039, P < 0.05; G’ST = 0.058, P < 0.05 Jost’s D = 0.016, P < 0.05). The bottleneck analysis using the M ratio (Chambal = 0.31 ± 0.06; Girwa = 0.41 ± 0.12) suggested the presence of a genetic bottleneck in both populations. The mitochondrial CR also showed a low level of variation, with two haplotypes observed in the Girwa population. This study highlights the low level of genetic diversity in the two largest managed gharial populations in the wild. Hence, it is recommended to assess the genetic status of extant wild and captive gharial populations for planning future translocation programmes to ensure long-term survival in the wild.

scholarly journals Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey

2016 ◽  
Vol 3 (2) ◽  
pp. 150250 ◽  
Author(s):  
Claudio Ottoni ◽  
Rita Rasteiro ◽  
Rinse Willet ◽  
Johan Claeys ◽  
Peter Talloen ◽  
...  
Keyword(s):  
Demographic History ◽  
Population Decline ◽  
Fifth Century ◽  
Seventh Century ◽  
Human Occupation ◽  
Dna Variation ◽  
Genetic Discontinuity ◽  
History Of ◽  
The City ◽  
Modern Sample

More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake.

scholarly journals Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator

2014 ◽  
Vol 281 (1795) ◽  
pp. 20141558 ◽  
Author(s):  
Marie Louis ◽  
Michael C. Fontaine ◽  
Jérôme Spitz ◽  
Erika Schlund ◽  
Willy Dabin ◽  
...  
Keyword(s):  
Population Structure ◽  
Mediterranean Sea ◽  
Environmental Changes ◽  
Demographic History ◽  
World Ocean ◽  
Ecological Niches ◽  
Morphological Divergence ◽  
Evolutionary Diversification ◽  
The Mediterranean ◽  
Population Demographic

Environmental conditions can shape genetic and morphological divergence. Release of new habitats during historical environmental changes was a major driver of evolutionary diversification. Here, forces shaping population structure and ecotype differentiation (‘pelagic’ and ‘coastal’) of bottlenose dolphins in the North-east Atlantic were investigated using complementary evolutionary and ecological approaches. Inference of population demographic history using approximate Bayesian computation indicated that coastal populations were likely founded by the Atlantic pelagic population after the Last Glacial Maxima probably as a result of newly available coastal ecological niches. Pelagic dolphins from the Atlantic and the Mediterranean Sea likely diverged during a period of high productivity in the Mediterranean Sea. Genetic differentiation between coastal and pelagic ecotypes may be maintained by niche specializations, as indicated by stable isotope and stomach content analyses, and social behaviour. The two ecotypes were only weakly morphologically segregated in contrast to other parts of the World Ocean. This may be linked to weak contrasts between coastal and pelagic habitats and/or a relatively recent divergence. We suggest that ecological opportunity to specialize is a major driver of genetic and morphological divergence. Combining genetic, ecological and morphological approaches is essential to understanding the population structure of mobile and cryptic species.

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