scholarly journals Population and conservation genomics of the world's rarest hyena species, the brown hyena (Parahyena brunnea)

2017 ◽  
Author(s):  
Michael Westbury ◽  
Stefanie Hartmann ◽  
Axel Barlow ◽  
Ingrid Wiesel ◽  
Viyanna Leo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Perceived Risk ◽  
Nuclear Dna ◽  
Conservation Status ◽  
Mammalian Species ◽  
Phylogeographic Structure ◽  
Risk Of Extinction ◽  
Nuclear Genomes ◽  
Brown Hyena

AbstractWith an estimated population size of less than 10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) has been listed as ‘near threatened’ by the IUCN. Despite this rank, studies involving DNA analyses of the brown hyena are limited. Little consideration has been focussed towards population structure within the brown hyena, which could provide valuable insights about its evolutionary history and aid in conservation efforts of the species. Here we report both mitochondrial and nuclear genomes of wild-caught brown hyena individuals from across southern Africa. Mitochondrial DNA shows little to no phylogeographic structure, whereas low-coverage nuclear genomes reveal several potential sub-populations. Moreover, we find that brown hyenas harbour the lowest genetic diversity for a species on both the mitochondrial and nuclear level when compared to a number of mammalian species for which such information is currently available. Our data also reveal that at least on the nuclear DNA level, this low diversity could be the result of a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene. Moreover, our findings also show that the correlation between genetic diversity and the perceived risk of extinction is not particularly strong, since many species with higher genetic diversity than the brown hyena are considered to be at greater risk of extinction. Taken together, our results have important implications for the conservation status and conservation approaches of the brown hyena.

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.

Population viability analysis of common marsupials, Didelphis marsupialis and Didelphis virginiana, in a scenario of constant loss of native vegetation

Mammalia ◽  
2020 ◽  
Vol 84 (5) ◽  
pp. 475-482
Author(s):  
Bárbara Cruz-Salazar ◽  
Lorena Ruiz-Montoya
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Forest Cover ◽  
Environmental Changes ◽  
Mammalian Species ◽  
Population Viability Analysis ◽  
Population Viability ◽  
Didelphis Virginiana ◽  
Metapopulation Dynamics ◽  
Viability Analysis

AbstractWe studied the population viability of two common marsupials, Didelphis marsupialis and Didelphis virginiana, based on field data and published ecological and genetic information. Using the VORTEX v. 10. 2.6 program, a 100-year simulation was performed with 1000 iterations for five populations of D. marsupialis and six of D. virginiana. A low probability of extinction was observed in both species, particularly for D. virginiana (0.000–0.007). Population size is higher considering a metapopulation dynamics approach versus individual populations for the two marsupials: 498.25 individuals for D. marsupialis and 367.41 individuals for D. virginiana. The estimated mean genetic diversity was high for both D. marsupialis (He = 0.77–0.78) and D. virginiana (He = 0.79–0.82). The survival of both species over time could be expected to increase if a metapopulation dynamics is favored over the coming decades, despite a 1.3% loss rate of forest cover. The monitoring of population size and genetic diversity is highly recommended to validate the trends suggested by the model; this is especially true for D. marsupialis, a species associated with conserved areas that are becoming progressively less abundant. This research provides information on the responses of common mammalian species to environmental changes such as deforestation.

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 Conservation biology of threatened Mediterranean chasmophytes: The case of Asperula naufraga endemic to Zakynthos island (Ionian islands, Greece)

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246706 ◽  
Author(s):  
Anna-Thalassini Valli ◽  
Vassiliki Lila Koumandou ◽  
Gregoris Iatrou ◽  
Marios Andreou ◽  
Vasileios Papasotiropoulos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Extinction Risk ◽  
Conservation Status ◽  
Small Population ◽  
Ex Situ ◽  
Current Conservation ◽  
Ionian Islands ◽  
Small Population Size ◽  
Area Of Occupancy

Asperula naufraga is a rare and threatened obligate chasmophyte, endemic to Zakynthos island (Ionian islands, Greece). In this study, we provide a combined approach (including monitoring of demographic and reproductive parameters and study of genetic diversity) to assess the current conservation status of the species and to estimate its future extinction risk. The five subpopulations of A. naufraga were monitored for five years (2014–2018). Population size markedly fluctuated between 68–130 mature individuals during the monitoring period. The extent of occurrence (EOO) was estimated at 28.7 km2 and the area of occupancy (AOO) was 8 km2. Stage-structure recordings were similar for all subpopulations, characterized by high proportions of adult and senescent individuals, following a common pattern, which has been observed in other cliff-dwelling plants. Preliminary genetic analysis with SSRs markers revealed low heterozygosity within subpopulations and significant departure from H-W equilibrium, which combined with small population size suggest increased threat of genetic diversity loss. Our results indicate that the species should be placed in the Critically Endangered (CR) IUCN threat category, while according to Population Viability Analysis results its extinction risk increases to 47.8% in the next 50 years. The small population size combined with large fluctuations in its size, low recruitment and low genetic diversity, indicate the need of undertaking effective in situ and ex situ conservation measures.

scholarly journals Population genetics and phylogeography of Tabanus bromius (Diptera: Tabanidae)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sumeyra Nur Sanal Demirci ◽  
Volkan Kilic ◽  
Serap Mutun ◽  
A. Yavuz Kilic
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Population Expansion ◽  
Its Region ◽  
Early Pleistocene ◽  
Phylogeographic Structure ◽  
The Past ◽  
Haplotype Allele

Abstract Background Tabanus bromius (Diptera: Tabanidae) is one of the most notable Tabanidae species of veterinary and medical importance distributed throughout the Palearctic region. In this study, we investigate the genetic diversity and the phylogeographic structure of T. bromius sampled from Turkey, Croatia, and Iran. Methods For this purpose, a 686-base-pair (bp) fragment of mitochondrial DNA cytochrome oxidase I gene (COI) and 1339 bp of the nuclear DNA internal transcribed spacer (ITS) were sequenced from 247 individuals representing 15 populations. Results The sequences generated 169 COI haplotypes and 90 ITS alleles. A higher haplotype/allele diversity (h = 0.9909 for the COI gene and Ad = 0.8193 for the ITS region) compared to a low nucleotide diversity (π = 0.020605 for COI gene and π = 0.013667 for the ITS region), present for a high number of singleton and private haplotypes/alleles imply population expansion in the past. The results of phylogenetic analysis led to the uncovering of geographically significant groupings of lineages with regard to the entrance of the species into Anatolia and the location of major geographic barriers. According to current data, the species appears to have entered Turkey from Caucasia and Iran. A molecular clock applied to the COI data suggests that T. bromius diverged from the outgroup species nearly 8.83 million years ago, around the end of the Miocene era. Conclusions The results of this study indicate remarkable genetic diversity across the studied range of the species. High haplotype/allele versus low nucleotide diversity and demographic analyses implied that the T. bromius populations have undergone a series of expansions and retreats in the past. Our current findings suggest that T. bromius split from outgroups around the Late Miocene. Subsequent diversification events during the climatic and environmental fluctuation times of the Late Pliocene and Early Pleistocene periods also significantly influenced the species, resulting in the formation of some major genetic lineages. The phylogenetic analyses indicate that T. bromius most likely entered Turkey from the Caucasus region and Iran. Graphical Abstract

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 Giant otter Pteronura brasiliensis density and abundance in Llanos Orientales de Colombia in the Orinoco basin

Oryx ◽  
2020 ◽  
pp. 1-4
Author(s):  
Germán Garrote ◽  
Beyker Castañeda ◽  
Jose Manuel Escobar ◽  
Laura Pérez ◽  
Brayan Marín ◽  
...  
Keyword(s):  
South America ◽  
Population Size ◽  
20Th Century ◽  
Conservation Status ◽  
Species Conservation ◽  
Iucn Red List ◽  
Red List ◽  
Recreational Fishing ◽  
Pteronura Brasiliensis ◽  
Direct Counts

Abstract The giant otter Pteronura brasiliensis, categorized as Endangered on the IUCN Red List, was once widely distributed throughout South America. By the middle of the 20th century the giant otter had become locally extinct along the main rivers of the Orinoco basin. Although some populations seem to have recovered, the paucity of information available does not permit a full evaluation of the species' conservation status. The objective of this study was to estimate the abundance and density of the giant otter population along the Orinoco river in the municipality of Puerto Carreño, Vichada, Colombia, where there is important commercial and recreational fishing. Thirty-nine linear km were surveyed, repeatedly, with a total of 315 km of surveys. Population size was estimated by direct counts of individuals. All individuals detected were photographed and identified individually from their throat pelage patterns. In total, 30 otters were identified, giving a minimum density of 0.77 individuals per km, one of the highest reported for the species in Colombia. Given the high density in this well-developed area, our results highlight the importance of this population for the conservation of the species.

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