scholarly journals Genetic Diversity and Relatedness among Captive African Painted Dogs in North America

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1463
Author(s):  
Cassandra M. Miller-Butterworth ◽  
Karen Vacco ◽  
Amy L. Russell ◽  
Joseph C. Gaspard
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Mhc Class Ii ◽  
Captive Breeding ◽  
Management Plan ◽  
Captive Population ◽  
Effective Population ◽  
Breeding Programs ◽  
Low Genetic Diversity ◽  
Population Size Estimates

African painted dogs (Lycaon pictus, APD) are highly endangered, with fewer than 7000 remaining in nature. Captive breeding programs can preserve a genetically diverse population and provide a source of individuals for reintroductions. However, most programs are initiated from few founders and suffer from low genetic diversity and inbreeding. The aims of this study were to use molecular markers to assess genetic variation, inbreeding, and relatedness among APDs in the North American captive population, to use these data to realign studbook records, and to compare these data to wild populations and to the European captive population to facilitate the development of a global management plan. We sequenced mitochondrial and major histocompatibility (MHC) class II loci and genotyped 14 microsatellite loci from 109 APDs from 34 institutions in North America. We identified three likely studbook errors and resolved ten cases of uncertain paternity. Overall, microsatellite heterozygosity was higher than reported in Europe, but effective population size estimates were lower. Mitochondrial sequence variation was extremely limited, and there were fewer MHC haplotypes than in Europe or the wild. Although the population did not show evidence of significant inbreeding overall, several individuals shared high relatedness values, which should be incorporated into future breeding programs.

scholarly journals Conservation Genetics and Gut Microbial Communities’ Variability of the Critically Endangered European Mink Mustela Lutreola: Implications for Captive Breeding Programs

2021 ◽  
Author(s):  
Pauline ML van Leeuwen ◽  
Albrecht I. Schulte-Hostedde ◽  
Christine Fournier-Chambrillon ◽  
Carmen M. Aranda ◽  
Laurie Berthomieu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gut Microbiota ◽  
Mhc Class I ◽  
Mhc Class Ii ◽  
Captive Breeding ◽  
Mustela Lutreola ◽  
Breeding Programs ◽  
European Mink ◽  
In Captivity ◽  
Captive Breeding Programs

Abstract Host’s fitness can be affected by its genotype and gut microbiota, defined as the microbes living in the host’s intestinal tract. This study explored how the genetic diversity of the host influences its bacterial communities in the context of captive breeding programs, for the critically endangered European mink (Mustela lutreola). As stated by the ecosystem on a leash model, loss of host genetic diversity may lead to changes in immunomodulation and will therefore induce modifications of the gut microbiota. We investigated variation in the gut bacteria through 16S rRNA metabarcoding, related to the genetic diversity of European mink held in captivity in two breeding centers representing separate breeding stocks originating from the western and eastern populations. The genetic diversity of the host was assessed through diversity analysis of the adaptive MHC class I and II genes as well as neutral microsatellite markers. Results indicate lower diversity in neutral and MHC class I genes for the western population, and the opposite for MHC class II. A lower MHC class II gene variability led to an increase in microbial phylogenetic diversity and in abundance depending on the presence of specific MHC-II motifs. Those results seem to be linked to management practices that differs between the two programs, especially the number of generations in captivity. Long term Ex situ conservation practices can thus modulate gut microbial communities, that might potentially have consequences on the survival of reintroduced animals. We suggest strategies to foster genetic diversity in captive breeding program to mitigate the effects of genetic drift on those small, isolated populations.

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, population structure, and effective population size in two yellow bat species in south Texas

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10348
Author(s):  
Austin S. Chipps ◽  
Amanda M. Hale ◽  
Sara P. Weaver ◽  
Dean A. Williams
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
North America ◽  
Wind Energy ◽  
Population Size ◽  
Effective Population Size ◽  
Microsatellite Loci ◽  
South Texas ◽  
Population Substructure ◽  
Effective Population

There are increasing concerns regarding bat mortality at wind energy facilities, especially as installed capacity continues to grow. In North America, wind energy development has recently expanded into the Lower Rio Grande Valley in south Texas where bat species had not previously been exposed to wind turbines. Our study sought to characterize genetic diversity, population structure, and effective population size in Dasypterus ega and D. intermedius, two tree-roosting yellow bats native to this region and for which little is known about their population biology and seasonal movements. There was no evidence of population substructure in either species. Genetic diversity at mitochondrial and microsatellite loci was lower in these yellow bat taxa than in previously studied migratory tree bat species in North America, which may be due to the non-migratory nature of these species at our study site, the fact that our study site is located at a geographic range end for both taxa, and possibly weak ascertainment bias at microsatellite loci. Historical effective population size (NEF) was large for both species, while current estimates of Ne had upper 95% confidence limits that encompassed infinity. We found evidence of strong mitochondrial differentiation between the two putative subspecies of D. intermedius (D. i. floridanus and D. i. intermedius) which are sympatric in this region of Texas, yet little differentiation using microsatellite loci. We suggest this pattern is due to secondary contact and hybridization and possibly incomplete lineage sorting at microsatellite loci. We also found evidence of some hybridization between D. ega and D. intermedius in this region of Texas. We recommend that our data serve as a starting point for the long-term genetic monitoring of these species in order to better understand the impacts of wind-related mortality on these populations over time.

Captive management and the maintenance of genetic diversity in a vulnerable marsupial, the greater bilby

2015 ◽  
Vol 37 (2) ◽  
pp. 170 ◽  
Author(s):  
Emily J. Miller ◽  
Mark D. B. Eldridge ◽  
Keith Morris ◽  
Neil Thomas ◽  
Catherine A. Herbert
Keyword(s):  
Genetic Diversity ◽  
Captive Breeding ◽  
Natural Habitat ◽  
Species Conservation ◽  
Molecular Data ◽  
Breeding Programs ◽  
Captive Populations ◽  
Genetic Impact ◽  
Captive Breeding Programs

The endemic Australian greater bilby (Macrotis lagotis) is a vulnerable and iconic species. It has declined significantly due to habitat loss, as well as competition and predation from introduced species. Conservation measures include a National Recovery Plan that incorporates several captive breeding programs. Two of these programs were established within 12 months of one another (1997/98), with the same number and sex ratio of founding individuals, but executed different breeding strategies: (1) unmanipulated mating in semi–free range natural habitat versus (2) minimising mean kinship in large enclosures, with the supplementation of new individuals into both populations. This study evaluates the long-term genetic impact of these programs and examines the congruency between the pedigree studbook estimates of diversity and molecular data. Our data demonstrate that genetic diversity was maintained in both populations, with the supplementation of new individuals contributing to the gene pool. The studbook estimates of diversity and inbreeding are not consistent with the microsatellite data and should not solely be relied upon to evaluate the genetic health of captive populations. Our analyses suggest that captive breeding programs may not require costly and intensive management to effectively maintain long-term genetic diversity in a promiscuous species.

Cryptic Lineages and a Population Dammed to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish

2019 ◽  
Vol 110 (5) ◽  
pp. 535-547 ◽  
Author(s):  
Amanda S Ackiss ◽  
Binh T Dang ◽  
Christopher E Bird ◽  
Ellen E Biesack ◽  
Phen Chheng ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Natural Populations ◽  
Principal Component ◽  
Flood Pulse ◽  
Mekong River ◽  
Effective Population ◽  
Long Distance ◽  
Genetic Lineages ◽  
Low Genetic Diversity ◽  
Population Size Estimates

Abstract An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller subpopulations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development—the Mekong River basin. Our results revealed the presence of 2 highly divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal component analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically important resources.

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.

Genetic diversity at the Major Histocompatibility Complex class II DZB gene, and geographical distribution of alleles, in platypuses in a Tasmanian river catchment.

2019 ◽  
Vol 40 (2) ◽  
pp. 241-250
Author(s):  
J.W. Macgregor ◽  
C. Holyoake ◽  
S. Munks ◽  
J.H. Connolly ◽  
I.D. Robertson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Major Histocompatibility Complex ◽  
Mhc Class Ii ◽  
Class Ii ◽  
Major Histocompatibility ◽  
Island Populations ◽  
Low Genetic Diversity ◽  
Histocompatibility Complex ◽  
Wildlife Populations ◽  
River Catchments

Genetic diversity at loci concerned with fitness is an important part of the ability of a wild population to adapt to changes in its environment, including climatic events, disease and pollution. Research into the effects of genetic diversity on the impacts of disease on wildlife populations has focussed on genes of the major histocompatibility complex (MHC). This study investigated the genetic diversity at the MHC class II DZB gene, as well as the distribution of alleles of the same gene, for platypuses Ornithorhynchus anatinus in the Seabrook Creek Catchment in northwest Tasmania. This study detected 10 previously identified alleles and two previously unreported alleles at the MHC Class II DZB locus in 18 platypuses from the Seabrook Creek Catchment. An additional sequence isolated from two individuals was consistent with a pseudogene. Alleles were reasonably well distributed geographically through the catchment, but there was evidence of a degree of isolation at one site. Consistent with evidence that smaller wildlife populations have relatively low genetic diversity, and that there is relatively slow gene flow between river catchments, the observed genetic diversity at the MHC Class II locus was lower than those in larger previously studied river catchments but higher than those in two island populations. Consequently, this population of platypuses may have a limited capacity to respond to new infectious challenges, such as the fungal disease mucormycosis.

scholarly journals Low genetic diversity contrasts with high phenotypic variability in heptaploidSpartina densiflorapopulations invading the Pacific coast of North America

2018 ◽  
Vol 8 (10) ◽  
pp. 4992-5007 ◽  
Author(s):  
Jesús M. Castillo ◽  
Blanca Gallego-Tévar ◽  
Enrique Figueroa ◽  
Brenda J. Grewell ◽  
Dominique Vallet ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Pacific Coast ◽  
Phenotypic Variability ◽  
Low Genetic Diversity ◽  
The Pacific

Nuclear and cytoplasmic genetic diversity reveals long-term population decline in Abies semenovii, an endemic fir of central Asia

2012 ◽  
Vol 42 (12) ◽  
pp. 2142-2152 ◽  
Author(s):  
Svetlana A. Semerikova ◽  
Martin Lascoux ◽  
Vladimir L. Semerikov
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Population Decline ◽  
Population Expansion ◽  
Nuclear Marker ◽  
Effective Population ◽  
Species Status ◽  
Siberian Fir ◽  
Low Genetic Diversity

The genus Abies is one of the largest conifer genera and many of the marginal species remain poorly characterized. Abies semenovii B. Fedtsch. is a rare mountain fir species from central Asia, and its species status is still disputed. We used both nuclear (allozymes and AFLP) and chloroplastic (cpSSR) markers to show that A. semenovii deserves to be considered as a species and that its low genetic diversity justifies more a proactive conservation policy. First, A. semenovii was significantly differentiated from the Siberian fir Abies sibirica Ledeb. and we did not detect gene flow between the two species. Second, A. semenovii has a very low nuclear genetic diversity, suggesting a prolonged restricted effective population size. Abies semenovii had low cpSSR diversity too but the identification of seven closely related haplotypes suggests that these mutations accumulated recently during a phase of population expansion. This agrees well with the palynological record and is in contrast with the situation observed in another rare Eurasian fir endemic to Kamchatka, Abies gracilis Kom., which was devoid of variation in cpSSRs but that also had a more substantial nuclear marker diversity than A. semenovii, thereby suggesting a more recent but less severe population bottleneck.

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