Current genetic conservation of Chinese indigenous horses revealed with Y-chromosomal and mitochondrial DNA polymorphisms

Abstract To investigate the genetic diversity of Chinese indigenous horses and determine the genetic status of extant horse breeds, novel Y chromosomal microsatellite markers and known Y chromosomal SNPs and mtDNA loop sequences, were employed to study the genetic diversity levels of 13 Chinese indigenous horse populations and four introduced breeds. Sixteen Y-chromosomal microsatellite markers, including seven newly identified loci, were used in the genotyping. The results showed that 4 out of the 16 loci were highly polymorphic in Chinese indigenous horse populations, in which the polymorphisms of 3 loci, ECAYP12, ECAYP13, and ECAYCAU3, were first reported in the present study. The polymorphic Y chromosomal microsatellite markers result in 19 haplotypes in the studied horses and formed 24 paternal lines when merged with the 14 Y chromosomal SNPs reported previously. The haplotypes CHT18 and SS24 harboring AMELY gene mutation were the ancestral haplotypes, and other haplotypes were derived from them by one or more mutation steps. The horse populations in mountainous and remote areas of southwestern China have the most ancient paternal lines, which suggests that ancient paternal lines preserved in local populations attributed to less human interventions. Our results also showed that the northern local breeds had higher mtDNA diversity than the southern ones in China. The frequency of haplogroup B, F, and G of mtDNA in Chinese indigenous horses has declined in recent years, and some breeds are in endangered status mainly due to small population sizes. Urgent actions should be taken to conserve the genetic diversity of the indigenous horse populations, especially the rare paternal lines. Our findings help to elucidate the genetic diversity and evolutionary history of Chinese domestic horses, which will facilitate the conservation of the indigenous horses in the future.

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Genetic Diversities and Historical Dynamics of Native Ethiopian Horse Populations (Equus caballus) Inferred from Mitochondrial DNA Polymorphisms

Genes ◽

10.3390/genes12020155 ◽

2021 ◽

Vol 12 (2) ◽

pp. 155

Author(s):

Kefena Effa ◽

Sonia Rosenbom ◽

Jianlin Han ◽

Tadelle Dessie ◽

Albano Beja-Pereira

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Genetic Differentiation ◽

Sequence Divergence ◽

Dna Polymorphisms ◽

Base Pairs ◽

Feral Horses ◽

Domestic Horses ◽

D Loop ◽

Diversity Estimates

Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA D-loop sequences were characterized by 15 variable sites that defined five different haplotypes. All genetic diversity estimates, including Reynolds’ linearized genetic distance, genetic differentiation (FST) and nucleotide sequence divergence (DA), revealed a low genetic differentiation in native Ethiopian horse populations. However, Kundido feral and Borana domestic horses were slightly diverged from the rest of the Ethiopian horse populations. We also tried to shed some light on the matrilineal genetic root of native Ethiopian horses from a network constructed by combining newly generated haplotypes and reference haplotypes deposited in the GenBank for Eurasian type Turkish Anatolian horses that were used as a genetic conduit between Eurasian and African horse populations. Ninety-two haplotypes were generated from the combined Ethio-Eurasian mtDNA D-loop sequences. A network reconstructed from the combined haplotypes using Median-Joining algorithm showed that haplotypes generated from native Ethiopian horses formed separate clusters. The present result encourages further investigation of the genetic origin of native African horses by retrieving additional mtDNA sequences deposited in the GenBank for African and Eurasian type horses.

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One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species

Frontiers in Plant Science ◽

10.3389/fpls.2021.730258 ◽

2021 ◽

Vol 12 ◽

Author(s):

Thais M. Teixeira ◽

Alison G. Nazareno

Keyword(s):

Genetic Diversity ◽

Missing Data ◽

Plant Species ◽

Threatened Species ◽

Demographic History ◽

Small Population ◽

Narrow Endemic ◽

Population Genomic ◽

Genomic Study ◽

History Of

Intraspecific genetic variation plays a fundamental role in maintaining the evolutionary potential of wild populations. Hence, the assessment of genetic diversity patterns becomes essential to guide biodiversity conservation policies, particularly for threatened species. To inform management strategies for conservation of Mimosa catharinensis – a narrow endemic, critically endangered plant species – we identified 1,497 unlinked SNP markers derived from a reduced representation sequencing method (i.e., double digest restriction site associated DNA sequencing, or ddRADseq). This set of molecular markers was employed to assess intrapopulation genetic parameters and the demographic history of one extremely small population of M. catharinensis (N=33) located in the Brazilian Atlantic Forest. Contrary to what is expected for narrow endemic and threatened species with small population sizes, we observed a moderate level of genetic diversity for M. catharinensis [uHE(0%missing data)=0.205, 95% CI (0.160, 0.250); uHE(30%missing data)=0.233, 95% CI (0.174, 0.292)]. Interestingly, M. catharinensis, which is a lianescent shrub with no indication of seed production for at least two decades, presented high levels of outcrossing [t(0%missing data)=0.883, SE±0.0483; t(30%missing data)=0.909, SE±0.011] and an apparent absence of inbreeding [F(0%missing data)=−0.145, 95% CI (−0.189, −0.101); F(30%missing data)=−0.105, 95% CI (−0.199, −0.011)]. However, the reconstruction of demographic history of M. catharinensis indicated that the population should be suffered a recent bottleneck. Our population genomic study tackles a central issue in evolution and conservation biology and we expect that it will be useful to help safeguard the remaining genetic diversity reported for this unique genetic resource.

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Genetic diversity of seeds from four German Douglas fir (Pseudotsuga menziesii) seed orchards

European Journal of Forest Research ◽

10.1007/s10342-021-01419-3 ◽

2021 ◽

Author(s):

Birte Pakull ◽

Pascal Eusemann ◽

Janine Wojacki ◽

Diana Ahnert ◽

Heike Liesebach

Keyword(s):

Genetic Diversity ◽

Pseudotsuga Menziesii ◽

Seed Orchard ◽

Small Population ◽

Douglas Fir ◽

Next Generation ◽

Seed Orchards ◽

Population Sizes ◽

Spatial Isolation ◽

Offspring Generation

AbstractIn Germany, Douglas fir (Pseudotsuga menziesii Franco) is seen as a valuable species for future cultivation in times of climate change. Local seed production in seed stands and seed orchards may secure that local adaptation is transferred to the next generation, but small population sizes could lower genetic diversity and thus future adaptability. Here we analyse the transfer of genetic diversity from parent to offspring generation in four older German seed orchards. We detected low pollen contamination rates due to high levels of spatial isolation. Even with a relatively low number of 40 clones, seed orchard design with randomized and repeated planting of clones led to low selfing rates, and despite uneven parental contributions, the number of successful parents and the level of genetic intermixture were high enough to allow the transfer of an adequate part of the genetic diversity to the next generation. Larger numbers, however, might be needed to reliably conserve the entire genetic diversity over succeeding generations. Conclusions on the establishment of future seed orchards and regarding areas requiring further research are drawn at the end of the paper.

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Classification of Genus Acanthopanax in Korea and Genetic Diversity Using Allozymes

Silvae Genetica ◽

10.1515/sg-2005-0030 ◽

2005 ◽

Vol 54 (1-6) ◽

pp. 206-210 ◽

Cited By ~ 2

Author(s):

M. K. Huh ◽

H. W. Huh

Keyword(s):

Genetic Diversity ◽

Representative Sample ◽

Genetic Relationships ◽

Woody Species ◽

Small Population ◽

Geographic Ranges ◽

Low Level ◽

Low Genetic Diversity ◽

Population Sizes

Abstract Genus Acanthopanax is a long-lived woody species that is primarily distributed throughout Asia. Many species of this genus are regarded as medically and ecologically important. We evaluated a representative sample of the nine taxa with allozymes to estimate genetic relationships within the genus. As some Korean populations were isolated and patchily distributed, they exhibited a low level of genetic diversity. The narrow geographic ranges, artificial distribution of habitats, and small population sizes are proposed as factors contributing to low genetic diversity. Acanthopanax seoulense was similar to A. sessiliflorus, while a cluster of the A. rufinerve population is distant from any other species. A. senticosus is closely related to A. seoulense and A. sessiliflorus, whereas other species (A. koreanum) are more distinct from the Korean populations. Korean species are clustered together and clearly differentiated from the Chinese and Russian Acanthopanax taxa, genus Acanthopanax

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Genetics of reintroduced populations of the narrowly endemic thistle, Cirsium pitcheri (Asteraceae)

Botany ◽

10.1139/cjb-2012-0232 ◽

2013 ◽

Vol 91 (5) ◽

pp. 301-308 ◽

Cited By ~ 12

Author(s):

Jeremie B. Fant ◽

Andrea Kramer ◽

Eileen Sirkin ◽

Kayri Havens

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Empirical Studies ◽

Small Population ◽

Native Plant ◽

Effective Population ◽

Term Survival ◽

Inbreeding Coefficients ◽

Native Populations ◽

Population Sizes

The aim of any reintroduction is to provide sufficient genetic variability to buffer against changing selection pressures and ensure long-term survival. To date, few empirical studies have compared levels of genetic diversity in reintroduced and native plant populations. Using microsatellite markers, we measured the genetic diversity within reintroduced and native populations of the threatened Cirsium pitcher (Eaton) Torrey and Gray. We found that the use of local mixed source was successful in establishing populations with significantly higher genetic diversity (P < 0.005) than the native populations (allelic richness is 3.39 in reintroduced and 1.84 in native populations). However, the reintroduced populations had significantly higher inbreeding coefficients (P < 0.002) (FIS is 0.405 and 0.213 in reintroduced and in native populations, respectively), despite having multiple genetic founders, population sizes equivalent to native populations and a positive growth rate. These results may be due to inbreeding or the Wahlund effect, driven by genetic substructuring. This suggests that the small population size of these reintroduced populations may lead to genetic issues in the future, given the low number of flowering individuals each year. This highlights the importance of considering not only the number of source individuals but the effective population size of the reintroduction.

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More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2010.0096 ◽

2010 ◽

Vol 365 (1556) ◽

pp. 3277-3288 ◽

Cited By ~ 53

Author(s):

Anne C. Stone ◽

Fabia U. Battistuzzi ◽

Laura S. Kubatko ◽

George H. Perry ◽

Evan Trudeau ◽

...

Keyword(s):

Demographic History ◽

Time Estimation ◽

Divergence Times ◽

Effective Population ◽

Founding Population ◽

Time Estimates ◽

Population Structures ◽

Population Sizes ◽

History Of ◽

Mtdna Diversity

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees ( Pan troglodytes ) from each of the three established subspecies ( P. t. troglodytes , P. t. schweinfurthii and P. t. verus ) and the proposed fourth subspecies ( P. t. ellioti ). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human–chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1–1.5, 1.1–0.76 and 0.25–0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.

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Low genetic diversity and inbreeding depression in Queensland Koalas

Wildlife Research ◽

10.1071/wr9930177 ◽

1993 ◽

Vol 20 (2) ◽

pp. 177 ◽

Cited By ~ 29

Author(s):

JMW Wilmer ◽

A Melzer ◽

F Carrick ◽

C Moritz

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Inbreeding Depression ◽

Natural Populations ◽

Small Population ◽

Phascolarctos Cinereus ◽

Low Genetic Diversity ◽

History Of ◽

Biased Sex Ratio ◽

Two Populations

The amount of genetic variation in two natural populations of Queensland koalas (Phascolarctos cinereus adustus) was assessed by analysis of mitochondrial DNA. Levels and any adverse effects of inbreeding (inbreeding depression) were estimated from the pedigree of a well-characterised captive colony. Genetic diversity of mitochondrial DNA was found to be exceedingly low both within and between the two populations, but the variation detected was found to be strongly structured geographically. Inbreeding levels in the captive colony were moderate to high yet the only apparent evidence of inbreeding depression was a male-biased sex ratio. There was no evidence for decreased juvenile survivorship or growth rate with inbreeding. Because of the limited data it would be premature to conclude that koalas are relatively resistant to the effects of inbreeding. However, we suggest the hypothesis that koalas have a history of small population size, resulting in reduced susceptibility to inbreeding depression.

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The Last Two Remaining Populations of the Critically Endangered Estuarine Pipefish Are Inbred and Not Genetically Distinct

Frontiers in Marine Science ◽

10.3389/fmars.2021.756595 ◽

2022 ◽

Vol 8 ◽

Author(s):

Sven-Erick Weiss ◽

Arsalan Emami-Khoyi ◽

Horst Kaiser ◽

Paul D. Cowley ◽

Nicola C. James ◽

...

Keyword(s):

Genetic Diversity ◽

Extinction Risk ◽

Significant Risk ◽

Small Population ◽

Environmental Stochasticity ◽

Critically Endangered ◽

Conservation Strategy ◽

Genome Wide Data ◽

Significant Genetic Structure ◽

Population Sizes

The critically endangered estuarine pipefish, Syngnathus watermeyeri, is one of Africa’s rarest fish species and currently faces a significant risk of extinction. A combination of anthropogenic and natural factors threaten submerged macrophyte beds in the two South African estuaries (Bushmans and Kariega) in which the species’ only two known remaining populations reside. Here, we genotyped 34 pipefish from both populations using genome-wide data to determine whether the two estuaries harbour distinct genetic diversity, such that translocating individuals between them might improve the genetic health of both. Our results show that both populations are highly inbred, and no statistically significant genetic structure was found between them. Moreover, individuals both within and between estuaries were very closely related to each other. These results indicate that the remaining populations of the estuarine pipefish suffer from the adverse genetic effects of small population sizes. Even though recent surveys have estimated population sizes in the order of thousands of individuals, these may fluctuate considerably. Although the translocation of genetically similar individuals between habitats will not increase local genetic diversity, the creation of additional populations across the species’ historical range may be a suitable conservation strategy to prevent further loss of genetic diversity, and to minimise the overall extinction risk posed by environmental stochasticity.

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Assessment of genetic diversity among Egyptian and Saudi chicken ecotypes and local Egyptian chicken breeds using microsatellite markers

Journal of Environmental Biology ◽

10.22438/jeb/42/1/mrn-1572 ◽

2021 ◽

Vol 42 (1) ◽

pp. 33-39

Author(s):

A. Sabry ◽

◽

S. Ramadan ◽

M.M. Hassan ◽

A.A. Mohamed ◽

...

Keyword(s):

Genetic Diversity ◽

Saudi Arabia ◽

Microsatellite Markers ◽

Rhode Island ◽

Polymorphic Information Content ◽

Genetic Distances ◽

Native Chicken ◽

Hardy Weinberg Equilibrium ◽

Chicken Breeds ◽

Endangered Status

Aim: To assess genetic diversity of two chicken ecotypes from Egypt and Saudi Arabia and compare these ecotypes to six local Egyptian and two exotic pure chicken breeds using 14 microsatellite markers. Methodology: Dataset consisted of two subsets. First subset represented two ecotypes from Saudi Arabia and Egypt. Second dataset consisted birds six Egyptian native chicken strains: Fayoumi (FAY), Dandarawy (DAN), Baladi (BAL), Sinai (Sini), El-Salam (Els) and Golden Montazah (GG), and two commercial strains: White Leghorn (WL) and Rhode Island Red (RIR). fourteen microsatellites markers were utilized to assess DNA polymorphism. Data analyses of the results were carried out using R statistical environment. Results: The obtained results indicated that number of alleles per locus averaged 11.4 ± 5.0. Polymorphic information content was informative (> 50%) for the local breeds, but not for two ecotypes. The observed and expected heterozygosity averaged 0.46 and 0.75, both ecotypes had the lowest estimates. All breeds showed significant deviation from Hardy–Weinberg equilibrium expectation. The average population differentiation index (FST) was 0.143, overall heterozygosity deficiency (FIT) was 0.156, and global inbreeding of individuals within breeds (FIS) was 0.319. Interpretation: This study revealed that both Egyptian and Saudi ecotypes have an endangered status. Lower genetic distances and lower FST values were reported for the Egyptian indigenous breeds. Phylogenetic and principle components showed that both ecotypes were genetically closer to each other when compared with other breeds. It also showed that the Dandarawy native Egyptian chicken breed was genetically the closest breed to both the Egyptian and Saudi ecotypes. Key words: Chicken, Ecotypes, Genetic diversity, Microsatellites, Phylogenetics

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Population genetics data help to guide the conservation of palm species with small population sizes and fragmented habitats in Madagascar

PeerJ ◽

10.7717/peerj.3248 ◽

2017 ◽

Vol 5 ◽

pp. e3248 ◽

Cited By ~ 3

Author(s):

Lauren M. Gardiner ◽

Mijoro Rakotoarinivo ◽

Landy R. Rajaovelona ◽

Colin Clubbe

Keyword(s):

Genetic Diversity ◽

Protected Area ◽

Conservation Management ◽

Low Cost ◽

Large Population ◽

Small Population ◽

Ex Situ ◽

Palm Species ◽

In The Wild ◽

Population Sizes

BackgroundThe need to incorporate genetic data into conservation management decisions is increasingly recognised. However, many published studies represent a ‘gold standard’ of sampling, techniques, and analyses. Such rigour is often not possible with limited funding and resourcing available for developing plans for the increasing number of threatened species requiring conservation management. Two endemic palm species of the Itremo Massif in central Madagascar,Dypsis ambositraeandD. decipiens, are known to be threatened with extinction and conservation management for these species is a priority for the newly created protected area in the region.MethodsThe genetic diversity of these two species was studied using the relatively low-cost and rapid AFLP technique. DNA fragments generated using three primer combinations were analysed for 20 and 50 individuals of the two species, respectively, from across their ranges.ResultsGenetic diversity was relatively low for both species. The two sites where the highly restrictedD. ambositraegrows were found to be genetically distinct (although overall heterozygosity was low). Despite having a much wider distribution and relatively large population,D. decipiensdid not show clear geographical nor genetic groupings and had similarly low genetic heterozygosity toD. ambositrae.Discussion and RecommendationsWith so few individuals remaining in the wild and two genetically distinct subpopulations, it is recommended that both sites ofD. ambositraeare conserved and that seed are collected from both forex situconservation and potential future reintroduction. It may be less important to focus resources on conserving or collectingex situmaterial from all sites whereD. decipiensis found, as the genetic diversity represented by each subpopulation is limited and increasing sampling may not protect significantly higher levels of genetic diversity. This study provides data that inform and support conservation decisions taken for both species within this region, and in the management of the newly designated Itremo Massif Protected Area, which covers most of the sites where these two species remain in the wild.

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