Genetic structure of the oriental white stork (Ciconia boyciana): implications for a breeding colony in a non‐breeding area

The oriental white stork (Ciconia boyciana) is a threatened species, and their numbers are still in decline due to habitat loss and poaching. China is a breeding and main wintering area for this animal and in recent years some individuals have been found breeding in wintering areas and at some stopover sites. These new breeding colonies are an exciting sign, however, little is understood of the genetic structure of this species. Based on the analysis of a 463‐bp mitochondrial DNA (mtDNA) control region, we investigated the genetic structure and genetic diversity of 66 wild oriental white storks from a Chinese population. We analyzed the sequences of 66 storks obtained in this study and the data of 17 storks from a Japanese population. Thirty‐seven different haplotypes were detected among the 83 samples. An analysis of molecular variance showed a significant population subdivision between the two populations (F_ST= 0.316, P < 0.05). However, the phylogenetic analysis revealed that the samples from the different populations did not form separate clusters and that there were genetic exchanges between the two populations. Compared with the Japanese population, the Chinese population had a relatively higher genetic diversity with a haplotype diversity (hπ SD) of 0.953 ± 0.013 and a nucleotide diversity (π± SD) of 0.013 ± 0.007. The high haplotype diversity and low nucleotide diversity indicate that this population might be in a rapidly increasing period from a small effective population. A neighbor‐joining tree analysis indicated that genetic exchange had occurred between the newly arisen southern breeding colony and the northern breeding colony wintering in the middle and lower Yangtze River floodplain. These results have important implications for the conservation of the oriental white stork population in China.     

Genetic monitoring of ex situ African Penguin (Spheniscus demersus) populations in South Africa

The African Penguin (Spheniscus demersus) has suffered population declines and is listed in the IUCN Red List as Endangered. The species is endemic to the coast of southern Africa, and breeding colonies are distributed on the south-western coast of Africa. Currently, African Penguins are being kept in zoo and aquarium facilities throughout South Africa. In this study, molecular genetic data based on 12 microsatellite markers from 1 119 African Penguin samples from four facilities were generated in order to determine the level of genetic variation, population structure and differentiation, and effective population size to assist in the development of an effective captive management plan. Expected heterozygosity ranged from 0.57 to 0.62, and allelic richness from 4.2 to 5.1. However, based on differences between first- and second-generation captive birds, we conclude that the ex situ population is at risk of losing genetic variability in the future and management programmes should include exchange of birds between captive facilities in order to induce gene flow and increase effective population size. Adding individuals from in situ populations should also be considered in the future in cases where these birds cannot be rehabilitated. Molecular genetic analyses of wild penguin populations should be carried out for comparison, and to ascertain to what degree ‘in situ genetic diversity’ is represented among ex situ populations. With regular resampling and analyses, the extent of the effect of processes such as genetic drift on diversity in the ex situ penguin populations will become evident.     

Genetic diversity and differentiation of Mongolian and Russian yak populations

In this study we examined the genetic diversity of yak populations in the northernmost part of their current global distribution. Five Mongolian and one Russian yak populations as well as one Chinese yak population from the Qinghai–Tibetan Plateau, the putative centre of yak domestication, were analysed with 15 microsatellite loci to determine the level of genetic variation within populations as well as the genetic differentiation and relationship between populations. A total of 116 microsatellite alleles were identified. The mean number of alleles per locus (MNA) across populations was 7.73 ± 1.98 and the mean expected heterozygosity (H_E) was 0.696 ± 0.026. The relative magnitude of gene differentiation (F_ST) among populations was 4.1%, and all genetic differentiations (F_ST) between populations were significant (p < 0.001). A significant inbreeding effect (F_IS) was detected in the Hovsgol yak (p < 0.01). There was no indication of a recent bottleneck in any of the populations studied. The results showed that yak populations in Mongolia and Russia have maintained high genetic diversity within populations and a low, although significant, genetic differentiation between populations. Both phylogenetic and principal component analyses support a close genetic relationship between the Gobi Altai, south Gobi and north Hangai populations, and between the Hovsgol and Buryatia populations respectively. Our results indicate that these yak populations should be considered as distinct genetic entities in respect of conservation and breeding programmes.     

Genetic structure and recent population demographic history of Taihangshan macaque (Macaca mulatta tcheliensis), North China

Massive actions have been and are being taken into protecting the world's primates from extinction, while the study of the properties of genetic diversity, demographic history, and ecological relationships will benefit the understanding of the long-term survival of a species. The Taihangshan macaque (Macaca mulatta tcheliensis), a subspecies of rhesus macaque (Macaca mulatta), is endemic to China and currently restricted to southern Mt. Taihangshan area. Herein, we evaluated the genetic diversity, population structure, and demographic history of this subspecies using mitochondrial (Cytb and high variable region I: HVR I) and nuclear markers (microsatellite loci) of 131 individuals collected from 9 localities covering the distribution range of this subspecies. Both phylogenetic analyses and genetic assignment revealed that the wild populations of Taihangshan macaques could be divided into 2 major highly divergent clades, THS-east and THS-west. Low genetic diversity (π: 0.00266 ± 0.00016) but high haplotype diversity (H_d: 0.80352 ± 0.015) were detected in the Taihangshan macaques, particularly in THS-east. Analyses of demographic history suggested that the Taihangshan macaques experienced first a stable historical population size from Holocene to early 19th century but a subtle decline and then slight growth in the recent 200 years. We suggest that bridging the neighbor populations (i.e. setting corridors) would facilitate the male-mediated gene flow and subsequently increase the genetic diversity of the Taihangshan macaque populations.     

Analysis of genetic diversity in Bolivian llama populations using microsatellites

South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (F_ST range: 0.003–0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise F_ST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations.     

Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers

The purpose of this study was to assess genetic diversity, phylogenetic relationship and population structure among nine Eurasian cattle populations using 58 single nucleotide polymorphism (SNP) markers. The calculated distribution of minor allele frequencies and heterozygosities suggested that the genetic diversity of Bos indicus populations was lower than that of Bos taurus populations. Phylogenetic analyses revealed the main divergence between the Bos taurus and Bos indicus populations, and subsequently between Asian and European populations. By principal components analysis, the Bos taurus and Bos indicus populations were clearly distinguished with PC1 (61.1%); however, six Bos taurus populations clustered loosely and the partial separation between European and Asian groups was observed by PC2 (12.5%). The structure analysis was performed using the STRUCTURE program. Distinct separation between Bos taurus and Bos indicus was shown at K = 2, and that between European and Asian populations at K = 3. At K = 4, 5 and 6, Mongolian population showed an admixture pattern with different ancestry of Asian and European cattle. At K = 7, all Bos taurus populations showed each cluster with little proportion of admixture. In conclusion, 58 SNP markers in this study could sufficiently estimate the genetic diversity, relationship and structure for nine Eurasian cattle populations, especially by analyses of principal components and STRUCTURE.     

Diversity analysis of sheep breeds from Southern peninsular and Eastern regions of India

Information is presented on the genetic diversity and relationship among six Indian sheep breeds/populations belonging to the Southern peninsular and Eastern agroecological zones, based on microsatellite markers. Parameters of genetic variation, viz., allele diversity, observed heterozygosity, gene diversity and population inbreeding estimates, were calculated for the six breeds. The allele diversity ranged from 6.40 to 7.92, whereas the gene diversity varied from 0.617 to 0.727. The highest allele and gene diversity was observed for Nellore sheep, while the lowest was exhibited by Garole breed. Within population inbreeding estimate (F _IS) revealed a significant deficit of heterozygotes in Deccani, Madgyal, Nellore and Garole, whereas Ganjam and Chhotanagpuri sheep showed an excess of heterozygotes. The contribution of each breed to the total diversity of the breeds was quantified by the Weitzman approach. The marginal loss of diversity incurred with removal of Nellore and Garole breeds was higher (>27%), whereas removal of Deccani breed resulted in lowest loss of diversity (3.84%) from the set. Estimation of the genetic differentiation (F _ST) and genetic distance (D _A) between the pairs of breeds revealed a close relationship between Deccani and Madgyal sheep (F _ST = 0.017; D _A = 0.080) and greatest demarcation between Madgyal and Garole breeds (F _ST = 0.110; D _A = 0.622). The information generated would help in shaping genetic management and conservation programs for the sheep breeds under consideration.     

Can low densities of carnivores result in genetic depletion? An investigation within French polecat populations

Carnivores as top predators are commonly found in relatively low densities even in optimal habitats. Despite a lack of empirical studies, it could be suspected that long‐term low density could result in genetic depletion. The genetic structure of European polecat Mustela putorius natural populations was investigated by allozyme electrophoresis in five distinct areas. Density estimates significantly differed among sites from 0.17 to 0.83 individuals/km² with an average of 0.56 individuals per km², resulting in a scattered distribution. Genetic structure varied among distinct populations both in number of polymorphic loci and heterozygosity. Polecats from Brittany revealed a very low observed heterozygosity (H_O = 0.028) whereas mean heterozygosity reached H_O = 0.072 in Brière. That the lowest heterozygosity levels and highest inbreeding coefficient F_IS were significantly associated with the lowest densities suggests that low densities may affect populations of carnivores. Both the loss of polymorphic loci and the reduction in heterozygosity rates suggest a density‐dependent effect and population density can be arguably regarded as a factor affecting genetic diversity in top carnivores.     

Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number of alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour‐joining dendrogram obtained from Nei's standard genetic distance differentiated eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations.     

Genomic differentiation with isolation by distance along a latitudinal gradient in the spotted-leg treefrog Polypedates megacephalus

The patterns of isolation by distance (IBD) entailing increased genetic differentiation among populations have aroused extensive concerns for evolutionary biologists. Although the IBD may act on spatial processes contributing to the genetic differentiation among populations in anuran species, the factors shaping the IBD of frogs among populations in natural systems are largely unknown. Here, we studied the genetic differentiation among six populations with 24 individuals of the spotted-leg treefrog along a latitudinal gradient (1860.31 km) based on 1020 single nucleotide polymorphisms from restriction site-associated DNA sequencing. The results showed that the genetic diversity differed significantly among populations and that the insular populations had higher genetic diversity than the mainland populations. Furthermore, we also found a significant genetic differentiation among populations (F_ST = 0.277) and no sign of inbreeding (F_UNI = −0.145). The IBD was detected for all populations, and a higher degree of the IBD was indicated when controlling for the effects of the isolation between Hainan and mainland populations caused by the Qiongzhou Strait. Our findings suggest that the form of the Qiongzhou Strait plays a key role in shaping the genetic diversity and population differentiation in treefrogs.     

Population genomics provides insights into the evolution and adaptation of tree shrews (Tupaia belangeri) in China

Physiological adaptation of tree shrews (Tupaia belangeri) to changing environmental temperature has been reported in detail. However, the T. belangeri origin (mainland or island), population history, and adaptation to historical climate change remain largely unknown or controversial. Here, for the first time, we sequenced the simplified genome of 134 T. belangeri individuals from 12 populations in China and further resequenced one individual from each population. Using population genomic approaches, we first observed considerable genetic variation in T. belangeri. Moreover, T. belangeri populations formed obvious genetic structure and reflected different demographic histories; they generally exhibited high genetic diversity, although the isolated populations had relatively low genetic diversity. The results presented in this study indicate that T. b. modesta and T. b. tonquinia were separated recently and with a similar population dynamics. Second, physical barriers rather than distance were the driving factors of divergence, and environmental heterogeneity may play an important role in genetic differentiation in T. belangeri. Moreover, our analyses highlight the role of historical global climates in the T. belangeri population dynamics and indicate that the decrease of the T. belangeri population size may be due to the low temperature. Finally, we identified the olfaction-associated adaptive genes between different altitude populations and found that olfactory-related genes of high-altitude populations were selectively eliminated. Our study provides demographic history knowledge of T. belangeri; their adaption history offers new insights into their evolution and adaptation, and provides valuable baseline information for conservation measures.     

Genetic diversity of Indian native cattle breeds as analysed with 20 microsatellite loci

The aim of the present study was to assess the genetic variation and establish the relationship amongst the three Indian zebu cattle breeds using 20 bovine‐specific microsatellite markers. A total of 136 unrelated DNA samples from Sahiwal (SC), Hariana (HC) and Deoni (DC) breeds of cattle were genotyped to estimate within and between breed genetic diversity indices. The estimated mean allelic diversity was 5.2, 6.5 and 5.9 in SC, HC and DC, respectively, with a total of 167 alleles. The average observed and expected heterozygosity for the population varied from 0.42 (SC) to 0.59 (DC), and from 0.61 (SC) to 0.70 (DC), respectively. Low values of genetic variability estimates were observed in SC when compared with DC and HC, indicating some loss of variability because of its relatively small population size. From global F‐statistics a significant deficit of heterozygotes of 24.2% (p < 0.05) was observed for each one of the analysed breeds whereas the total population had a 32.8% (p < 0.05) deficit of heterozygotes. The F_ST estimates demonstrated that approximately 88.7% of the total genetic variation was because of the genetic differentiation within each breed. Pair‐wise breed differentiation, Nei's standard and D_A genetic distance estimates revealed relatively close genetic similarity between HC and DC in comparison with SC. In the UPGMA‐based phylogenetic tree constructed from the genetic distances, HC and DC were grouped together in one cluster and SC in the other. The estimated time of divergence suggested a separation time of approximately 776 years between DC and HC, and a comparatively longer period (1296 years) between DC and SC.     

Genetic diversity and structure in Asian native goat analyzed by newly developed SNP markers

In the current study, a total of 65 single nucleotide polymorphisms (SNPs) within the intron region were developed in goat (Capra hircus) by utilizing genomic information of cattle and sheep due to poor available genomic information on goat. Using these markers, we carried out genetic diversity and structure analyses for 10 Asian goat populations. The phylogenetic tree and principal components analysis showed good correspondence between clustered populations and their geographic locations. The STRUCTURE software analysis illustrated six divergent genetic structures among 10 populations. Myanmar and Cambodia populations showed high admixture patterns with different ancestry, suggesting genetic introgression into native goat populations. We also investigated the correlation between genetic diversity and geographic distance from a domestication center. This result showed a decreasing trend of genetic diversity according to the distance (P = 0.014). This result supported common consensus that western Asia is one of the centers of origin for modern Asian domestic goat.     

Genetic diversity decreases as population density declines: Implications of temporal variation in mitochondrial haplotype frequencies in a natural population of Tscherskia triton

Although the spatial genetic differentiation that occurs in animal populations has been extensively studied, information on temporal variations in genetic structure and diversity is still lacking, especially for animals with oscillating populations. In the present study, we used the mtDNA D‐loop sequence to assess the temporal genetic variation in samples from six successive years for the greater long‐tailed hamster, Tscherskia triton. Sampling was carried out between 1998 and 2003 in cropland on the North China Plain, China. A total of 108 individuals were analyzed. The temporal samples showed a high level of genetic diversity. Substantial genetic changes in haplotype frequencies over time were detected for the hamster population. Random genetic drift and migration are likely to be the major factors responsible for the observed temporal pattern. The genetic diversity of the hamster population was higher in years with higher population density, and lower in years with lower population density. The result supports our hypothesis that genetic diversity decreases when population density declines in animals whose population oscillates greatly between years. The combined effects of inbreeding and genetic drift caused by reproduction, dispersal and population size might play important roles in the observed changes in genetic structure and diversity between years.     

Applying molecular genetic tools to tiger conservation

The utility of molecular genetic approaches in conservation of endangered taxa is now commonly recognized. Over the past decade, conservation genetic analyses based on mitochondrial DNA sequencing and microsatellite genotyping have provided powerful tools to resolve taxonomy uncertainty of tiger subspecies, to define conservation units, to reconstruct phylogeography and demographic history, to examine the genetic ancestry of extinct subspecies, to assess population genetic status non-invasively, and to verify genetic background of captive tigers worldwide. The genetic status of tiger subspecies and populations and implications for developing strategies for the survival of this charismatic species both in situ and ex situ are discussed.     

Population Structure Among Progeny-tested Bulls of the Red Dairy Breeds in Finland,Norway and Sweden

Abstract

The Icelandic cattle breed is believed to have been brought to Iceland from Norway around 1100 years ago. Since then it is thought to have been almost completely isolated and to have gone through large fluctuations in population size. Here molecular markers were used to assess the breed's genetic diversity and the current within-population genetic structure using a randomly selected unbiased sample from the population as verified by calculations of the coefficient of relationship (R). Measures of genetic diversity suggest that there is considerable diversity within the breed despite long-term isolation and the effective population size is high considering the isolation and the breeding system used in recent years. No evidence of recent bottlenecks was found and analysis of population structure suggests that the population is uniform in structure.     

Using genetic tools to inform conservation of fragmented populations of Asian elephants (Elephas maximus) across their range in China

A herd of 15 Chinese elephants attracted international attention during their 2021 northward trek, motivating the government to propose establishment of an Asian elephant national park. However, planning is hampered by a lack of genetic information on the remaining populations in China. We collected DNA from 497 dung samples from all 5 populations encompassing the entire range of elephants in China and used mitochondrial and microsatellite markers to investigate their genetic and demographic structure. We identified 237 unique genotypes (153 females, 84 males), representing 81% of the known population. However, the effective population size was small (28, range 25–32). Historic demographic contraction appeared to account for low haplotype diversity (H_d = 0.235), but moderate nucleotide and nuclear diversity (π = 0.6%, H_e = 0.55) was attributable to post-bottleneck recovery involving recent population expansion plus historical gene exchange with elephants in Myanmar, Lao PDR, and Vietnam. The 5 populations fell into 3 clusters, with Nangunhe elephants differing consistently from the other 4 populations (F_ST = 0.23); elephants from Mengyang, Simao, and Jiangcheng belonged to a single population (henceforth, MSJ), and differed from the Shangyong population (F_ST = 0.11). Interpopulation genetic variation reflected isolation by distance and female-biased dispersal. Chinese elephants should be managed as 2 distinct units: Nangunhe and another combining Shangyong and MSJ; their long-term viability will require restoring gene flow between Shangyong and MSJ, and between elephants in China and neighboring countries. Our results have the potential to inform conservation planning for an iconic megafaunal species.     

An insight into population structure and gene flow within pure‐bred cats

Investigation of genetic structure on the basis of pedigree information requires indicators adapted to the specific context of the populations studied. On the basis of pedigree‐based estimates of diversity, we analysed genetic diversity, mating practices and gene flow among eight cat populations raised in France, five of them being single breeds and three consisting of breed groups with varieties that may interbreed. When computed on the basis of coancestry rate, effective population sizes ranged from 127 to 1406, while the contribution of founders from other breeds ranged from 0.7 to 16.4%. In the five breeds, F_IS ranged between 0.96 and 1.83%, with this result being related to mating practices such as close inbreeding (on average 5% of individuals being inbred within two generations). Within the three groups of varieties studied, F_IT ranged from 1.59 to 3%, while values were estimated between 0.04 and 0.91%, which was linked to various amounts of gene exchanges between subpopulations at the parental level. The results indicate that cat breeds constitute populations submitted to low selection intensity, contrasting with relatively high individual inbreeding level caused by close inbreeding practices.     

Evaluation of the genetic structure of sika deer (Cervus nippon) in Japan's Kanto and Tanzawa mountain areas,based on microsatellite markers

The browsing habits of sika deer (Cervus nippon) in Japan have caused serious ecological problems. Appropriate management of sika deer populations requires understanding the different genetic structures of local populations. In the present study, we used 10 microsatellite polymorphisms to explore the genetic structures of sika deer populations (162 individuals) living in the Kanto region. The expected heterozygosity of the Tanzawa mountain range population (Group I) was lower than that of the populations in the Kanto mountain areas (Group II). Our results suggest that moderate gene flow has occurred between the sika deer populations in the Kanto mountain areas (Group II), but not to or from the Tanzawa mountain range population (Group I). Also, genetic structure analysis showed that the Tanzawa population was separated from the other populations. This is probably attributable to a genetic bottleneck that developed in the Tanzawa sika deer population in the 1950s. However, we found that the Tanzawa population has since recovered from the bottleneck situation and now exhibits good genetic diversity. Our results show that it is essential to periodically evaluate the genetic structures of deer populations to develop conservation strategies appropriate to the specific structures of individual populations at any given time.     

Genetic structure of wild and domesticated grasscutters (Thryonomys swinderianus) from south-western Nigeria

Grasscutter (Thryonomys swinderianus) is a large rodent distributed across sub-Saharan Africa that is highly valued as a source of protein. There has been little effort to evaluate the genetic structure of grasscutters despite long-term harvesting pressure and over 40 years of grasscutter domestication in West Africa. Our objectives were to quantify the genetic structure of wild grasscutters, and to compare genetic variation from wild samples to those from various farmed samples within south-western Nigeria. We genotyped 145 wild and 88 domesticated individuals at 11 microsatellite loci and present results quantifying regional genetic structuring and the relative patterns of diversity among wild and domesticated grasscutter populations. Our data reflect high differentiation between wild and domesticated grasscutters, and significantly greater allelic richness and gene diversity in the former. Despite this, domesticated populations appear to have similar levels of observed heterozygosity and comparable levels of differentiation among domesticated samples relative to wild samples. This may be the result of high turnover within captive colonies, or frequent infusion of new animals. More detailed molecular and quantitative genetic studies are recommended on this species to be able to understand their natural variation, degree of connectivity and to improve strategies for domestication.