Fluctuating fine-scale spatial genetic structure in the common shrews (Eulipotyphla,Mammalia)

The spatial genetic structure is a topical issue in the studies of various aspects of ecology and evolution. Using the multilocus autocorrelation method with hypervariable microsatellite genetic markers, we investigated a fine-scale pattern of genetic structure in 5 local populations of the common shrew Sorex araneus separated by distances of 300–1000 m (the Moscow chromosomal race). Spatial genetic autocorrelation analysis based on 5 microsatellite loci (expected heterozygosity >0.79) with 90 alleles revealed a consistent pattern of significant positive genetic structure. By testing the autocorrelation at multiple scales from 25 to 500 m, we found that positive spatial genetic structure is detectable in distance classes of <500 m. The weaker spatial genetic structure positively correlated with a higher ratio of nonresident individuals to residents’ activity (number of captures). In contrast to nonresident animals, the residents demonstrated prominent genetic structure. Genetic difference (F_ST) between the populations was significant (0.016–0.051) and comparable with that between populations of different races analyzed previously (0.016–0.038). F_ST was not associated with geographic distance. These demographic patterns allowed us to propose a scheme of genetic-structure dynamics involving periodic appearance of more related local groups and renewal of allelic profiles from а common pool where the alleles are mixed. The scheme predicts fluctuating genetic structure and random similar differences among local 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.     

Assessment of genetic diversity and conservation priority of Omani local chickens using microsatellite markers

Designing strategies for conservation and improvement livestock should be based on assessment of genetic characteristics of populations under consideration. In Oman, conservation programs for local livestock breeds have been started. The current study assessed the genetic diversity and conservation potential of local chickens from Oman. Twenty-nine microsatellite markers were analyzed in 158 birds from six agroecological zones: Batinah, Dhofar, North Hajar, East Hajar, Musandam, and East Coast. Overall, a total of 217 alleles were observed. Across populations, the average number of alleles per locus was 7.48 and ranged from 2 (MCW98 and MCW103) to 20 (LEI094). The mean expected heterozygosity (H _E) was 0.62. Average fixation index among populations (F _ST) was 0.034, indicating low population differentiation, while the mean global deficit of heterozygotes across populations (F _IT) was 0.159. Based on Nei’s genetic distance, a neighbor-joining tree was constructed for the populations, which clearly identified the Dhofar population as the most distant one of the Omani chicken populations. The analysis of conservation priorities identified Dhofar and Musandam populations as the ones that largely contribute to the maximal genetic diversity of the Omani chicken gene pool.     

Microsatellite-based diversity analysis and genetic relationships of three Indian sheep breeds

The genetic structure of three Indian sheep breeds from two different geographical locations (Nali, Chokla from north‐western arid and semi‐arid region; Garole from eastern saline marshy region) of India was investigated by means of 11 ovine‐specific microsatellite markers as proposed in FAOs MoDAD programme. Microsatellite analysis revealed high allelic and gene diversity in all the three breeds. Nali sheep showed higher mean number of alleles and gene diversity (6.27 and 0.65) than Chokla (5.63 and 0.64) and Garole (5.63 and 0.59). High within population inbreeding estimates observed in the three breeds (F_IS, Chokla = 0.286, Nali = 0.284, Garole = 0.227) reflected deficit of heterozygotes. The overall estimates for F‐statistics were significantly (p < 0.05) different from zero. High values of F_ST (0.183) across all the loci revealed substantial degree of breed differentiation. Based on pair wise F_ST and N_m between different breeds, Nali and Chokla (F_ST = 6.62% and N_m = 4.80) were observed to be the closest followed by Garole and Nali (F_ST = 20.9% and N_m = 1.80), and Garole and Chokla (F_ST = 21.4% and N_m = 1.71). In addition, genetic distance estimates, phylogeny analysis and individual assignment test used to evaluate interbreed genetic proximity and population structure also revealed substantial genetic differentiation between Garole and the other two Rajasthani (Nali and Chokla) sheep. This divergent status of Garole sheep indicated genetic uniqueness of this breed suggesting higher priority for its conservation.     

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.     

Molecular characterization and differentiation of five horse breeds raised in Algeria using polymorphic microsatellite markers

In this study, genetic analyses of diversity and differentiation were performed on five horse breeds raised in Algeria (Barb, Arab‐Barb, Arabian, Thoroughbred and French Trotter). All microsatellite markers were highly polymorphic in all the breeds. A total of 123 alleles from 14 microsatellite loci were detected in 201 horses. The average number of alleles per locus was the highest in the Arab‐Barb horses (7.86) and lowest in the thoroughbred breed (5.71), whereas the observed and expected heterozygosities per breed ranged from 0.71 (Thoroughbred) to 0.752 (Barb) and 0.71 (Thoroughbred) to 0.77 (Arab‐Barb), respectively. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (F_ST). Three different approaches for evaluating the genetic relationships were applied. Genetic distances, the factorial correspondence analysis and structure analysis showed that a significant amount of genetic variation is maintained in the native horse populations and the other breeds. The Barb and Arab‐Barb breeds seem to be the most genetically related and support the decision to consider the breeds as same population.     

Genetic diversity of Forest and Savannah chicken populations of Ghana as estimated by microsatellite markers

The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco‐zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations – a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright's F‐statistics revealed negligible genetic differentiation (F_ST) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south‐north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement.     

Evaluation of genetic variability and mutation drift equilibrium of Banni buffalo using multi locus microsatellite markers

The present study was conducted to evaluate genetic diversity of Banni buffalo and its relationship/differentiation with Murrah using genotypic data on 24 heterologus bovine specific microsatellite marker loci. A total of 138 alleles were observed with a mean of 5.75 alleles/locus across two populations. The mean observed and expected heterozygosities were found to be 0.441 and 0.572 respectively in Banni buffaloes while it was 0.464 and 0.610 respectively in Murrah buffaloes. The average heterozygosity deficit was significantly positive with substantially higher values observed in Banni (22.3%) and Murrah (24%) buffalo populations. Banni buffalo population, when evaluated for mutation drift equilibrium revealed significant heterozygosity excess under IAM while no such excess was observed under SMM and TPM. The qualitative graphical test revealed a normal L-shaped distribution of allele frequencies indicating the absence of genetic bottleneck in Banni buffaloes. The mean estimates of F-statistics over all the loci were 0.376 for F_IT, 0.187 for F_ST and 0.232 for F_IS respectively. Analysis of molecular variance (AMOVA) revealed 18.95% of the total variation being explained by between breed differences while 14.36% of the variation explained differences between individuals within each breed. Genotype assignment test revealed distinct clustering of Banni and Murrah buffaloes. Genetic distance was estimated using three different methods, the results of which revealed considerable genetic differentiation between these two buffalo populations. The divergence time between Banni and Murrah buffaloes was estimated to be around 7286 years. The results of the present study may be helpful in decision making for conservation programs as Banni buffalo population is on decline.     

Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese indigenous cattle populations, using microsatellite markers. A total of 410 individuals from six indigenous cattle populations and an exotic breed was characterized using 27 microsatellite markers A total of 362 alleles was detected and the number of alleles per locus ranged from 8 (INRA005 and ILSTS005) to 17 (ETH185). The level of gene diversity was high indicated by a mean expected heterozygosity (He) across populations and loci of 0.73. Level of inbreeding (mean F_IS=0.05) and genetic differentiation (mean F_ST=0.04) was moderate. The phylogenetic tree based on Reynolds genetic distance reflected geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels of genetic diversity and distinct genetic structures. Based on these results, we recommend that for conservation homogenous populations (Nghe An, Thanh Hoa and Phu Yen) can be grouped to reduce costs and U Dau Riu, Lang Son and Ha Giang populations should be conserved separately to avoid loss of genetic diversity.     

Genetic characterization of Thai indigenous chickens compared with commercial lines

A total of 210 chicken samples, from seven strains, were genotyped using 20 microsatellite loci of which 16 are recommended by the Food and Agriculture Organization. The genetic variability and divergence of four Thai indigenous strains and three commercial lines were assessed to generate baseline information for conservation, promotion, and make sustainable utilization of indigenous chicken resources in Thailand. A total of 227 alleles were distributed ranging from six (MCW 111) to 16 (MCW 183 and LEI 166) alleles per locus. The highest (0.81) and lowest (0.77) average of expected heterozygosities were observed in indigenous chicken (Dang) and commercial layer (Isa Brown), respectively. All microsatellite loci were in the Hardy–Weinberg equilibrium, except for MCW111 and ADL372 in the Isa Brown line. The subpopulation division coefficient (F _ST ) was strong with the value of 0.183 indicating the genetic differentiation among the studied groups. Four genetic clusters were detected: the first group consisted of layers (Isa Brown and White Leghorn); the second group was broiler; the third group consisted of non-black feather indigenous chicken (Chee, Dang, and Leung Hang Khoa); and the fourth group was black feather indigenous chicken (Pradu Hang Dam). The results of this study also suggested that Pradu Hang Dam is suitable to be developed as a meat type chicken due to lower genetic distance between Pradu Hang Dam and broiler.     

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.     

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Selective breeding has led to modifications in the genome of many livestock breeds. In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case–control genome‐wide association study (GWAS), the Bayesian population differentiation analysis (F_ST) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and F_ST and one marker between GWAS and Rsb. Three markers detected by Rsb were also located near (<2 Mb) to highly significant regions identified by GWAS and F_ST analyses. Moreover, one candidate marker identified by GWAS and F_ST approaches was located in a run of homozygosity island that was shared by both breeds. We identified several genes involved in many phenotypic differences (such as stature and growth, reproduction, ear size, coat colour, behaviour) between the two analysed breeds. This study shows that combining several genome‐wide approaches could improve discovery of regions involved in the variability of breeding traits and responsible for the phenotypic diversity even between closely related breeds. Overall, the combination of such genome‐wide methods can be extended to other livestock breeds that share between them a similar genetic background, to understand the process that shapes the patterns of genetic variability between closely related populations.     

Is the ballan wrasse (Labrus bergylta) two species? Genetic analysis reveals within‐species divergence associated with plain and spotted morphotype frequencies

The ballan wrasse (Labrus bergylta) is a marine fish belonging to the family Labridae characterized by 2 main morphotypes that occur in sympatry: spotty and plain. Previous studies have revealed differences in their life‐history traits, such as growth and maturation; however, the genetic relationship between forms is presently unknown. Using 20 recently developed microsatellite markers, we conducted a genetic analysis of 41 and 48 spotty and plain ballan wrasse collected in Galicia (northwest Spain). The 2 morphotypes displayed highly significant genetic differences to each other (F_ST = 0.018, P < 0.0001). A similar degree of genetic differentiation (F_ST = 0.025, P < 0.0001) was shown using the STRUCTURE clustering approach with no priors at K = 2. In this case, the frequency of spotty and plain morphotypes was significantly different (χ² = 9.46, P = 0.002). It is concluded that there is significant genetic heterogeneity within this species, which appears to be highly associated with the spotty and plain forms, but not completely explained by them. Given the previously demonstrated biological differences between morphotypes, and the present genetic analyses, we speculate about the convenience of a taxonomic re‐evaluation of this species.     

Genetic diversity,population structure,and correlations between locally adapted zebu and taurine breeds in Brazil using SNP markers

Genetic diversity is one of the most important issues in studies on conservation of cattle breeds and endangered species. The objective of this study was to estimate the levels of genetic differentiation between locally adapted taurine (Bos taurus taurus) and zebu (Bos taurus indicus) breeds in Brazil, which were genotyped for more than 777,000 SNPs. The fixation index (F _ST), principal component analysis (PCA), and Bayesian clustering were estimated. The F _ST highlighted genetic differentiation between taurine and zebu breeds. The taurine lines, Caracu and Caracu Caldeano, had significant genetic differentiation (F _ST close to 5%) despite their recent selection for different uses (meat and milk). This genetic variability can be used for conservation of locally adapted animals, as well as for breeding programs on zebu breeds. Introgression of zebu in locally adapted breeds was identified, especially in Curraleiro Pé-Duro breed. The Gyr breed, however, had low breed purity at genomic level due to its very heterogeneous mixing pattern.     

Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms

Level of genetic differentiation, gene flow and genetic structuring of nine Bos indicus and three Bos taurus cattle breeds in Cameroon and Nigeria were estimated using the genetic information from 16 microsatellite, five blood protein and seven milk protein markers. The global heterozygote deficit across all populations (F_it) amounted to 11.7% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds (F_is) amounted to 6.1%. The breeds were moderately differentiated (F_st = 6%, p < 0.001) with all loci except CSN1S2 contributing significantly to the F_st value. The 12 populations belong to two genetic clusters, a zebu and a taurine cluster. While inferred sub‐clusters within the taurine group corresponded extremely well to predefined breed categorizations, no real sub‐clusters, corresponding to predefined breeds, existed within the zebu cluster. With the application of prior population information, cluster analysis achieved posterior probabilities from 0.962 to 0.994 of correctly assigning individuals to their rightful populations. High gene flow was evident between the zebu populations. Positive and negative implications of the observed genetic structure of the breeds on their development, improvement and conservation are discussed. The study shows that the breeds are threatened by uncontrolled breeding and therefore are at risk to become genetically uniform in the future. This situation can be avoided by putting in place effective breeding and management measures aimed at limiting uncontrolled mating between the breeds and to preserve special characteristics, genetic as well as breed biodiversity. The first step towards realizing these goals might be to geographically demarcate the breeds.     

An evaluation of genetic diversity indices of the Red Bororo and White Fulani cattle breeds with different molecular markers and their implications for current and future improvement options

The genetic diversity of the Red Bororo and White Fulani cattle breeds of Cameroon and Nigeria was assessed with a panel of 32 markers. Estimates for the various indices of genetic diversity, total number of alleles (TNA), mean observed number of alleles (MNA), mean effective number of alleles (MNE), observed heterozygosity (H _ob) and expected heterozygosity (H _ex), were higher at microsatellite loci than at protein loci. Mean H _ex values were above 71% at microsatellite loci in all the breeds and ranged from 37% to 41.6% at milk protein loci and from 40.9% to 45.6% at blood protein loci. The highest TNA and MNA of microsatellites were recorded for the Nigerian White Fulani. MNE of milk protein loci was highest in the Cameroonian Red Bororo, while TNA of blood protein loci was highest in the Cameroonian White Fulani. The high genetic diversity levels indicate the presence of the necessary ingredients for improvement breeding and conservation. Multi-locus estimates of within-population inbreeding (f), total inbreeding (F) and population differentiation (θ) of the breeds were significantly different from zero, except for θ of blood proteins. A high level of gene flow was found between the breeds (5.829). The phylogenetic relationship existing among the four breeds is greatly influenced by location. The high gene flow between the breeds may lead to a loss of genetic diversity through genetic uniformity and a reduction in opportunities for future breed development. We propose an improvement scheme with aims to prevent loss of genetic diversity, improve productivity and reduce uncontrolled genetic exchanges between breeds.     

Genetic population structure of red snapper (Lutjanus malabaricus) and orange‐spotted grouper (Epinephelus coiodes) in Brunei and Sabah

The genetic population structure of red snapper Lutjanus malabaricus and orange‐spotted grouper Epinephelus coiodes in Brunei and Sabah was investigated using allozyme electrophoresis. Samples were collected from three sites in Brunei for E. coiodes and from three sites in Brunei and Sabah for L. malabaricus. A total of 22 loci and 16 loci were scored, respectively. The index of fixation (F_ST) for the E. coiodes population was 0.176 but, in general, it lacked within‐population structuring. The F_ST was particularly high between Brunei Bay/Jerudong and Brunei Bay/ Kuala Belait, suggesting genetic subdivision on a small spatial scale. Isolation of Brunei Bay from the South China Sea may constrain the movement of adult fishes and larval dispersal, thereby reducing homogeneity among subpopulations. All variable loci for E. coiodes were in Hardy‐Weinberg equilibrium except for MDH* and GTDHP* (P < 0.01), in which two subpopulations showed an excess of heterozygotes (P < 0.01). The study on the L. malabaricus population showed a heterozygote deficit of approximately 60% in variable loci (F_ST genetic variation within population = 0.45; P < 0.05); however, the mean observed heterozygosity for the population far exceeded L. malabaricus populations in Australia and Indonesia. A F_ST value of 0.076 revealed moderate genetic differentiation among subpopulations of L. malabaricus. The genotypes were likely to be drawn from the same distribution in Jerudong and Kuala Belait. This study infers that sustainable management of snapper and grouper resources in Brunei waters must take into account the presence of a single stock and two stocks, respectively.     

Milk protein polymorphisms in cattle (Bos indicus), mithun (Bos frontalis) and yak (Bos grunniens) breeds and their hybrids indigenous to Bhutan

In the current study, milk protein variation was examined in cattle (Bos indicus), mithun (Bos frontalis), yak (Bos grunniens) and their hybrid populations in Bhutan to estimate genetic variability, conduct genetic characterization and assess the possibility of gene flow between mithun and cattle. Isoelectric focusing of 372 milk samples from 11 populations detected four molecular types of β‐lactoglobulin (A, B, E and M), five molecular types of α_S1‐casein (A, B, C, E and X) and three molecular types of k‐casein (A, B and X). Mithun and yak shared alleles but were found to exhibit different allele frequencies for the proteins studied. The degree of genetic variability within populations was measured by average heterozygosity and ranged from 24–40% in cattle, 26% for yak and 33% for mithun. We also resolved the traditional mithun and cattle hybridization system via principal component analysis. Our results suggested secondary introgression of mithun genes to the village Thrabum population, and a close genetic relationship between Bhutanese indigenous cattle and Indian cattle.     

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.     

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.