Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing

The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independently reported in two Asian primate research centers.Nevertheless,the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated.Here,we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing.We identified 14558184 single nucleotide polymorphisms(SNPs)from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples.Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers.In addition,SNP and copy number variation(CNV)analyses suggested that the WW domain-containing oxidoreductase(WWOX)and Tyrosine-protein phosphatase nonreceptor type 21(PTPN21)genes may be associated with epilepsy in marmosets.Notably,KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets.This study provides valuable population genomic resources for marmosets in two Asian primate centers.Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers,while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.

Molecular phylogenetics and population demographic history of Amphioctopus fangsiao,inferred from mitochondrial and microsatellite DNA markers

Amphioctopus fangsiao(Cephalopoda:Octopodidae)is an important commercial species in the coastal waters of China.In recent years,however,the resource of A.fangsiao have declined because of habitat destruction and overfishing.To analyze the genetic variations of A.fangsiao caused by the fluctuation of resources,the population genetic structure of nine sampling locations collected from the Bohai Sea to the South China Sea were investigated,using mtDNA COI fragments and microsatellite DNA.The results of F-statistics,AMOVA,STRUCTURE and PCA analyses showed three phylogeographic clades(Clades A,B and C),revealing limited genetic exchange between north and south populations.These clades diverged in 2.23(Clades A and B)and 3.67(Clades A,B and C)million years ago,during the dramatic environmental fluctuations,such as sea level and temperature changes,have exerted great influence on the survival distribution pattern of global organisms.Our results for low genetic connectivity among A.fangsiao populations provide insights into the development of management strategies,that is,to manage this species as separate management unit.

Haplotype and Genetic Analysis of 41 Y-STR Loci in the Wuwei Han Population from Gansu Province,China

Objective Y-Chromosomal short tandem repeat polymorphism(Y-STR)analysis plays an indispensable role in the identification of male individuals,population genetics,and biogeographic research.While profiles of many populations based on Y-STR markers in human genomes are ample,haplotype data for the Wuwei Han are still scarce.Methods In this study,2180 unrelated Wuwei Han male individuals residing in Gansu Province,China were collected and genotyped using the novel Microreader™40Y Plus ID system.Phylogenetic relationship reconstructions,multidimensional scaling(MDS),and heatmap analysis were performed based on the genetic distance(Rst)values between our studied population and other populations of the Ymax module in the Y-STR Haplotype Reference Database(YHRD).Results A total of 2129 unique haplotypes were obtained,and the haplotype diversity(HD)and discrimination capacity(DC)for the Wuwei Han were 0.9999 and 0.9931,respectively.Conclusion Our results demonstrate that the Wuwei Han population had intimate genetic relationships with East Asians,especially the geographically close Han populations.Overall,this Y-Chromosomal assay gives valuable information about paternal lineages in male individual tracking and genealogical database construction.

Genetic Structure of Malus sieversii Population from Xinjiang,China,Revealed by SSR Markers

One hundred and nine Malus sieversii accessions from four geographical populations located at Kuerdening in Mohe town, Gongliu County, Jiaowutuohai, in Xinyuan County, Daxigou in Houcheng County of Ily State, and Baerluke Mountain in Yumin County of Tacheng State, Xinjiang Uygur Autonomous Region of China were studied by SSR markers. The purpose of the study was to determine the genetic structure and diversity in these eco-geographical populations with eight pair SSR primers of apple. The results indicated that： an average of 16 bands was detected in the four populations. The percentage of polymorphic bands in Gongliu population （89.06%） was the highest in the four populations. The average Nei＇s gene diversity index was 0.257 for all the loci. Totally, 128 polymorphic loci were detected and the percentage of polymorphic loci （P） was 100%, 88.28%, 84.83%, 87.50%, and 87.12%, respectively, at the species level and Gongliu, Xinyuan, Huocheng, and Yumin population levels. The Nei＇s gene diversity index （H = 0.2619） and Shannon＇s information index （1 = 0.4082） in the species level were higher than in the population level. The Nei＇s gene diversity index and Shannon＇s information index in the four populations were Gongliu 〉 Huocheng 〉 Xinyuan 〉 Yumin. Gongliu population and Xinyuan population were the highest in genetic identity and the closest in genetic distance. Gene flow between the populations was 7.265 based on genetic differentiation coefficient （GST = 0.064）. The UPGMA cluster analysis indicated that the genetic relationships between the Gongliu and Xinyuan population were the closest, and the Yumin population were the farthest with the other three populations. The UPGMA cluster analysis indicated that the four geographical populations located in Gongliu, Xinyuan, Huocheng, and Yumin were relatively independent populations. Concurrently, there was also mild gene exchange between the populations. On the basis of the study of population genetic structure and the highest genetic diversity, Gongliu population should be given a high priority consideration in Malus sieversii population＇s in situ germplasm conservation.

Population Genetic Diversity in Chinese Pomegranate (Punica granatum L.) Cultivars Revealed by Fluorescent-AFLP Markers

Eighty-five pomegranate （Punica granatum L.） cultivars from six geographical populations located at Shandong, Anhui, Shaanxi, Henan, Yunnan, and Xinjiang Provinces were studied for its population genetic diversity by means of fluorescent-AFLP markers. The results indicated that 135-185 polymorphic loci were amplified by eight pairs of primers at species level. An average of 158.25 polymorphic loci was amplified for each primer combination. The polymorphism percentage ranged from 62.5% to 86.11%, and the average polymorphism percentage was 73.26%. This indicated that there was plentiful genetic diversity in pomegranate cultivars. The genetic diversity at the species level was higher than that at the population level. The order of the genetic diversity was Henan population 〉 Xinjiang population 〉 Shaanxi population 〉 Anhui population 〉 Shandong population 〉 Yunnan population. Variance analysis showed that there was significant difference between populations in genetic diversity. The genetic differentiation coefficient between populations （Gsr） was 0.2018, which indicated that gene differentiation was mainly within the population, and between populations, it accounted for 20.18% of the total variation. Gene flow （Nm） between the populations measured was 1.9027 based on the genetic differentiation coefficient between populations, indicating that there was mild gene flow between populations. The UPGMA cluster analysis showed that most accessions from the same population were clustered together, but there was partly gene exchange. All genetic parameters indicated that there was plentiful genetic diversity in pomegranate cultivars in China, of which Henan population was significantly higher than the other populations, and it had wide application foreground in pomegranate breeding in China.

Genetic Structure of Three Populations of Oxya chinensis in Shanxi,China

Starch gel electrophoresis was used to analyze genetic structure of three populations of Oxya chinensis from Shanxi Province,China.Four allozyme polymorphic loci (MDH-1,MDH-2,LDH,ME) were found.The data suggest that two populations of O.chinensis about 41 kilometers apart are genetically similar,but differentiated from the third population with a geographic distance of 357 kilometers.However,the heterozygosity levels of those two genetically similar populations were much different.The Nei's genetic distance between two geographically close populations is 0.068,which is much smaller than those of geographically distant populations (0.23 in average).The observed overlap of geographical distance and genetic distance implies that for O.chinensis population divergence may correlate with geographic isolation.

Population genetic diversity and regional differentiation of Chinese forest frog s (Rana chensinensis) in Heilongjiang Province

The Random Amplified Polymorphism DNA (RAPD) markers were used to stu dy the intra-specific diversity and regional differentiation of the Chinese fore st frogs (Rana chensinensis), which were sampled from the fields of 8 regions in Heilongjiang Province. Totally 78 polymorphic DNA loci were amplified by 10 RAP D primers. By genetic distance analysis and phylogenetic tree reconstruction wit h the Neighbor-Joining (NJ) method the results showed that the populations of Ch inese forest frogs distributed in 8 regions existed great differentiation (Avera ge Fst=0.347, SD=0.235) while there was the paradox between geographic distances and genetic distances. Based on geographic and geological data, a hypothesis wa s posed that it is very possible that the hilly lands in the downstream of the S onghua River and the Heilong River were the center of the origin of the Chinese forest frogs in Heilongjiang Province. And mainly through the Songhua River syst em, the Chinese forest frogs dispersed into the Songneng Plain from the Sanjiang Plain whereas the Fangzheng region became a sub-center for the western dispersi on.

Genetic variation of Laminaria japonica (Phaeophyta) populations in China as revealed by RAPD markers

For the population genetics analysis of the naturally grown brown seaweed Laminaria japonica （Laminariales,Phaeophyta） sampled from Dalian,Yantai,Weihai,Rongcheng and Qingdao in China,ten primers were employed to produce 88 bands as revealed by randomly amplified polymorphic DNA （RAPD） markers,and all these bands were polymorphic.According to these band patterns,there were 94 distinct phenotypes occurred in 100 samples indicating the high heterozygosity of this kelp.Dalian population samples showed the highest percentage of polymorphism （71.67%）,and also the higher diversity estimated on the basis of the Shannon’s index （8.498）,suggesting that this population could be chosen as the best resource for genetic breeding.The highest diversity of Yantai population possibly resulted from the introduction of L.longissima used for interspecific cross breeding with L.japonica cultivated in China.From Dalian southwards to Qingdao,the genetic variation of the five populations became less with a decrease in latitude,possibly due to the natural selection especially of high temperature.The genetic distance （Φ ST values） of the five populations was a little significantly correlated with the geographical distance （r=0.496） at P =0.05 by Mantel’s test.Weihai,Rongcheng and Yantai populations were closely grouped genetically together by Neighbor-joining cluster analysis probably in that the dispersal of the kelp by propagules more easily occurring in the range of relatively short distance.The analysis of molecular variance （AMOVA） also demonstrated that the relatively higher variation occurred among populations （71.49%） at an extremely significant level （P 0.000 1）.All these evidence showed that there was a relatively distinct genetic differentiation among the sampled kelp populations,and L.japonica grown in China was also rather heterozygous in heredity.

Molecular phylogeography and population genetic structure of the planktonic copepod Calanus sinicus Brodsky in the coastal waters of China

Planktonic copepod Calanus sinicus is the dominant meso-zooplankton in the Northwest Pacific Ocean. To better understand its population dynamics and phylogeographic patterns, 243 C. sinicus individuals were collected from seven locations across the shelf waters of China and its population genetics was studied by mitochondrial DNA cytochrome oxidase I（mtCOI） sequences analyses. Thirty-nine different sequences, or haplotypes, were detected with moderate haplotype diversity（h=0.749） and low nucleotide diversity（π=0.003） for all populations. The evolutionary divergence between geographic populations varied from 0.24% to 0.37%, indicative of very limited genetic differentiation. Visualized minimum spanning network（MSN） and phylogenetic analysis of all the detected haplotypes did not reveal any clear phylogeographic pattern. Furthermore, AMOVA data showed no significant spatial population differentiation existed among the individuals collected across China shelf waters. Pairwise FST values showed that population collected from northwest of the East China Sea（ECS） displayed a low difference to other populations. Mismatch distribution analyses and neutrality tests indicated that C. sinicus might undergo a demographic/population expansion. No significant population genetic structuring was detected, indicating an extensive gene flow among the C. sinicus populations. Our results provide molecular evidence for the hypothesis that C. sinicus in the northwestern South China Sea in winter is transported from the East China Sea and the Yellow Sea by the China Coastal Current during the northeast monsoon period.

Population genetic studies in the genomic sequencing era

Recent advances in high-throughput sequencing technologies have revolutionized the field of population genetics. Data now routinely contain genomic level polymorphism information, and the low cost of DNA sequencing enables researchers to investigate tens of thousands of subjects at a time. This provides an unprecedented opportunity to address fundamental evolutionary questions, while posing challenges on traditional population genetic theories and methods. This review provides an overview of the recent methodological developments in the field of population genetics, specifically methods used to infer ancient population history and investigate natural selection using large-sample, large-scale genetic data. Several open questions are also discussed at the end of the review.

Population Genetic Structure and Genetic Differentiation of the Pufferfish Takifugu Rubripes and Takifugu Pseudommus Revealed by RAPD Analysis

RAPD analysis is used to assay the population genetic structure and genetic differentiation of pufferfish T. rubripes and T. pseudammus. One hundred and twenty fragments are amplified with 21 random sequence 10-mer primers. The proportion of polymorphic fragments of T. rubripes populations from the coast of China (TRC), the coast of Japan (TRJ), general population of T. rubripes both from China and Japan (TRCJ), and the population of T. pseudommus are 31.7%, 33.3%, 35.0% and 39.2 % respectively. The mean expected heterozygositiee of the four populations are 0. 116, 0. 125, 0. 126, and 0. 144, respectively. Low genetic distances (ranging from 0.0118 to 0.0309) and Fst estimates (0.020 to 0.024) among the populations in-dicated that there is no significant differentiation between T. rubripes and T. pseudommus and suggested that only one species is involved.

Genetic diversity analysis of spawner and recaptured populations of Chinese shrimp(Fenneropenaeus chinensis)during stock enhancement in the Bohai Bay based on an SSR marker

Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles（N_a） were 8–63 and 6–60, respectively. The numbers of effective alleles（N_e） were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity（H_o） values（0.638–0.910 and 0.712–0.927） were lower than the expected heterozygosity（H_e） values（0.603–0.954 and 0.625–0.952）, which indicated that the two populations possessed a rich genetic diversity. In 16 tests（2 populations×8 loci）, 13 tests deviated from the HardyWeinberg equilibrium. F_（is） values were positive at seven loci and the inbreeding coefficients（F） of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_（st） values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes（3 060.2 and 3 842.8） were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.

Population genetics of Sargassum horneri (Fucales, Phaeophyta) in China revealed by ISSR and SRAP markers

Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR (inter simple sequence repeat) and SRAP (sequence related amplified polymorphism) markers were used to analyze the population genetics among nine natural populations of S. horneri. The nine studied populations were distributed over 2 000 km from northeast to south China. The percentage of polymorphic loci P% (ISSR, 99.44%; SRAP, 100.00%), Nei's genetic diversity H (ISSR, 0.107-0.199; SRAP, 0.100-0.153), and Shannon's information index I (ISSR, 0.157-0.291; SRAP, 0.148-0.219) indicated a fair amount of genetic variability among the nine populations. Moreover, the high degree of gene differentiation G st (ISSR, 0.654; SRAP, 0.718) and low gene flow N m (ISSR, 0.265; SRAP, 0.196) implied that there was significant among-population differentiation, possibly as a result of habitat fragmentation. The matrices of genetic distances and fixation indices (F st ) among the populations correlated well with their geographical distribution (Mantel test R=0.541 5, 0.541 8; P=0.005 0, 0.002 0 and R=0.728 6, 0.641 2; P=0.001 0, 0.001 0, respectively); the Rongcheng population in the Shandong peninsula was the only exception. Overall, the genetic differentiation agreed with the geographic isolation. The fair amount of genetic diversity that was revealed in the S. horneri populations in China indicated that the seaweed resources had not been seriously affected by external factors.

Genetic variation and population structure of the mushroom Pleurotus ferulae in China inferred from nuclear DNA analysis

To investigate the genetic diversity of an edible fungus Pleurotus ferulae, a total of 89 wild samples collected from six geographical locations in the Xinjiang Uygur Autonomous Region of China and two geographical locations in Italy, were analyzed using three DNA fragments including the translation elongation factor（EF1α）, the second largest subunit of t he RNA polymerase II（RPB2） and the largest subunit of the RNA polymerase II（RPB1）. The results indicated relatively abundant genetic variability in the wild resources of P. ferulae. The analysis of molecular variance（AMOVA） showed that the vast majority of the genetic variation was found within geographical populations. Both the Chinese populations and the Italian populations of P. ferulae displayed a limited genetic differentiation. The degree of differentiation between the Chinese populations and the Italian populations was obviously higher than that between the populations from the same region, and moreover the genetic differentiation among all the tested populations was correlated to the geographical distance. T he phylogeny analyses confirmed that samples from China and Italy belonged to another genetic group separated from Pleurotus eryngii. They were closely related to each other but were clustered according to their geographical origins, which implied the Chinese populations were highly differentiated from the Italian populations because of distance isolation, and the two populations from different regions might be still in the process of allopatric divergence.

Genetic Differentiation of Japanese Sardinella(Sardinella zunasi) Populations in the Northwest Pacific Revealed by ISSR Analysis

Knowledge of population genetic structure plays an important role in fisheries management.In this research,In-ter-Simple-Sequence-Repeat(ISSR)markers were employed to evaluate the genetic structure of Japanese sardinella(Sardinella zun-asi)populations in the Northwest Pacific.Eighty seven individuals from 5 locations were screened using 4 highly polymorphic prim-ers.A total of 173 polymorphic loci were detected out of 191 loci amplified.Small but significant genetic differentiation was de-tected between the Chinese and Japanese populations by both AMOVA and pairwise FST analyses,which was further supported by cluster analysis.We consider that climate change during glaciations should be responsible for the genetic differentiation.Isolation by geographic distance among populations was observed,indicating that the distance might also lead to the genetic differentiation.However,no genetic structure was found within the populations off both the Chinese and Japanese coasts,indicating a high-level along-coast gene flow,which might result from ocean current transport and common ground for over-wintering.

Genetic Diversity and Population Structure in Landraces and Improved Rice Varieties from India

A set of 50 rice genotypes comprising landraces, local selections, and improved varieties were characterized using simple sequence repeat（SSR） and inter simple sequence repeat（ISSR） markers to study genetic diversity and population structure. Following unweighted pair group method with arithmetic mean based clustering using binary data of polymorphic markers, the genotypes were grouped into 5 clusters and 11 sub-clusters, whereas population structure analysis separated 50 rice genotypes into 5 sub-populations. Grouping of rice genotypes showed better resemblance with the pedigree information of the genotypes. Both genetic diversity and population structure analysis separated majority of the improved varieties from landraces and local selections. Some of the SSR markers amplified unique alleles which were specific to a particular genotype and could distinguish them from the rest. The results indicate that these rice genotypes exhibit a higher genetic diversity and can be very useful in rice improvement program.

Genetic diversity and population genetic structure of Python bivittatus in China

The Burmese python （Python bivittatus） has recently suffered large population declines in the wild in China due to illegal capture, overexploitation, deforestation and the loss of its natural habitat. Greater knowledge of the genetic diversity and structure of wild P. bivittatus populations is needed to help ensure its effective management. In this study, we investigated the genetic diversity and population genetic structure of wild P. bivittatus in China in detail. 109 P. bivittatus individuals from five distribution areas in Guangdong （GD）, Guangxi （GX）, Hainan （HN）, Fujian （FJ） and Yunnan （YN） province of China were collected, and their genetic structure and diversity were analyzed. Eight highly polymorphic microsatellite loci were utilized to reveal high levels of genetic diversity in the P. bivittatus population. Genetic diversity was highest in GX, and lowest in GD. All geographic populations demonstrated a bottleneck effect indicating recent population decline. Fst and AMOVA analyses revealed that there was moderate genetic differentiation among the five populations, and that only 10.59 % of total genetic diversity occurred among populations. Fst values between pop- ulations were positively correlated with their geographical distances. Genetic structure analyses revealed that the HN, GX and GD populations, which were geographically closest, were assigned to a genetic cluster, while the YN and FJ populations constituted a single cluster, respectively.

Reveal the Population Genetic Characteristics of Bombay Duck (Harpadon nehereus) in Coastal Waters of China with Genotyping-by-Sequencing Technique

Bombay duck(Harpadon nehereus)is an economically important species in the estuarine and coastal offshore waters of the Indo-West Pacific.This study aims to reveal the genome-wide genetic characteristics of five populations of H.nehereus from the coastal areas of China by using the genotyping-by-sequencing technique.After strict filtering,32088 high-quality single-nucleotide polymorphism markers were detected and analyzed.The average observed heterozygosity and expected heterozygosity ranged from 0.41651 to 0.56725 and from 0.30998 to 0.45531,respectively,indicating that heterozygosity excess occurred in H.nehereus populations.The nucleotide diversity ranged from 0.63664 to 0.74868,which was larger than those from other marine fishes.No obvious genetic structure was detected among H.nehereus populations,and the genetic variation originated within individuals.Extensive gene exchange caused by longshore currents in the reproductive season might be the primary reason for the weak genetic differentiation.Among various environmental factors,water temperature might be the key element affecting the genetic structure of H.nehereus.Due to the destruction and overfishing of spawning grounds,the fishery resources declined in recent years.This study could serve as a reference for the resource protection and rational utilization of H.nehereus.

Microsatellite marker development and population genetic analysis revealed high connectivity between populations of a periwinkle Littoraria sinensis(Philippi,1847)

Periwinkle Littoraria sinensis is a widely distributed gastropod in rocky intertidal zone of the northwestern Pacifi c.To examine genetic diversity and genetic connectivity among coastal populations of L.sinensis in China,1636 pairs of primers were successfully designed using whole-genome shotgun sequencing,de novo assembly,and a bioinformatics pipeline QDD.Twelve highly variable polymorphic markers were selected to genotype 351 individuals from 15 populations.Data of nine microsatellite loci were retained for population genetic analysis,and weak genetic differentiation among populations were detected,suggesting high gene flow among populations.The long planktonic larval duration of L.sinensis might have played an important role in the high gene flow among populations.A tendency of genetic differentiation between north and south populations of L.sinensis was detected,which might be resulted from isolation due to lowered sea level in the last glacial maximum.Furthermore,the newly founded populations along the coast of Jiangsu Province were closely related to populations to the south of the Changjiang(Yangtze)River estuary,suggesting that the main source of the newly founded populations is from natural rocky populations south of the estuary.

Population Genetic Analysis of Sillago nigrofasciata (Perciformes:Sillaginidae) Along the Coast of China by Sequencing Mitochondrial DNA Control Region

Sillago nigrofasciata, a small to moderate size nearshore species, is newly found along the eastern and southern coasts of China. The present study is carried out in order to analyze the population genetics of the S. nigrofasciata. The control region sequence of mitochondrial DNA revealing 73 haplotypes were obtained from 162 individuals collected at 8 locations along the coast of China. The whole S. nigrofasciata population along the coast of China showed a low nucleotide diversity(0.012) and a high population diversity(haplotype diversity)(0.943), and all the 8 local populations showed low nucleotide diversities(0.014 – 0.001), suggesting the protective measures are effective. The haplotypes of the 8 local populations were widely distributed in haplotype network diagram and neighbor-joining phylogenetic tree, while no branch associating with sampling locations was detected. Recent gene flow analysis showed asymmetric gene exchanges among local populations. The pairwise FST values and unweighted pair-group method with arithmetic mean(UPGMA) tree revealed a certain amount of genetic difference among local populations. Moreover, analysis of molecular variance(AMOVA) reflected genetic differences between hypothetical subdivision groups. Neutral test and mismatch distribution of pairwise nucleotide suggested S. nigrofasciata may have experienced recent population expansion events. The historical geographic events associating with ice age may be the main explanation to the heterogeneity among local populations with short geographic distances, and the homogeneity among local populations with long geographic distances.