Strong Gene Flow Research Articles

When maladaptive gene flow does not increase selection.

Populations receiving high maladaptive gene flow are expected to experience strong directional selection-because gene flow pulls mean phenotypes away from local fitness peaks. We tested this prediction by means of a large and replicated mark-recapture study of threespine stickleback (Gasterosteus aculeatus) in two stream populations. One of the populations (outlet) experiences high gene flow from the lake population and its morphology is correspondingly poorly adapted. The other population (inlet) experiences very low gene flow from the lake population and its morphology is correspondingly well adapted. Contrary to the above prediction, selection was not stronger in the outlet than in the inlet, a result that forced us to consider potential reasons for why maladaptive gene flow might not increase selection. Of particular interest, we show by means of a simple population genetic model that maladaptive gene flow can-under reasonable conditions-decrease the strength of directional selection. This outcome occurs when immigrants decrease mean fitness in the resident population, which decreases the strength of selection against maladapted phenotypes. We argue that this previously unrecognized effect of gene flow deserves further attention in theoretical and empirical studies.

Genetic differentiation of European larch along an altitudinal gradient in the French Alps

Despite variable dynamics of genetic diversification at the different altitudinal levels, strong gene flow tends to standardize larch genetic diversity: the larch forest distributed along the altitudinal gradient can be regarded as a single population. While in forest tree species many studies focus on the structure of the genetic diversity at the natural range and at the forest stand levels, few studies have worked at intermediate levels like the landscape level. We tried to determine to what degree altitude variation can affect the genetic diversity and the local structure of the genetic diversity of European larch (Larix decidua Miller) at the landscape level. Using microsatellite markers, we determined the between- and within-plot genetic structure and the spatial genetic structure (SGS) of four altitudinal plots distributed between 1,350 and 2,300 m a.s.l. in a European larch forest located in the French Alps. A homogenous neutral genetic structure was detected along this gradient. The intensity of the SGS was found to be stronger at 2,300 m and decreased at the 2,000-m plot. It was low or non-existent at the 1,700- and 1,350-m altitudinal levels. Our results suggest that the genetic structure observed at the landscape level in this European larch forest was only slightly affected by climatic variation, human activities, or historical events. However, the variation of intensity of the SGS within the altitudinal plots indicates the existence of variable genetic dynamics, despite the globally uniform genetic structure along the altitudinal gradient.

Population genetic structure of serotine bats (Eptesicus serotinus) across Europe and implications for the potential spread of bat rabies (European bat lyssavirus EBLV-1).

Understanding of the movements of species at multiple scales is essential to appreciate patterns of population connectivity and in some cases, the potential for pathogen transmission. The serotine bat (Eptesicus serotinus) is a common and widely distributed species in Europe where it frequently harbours European bat lyssavirus type 1 (EBLV-1), a virus causing rabies and transmissible to humans. In the United Kingdom, it is rare, with a distribution restricted to south of the country and so far the virus has never been found there. We investigated the genetic structure and gene flow of E. serotinus across the England and continental Europe. Greater genetic structuring was found in England compared with continental Europe. Nuclear data suggest a single population on the continent, although further work with more intensive sampling is required to confirm this, while mitochondrial sequences indicate an east-west substructure. In contrast, three distinct populations were found in England using microsatellite markers, and mitochondrial diversity was very low. Evidence of nuclear admixture indicated strong male-mediated gene flow among populations. Differences in connectivity could contribute to the high viral prevalence on the continent in contrast with the United Kingdom. Although the English Channel was previously thought to restrict gene flow, our data indicate relatively frequent movement from the continent to England highlighting the potential for movement of EBLV-1 into the United Kingdom.

Genetic differentiation in the barnacle Catomerus polymerus despite migration across a biogeographic barrier

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 524:213-224 (2015) - DOI: https://doi.org/10.3354/meps11177 Genetic differentiation in the barnacle Catomerus polymerus despite migration across a biogeographic barrier L. A. Aguilar*, D. G. Roberts, T. E. Minchinton, D. J. Ayre Institute for Conservation Biology and Environmental Management, School of Biological Sciences, University of Wollongong, Wollongong NSW 2522, Australia *Corresponding author: laa045@uowmail.edu.au ABSTRACT: Biogeographic barriers can set range limits for marine organisms by restricting migration, or because subsequent recruitment may be prevented by post-settlement selection. We used microsatellite and mtDNA data for adults and juveniles of the barnacle Catomerus polymerus to test the hypothesis that persistent differentiation of populations occurring to the northeast as compared with south and west of the southeast Australian biogeographic barrier (SEABB) is maintained by selection rather than dispersal limitation. We also explored the dispersal of C. polymerus along uninterrupted linear stretches of coastline (1440 km) to the east and west (120 km) of the SEABB. Within the regions flanking the SEABB, we found little genetic differentiation (FST < 0.006), implying strong gene flow. In contrast, adults to the northeast were significantly differentiated from those to the south and southwest of the SEABB (FST = 0.10), confirming some restriction of gene flow by the SEABB. Similarly, Bayesian analyses revealed eastern and western clusters of adults and juveniles, with the great majority assigning strongly to their region of collection. Nevertheless, 5 of 556 adults, and 10 of 537 juveniles, had genotypes that aligned more strongly with the genetic cluster of the opposite side of the SEABB, implying that migration does occur. Mitochondrial DNA sequence data (n = 71) revealed one additional eastern adult with an immigrant western haplotype. Our data imply that differentiation of eastern and western lineages reflects both restricted dispersal and possibly regional-scale selection acting on immigrant genotypes. KEY WORDS: Australia · Gene flow · Marine invertebrate · Recruitment · Rocky intertidal shores · Range limits Full text in pdf format PreviousNextCite this article as: Aguilar LA, Roberts DG, Minchinton TE, Ayre DJ (2015) Genetic differentiation in the barnacle Catomerus polymerus despite migration across a biogeographic barrier. Mar Ecol Prog Ser 524:213-224. https://doi.org/10.3354/meps11177 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 524. Online publication date: March 30, 2015 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2015 Inter-Research.

Wide-range genetic connectivity of Coney, Cephalopholis fulva (Epinephelidae), through oceanic islands and continental Brazilian coast.

The Epinephelidae form a group of species of high biological and economical interests. It´s phylogeographic patterns are not well known especially the distributed populations in the western region of the Atlantic Ocean. Among the representatives is a small species called Cephalopholis fulva, Coney, which presents a wide geographical distribution, polychromia, hermaphroditism and is quickly becoming a large target for the exploration of commercial fishing. The genetic and historical demography were obtained through the partial sequence analysis of Control Region from six locations on the coastline of Brazil from the northeast coast to the southwest coast, including the oceanic islands of Rocas Atoll and Fernando de Noronha Archipelago. The analyzed samples revealed a high genetic variability and a strong gene flow among the sampled locations. Additionally, the genetic data revealed that population expansions probably occurred due to the changes in the sea levels that occurred during the Pleistocene. The large population connectivity found in Coney constitutes relevant conditions for their biological conservation.

Hybridization and mitochondrial genome introgression betweenRana chensinensisandR. kukunoris

Mitochondrial genome (mito-genome) introgression among metazoans is commonplace, and several biological processes may promote such introgression. We examined two proposed processes for the mito-genome introgression between Rana chensinensis and R. kukunoris: natural hybridization and sex-biased dispersal. We sampled 477 individuals from 28 sites in the potential hybrid zone in the western Tsinling Mountains. Mitochondrial gene (cyt-b) trees were used to examine the introgression events. Microsatellite DNA loci, cyt-b and morphological data were used to identify hybrids and to examine the extent of natural hybridization. We detected rampant bidirectional introgressions, both ancient and recent, between the two species. Furthermore, we found a wide hybrid zone, and frequent and asymmetric hybridization. The hybrid zone cline analysis revealed a clear mitochondrial-nuclear discordance; while most nuclear markers displayed similar and steep clines, cyt-b had a displaced cline centre and a more gradual and wider cline. We also detected strong and asymmetric historical maternal gene flow across the hybrid zone. This widespread hybridization and detected low mito-nuclear conflicts may, at least partially, explain the high frequency of introgression. Lastly, microsatellite data and population genetic methods were used to assess sex-biased dispersal. A weak pattern of female-biased dispersal was detected in both species, suggesting it may not play an important role in the observed introgression. Our data are consistent with the hybridization hypothesis, but support for the sex-biased dispersal hypothesis is weak. We further suggest that selective advantages of the R. kukunoris-type mito-genome in thermal adaptation may also contribute to the introgression between the two species.

Genetic structure of Saxifraga rosacea subsp. sponhemica, a rare endemic rock plant of Central Europe

We used RAPD markers to study the population genetic structure and diversity of Saxifraga rosacea subsp. sponhemica, a rare Central European endemic rock plant with a highly disjunct distribution. Because of strong isolation current gene flow between populations is very low or absent. However, an isolation by distance pattern of genetic differentiation suggested historical gene flow during the last glaciation when suitable habitats for S. sponhemica were much more abundant. In most populations, considerable genetic variability has been preserved due to the longevity of S. sponhemica. Our results suggest that long-lived plant species can maintain historic genetic patterns despite small size and strong isolation of populations. Several RAPD loci were identified to be non-neutral and their frequencies correlated with climatic gradients, indicating natural selection. Adaptive genetic variation could be important for adaptation to environmental changes like ongoing climate change. The taxon does not appear to be genetically threatened in the short term, but populations are threatened by habitat destruction. The establishment of new populations in suitable habitats with seeds from the same region may be a suitable conservation measure avoiding potential maladaptation due to local adaptation.

Phylogeography and genetic diversity ofOphidiaster ophidianus(Echinodermata: Asteroidea)—evidence for a recent range expansion in the Azores

The seastarOphidiaster ophidianusis a vulnerable and protected species in the Mediterranean Sea but is common on North Atlantic islands such as the Azores and Madeira archipelagos. This work presents new insights into the phylogeography and genetic diversity ofO. ophidianusfrom the Azores, based on 67 sequences of the 16S mitochondrial gene and 46 sequences of the nuclear ATP intron 5 gene. Twenty-six samples from the Mediterranean and seven samples from Madeira were used as out-groups. The results revealed that there is a lack of genetic differentiation betweenO. ophidianusfrom the Azores and the out-groups. All, therefore, belong to the same lineage and argue for a fast and recent range expansion of this species into the Azores. Our results also suggest the existence of distinctive periods of strong gene flow followed by periods of either low or non-existent gene flow between the Mediterranean Sea and this archipelago, which could explain the presence of private haplotypes in all studied areas.

Genetic diversity and taxol content variation in the Chinese yew Taxus mairei

Taxus mairei is an endangered plant with high medicinal value in China. In the present study, inter-simple sequence repeat markers and high-performance liquid chromatography (HPLC) were used to investigate genetic diversity, taxol content, and the inter-relationship of these two variables in 11 populations. Genetic diversity was high at the species level [percentage of polymorphic bands (PPB) = 91.73 %; Nei’s gene diversity (h) = 0.2428; Shannon’s information index (I) = 0.3771], but relatively lower at the population level (PPB = 54.14–67.67 %; h = 0.1809–0.2121; I = 0.2721–0.3211). Hierarchical analysis of molecular variance (AMOVA) revealed moderate genetic differentiation among populations (OST = 16.13 %), in line with the low gene differentiation coefficient (GST = 0.1697) and relatively strong gene flow (Nm = 2.4480). Both UPGMA and principal coordinates analysis supported the clustering of all 11 populations into three groups. A Mantel test indicated a significant correlation between geographic and genetic distances (r = 0.405; P < 0.005). Taxol content varied significantly among populations, ranging from 0.0069 to 0.0127 % based on the HPLC analysis. The taxol content was not significantly associated with genetic diversity, but was significantly, negatively associated with population latitude (r = −0.620; P < 0.005). This implies that local temperature may significantly affect the taxol content, although the role of heredity cannot be neglected. Our findings provided important references for resource protection and sustainable management of this valuable plant.

Genetic diversity and population differentiation of the Chinese soft-shelled turtle (Pelodiscus sinensis) in three geographical populations

The Chinese soft-shelled turtle (Pelodiscus sinensis) is one of the most important economical chelonians in the world. To understand the genetic variations of the Chinese soft-shelled turtle in China, 62 individuals were sampled from three localities and 18 polymorphic microsatellite loci tested were used to detect genetic diversity and population structure. Results showed that the genetic diversity of the wild P. sinensis was high. Except for the Wuhu populations, the majority of microsatellite loci are not deviation from Hardy–Weinberg equilibrium in the other two populations. AMOVA analysis indicated that genetic variations occurred mainly within populations (97.4%) rather than among populations (2.6%). The gene flow estimates (Nm) among three geographic populations demonstrated that strong gene flow existed (Nm > 1, mean 6). The present study supported that different habitats, breed turtles escaped, multiple paternity and long evolutionary history may be responsible for the current genetic diversity and differentiation in the wild Chinese soft-shelled turtle.

Microsatellite and mitochondrial markers reveal strong gene flow barriers for Anopheles farauti in the Solomon Archipelago: implications for malaria vector control

Anopheles farauti is the primary malaria vector throughout the coastal regions of the Southwest Pacific. A shift in peak biting time from late to early in the night occurred following widespread indoor residue spraying of dichlorodiphenyltrichloro-ethane (DDT) and has persisted in some island populations despite the intervention ending decades ago. We used mitochondrial cytochrome oxidase I (COI) sequence data and 12 newly developed microsatellite markers to assess the population genetic structure of this malaria vector in the Solomon Archipelago. With geographically distinct differences in peak A. farauti night biting time observed in the Solomon Archipelago, we tested the hypothesis that strong barriers to gene flow exist in this region. Significant and often large fixation index (FST) values were found between different island populations for the mitochondrial and nuclear markers, suggesting highly restricted gene flow between islands. Some discordance in the location and strength of genetic breaks was observed between the mitochondrial and microsatellite markers. Since early night biting A. farauti individuals occur naturally in all populations, the strong gene flow barriers that we have identified in the Solomon Archipelago lend weight to the hypothesis that the shifts in peak biting time from late to early night have appeared independently in these disconnected island populations. For this reason, we suggest that insecticide impregnated bed nets and indoor residue spraying are unlikely to be effective as control tools against A. farauti occurring elsewhere, and if used, will probably result in peak biting time behavioural shifts similar to that observed in the Solomon Islands.

High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid.

BackgroundGene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci.ResultsWe expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) ‘outlier’ loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations.ConclusionsThe findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe.

Variable salinity tolerance in ascidian larvae is primarily a plastic response to the parental environment

Both phenotypic plasticity and local genetic adaptation may contribute to a species’ ability to inhabit different environmental conditions. While phenotypic plasticity is usually considered costly, local adaptation takes generations to respond to environmental change and may be constrained by strong gene flow. The majority of marine species have complex life-cycles with pelagic stages that might be expected to promote gene flow and plastic responses, and yet several notable examples of local adaptation have been found in species with broadcast larvae. In the ascidian, Ciona intestinalis (Linnaeus, 1767),—a common marine species with broadcast spawning and a short larval stage—previous studies have found marked differences in salinity tolerance of early life-history stages among populations from different salinity regimes. We used common-garden experiments to test whether observed differences in salinity tolerance could be explained by phenotypic plasticity. Adult ascidians from two low salinity populations [2–5 m depth, ~25 practical salinity units (PSU)], and two full salinity populations (25–27 m depth, ~31 PSU) were acclimated for 2–4 weeks at both 25 and 31 PSU. Gametes were fertilized at the acclimation salinities, and the newly formed embryos were transferred to 10 different salinities (21–39 PSU) and cultured to metamorphosis. Adult acclimation salinity had an overriding and significant effect on larval metamorphic success: tolerance norms for larvae almost fully matched the acclimation salinity of the parents, independent of parental origin (deep or shallow). However we also detected minor population differences that could be attributed to either local adaptation or persistent environmental effects. We conclude that differences in salinity tolerance of C. intestinalis larvae from different populations are driven primarily by transgenerational phenotypic plasticity, a strategy that seems particularly favourable for an organism living in coastal waters where salinity is less readily predicted than in the open oceans.

Evidence for Divergence in Populations of Bonobos (Pan paniscus) in the Lomami-Lualaba and Kasai-Sankuru Regions Based on Preliminary Analysis of Craniodental Variation

Historical climatic events and riverine barriers influence the distribution of primates. The River Congo exerts the most significant influence on primate distribution in equatorial Africa, but the extent to which the inner basin of the Congo provided a refuge against Plio-Pleistocene climatic fluctuation is poorly understood. In this study we use cranial and dental morphometrics to examine how riverine barriers affect population patterns in bonobos (Pan paniscus). Bonobos and chimpanzees (Pan troglodytes) are sister species and share the distinction of being the closest evolutionary relatives of humans, yet comparatively little is known about bonobo morphological diversity. We selected 55 adult bonobo crania with well-preserved postcanine dentitions and divided them into regions separated by the rivers Lukenie, Kasai, Lomami, and Lualaba. We found good discrimination among these regions in cranial and dental metrics, but whereas the discriminant functions from cranial metrics were statistically significant, the discriminant functions from dental metrics were not. Mean classification accuracy was 89% for craniometrics, and ranged between 72% and 93% for dental metrics. On average 84–97% of phenetic variation was encountered within regions. Our results mirror molecular studies in suggesting that bonobos are characterized by a long-term stable demographic history allowing strong gene flow between regions and precluding drift and population differentiation. There are some indications that the bonobos from the Lomami-Lualaba and the Kasai-Sankuru regions are divergent, but modest sample sizes do not allow us to be conclusive. We would welcome the opportunity to work with field researchers to augment our sample sizes and reanalyze our data.

GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON?

Gene flow among populations can enhance local adaptation if it introduces new genetic variants available for selection, but strong gene flow can also stall adaptation by swamping locally beneficial genes. These outcomes can depend on population size, genetic variation, and the environmental context. Gene flow patterns may align with geographic distance (IBD--isolation by distance), whereby immigration rates are inversely proportional to the distance between populations. Alternatively gene flow may follow patterns of isolation by environment (IBE), whereby gene flow rates are higher among similar environments. Finally, gene flow may be highest among dissimilar environments (counter-gradient gene flow), the classic "gene-swamping" scenario. Here we survey relevant studies to determine the prevalence of each pattern across environmental gradients. Of 70 studies, we found evidence of IBD in 20.0%, IBE in 37.1%, and both patterns in 37.1%. In addition, 10.0% of studies exhibited counter-gradient gene flow. In total, 74.3% showed significant IBE patterns. This predominant IBE pattern of gene flow may have arisen directly through natural selection or reflect other adaptive and nonadaptive processes leading to nonrandom gene flow. It also precludes gene swamping as a widespread phenomenon. Implications for evolutionary processes and management under rapidly changing environments (e.g., climate change) are discussed.

Distinct subspecies or phenotypic plasticity? Genetic and morphological differentiation of mountain honey bees in East Africa

Identifying the forces shaping intraspecific phenotypic and genotypic divergence are of key importance in evolutionary biology. Phenotypic divergence may result from local adaptation or, especially in species with strong gene flow, from pronounced phenotypic plasticity. Here, we examine morphological and genetic divergence among populations of the western honey bee Apis mellifera in the topographically heterogeneous East African region. The currently accepted “mountain refugia hypothesis” states that populations living in disjunct montane forests belong to a different lineage than those in savanna habitats surrounding these forests. We obtained microsatellite data, mitochondrial sequences, and morphometric data from worker honey bees collected from feral colonies in three montane forests and corresponding neighboring savanna regions in Kenya. Honey bee colonies from montane forests showed distinct worker morphology compared with colonies in savanna areas. Mitochondrial sequence data did not support the existence of the two currently accepted subspecies. Furthermore, analyses of the microsatellite data with a Bayesian clustering method did not support the existence of two source populations as it would be expected under the mountain refugia scenario. Our findings suggest that phenotypic plasticity rather than distinct ancestry is the leading cause behind the phenotypic divergence observed between montane forest and savanna honey bees. Our study thus corroborates the idea that high gene flow may select for increased plasticity.

Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon.

Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by FST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (HE = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (HE = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.

Population genetics, gene flow, and biogeographical boundaries ofCarcinus aestuarii(Crustacea: Brachyura: Carcinidae) along the European Mediterranean coast

Carcinus aestuarii Nardo, 1847 is a widespread coastal crab species throughout the Mediterranean Sea with a pelagic larval phase. This species tolerates a wide range of environmental conditions and typically inhabits fragmented habitats, such as embayments, lagoons and estuaries. It is therefore a good candidate species for studying and testing different phylogeographical hypotheses in the Mediterranean Sea. By contrast to its Atlantic sister species, Carcinus maenas, studies on the population genetic structure of C. aestuarii in its native range are still scarce. In the present study, specimens from along the European Mediterranean Sea were collected and DNA-sequenced and analyses were applied to discriminate between present day and historical factors influencing the population genetic structure of this species. The results obtained demonstrate the existence of two genetically distinct geographical groups, corresponding to the eastern and western Mediterranean, with further subdivision within the East Mediterranean Basin. A strong asymmetric gene flow was recorded toward the Eastern Basin, which may play a crucial role in shaping the present day biogeographical patterns of this species and potentially other sympatric ones with pelagic larvae. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 771‐790. ADDITIONAL KEYWORDS: biodiversity ‐ cox1 ‐ demographic history ‐ larval dispersal ‐ Mediterranean Sea ‐ phylogeography.

Mitochondrial DNA diversity and the origin of Chinese indigenous sheep

Large-scale mitochondrial DNA (mtDNA) D-loop sequences data from previous studies were investigated to obtain genetic information which contributes to a better understanding of the genetic diversity and history of modern sheep. In this study, we analyzed mtDNA D-loop sequences of 963 individuals from 16 Chinese indigenous breeds that distributed seven geographic regions. Phylogenetic analysis showed that all three previously defined haplogroups A, B, and C were found in all breeds among different regions except in Southwest China mountainous region, which had only the A and B haplogroups. The weak phylogeographic structure was observed among Chinese indigenous sheep breeds distribution regions and this could be attributable to long-term strong gene flow among regions induced by the human migration, commercial trade, and extensive transport of sheep. The estimation of demographic parameters from mismatch analyses showed that haplogroups A and B had at least one demographic expansion of indigenous sheep in China.

Phylogeography and Domestication of Chinese Swamp Buffalo

To further probe into whether swamp buffaloes were domesticated once or multiple times in China, this survey examined the mitochondrial DNA (mtDNA) Control Region (D-loop) diversity of 471 individuals representing 22 populations of 455 Chinese swamp buffaloes and 16 river buffaloes. Phylogenetic analysis revealed that Chinese swamp buffaloes could be divided into two distinct lineages, A and B, which were defined previously. Of the two lineages, lineage A was predominant across all populations. For predominant lineage A, Southwestern buffalo populations possess the highest genetic diversity among the three hypothesized domestication centers (Southeastern, Central, and Southwestern China), suggesting Southwestern China as the most likely location for the domestication of lineage A. However, a complex pattern of diversity is detected for the lineage B, preventing the unambiguous pinpointing of the exact place of domestication center and suggesting the presence of a long-term, strong gene flow among swamp buffalo populations caused by extensive migrations of buffaloes and frequent human movements along the Yangtze River throughout history. Our current study suggests that Southwestern China is the most likely domestication center for lineage A, and may have been a primary center of swamp buffalo domestication. More archaeological and genetic evidence is needed to show the process of domestication.