Phylogeography and population structure of the endangered Tehuantepec jackrabbit <Emphasis Type="Italic">Lepus flavigularis</Emphasis>: implications for conservation

The Tehuantepec jackrabbit (Lepus flavigularis) is an endangered species restricted to a small area in the Isthmus of Tehuantepec, Oaxaca, Mexico. To evaluate its phylogeographic structure, population genetics, and demographic history we sequenced the mitochondrial Control Region hypervariable domain (CR-1) for 42 individuals representing the entire species range. Phylogenetic patterns indicated that this species is subdivided into two highly divergent clades, with an average nucleotide genetic distance of 3.7% (TrN) between them. Clades A and B are geographically distributed in non-overlapping areas to the west and to the east of the Isthmus of Tehuantepec, respectively. Genetic diversity indices showed reduced genetic variability in L. flavigularis when compared to other species of Lepus within main clades and within populations. This low genetic diversity coupled with the restricted distribution to very small areas of occurrence and limited gene flow suggest that genetic drift has played an important role in the evolution of this species. Historical demographic analysis also pointed out that these two clades underwent a recent population expansion that started about 9,000 years ago for clade A and 3,200 years ago for clade B during the Holocene. Consequently, from the conservation perspective our results suggest that populations included in clades A and B should be regarded as distinct evolutionary lineages.     

Hidden endemism,deep polyphyly,and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)

Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White‐collared Seedeater (Sporophila torqueola) of Central America and Mexico. We combine measurements of morphology and plumage patterning with thousands of nuclear loci derived from ultraconserved elements (UCEs) and mitochondrial DNA to evaluate population differentiation. We find deep levels of molecular divergence between two S. torqueola lineages that are phenotypically diagnosable: One corresponds to S. t. torqueola along the Pacific coast of Mexico, and the other includes S. t. morelleti and S. t. sharpei from the Gulf Coast of Mexico and Central America. Surprisingly, these two lineages are strongly differentiated in both nuclear and mitochondrial markers, and each is more closely related to other Sporophila species than to one another. We infer low levels of gene flow between these two groups based on demographic models, suggesting multiple independent evolutionary lineages within S. torqueola have been obscured by coarse‐scale similarity in plumage patterning. These findings improve our understanding of the biogeographic history of this lineage, which includes multiple dispersal events out of South America and across the Isthmus of Tehuantepec into Mesoamerica. Finally, the phenotypic and genetic distinctiveness of the range‐restricted S. t. torqueola highlights the Pacific Coast of Mexico as an important region of endemism and conservation priority.     

Incipient genetic divergence or cryptic speciation? Procamallanus (Nematoda) in freshwater fishes (Astyanax)

Hosts provide the main environmental traits parasites have to deal with, resulting in covariation between both associates at both micro- and macro-evolutionary scales; phylogenetic analyses of highly host-specific parasites have shown that parasite and host phylogeny might be highly congruent, and adaptation of a host species to new environments may lead to concordant changes of their parasites. Procamallanus (Spirocamallanus) neocaballeroi is a highly host-specific parasitic nematode of the Neotropical freshwater fish genus Astyanax in Mexico. One of the host species of the nematode is the emblematic Mexican tetra, A. mexicanus, which exhibits two contrasting phenotypes, a cave-dwelling morph (with troglomorphic features), and the surface-dwelling morph; other congeneric species inhabit rivers and lakes, and some of them occur in sympatry, displaying trophic specializations. Here, we explored the hypothesis that contrasting environments (surface rivers vs cave rivers), and host morphological divergence (sympatric ecomorphs in a lacustrine environment) might result in the divergence of their parasites, even though the hosts maintain a cohesive genetic structure as the same species. To test the hypothesis, several populations of Astyanax spp. were sampled to search for P. (S.) neocaballeroi. The nematode was found in 10 of the 52 sampled sites; two localities corresponded to cave populations. The phylogenetic analysis based on COI sequences yielded three major lineages for P. (S.) neocaballeroi. We found no concordance between the three lineages and the habitat where they occur in Astyanax mexicanus, even considering those living in drastic environmental conditions (caves), or between these lineages and lacustrine ecomorphs of Astyanax aeneus and A. caballeroi occurring in sympatry. Instead, genetic lineages of the nematode exhibit a clearer pattern of host species association and geographical distribution; our results showed that P. (S.) neocaballeroi is experiencing an incipient divergence although the morphological study of lineages shows no conspicuous differences.     

Intricate evolutionary histories in montane species: a phylogenetic window into craniodental discrimination in the Peromyscus mexicanus species group (Mammalia: Rodentia: Cricetidae)

Mountain‐associated species, which exhibit allopatric distributions associated with elevation, endemisms and complex evolutionary histories, pose challenging evolutionary scenarios in which to discern the diversification of species. The Peromyscus mexicanus mice group, distributed along mountains in southern Mexico and Central America, is morphometrically variable, a key rationale for the ongoing controversy regarding its species delimitation. Based on the recognized 15 mitochondrial lineages for the group, we analysed external and craniodental morphometric variables to test whether lineages can be differentiated morphometrically and allow for the delimitation of species. We also aimed to test the prediction that the phylogenetic structure of the morphometric data is concordant with that of the molecular information. Based on 19 craniodental measurements from 521 specimens, multivariate and discriminant analyses showed that lineages are morphometrically discernible, representing distinct phenotypes, and that overall size and mandible measurements are significant features that discriminate lineages, supporting hypotheses about differences in feeding habits between species. Also, a pattern of increasing size with elevation was observed, further supported by specific morphological differences exhibited between highland and lowland lineages inhabiting the same mountain. Our results demonstrate that P. mexicanus is both genetically and morphometrically variable, where most highland montane species are differentiated from lowland species; also, a significant correlation between mitochondrial and morphometric information is indicative of phenetic concordance, altogether in agreement with a recent taxonomic proposal for the group. We suggest that the group's intricate diversification responds to ecological diversification and adaptation to a variety of mountain habitats and Pleistocene biogeographic climatic dynamics.     

Patterns of morphological and ecological similarities of small-eared shrews (Soricidae,Cryptotis) in tropical montane cloud forests from Mesoamerica

It has been proposed that high morphological similarity between closely related species of small-eared shrews resulted from a recent divergence and intermittent population connectivity, presumably due to Pleistocene climatic fluctuations and associated changes in forest habitat distribution. Here we examined the morphological variation of two sister species of small-eared shrews inhabiting cloud forests from Mexico, Cryptotis obscurus and C. mexicanus. We then used ecological niche modelling to provide compelling evidence for current environmental barriers for population connectivity, and for detecting divergent ecological niches between candidate species. Our results indicated that the species boundaries in this clade should be subject to change. High morphological similarity suggested that populations of C. obscurus and C. mexicanus located west of the Isthmus of Tehuantepec, a major geographic barrier for montane species, are conspecific. Niche divergence between these two putative species was not supported indicating niche conservatism across the evolutionary history of these small-eared shrews. In addition, several barriers seem to play a main role for current lineage divergence between populations within this clade. The population located east of the Isthmus, previously referred to C. mexicanus, might prove to represent a new species based on morphological distinction and current geographic isolation. We have highlighted that estimating species’ potential distributions provides insights to evaluating the effect of geographic barriers on lineage divergence and making stronger inferences when delimiting species.     

Coalescent analyses show isolation without migration in two closely related tropical orioles: the case of Icterus graduacauda and Icterus chrysater

The Isthmus of Tehuantepec has played an important role in shaping the avian diversity of Mexico, as well as the rest of the Western Hemisphere. It has been both a barrier and a land connector between North and South America for many groups of birds. Furthermore, climatic change over the Pleistocene has resulted in ecological fluctuations that led to periods of connection and isolation of the highlands in this area. Here we studied the divergence of two species of orioles whose distribution in the highlands is separated by the lowlands of the Isthmus of Tehuantepec: Icterus graduacauda (west of the Isthmus) and Icterus chrysater (east of the Isthmus). We sequenced multiple loci (one mitochondrial gene and six nuclear introns) and performed coalescent analyses (Isolation with Migration) to test whether their divergence resulted from prior occupancy of the ancestral area followed by a vicariant event or recent dispersal from one side or the other of this Isthmus. Results strongly indicate a vicariant event roughly 300,000 years ago in the Pleistocene followed by little or no gene flow. Both mitochondrial and nuclear genes show that the Isthmus of Tehuantepec is a strong barrier to gene flow. Thus, these two species appear to not exchange genes despite their recent divergence and the close geographic proximity of their ranges.     

Historical biogeography of lowland species of toads (Bufo) across the Trans-Mexican Neovolcanic Belt and the Isthmus of Tehuantepec

Aim In this study, we investigate phylogeographic structure in two different species groups of lowland toads. First, we further investigate strict parapatry of the Pliocene‐vicariant Bufo valliceps/B. nebulifer species pair. Secondly, we test for similar phylogeographic structure in the distantly related toad B. marinus, a species we hypothesize will show a Pleistocene dispersal across the same area. Location The eastern extension of the Trans‐Mexican Neovolcanic Belt (TMNB) contacts the Atlantic Coast in central Veracruz, Mexico. Although it is not a massive structure at this eastern terminus, the TMNB has nonetheless effected vicariance and subsequent speciation in several groups of animals. The Isthmus of Tehuantepec unites the North American continent with Nuclear Central America and is also known to be a biogeographic barrier for many taxa. Methods We use sequence data from two mitochondrial DNA genes (c. 550 base‐pairs (bp) of 16S and c. 420 bp of cyt b) from 58 individuals of the B. valliceps/nebulifer complex, collected from 24 localities. We also present homologous sequence data from 23 individuals of B. marinus, collected from 12 localities. We conduct maximum‐parsimony, maximum‐likelihood and Bayesian analyses to investigate phylogeographic structure. We then use parsimony‐ and likelihood‐based topology tests to assess alternative phylogenetic hypotheses and use a previously calibrated molecular rate of evolution to estimate dates of divergence. Results Our results further define the parapatric contact zone across the TMNB between the Pliocene‐vicariant sister species B. valliceps and B. nebulifer. In contrast, phylogenetic structure among populations of B. marinus across the TMNB is much shallower, suggesting a more recent Pleistocene dispersal in this species. In addition, we found phylogeographic structure associated with the Isthmus of Tehuantepec in both species groups. Main conclusions The existence of a Pliocene–Pleistocene seaway across the Isthmus of Tehuantepec has been controversial. Our data depict clades on either side of the isthmus within two distinct species (B. valliceps and B. marinus), although none of the clades associated with the isthmus, for either species, are reciprocally monophyletic. In the B. valliceps/B. nebulifer complex, the TMNB separation appears to predate the isthmian break, whereas in B. marinus dispersal across the TMNB has occurred subsequent to the presence of a barrier at the Isthmus of Tehuantepec.     

Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers

The American cockroach (Periplaneta americana) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of P. americana. Our study analyzed 1,053 P. americana and other Periplaneta species' samples from different locations in China and the United States. A traditional tree‐based method using 17 unique mitochondrial COI haplotypes of P. americana and 20 haplotypes of the other Periplaneta species accurately identified P. americana with a barcoding threshold of 5.1%. To identify the population genetic structure of P. americana, we investigated wingless gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. The analysis of molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that P. americana had very little global genetic differentiation. The weak geographic genetic structure might reflect the human‐mediated dispersal of P. americana. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct P. americana haplotype groups, showing four ancient maternal lineages of P. americana in China and the United States.     

Mitogenomic phylogeny of Nassarius (Gastropoda: Neogastropoda)

Nassariids (Family Nassariidae) are a group of marine snails that are distributed worldwide, with their maximum species diversity in tropical regions, particularly the Indo‐Pacific. However, the traditional taxonomy of Nassariidae defined by shell or radula characters is usually inconsistent with little phylogenetic signal. In the present study, the complete mitochondrial (mt) genomes of nine Nassarius species were sequenced and compared with other eight nassariid species previously reported. All nassariid mt genomes showed the same gene order as in most caenogastropods and shared a very similar pattern with respect to genome size, nucleotide composition and AT contents. A deletion of three nucleotides in nad6 gene was detected in Nassarius jacksonianus and Nassarius acuticostus, and this feature also provided implications for nassariid phylogeny. The genetic distance analysis and reconstructed phylogeny revealed a distant relationship between N. jacksonianus or N. acuticostus and other members in Nassarius. The mitogenomic phylogeny recovered the evolutionary relationships within Nassarius with high statistical support. In addition, a chronogram was reconstructed under an uncorrelated relaxed molecular clock, which dated the divergence among main lineages of Nassarius during ~31 MYA.     

Species distribution modelling and cpSSR reveal population history of the Neotropical annual herb Tithonia rotundifolia (Asteraceae)

• The impacts of the historical geologic and climatic events on the diversity and genetic structure of Neotropical taxa have recently become a subject of study. However, annual plants associated with tropical dry forests remain under‐studied. The exploration of additional taxa in contrasting environments will improve the current understanding of responses of the Neotropical biota to these events. Here, we explore the species distribution and geographic structure of the annual herb Tithonia rotundifolia.
• We sampled 175 individuals from 19 populations of T. rotundifolia. Species distribution modelling and six microsatellite chloroplast loci were used to infer its population history. We identified areas of historical climate suitability and then tested if there is genetic structuring among these areas.
• Haplotypes showed strong phylogeographic structure. Historical climatic suitability areas were found along the Pacific coast; however, a gap was found at the Isthmus of Tehuantepec (IT). Although Bayesian analysis showed population structuring, amova revealed that the IT is not its main driver. Instead, a subdivision into a higher number of regions had higher F_CT values. Also, populations to the east of the IT showed evidence of recent population expansion and migration in a south–north direction.
• Pleistocene climate fluctuations partially explain the geographic structure of T. rotundifolia. However, life‐history characteristics such as limited seed dispersal and the patchy distribution of suitable habitats explain the high haplotype diversity and population sub‐structuring and diversity. Lastly, the absence of geographic structure of some haplotypes may indicate long‐distance dispersal, or hybridisation with the closely related T. tubaeformis.

     

Evolutionary history of the genus Sorex (Soricidae,Eulipotyphla) as inferred from multigene data

The genus Sorex is one of the most diverse and ecologically successful lineages of the family Soricidae. We present the first multilocus nuclear phylogeny focusing on the nominal subgenus Sorex s.str., which is distributed mainly in the northern Palearctic. The nuclear tree (six exons) provides more resolution than the mitochondrial data (cytb) and supports subdivision into eight species groups within Sorex s.str., most of which correspond to those recognized from chromosome data. The European species S. alpinus is consistently placed as the basal lineage in the Palearctic clade, while the next split separates the east‐Tibetan group of striped shrews (S. aff. cylindricauda, S. bedfordiae, S. excelsus). Within the remaining species, the following well‐supported clades are identified at the supra‐group level: “araneus” species group+S. samniticus; the “caecutiens” group+the “minutus” group, the latter also including S. minutissimus, S. gracillimus and S. thibetanus. S. raddei and S. roboratus represent separate lineages with no close relatives. The fossil‐calibrated molecular clock placed the divergence between Sorex s.str. and Otisorex at the Early/Middle Miocene boundary. Basal radiation of the crown Sorex s.str. was estimated to have occurred in the middle of the Late Miocene. A more than threefold increase in the diversification rate is inferred for the Early Pliocene. Taxonomic implications including potential genus ranks for Sorex s.str. and Otisorex are discussed. S. alpinus is placed in the monotypic subgenus Homalurus. The full species status of S. buchariensis and S. thibetanus and close relationships between S. cf. cansulus and S. caecutiens are confirmed.     

A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico

Hybrid speciation may contribute significantly to generating biodiversity, but only a few well‐documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish, Xiphophorus clemenciae, shows common hallmarks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (Xiphophorus hellerii and Xiphophorus maculatus). Xiphophorus clemenciae provides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here, we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range of X. clemenciae– the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise to X. clemenciae appears to be rather ancient, and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, because they now occupy distinct ecological niches, and a common haplotype is shared by most populations of X. clemenciae. The population structure within these species shows an isolation‐by‐distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations of X. clemenciae and X. helleriii and provide preliminary information to aid in conservation management of this geographically restricted hybrid species, X. clemenciae.     

Isolation and characterization of eight microsatellite loci from the house finch (Carpodacus mexicanus)

I isolated the first set of polymorphic microsatellite markers from the house finch, Carpodacus mexicanus, a well‐studied North American bird species, as part of an effort to compare levels of genetic diversity in introduced and native populations. Here, I describe eight independently assorting microsatellite loci screened for polymorphism using 40 house finches. Polymorphism levels ranged from six to 14 alleles (mean = 10.6), making these markers a powerful tool for paternity and population level analyses of this widely distributed North American species.     

Radiation of the Drosophila nannoptera species group in Mexico

The Drosophila nannoptera species group, a taxon of Mexican cactophilic flies, is an excellent model system to study the influence of abiotic and biotic factors on speciation, the genetic causes of ecological specialization and the evolution of unusual reproductive characters. However, the phylogenetic relationships in the nannoptera species group and its position within the virilis‐repleta phylogeny have not been thoroughly investigated. Using a multilocus data set of gene coding regions of eight nuclear and three mitochondrial genes, we found that the four described nannoptera group species diverged rapidly, with very short internodes between divergence events. Phylogenetic analysis of repleta group lineages revealed that D. inca and D. canalinea are sister to all other repleta group species, whereas the annulimana species D. aracataca and D. pseudotalamancana are sister to the nannoptera and bromeliae species groups. Our divergence time estimates suggest that the nannoptera species group radiated following important geological events in Central America. Our results indicate that a single evolutionary transition to asymmetric genitalia and to unusual sperm storage may have occurred during evolution of the nannoptera group.     

Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood

Mice of the Peromyscus aztecus species group occur at mid to high elevations in several mountain ranges in the highlands of Middle America (Mexico and Central America), a region of high endemicity. We examined the biogeography of this group by conducting phylogenetic analyses of 668 bp of the mitochondrial cytochrome b (cyt b) gene. Phylogenetic analyses under both parsimony and likelihood frameworks produced the same topologies, but estimates of nodal support were artificially high in weighted parsimony analyses. This difference is attributed to the inability of parsimony to optimize branch lengths when evaluating topologies. These data indicate that the P. aztecus-like populations from south and east of the Isthmus of Tehuantepec currently assigned to P. a. oaxacensis represent a distinct species, with genetic distances as high as 0.091. In addition, P. hylocetes is strongly divergent from Mexican populations of P. aztecus (genetic distances of 0.044-0.069), supporting the recognition of this taxon as a distinct species. The history of divergence in this group can be explained by a series of apparently early to middle Pleistocene vicariance events associated with glacial cycles. The Sierra Madre Occidental and Cordillera Transvolcanica each appear to be faunistically isolated, the Isthmus of Tehuantepec appears to have been a strong Pleistocene barrier, and the Sierra Madre Oriental has affinities with the Sierra Madre del Sur and the highlands of central Oaxaca.     

Competitive interactions between felid species may limit the southern distribution of bobcats Lynx rufus

Bobcats are opportunistic felids occurring in a diverse range of habitats and with a widespread distribution from southern Canada to southern Mexico. To explore why the bobcat's distribution stops at the Isthmus of Tehuantepec, we modelled the ecological niches, projected as potential distributions, of the felid community (bobcat Lynx rufus, puma Puma concolor, jaguar Panthera onca, margay Leopardus wiedii, jaguarundi Herpailurus yagouaroundi, and ocelot Leopardus pardalis) in southern Mexico, using occurrence data, environmental maps, the computer algorithm GARP, and a GIS platform. The resulting geographical projection of the ecological niche of bobcats extends south of the Isthmus of Tehuantepec, suggesting that ecological conditions exist for the establishment of populations. The overlap of the modelled distribution of the bobcat was large with that of the puma (97%), but low with that of the ocelot (44%), margay (46%), jaguar (49%), and jaguarundi (52%), the latter three having relatively similar size and feeding habits to bobcats. Moreover, an independent analysis computing a geographic co‐occurrence index showed a similar trend of geographic avoidance (values 0.15), while all felids, except bobcats, showed a geographic co‐occurrence in southern Mexico (values ranging from ?1.91 to 4.71). The Isthmus of Tehuantepec, a lowland region with subtropical habitat, is unlikely to serve as a geographic and ecological barrier to bobcats. As mammal inventories have been conducted for over a century in this region with no records of bobcats, it is unlikely that bobcats are present but have just not been seen. Fossil records also provide no support for the presence of bobcats in that region in the past. Thus, competitive interactions with other felid species appear important in limiting the southern distribution of bobcats, preventing dispersal to a suitable but geographically reduced area south of the Isthmus of Tehuantepec.     

Long‐term survival and diversification of an endemic Melitaea species in mountains of Iran and adjacent areas

Disjunct distribution patterns regularly resulted in the separation of different genetic lineages in glacial refugia. Recent patterns of survival and expansion have been often revealed by climatic niche modelling. We used the combination of genetic markers, geometric morphometry and climatic niche modelling to clear up the taxonomy and reconstruct the potential range of an endemic Iranian, taxonomically disputed Melitaea species in climatically different epochs. Our results show that this species (Melitaea abbas Gross and Ebert 1975, comb. n. = M. zagrosi Tóth and Varga syn. nova) is clearly separated from all taxa of the Melitaea phoebe species group and only occurs in Iran and Azerbaijan but were also predicted for some adjacent regions. Molecular markers and distribution modelling show consistently that this species should have had a long‐term survival in this area, and its range could have been slightly larger during the last glacial maximum than currently. Based on the studied molecular markers, three main groups in M. abbas can be recognized: those of steppic area of Azerbaijan, western Iran and northeastern Iran. Each group is characterized by own mitochondrial haplotypes, but also a high level of genetic diversity appears in the central part of the distribution area (Zagros Mts.).     

Effect of Yangtze River on population genetic structure of the relict plant Parrotia subaequalis in eastern China

Parrotia subaequalis (Hamamelidaceae) is a Tertiary relic species endemic in eastern China. We used inter‐simple sequence repeat (ISSR) markers to access genetic diversity and population genetic structure in natural five populations of P. subaequalis. The levels of genetic diversity were higher at species level (H = 0.2031) but lower at population level (H = 0.1096). The higher genetic diversity at species levels might be attributed to the accumulation of distinctive genotypes which adapted to the different habitats after Quaternary glaciations. Meanwhile, founder effects on the early stage, and subsequent bottleneck of population regeneration due to its biological characteristics, environmental features, and human activities, seemed to explain the low population levels of genetic diversity. The hierarchical AMOVA revealed high levels (42.60%) of among‐population genetic differentiation, which was in congruence with the high levels of Nei's genetic differentiation index (G_ST = 0.4629) and limited gene flow (N_m = 0.5801) among the studied populations. Mantel test showed a significant isolation‐by‐distance, indicating that geographic isolation has a significant effect on genetic structure in this species. Unweighted pair‐group method with arithmetic average clustering, PCoA, and Bayesian analyses uniformly recovered groups that matched the geographical distribution of this species. In particular, our results suggest that Yangtze River has served as a natural barrier to gene flow between populations occurred on both riversides. Concerning the management of P. subaequalis, the high genetic differentiation among populations indicates that preserving all five natural populations in situ and collecting enough individuals from these populations for ex situ conservation are necessary.