Phylogeography of northern Dolly Varden Salvelinus malma malma based on analysis of mitochondrial DNA

The northern Dolly Varden, Salvelinus malma malma, is a typical representative of arctic fauna distributed in northeastern Asia and northwestern North America. Because its spawning habitats were affected by Pleistocene glacial advances over most of its natural range, S. m. malma is among the most interesting objects of phylogeographic and microevolutionary studies. We reconstructed the genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of glacial and geological vicariance events on the contemporary population genetic structure, phylogeographic subdivision and distribution of the northern Dolly Varden. Analysis of restriction site states in three PCR‐amplified mtDNA regions (ND1/ND2, ND5/ND6, Cytb/D‐loop; 47% of the mitochondrial genome) resolved 75 haplotypes in 436 fish. Similar patterns of subspecific variation apparent from hierarchical diversity and nested clade analyses of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. Our results suggest that (1) demographic history has been influenced by historical range expansions and recent isolation by distance, (2) present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon's ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period.     

Population genetic structure of northern Dolly Varden char <Emphasis Type="Italic">Salvelinus malma malma</Emphasis> in Asia and North America

The level of genetic differentiation of northern Dolly Varden char Salvelinus malma malma from Asia and North America was evaluated using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D-loop) obtained by means of PCR-RFLP analysis. For S. m. malma, the mean values of haplo-type and nucleotide diversity were 0.5261 ± 0.00388 and 0.001558, respectively. The mean estimate of the population nucleotide divergence constituted 0.055%. It was demonstrated that S. m. malma on the most part of the species range examined (drainages of the Beaufort Sea, Chukotka Sea, Bering Sea, and the Sea of Okhotsk) was characterized by the population genetic structure with the low level of genetic differentiation and divergence. At the same time, populations from the Pacific Ocean Gulf of Alaska demonstrated marked genetic differentiation, supported by the high pairwise G4ST values (from 0.4198 to 0.5211) and nucleotide divergence estimates (mean divergence, 0.129%), from Asian and North American populations. Analysis of molecular variance (AMOVA) showed that most of the mtDNA variation in S. m. malma fell in the intrapopulation component (72.5%). At the same time, the differences between the populations (21.1%) and between the regions (6.4%) made lower contribution to the total variation.     

Differentiation of Dolly Varden Char <Emphasis Type="Italic">Salvelinus malma</Emphasis> from Asia and North America Inferred from PCR-RFLP Analysis of Mitochondrial DNA

Genetic differentiation of Dolly Varden char Salvelinus malma Walbaum from the Asian and North American Pacific coasts was studied. We examined restriction fragment length polymorphism of three mitochondrial DNA (mtDNA) fragments amplified in polymerase chain reaction, which encoded four NADH dehydrogenase subunits, the cytochrome b gene, and a D-loop segment. The mtDNA haplotypes were shown to form three phylogenetic groups, whose geographic distribution corresponded to three Dolly Varden subspecies: S. malma malma, S. malma krascheninnikovi, and S. malma lordi. The nucleotide sequence divergence between S. malma malma and S. malma krascheninnikovi was 3.8%; between S. malma malma and S. malma lordi, 3.1%; and between S. malma krascheninnikovi and S. malma lordi, 2.5%. The northern Dolly Varden S. malma malma from Asia was shown to be genetically identical to that from North America.__________Translated from Genetika, Vol. 41, No. 5, 2005, pp. 626–634.Original Russian Text Copyright © 2005 by Oleinik, Skurikhina, Brykov, Crane, Wenburg.     

Phylogeography of northern Dolly Varden Salvelinus malma (Salmoniformes: Salmonidae) from Asia and North America: An analysis based on the mitochondrial DNA genealogy

Spawning in habitats affected by Pleistocene glacial advances over most of its natural range, northern Dolly Varden Salvelinus malma malma typifies Arctic fauna distributed in northeastern Asia and northwestern North America. We reconstructed a genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of historical events on the phylogeography and contemporary population genetic structure. Analysis of molecular variance partitioned most of the mtDNA variability to the intrapopulation component (72.5%) with much reduced differences between populations (21.1%) and regions (6.4%). Similar patterns of variation apparent from hierarchical diversity and nested clade phylogeographical analysis (NCPA) of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. These findings suggest (1) that demographic history has been influenced by historical range expansions and recent isolation by distance, (2) that present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon’s ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period. The genealogical and NCPA analyses, and mismatch distribution of S. m. malma mtDNA haplotypes do not confirm the assumptions about presence of the two refugia on the territories of the Beringian Land, in which allopatric S. m. malma ancestral populations evolved, and independent origin of the Sea of Okhotsk populations.     

Introgressive hybridization of chars of the genus <Emphasis Type="Italic">Salvelinus</Emphasis> as inferred from mitochondrial DNA variation

Nucleotide sequence analysis of the mitochondrial cytochrome b gene in the genus Salvelinus revealed hybrids with S. leucomaenis in S. malma malma populations of the Northern Okhotsk Sea basin. Hybrids of S. m. malma and S. m. krascheninnikovi were found in S. m. malma populations from the Northern Okhotsk Sea basin and Kamchatka. The findings testify to a secondary contact and mtDNA transfer between these species and forms. It was assumed that introgressive hybridization took place both long ago and relatively recently and occurred in one direction: from S. leucomaenis or S. m. krascheninnikovi to S. m. malma.Translated from Genetika, Vol. 40, No. 12, 2004, pp. 1678–1685.Original Russian Text Copyright © 2004 by Radchenko.     

Effect of isolation on the genetic characteristics of populations in charrs of the genus Salvelinus

To study the effect of isolation on the genetic variation of mDNA, Salvelinus malma krascheninnikovi and S. malma malma nonanadromous populations from different model ecosystems were examined by RFLI-PCR. The haplotype and nucleotide diversities of mtDNA were significantly decreased in three isolated populations as a result of random gene drift. The genealogy of mtDNA haplotypes was reconstructed. The formation of the modern structure of the isolated populations is discussed in terms of phylogeography.     

Polymorphism of mtDNA regions in brown hare (Lepus europaeus) populations from Vojvodina (Serbia and Montenegro)

It is well known that there is heterogeneity of mitochondrial DNA (mtDNA) within and among natural populations of same species. The polymorphism level of particular regions of mtDNA gives valuable results in detection of population genetic structure. The aim of this paper was to detect polymorphism of three mtDNA regions: cytochrome oxidase I (COI), Control region, and 12S/16S rRNA, by the mtDNA RFLP-PCR method, in three Lepus europaeus populations from Vojvodina province (Serbia and Montenegro). Polymorphism was detected within the two regions, COI and Control region, while 12S/16S rRNA region was monomorphic in all 77 individuals. Eight haplotypes were detected in the brown hare population in Vojvodina, and three were unique for the Srem brown hare population.     

Genetic diversity in the Japanese rosy bitterling, Rhodeus ocellatus kurumeus (Cyprinidae)

Comparison of meristic characters (pored lateral line scales, vertebrae, and fin rays), and PCR-RFLP analysis in the D-loop and ND1 regions of mitochondrial DNA were performed to estimate the genetic diversity in local populations of the Japanese rosy bitterling, Rhodeus ocellatus kurumeus. In terms of meristic characters, the Fukuoka population was the largest in both range and variance of the number of pored lateral line scales and vertebrae (abdominal and caudal), and Osaka was the second, whereas the Kagawa population showed the smallest range and variance in these characters. In PCR-RFLP analysis, 11 haplotypes (3 in Fukuoka, 2 in Okayama, 2 in Kagawa, and 4 in Osaka) were observed, and nucleotide sequence divergence (NSD) was approximately two times larger in ND1 (mean, 0.61%) than in D-loop (mean, 0.31%). In the neighbor-joining (NJ) tree, based upon the NSD value in ND1, haplotypes were arranged into four clades, which corresponded to the locality of each haplotype. The Fukuoka population was conspicuously apart from the other populations (mean, 0.90% in NSD), but the remaining three showed a similar genetic distance with each other (mean, 0.48%–0.52% in NSD). In haplotype diversity of mtDNA, half the stations in Osaka and all in Kagawa were monomorphic. Especially, two haplotypes endemic to Kagawa were randomly distributed, irrespective of drainages. Rhodeus o. kurumeus in Fukuoka inhabits small rivers and creeks (open water systems), while that in Kagawa and Osaka lives in small ponds (closed water systems). Taking the information of morphology, mtDNA, and habitat into consideration, the low genetic diversity in Kagawa and Osaka populations of R. o. kurumeus is thought to be mainly the result of the isolation of their habitat. Received: January 14, 2001 / Revised: June 14, 2001 / Accepted: July 1, 2001     

Genetic variation in populations of the endangered fish Ladigesocypris ghigii and its implications for conservation

1. The genetic variation of the endangered freshwater fish Ladigesocypris ghigii, endemic to the island of Rhodes (Greece), was investigated for nine populations, originating from seven different stream systems and a reservoir, both at the mtDNA and nuclear level, in order to suggest conservation actions. 2. Both restriction fragment length polymorphism analysis of five segments of mitochondrial DNA (ND‐5/6, COI and 12S‐16S rRNA) amplified by polymerase chain reaction, and random amplified polymorphic DNA analysis, revealed extremely low levels of intra‐population polymorphism. It is highly likely that the low intra‐population variability is the result of successive bottleneck events evident in shrinkage and expansion of the populations year after year, which may have led to a complete loss of several genotypes and haplotypes, and an increased degree of inbreeding. 3. Inter‐population genetic structuring was high, with fixation of haplotypes within six of the nine populations and fixation of alleles within populations originating from different waterbodies. It is probable that all haplotypes and/or alleles found were initially represented in all populations. However, because of the long time of isolation coupled with successive bottleneck and subsequent genetic drift, common mtDNA haplotypes and alleles among the populations may have become rare or extinct through stochastic lineage loss. 4. Although nucleotide divergence among haplotypes was very shallow, half of the haplotypes recorded (three of six), resulted from nucleotide changes on the 12S–16S rRNA segments, which are the most conserved part of the mitochondrial genome. This fact may indicate that the observed genetic variation did not necessarily result only from the retention of ancestral polymorphism, but may have arisen through mutation and complete lineage sorting over a relatively small number of generations, once the populations had become isolated from one another. 5. Our data suggest that two of the L. ghigii populations may be on independent evolutionary trajectories. Considering that each population appears so far well adapted within each site, all populations should be managed and conserved separately.     

Population genetic structure of northern Dolly Varden char Salvelinus malma malma in Asia and North America

The level of genetic differentiation of northern Dolly Varden char Salvelinus malma malma from Asia and North America was evaluated using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D loop) obtained by means of PCR-RFLP analysis. For S. m. malma, the mean values of haplotype and nucleotide diversity were 0.5261 +/- 0.00388 and 0.001558, respectively. The mean estimate of the population nucleotide divergence constituted 0.055%. It was demonstrated that S. m. malma on the most part of the species range examined (drainages of the Beaufort Sea, Chukotka Sea, Bering Sea, and the Sea of Okhotsk) was characterized by the population genetic structure with the low level of genetic differentiation and divergence. At the same time, populations from the Pacific Ocean Gulf of Alaska demonstrated marked genetic differentiation, supported by the high pairwise phi(ST) values (from 0.4198 to 0.5211) and nucleotide divergence estimates (mean divergence, 0.129%), from Asian and North American populations. Nested analysis of molecular variance (AMOVA) showed that most of the mtDNA variation in S. m. malma fell in the intrapopulation component (72.5%). At the same time, the differences between the populations (21.1%) and between the regions (6.4%) made lower contribution to the total variation.     

Spatial and temporal variation in invertebrate consumer diets in forested and herbaceous wetlands

Lake Kronotskoye (the Kronotsky Biosphere State Reserve, south-eastern Kamchatka Peninsula) contains three closely related resident morphotypes charrs, which are considered to be either independent species (white charr Salvelinus albus, longhead charr Salvelinus kronocius, Schmidt’s charr Salvelinus schmidti) or a united lacustrine-riverine charrs, represented by several phenotypes. Salvelinus malma malma is isolated from the lake charr populations by an upstream migration barrier in the Kronotskaya River, which flows out of the lake. We examined the level of genetic variability and divergence of mtDNA both between charrs from Kronotsky Lake and between resident lacustrine charrs and the hypothetical ancestor species S. m. malma. The RFLP-PCR analysis was used to examine six regions (ND1/ND2, ND3/ND4L/ND4, ND5/ND6, COI/COII/A8, A8/A6/COIII/ND3, and Cytb/D-loop), comprising ~80% of the mtDNA. Significantly different levels of diversity were found among the populations of lacustrine charrs. S. albus and S. schmidti had the highest indices of mtDNA diversity among the investigated populations from the different habitats. Heterogeneity tests revealed highly significant differentiation among lake populations and among riverine (Kronotskaya River) and lake (Lake Kronotskoye) populations of charrs, indicating their reproductive isolation. Hierarchical analysis of molecular variance revealed the following regularities of diversity distribution: the high proportion of interpopulation variation (93.25%) and low but statistically significant subdivision between charr populations (6.75%, P < 0.001). Results of the present study suggest that the populations of S. albus, S. kronocius, S. schmidti belong to the S. m. malma phylogenetic group. The divergence value of mtDNA of resident charrs (0.0357–0.0010%) does not exceed the intraspecific variability of S. m. malma. The analysis of the mtDNA haplotypes genealogy of charrs showed that the low values of nucleotide divergence reflect a short period from the beginning of divergence from the ancestral lineages and are due to ancestral polymorphism, as well as to haplotype exchange between the diverged phylogenetic groups as a result of introgressive hybridization.     

Phylogenetic relationships of Sakhalin taimen <Emphasis Type="Italic">Parahucho perryi</Emphasis> inferred from PCR-RFLP analysis of mitochondrial DNA

RFLP analysis of three amplified mtDNA fragments (Cytb/D-loop, ND1/ND2, and ND3/ND4L/ND4) was performed in the following taxa: Parahucho perryi, Hucho taimen, Brachymystax lenok, B. tumensis, Salmo salar, Salvelinus leucomaenis, and S. levanidovi. For mtDNA of P. perryi, a substantial decrease in the haplotype and nucleotide diversity was observed as a result of random genetic drift, caused by a reduction in the effective population size. Nucleotide divergence estimates between the mtDNA haplotypes were determined. Sakhalin taimen P. perryi was found to be approximately equally diverged from S. salar and from the charrs of the genus Salvelinus, by 11.0 and 10.0%, respectively. The divergence between P. perryi and H. taimen constituted 14.6%, between P. perryi and lenoks of the genus Brachymystax, 14.2%, and between H. taimen and Brachymystax, 7.7%. The analysis of possible phylogenetic relationships of the mtDNA from P. perryi among the group of taxa examined confirmed validity of the genus Parahucho. Phylogenetic reconstructions performed showed that robustness of the trees constructed for the complex of phylogenetically informative characters over three mtDNA fragments was considerably higher than that of the trees constructed for individual genes.     

Population genetic structure of the point-head flounder, <Emphasis Type="Italic">Cleisthenes herzensteini</Emphasis>, in the Northwestern Pacific

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5′ end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94–376 kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.     

Changes in genetic diversity and differentiation in Red‐cockaded woodpeckers (Dryobates borealis) over the past century

Red‐cockaded woodpeckers (RCW; Dryobates borealis) declined after human activities reduced their fire‐maintained pine ecosystem to <3% of its historical range in the southeastern United States and degraded remaining habitat. An estimated 1.6 million RCW cooperative breeding groups declined to about 3,500 groups with no more than 10,000 birds by 1978. Management has increased RCW population abundances since they were at their lowest in the 1990s. However, no range‐wide study has been undertaken since then to investigate the impacts of this massive bottleneck or infer the effects of conservation management and recent demographic recoveries. We used mitochondrial DNA sequences (mtDNA) and nine nuclear microsatellite loci to determine if range‐wide demographic declines resulted in changes to genetic structure and diversity in RCW by comparing samples collected before 1970 (mtDNA data only), between 1992 and 1995 (mtDNA and microsatellites), and between 2010 and 2014 (mtDNA and microsatellites). We show that genetic diversity has been lost as detected by a reduction in the number of mitochondrial haplotypes. This reduction was apparent in comparisons of pre‐1970 mtDNA data with data from the 1992–1995 and 2010–2014 time points, with no change between the latter two time points in mtDNA and microsatellite analyses. The mtDNA data also revealed increases in range‐wide genetic differentiation, with a genetically panmictic population present throughout the southeastern United States in the pre‐1970s data and subsequent development of genetic structure that has remained unchanged since the 1990s. Genetic structure was also uncovered with the microsatellite data, which like the mtDNA data showed little change between the 1992–1995 and 2010–2014 data sets. Temporal haplotype networks revealed a consistent, star‐like phylogeny, suggesting that despite the overall loss of haplotypes, no phylogenetically distinct mtDNA lineages were lost when the population declined. Our results may suggest that management during the last two decades has prevented additional losses of genetic diversity.     

Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats

The Horn of Africa forms one of the two main historical entry points of domestics into the continent and Ethiopia is particularly important in this regard. Through the analysis of mitochondrial DNA (mtDNA) d‐loop region in 309 individuals from 13 populations, we reveal the maternal genetic variation and demographic dynamics of Ethiopian indigenous goats. A total of 174 variable sites that generated 231 haplotypes were observed. They defined two haplogroups that were present in all the 13 study populations. Reference haplotypes from the six globally defined goat mtDNA haplogroups show the two haplogroups present in Ethiopia to be A and G, the former being the most predominant. Although both haplogroups are characterized by an increase in effective population sizes (N_e) predating domestication, they also have experienced a decline in N_e at different time periods, suggesting different demographic histories. We observed seven haplotypes, six were directly linked to the central haplotypes of the two haplogroups and one was central to haplogroup G. The seven haplotypes were common between Ethiopia, Kenya, Egypt, and Saudi Arabia populations, suggesting common maternal history and the introduction of goats into East Africa via Egypt and the Arabian Peninsula, respectively. While providing new mtDNA data from a historically important region, our results suggest extensive intermixing of goats mediated by human socio‐cultural and economic interactions. These have led to the coexistence of the two haplogroups in different geographic regions in Ethiopia resulting in a large caprine genetic diversity that can be exploited for genetic improvement.     

PCR–RFLP analysis of mitochondrial DNA in tench Tinca tinca

Polymorphism was detected at ND1, ND6, D‐loop and cyt b segments of mtDNA in 105 tench (Tinca tinca L.), using the polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) technique and five composite haplotypes were identified. The diversity indices and the results of the population comparisons revealed that the identified markers provide a powerful tool for further studies on this species.     

Morphology and mitochondrial DNA variation of the Siberian whitefish <Emphasis Type="Italic">Coregonus lavaretus pidschian</Emphasis> (Gmelin) in the upstream water bodies of the Ob and Yenisei Rivers

Combining morphological, ecological and genetic analyses, we compared patterns of diversification within and among populations of the southern Siberian whitefish species Coregonus lavaretus pidschian (Gmelin) to illuminate their evolutionary history. Using sequencing data from 1,930 bp of NADH dehydrogenase subunit 1 (ND1) mitochondrial DNA regions, we documented phylogeographic relationships among populations and developed a phylogeny of mtDNA haplotypes. We found significant differences in the perforated lateral-line scale numbers within and between some populations. Clear differences in the number of gill rakers on the first branchial arch were only exhibited between populations of C. l. pidschian and Coregonus lavaretus pravdinellus Dulkeit. Concordance between different morphological groups based on two meristic traits and mtDNA patterns was also tested.     

Intraspecific mitochondrial DNA variation in the Colorado potato beetle,Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

Restriction endonuclease analyses of mitochondrial DNA (mtDNA) were used to examine genetic variability and population structure inLeptinotarsa decemlineata (Say). A group of three enzymes, EcoRI, HpaI, and PstI, was used to reveal polymorphism both within and among some of the 10 populations tested, yielding 16 haplotypes in combination. The frequencies of these 16 haplotypes differed significantly across geographic regions, indicating some partitioning of mtDNA haplotypes. Estimates of mtDNA sequence divergence (δ) between haplotypes ranged from 0.016 to 0.135%, suggesting local differentiation of mtDNA in some populations. Analysis of these data suggests that Texas was colonized by more than one mtDNA lineage, most likely originating in Mexico. We hypothesize that a larger founder size for the initial introductions or high levels of variability in the parent population at the edge of the CPB expanding range led to the initial partitioning of haplotypes observed in samples from Texas.     

Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific

The population structure of variation in a nuclear actin intron and the control region of mitochondrial DNA is described for humpback whales from eight regions in the North Pacific Ocean: central California, Baja Peninsula, nearshore Mexico (Bahia Banderas), offshore Mexico (Socorro Island), southeastern Alaska, central Alaska (Prince Williams Sound), Hawaii and Japan (Ogasawara Islands). Primary mtDNA haplotypes and intron alleles were identified using selected restriction fragment length polymorphisms of target sequences amplified by the polymerase chain reaction (PCR–RFLP). There was little evidence of heterogeneity in the frequencies of mtDNA haplotypes or actin intron alleles due to the year or sex composition of the sample. However, frequencies of four mtDNA haplotypes showed marked regional differences in their distributions (Φ_ST = 0.277; P < 0.001; n = 205 individuals) while the two alleles showed significant, but less marked, regional differences (Φ_ST = 0.033; P < 0.013; n = 400 chromosomes). An hierarchical analysis of variance in frequencies of haplotypes and alleles supported the grouping of six regions into a central and eastern stock with further partitioning of variance among regions within stocks for haplotypes but not for alleles. Based on available genetic and demographic evidence, the southeastern Alaska and central California feeding grounds were selected for additional analyses of nuclear differentiation using allelic variation at four microsatellite loci. All four loci showed significant differences in allele frequencies (overall F_ST = 0.043; P < 0.001; average n = 139 chromosomes per locus), indicating at least partial reproductive isolation between the two regions as well as the segregation of mtDNA lineages. Although the two feeding grounds were not panmictic for nuclear or mitochondrial loci, estimates of long-term migration rates suggested that male-mediated gene flow was several-fold greater than female gene flow. These results include and extend the range and sample size of previously published work, providing additional evidence for the significance of genetic management units within oceanic populations of humpback whales.     

Patterns of genetic diversity in the critically endangered Central American river turtle: human influence since the Mayan age?

We conducted a phylogeographic analysis of the strictly aquatic and critically endangered Central American river turtle, Dermatemys mawii, as part of a conservation management program for the species. We sampled 238 individuals from 15 different localities throughout the species range. Using sequence fragments from the mtDNA Cyt b and ND4 genes, we identified 16 different haplotypes. Overall, our results reveal a signal of phylogeographic structure throughout the range, which appears to have been secondarily blurred by extensive gene flow. Notably, this also applies to genetic structuring across three major hydrological basins that pose biogeographic breaks in other aquatic taxa. Divergence times of mtDNA haplotypes in D. mawii suggest that the main lineages split in the Pliocene–Pleistocene (3.73–0.227 MA) and demographic tests indicate that the species has undergone drastic demographic size fluctuations since this time period. One ancient haplotype (1D) was found to exhibit sequence divergence of up to 2% from other haplogroups. Divergence of this magnitude is indicative of species level differentiation in other turtle genera. Haplotype 1D was found in only two localities, Sarstun and Salinas, but specimens with other haplotypes were also found in those localities. It is not known whether the individuals with the 1D haplotype interbreed with non-1D individuals. Our results suggest that human activity, such as harvesting and long distance transport of animals, may have influenced the current patterns of genetic diversity. For more than 2000 years, D. mawii has been consumed by people from Middle American cultures, and the archeological record contains strong evidence that the Mayans transported animals between villages and far away from their natural distribution range. Therefore, the large-scale pattern of haplotype sharing even across hydrological barriers, the observed low haplotype diversity in some populations and the contemporary absence of a pronounced phylogeographic pattern is likely due to a combination of population expansions, gene flow, extensive human-mediated-movements and recent bottlenecks resulting from over-harvesting.