Genetic and ecological data reveal species boundaries between viviparous and oviparous lizard lineages

Identification of cryptic species is an essential aim for conservation biologists to avoid premature extinctions of ‘unrecognized'' species. Integrating different types of data can undoubtedly aid in resolving the issue of species delimitation. We studied here two lineages of the common lizard Zootoca vivipara that display different reproductive mode (the viviparous Z. v. vivipara and the oviparous Z. v. carniolica) and that overlap their distributional ranges in the European Alps. With the purpose of delimiting species'' boundaries, we analyzed their ecological, genetic and natural history features. More than 300 samples were collected and analyzed at cytochrome b and 11 microsatellites loci for investigating genetic variation, population structure, individual relatedness and evolutionary histories of the two lineages. Additionally, we compared their ecological niches using eight ecological variables. Genetic data showed contrasting patterns of genetic structure between the two lineages, different demographic dynamics and no hybridization events. Also strong ecological differences (such as temperature) emerged between the two lineages, and niche overlap was limited. Taken together, these results indicate that Z. v. vivipara and Z. v. carniolica should be recognized as two separate species, and particular conservation consideration should be given to the oviparous lineage that tends to live in areas threatened by increasing impact of human activities. However, recent and rapid climate warming might determine an increasing risk for the persistence of the viviparous lineage, being adapted to cold environments.     

Intraspecific Phylogeography of Lacerta vivipara and the Evolution of Viviparity

The lacertid lizard Lacerta vivipara is one of the few squamate species with two reproductive modes. We present the intraspecific phylogeny obtained from neighbor-joining and maximum-parsimony analyses of the mtDNA cytochrome b sequences for 15 individuals from Slovenian oviparous populations, 34 individuals from western oviparous populations of southern France and northern Spain, 92 specimens from European and Russian viviparous populations, and 3 specimens of the viviparous subspecies L. v. pannonica. The phylogeny indicates that the evolutionary transition from oviparity to viviparity probably occurred once in L. vivipara. The western oviparous group from Spain and southern France is phylogenetically most closely related to the viviparous clade. However, the biarmed W chromosome characterizing the western viviparous populations is an apomorphic character, whereas the uniarmed W chromosome, existing both in the western oviparous populations and in the geographically distant eastern viviparous populations, is a plesiomorphic character. This suggests an eastern origin of viviparity. Various estimates suggest that the oviparous and viviparous clades of L. vivipara split during the Pleistocene. Our results are discussed in the framework of general evolutionary models: the concept of an oviparity–viviparity continuum in squamates, the cold climate model of selection for viviparity in squamates, and the contraction–expansion of ranges in the Pleistocene resulting in allopatric differentiation.     

Reproductive isolation between oviparous and viviparous lineages of the Eurasian common lizard Zootoca vivipara in a contact zone

Contact zones between two evolutionary lineages are often useful for understanding the process of speciation because the observed genetic pattern reflects the history of differentiation. The Eurasian lacertid lizard Zootoca vivipara is a potentially interesting model for studying the role of reproductive mode in the speciation of squamate reptiles because it has both oviparous (Zootoca vivipara carniolica) and viviparous (Zootoca vivipara vivipara) populations that have recently been shown to be genetically distinct. We studied a newly‐discovered syntopic area of these two Zootoca subspecies in the central Italian Alps using genetic markers to investigate the level of introgression between them. Patterns of genetic differentiation in a fragment of the mitochondrial DNA cytb gene and a set of nuclear microsatellites show that the speciation process is complete in this area, with no evidence of recent introgression. Phylogenetic and genotypic divergence suggests that the two subspecies have experienced long independent evolutionary histories, during which genetic and phenotypic differences evolved. The possible roles of biogeography, reproductive mode, and cytogenetic differentiation in this speciation process are discussed. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 566–573.     

Intraspecific phylogeography of Lacerta vivipara and the evolution of viviparity

The lacertid lizard Lacerta vivipara is one of the few squamate species with two reproductive modes. We present the intraspecific phylogeny obtained from neighbor-joining and maximum-parsimony analyses of the mtDNA cytochrome b sequences for 15 individuals from Slovenian oviparous populations, 34 individuals from western oviparous populations of southern France and northern Spain, 92 specimens from European and Russian viviparous populations, and 3 specimens of the viviparous subspecies L. v. pannonica. The phylogeny indicates that the evolutionary transition from oviparity to viviparity probably occurred once in L. vivipara. The western oviparous group from Spain and southern France is phylogenetically most closely related to the viviparous clade. However, the biarmed W chromosome characterizing the western viviparous populations is an apomorphic character, whereas the uniarmed W chromosome, existing both in the western oviparous populations and in the geographically distant eastern viviparous populations, is a plesiomorphic character. This suggests an eastern origin of viviparity. Various estimates suggest that the oviparous and viviparous clades of L. vivipara split during the Pleistocene. Our results are discussed in the framework of general evolutionary models: the concept of an oviparity-viviparity continuum in squamates, the cold climate model of selection for viviparity in squamates, and the contraction-expansion of ranges in the Pleistocene resulting in allopatric differentiation.     

Variation of Reproductive Traits and Female Body Size in the Most Widely-Ranging Terrestrial Reptile: Testing the Effects of Reproductive Mode, Lineage, and Climate

The European common lizard, Zootoca vivipara, is the most widespread terrestrial reptile in the world. It occupies almost the entire Northern Eurasia and includes four viviparous and two oviparous lineages. We analysed how female snout-vent length (SVL), clutch size (CS), hatchling mass (HM), and relative clutch mass (RCM) is associated with the reproductive mode and climate throughout the species range and across the evolutionary lineages within Z. vivipara. The studied variables were scored for 1,280 females and over 3,000 hatchlings from 44 geographically distinct study samples. Across the species range, SVL of reproductive females tends to decrease in less continental climates, whereas CS corrected for female SVL and RCM tend to decrease in climates with cool summer. Both relationships are likely to indicate direct phenotypic responses to climate. For viviparous lineages, the pattern of co-variation between female SVL, CS and HM among populations is similar to that between individual females within populations. Consistent with the hypothesis that female reproductive output is constrained by her body volume, the oviparous clade with shortest retention of eggs in utero showed highest HM, the oviparous clade with longer egg retention showed lower HM, and clades with the longest egg retention (viviparous forms) had lowest HM. Viviparous populations exhibited distinctly lower HM than the other European lacertids of similar female SVL, many of them also displaying unusually high RCM. This pattern is consistent with Winkler and Wallin’s model predicting a negative evolutionary link between the total reproductive investment and allocation to individual offspring.     

Comparisons of mitochondrial DNA (mtDNA) sequences (16S rRNA gene) between oviparous and viviparous strains of Lacerta vivipara: a preliminary study

The lizard Lacerta vivipara has allopatric oviparous and viviparous populations. The mitochondrial DNA (mtDNA) gene coding for the 16S rRNA was sequenced for several viviparous lizard populations from France, Switzerland, Bulgaria, Czech Republic, The Netherlands, Sweden, and for oviparous lizard populations from the Pyrenean and Cantabric Mountains. Seven distinct groups (three oviparous and four viviparous) were identified. The net nucleotide divergence between oviparous and viviparous haplotypes was 1.3% +/- 0.5 (mean +/- standard deviation). These results on mtDNA, together with other data obtained previously, led us to formulate a biogeographical scenario that could be tested by further research.     

Length of activity season drives geographic variation in body size of a widely distributed lizard

Understanding the factors that drive geographic variation in life history is an important challenge in evolutionary ecology. Here, we analyze what predicts geographic variation in life‐history traits of the common lizard, Zootoca vivipara, which has the globally largest distribution range of all terrestrial reptile species. Variation in body size was predicted by differences in the length of activity season, while we found no effects of environmental temperature per se. Females experiencing relatively short activity season mature at a larger size and remain larger on average than females in populations with relatively long activity seasons. Interpopulation variation in fecundity was largely explained by mean body size of females and reproductive mode, with viviparous populations having larger clutch size than oviparous populations. Finally, body size‐fecundity relationship differs between viviparous and oviparous populations, with relatively lower reproductive investment for a given body size in oviparous populations. While the phylogenetic signal was weak overall, the patterns of variation showed spatial effects, perhaps reflecting genetic divergence or geographic variation in additional biotic and abiotic factors. Our findings emphasize that time constraints imposed by the environment rather than ambient temperature play a major role in shaping life histories in the common lizard. This might be attributed to the fact that lizards can attain their preferred body temperature via behavioral thermoregulation across different thermal environments. Length of activity season, defining the maximum time available for lizards to maintain optimal performance, is thus the main environmental factor constraining growth rate and annual rates of mortality. Our results suggest that this factor may partly explain variation in the extent to which different taxa follow ecogeographic rules.     

Development and characterization of 79 nuclear markers amplifying in viviparous and oviparous clades of the European common lizard

The European common lizard (Zootoca vivipara) is a widely distributed species across Europe and Asia exhibiting two reproductive modes (oviparity/viviparity), six major lineages and several sublineages. It has been used to tackle a large variety of research questions, nevertheless, few nuclear DNA sequence markers have been developed for this species. Here we developed 79 new nuclear DNA sequence markers using a clonation protocol. These markers were amplified in several oviparous and viviparous specimens including samples of all extant clades, to test the amplification success and their diversity. 49.4% of the markers were polymorphic and of those, 51.3% amplified in all and 94.9% amplified in 5–7 of the extant Z. vivipara clades. These new markers will be very useful for the study of the population structure, population dynamics, and micro/macro evolution of Z. vivipara. Cross-species amplification in four lizard species (Psammodromus edwardsianus, Podarcis muralis, Lacerta bilineata, and Takydromus sexlineatus) was positive in several of the markers, and six makers amplified in all five species. The large genetic distance between P. edwardsianus and Z. vivipara further suggests that these markers may as well be employed in many other species.     

Evolutionary and biogeographical implications of the karyological variations in the oviparous and viviparous forms of the lizard Lacerta (Zootoca) vivipara

The lizard Lacerta ( Zootoca ) vivipara has two modes of reproduction and is variable karyologically. We describe its karyological variation from literature data and from new data on two viviparous populations from France, on two oviparous populations from the Pyrenees in south-western France and on three oviparous populations recently discovered in Slovenia. Males have 36 chromosomes, whereas females have only 35 chromosomes in all viviparous populations and in the Pyrenean oviparous populations. This karyotype has been interpreted to result from a fusion of an ancestral sexual W chromosome with an autosome from the Zl or from the Z2 pair. The karyotype formula is 32 autosomes + ZIZ2W for the female and 32 autosomes + Z1Z1Z2Z2 for the male. The karyotype of the Slovenian oviparous populations, 34 autosomes + ZW in the male and 34 autosomes +ZW in the female, represents an evolutionary stage that preceded the chromosomal fusion. There is minor karyological variation, mainly concerning the W and Z2 chromosomes, within the Pyrenean oviparous populations. This parallels the geographic variation of the W-linked alleles of the MPI enzyme and suggests that allopatric differentiation of these oviparous populations might have occurred in the vicinity of the Pyrenees during the Pleistocene.
The viviparous populations from western Europe carry a metacentric W chromosome, whereas oviparous populations from south-western Europe and eastern viviparous populations both show an acrocentrie, or a subtelocentrie. W chromosome. This suggests that the acrocentric-subtelocentric W is a primitive character and that viviparity probably arose in an eastern lineage of the species.     

MITOCHONDRIAL DNA SEQUENCE-BASED PHYLOGENY AND THE EVOLUTION OF VIVIPARITY IN THE SCELOPORUS SCALARIS GROUP (REPTILIA,SQUAMATA)

The lizard genus Sceloporus contains both oviparous and viviparous species. The scalaris complex is the only monophyletic group within the genus that includes both reproductive modes, thus it is particularly well suited for studies of the evolution of viviparity. Approximately 874 nucleotides of mtDNA sequence data, collected from 38 specimens, comprising 25 populations of all five recognized species within the group, were used in a phylogenetic analysis of the origin of viviparity. Viviparity appears to have evolved twice in this group: once in S. goldmani, included in a clade formed by a northern group consisting of S. scalaris, S. chaneyi, and S. goldmani, and one more time in S. bicanthalis, included in the southern group formed by S. bicanthalis and S. aeneus. An oviparous population of S. bicanthalis nested within that viviparous clade, indicates that reversal from viviparity to oviparity may be possible. Degree of sequence divergence among several S. bicanthalis individuals pertaining to a population in which both parity modes occur, was no larger between oviparous and viviparous lizards than among viviparous lizards. This suggests that this population is a single species, and it may represent a transition from oviparity to viviparity or vice-versa.     

Plasticity and limitations of extended egg retention in oviparous Zootoca vivipara (Reptilia: Lacertidae)

The transition between oviparity and viviparity in reptiles is generally accepted to be a gradual process, the result of selection for increasingly prolonged egg retention within the oviduct. We examined egg retention plasticity in an oviparous strain of the lacertid lizard Zootoca vivipara, a species having both oviparous and viviparous populations. We forced a group of female Z. vivipara to retain their clutch in utero by keeping them in dry substrata, and assessed the effect on embryonic development and hatching success, along with offspring phenotype and locomotor performance. Forced egg retention for one additional week affected the developmental stage of embryos at oviposition, as well as hatchling robustness and locomotor performance. However, embryos from forced clutch retention treatment reached one stage unit more than control embryos at oviposition time. Embryos from control eggs were more developed than embryos from experimental eggs after approximately the same period of external incubation, showing that embryonic development is retarded during the period of extended egg retention, despite the high temperature inside the mother's body. Significant differences in external incubation time were only found in one of the two years of study. Hatching success was much lower in the experimental group with forced egg retention (21.1%) than in the control group (95.4%). Therefore, we conclude that there are limitations that hinder the advance of intrauterine embryonic development beyond the normal time of oviposition, and that extended egg retention does not represent clear advantages in this population of Z. vivipara. Nevertheless, the fact that some eggs are successful after forced egg retention could be advantageous for the females that are able to retain their clutch under unfavourable climatic conditions. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 75–82.     

Metaphase and meiotic chromosomes,synaptonemal complexes (SC) of the lizard <Emphasis Type="Italic">Zootoca vivipara</Emphasis>

Somatic mitotic and meiotic chromosomes at the pachytene and at the metaphase I of the males of the viviparous lizard, Zootoca vivipara (Lichtenstein, 1823), from northwestern Russia, belonging to the Russian form of Z. v. vivipara, are examined. The spreading of synaptonemal complexes (SC) of their chromosomes are obtained and analyzed for the first time. Eighteen SC are observed, including SC of the Z₁Z₁ (pairs 5 or 6) and the Z₂Z₂ (pair 13) sex chromosomes. Characteristics of SC are compared with the number and the shape of bivalents and with those of the karyotype structure. In the studied Russian form of Z. v. vivipara, the length ratios of bivalents correlate with that of mitotic chromosomes (2n = 36); however, some specificity in the morphology of SC of the Z₁Z₁ sex chromosomes is reported in this article.     

Variation in body size and sexual size dimorphism in the most widely ranging lizard: testing the effects of reproductive mode and climate

Reproductive mode, ancestry, and climate are hypothesized to determine body size variation in reptiles but their effects have rarely been estimated simultaneously, especially at the intraspecific level. The common lizard (Zootoca vivipara) occupies almost the entire Northern Eurasia and includes viviparous and oviparous lineages, thus representing an excellent model for such studies. Using body length data for >10,000 individuals from 72 geographically distinct populations over the species' range, we analyzed how sex‐specific adult body size and sexual size dimorphism (SSD) is associated with reproductive mode, lineage identity, and several climatic variables. Variation in male size was low and poorly explained by our predictors. In contrast, female size and SSD varied considerably, demonstrating significant effects of reproductive mode and particularly seasonality. Populations of the western oviparous lineage (northern Spain, south‐western France) exhibited a smaller female size and less female‐biased SSD than those of the western viviparous (France to Eastern Europe) and the eastern viviparous (Eastern Europe to Far East) lineages; this pattern persisted even after controlling for climatic effects. The phenotypic response to seasonality was complex: across the lineages, as well as within the eastern viviparous lineage, female size and SSD increase with increasing seasonality, whereas the western viviparous lineage followed the opposing trends. Altogether, viviparous populations seem to follow a saw‐tooth geographic cline, which might reflect the nonmonotonic relationship of body size at maturity in females with the length of activity season. This relationship is predicted to arise in perennial ectotherms as a response to environmental constraints caused by seasonality of growth and reproduction. The SSD allometry followed the converse of Rensch's rule, a rare pattern for amniotes. Our results provide the first evidence of opposing body size—climate relationships in intraspecific units.     

Subspecies of the Central American Squirrel Monkey (Saimiri oerstedii) as Units for Conservation

The accurate diagnosis of conservation units now typically includes recognition of genetic diversity and unique evolutionary lineages and is necessary to inform the conservation management of endangered species. We evaluated whether the two currently recognized subspecies of the endangered Central American squirrel monkey (Saimiri oerstedii) in Costa Rica are evolutionarily significant units (ESUs) that should be managed separately in conservation efforts. We used previously published sequences of 50 individuals of Saimiri oerstedii for 880 bp of the mtDNA d-loop and genotypes of 244 individuals for 16 microsatellites and conducted novel analyses to characterize genetic differentiation between subspecies of Saimiri oerstedii. We measured sequence differentiation and inferred an intraspecific molecular phylogeny and a haplotype network, and found consistent results supporting statistically significant divergence and reciprocal monophyly between subspecies. A population aggregation analysis also supported Saimiri oerstedii citrinellus and S. o. oerstedii as diagnosably distinct units. These results confirm previous genetic studies with smaller sample sizes and are consistent with other factors including differences in pelage and morphology and divergence at nuclear markers. Conservation managers should manage these subspecies separately to prevent the loss of genetic diversity via artificially induced outbreeding. High levels of genetic diversity may buffer populations against outside extinction pressures, to which Saimiri oerstedii are vulnerable because of their dwindling habitat and small population size.     

Chemical composition of femoral secretions of oviparous and viviparous types of male common lizards Lacerta vivipara

In spite of the importance of chemoreception in intraspecific communication of lizards, only a few studies have examined chemical composition of secretions of lizards. The secretion of the femoral glands of adult male lizards Lacerta vivipara contains a relatively low number (18) of lipophilic compounds in comparison with other related lacertid lizards. These compounds were identified on the basis of mass spectra, obtained by GC-MS. Chemicals included ten steroids (mainly cholesterol) and four carboxylic acids between n-C₁₂ and n-C₁₈, and minor components such as squalene, α-tocopherol, and two waxy esters, which may contribute to avoid oxidation of other lipophilic components in the fairly humid environments occupied by this lizard. Secretions of adult males from oviparous and viviparous populations did not differ in the numbers and quality of chemical compounds, but there were some differences in the relative proportion of some compounds. Males from oviparous populations had lower proportions of hexadecanoic acid and cholestan-3-one, and higher proportions of squalene than viviparous males. These differences might be explained by either small genetic differences between types or due to different microclimatic conditions in the original populations.     

Karyological investigations of populations of the lizard Zootoca vivipara (Juaquin, 1787) from the Baltic Sea basin (western region of Russia)

Populations of the lizard Zootoca vivipara (Juaquin, 1787) (Lacertidae, Sauria) from Western and Central Europe are poorly differentiated in morphology. However, they differ from each other by several karyotype markers and their reproductive mode (oviparous and viviparous types). Here we report for the first time the results of combined investigations of Z. vivipara from Eastern Europe (the Baltic Sea basin of Western Russia). The karyotype and reproductive mode of the specimens from four previously not examined populations in Kaliningrad region have been studied. It has been shown that these lizards have viviparous mode of reproduction and their karyotypes vary on morphology of W-sex chromosomes. Females possess 2n = 35 : 32 A + Z1Z2W, with W--SV and 2n = 35 : 32 A + Z1Z2W, with W--A/ST. We have identified these populations karyologically and have first revealed that they belong to two different viviparous forms of nominative subspecies Z. v. vivipara, namely to its "western" and "Russian (eastern)" forms. These data have confirmed that the Baltic Sea basin in Eastern Europe is a zone of secondary contact of these chromosomal forms of Z. v. vivipara. The results obtained do not now allow us to speak about their sympatry, parapatry and (or) hybridization events. The results suggest that during postglasial time "western" form might colonize this region from western Europe whereas "Russian (eastern)" form might do it from Southern-Eastern Europe. It has been recommended to save the biodiversity of Z. vivipara in Kaliningrad region, namely the peripheral and very rare on vast territory of Russia "western" form and unique for western region of Russia "Russian (eastern)" form.     

Subspecies boundaries and recent evolution history of the common pheasant (Phasianus colchicus) across China

The mitochondrial DNA (mtDNA) control region of two hundreds and thirty-six common pheasants (belonging to fourteen subspecies collected at twenty-eight localities) was used to investigate the subspecies status of Phasianus colchicus. Eighty-nine variable sites defined one hundred and thirty-nine haplotypes. Phylogenetic analysis of haplotypes revealed that P. c. shawii, P. c. mongolicus and P. c. suehschanensis were monophyletic. P. c. shawii and P. c. mongolicus were isolated by the Taklimakan, the Bardain, the Jaran and the Gurbantonggut Deserts where the two subspecies evolved independently. P. c. suehschanensis was isolated by the forest and mountains in the Sichuan Basin where it evolved independently. Further eleven subspecies were identified and split into the western and eastern groups. The divergence occurred in the late Pleistocene when the arid, semi-arid and monsoon regions formed, and it was induced by the isolation from the Qinling and Taihang Mountains. Fst-values decreased from 0.543 (for twenty-eight populations) to 0.541 (for fourteen subspecies). In light of these results, we suggest that the currently recognized subspecies do not reflect the evolutionary history of the common pheasant.     

Comparison of the cold hardiness capacities of the oviparous and viviparous forms of Lacerta vivipara

The lizard Lacerta vivipara has allopatric oviparous and viviparous populations. The cold hardiness strategy of L. vivipara has previously been studied in viviparous populations, but never in oviparous ones. The present study reveals that both the oviparous and viviparous individuals of this species are able to survive in a supercooled state at -3 degrees C for at least one week when kept on dry substrates. The mean crystallisation temperatures of the body, around -4 degrees C on dry substrata and -2 degrees C on wet substrata, do not differ between oviparous and viviparous individuals. All the individuals are able to tolerate up to 48-50% of their body fluid converted into ice, but only viviparous individuals were able to stabilize their body ice content at 48%, and hence were able to survive even when frozen at -3 degrees C for times of up 24 hours. Ice contents higher than 51% have been constantly found lethal for oviparous individuals. This suggests that, in L. vivipara, the evolution towards a higher degree of freezing tolerance could parallel the evolution of the viviparous reproductive mode, a feature believed to be strongly selected under cold climatic conditions. This is the first report, among reptiles, of an intraspecific variation regarding the freeze tolerance capacities.     

Phylogeny of mitochondrial DNA clones in tassel-eared squirrels Sciurus aberti

The tassel-eared squirrel, Sciurus aberti , includes six subspecies which occupy restrictive and apparently identical habitats in Ponderosa pine forests in the south-western United States and Mexico; the strict habitat requirement of this species is based on dietary requirements which are only fulfilled in these forests. To examine evolutionary relationships among certain subspecies of S. aberti , we obtained estimates of nucleotide diversity within subspecies as well as nucleotide divergence between subspecies using mitochondrial DNA (mtDNA) analysis. Restriction site polymorphisms were identified in samples of the four US subspecies: S. a. aberti (Abert), S. a. kaibabensis (Kaibab), S. a. ferreus (Ferreus), and S. a. chuscensis (Chuska) Fourteen mtDNA clones were resolved that were, with one exception, uniquely subspecific. Dendrograms constructed by neighbour-joining and maximum parsimony methods revealed two major assemblages: (1) an Abert/Kaibab group; and (2) a Ferreus/Chuska group. The Abert vs. Ferreus clones exhibited the greatest net nucleotide divergence, with a lineage separation estimate approximating 572 000 years ago assuming a nucleotide substitution rate of 7.15 × 10^-9/year/site. Five out of ten Chuska squirrels shared a clone with one Abert sample; the relative sizes of these two populations and their respective ranges as well as their close proximity support the proposal for relatively recent intermixing of Abert and Chuska populations resulting in what appears to be Abert → Chuska migration. Nucleotide diversity within subspecies ranked as Kaibab < Ferreus < Abert < Chuska; the relatively high diversity for the Chuska sample is based on the apparent introgression of Abert mtDNA. The relative diversity exhibited by Kaibab, Ferreus and Aberti samples corresponds to the range size of the respective subspecies.     

Recombination and Evolution of Duplicate Control Regions in the Mitochondrial Genome of the Asian Big-Headed Turtle,Platysternon megacephalum

Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3′ end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum.