The rate of mitochondrial 12S rRNA gene evolution is similar in freshwater turtles and marsupials

The determinants of the molecular substitution process in turtles

Neutral rates of molecular evolution vary across species, and this variation has been shown to be related to biological traits. One of the first patterns to be observed in vertebrates has been an inverse relationship between body mass (BM) and substitution rates. The effects of three major life-history traits (LHT) that covary with BM - metabolic rate, generation time and longevity (LON) - have been invoked to explain this relationship. However, most of the theoretical and empirical evidence supporting this relationship comes from endothermic vertebrates, that is, mammals and birds, in which the environmental conditions, especially temperature, do not have a direct impact on cellular and molecular biology. We analysed the variations in mitochondrial and nuclear rates of synonymous substitution across 224 turtle species and examined their correlation with two LHT (LON and BM) and two environmental variables [latitude (LAT) and habitat]. Our analyses indicate that in turtles, neutral rates of molecular evolution are hardly correlated with LON or BM. Rather, both the mitochondrial and nuclear substitution rates are significantly correlated with LAT - faster evolution in the tropics - and especially so for aquatic species. These results question the generality of the relationships reported in mammals and birds and suggest that environmental factors might be the strongest determinants of the mutation rate in ectotherms.

Fast molecular evolution associated with high active metabolic rates in poison frogs

Molecular evolution is simultaneously paced by mutation rate, genetic drift, and natural selection. Life history traits also affect the speed of accumulation of nucleotide changes. For instance, small body size, rapid generation time, production of reactive oxygen species (ROS), and high resting metabolic rate (RMR) are suggested to be associated with faster rates of molecular evolution. However, phylogenetic correlation analyses failed to support a relationship between RMR and molecular evolution in ectotherms. In addition, RMR might underestimate the metabolic budget (e.g., digestion, reproduction, or escaping predation). An alternative is to test other metabolic rates, such as active metabolic rate (AMR), and their association with molecular evolution. Here, I present comparative analyses of the associations between life history traits (i.e., AMR, RMR, body mass, and fecundity) with rates of molecular evolution of and mitochondrial loci from a large ectotherm clade, the poison frogs (Dendrobatidae). My results support a strong positive association between mass-specific AMR and rates of molecular evolution for both mitochondrial and nuclear loci. In addition, I found weaker and genome-specific covariates such as body mass and fecundity for mitochondrial and nuclear loci, respectively. No direct association was found between mass-specific RMR and rates of molecular evolution. Thus, I provide a mechanistic hypothesis of the link between AMRs and the rate of molecular evolution based on an increase in ROS within germ line cells during periodic bouts of hypoxia/hyperoxia related to aerobic exercise. Finally, I propose a multifactorial model that includes AMR as a predictor of the rate of molecular evolution in ectothermic lineages.

Population genetics analysis of Podocnemis sextuberculata (Testudines, Podocnemidae): lack of population structure in the central Amazon Basin

The chelonians are, in general, important for the economy of the traditional populations of the Amazon region, especially as a source of animal protein. Furthermore, sub-products, such as eggs and fat, are utilized in the manufacture of cosmetics, and the plastron and carapace are used in the manufacture of adornments. The freshwater turtle species Podocnemis sextuberculata, locally known as "iaçá" or "pitiú", is widely distributed in the Amazon Basin in Brazil and also in Colombia and Peru. This species is on the International Union for Conservation of Nature Red List in the category of vulnerable species. We examined the genetic variability and population structure of three populations represented by 64 individuals sampled from Reserva Federal de Abufari, Tapauá, Amazonas State; Reserva de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas State, and Terra Santa, Pará State. All of these are over 1000 km from each other. A partial 415-bp sequence of the mitochondrial gene ND1 was utilized as a molecular marker. Seven haplotypes were observed; the most common haplotype was shared by all the areas sampled, while the rarest haplotypes were represented by a single individual and were thus restricted to a single locality. The sharing of the most common haplotype, the high number of migrants (Nm) and the AMOVA results indicate a lack of genetic structure among the sampling localities. The levels of genetic variability observed were homogeneous among the sampling localities. These results (Ө(ST) and Nm) are compatible with what is known about the ecology of this species, which has a great migratory capacity.

Species identification using the cytochrome b gene of commercial turtle shells

Turtle shells and their gelled products are familiar in some countries as foods, tonics and medicines. These shells may come from endangered and protected species, requiring the identification of the species present to enforce national and international legislation. We report on the design of five combinations of primer pairs for the identification of turtle shells and shell fragments used as ornaments, food products and medicines. The types of samples used are those encountered frequently and will typically contain highly degraded DNA. The success rate for species identification using the test described is dependent upon the choice of primer sets used and the length of the expected amplification product. Gelled products were simulated by the process of decoction for up to 12 h, after which all the turtle species could be identified from the liquid samples. This study establishes a method for the identification of commercial turtle shells and illustrates a simulated case using gelled products.

Complete mitochondrial genomes of three neobatrachian anurans: a case study of divergence time estimation using different data and calibration settings

We sequenced the whole mitochondrial (mt) genomes of three neobatrachian species: Japanese tree frog Hyla japonica, Japanese common toad Bufo japonicus, and narrow-mouthed toad Microhyla okinavensis. The gene arrangements of these genomes diverged from that of basal anurans (suborder Archaeobatrachia), but are the same as that of the members of derived frogs (i.e., superfamily Hyloidae and Ranoidae in suborder Neobatrachia), suggesting the one-time occurrence of a gene rearrangement event in an ancestral lineage of derived anurans. Furthermore, several distinct repeat motifs including putative termination-associated sequences (TASs) and conserved sequence blocks (CSBs) were observed in the control regions (CRs) of B. japonicus and H. japonica, while no repeat motifs were found in that of M. okinavensis. Phylogenetic analyses using both nucleotide and amino acid data of mt genes support monophyly of neobatrachians. The estimated divergence time based on amino acid data with multiple reference points suggests that the three living amphibian orders may have originated in the Carboniferous period, and that the divergences of anurans had occurred between the Permian and Tertiary periods. We also checked the influence of the data types and the settings of reference times on divergence time estimation. The resultant divergence times estimated from several datasets and reference time settings suggest that the substitution saturation of nucleotide data may lead to overestimated (i.e., older) branching times, especially for early divergent taxa. We also found a highly accelerated substitution rate in neobatrachian mt genes, and fast substitution possibly resulted in overestimation. To correct this erroneous estimation, it is efficient to apply several reference points among neobatrachians.

The complete mitochondrial genome of the Korean soft-shelled turtle Pelodiscus sinensis (Testudines, Trionychidae)

We isolated Korean soft-shelled turtle, Pelodiscus sinensis, mitochondrial DNA by long-polymerase chain reaction (long-PCR) with conserved primers and sequenced this mitochondrial genome (mitogenome) with primer walking using flanking sequences. The P. sinensis mitochondrial DNA has 17,042 bp and its structural organization is conserved compared to those of other reptiles and mammals. To unveil the phylogenetic relationship of the turtles, we used the NJ, MP, and ML analysis methods after inferring those sequences from the mitochondrial 16S rRNA gene. We also compared two P. sinensis variants from Korea and China using the mitochondrial genome. In this study, we report the basic characteristics of the P. sinensis mitochondrial genome, including structural organization and base composition of the rRNAs, tRNAs and protein-coding genes, as well as characteristics of tRNAs. These features are applicable for the study of phylogenetic relationships in turtles.

Species identification of Kachuga tecta using the cytochrome b gene

A DNA technique has been established for the identification to species level of tortoises. The test on the shell of the animal was used to identify samples from the species Kachuga tecta. A total of 100 tortoise shell specimens collected from the National Council of Agriculture (COA), Taiwan, were used in this study. Primer pairs were designed to amplify partial DNA fragments of cytochrome b within the mitochondrial genome. The DNA data showed that among the 100 samples, there were four distinct haplotype DNA sequences, within which there were a total of 90 variable sites. Between haplotypes I and II, there was only 1 nucleotide difference at position 228. Between haplotypes I and III, 65 nucleotide differences were observed; haplotypes I and IV, 62 nucleotide differences; and haplotypes III and IV, 56 nucleotide differences were observed. There were 66 and 63 nucleotide differences between haplotypes II and III and haplotypes II and IV respectively. All four haplotypes were compared with the DNA sequences held at the GenBank and EMBL databases. The most similar species were K. tecta (haplotype I and II), Morenia ocellata (haplotype III) and Geoclemys hamiltonii (haplotype IV), and their respective mtDNA similarities were 99.5%, 99.3%, 89.9% and 99.5%. However, as haplotype III was only 89.9% homologous with M. ocellata, it would seem that this haplotype shows only a limited relationship with a similar species registered currently in these databases. The method established by this study is an additional method for the identification of samples protected under Convention International Trade in Endangered Species (CITES) and will improve the work for the preservation of the endangered species.

A previously unrecognized radiation of ranid frogs in Southern Africa revealed by nuclear and mitochondrial DNA sequences

In sub-Saharan Africa, amphibians are represented by a large number of endemic frog genera and species of incompletely clarified phylogenetic relationships. This applies especially to African frogs of the family Ranidae. We provide a molecular phylogenetic hypothesis for ranids, including 11 of the 12 African endemic genera. Analysis of nuclear (rag-1, rag-2, and rhodopsin genes) and mitochondrial markers (12S and 16S ribosomal RNA genes) provide evidence for an endemic clade of African genera of high morphological and ecological diversity thus far assigned to up to five different subfamilies: Afrana, Cacosternum, Natalobatrachus, Pyxicephalus, Strongylopus, and Tomopterna. This clade has its highest species diversity in southern Africa, suggesting a possible biogeographic connection with the Cape Floral Region. Bayesian estimates of divergence times place the initial diversification of the southern African ranid clade at approximately 62-85 million years ago, concurrent with the onset of the radiation of Afrotherian mammals. These and other African ranids (Conraua, Petropedetes, Phrynobatrachus, and Ptychadena) are placed basally within the Ranoidae with respect to the Eurasian groups, which suggests an African origin for this whole epifamily.

Initial Diversification of Living Amphibians Predated the Breakup of Pangaea

The origin and divergence of the three living orders of amphibians (Anura, Caudata, Gymnophiona) and their main lineages are one of the most hotly debated topics in vertebrate evolution. Here, we present a robust molecular phylogeny based on the nuclear RAG1 gene as well as results from a variety of alternative independent molecular clock calibrations. Our analyses suggest that the origin and early divergence of the three living amphibian orders dates back to the Palaeozoic or early Mesozoic, before the breakup of Pangaea, and soon after the divergence from lobe-finned fishes. The resulting new biogeographic scenario, age estimate, and the inferred rapid divergence of the three lissamphibian orders may account for the lack of fossils that represent plausible ancestors or immediate sister taxa of all three orders and the heretofore paradoxical distribution of some amphibian fossil taxa. Furthermore, the ancient and rapid radiation of the three lissamphibian orders likely explains why branch lengths connecting their early nodes are particularly short, thus rendering phylogenetic inference of implicated relationships especially difficult.

Mitochondrial haplotype diversity in the tortoise species Testudo graeca from North Africa and the Middle East

BACKGROUND

To help conservation programs of the endangered spur-thighed tortoise and to gain better insight into its systematics, genetic variation and evolution in the tortoise species Testudo graeca (Testudines: Testudinidae) was investigated by sequence analysis of a 394-nucleotide fragment of the mitochondrial 12S rRNA gene for 158 tortoise specimens belonging to the subspecies Testudo graeca graeca, Testudo graeca ibera, Testudo graeca terrestris, and a newly recognized subspecies Testudo graeca whitei. A 411-nucleotide fragment of the mitochondrial D-loop was additionally sequenced for a subset of 22 T. graeca, chosen because of their 12S gene haplotype and/or geographical origin.

RESULTS

Haplotype networks generated by maximum-likelihood and neighbor-joining analyses of both the separate and the combined sequence data sets suggested the existence of two main clades of Testudo graeca, comprising Testudo graeca from northern Africa and Testudo graeca from the Turkey and the Middle East, respectively.

CONCLUSION

Mitochondrial DNA haplotyping suggests that the tortoise subspecies of T. g. graeca and T. g. ibera are genetically distinct, with a calculated divergence time in the early or middle Pleistocene. Other proposed subspecies could not clearly be recognized based upon their mt haplotypes and phylogenetic position, and were either part of the T. g. graeca or of the T. g. ibera clade, suggesting that genetic evidence for the existence of most of the 15 proposed subspecies of T. graeca is weak.

Phylogenetic relationships among the species of the genus Testudo (Testudines: Testudinidae) inferred from mitochondrial 12S rRNA gene sequences

To test phylogenetic relationships within the genus Testudo (Testudines: Testudinidae), we have sequenced a fragment of the mitochondrial (mt) 12S rRNA gene of 98 tortoise specimens belonging to the genera Testudo, Indotestudo, and Geochelone. Maximum likelihood and neighbor-joining methods identify two main clades of Mediterranean tortoises, one composed of the species Testudo graeca, Testudo marginata, and Testudo kleinmanni and a second of Testudo hermanni, Testudo horsfieldii, and Indotestudo elongata. The first clade, but not the second, was also supported by maximum parsimony analysis. Together with the genus Geochelone, a star-like radiation of these clades was suggested, as a sister-group relationship between the two Testudo clades could not be confirmed. The intraspecies genetic variation was examined by sequencing the mt 12S rRNA fragment from 28 specimens of T. graeca and 49 specimens of T. hermanni from various geographic locations. Haplotype diversity was found to be significantly larger in T. graeca compared with T. hermanni, suggestive of reduced genetic diversity in the latter species, perhaps due to Pleistocene glaciations affecting northern and middle Europe or other sources of lineage reduction. No ancient mt 12S rRNA gene haplotypes were identified in T. graeca and/or T. hermanni originating from islands in the Mediterranean Sea, suggesting that these islands harbor tortoise populations introduced from the European and African mainland.

Lineage-specific evolutionary rate in mammalian mtDNA

The existence of a lineage-specific nucleotide substitution rate in mammalian mtDNA has been investigated by analyzing the mtDNA of all available species, that is, 35 complete mitochondrial genomes from 14 mammalian orders. A detailed study of their evolutionary dynamics has been carried out on both ribosomal RNA and first and second codon positions (P12) of H-strand protein-coding genes by using two different types of relative-rate tests. Results are quite congruent between ribosomal and P12 sites. Significant rate variations have been observed among orders and among species of the same order. However, rate variation does not exceed 1.8-fold between the fastest (Proboscidea and Primates) and the slowest (Perissodactyla) evolving orders. Thus, the observed mitochondrial rate variations among taxa do not invalidate the suitability of mtDNA for drawing mammalian phylogeny. Dependence of evolutionary rate differences on variations in mutation and/or fixation rates was examined. Body size, generation time, and metabolic rate were tested, and no significant correlation was observed between them and the taxon-specific evolutionary rates, most likely because the latter might be influenced by multiple overlapping variable constraints.

Comparative molecular phylogeography of North American softshell turtles (Apalone): implications for regional and wide-scale historical evolutionary forces

We use a comparative analysis of partial cytochrome b sequences to evaluate the evolutionary forces shaping wide-scale phylogeographic patterns of all three North American softshell turtles (Apalone ferox, A. mutica, and A. spinifera). The overall phylogeographic patterns are concordant with results from both extensive regional studies of southeastern species, implicating historical vicariant processes during the Pliocene and Pleistocene, and investigations of more northerly distributed species, indicating a bottleneck effect of recent dispersal into postglacial habitat. We also resolved a novel, shared genetic break between northern-western and southeastern populations within both A. mutica and A. spinifera, demonstrating the value of using widespread taxa to evaluate both regional and wider scale phylogeographic patterns. The extensive phylogenetic structure and sequence divergences within both A. mutica and A. spinifera contrast sharply with most previous studies of turtles and with the hypothesis that turtles in general have slow rates of mtDNA evolution.