Whole-genome survey reveals extensive variation in genetic diversity and inbreeding levels among peregrine falcon subspecies.

In efforts to prevent extinction, resource managers are often tasked with increasing genetic diversity in a population of concern to prevent inbreeding depression or improve adaptive potential in a changing environment. The assumption that all small populations require measures to increase their genetic diversity may be unwarranted, and limited resources for conservation may be better utilized elsewhere. We test this assumption in a case study focused on the peregrine falcon (Falco peregrinus), a cosmopolitan circumpolar species with 19 named subspecies. We used whole-genome resequencing to generate over two million single nucleotide polymorphisms (SNPs) from multiple individuals of all peregrine falcon subspecies. Our analyses revealed extensive variation among subspecies, with many island-restricted and nonmigratory populations possessing lower overall genomic diversity, elevated inbreeding coefficients (F ROH)-among the highest reported, and extensive runs of homozygosity (ROH) compared to mainland and migratory populations. Similarly, the majority of subspecies that are either nonmigratory or restricted to islands show a much longer history of low effective population size (N e). While mutational load analyses indicated an increased proportion of homozygous-derived deleterious variants (i.e., drift load) among nonmigrant and island populations compared to those that are migrant or reside on the mainland, no significant differences in the proportion of heterozygous deleterious variants (i.e., inbreeding load) was observed. Our results provide evidence that high levels of inbreeding may not be an existential threat for some populations or taxa. Additional factors such as the timing and severity of population declines are important to consider in management decisions about extinction potential.

Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae.

Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication-Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny.

Geography-Dependent Horizontal Gene Transfer from Vertebrate Predators to Their Prey.

Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from predators (snakes) to their prey (frogs). At least 54 instances of BovB HT were detected, which we estimate to have occurred across time between 85 and 1.3 Ma. Using comprehensive transcontinental sampling, our study demonstrates that BovB HT is highly prevalent in one geographical region, Madagascar, suggesting important regional differences in the occurrence of HTs. We discovered parasite vectors that may plausibly transmit BovB and found that the proportion of BovB-positive parasites is also high in Madagascar where BovB thus might be physically transported by parasites to diverse vertebrates, potentially including humans. Remarkably, in two frog lineages, BovB HT occurred after migration from a non-HT area (Africa) to the HT hotspot (Madagascar). These results provide a novel perspective on how the prevalence of parasites influences the occurrence of HT in a region, similar to pathogens and their vectors in some endemic diseases.

Karyotype Analysis of Four Blind Snake Species (Reptilia: Squamata: Scolecophidia) and Karyotypic Changes in Serpentes.

The suborder Serpentes is divided into 2 infraorders, Scolecophidia and Alethinophidia, which diverged at an early stage of snake diversification. In this study, we examined karyotypes of 4 scolecophidian species (Letheobia simonii, Xerotyphlops vermicularis, Indotyphlops braminus, and Myriopholis macrorhyncha) and performed FISH with 18S-28S rDNA as well as microchromosomal and Z chromosome-linked genes of Elaphe quadrivirgata (Alethinophidia) to investigate the karyotype evolution in the scolecophidian lineage. Diploid chromosome numbers of X. vermicularis and L. simonii were 30 (16 macrochromosomes and 14 microchromosomes) and 32 (16 macrochromosomes and 16 microchromosomes), respectively. The karyotype of a female M. macrorhyncha consisted of 15 macrochromosomes and 19 microchromosomes, including a heterochromatic microchromosome, indicating the presence of a heteromorphic chromosome pair. E. quadrivirgata Z-linked genes mapped to chromosome 4 of M. macrorhyncha, not to the heteromorphic pair. Therefore, M. macrorhyncha may have differentiated ZW sex chromosomes which are not homologous to those of E. quadrivirgata. One of the E. quadrivirgata microchromosomal genes mapped to the terminal region of chromosome 4q in X. vermicularis, suggesting that fusions between microchromosomes and macrochromosomes occurred in this species. rDNA was localized in different macrochromosomal pairs in the 2 diploid scolecophidian snakes examined here, whereas the gene location in a microchromosomal pair was conserved in 5 alethinophidian species examined. These results might imply the occurrence of chromosome fusions in the scolecophidian lineages. In I. braminus, a unique parthenogenetic snake with a triploid karyotype (21 macrochromosomes and 21 microchromosomes), morphological heteromorphisms were identified in chromosomes 1 and 7. Such heteromorphisms in 2 chromosomes were also observed in individuals from distant locations in the broad distribution range of this species, suggesting that the heteromorphisms were fixed in the genome at an early stage of its speciation.

Incubation and water temperatures influence the performances of loggerhead sea turtle hatchlings during the dispersal phase.

Artificial manipulation of incubation temperature has been proposed as a potential strategy for mitigating the effects of climate change on sea turtles for which sex determination is temperature-dependent, but thermal manipulation may also affect hatchling survival. Here, we demonstrated that incubation and water temperatures influenced several performance traits that contribute to the survival of loggerhead sea turtles (Caretta caretta) during the post-hatchling dispersal phase. Hatchlings from warm incubation temperatures (31 °C) had significantly shorter incubation periods, higher initial swimming performance, lower sustained swimming performance, and lower growth rates during the first three weeks post-hatching, as well as higher blood glucose concentrations, than those from cool incubation temperatures (27.5 °C). Hatchlings in warm water temperatures (30 °C) exhibited significantly greater swimming performance than those in cool water temperatures (27 °C). Our results indicated that altering incubation temperatures indirectly influences the survival of loggerhead hatchlings by modifying their swimming performance and growth rates, which may affect hatchling predator-avoidance capability. Moreover, thermal manipulation may alter the incubation period, exposing hatchling to water temperatures that they would not otherwise normally experience, which may affect swimming performance. Our results suggest that such conservation strategies may influence their survival, and thus should be carefully considered.

The complete mitochondrial DNA sequence of Pectenocypris sp. (Actinopterygii: Cyprinidae) from Serkap River, Sumatra, Indonesia.

The whole mitochondrial genome of a small cyprinid freshwater fish Pectenocypris sp. collected from Serkap River, Central Sumatra, Indonesia was sequenced. This mitochondrial genome consisted of 16,589 bp and included 37 genes in the same order as in many other vertebrates including the human. Phylogenetic analysis suggested that this taxon clusters with Boraras maculatus among several Rasbora species.

Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing.

BACKGROUND: Genes encoded in vertebrate mitochondrial DNAs are transcribed as a polycistronic transcript for both strands, which is later processed into individual mRNAs, rRNAs and tRNAs, followed by modifications, such as polyadenylation at the 3' end of mRNAs. Although mechanisms of the mitochondrial transcription and RNA processing have been extensively studied using some model organisms, structural variability of mitochondrial mRNAs across different groups of vertebrates is poorly understood. We conducted the high-throughput RNA sequencing to identify major polyadenylation sites for mitochondrial mRNAs in the Japanese grass lizard, Takydromus tachydromoides and compared the polyadenylation profiles with those identified similarly for 23 tetrapod species, featuring sauropsid taxa (reptiles and birds). RESULTS: As compared to the human, a major polyadenylation site for the NADH dehydrogenase subunit 5 mRNA of the grass lizard was located much closer to its stop codon, resulting in considerable truncation of the 3' untranslated region for the mRNA. Among the other sauropsid taxa, several distinct polyadenylation profiles from the human counterpart were found for different mRNAs. They included various truncations of the 3' untranslated region for NADH dehydrogenase subunit 5 mRNA in four taxa, bird-specific polyadenylation of the light-strand-transcribed NADH dehydrogenase subunit 6 mRNA, and the combination of the ATP synthase subunit 8/6 mRNA with a neighboring mRNA into a tricistronic mRNA in the side-necked turtle Pelusios castaneus. In the last case of P. castaneus, as well as another example for NADH dehydrogenase subunit 1 mRNAs of some birds, the association between the polyadenylation site change and the gene overlap was highlighted. The variations in the polyadenylation profile were suggested to have arisen repeatedly in diverse sauropsid lineages. Some of them likely occurred in response to gene rearrangements in the mitochondrial DNA but the others not. CONCLUSIONS: These results demonstrate structural variability of mitochondrial mRNAs in sauropsids. The efficient and comprehensive characterization of the mitochondrial mRNAs will contribute to broaden our understanding of their structural and functional evolution.

Complete mitogenome sequence of Rasbora argyrotaenia (Actinopterygii: Cyprinidae).

The mitochondrial genome of a small freshwater fish Rasbora argyrotaenia from Java Island, Indonesia, was completely sequenced. This mitochondrial genome had 16,740 bp in length and consisted of 37 genes in the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis showed that R. argyrotaenia is more closely related to R. borapetensis than to other Javanese rasboras, R. aprotaenia and R. lateristriata.

Sex chromosome evolution in snakes inferred from divergence patterns of two gametologous genes and chromosome distribution of sex chromosome-linked repetitive sequences.

BACKGROUND: The discovery of differentially organized sex chromosome systems suggests that heteromorphic sex chromosomes evolved from a pair of homologous chromosomes. Whereas karyotypes are highly conserved in alethinophidian snakes, the degeneration status of the W chromosomes varies among species. The Z and W chromosomes are morphologically homomorphic in henophidian species, whereas in snakes belonging to caenophidian families the W chromosomes are highly degenerated. Snakes therefore are excellent animal models in which to study sex chromosome evolution. Herein, we investigated the differentiation processes for snake sex chromosomes using both coding and repetitive sequences. We analyzed phylogenetic relationships of CTNNB1 and WAC genes, localized to the centromeric and telomeric regions, respectively, of the long arms on snake sex chromosomes, and chromosome distribution of sex chromosome-linked repetitive sequences in several henophidian and caenophidian species. RESULTS: Partial or full-length coding sequences of CTNNB1 and WAC were identified for Z homologs of henophidian species from Tropidophiidae, Boidae, Cylindrophiidae, Xenopeltidae, and Pythonidae, and for Z and W homologs of caenophidian species from Acrochordidae, Viperidae, Elapidae, and Colubridae. Female-specific sequences for the two genes were not found in the henophidian (boid and pythonid) species examined. Phylogenetic trees constructed using each gene showed that the Z and W homologs of the caenophidian species cluster separately. The repetitive sequence isolated from the W chromosome heterochromatin of the colubrid Elaphe quadrivirgata and a microsatellite motif (AGAT)8 were strongly hybridized with W chromosomes of the viperid and colubrid species examined. CONCLUSION: Our phylogenetic analyses suggest that the cessation of recombination between the Z and W homologs of CTNNB1 and WAC predated the diversification of the caenophidian families. As the repetitive sequences on the W chromosomes were shared among viperid and colubrid species, heterochromatinization of the proto-W chromosome appears to have occurred before the splitting of these two groups. These results collectively suggest that differentiation of the proto-Z and proto-W chromosomes extended to wide regions on the sex chromosomes in the common ancestor of caenophidian families during a relatively short period.

Molecular phylogeny and historical biogeography of the Indonesian freshwater fish Rasbora lateristriata species complex (Actinopterygii: Cyprinidae): Cryptic species and west-to-east divergences.

Rasbora lateristriata is a primary freshwater fish described from Java Island of Indonesia but its taxonomy, phylogeny, and distributional boundary have not been fully studied. Rasbora baliensis was described as a species endemic to Balinese lakes but its taxonomic status has been controversial in relation to R. lateristriata. Here, we collected Rasbora fishes from various freshwater localities of Java Island, as well as five neighboring islands to conduct molecular and morphological analyses on their phylogenetic relationships. Both molecular analyses using two mitochondrial and two nuclear gene sequences and morphological analyses featuring the body color pattern consistently support that the currently recognized R. lateristriata forms a species complex including at least four major lineages that possibly represent different species. In one of the major lineages, Balinese individuals cluster with those from East Javanese, Lombok and Sumbawa localities, calling for taxonomic revision on R. baliensis. The other three major lineages occur in distinct regions of central, west-central, and western Java and they can be clearly distinguished by the combination of pigmentation patterns in the basicaudal blotch and the supra anal pigment. Our molecular phylogeny suggests west-to-east divergences of the R. lateristriata species complex in Java Island from the late Miocene to Plio-Pleistocene before it finally crossed Wallace's Line, colonizing Lombok and Sumbawa Islands very recently.

Complete mitochondrial genome sequences of two Indonesian rasboras (Rasbora aprotaenia and Rasbora lateristriata).

Complete mitochondrial genome sequences were determined for two Indonesian freshwater fishes, Rasbora aprotaenia and Rasbora lateristriata. These genomes are 16,541 bp and 16,539 bp in length, respectively and encode 37 genes in the typical vertebrate gene arrangement. Phylogenetic analyses supported a view that these species are very closely related to each other.

DNA barcoding of Japanese click beetles (Coleoptera, Elateridae).

Click beetles (Coleoptera: Elateridae) represent one of the largest groups of beetle insects. Some click beetles in larval form, known as wireworms, are destructive agricultural pests. Morphological identification of click beetles is generally difficult and requires taxonomic expertise. This study reports on the DNA barcoding of Japanese click beetles to enable their rapid and accurate identification. We collected and assembled 762 cytochrome oxidase subunit I barcode sequences from 275 species, which cover approximately 75% of the common species found on the Japanese main island, Honshu. This barcode library also contains 20 out of the 21 potential pest species recorded in Japan. Our analysis shows that most morphologically identified species form distinct phylogenetic clusters separated from each other by large molecular distances. This supports the general usefulness of the DNA barcoding approach for quick and reliable identification of Japanese elaterid species for environmental impact assessment, agricultural pest control, and biodiversity analysis. On the other hand, the taxonomic boundary in dozens of species did not agree with the boundary of barcode index numbers (a criterion for sequence-based species delimitation). These findings urge taxonomic reinvestigation of these mismatched taxa.

Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes.

BACKGROUND: Vertebrate mitochondrial genomes (mitogenomes) are 16-18 kbp double-stranded circular DNAs that encode a set of 37 genes. The arrangement of these genes and the major noncoding region is relatively conserved through evolution although gene rearrangements have been described for diverse lineages. The tandem duplication-random loss model has been invoked to explain the mechanisms of most mitochondrial gene rearrangements. Previously reported mitogenomic sequences for geckos rarely included gene rearrangements, which we explore in the present study. RESULTS: We determined seven new mitogenomic sequences from Gekkonidae using a high-throughput sequencing method. The Tropiocolotes tripolitanus mitogenome involves a tandem duplication of the gene block: tRNAArg, NADH dehydrogenase subunit 4L, and NADH dehydrogenase subunit 4. One of the duplicate copies for each protein-coding gene may be pseudogenized. A duplicate copy of the tRNAArg gene appears to have been converted to a tRNAGln gene by a C to T base substitution at the second anticodon position, although this gene may not be fully functional in protein synthesis. The Stenodactylus petrii mitogenome includes several tandem duplications of tRNALeu genes, as well as a translocation of the tRNAAla gene and a putative origin of light-strand replication within a tRNA gene cluster. Finally, the Uroplatus fimbriatus and U. ebenaui mitogenomes feature the apparent loss of the tRNAGlu gene from its original position. Uroplatus fimbriatus appears to retain a translocated tRNAGlu gene adjacent to the 5' end of the major noncoding region. CONCLUSIONS: The present study describes several new mitochondrial gene rearrangements from Gekkonidae. The loss and reassignment of tRNA genes is not very common in vertebrate mitogenomes and our findings raise new questions as to how missing tRNAs are supplied and if the reassigned tRNA gene is fully functional. These new examples of mitochondrial gene rearrangements in geckos should broaden our understanding of the evolution of mitochondrial gene arrangements.

Molecular phylogeny and biogeography of air sac catfishes of the Heteropneustes fossilis species complex (Siluriformes: Heteropneustidae).

The air sac catfish, Heteropneustes fossilis (Siluriformes: Heteropneustidae), is widely distributed in freshwaters of the Indian subcontinent and mainland southeast Asia. No comprehensive molecular studies that cover the broad distributional areas have been carried out to date. Here, we conducted molecular phylogenetic analyses using both mitochondrial and nuclear gene sequences to suggest that the Heteropneustes fossilis species complex consists of three clades that may potentially be separate species with distinct geographical distribution (southeast Asia, northeastern India, and southwestern India). The first and second clades are more closely related to each other than they are to the third clade. Within the first clade there is a basal divergence of a subclade consisting of individuals from the Upper Irrawaddy River basin of Myanmar, which share some morphological traits with members of the Indian clades. Our molecular and morphological data are congruent with hypotheses that the Early-Middle Miocene disconnection between the paleo-Tsangpo River and the Irrawaddy River caused the vicariant divergence between southeast Asian and northeastern Indian clades, and that the southeast Asian Heteropneustes originated from the Upper Irrawaddy.

Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake.

BACKGROUND: Extant sauropsids (reptiles and birds) are divided into two major lineages, the lineage of Testudines (turtles) and Archosauria (crocodilians and birds) and the lineage of Lepidosauria (tuatara, lizards, worm lizards and snakes). Karyotypes of these sauropsidan groups generally consist of macrochromosomes and microchromosomes. In chicken, microchromosomes exhibit a higher GC-content than macrochromosomes. To examine the pattern of intra-genomic GC heterogeneity in lepidosaurian genomes, we constructed a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 183 cDNA clones by fluorescence in situ hybridization, and examined the correlation between the GC-content of exonic third codon positions (GC3) of the genes and the size of chromosomes on which the genes were localized. RESULTS: Although GC3 distribution of snake genes was relatively homogeneous compared with those of the other amniotes, microchromosomal genes showed significantly higher GC3 than macrochromosomal genes as in chicken. Our snake cytogenetic map also identified several conserved segments between the snake macrochromosomes and the chicken microchromosomes. Cross-species comparisons revealed that GC3 of most snake orthologs in such macrochromosomal segments were GC-poor (GC3 < 50%) whereas those of chicken orthologs in microchromosomes were relatively GC-rich (GC3 ≥ 50%). CONCLUSION: Our results suggest that the chromosome size-dependent GC heterogeneity had already occurred before the lepidosaur-archosaur split, 275 million years ago. This character was probably present in the common ancestor of lepidosaurs and but lost in the lineage leading to Anolis during the diversification of lepidosaurs. We also identified several genes whose GC-content might have been influenced by the size of the chromosomes on which they were harbored over the course of sauropsid evolution.

Mitochondrial genomes of two African geckos of genus Hemitheconyx (Squamata: Eublepharidae).

Mitochondrial genomes of two eyelid geckos (Hemitheconyx caudicinctus and Hemitheconyx taylori) were sequenced. Although these genomes conserve a typical vertebrate gene organization, tRNA(Gln) gene of the former appears to have been pseudogenized. A very extensive RNA editing may restore its function in the RNA level or a functional tRNA(Gln) encoded in the nuclear chromosome may be imported into mitochondria.

Characterization of squamate olfactory receptor genes and their transcripts by the high-throughput sequencing approach.

The olfactory receptor (OR) genes represent the largest multigene family in the genome of terrestrial vertebrates. Here, the high-throughput next-generation sequencing (NGS) approach was applied to characterization of OR gene repertoires in the green anole lizard Anolis carolinensis and the Japanese four-lined ratsnake Elaphe quadrivirgata. Tagged polymerase chain reaction (PCR) products amplified from either genomic DNA or cDNA of the two species were used for parallel pyrosequencing, assembling, and screening for errors in PCR and pyrosequencing. Starting from the lizard genomic DNA, we accurately identified 56 of 136 OR genes that were identified from its draft genome sequence. These recovered genes were broadly distributed in the phylogenetic tree of vertebrate OR genes without severe biases toward particular OR families. Ninety-six OR genes were identified from the ratsnake genomic DNA, implying that the snake has more OR gene loci than the anole lizard in response to an increased need for the acuity of olfaction. This view is supported by the estimated number of OR genes in the Burmese python's draft genome (∼280), although squamates may generally have fewer OR genes than terrestrial mammals and amphibians. The OR gene repertoire of the python seems unique in that many class I OR genes are retained. The NGS approach also allowed us to identify candidates of highly expressed and silent OR gene copies in the lizard's olfactory epithelium. The approach will facilitate efficient and parallel characterization of considerable unbiased proportions of multigene family members and their transcripts from nonmodel organisms.

Mitochondrial DNA Variability within Uromastyx ornata philbyi (Agamidae: Squamata) from Southwestern Saudi Arabia.

Approximately 2.4 kbp of mitochondrial DNA was sequenced from 9 individuals of Uromastyx ornata philbyi originating from Taif, Namas, Al-Baha, and Jazan in southwestern Saudi Arabia. The sequenced regions cover eight tRNA genes (tRNA(Gln), tRNA(Ile), tRNA(Met), tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), and tRNA(Tyr)) and two protein-coding genes (NADH dehydrogenase subunit 2 and cytochrome b). U. ornata philbyi had an insertion of 170 bp length between tRNA(Gln) and tRNA(Ile) genes. The first 128 bp of this insertion was similar to the one identified earlier in U. ornata ornata and can be folded into a stem-and-loop structure, which was less stable in U. ornata philbyi than in U. ornata ornata, or the second tRNA(Gln) gene. The next 42 bp of the insertion was unique in U. ornata philbyi and additionally retained a stable stem-and-loop structure. Most base substitutions found in the sequenced genes were synonymous transitions rather than transversions. Tree analyses supported the sister group relationship between the two U. ornata subspecies and divided U. ornata philbyi into two groups: Taif+Namas group in the east of Sarawat and Al-Baha+Jazan group in the west of Sarawat. These molecular data are in agreement with current classification of U. ornata.

Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications.

BACKGROUND: Acrodonta consists of Agamidae and Chamaeleonidae that have the characteristic acrodont dentition. These two families and Iguanidae sensu lato are members of infraorder Iguania. Phylogenetic relationships and historical biogeography of iguanian lizards still remain to be elucidated in spite of a number of morphological and molecular studies. This issue was addressed by sequencing complete mitochondrial genomes from 10 species that represent major lineages of acrodont lizards. This study also provided a good opportunity to compare molecular evolutionary modes of mitogenomes among different iguanian lineages. RESULTS: Acrodontan mitogenomes were found to be less conservative than iguanid counterparts with respect to gene arrangement features and rates of sequence evolution. Phylogenetic relationships were constructed with the mitogenomic sequence data and timing of gene rearrangements was inferred on it. The result suggested highly lineage-specific occurrence of several gene rearrangements, except for the translocation of the tRNAPro gene from the 5' to 3' side of the control region, which likely occurred independently in both agamine and chamaeleonid lineages. Phylogenetic analyses strongly suggested the monophyly of Agamidae in relation to Chamaeleonidae and the non-monophyly of traditional genus Chamaeleo within Chamaeleonidae. Uromastyx and Brookesia were suggested to be the earliest shoot-off of Agamidae and Chamaeleonidae, respectively. Together with the results of relaxed-clock dating analyses, our molecular phylogeny was used to infer the origin of Acrodonta and historical biogeography of its descendant lineages. Our molecular data favored Gondwanan origin of Acrodonta, vicariant divergence of Agamidae and Chamaeleonidae in the drifting India-Madagascar landmass, and migration of the Agamidae to Eurasia with the Indian subcontinent, although Laurasian origin of Acrodonta was not strictly ruled out. CONCLUSIONS: We detected distinct modes of mitogenomic evolution among iguanian families. Agamidae was highlighted in including a number of lineage-specific mitochondrial gene rearrangements. The mitogenomic data provided a certain level of resolution in reconstructing acrodontan phylogeny, although there still remain ambiguous relationships. Our biogeographic implications shed a light on the previous hypothesis of Gondwanan origin of Acrodonta by adding some new evidence and concreteness.

The historical biogeography of the freshwater knifefishes using mitogenomic approaches: a mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha).

The continental distributions of freshwater fishes in the family Notopteridae (Osteoglossomorpha) across Africa, India, and Southeast Asia constitute a long standing and enigmatic problem of freshwater biogeography. The migrational pathway of the Asian notopterids has been discussed in light of two competing schemes: the first posits recent transcontinental dispersal while the second relies on distributions being shaped by ancient vicariance associated with plate-tectonic events. In this study, we determined complete mitochondrial DNA sequences from 10 osteoglossomorph fishes to estimate phylogenetic relationships using partitioned Bayesian and maximum likelihood methods and divergence dates of the family Notopteridae with a partitioned Bayesian approach. We used six species representing the major lineages of the Notopteridae and seven species from the remaining osteoglossomorph families. Fourteen more-derived teleosts, nine basal actinopterygians, two coelacanths, and one shark were used as outgroups. Phylogenetic analyses indicated that the African and Asian notopterids formed a sister group to each other and that these notopterids were a sister to a clade comprising two African families (Mormyridae and Gymnarchidae). Estimated divergence time between the African and Asian notopterids dated back to the early Cretaceous when India-Madagascar separated from the African part of Gondwanaland. Thus, estimated time of divergence based on the molecular evidence is at odds with the recent dispersal model. It can be reconciled with the geological and paleontological evidence to support the vicariance model in which the Asian notopterids diverged from the African notopterids in Gondwanaland and migrated into Eurasia on the Indian subcontinent from the Cretaceous to the Tertiary. However, we could not exclude an alternative explanation that the African and Asian notopterids diverged in Pangea before its complete separation into Laurasia and Gondwanaland, to which these two lineages were later confined, respectively.