Antifertility effects of EP-1 (quinestrol and levonorgestrel) on Pacific rats (Rattus exulans).

Pest rodents pose a serious threat to island biodiversity. Fertility control could be an alternative approach to control the impact of rodents on these islands. In this study, we examined the antifertility effects of EP-1 baits containing quinestrol (E) and levonorgestrel (P) using a dose of 50 ppm E and P at three different ratios (E:P ratio = 1:2, 1:1, and 2:1) on Pacific rats (Rattus exulans) in the Xisha Islands, Hainan, China. Compared to the control group, all animals in EP-1 treatment groups showed significantly decreased food intake and body weight. In treated males, there were obvious abnormalities in testis structure and a significant decrease of relative seminal vesicle weight, but no significant effect on relative uterine and ovarian weights (g kg-1 body weight), or ovarian structure in females. Adding 8% sucrose to the original 50-ppm baits (E:P ratio = 1:1) significantly increased bait palatability for males and females. This dose induced uterine edema and abnormalities of ovarian structure in females but had no significant negative effect on the relative testis, epididymis, and seminal vesicle weights (g kg-1 body weight) or sperm density in males. In summary, 50-ppm EP-1 (1:1) baits have the potential to disrupt the fertility of females, and 8% sucrose addition to the EP-1 baits (E:P ratio = 1:1) could improve bait palatability. This dose disrupted the testis structure in males. Future studies are needed to improve bait acceptance and assess the antifertility effects of EP-1 (1:1) on Pacific rats in captive breeding trials and under field conditions.

The complete mitochondrial genome of the Hainan Island Shrew, Crocidura wuchihensis.

The Hainan Island Shrew Crocidura wuchihensis is a small-bodied insectivore species belonging to the Soricidae family. In this study, we determined its the complete mitochondrial genome. The whole mitochondrial genome was found to be 17,253 bp in length and comprises 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a control region. The base composition of the C. wuchihensis total mitogenome as follows: A, 32.8%; G, 13.0%; T, 32.1%; and C, 22.1%, with an A + T content of 64.9%. Notably, a tandem repeat sequence (5'-CAC ACG TGT ACA-3') was identified in the control region with 24 copy numbers. Additionally, phylogenetic analysis indicated that C. wuchihensis is closely related to Crocidura tanakae and Crocidura dongyangjiangensis based on the concatenated sequences of the 13 protein-coding genes. The characterization of the shrew's mitogenome will provide the foundation for its use in population genomics and systematic studies of Soricidae.

Geographical variation of the acoustic signals in the spot-legged treefrog (Polypedates megacephalus) of Hainan Island.

Geographical divergence in acoustic signals is often affected by multiple selective pressures. Environmental factors are expected to shape signals by adjusting for greater propagation efficiency. Nevertheless, such habitat-driven hypotheses have not been well-examined with multi-signal and multi-habitat types included simultaneously. In this study, we evaluated call similarity of the spot-legged treefrog (Polypedates megacephalus), characterized by multiple call types, from 11 geographic populations across Hainan Island. We also examined multiple factors (i.e. body mass, temperature, altitude, and vegetation) among different acoustical geographic clusters, and tested whether the variation in acoustic length and frequency among different habitats was in accordance with the prediction derived from the acoustic adaptation hypothesis. We showed that P. megacephalus from Hainan Island included 3 acoustic geographic clusters: the northeastern flatlands, the southwest mountains, and the hills around the mountains. We also showed that environmental factors (i.e. altitude and vegetation) varied across these 3 acoustically distinct areas. Moreover, the duration of the different call types supported the hypothesis that they should have optimal transmission in their own habitats. Thus, our results reveal the roles of ecological selection in the geographical divergence of anuran acoustic signals.

A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history.

The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.

Complete mitogenome of Intermediate Egret Ardea intermedia (Ciconiiformes: Ardeidae).

The Intermediate Egret Ardea intermedia belongs to family Ardeidae, and it is widely distributed over east Africa across the Indian subcontinent to Southeast Asia and Australia. In the present study, the total mitochondrial genome of A. intermedia was determined. The genome is 18,578 bases in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (CR and CRR), with a base composition of A 30.8%, G 14.0%, T 24.3% and C 30.9%. The dn/ds values of ten PCGs (ND1, ND2, ATP8, ATP6, Cox3, ND3, ND4L, ND4, ND5 and ND6) are below 1. Bayesian inference (BI) and maximum likelihood (ML) methods generated similar topologies. Phylogenies showed that Ardea novaehollandiae and A. intermedia should be assign to Egretta and Ardea, respectively. The mitogenomic data of A. intermedia will be useful in the conservation genetics and phylogeny of the species.

Mitogenome of a cryptic species within Uropsilus and divergence time estimation.

Uropsilus sp. 4 is a new cryptic species, collected in Changyang county, Hubei province, China. In this study, the whole mitochondrial genome of Uropsilus sp. 4 was first determined and characterized. The genome is 16,542 bp in length, containing 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Base on NJ, ML, and BI methods, we obtained the same topologies. U. sp. 4 clustered with U. gracilis and the divergence time was 1.78 Ma (95% CI 1.24-2.32 Ma), in concordance with the third period of last orogenic push of the Qinghai-Tibetan Plateau, might contribute to the speciation of U. sp. 4.

DNA barcoding and phylogeny of Calidris and Tringa (Aves: Scolopacidae).

The avian genera Calidris and Tringa are the largest of the widespread family of Scolopacidae. The phylogeny of members of the two genera is still a matter of controversial. Mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification and phylogeny of animal species. In this study, we analyzed the COI barcodes of thirty-one species of the two genera. All the species had distinct COI sequences. Two hundred and twenty-one variable sites were identified. Kimura two-parameter distances were calculated between barcodes. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. All the species could be discriminated by their distinct clades in the phylogenetic trees. The phylogenetic trees grouped all the species of Calidris and Tringa into different monophyletic clade, respectively. COI data showed a well-supported phylogeny for Calidris and Tringa species.

Complete mitochondrial genome of Chinese bamboo rat, Rhizomys sinensis and species divergence comparison.

The Chinese bamboo rat Rhizomys sinensis belongs to family Spalacidae, and is distributed in China, Myanmar, and Vietnam. In this study, the entire mitochondrial genome of R. sinensis was firstly determined. The genome is 16,564 bases in length, containing 13 protein coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a putative control region. The composition and arrangement of its genes are identical to most other mammals. The whole base composition of the mitogenome is A 31.9%, G 12.0%, T 31.2% and C 24.9%, with an A+T rich pattern. The species divergence between R. sinensis and R. pruinosus is 0.113, in accordance with a "10× rule", as the intraspecific barcode variation averaged 1%. The mitogenome data of R. sumatrensis is required to better understand the phylogenetic relationships within Rhizomys.

Characterization of the mitogenome of Uropsilus gracilis and species delimitation.

The species diversity within the genus Uropsilus were underestimated: 10 species among the genus Uropsilus have been proposed. In this study, the complete mitochondrial genome of U. gracilis, with the topotype, was determined. It is 16,536 bp in length, comprising of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and 1 control region. The composition and arrangement of its genes are similar to most other mammals. The total base composition of the mitogenome is A, 33.4%; T, 30.3%; C, 22.7% and G, 13.6%, with a rich content of A+T pattern. We performed the similarity comparison based on 13 PCGs of three species of Asiatic shrew-like mole, U. gracilis, U. sp. 1 and U. soricipes. Pairwise sequence alignment showed that similarity data of U. gracilis versus U. sorcipes are significantly higher than those of U. gracilis versus U. sp.1. This pointed toward a cryptic species (U. sp.1) from Jiajin Mountains rather than U. gracilis.

Description of the mitogenome of Gansu mole (Scapanulus oweni).

The Gansu mole Scapanulus oweni belongs to family Talpidae, and is distributed in the Central and Southwest China. In this study, the total mitochondrial genome of S. oweni was firstly determined. The genome is 16,826 bases in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a displacement loop region, with a base composition of A 34.0%, G 13.5%, T 28.7% and C 23.9%. All of the protein-coding genes initiate with the orthodox ATG start codon execpt for Nd2 and Nd3 begin with ATT, Nd4 and Nd5, start with GTG and ATA, respectively. Four types of stop codons are used by the coding genes, including TAA for Nd1, Cox1, Cox2, Atp8, Atp6, Nd4L, Nd5, Nd6, TAG for Nd2, AGA for Cytb, and an incomplete stop codon T for Cox3, Nd3 and Nd4. The mito-genomic data of Gansu mole, S. oweni will be useful in determining its taxonomic status within Talpidae.

Determination of the complete mitogenome of Spotted Dove, Spilopelia chinensis (Columbiformes: Columbidae).

The Spotted Dove Spilopelia chinensis (Columbiformes: Columbidae) is widely distributed in Southeast Asia. In the present study, we investigated the complete mitochondrial genome of S. chinensis and the mitogenome is 16,964 bp in length, consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region, with the base composition of A 31.1%, G 13.9%, T 23.9%, and C 32.1%. A single extra base "C" at position 174 is inserted in gene Nd3, similar to some other birds and turtles. The phylogenetic relationships using partitioned Bayesian inference based on the 12 concatenated PCGs indicated that ((((Spilopelia, Columba) Ectopistes) (Geotrygon (Leptotila, Zenaida))) Hemiphaga). While, more complete mitogenome sequences should be determined to confirm the phylogenetic status of Spilopelia within family Columbidae.

Molecular phylogenetics and phylogeographic structure of Sorex bedfordiae based on mitochondrial and nuclear DNA sequences.

The southeastern margin of the Tibetan Plateau is characterized by complex topography and a discontinuous landscape, creating a sky island situation. However, the way topography shapes genetic structures and demographic histories of endemic species has not been well studied. We examined the phylogeographic pattern and demographic histories of Sorex bedfordiae, a dispersal-limited small mammal, using three nuclear genes [1977bp] and two mitochondrial genes [1794bp] with comprehensive molecular approaches. We recovered five well-supported clades whose distributions are along mountain ridges and roughly subdivided by large rivers. Demographic expansions in the middle Pleistocene were strongly supported by both nuclear and mitochondrial genes. Our results support the hypothesis that sky island topography and river systems strongly affect the genetic structure of non-aquatic terrestrial species. We further clarify that S. bedfordiae and S. cylindricauda are valid sibling species, whereas S. excelsus is most likely a geographic subspecies of S. bedfordiae.

The complete mitogenome of Stripe-Backed Shrew, Sorex cylindricauda (Soricidae).

The Stripe-Backed Shrew, Sorex cylindricauda belongs to the family Soricidae, and distributes in northwestern Yunnan, central Sichuan, southern Gansu and Shaanxi. In this study, the complete mitochondrial genome sequence of S. cylindricauda was determined. The mitogenome is 17,191 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region, with a base composition of 33.2% A, 30.2% T, 23.8% C and 12.8% G. The study contributes to illuminating taxonomic status of Stripe-Backed Shrew Sorex cylindricauda.

Taxonomic status of Tetraophasis obscurus and Tetraophasis szechenyii (Aves: Galliformes: Phasianidae) based on the complete mitochondrial genome.

Tetraophasis szechenyii and T. obscurus are endangered phasianid birds endemic to China. Historically, the question of whether T. obscurus and T. szechenyii are valid species or subspecies has been controversial. In order to clarify their phylogenetic relationship, we sequenced the complete mitochondrial genome of T. obscurus and, using the complete mitochondrial genome of T. szechenyii, which our lab had already sequenced, conducted Bayesian and maximum-likelihood phylogenetic analyses based on the sequences of 12 concatenated heavy-strand encoded protein-coding genes. Genetic distance and divergence time between the two species were also calculated. The complete mitochondrial genome of T. obscurus was 16,707 bases (accession no.: NC_018034), and its structure was similar to mitochondrial genomes reported for other phasianids. The genetic distance between T. obscurus and T. szechenyii was 0.028, and the divergence time of T. obscurus and T. szechenyii was 1.75 Myr. Considering the genetic distance and divergence time, as well as geographical distribution and morphological differences, we suggest that T. obscurus and T. szechenyii are two valid species. The Pleistocene glacial events in the Hengduan Mountains region may have played an important role in the speciation of T. obscurus and T. szechenyii.

Complete mitochondrial genome of Hainan partridge, Arborophila ardens (Galliformes: Phasianidae).

The Hainan partridge, Arborophila ardens belongs to family Phasianidae, and distributes only in Hainan, China. In this study, the complete mitochondrial genome of A. ardens was first sequenced and characterized. The genome is 16,727 bases in length. Bayesian inference, maximum likelihood and maximum parsimony methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes located on the heavy strand. Phylogenetic analyses further confirm the Arborophila placed at the root of Phasianidae. Arborophila ardens show closer relationship with A. rufipectus than A. rufogularis and A. gingica which cluster as sister group to A. ardens and A. rufipectus.

Phylogenetic analysis of the Mustela altaica (Carnivora: Mustelidae) based on complete mitochondrial genome.

The mountain weasel (Mustela altaica) belongs to family Mustelidae, which is the near threatened species in the IUCN Red List. In this study, the complete mitochondrial genome of M. altaica was sequenced and characterized. The genome is 16,521 bases in length (GenBank accession no. KC815122). The nucleotide sequence data of 12 heavy-strand protein-coding genes of M. altaica and other 20 Mustelidae species were used for phylogenetic analyses. Trees constructed by using Bayesian inference, maximum parsimony and maximum likelihood demonstrated that M. altaica was close to Mustela nivalis and they were sister to Mustela putorius and Mustela sibirica.

Complete mitochondrial genome sequence of Nectogale elegans.

The elegant water shrew (Nectogale elegans) belongs to the family Soricidae, and distributes in northern South Asia, central and southern China and northern Southeast Asia. In this study, the complete mitochondrial genome of N. elegans was sequenced. It was determined to be 17,460 bases, and included 13 protein-coding genes (PCGs), 22 tRNA genes, 2 ribosomal RNA genes and one non-coding region, which is similar to other mammalian mitochondrial genomes. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 heavy-strand concatenated PCGs. Phylogenetic analyses further confirmed that Crocidurinae diverged prior to Soricinae, and Sorex unguiculatus differentiated earlier than N. elegans.

Complete mitochondrial genome of blood pheasant (Ithaginis cruentus).

The blood pheasant Ithaginis cruentus belongs to the family Phasianidae and distributes in the eastern Himalayas, India, Nepal, Bhutan and China. In this study, the total mitochondrial genome of I. cruentus was firstly determined. The genome is 16,683 bases in length. Bayesian inference, maximum likelihood and maximum parsimony methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes on the heavy strand. Phylogenetic analyses further confirmed that Ithaginis clearly diverged later than Arborophila, and Arborophila was a basal branch within Phasianidae.

The complete mitochondrial genome sequence of Shrew Gymnure, Neotetracus sinensis.

The Shrew Gymnure Neotetracus sinensis belongs to family Erinaceidae, and distributes in China, Myanmar, and northern Vietnam. In this study, the whole mitochondrial genome of N. sinensis was first sequenced and characterized. The genome is 16,982 bases in length. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes on the heavy strand. Phylogenetic analyses further confirm the subfamily Galericinae diverged prior to the subfamily Erinaceinae, support the species N. sinensis was in distinct genus Neotetracus rather than Hylomys, and N. sinensis diverged later than Echinosorex gymnura.

The complete mitochondrial genome sequence of the Gracile shrew mole, Uropsilus gracilis (Soricomorpha: Talpidae).

The Gracile shrew mole (Uropsilus gracilis) belongs to the family Talpidae, which distributes in southwestern China, extending to northern Myanmar. In this study, the complete mitochondrial genome of U. gracilis was sequenced. It was determined to be of 16,533 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of U. gracilis and other 12 insectivores were used for phylogenetic analysis. Phylogenetic trees were constructed by using Bayesian and maximum likelihood methods, which showed that U. gracilis was clustered together with U. soricipes, and Urotrichus should be prior to Galemys.