Mitogenome of a cryptic species within <i>Uropsilus</i> and divergence time estimation

<p><i>Uropsilus</i> sp. 4 is a new cryptic species, collected in Changyang county, Hubei province, China. In this study, the whole mitochondrial genome of <i>Uropsilus</i> 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. <i>U.</i> sp. 4 clustered with <i>U. gracilis</i> 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 <i>U</i>. sp. 4.</p

Characterization of the mitogenome of <i>Uropsilus gracilis</i> and species delimitation

<p>The species diversity within the genus <i>Uropsilus</i> were underestimated: 10 species among the genus <i>Uropsilus</i> have been proposed. In this study, the complete mitochondrial genome of <i>U. gracilis,</i> 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, <i>U. gracilis, U.</i> sp. 1 and <i>U. soricipes</i>. Pairwise sequence alignment showed that similarity data of <i>U. gracilis</i> versus <i>U. sorcipes</i> are significantly higher than those of <i>U. gracilis</i> versus <i>U.</i> sp.1. This pointed toward a cryptic species (<i>U.</i> sp.1) from Jiajin Mountains rather than <i>U. gracilis.</i></p

Complete mitogenome of Intermediate Egret <i>Ardea intermedia</i> (Ciconiiformes: Ardeidae)

<p>The Intermediate Egret <i>Ardea intermedia</i> 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 <i>A. intermedia</i> 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 <i>Ardea novaehollandiae</i> and <i>A. intermedia</i> should be assign to <i>Egretta</i> and <i>Ardea</i>, respectively. The mitogenomic data of <i>A. intermedia</i> will be useful in the conservation genetics and phylogeny of the species.</p

Taxa and sequence Genbank accession numbers of the 45 species used for phylogenetic analysis.

<p>Taxa and sequence Genbank accession numbers of the 45 species used for phylogenetic analysis.</p

Species tree with estimated divergence time.

<p>The divergence times were estimated in BEAST with five fossil calibrations (C1-C5). Mean ages are included beside corresponding nodes. Horizontal gray bars on each node indicate the 95% credible interval of divergence time in millions of years, with the unit of divergence time as Mya.</p

Geographic distribution of the five hill partridges within this study in comparison to the overall distribution of the other 17 hill partridges in South-east Asia.

<p>The five studied hill partridge distributions have been assigned different colors while the others 17 are all colored midnight blue. Elevation information (altitude: meters above sea level) is represented by different heat colors.</p

Molecular phylogenetic tree based on 13 mitochondrial protein-coding genes using Bayesian inference (BI) and maximum likelihood (ML) analysis.

<p>The numbers beside the nodes are Bayesian posterior probabilities and ML bootstrap proportions. <i>Anseranas semipalmata</i> and <i>Anas platyrhynchos</i> were set as outgroups.</p

A novel mitochondrial genome of <i>Arborophila</i> and new insight into <i>Arborophila</i> evolutionary history

<div><p>The lineage of the Bar-backed Partridge (<u><i>Arborophila brunneopectus</i></u>) was investigated to determine the phylogenetic relationships within <i>Arborophila</i> 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 <i>A</i>. <i>brunneopectus</i> 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 <i>Arborophila</i> using combined datasets composed of their 13-protein coding sequences. <i>Arborophila</i> is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. <i>A</i>. <i>rufipectus</i> shares a closer relationship with <i>A</i>. <i>ardens</i> and <i>A</i>. <i>brunneopectus</i> compared to <i>A</i>. <i>gingica</i> and <i>A</i>. <i>rufogularis</i>, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (<i>ND5</i>). The intragenus divergence of all five <i>Arborophila</i> 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 (<i>ND3</i>) found in all <i>Arborophila</i> 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.</p></div

Phylogenetic analyses using jackknifing of single mitogene.

<p>Phylogenetic analyses using jackknifing of single mitogene.</p