Three new species of Entomobryidae (Collembola, Entomobryoidea) from China.

Three new species of entomobryid springtails (Collembola) from China are described here. Homidiapseudozhangisp. nov. is characterised by a narrow irregular longitudinal stripe on the body, smooth chaetae e and l1 of the labial base, and the relative position of the specialized microchaeta on Abd. I; H.qianensissp. nov. by its colour pattern on the antennae and nine sutural macrochaetae on the head; and Entomobryashaanxiensissp. nov. by its colour pattern, labral papillae and the lateral process of labial papilla E. Specimens of Akabosiamatsudoensis Kinoshita, 1919 from China are redescribed, including description of some characters for the first time.

Description of three new species of Callyntrura (Japonphysa) (Collembola, Entomobryidae) from China with the aid of DNA barcoding.

Callyntrura(s.l.) Börner, 1906 is the largest genus of the subfamily Salininae and contains 11 subgenera and 98 species from all over the world (mainly Asia), with eight species recorded from China. In the present paper, three new species of Callyntrura(s.l.) are described from China: C. (Japonphysa) xinjianensissp. nov.; C. (J.) tongguensissp. nov. and C. (J.) raoisp. nov. Their differences in colour pattern, chaetotaxy and other characters are slight, however distances of COI mtDNA support their validation as three new distinct species. A key to the Chinese Callyntrura(s.l.) is provided.

Comparative phylogeography of two commensal rat species (Rattus tanezumi and Rattus norvegicus) in China: Insights from mitochondrial DNA, microsatellite, and 2b-RAD data.

Rattus norvegicus and Rattus tanezumi are dominant species of Chinese house rats, but the colonization and demographic history of two species in China have not been thoroughly explored. Phylogenetic analyses with mitochondrial DNA including 486 individuals from 31 localities revealed that R. norvegicus is widely distributed in China, R. tanezumi is mainly distributed in southern China with currently invading northward; northeast China was the natal region of R. norvegicus, while the spread of R. tanezumi in China most likely started from the southeast coast. A total of 123 individuals from 18 localities were subjected to 2b-RAD analyses. In neighbor-joining tree, individuals of R. tanezumi grouped into geographic-specific branches, and populations from southeast coast were ancestral groups, which confirmed the colonization route from southeast coast to central and western China. However, individuals of R. norvegicus were generally grouped into two clusters instead of geographic-specific branches. One cluster comprised inland populations, and another cluster included both southeast coast and inland populations, which indicated that spread history of R. norvegicus in China was complex; in addition to on-land colonization, shipping transportation also have played great roles. ADMIXTURE and principal component analyses provided further supports for the colonization history. Demographic analyses revealed that climate changes at ~40,000 to 18,000 years ago and ~4000 years ago had led to population declines of both species; the R. norvegicus declined rapidly while the population of R. tanezumi continuously expanded since ~1500 years ago, indicating the importance of interspecies' competition in their population size changes. Our study provided a valuable framework for further investigation on phylogeography of two species in China.

Two new species and two new records of Homidia (Collembola, Entomobryidae) from China.

Homidia, one of the largest genera of the family Entomobryidae, is widely distributed in China. To date, 46 species of this genus are present in China and account for approximately 60 % of all known species of the genus. In the present paper, two new species of Homidia are described from China: H.acutus sp. nov. and H.changensis sp. nov. The former is discriminated by the brown to blue-violet pigment present on whole dorsal body and by pointed tenent hairs. The latter is characterised by having only scattered traces of brown pigment on tergites, and by the special macrochaetal formula of coxae. Additionally, two known species of the genus, H.linhaiensis Shi, Pan & Qi, 2009 and H.socia Denis, 1929, are reported from Jiangxi Province for the first time, and some of their taxonomic characters are described. A key to the Chinese species of the genus is provided.

Genomic analysis unveils mechanisms of northward invasion and signatures of plateau adaptation in the Asian house rat.

The Asian house rat (AHR), Rattus tanezumi, has recently invaded the northern half of China. The AHR is a highly adaptive rat species that has also successfully conquered the Qinghai-Tibet Plateau (QTP) and replaced the brown rat (BR), R. norvegicus, at the edge of the QTP. Here, we assembled a draft genome of the AHR and explored the mechanisms of its northward invasion and the genetic basis underlying plateau adaptation in this species. Population genomic analyses revealed that the northwardly invasive AHRs consisted of two independent and genetically distinct populations which might result from multiple independent primary invasion events. One invasive population exhibited reduced genetic diversity and distinct population structure compared with its source population, while the other displayed preserved genetic polymorphisms and little genetic differentiation from its source population. Genes involved in G-protein coupled receptors and carbohydrate metabolism may contribute to the local adaptation of northern AHRs. In particular, RTN4 was identified as a key gene for AHRs in the QTP that favours adaptation to high-altitude hypoxia. Coincidently, the physiological performance and transcriptome profiles of hypoxia-exposed rats both showed better hypoxia adaptation in AHRs than in BRs that failed to colonize the heart of the QTP, which may have facilitated the replacement of the BR population by the invading AHRs at the edge of the QTP. This study provides profound insights into the multiple origins of the northwardly invasive AHR and the great tolerance to hypoxia in this species.

Characterization of three new mitochondrial genomes of Coraciiformes (Megaceryle lugubris, Alcedo atthis, Halcyon smyrnensis) and insights into their phylogenetics.

Coraciiformes contains more than 200 species with great differences on external morphology and life-style. The evolutionary relationships within Coraciiformes and the phylogenetic placement of Coraciiformes in Aves are still questioned. Mitochondrial genome (mitogenome) sequences are popular markers in molecular phylogenetic studies of birds. This study presented the genome characteristics of three new mitogenomes in Coraciiformes and explored the phylogenetic relationships among Coraciiformes and other five related orders with mitogenome data of 30 species. The sizes of three mitogenomes were 17,383 bp (Alcedo atthis), 17,892 bp (Halcyon smyrnensis) and 17,223 bp (Megaceryle lugubris). Each mitogenome contained one control region and 37 genes that were common in vertebrate mitogenomes. The organization of three mitogenomes was identical to the putative ancestral gene order in Aves. Among 13 available Coraciiform mitogenomes, 12 protein coding genes showed indications of negative selection, while the MT-ND6 presented sign of positive selection or relaxed purifying selection. The phylogenetic results supported that Upupidae and Bucerotidae should be separated from Coraciiformes, and that Coraciiformes is more closely related to Piciformes than to Strigiformes, Trogoniformes and Cuculiformes. Our study provide valuable data for further phylogenetic investigation of Coraciiformes.

[Biocatalysis of formaldehyde to L-xylose].

It is of great significance to use biosynthesis to transform the inorganic substance formaldehyde into organic sugars. Most important in this process was to find a suitable catalyst combination to achieve the dimerization of formaldehyde. In a recent report, an engineered glycolaldehyde synthase was reported to catalyze this reaction. It could be combined with engineered D-fructose-6-phosphate aldolase, a "one-pot enzyme" method, to synthesize L-xylose using formaldehyde and the conversion rate could reach up to 64%. This process also provides a reference for the synthesis of other sugars. With the increasing consumption of non-renewable resources, it was of great significance to convert formaldehyde into sugar by biosynthesis.

Genetic diversity and population structure of penis fish (Urechis unicinctus) based on mitochondrial and nuclear gene markers.

Urechis unicinctus is distributed only in Bohai Gulf of China and Korean and Japanese coast. The wild populations of this species have sharply declined in China and Japan. We collected 105 samples from six localities of Bohai Gulf and Korea coast, and investigated genetic diversity and population structure with mitochondrial COI, 16S-rRNA and nuclear 28S-rRNA gene fragments. Genetic diversity of U. unicinctus based on COI sequences was still high (Hd: 0.9595, π: 0.0101), however, 28S-rRNA gene sequences showed low level of genetic diversity (Hd: 0.4084, π: 0.0007). Based on COI sequences, FST values between populations ranged from -0.00204 to 0.05210, and 99.12% genetic diversity was contributed by different individuals within population. Both phylogenetic trees and median-joining network did not show clear geographic cluster, haplotypes from different populations were mixed. Our results indicated low level of genetic divergence among different localities of U. unicinctus, and this species should be treated as a whole population among China, Japan and Korea coast during species conservation.

Two mitochondrial genomes in Alcedinidae (Ceryle rudis/Halcyon pileata) and the phylogenetic placement of Coraciiformes.

Coraciiformes comprises 209 species belonging to ten families with significant divergence on external morphologies and life styles. The phylogenetic placement of Coraciiformes was still in debate. Here, we determined the complete mitochondrial genomes (mitogenomes) of Crested Kingfisher (Ceryle rudis) and Black-capped Kingfisher (Halcyon pileata). The mitogenomes were 17,355 bp (C. rudis) and 17,612 bp (H. pileata) in length, and both of them contained 37 genes (two rRNA genes, 22 tRNA genes and 13 protein-coding genes) and one control region. The gene organizations and characters of two mitogenomes were similar with those of other mitogenomes in Coraciiformes, however the sizes and nucleotide composition of control regions in different mitogenomes were significantly different. Phylogenetic trees were constructed with both Bayesian and Maximum Likelihood methods based on mitogenome sequences from 11 families of six orders. The trees based on two different data sets supported the basal position of Psittacidae (Psittaciformes), the closest relationship between Cuculiformes (Cuculidae) and Trogoniformes (Trogonidae), and the close relationship between Coraciiformes and Piciformes. The phylogenetic placement of the clade including Cuculiformes and Trogoniformes has not been resolved in present study, which need further investigations with more molecular markers and species. The mitogenome sequences presented here provided valuable data for further taxonomic studies on Coraciiformes and other related groups.

The complete mitochondrial genome sequence of the little egret (Egretta garzetta).

Many phylogenetic questions in the Ciconiiformes remain unresolved and complete mitogenome data are urgently needed for further molecular investigation. In this work, we determined the complete mitogenome sequence of the little egret (Egretta garzetta). The genome was 17,361 bp in length and the gene organization was typical of other avian mtDNA. In protein-coding genes (PCGs), a C insertion was found in ND3, and COIII and ND4 terminated with incomplete stop codons (T). tRNA-Val and tRNA-Ser (AGY) were unable to fold into canonical cloverleaf secondary structures because they had lost the DHU arms. Long repetitive sequences consisting of five types of tandem repeats were found at the 3' end of Domain III in the control region. A phylogenetic analysis of 11 species of Ciconiiformes was done using complete mitogenome data and 12 PCGs. The tree topologies obtained with these two strategies were identical, which strongly confirmed the monophyly of Ardeidae, Threskiorothidae and Ciconiidae. The phylogenetic analysis also revealed that Egretta was more closely related to Ardea than to Nycticorax in the Ardeidae, and Platalea was more closely related to Threskiornis than to Nipponia in the Threskiornithidae. These findings contribute to our understanding of the phylogenetic relationships of Ciconiiformes based on complete mitogenome data.

Phylogeography of Chinese house mice (Mus musculus musculus/castaneus): distribution, routes of colonization and geographic regions of hybridization.

House mice (Mus musculus) are human commensals and have served as a primary model in biomedical, ecological and evolutionary research. Although there is detailed knowledge of the biogeography of house mice in Europe, little is known of the history of house mice in China, despite the fact that China encompasses an enormous portion of their range. In the present study, 535 house mice caught from 29 localities in China were studied by sequencing the mitochondrial D-loop and genotyping 10 nuclear microsatellite markers distributed on 10 chromosomes. Phylogenetic analyses revealed two evolutionary lineages corresponding to Mus musculus castaneus and Mus musculus musculus in the south and north, respectively, with the Yangtze River approximately representing the boundary. More detailed analyses combining published sequence data from mice sampled in neighbouring countries revealed the migration routes of the two subspecies into China: M. m. castaneus appeared to have migrated through a southern route (Yunnan and Guangxi), whereas M. m. musculus entered China from Kazakhstan through the north-west border (Xinjiang). Bayesian analysis of mitochondrial sequences indicated rapid population expansions in both subspecies, approximately 4650-9300 and 7150-14 300 years ago for M. m. castaneus and M. m. musculus, respectively. Interestingly, the migration routes of Chinese house mice coincide with the colonization routes of modern humans into China, and the expansion times of house mice are consistent with the development of agriculture in southern and northern China, respectively. Finally, our study confirmed the existence of a hybrid zone between M. m. castaneus and M. m. musculus in China. Further study of this hybrid zone will provide a useful counterpart to the well-studied hybrid zone between M. m. musculus and Mus musculus domesticus in central Europe.

The complete mitochondrial genome sequence of the black-capped capuchin (Cebus apella).

The phylogenetic relationships of primates have been extensively investigated, but key issues remain unresolved. Complete mitochondrial genome (mitogenome) data have many advantages in phylogenetic analyses, but such data are available for only 46 primate species. In this work, we determined the complete mitogenome sequence of the black-capped capuchin (Cebus apella). The genome was 16,538 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs and a control region. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other primates. The control region contained several distinct repeat motifs, including a putative termination-associated sequence (TAS) and several conserved sequence blocks (CSB-F, E, D, C, B and 1). Among the protein-coding genes, the COII gene had lower nonsynonymous and synonymous substitutions rates while the ATP8 and ND4 genes had higher rates. A phylogenetic analysis using Maximum likelihood and Bayesian methods and the complete mitogenome data for platyrrhine species confirmed the basal position of the Callicebinae and the sister relationship between Atelinae and Cebidae, as well as the sister relationship between Aotinae (Aotus) and Cebinae (Cebus/Saimiri) in Cebidae. These conclusions agreed with the most recent molecular phylogenetic investigations on primates. This work provides a framework for the use of complete mitogenome information in phylogenetic analyses of the Platyrrhini and primates in general.

Phylogenetic relationships in genus Niviventer (Rodentia: Muridae) in China inferred from complete mitochondrial cytochrome b gene.

Chinese species of the genus Niviventer, predominantly distributed in the southeastern Tibetan Plateau and in Taiwan, are a diverse group and have not yet received a thorough molecular phylogenetic analysis. Here, we reconstructed the phylogenetic relationships of 32 specimens representing nine Chinese species of Niviventer, based on sequences of the complete mitochondrial cytochrome b gene. Maximum parsimony, maximum likelihood and Bayesian analysis resulted in three consistent trees, each supported by high bootstrap values. The results showed that the Niviventer species included here are monophyletic. The nine species were classified into three distinct clades: clade A with Niviventer brahma, N. confucianus, N. coxingi, N. culturatus, N. eha and N. fulvescens; clade B with N. andersoni and N. excelsior; clade C with N. cremoriventer. Our results also suggested that N. culturatus should be a valid species rather than a subspecies of N. confucianus. Divergence times among species were calibrated according to the middle-late Pleistocene (1.2-0.13 Mya) fossil records of N. confucianus. The results demonstrated that the first radiation event of the genus Niviventer occurred in early Pleistocene (about 1.66 Mya), followed by the divergence of clades A and B at about 1.46 Mya. Most of the extant Niviventer species appeared during early to middle Pleistocene (about 1.29-0.67 Mya). These divergence times are coincidental with the last uplift events of the Tibetan Plateau, Kun-Huang movement, Pleistocene glaciations and the vicariant formation of Taiwan Strait. Consequently geographical events and Pleistocene glaciations have played a great role in the diversification of Niviventer.

Cross-species chromosome painting unveils cytogenetic signatures for the Eulipotyphla and evidence for the polyphyly of Insectivora.

Insectivore-like animals are traditionally believed among the first eutherian mammals that have appeared on the earth. The modern insectivores are thus crucial for understanding the systematics and phylogeny of eutherian mammals as a whole. Here cross-species chromosome painting, with probes derived from flow-sorted chromosomes of human, was used to delimit the homologous chromosomal segments in two Soricidae species, the common shrew (Sorex araneus, 2n = 20/21), and Asiatic short-tailed shrew (Blarinella griselda, 2n = 44), and one Erinaceidae species, the shrew-hedgehog (Neotetracus sinensis, 2n = 32), and human. We report herewith the first comparative maps for the Asiatic short-tailed shrew and the shrew-hedgehog, in addition to a refined comparative map for the common shrew. In total, the 22 human autosomal paints detected 40, 51 and 58 evolutionarily conserved segments in the genomes of common shrew, Asiatic short-tailed shrew, and shrew-hedgehog, respectively, demonstrating that the common shrew has retained a conserved genome organization while the Asiatic short-tailed shrew and shrew-hedgehog have relatively rearranged genomes. In addition to confirming the existence of such ancestral human segmental combinations as HSA 3/21, 12/22, 14/15 and 7/16 that are shared by most eutherian mammals, our study reveals a shared human segmental combination, HSA 4/20, that could phylogenetically unite the Eulipotyphlan (i.e., the core insectivores) species. Our results provide cytogenetic evidence for the polyphyly of the order Insectivora and additional data for the eventual reconstruction of the ancestral eutherian karyotype.