摘要: The analysis of molecular variance (AMOVA) is a widely used statistical method in population genetics and molecular ecology. The classic framework of AMOVA only supports haploid and diploid data, in which the number of hierarchies ranges from two to four. In practice, natural populations can be classified into more hierarchies, and polyploidy is frequently observed in extant species. The ploidy level may even vary within the same species, and/or within the same individual. We generalized the framework of AMOVA such that it can be used for any number of hierarchies and any level of ploidy. Based on this framework, we present four methods to account for data that are multilocus genotypic and allelic phenotypic (with unknown allele dosage). We use simulated datasets and an empirical dataset to evaluate the performance of our framework. We make freely available our methods in a new software package,polygene, which is freely available at .

摘要: The currently recognized Indo-Pacific humpback dolphin occurs in estuaries and surrounding shallow waters from the South China Sea to the Asian coast of the Indian Ocean. However, a recent study suggested that the humpback dolphin from the Bay of Bengal may represent a distinct phylogenetic species. In this study, we sequenced 915-bp mtDNA segments from five geographic populations in both Chinese and Thai waters; together with previously published sequences, these data revealed that the ancestral Indo-Pacific humpback dolphin might have split during the transition from the Oligocene to Miocene (23.45 Mya, 95% HPD: 16.65-26.55 Mya), and then dispersed along the Pacific and Indian Ocean coasts of Asia. Genetic differentiation was detected between most of the examined populations, except for only a few pairwise populations in the northern South China Sea. Genetic differentiation/distance between the humpback dolphins from the northern and southern South China Sea met the sub-species threshold value proposed for marine mammals, whereas that between the humpback dolphins in the Pacific and the Indian Ocean was above the species threshold. Bayesian inference of historic gene flow indicated low but constant northward gene flow along the Indian Ocean coast; however, there was a recent abrupt increase in gene flow in the Pacific region, likely due to the shortening coastline at the low stand of sea level. Our results revealed that the current taxonomic classification of Indo-Pacific humpback dolphins may not reflect their phylogeography.

摘要: Cyrtodactylus geckos are one of the most speciose and diverse groups of extant lizards known, distributed throughout the Asian and Pacific realms. Using molecular phylogenetic methods and supporting morphological data, we describe a new species of Cyrtodactylus in Daweishan National Nature Reserve, Yunnan Province, China. Cyrtodactylus hekouensis sp. nov. can be morphologically distinguished from its nearby congeners by the following characters: maximum SVL 92.3 mm and TL 98.5 mm; 11-12 supralabials; 11-12 infralabials; 36-57 scale rows between the fifth supralabials; 10-13 dorsal tubercles rows; 3 postnasals on blunt and smooth front snout; precloacalfemoral pores in a continuous series of 33-39 (females with pitted scales) located under vent/cloaca and thighs in both sexes; precloacal groove absent; 3/3 postcloacal tubercles; subdigital lamellae under the fourth finger 21 or 22, under the fourth toe 20-23; smooth midbody with smooth venter and tuberculate dorsal scale rows, tubercles from head to tail base; dorsal transverse patterns are generally large, bilaterally symmetrical. The results of the phylogenetic analysis recover specimens of this new species as sister to a clade containing C. wayakonei and C. martini. Uncorrected pairwise intraspecific distances were < 1%, and distances between our new species and other Cyrtodactylus species from nearby countries ranged from 14.2% to 26.8%.

摘要: Comparisons of vertebrate mitochondrial genomes (mitogenomes) may yield significant insights into the evolution of organisms and genomes. However, no complete mitogenome from the snake family Psammophiidae has been reported. In this study, we sequenced and annotated the complete mitogenome of Psammophis lineolatus, representing the first mitogenome of Psammophiidae. The total length is 17 166 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (12S rRNA and 16S rRNA), and duplicate control regions (CRs). This gene arrangement belongs to the Type III pattern, which is a widely shared gene order in Alethinophidian snakes. All tRNAs exhibit cloverleaf structures with the exception of tRNA-Ser(AGY) and tRNA-Pro, which lack a dihydrouridine (DHU) arm/stem and T psi C loop, respectively. The13 PCGs include five start codons (ATG, GTG, ATA, ATT, and ATC), two complete stop codons (TAA and AGG), and two incomplete stop codon (T- and TA-). In addition, the Ka/Ks ratios indicate that all PCGs had undergone a strong purifying selection. Four types of CR domains rearrangement occurred among eight species of Elapoidea. The phylogenetic reconstructions with both Bayesian inference and maximum likelihood methods support the placement of Psammophiidae in the Elapoidea superfamily, with Homalopsidae being the sister taxon to Elapoidea and Colubroidea. However, the sister taxon of Psammophiidae is unclear due to the availability of Elapoidea mitogenomes being limited to the family Elapidae. More mitogenomes from different taxonomic groups in Elapoidea are needed to better understand the phylogenetic relationships within Elapoidea.

摘要: Understanding how organisms adapt to the environment is a compelling question in modern evolutionary biology. Genetic assimilation provides an alternative hypothesis to explain adaptation, in which phenotypic plasticity is first triggered by environmental factors, followed by selection on genotypes that reduce the plastic expression of phenotypes. To investigate the evidence of genetic assimilation in a high-altitude dweller, the toad-headed agama Phrynocephalus vlangalii, we conducted a translocation experiment by moving individuals from high- to low-altitude environments. We then measured their gene expression profiles by transcriptome sequencing in heart, liver and muscle, and compared them to two low-altitude species P. axillaris and P. forsythii. The results showed that the general expression profile of P. vlangalii was similar to its viviparous relative P. fors ythii, however, the differentially expressed genes in the liver of P. vlangalii showed a distinct pattern compared to both the low-altitude species. In particular, several key genes (FASN, ACAA2 and ECI2) within fatty acid metabolic pathway were no longer differentially expressed in P. valgnalii, suggesting the loss of plasticity for this pathway after translocation. This study provides evidence of genetic assimilation in fatty acid metabolism that may have facilitated the adaptation to high-altitude for P. vlangalii.