Molecular phylogeny of avian genus Syrmaticus based on the mitochondrial cytochrome B gene and control region

Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

Background

The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. This pheasant provides an opportunity to investigate evolutionary processes following geographic isolation. Currently, the genetic background and adaptive evolution of the Mikado pheasant remain unclear.

Results

We present the draft genome of the Mikado pheasant, which consists of 1.04 Gb of DNA and 15,972 annotated protein-coding genes. The Mikado pheasant displays expansion and positive selection of genes related to features that contribute to its adaptive evolution, such as energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. To investigate the molecular evolution of the major histocompatibility complex (MHC) across several avian species, 39 putative genes spanning 227 kb on a contiguous region were annotated and manually curated. The MHC loci of the pheasant revealed a high level of synteny, several rapidly evolving genes, and inverse regions compared to the same loci in the chicken. The complete mitochondrial genome was also sequenced, assembled, and compared against four long-tailed pheasants. The results from molecular clock analysis suggest that ancestors of the Mikado pheasant migrated from the north to Taiwan about 3.47 million years ago.

Conclusions

This study provides a valuable genomic resource for the Mikado pheasant, insights into its adaptation to high altitude, and the evolutionary history of the genus Syrmaticus, which could potentially be useful for future studies that investigate molecular evolution, genomics, ecology, and immunogenetics.

Reproductive biology and its impact on body size: comparative analysis of mammalian, avian and dinosaurian reproduction

Janis and Carrano (1992) suggested that large dinosaurs might have faced a lower risk of extinction under ecological changes than similar-sized mammals because large dinosaurs had a higher potential reproductive output than similar-sized mammals (JC hypothesis). First, we tested the assumption underlying the JC hypothesis. We therefore analysed the potential reproductive output (reflected in clutch/litter size and annual offspring number) of extant terrestrial mammals and birds (as "dinosaur analogs") and of extinct dinosaurs. With the exception of rodents, the differences in the reproductive output of similar-sized birds and mammals proposed by Janis and Carrano (1992) existed even at the level of single orders. Fossil dinosaur clutches were larger than litters of similar-sized mammals, and dinosaur clutch sizes were comparable to those of similar-sized birds. Because the extinction risk of extant species often correlates with a low reproductive output, the latter difference suggests a lower risk of population extinction in dinosaurs than in mammals. Second, we present a very simple, mathematical model that demonstrates the advantage of a high reproductive output underlying the JC hypothesis. It predicts that a species with a high reproductive output that usually faces very high juvenile mortalities will benefit more strongly in terms of population size from reduced juvenile mortalities (e.g., resulting from a stochastic reduction in population size) than a species with a low reproductive output that usually comprises low juvenile mortalities. Based on our results, we suggest that reproductive strategy could have contributed to the evolution of the exceptional gigantism seen in dinosaurs that does not exist in extant terrestrial mammals. Large dinosaurs, e.g., the sauropods, may have easily sustained populations of very large-bodied species over evolutionary time.

The phylogenetic position and speciation dynamics of the genus Perdix (Phasianidae, Galliformes)

The nuclear gene (c-mos) and mitochondrial genes (CYT B and ND2) sequences, representing 44 phasianid species and 26 genera (mainly distributed in China), were used to study the phylogeny of the genus Perdix, which comprises three partridge species. Maximum parsimony and Bayesian methods were employed, and the analysis of mitochondrial sequence data and the combined dataset showed that Perdix is specifically related either to typical pheasants or to Ithaginis. Phylogenetic trees also indicated that: (1) Perdix is monophyletic; (2) the Tibetan partridge (Perdix hodgsoniae) has been consistently placed as basal to all other Perdix, and the Daurian partridge (Perdix dauuricae) is placed sister to gray partridge (Perdix perdix); (3) the Daurian partridge subspecies przewalskii and Tibetan partridge subspecies hodgsoniae are basal to other subspecies in their species clade, respectively. Speciation in Perdix was likely promoted by the late Pliocene/early Pleistocene intensive uplift of the Tibetan Plateau and by Pleistocene glaciations.