To investigate the genetic diversity of Chinese indigenous horses and determine the genetic status of extant horse breeds, novel Y chromosomal microsatellite markers and known Y chromosomal SNPs and mtDNA loop sequences, were employed to study the genetic diversity levels of 13 Chinese indigenous horse populations and four introduced breeds. Sixteen Y-chromosomal microsatellite markers, including seven newly identified loci, were used in the genotyping. The results showed that 4 out of the 16 loci were highly polymorphic in Chinese indigenous horse populations, in which the polymorphisms of 3 loci, ECAYP12, ECAYP13, and ECAYCAU3, were first reported in the present study. The polymorphic Y chromosomal microsatellite markers result in 19 haplotypes in the studied horses and formed 24 paternal lines when merged with the 14 Y chromosomal SNPs reported previously. The haplotypes CHT18 and SS24 harboring AMELY gene mutation were the ancestral haplotypes, and other haplotypes were derived from them by one or more mutation steps. The horse populations in mountainous and remote areas of southwestern China have the most ancient paternal lines, which suggests that ancient paternal lines preserved in local populations attributed to less human interventions. Our results also showed that the northern local breeds had higher mtDNA diversity than the southern ones in China. The frequency of haplogroup B, F, and G of mtDNA in Chinese indigenous horses has declined in recent years, and some breeds are in endangered status mainly due to small population sizes. Urgent actions should be taken to conserve the genetic diversity of the indigenous horse populations, especially the rare paternal lines. Our findings help to elucidate the genetic diversity and evolutionary history of Chinese domestic horses, which will facilitate the conservation of the indigenous horses in the future.

Species of Artemia are regionally endemic branchiopod crustaceans composed of sexual species and parthenogenetic lineages, and represent an excellent model for studying adaptation and speciation to extreme and heterogeneous hypersaline environments. We tested hypotheses of whether populations from the Tibetan Plateau belong to A. tibetianaAbatzopoulos, Zhang & Sorgeloos,1998 and whether a population from Kazakhstan is a new species, using other Asian species of Artemia as outgroups. We conducted a multitrait phylogenetic study based on the complete mitogenome, mitochondrial (COI, 12S, 16S) and nuclear (microsatellites, ITS1) markers, and a suit of uni- and multivariate morphological traits. Our results led to the discovery of two new species, one from the Tibetan Plateau (Haiyan Lake) in China (Artemia sorgeloosin. sp.) and a second from Kazakhstan (Artemia amatin. sp.). Our analysis demonstrate that A. tibetiana and A. amatin. sp. are monophyletic, whereas A. sorgeloosin. sp., and A. tibetiana are polyphyletic. Evolutionary relationships based on mitochondrial and nSSR markers suggest that A. tibetiana may have arisen from a past hybridization event of a maternal ancestor of A. tibetiana with A. sorgeloosin. sp. or its ancestor. We present the complete mitogenome of A. tibetiana, A. amatin. sp., and A. sorgeloosin. sp. We also provide a novel taxonomic identification key based on morphology, emphasizing the phenotype as a necessary component of the species concept.

The crested ibis (Nipponia nippon) is endangered worldwide. Although a series of conservation measures have markedly increased the population size and distribution area of these birds, the high mortality of embryos and nestlings considerably decreases the survival potential of this bird species. High-throughput sequencing technology was utilized to compare whole genomes between ten samples from dead crested ibises (including six dead embryos and four dead nestlings aged 0–45 days) and 32 samples from living birds. The results indicated that the dead samples all shared the genetic background of a specific ancestral subpopulation. Furthermore, the dead individuals were less genetically diverse and suffered higher degrees of inbreeding compared with these measures in live birds. Several candidate genes (KLHL3, SETDB2, TNNT2, PKP1, AK1, and EXOSC3) associated with detrimental diseases were identified in the genomic regions that differed between the alive and dead samples, which are likely responsible for the death of embryos and nestlings. In addition, in these regions, we also found several genes involved in the protein catabolic process (UBE4A and LONP1), lipid metabolism (ACOT1), glycan biosynthesis and metabolism (HYAL1 and HYAL4), and the immune system (JAM2) that are likely to promote the normal development of embryos and nestlings. The aberrant conditions of these genes and biological processes may contribute to the death of embryos and nestlings. Our data identify congenital factors underlying the death of embryos and nestlings at the whole genome level, which may be useful toward informing more effective conservation efforts for this bird species.

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