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Fairy shrimp are the most divergent taxon of large branchiopod crustaceans and have a worldwide distribution. Yet the diversity and distribution of fairy shrimps in the "Roof of the World" remain poorly known. Here, based on morphology, we identified three species of fairy shrimp (Branchinecta orientalis, Chirocephalus graziellae and Branchipodopsis affinis), among 14 fairy-shrimp populations from the Tibetan Plateau, China. Their phylogenetic relationships were verified based on mitochondrial DNA sequences (cytochrome c oxidase subunit I gene) and two nuclear markers (18S ribosomal RNA gene and internal transcribed spacer 2). Syntopy of different species of fairy shrimp was observed. Some haplotypes were shared among populations, and sequences from B. affinis exhibited a star-like pattern in haplotype networks, suggesting a recent rapid expansion. Finally, a high genetic diversity of fairy shrimp was detected on the Tibetan Plateau. Obtained results contribute to a better knowledge of the diversity of high-altitude fairy shrimps. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • We explored lineage diversity and regional distribution of Moina in China. • Four Moina species complexes with eleven mtDNA lineages occurred across China. • Discordance between mtDNA and nuclear ITS-1 phylogenies of Moina was detected. • An mtDNA phylogeny showed apparent paraphyly in two Moina taxa. Abstract The distribution and genetic diversity of freshwater zooplankton is understudied in the Eastern Palearctic. Here, we explored the lineage diversity and regional distribution of the genus Moina in China. Members of this genus are often keystone components of freshwater ecosystems and have been frequently subjected to toxicological and physiological studies. Four species of Moina were identified, based on morphology, in 50 of 113 Chinese water bodies examined, and their phylogenetic position was analyzed using both a mitochondrial (mitochondrial cytochrome c oxidase subunit I; COI) and a nuclear marker (the nuclear internal transcribed spacer; ITS-1). Both molecular markers identified four clades corresponding broadly to the morphological species. Mitochondrial DNA analysis showed the presence of four species complexes with eleven lineages across China, five of which were new. However, some lineages (and even individual haplotypes) were widespread in Eurasia, suggesting an ability to disperse over long distances. In contrast, a few lineages exhibited restricted distributions. The nuclear phylogeny also recognized four species of Moina within China and seven very distinct clades. Interestingly, one specimen possessing Moina cf. micrura mtDNA had ITS-1 alleles of the M. cf. brachiata clade. This discordance between mtDNA and nuclear ITS-1 phylogenies is indicative of interspecific introgression and hybridization. Additionally, our COI phylogeny showed apparent paraphyly in two Moina species groups, suggesting introgression of their mitochondrial genomes. Our data shows the regional distribution/diversity of the Moina species complex in a Eurasian context. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Two distinct species complexes (D. pulex and D. mitsukuri) were documented. • Strikingly different patterns of clonal diversity were observed among populations. • Obligate parthenogenesis was confirmed by genotyping dormant ephippial eggs. • Obligate parthenogens probably originated through interspecific hybridization. Abstract Recent studies of the distribution and diversity of freshwater zooplankton have indicated that the previously understudied Eastern Palearctic region is an important biogeographic hotspot. Here, we explored the lineage diversity and reproductive modes of the Daphnia pulex species group across China. Members of this group are often keystone species of standing water bodies and are frequently used as a model system for ecological, evolutionary and, more recently, genomic studies. We found members of the D. pulex group in seven of seventy-six Chinese water bodies examined. We analyzed their phylogenetic position using mitochondrial markers, and explored the genetic structure of six populations using microsatellite markers. Mitochondrial DNA analysis suggested the presence of two distinct species complexes in China: the D. pulex complex that has a global distribution, and an apparently endemic Eastern Palearctic D. mitsukuri complex. Microsatellite analyses of six populations suggested that three of these reproduced by cyclical parthenogenesis, as evidenced by high clonal diversity and the absence of deviations from the Hardy-Weinberg equilibrium. In contrast, three other populations showed remarkably low diversity of multilocus genotypes. This suggests an obligate parthenogenetic reproductive mode, which was confirmed in one of the populations by comparison of genotypes of Daphnia adults and dormant embryos. All presumably obligate parthenogenetic clones were heterozygous at the majority of microsatellite loci, suggesting their hybrid origin. This was further supported by analyses of a small GTPase nuclear gene (rab4), as two alleles within single individuals belonged to different clades. Interestingly, one putatively obligate parthenogenetic clone carried three distinct alleles suggesting higher ploidy and potential gene flow between the D. pulicaria and D. mitsukuri complexes. Our data show that the expansion of the D. pulex complex in the Eastern Palearctic was associated with widespread hybridization. [ABSTRACT FROM AUTHOR]

Abstract Ancient DNA analysis of 24 archaeological bovid remains recovered from large Neolithic (6300 BP to 5000 calBP) pit and ditch features at Houtaomuga, Northeast China, identified 23 of these samples as aurochs (Bos primigenius). These DNA-based identifications contrast with the morphological analysis of the remains, which identified them as Bison exiguous. The abundance of auroch remains at this site contradicts the general assumption that this species was not present in large numbers in Neolithic China. It also suggests archaeologists need to revise the notion that wild aurochs played an insignificant role in the lifeways of Neolithic peoples in China. Furthermore, phylogenetic analyses of a 294 bp fragment of the mitochondrial DNA (mtDNA) D-loop indicate the identified aurochs belong to a unique haplogroup (Haplogroup C) that is indigenous to East Asia and made no direct contribution to modern domesticated cattle Bos taurus. Moreover, temporal changes in haplotype frequencies were observed among the identified aurochs, suggesting population fluctuations potentially caused by human hunting activities occurred among Chinese aurochs during the Neolithic. This study also identified one sample (HT31) radiocarbon dated to ca. 5500–5300 calBP as Bos taurus , making it one of the earliest known taurine cattle specimens in China. HT31's location in Northeast China and early date points to the existence of another entrance for domesticated cattle into China, the Northeast China Route via the Mongolian Steppe. Highlights • DNA confirms that aurochs were much more abundantly available in Neolithic China. • Many aurochs remains may have been mistakenly identified as Bison exiguous. • All aurochs belong to Haplogroup C and no direct contribution to modern cattle. • DNA identified one of the earliest Bos taurus remains in China. [ABSTRACT FROM AUTHOR]

Abstract: Domestic horses played a pivotal role in ancient China, but their exact origin remains controversial. To investigate the origin of Chinese domestic horses, we analyzed mitochondrial DNA (mtDNA) from 35 horse remains, aged between 4000 and 2000 years, excavated from nine archaeological sites in northern China. The Chinese ancient horses exhibited high matrilineal diversity, falling into all the seven haplogroups (A–G) observed in modern horses. These results suggest that several maternal lines were introduced into the gene pool of Chinese horses in the past. Haplogroups A and F were more prevalent in ancient horses than the other haplogroups. Interestingly, only haplogroups A and F were present in the samples older than 4000 years, while the more recent horses (between 2000 and 3000 years BP) fell into all seven haplogroups. Comparison with DNA data of present-day horses suggests that haplogroup F is like to be an ancient haplogroup of East Asian origin. These analyses also suggest that the origin of Chinese domestic horses is complex, and external mtDNA input occurred after initial domestication. Our results indicate that the Chinese ancient horses are more related to the modern Mongolian horses. Lastly, our results cannot support the previous hypothesis that early Chinese domestic horses were derived from the Przewalski horse. [Copyright &y& Elsevier]