Bingyao Chen

Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals

Abstract Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian mammals with draft genome sequences were reconstructed based on 1608 exons (2,175,102 bp). Our reconstructions resolve the interordinal relationships within Laurasiatheria and corroborate the clades Scrotifera, Fereuungulata, and Cetartiodactyla. Furthermore, we tested alternative topologies within Laurasiatheria, and among alternatives for the phylogenetic position of Perissodactyla, a sister-group relationship with Cetartiodactyla receives the highest support. Thus, Pegasoferae (Perissodactyla + Carnivora + Pholidota + Chiroptera) does not appear to be a natural group. Divergence time estimates from these genes were compared with published estimates for splits within Laurasiatheria. Our estimates were similar to those of several studies and suggest that the divergences among these orders occurred within just a few million years.

Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations

The baiji, or Yangtze River dolphin (Lipotes vexillifer), is a flagship species for the conservation of aquatic animals and ecosystems in the Yangtze River of China; however, this species has now been recognized as functionally extinct. Here we report a high-quality draft genome and three re-sequenced genomes of L. vexillifer using Illumina short-read sequencing technology. Comparative genomic analyses reveal that cetaceans have a slow molecular clock and molecular adaptations to their aquatic lifestyle. We also find a significantly lower number of heterozygous single nucleotide polymorphisms in the baiji compared to all other mammalian genomes reported thus far. A reconstruction of the demographic history of the baiji indicates that a bottleneck occurred near the end of the last deglaciation, a time coinciding with a rapid decrease in temperature and the rise of eustatic sea level.

Distribution and conservation of the Indo-Pacific humpback dolphin in China.

The Indo-Pacific humpback dolphin (Sousa chinensis Osbeck, 1765) is a threatened species inhabiting the waters of China. Despite being of conservation concern, the distribution and abundance of this species has not been comprehensively evaluated. From 1994 to 2008 we performed over 14 000 km of line-transect surveys and administered over 700 questionnaires to collect basic information on the geographic range and likely abundance of Indo-Pacific humpback dolphins along the southern and eastern coasts of China. Through our study we were able to establish a reporting network of stranding and incidental catches for this species. Our quantitative data suggests that only 76 animals remain around Xiamen, 39 in the Hepu Nature Reserve and 114 in the estuary of the Dafengjiang River. Qualitative data from local fishing people and government officials suggests that dolphins may exist year-round in waters off Ningde and Shantou. We found that wild populations of Sousa chinensis in this important region are clearly being affected by human disturbance and habitat deterioration, including underwater blasting, vessel collision, fishing, aquaculture and water pollution. Although some protected areas have been established and this species is protected under Chinese law, there remains virtually no protection for this animal.

High similarity at three MHC loci between the baiji and finless porpoise: trans-species or convergent evolution?

Two DRA alleles and six MHC-I alleles were identified from a group of 15 baiji (Lipotes vexillifer), the most threatened cetacean in the world. Little sequence variation was detected at the DRA locus but extensive variation at the MHC-I locus. In combination with data at the DQB locus previously reported, three MHC loci exon 2 of the baiji all revealed striking similarity with those of the finless porpoise. Especially, some identical alleles shared by both species at the MHC-I and DQB loci suggested the convergent evolution as a consequence of common adaptive solutions to similar environmental pressures in the Yangtze River. As for DRA locus, the identity alleles were shared not only by baiji and finless porpoise but by some other cetacean species of the families Phocoenidae and Delphinidae, suggesting trans-species evolution on this gene.

Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater

Cetaceans (whales, dolphins, and porpoises) are a group of mammals adapted to various aquatic habitats, from oceans to freshwater rivers. We report the sequencing, de novo assembly and analysis of a finless porpoise genome, and the re-sequencing of an additional 48 finless porpoise individuals. We use these data to reconstruct the demographic history of finless porpoises from their origin to the occupation into the Yangtze River. Analyses of selection between marine and freshwater porpoises identify genes associated with renal water homeostasis and urea cycle, such as urea transporter 2 and angiotensin I-converting enzyme 2, which are likely adaptations associated with the difference in osmotic stress between ocean and rivers. Our results strongly suggest that the critically endangered Yangtze finless porpoises are reproductively isolated from other porpoise populations and harbor unique genetic adaptations, supporting that they should be considered a unique incipient species.Whales, dolphins and porpoises are adapted to various aquatic habitats. Here, Zhou et al. show that polymorphisms associated with renal function and the urea cycle have undergone selection in the freshwater Yangtze finless porpoise and provide genomic evidence of incipient speciation.

Trace element concentrations, risks and their correlation with metallothionein genes polymorphism: A case study of narrow-ridged finless porpoises (Neophocaena asiaeorientalis) in the East China Sea

The concentration of trace elements (TEs) and their risk to narrow-ridged finless porpoises (Neophocaena asiaeorientalis) are still unclear. The present study determined the concentration of typical TEs in liver, kidney, and muscle tissues from porpoises in the East China Sea, assessed potential health risk of TEs to porpoises, and explored the relationship between TE concentration and metallothionein genes (MTs) polymorphism. It was found that Zn, Cu, Mn, Cd and Hg were highly accumulated in liver, and Cd was highly accumulated in kidney. The concentrations of Cr, As, Pb and Ni were very low in all three tissues. TE concentrations showed significant positive correlation with body length, and sexual variation. The levels of most TEs were higher in tissues of porpoises in Ningbo and Nantong than in Pingtan, which is likely related to the local environment pollution level. The risk assessment showed that porpoises from Nantong and Ningbo could face health risks due to Hg, As, Cd, Pb, and Cr exposure. Moreover, two polymorphic sites on the MT4 gene were found to be significantly associated with increased levels of Hg, Cd, Zn and Mn. Whether these two polymorphic sites are involved in expression of MTs, or other functional processes, needs further research.

Genomic organization and adaptive evolution of IGHC genes in marine mammals

HIGHLIGHTSThe genomic organization of IGHC genes in marine mammal is similar to that of terrestrial relatives.The number of the immunoglobulin heavy chain constant region genes vary among different mammals.Different levels of selective pressures were detected between marine and terrestrial mammalian lineages. ABSTRACT Immunoglobulins are important elements of the adaptive immune system that bind to an immense variety of microbial antigens to neutralize infectivity and specify effector functions. In the present study, the immunoglobulin heavy chain constant region (IGHC) genes from marine mammals were identified and compared with those of their terrestrial relatives to explore their genomic organization and evolutionary characteristics. The genomic organization of marine mammal IGHC genes was shown to be conservative with other eutherian mammals. Stronger signals of positive selection on IGHC were revealed in terrestrial mammals than that in marine mammals with the branch‐site model, displaying different selective pressure, which might suggest their divergent adaptations to contrasted environments.

Divergent Selection of Pattern Recognition Receptors in Mammals with Different Ecological Characteristics

Pattern recognition receptors (PRRs) are specialized receptors that represent a key component of the host innate immune system. Whether molecular evolutionary history of different PRR classes have involved different genetic mechanisms underlying diverse pathogen environment in mammals, and whether distinct ecology of mammals may have imposed divergent selective pressures on the evolution of the PRRs, remained unknown. To test these hypotheses, we investigated the characterization of 20 genes belonging to four PRR classes in mammals. Evidence of positive selection was found in most (17 of 20) PRR genes examined, and most positively selected sites (84%) undergoing radical changes were found to fall in important functional regions, consistent with the co-evolutionary dynamics between the hosts and their microbial counterparts. We found different evolutionary patterns in different PRR classes, with the highest level of positive selection in C-type lectin receptor (CLR) family, suggesting that the capability of CLRs in response to a wide variety of ligands might explain their malleability to selection pressures. Tests using branch models that partitioned the data along habitat and social behavior found significant evidence of divergent selective pressures of PRRs among mammalian groups. Interestingly, species-specific evolution was detected on RIG-I-like helicase genes (RLRs) in cetaceans, suggesting that RLRs might play a critical role in the defense against widespread marine RNA viruses during their divergence and radiation into marine habitats. This study provides a comprehensive look at the evolutionary patterns and implications of mammalian PRRs, and highlights the importance of ecological influences in molecular adaptation.