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Chernova OF, Zherebtsova OV. Hair microstructure in some rodent species of Diatomyidae, Ctenodactylidae, and Echimyidae (Ctenohystrica, Rodentia). ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ge D, Feijó A, Abramov AV, Wen Z, Liu Z, Cheng J, Xia L, Lu L, Yang Q. Molecular phylogeny and morphological diversity of the Niviventer fulvescens species complex with emphasis on species from China. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe Niviventer fulvescens species complex (NFSC), a group of abundant and taxonomically ambiguous rodent taxa, is distributed from Southeast Asia to south-eastern China. We combined molecular and morphological datasets to clarify the species composition and variation of the NFSC. Our phylogenetic analyses, using molecular data, recovered eight genetic lineages in the NFSC, including a novel, distinct lineage from Jilong, Tibet, China, which is described as a new species, N. fengi sp. nov. The species status of N. fengi is supported by a species delimitation analysis, and it is morphologically distinguished from other members of the NFSC by its greyish dorsal fur, soft hairs covering the whole body and a hairy tail. NFSC species bearing well-developed spines are found at lower elevations. A comprehensive taxonomic revision of the NFSC within China is provided, represented by five species: N. cremoriventer, N. fulvescens, N. huang, N. mekongis comb. nov. and N. fengi. A further study of this species complex, including samples from Southeast Asia, is needed.
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Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia; Joint Russian–Vietnamese Tropical Research and Technological Centre, Hanoi, Vietnam
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhengjia Liu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Marcovitz A, Turakhia Y, Chen HI, Gloudemans M, Braun BA, Wang H, Bejerano G. A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales. Proc Natl Acad Sci U S A 2019; 116:21094-21103. [PMID: 31570615 PMCID: PMC6800341 DOI: 10.1073/pnas.1818532116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. How much genomic molecular convergence (particularly of highly constrained coding sequence) contributes to convergent phenotypic evolution, such as echolocation in bats and whales, is a long-standing fundamental question. Like others, we find that convergent amino acid substitutions are not more abundant in echolocating mammals compared to their outgroups. However, we also ask a more informative question about the genomic distribution of convergent substitutions by devising a test to determine which, if any, of more than 4,000 tissue-affecting gene sets is most statistically enriched with convergent substitutions. We find that the gene set most overrepresented (q-value = 2.2e-3) with convergent substitutions in echolocators, affecting 18 genes, regulates development of the cochlear ganglion, a structure with empirically supported relevance to echolocation. Conversely, when comparing to nonecholocating outgroups, no significant gene set enrichment exists. For aquatic and high-altitude mammals, our analysis highlights 15 and 16 genes from the gene sets most affected by molecular convergence which regulate skin and lung physiology, respectively. Importantly, our test requires that the most convergence-enriched set cannot also be enriched for divergent substitutions, such as in the pattern produced by inactivated vision genes in subterranean mammals. Showing a clear role for adaptive protein-coding molecular convergence, we discover nearly 2,600 convergent positions, highlight 77 of them in 3 organs, and provide code to investigate other clades across the tree of life.
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Affiliation(s)
- Amir Marcovitz
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - Yatish Turakhia
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | | | - Benjamin A Braun
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University, Stanford, CA 94305;
- Department of Computer Science, Stanford University, Stanford, CA 94305
- Department of Pediatrics, Stanford University, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305
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