1
|
Ramos E, Selleghin-Veiga G, Magpali L, Daros B, Silva F, Picorelli A, Freitas L, Nery MF. Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians. J Mol Evol 2023; 91:865-881. [PMID: 38010516 DOI: 10.1007/s00239-023-10141-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 10/29/2023] [Indexed: 11/29/2023]
Abstract
The genetic basis underlying adaptive physiological mechanisms has been extensively explored in mammals after colonizing the seas. However, independent lineages of aquatic mammals exhibit complex patterns of secondary colonization in freshwater environments. This change in habitat represents new osmotic challenges, and additional changes in key systems, such as the osmoregulatory system, are expected. Here, we studied the selective regime on coding and regulatory regions of 20 genes related to the osmoregulation system in strict aquatic mammals from independent evolutionary lineages, cetaceans, and sirenians, with representatives in marine and freshwater aquatic environments. We identified positive selection signals in genes encoding the protein vasopressin (AVP) in mammalian lineages with secondary colonization in the fluvial environment and in aquaporins for lineages inhabiting the marine and fluvial environments. A greater number of sites with positive selection signals were found for the dolphin species compared to the Amazonian manatee. Only the AQP5 and AVP genes showed selection signals in more than one independent lineage of these mammals. Furthermore, the vasopressin gene tree indicates greater similarity in river dolphin sequences despite the independence of their lineages based on the species tree. Patterns of distribution and enrichment of Transcription Factors in the promoter regions of target genes were analyzed and appear to be phylogenetically conserved among sister species. We found accelerated evolution signs in genes ACE, AQP1, AQP5, AQP7, AVP, NPP4, and NPR1 for the fluvial mammals. Together, these results allow a greater understanding of the molecular bases of the evolution of genes responsible for osmotic control in aquatic mammals.
Collapse
Affiliation(s)
- Elisa Ramos
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Giovanna Selleghin-Veiga
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Letícia Magpali
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Beatriz Daros
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Felipe Silva
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Agnello Picorelli
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Lucas Freitas
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Mariana F Nery
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil.
| |
Collapse
|
2
|
Zhao X, Dai C, Qian S, Tang Q, Li L, Hao Y, Zhou Z, Ge X, Gong C, Yuan J. Viral Diversity and Epidemiology in Critically Endangered Yangtze Finless Porpoises (Neophocaena asiaeorientalis asiaeorientalis). Microbiol Spectr 2023; 11:e0081023. [PMID: 37265414 PMCID: PMC10434060 DOI: 10.1128/spectrum.00810-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
The Yangtze finless porpoise (YFP) (Neophocaena asiaeorientalis asiaeorientalis) is a critically endangered freshwater cetacean, with about 1,249 individuals thought to be left in the wild. However, viral entities and viral diseases of YFPs remain obscure. In this study, anal swabs for virome analysis were collected during the physical examination of YFPs in the Tian-E-Zhou Oxbow (TEO) ex situ reserve. A total of 19 eukaryotic viral species belonging to 9 families, including Papillomaviridae, Herpesviridae, Picornaviridae, Picobirnaviridae, Caliciviridae, Retroviridae, Parvoviridae, Virgaviridae, and Narnaviridae, and other unclassified viruses were identified based on metasequencing. Among these detected viruses, a novel herpesvirus (NaHV), two different kobuviruses (NaKV1-2), and six different papillomaviruses (NaPV1 to -6) were considered potential risks to YFPs and confirmed by PCR or reverse transcription-PCR (RT-PCR). Most YFPs sampled were found to harbor one or more kinds of detected viral genomes (52/58 [89.7%]). Surveillance results demonstrated that kobuvirus and herpesvirus displayed obvious age distribution and PVs showed significant gender difference in YFPs. According to species demarcation criteria in individual genera in Papillomaviridae, two novel species (referred to as Omikronpapillomavirus 2 and 3) and four novel isolates of PV were identified in YFPs. Further evolutionary analysis suggested that NaPVs would occupy the mucosal niche and that virus-host codivergence mixed with duplications and host-switching events drives the evolution of cetacean PVs. Divergence times of PVs in YFP and other cetacean reflect the incipient speciation of YFPs. In summary, our findings revealed the potential viral entities, their prevalence, and their evolutionary history in YFPs, which raises an important issue regarding effects of viral infection on the fitness of YFPs. IMPORTANCE The Yangtze finless porpoise (YFP) is the only cetacean species in freshwater following the functional extinction of the baiji (Lipotes vexillifer). Health management, disease treatment, and other special measures are important for maintaining the existing YFP populations, especially in in situ and ex situ reserves. The discovery of potential viral entities and their prevalence in YFPs raises an important issue regarding the effects of viral infection on the fitness of YFPs and may contribute to the conservation of YFPs. The evolutionary history of papillomaviruses in YFP and other cetaceans reflects the phylogeny of their hosts and supports the status of incipient species, opening a window to investigate the evolutionary adaptation of cetaceans to freshwater as well as their phylogeny to remedy the deficiency of fossil evidence.
Collapse
Affiliation(s)
- Xin Zhao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Caijiao Dai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Shiyu Qian
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Qing Tang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Lijuan Li
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, People’s Republic of China
| | - Yujiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zhijian Zhou
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Xingyi Ge
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Cheng Gong
- Tian-e-zhou National Reserve for Lipotes Vexillifer, Shishou, People’s Republic of China
| | - Junfa Yuan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, People’s Republic of China
| |
Collapse
|
3
|
Font-Porterias N, McNelis MG, Comas D, Hlusko LJ. Evidence of selection in the ectodysplasin pathway among endangered aquatic mammals. Integr Org Biol 2022; 4:obac018. [PMID: 35874492 PMCID: PMC9299678 DOI: 10.1093/iob/obac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/06/2022] [Accepted: 05/21/2022] [Indexed: 11/13/2022] Open
Abstract
Synopsis The ectodysplasin pathway has been a target of evolution repeatedly. Genetic variation in the key genes of this pathway (EDA, EDAR, and EDARADD) results in a rich source of pleiotropic effects across ectodermally-derived structures, including teeth, hair, sweat glands, and mammary glands. In addition, a non-canonical Wnt pathway has a very similar functional role, making variation in the WNT10A gene also of evolutionary significance. The adaptation of mammals to aquatic environments has occurred independently in at least 4 orders, whose species occupy a wide geographic range (from equatorial to polar regions) and exhibit great phenotypic variation in ectodermally-derived structures, including the presence or absence of fur and extreme lactational strategies. The role of the ectodysplasin pathway in the adaptation to aquatic environments has been never explored in mammalian species. In the present study, we analyze the genetic variation in orthologous coding sequences from EDA, EDAR, EDARADD, and WNT10A genes together with ectodermally-derived phenotypic variation from 34 aquatic and non-aquatic mammalian species to assess signals of positive selection, gene-trait coevolution, and genetic convergence. Our study reveals strong evidence of positive selection in a proportion of coding sites in EDA and EDAR genes in 3 endangered aquatic mammals (the Hawaiian monk seal, the Yangtze finless porpoise, and the sea otter). We hypothesize functional implications potentially related to the adaptation to the low-latitude aquatic environment in the Hawaiian monk seal and the freshwater in the Yangtze finless porpoise. The signal in the sea otter is likely the result of an increased genetic drift after an intense bottleneck and reduction of genetic diversity. Besides positive selection, we have not detected robust signals of gene-trait coevolution or convergent amino acid shifts in the ectodysplasin pathway associated with shared phenotypic traits among aquatic mammals. This study provides new evidence of the evolutionary role of the ectodysplasin pathway and encourages further investigation, including functional studies, to fully resolve its relationship with mammalian aquatic adaptation. Spanish La vía de la ectodisplasina ha sido objeto de la evolución repetidamente. La variación genética en los principales genes de esta vía (EDA, EDAR y EDARADD) da como resultado una gran diversidad de efectos pleiotrópicos en las estructuras derivadas del ectodermo, incluidos los dientes, el cabello, las glándulas sudoríparas y las glándulas mamarias. Además, una vía wnt no canónica tiene un papel funcional muy similar, por lo que la variación en el gen WNT10A también tiene importancia evolutiva. La adaptación de los mamíferos a los entornes acuáticos se ha producido de forma independiente en al menos cuatro órdenes, cuyas especies ocupan un amplio rango geográfico (desde regiones ecuatoriales a polares) y presentan una gran variación fenotípica en las estructuras derivadas del ectodermo, incluyendo la presencia o ausencia de pelaje y estrategias de lactancia muy diferentes. El papel de la vía de la ectodisplasina en la adaptación a entornos acuáticos no se ha explorado nunca en especies de mamíferos. En este estudio, analizamos la variación genética en las secuencias codificantes ortólogas de los genes EDA, EDAR, EDARADD y WNT10A junto con la variación fenotípica derivada del ectodermo de 34 especies de mamíferos acuáticos y no acuáticos para evaluar señales de selección positiva, coevolución gen-rasgo y convergencia genética. Nuestro estudio revela señales de selección positiva en regiones de las secuencias codificantes de los genes EDA y EDAR en tres mamíferos acuáticos en peligro de extinción (la foca monje de Hawái, la marsopa lisa y la nutria marina). Estas señales podrían tener implicaciones funcionales potencialmente relacionadas con la adaptación al entorno acuático de baja latitud en la foca monje de Hawái y el agua dulce en la marsopa lisa. La señal en la nutria marina es probablemente el resultado de una mayor deriva genética tras un intenso un cuello de botella y una reducción de la diversidad genética. A parte de selección positiva, no hemos detectado señales sólidas de coevolución gen-rasgo o cambios convergentes de aminoácidos en la vía de la ectodisplasina asociados a rasgos fenotípicos compartidos entre mamíferos acuáticos. Este estudio proporciona nuevas evidencias del papel evolutivo de la vía de la ectodisplasina y quiere promover futuras investigaciones con estudios funcionales para acabar de resolver la relación de esta vía con la adaptación acuática de los mamíferos.
Collapse
Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Madeline G McNelis
- Department of Integrative Biology, University of California Berkeley , California , USA
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley , California , USA
- National Research Center on Human Evolution (CENIEH) , Burgos , Spain
| |
Collapse
|
4
|
Robinson JA, Kyriazis CC, Nigenda-Morales SF, Beichman AC, Rojas-Bracho L, Robertson KM, Fontaine MC, Wayne RK, Lohmueller KE, Taylor BL, Morin PA. The critically endangered vaquita is not doomed to extinction by inbreeding depression. Science 2022; 376:635-639. [PMID: 35511971 PMCID: PMC9881057 DOI: 10.1126/science.abm1742] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In cases of severe wildlife population decline, a key question is whether recovery efforts will be impeded by genetic factors, such as inbreeding depression. Decades of excess mortality from gillnet fishing have driven Mexico's vaquita porpoise (Phocoena sinus) to ~10 remaining individuals. We analyzed whole-genome sequences from 20 vaquitas and integrated genomic and demographic information into stochastic, individual-based simulations to quantify the species' recovery potential. Our analysis suggests that the vaquita's historical rarity has resulted in a low burden of segregating deleterious variation, reducing the risk of inbreeding depression. Similarly, genome-informed simulations suggest that the vaquita can recover if bycatch mortality is immediately halted. This study provides hope for vaquitas and other naturally rare endangered species and highlights the utility of genomics in predicting extinction risk.
Collapse
Affiliation(s)
- Jacqueline A. Robinson
- Institute for Human Genetics, University of California, San Francisco; San Francisco, CA, USA
| | - Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles; Los Angeles, CA, USA
| | - Sergio F. Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav); Irapuato, Guanajuato, Mexico
| | | | - Lorenzo Rojas-Bracho
- Comisión Nacional de Áreas Naturales Protegidas/SEMARNAT; Ensenada, Mexico
- PNUD-Sinergia en la Comisión Nacional de Áreas Naturales Protegidas, Ensenada, B.C., México
| | - Kelly M. Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA ; La Jolla, CA, USA
| | - Michael C. Fontaine
- MIVEGEC, Université de Montpellier, CNRS, IRD; Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES); Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen; Groningen, The Netherlands
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles; Los Angeles, CA, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles; Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, USA
| | - Barbara L. Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA ; La Jolla, CA, USA
| | - Phillip A. Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA ; La Jolla, CA, USA
| |
Collapse
|
5
|
Taylor RS, Manseau M, Klütsch CFC, Polfus JL, Steedman A, Hervieux D, Kelly A, Larter NC, Gamberg M, Schwantje H, Wilson PJ. Population dynamics of caribou shaped by glacial cycles before the last glacial maximum. Mol Ecol 2021; 30:6121-6143. [PMID: 34482596 PMCID: PMC9293238 DOI: 10.1111/mec.16166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/04/2022]
Abstract
Pleistocene glacial cycles influenced the diversification of high‐latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger‐scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20–30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre‐LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high‐latitude species.
Collapse
Affiliation(s)
- Rebecca S Taylor
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Micheline Manseau
- Biology Department, Trent University, Peterborough, Ontario, Canada.,Landscape Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | | | - Jean L Polfus
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Audrey Steedman
- Parks Canada, Government of Canada, Winnipeg, Manitoba, Canada
| | - Dave Hervieux
- Department of Environment and Parks, Government of Alberta, Grande Prairie, Alberta, Canada
| | - Allicia Kelly
- Department of Environment and Natural Resources, Government of the Northwest Territories, Fort Smith, Northwest Territories, Canada
| | - Nicholas C Larter
- Department of Environment and Natural Resources, Government of the Northwest Territories, Fort Simpson, Northwest Territories, Canada
| | | | - Helen Schwantje
- BC Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Nanaimo, British Columbia, Canada
| | - Paul J Wilson
- Biology Department, Trent University, Peterborough, Ontario, Canada
| |
Collapse
|
6
|
Zhang P, Zhao Y, Li C, Lin M, Dong L, Zhang R, Liu M, Li K, Zhang H, Liu X, Zhang Y, Yuan Y, Liu H, Seim I, Sun S, Du X, Chang Y, Li F, Liu S, Lee SMY, Wang K, Wang D, Wang X, McGowen MR, Jefferson TA, Olsen MT, Stiller J, Zhang G, Xu X, Yang H, Fan G, Liu X, Li S. An Indo-Pacific Humpback Dolphin Genome Reveals Insights into Chromosome Evolution and the Demography of a Vulnerable Species. iScience 2020; 23:101640. [PMID: 33103078 PMCID: PMC7569330 DOI: 10.1016/j.isci.2020.101640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/25/2020] [Accepted: 09/30/2020] [Indexed: 01/12/2023] Open
Abstract
The Indo-Pacific humpback dolphin (Sousa chinensis) is a small inshore species of odontocete cetacean listed as Vulnerable on the IUCN Red List. Here, we report on the evolution of S. chinensis chromosomes from its cetruminant ancestor and elucidate the evolutionary history and population genetics of two neighboring S. chinensis populations. We found that breakpoints in ancestral chromosomes leading to S. chinensis could have affected the function of genes related to kidney filtration, body development, and immunity. Resequencing of individuals from two neighboring populations in the northwestern South China Sea, Leizhou Bay and Sanniang Bay, revealed genetic differentiation, low diversity, and small contemporary effective population sizes. Demographic analyses showed a marked decrease in the population size of the two investigated populations over the last ~4,000 years, possibly related to climatic oscillations. This study implies a high risk of extinction and strong conservation requirement for the Indo-Pacific humpback dolphin. Deducing chromosome evolution from ancestral Cetruminantia and ancestral Odontoceti Reconstructing the demographic history of Sousa chinensis Implying high risk of extinction and strong conservation requirement for S. chinensis
Collapse
Affiliation(s)
- Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Yong Zhao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Chang Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Mingli Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - Lijun Dong
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - Rui Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Mingzhong Liu
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - Kuan Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiaochuan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Yuan Yuan
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane 4102, Australia
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xiao Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yue Chang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Feida Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Ding Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Xianyan Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - Michael R. McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington DC 20560, USA
| | | | - Morten Tange Olsen
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen 1353, Denmark
| | - Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xun Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
- Corresponding author
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- BGI-Fuyang, BGI-Shenzhen, Fuyang, Anhui 236009, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guandong 518083, China
- Corresponding author
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
- Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore
- Corresponding author
| |
Collapse
|
7
|
Russello M, Amato G, DeSalle R, Knapp M. Conservation Genetics and Genomics. Genes (Basel) 2020; 11:genes11030318. [PMID: 32192054 PMCID: PMC7140847 DOI: 10.3390/genes11030318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 11/16/2022] Open
Affiliation(s)
- Michael Russello
- Department of Biology, The University of British Columbia, 3247 University Way, FIP346, Kelowna, BC V1V 1V7, Canada;
| | - George Amato
- Conservation Genomics, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024-5102, USA;
- Correspondence:
| | - Robert DeSalle
- Conservation Genomics, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024-5102, USA;
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand;
| |
Collapse
|
8
|
Tian R, Seim I, Zhang Z, Yang Y, Ren W, Xu S, Yang G. Distinct evolution of toll-like receptor signaling pathway genes in cetaceans. Genes Genomics 2019; 41:1417-1430. [PMID: 31535317 DOI: 10.1007/s13258-019-00861-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The relatively rapid spread and diversity of marine pathogens posed an initial and ongoing challenge for cetaceans (whales, dolphins, and porpoises), descendants of terrestrial mammals that transitioned from land to sea approximately 56 million years ago. Toll-like receptors (TLRs) play important roles in regulating immunity against pathogen infections by detecting specific molecular patterns and activating a wide range of downstream signaling pathways. The ever-increasing catalogue of mammalian genomes offers unprecedented opportunities to reveal genetic changes associated with evolutionary and ecological processes. OBJECTIVE This study aimed to explore the molecular evolution of TLR signaling pathway genes in cetaceans. METHODS Genes involved in the TLR signaling pathway were retrieved by BLAST searches using human coding sequences as queries. We tested each gene for positive selection along the cetacean branches using PAML and Hyphy. Physicochemical property changes of amino acids at all positively selected residues were assessed by TreeSAAP and visualized with WebLogo. Bovine and dolphin TLR4 was assessed using human embryonic kidney cell line HEK293, which lacks TLR4 and its co-receptor MD-2. RESULTS We demonstrate that eight TLR signaling pathway genes are under positive selection in cetaceans. These include key genes in the response to Gram-negative bacteria: TLR4, CD14, and LY96 (MD-2). Moreover, 41 out of 65 positively selected sites were inferred to harbor substitution that dramatically changes the physicochemical properties of amino acids, with most of them situated in or adjacent to functional regions. We also found strong evidence that positive selection occurred in the lineage of the Yangtze finless porpoise, likely reflecting relatively recent adaptions to a freshwater milieu. Species-specific differences in TLR4 response were observed between cetacean and terrestrial species. Cetacean TLR4 was significantly less responsive to lipopolysaccharides from a terrestrial E. coli strain, possibly a reflection of the arms race of host-pathogen co-evolution faced by cetaceans in an aquatic environment. CONCLUSION This study provides further impetus for studies on the evolution and function of the cetacean immune system.
Collapse
Affiliation(s)
- Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.,Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.,Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Zepeng Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Ying Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
| |
Collapse
|
9
|
Fumagalli M, Camus SM, Diekmann Y, Burke A, Camus MD, Norman PJ, Joseph A, Abi-Rached L, Benazzo A, Rasteiro R, Mathieson I, Topf M, Parham P, Thomas MG, Brodsky FM. Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism. eLife 2019; 8:41517. [PMID: 31159924 PMCID: PMC6548504 DOI: 10.7554/elife.41517] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 05/01/2019] [Indexed: 01/29/2023] Open
Abstract
CHC22 clathrin plays a key role in intracellular membrane traffic of the insulin-responsive glucose transporter GLUT4 in humans. We performed population genetic and phylogenetic analyses of the CHC22-encoding CLTCL1 gene, revealing independent gene loss in at least two vertebrate lineages, after arising from gene duplication. All vertebrates retained the paralogous CLTC gene encoding CHC17 clathrin, which mediates endocytosis. For vertebrates retaining CLTCL1, strong evidence for purifying selection supports CHC22 functionality. All human populations maintained two high frequency CLTCL1 allelic variants, encoding either methionine or valine at position 1316. Functional studies indicated that CHC22-V1316, which is more frequent in farming populations than in hunter-gatherers, has different cellular dynamics than M1316-CHC22 and is less effective at controlling GLUT4 membrane traffic, altering its insulin-regulated response. These analyses suggest that ancestral human dietary change influenced selection of allotypes that affect CHC22's role in metabolism and have potential to differentially influence the human insulin response.
Collapse
Affiliation(s)
- Matteo Fumagalli
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom.,Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom.,Research Department of Genetics, Evolution and Environment, Division of Biosciences, University College London, London, United Kingdom.,UCL Genetics Institute, University College London, London, United Kingdom
| | - Stephane M Camus
- Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, Division of Biosciences, University College London, London, United Kingdom.,UCL Genetics Institute, University College London, London, United Kingdom
| | - Alice Burke
- Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Marine D Camus
- Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Paul J Norman
- Division of Bioinformatics and Personalized Medicine, University of Colorado, Aurora, United States.,Department of Microbiology and Immunology, University of Colorado, Aurora, United States
| | - Agnel Joseph
- Institute of Structural and Molecular Biology, Birkbeck College and University College London, London, United Kingdom
| | - Laurent Abi-Rached
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, CNRS, Marseille, France
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Rita Rasteiro
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck College and University College London, London, United Kingdom
| | - Peter Parham
- Department of Structural Biology, Stanford University, Stanford, CA, United States.,Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, Division of Biosciences, University College London, London, United Kingdom.,UCL Genetics Institute, University College London, London, United Kingdom
| | - Frances M Brodsky
- Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College and University College London, London, United Kingdom
| |
Collapse
|
10
|
Autenrieth M, Hartmann S, Lah L, Roos A, Dennis AB, Tiedemann R. High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena). Mol Ecol Resour 2018; 18:1469-1481. [PMID: 30035363 DOI: 10.1111/1755-0998.12932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 11/27/2022]
Abstract
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.
Collapse
Affiliation(s)
- Marijke Autenrieth
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Ljerka Lah
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Anna Roos
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Alice B Dennis
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| |
Collapse
|