1
|
Black AN, Mularo AJ, Jeon JY, Haukos D, Bondo KJ, Fricke KA, Gregory A, Grisham B, Lowe ZE, DeWoody JA. Discordance between taxonomy and population genomic data: An avian example relevant to the United States Endangered Species Act. PNAS NEXUS 2024; 3:pgae298. [PMID: 39131912 PMCID: PMC11313583 DOI: 10.1093/pnasnexus/pgae298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/03/2024] [Indexed: 08/13/2024]
Abstract
Population genomics can reveal cryptic biological diversity that may impact fitness while simultaneously serving to delineate relevant conservation units. Here, we leverage the power of whole-genome resequencing for conservation by studying 433 individual lesser prairie-chicken (Tympanuchus pallidicinctus; LEPC, a federally endangered species of conservation concern in the United States) and greater prairie-chicken (Tympanuchus cupido; GRPC, a legally huntable species throughout much of its range). The genomic diversity of two formally recognized distinct population segments (DPSs) of LEPCs is similar, but they are genetically distinct. Neither DPS is depleted of its genomic diversity, neither is especially inbred, and temporal diversity is relatively stable in both conservation units. Interspecific differentiation between the two species was only slightly higher than that observed between LEPC DPSs, due largely to bidirectional introgression. The high resolution provided by our dataset identified a genomic continuum between the two species such that individuals sampled from the hybrid zone were imperfectly assigned to their presumptive species when considering only their physical characteristics. The admixture between the two species is reflected in the spectrum of individual ancestry coefficients, which has legal implications for the "take" of individuals under the Endangered Species Act. Overall, our data highlight the recurring dissonance between static policies and dynamic species boundaries that are increasingly obvious in the population genomic era.
Collapse
Affiliation(s)
- Andrew N Black
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
- Western Association of Fish and Wildlife Agencies, Boise, ID 83719, USA
| | - Andrew J Mularo
- Department of Biological Sciences, Purdue University, West Lafayette, IN 66506, USA
| | - Jong Yoon Jeon
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
| | - David Haukos
- U.S. Geological Survey, Kansas Cooperative Fish and Wildlife Research Unit, Kansas State University, Manhattan, KS 66506, USA
| | - Kristin J Bondo
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX 79410, USA
| | - Kent A Fricke
- Kansas Department of Wildlife and Parks, Emporia, KS 66801, USA
| | - Andy Gregory
- Department of Biological Sciences, University of North Texas, Denton, TX 76201, USA
| | - Blake Grisham
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX 79410, USA
| | - Zachary E Lowe
- Western Association of Fish and Wildlife Agencies, Boise, ID 83719, USA
| | - J Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 66506, USA
| |
Collapse
|
2
|
Jia P, Nurziya Y, Luo Y, Jia W, Zhu Q, Tian M, Sun L, Zhang B, Qi Z, Zhao Z, Dai Y, Fu Y, Li Y. Evolution and Genetic Differentiation of Pleurotus tuoliensis in Xinjiang, China, Based on Population Genomics. J Fungi (Basel) 2024; 10:472. [PMID: 39057357 PMCID: PMC11278092 DOI: 10.3390/jof10070472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Pleurotus tuoliensis is a unique species discovered in Xinjiang, China, which is recognized for its significant edible, medicinal, and economic value. It has been successfully incorporated into industrial production. Controversy has emerged concerning the evolution and environmental adaptability of this species due to inadequate interspecific ecology and molecular data. This study examines the germplasm resources of P. tuoliensis in the Xinjiang region. A total of 225 wild and cultivated strains of P. tuoliensis were gathered from seven representative regions. Phylogenetic analysis revealed that seven populations were notably segregated into three distinct groups, primarily attributed to environmental factors as the underlying cause for this differentiation. Population historical size data indicate that P. tuoliensis underwent two expansion events, one between 2 and 0.9 Mya (Miocene) and the other between 15 and 4 Mya (Early Pleistocene). The ancient climate fluctuations in the Xinjiang region might have contributed to the comparatively modest population size during the Pliocene epoch. Moreover, through the integration of biogeography and ancestral state reconstruction, it was determined that group C of P. tuoliensis emerged initially and subsequently dispersed to groups D and B, in that order. Subsequently, group D underwent independent evolution, whereas group B continued to diversify into groups A and EFG. The primary factor influencing this mode of transmission route is related to the geographical conditions and prevailing wind direction of each group. Subsequent research endeavors focused on assessing the domestication adaptability of P. tuoliensis to different substrates. It was found that the metabolic processes adapted during the domestication process were mainly related to energy metabolism, DNA repair, and environmental adaptability. Processes adapted to the host adaptability include responses to the host (meiosis, cell cycle, etc.) and stress in the growth environment (cysteine and methionine metabolism, sulfur metabolism, etc.). This study analyzed the systematic evolution and genetic differentiation of P. tuoliensis in Xinjiang. The identified loci and genes provide a theoretical basis for the subsequent improvement of germplasm resources and conducting molecular breeding.
Collapse
Affiliation(s)
- Peisong Jia
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China (L.S.); (B.Z.); (Z.Q.); (Y.D.)
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.N.); (Y.L.); (W.J.); (Q.Z.); (Z.Z.)
| | - Yarmamat Nurziya
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.N.); (Y.L.); (W.J.); (Q.Z.); (Z.Z.)
| | - Ying Luo
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.N.); (Y.L.); (W.J.); (Q.Z.); (Z.Z.)
| | - Wenjie Jia
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.N.); (Y.L.); (W.J.); (Q.Z.); (Z.Z.)
| | - Qi Zhu
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.N.); (Y.L.); (W.J.); (Q.Z.); (Z.Z.)
| | - Meng Tian
- College of Life Sciences, Xinjiang Agricultural University, Urumqi 830091, China;
| | - Lei Sun
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China (L.S.); (B.Z.); (Z.Q.); (Y.D.)
| | - Bo Zhang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China (L.S.); (B.Z.); (Z.Q.); (Y.D.)
| | - Zhengxiang Qi
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China (L.S.); (B.Z.); (Z.Q.); (Y.D.)
| | - Zhenhao Zhao
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.N.); (Y.L.); (W.J.); (Q.Z.); (Z.Z.)
| | - Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China (L.S.); (B.Z.); (Z.Q.); (Y.D.)
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China (L.S.); (B.Z.); (Z.Q.); (Y.D.)
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China (L.S.); (B.Z.); (Z.Q.); (Y.D.)
| |
Collapse
|
3
|
An ZX, Shi LG, Hou GY, Zhou HL, Xun WJ. Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data. Animal 2024; 18:101147. [PMID: 38843669 DOI: 10.1016/j.animal.2024.101147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 06/22/2024] Open
Abstract
Understanding the genetic characteristics of indigenous goat breeds is crucial for their conservation and breeding efforts. Hainan black goats, as a native breed of south China's tropical island province of Hainan, possess distinctive traits such as black hair, a moderate growth rate, good meat quality, and small body size. However, they exhibit exceptional resilience to rough feeding conditions, possess high-quality meat, and show remarkable resistance to stress and heat. In this study, we resequenced the whole genome of Hainan black goats to study the economic traits and genetic basis of these goats, we leveraged whole-genome sequencing data from 33 Hainan black goats to analyze single nucleotide polymorphism (SNP) density, Runs of homozygosity (ROH), Integrated Haplotype Score (iHS), effective population size (Ne), Nucleotide diversity Analysis (Pi) and selection characteristics. Our findings revealed that Hainan black goats harbor a substantial degree of genetic variation, with a total of 23 608 983 SNPs identified. Analysis of ROHs identified 53 710 segments, predominantly composed of short fragments, with inbreeding events mainly occurring in ancient ancestors, the estimates of inbreeding based on ROH in Hainan black goats typically exhibit moderate values ranging from 0.107 to 0.186. This is primarily attributed to significant declines in the effective population size over recent generations. Moreover, we identified 921 candidate genes within the intersection candidate region of ROH and iHS. Several of these genes are associated with crucial traits such as immunity (PTPRC, HYAL1, HYAL2, HYAL3, CENPE and PKN1), heat tolerance (GNG2, MAPK8, CAPN2, SLC1A1 and LEPR), meat quality (ACOX1, SSTR1, CAMK2B, PPP2CA and PGM1), cashmere production (AKT4, CHRM2, OXTR, AKT3, HMCN1 and CDK19), and stress resistance (TLR2, IFI44, ENPP1, STK3 and NFATC1). The presence of these genes may be attributed to the genetic adaptation of Hainan black goats to local climate conditions. The insights gained from this study provide valuable references and a solid foundation for the preservation, breeding, and utilization of Hainan black goats and their valuable genetic resources.
Collapse
Affiliation(s)
- Z X An
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - L G Shi
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - G Y Hou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - H L Zhou
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524000, China
| | - W J Xun
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| |
Collapse
|
4
|
Teixeira H, Le Corre M, Michon L, Nicoll MAC, Jaeger A, Nikolic N, Pinet P, Couzi FX, Humeau L. Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts. Sci Rep 2024; 14:1960. [PMID: 38263429 PMCID: PMC10805739 DOI: 10.1038/s41598-024-52556-9] [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: 10/04/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.
Collapse
Affiliation(s)
- Helena Teixeira
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France.
| | - Matthieu Le Corre
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | - Laurent Michon
- Université de La Réunion, Laboratoire Géosciences Réunion, 97744, Saint Denis, France
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, 75005, Paris, France
| | - Malcolm A C Nicoll
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Audrey Jaeger
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | | | - Patrick Pinet
- Parc National de La Réunion, Life+ Pétrels, 258 Rue de la République, 97431, Plaine des Palmistes, Réunion Island, France
| | - François-Xavier Couzi
- Société d'Etudes Ornithologiques de La Réunion (SEOR), 13 ruelle des Orchidées, 97440, Saint André, Réunion Island, France
| | - Laurence Humeau
- UMR PVBMT (Université de La Réunion, CIRAD), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| |
Collapse
|
5
|
Kimmitt AA, Pegan TM, Jones AW, Wacker KS, Brennan CL, Hudon J, Kirchman JJ, Ruegg K, Benz BW, Herman R, Winger BM. Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum. Proc Biol Sci 2023; 290:20221334. [PMID: 36695033 PMCID: PMC9874272 DOI: 10.1098/rspb.2022.1334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023] Open
Abstract
Pleistocene climate cycles are well documented to have shaped contemporary species distributions and genetic diversity. Northward range expansions in response to deglaciation following the Last Glacial Maximum (LGM; approximately 21 000 years ago) are surmised to have led to population size expansions in terrestrial taxa and changes in seasonal migratory behaviour. Recent findings, however, suggest that some northern temperate populations may have been more stable than expected through the LGM. We modelled the demographic history of 19 co-distributed boreal-breeding North American bird species from full mitochondrial gene sets and species-specific molecular rates. We used these demographic reconstructions to test how species with different migratory strategies were affected by glacial cycles. Our results suggest that effective population sizes increased in response to Pleistocene deglaciation earlier than the LGM, whereas genetic diversity was maintained throughout the LGM despite shifts in geographical range. We conclude that glacial cycles prior to the LGM have most strongly shaped contemporary genetic diversity in these species. We did not find a relationship between historic population dynamics and migratory strategy, contributing to growing evidence that major switches in migratory strategy during the LGM are unnecessary to explain contemporary migratory patterns.
Collapse
Affiliation(s)
- Abigail A. Kimmitt
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Teresa M. Pegan
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew W. Jones
- Department of Ornithology, Cleveland Museum of Natural History, Cleveland, OH 44106, USA
| | - Kristen S. Wacker
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Courtney L. Brennan
- Department of Ornithology, Cleveland Museum of Natural History, Cleveland, OH 44106, USA
| | - Jocelyn Hudon
- Royal Alberta Museum, Edmonton, Alberta Canada, T5J 0G2
| | | | - Kristen Ruegg
- Biology Department, Colorado State University, Fort Collins, CO 80521, USA
| | - Brett W. Benz
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rachael Herman
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Benjamin M. Winger
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
6
|
Zhang J, Richards ZT, Adam AAS, Chan CX, Shinzato C, Gilmour J, Thomas L, Strugnell JM, Miller DJ, Cooke I. Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum. Mol Biol Evol 2022; 39:msac201. [PMID: 36219871 PMCID: PMC9578555 DOI: 10.1093/molbev/msac201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera. We show that three genetically distinct populations are present in northwestern Australia, and that their rapid divergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid divergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.
Collapse
Affiliation(s)
- Jia Zhang
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Collections and Research, Western Australian Museum, 49 Kew Street Welshpool, WA 6106, Australia
| | - Arne A S Adam
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Cheong Xin Chan
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, QLD 4072, Australia
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo277-8564, Chiba, Japan
| | - James Gilmour
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
| | - Luke Thomas
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
- Oceans Graduate School, The UWA Oceans Institute, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jan M Strugnell
- Department of Marine Biology and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
| | - David J Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan 904-0495
| | - Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
| |
Collapse
|
7
|
Dong F, Zhang Q, Chen YL, Lei FM, Li SH, Wu F, Yang XJ. Potential millennial-scale avian declines by humans in southern China. GLOBAL CHANGE BIOLOGY 2022; 28:5505-5513. [PMID: 35665575 DOI: 10.1111/gcb.16289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Mounting observational records demonstrate human-caused faunal decline in recent decades, while accumulating archaeological evidence suggests an early biodiversity impact of human activities during the Holocene. A fundamental question arises concerning whether modern wildlife population declines began during early human disturbance. Here, we performed a population genomic analysis of six common forest birds in East Asia to address this question. For five of them, demographic history inference based on 25-33 genomes of each species revealed dramatic population declines by 4- to 48-fold over millennia (e.g. 2000-5000 thousand years ago). Nevertheless, summary statistics detected nonsignificant correlations between these population size trajectories and Holocene temperature variations, and ecological niche models explicitly predicted extensive range persistence during the Holocene, implying limited demographic consequence of Holocene climate change. Further analyses suggest high negative correlations between the reconstructed population declines and human disturbance intensities and indicate a potential driver of human activities. These findings provide a deep-time and large-scale insight into the recently recognized avifaunal decline and support an early origin hypothesis of human effects on biodiversity. Overall, our study sheds light on the current biodiversity crisis in the context of long-term human-environment interactions and offers a multi-evidential framework for quantitatively assessing the ecological consequences of human disturbance.
Collapse
Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yi-Lin Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Fei Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
8
|
Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation. Commun Biol 2022; 5:821. [PMID: 36008681 PMCID: PMC9411537 DOI: 10.1038/s42003-022-03757-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/22/2022] [Indexed: 11/18/2022] Open
Abstract
Poaching and trafficking have a substantial negative impact on the population growth and range expansion of the Chinese pangolin (Manis pentadactyla). However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicate a promising sign for the recovery of this threatened species. Here, we re-sequence genomes of 15 individuals and perform comprehensive population genomics analyses with previously published 22 individuals. These Chinese pangolins are found to be divided into three distinct populations. Multiple lines of evidence indicate the existence of a newly discovered population (CPA) comprises entirely of individuals from Guangdong province. The other two populations (CPB and CPC) have previously been documented. The genetic differentiation of the CPA and CPC is extremely large (FST = 0.541), which is larger than many subspecies-level differentiations. Even for the closer CPA and CPB, their differentiation (FST = 0.101) is still comparable with the population-level differentiation of many endangered species. Further analysis reveals that the CPA and CPB populations separate 2.5–4.0 thousand years ago (kya), and on the other hand, CPA and CPC diverge around 25–40 kya. The CPA population harbors more runs of homozygosity (ROHs) than the CPB and CPC populations, indicating that inbreeding is more prevalent in the CPA population. Although the CPC population has less mutational load than CPA and CPB populations, we predict that several Loss of Function (LoF) mutations will be translocated into the CPA or CPB populations by using the CPC as a donor population for genetic rescue. Our findings imply that the conservation of Chinese pangolins is challenging, and implementing genetic rescue among the three groups should be done with extreme caution. Whole-genome resequencing of Chinese pangolins reveals a new population CPA that is genetically distinct from and harbor more homozygosity than CPB and CPC populations, indicating prevalence in inbreeding and implying challenges in conservation.
Collapse
|
9
|
Carrera L, Pavia M, Varela S. Birds adapted to cold conditions show greater changes in range size related to past climatic oscillations than temperate birds. Sci Rep 2022; 12:10813. [PMID: 35752649 PMCID: PMC9233688 DOI: 10.1038/s41598-022-14972-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Investigation of ecological responses of species to past climate oscillations provides crucial information to understand the effects of global warming. In this work, we investigated how past climate changes affected the distribution of six bird species with different climatic requirements and migratory behaviours in the Western Palearctic and in Africa. Species Distribution Models and Marine Isotopic Stage (MIS) 2 fossil occurrences of selected species were employed to evaluate the relation between changes in range size and species climatic tolerances. The Last Glacial Maximum (LGM) range predictions, generally well supported by the MIS 2 fossil occurrences, suggest that cold-dwelling species considerably expanded their distribution in the LGM, experiencing more pronounced net changes in range size compared to temperate species. Overall, the thermal niche proves to be a key ecological trait for explaining the impact of climate change in species distributions. Thermal niche is linked to range size variations due to climatic oscillations, with cold-adapted species currently suffering a more striking range reduction compared to temperate species. This work also supports the persistence of Afro-Palearctic migrations during the LGM due to the presence of climatically suitable wintering areas in Africa even during glacial maxima.
Collapse
Affiliation(s)
- Lisa Carrera
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, University of Bologna, Via Zamboni 67, 40126, Bologna, Italy.
| | - Marco Pavia
- Dipartimento di Scienze della Terra, Museo di Geologia e Paleontologia, University of Torino, Via Valperga Caluso 35, 10125, Turin, Italy
| | - Sara Varela
- MAPAS Lab, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain
| |
Collapse
|
10
|
Robin M, Ferrari G, Akgül G, Münger X, von Seth J, Schuenemann VJ, Dalén L, Grossen C. Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex. Mol Ecol 2022; 31:3548-3565. [PMID: 35560856 PMCID: PMC9328357 DOI: 10.1111/mec.16503] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/13/2022] [Accepted: 05/04/2022] [Indexed: 11/27/2022]
Abstract
Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. Understanding of historic population size and standing genetic variation prior to a contraction allows estimating the impact of a bottleneck on the species genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10-20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1-2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations from the emergence of a species through its near extinction up to the recent past.
Collapse
Affiliation(s)
- Mathieu Robin
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland.,Institute of Evolutionary Medicine, University of Zurich, Zürich, Switzerland
| | - Giada Ferrari
- Institute of Evolutionary Medicine, University of Zurich, Zürich, Switzerland
| | - Gülfirde Akgül
- Institute of Evolutionary Medicine, University of Zurich, Zürich, Switzerland
| | - Xenia Münger
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Christine Grossen
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| |
Collapse
|
11
|
Brüniche-Olsen A, Kellner KF, Belant JL, DeWoody JA. Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation. Proc Biol Sci 2021; 288:20211441. [PMID: 34702080 PMCID: PMC8548786 DOI: 10.1098/rspb.2021.1441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022] Open
Abstract
More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes (Ne) and current genomic variability (H), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that Ne and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.
Collapse
Affiliation(s)
- Anna Brüniche-Olsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 KBH N Copenhagen, Denmark
| | - Kenneth F. Kellner
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Jerrold L. Belant
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47905, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47905, USA
| |
Collapse
|
12
|
Song K, Gao B, Halvarsson P, Fang Y, Klaus S, Jiang YX, Swenson JE, Sun YH, Höglund J. Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change. BMC Ecol Evol 2021; 21:194. [PMID: 34689746 PMCID: PMC8543876 DOI: 10.1186/s12862-021-01921-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
Background The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To understand the possible effects of on-going and future climate change it would be useful to reconstruct past population size changes and relate such to climatic events in the past. We sequenced the genomes of 32 individuals from two forest inhabiting bird species, Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of two outgroup species from Europe and China. Results We estimated the divergence time of Chinese Grouse and Hazel Grouse to 1.76 (0.46–3.37) MYA. The demographic history of different populations in these two sibling species was reconstructed, and showed that peaks and bottlenecks of effective population size occurred at different times for the two species. The northern Qilian population of Chinese Grouse became separated from the rest of the species residing in the south approximately 250,000 years ago and have since then showed consistently lower effective population size than the southern population. The Chinese Hazel Grouse population had a higher effective population size at the peak of the Last Glacial Period (approx. 300,000 years ago) than the European population. Both species have decreased recently and now have low effective population sizes. Conclusions Combined with the uplift history and reconstructed climate change during the Quaternary, our results support that cold-adapted grouse species diverged in response to changes in the distribution of palaeo-boreal forest and the formation of the Loess Plateau. The combined effects of climate change and an increased human pressure impose major threats to the survival and conservation of both species. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01921-7.
Collapse
Affiliation(s)
- Kai Song
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden. .,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China.
| | - Bin Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | - Peter Halvarsson
- Unit of Parasitology, Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, PO Box 7036, 75007, Uppsala, Sweden
| | - Yun Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | | | - Ying-Xin Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | - Jon E Swenson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, PO Box 5003, 1432, Ås, Norway
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China.
| | - Jacob Höglund
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
| |
Collapse
|
13
|
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
|
14
|
Wang P, Burley JT, Liu Y, Chang J, Chen D, Lu Q, Li SH, Zhou X, Edwards S, Zhang Z. Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant. Mol Biol Evol 2021; 38:263-273. [PMID: 32853368 PMCID: PMC7783171 DOI: 10.1093/molbev/msaa213] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Population genetic theory and empirical evidence indicate that deleterious alleles can be purged in small populations. However, this viewpoint remains controversial. It is unclear whether natural selection is powerful enough to purge deleterious mutations when wild populations continue to decline. Pheasants are terrestrial birds facing a long-term risk of extinction as a result of anthropogenic perturbations and exploitation. Nevertheless, there are scant genomics resources available for conservation management and planning. Here, we analyzed comparative population genomic data for the three extant isolated populations of Brown eared pheasant (Crossoptilon mantchuricum) in China. We showed that C. mantchuricum has low genome-wide diversity and a contracting effective population size because of persistent declines over the past 100,000 years. We compared genome-wide variation in C. mantchuricum with that of its closely related sister species, the Blue eared pheasant (C. auritum) for which the conservation concern is low. There were detrimental genetic consequences across all C. mantchuricum genomes including extended runs of homozygous sequences, slow rates of linkage disequilibrium decay, excessive loss-of-function mutations, and loss of adaptive genetic diversity at the major histocompatibility complex region. To the best of our knowledge, this study is the first to perform a comprehensive conservation genomic analysis on this threatened pheasant species. Moreover, we demonstrated that natural selection may not suffice to purge deleterious mutations in wild populations undergoing long-term decline. The findings of this study could facilitate conservation planning for threatened species and help recover their population size.
Collapse
Affiliation(s)
- Pengcheng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China.,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Department of Organismic and Evolutionary Biology/Museum of Comparative Zoology, Harvard University, Cambridge, MA
| | - John T Burley
- Department of Ecology and Evolutionary Biology/Institute at Brown for Environment and Society, Brown University, Providence, RI
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-Sen University, Guangzhou, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - De Chen
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qi Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Shou-Hsien Li
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Scott Edwards
- Department of Organismic and Evolutionary Biology/Museum of Comparative Zoology, Harvard University, Cambridge, MA
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
15
|
Appenroth D, Wagner GC, Hazlerigg DG, West AC. Evidence for circadian-based photoperiodic timekeeping in Svalbard ptarmigan, the northernmost resident bird. Curr Biol 2021; 31:2720-2727.e5. [PMID: 33930302 DOI: 10.1016/j.cub.2021.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 02/09/2021] [Accepted: 04/07/2021] [Indexed: 01/24/2023]
Abstract
The high Arctic archipelago of Svalbard (74°-81° north) experiences extended periods of uninterrupted daylight in summer and uninterrupted night in winter, apparently relaxing the major driver for the evolution of circadian rhythmicity. Svalbard ptarmigan (Lagopus muta hyperborea) is the only year-round resident terrestrial bird species endemic to the high Arctic and is remarkably adapted to the extreme annual variation in environmental conditions.1 Here, we demonstrate that, although circadian control of behavior disappears rapidly upon transfer to constant light conditions, consistent with the loss of daily activity patterns observed during the polar summer and polar night, Svalbard ptarmigans nonetheless employ a circadian-based mechanism for photoperiodic timekeeping. First, we show the persistence of rhythmic clock gene expression under constant light within the mediobasal hypothalamus and pars tuberalis, the key tissues in the seasonal neuroendocrine cascade. We then employ a "sliding skeleton photoperiod" protocol, revealing that the driving force behind seasonal biology of the Svalbard ptarmigan is rhythmic sensitivity to light, a feature that depends on a functioning circadian rhythm. Hence, the unusual selective pressures of life in the high Arctic have favored decoupling of the circadian clock from organization of daily activity patterns, while preserving its importance for seasonal synchronization.
Collapse
Affiliation(s)
- Daniel Appenroth
- Arctic Seasonal Timekeeping Initiative (ASTI), Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Framstredet 42, 9019 Tromsø, Norway
| | - Gabriela C Wagner
- Arctic Seasonal Timekeeping Initiative (ASTI), Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Framstredet 42, 9019 Tromsø, Norway; Divisjon for skog og utmark, NIBIO, Holtveien 66, 9016 Tromsø, Norway
| | - David G Hazlerigg
- Arctic Seasonal Timekeeping Initiative (ASTI), Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Framstredet 42, 9019 Tromsø, Norway.
| | - Alexander C West
- Arctic Seasonal Timekeeping Initiative (ASTI), Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Framstredet 42, 9019 Tromsø, Norway.
| |
Collapse
|
16
|
Guo X, He XX, Chen H, Wang ZC, Li HF, Wang JX, Wang MS, Jiang RS. Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses. Zool Res 2021; 42:43-50. [PMID: 33269825 PMCID: PMC7840458 DOI: 10.24272/j.issn.2095-8137.2020.133] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although domestic ducks have been important poultry species throughout human history, their origin remains enigmatic, with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s) of domestic ducks. Here, we analyzed 118 whole genomes from mallard, Chinese spot-billed, and domestic ducks to reconstruct their evolutionary history. We found pervasive introgression patterns among these duck populations. Furthermore, we showed that domestic ducks separated from mallard and Chinese spot-billed ducks nearly 38 thousand years ago (kya) and 54 kya, respectively, which is considerably outside the time period of presumed duck domestication. Thus, our results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled, rather than from present-day mallard and/or Chinese spot-billed ducks, as previously thought. Overall, this study provides new insight into the complex evolution of ducks.
Collapse
Affiliation(s)
- Xing Guo
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xin-Xin He
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hong Chen
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zhi-Cheng Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hui-Fang Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Jiang-Xian Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA 95064, USA. E-mail:
| | - Run-Shen Jiang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China. E-mail:
| |
Collapse
|
17
|
Natesh M, Vinay KL, Ghosh S, Jayapal R, Mukherjee S, Vijay N, Robin VV. Contrasting Trends of Population Size Change for Two Eurasian Owlet Species—Athene brama and Glaucidium radiatum From South Asia Over the Late Quaternary. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.608339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Climatic oscillations over the Quaternary have had a lasting impact on species’ distribution, evolutionary history, and genetic composition. Many species show dramatic population size changes coinciding with the last glacial period. However, the extent and direction of change vary across biogeographic regions, species-habitat associations, and species traits. Here we use genomic data to assess population size changes over the late Quaternary using the Pairwise Sequential Markovian Coalescent (PSMC) approach in two Eurasian Owlet species—the Spotted Owlet, Athene brama, and the Jungle Owlet, Glaucidium radiatum. While Spotted Owlets are typically associated with open habitats, Jungle Owlets are found in deciduous forests and scrublands. We find that the effective population size for the Spotted Owlet increased after the Interglacial period till the Last Glacial Maxima and subsequently declined toward the Mid-Holocene. On the other hand, effective population size estimates for the Jungle Owlet increased gradually throughout this period. These observations are in line with climatic niche model-based predictions for range size change for both species from a previous study and suggest that habitat associations at the local scale are important in determining responses to past climatic and vegetational changes. The Spotted Owlet result also aligns well with the expectation of open habitat expansion during the arid Glacial Maxima, whereas for the Jungle Owlet the contrasting expectation does not hold. Therefore, assessing the impacts of glacial history on population trajectories of multiple species with different habitat associations is necessary to understand the impacts of past climate on South Asian taxa.
Collapse
|
18
|
Song K, Gao B, Halvarsson P, Fang Y, Jiang YX, Sun YH, Höglund J. Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese Grouse Tetrastes sewerzowi. BMC Genomics 2020; 21:581. [PMID: 32847513 PMCID: PMC7450560 DOI: 10.1186/s12864-020-06957-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 07/27/2020] [Indexed: 11/20/2022] Open
Abstract
Background The Quaternary had worldwide consequences in forming the contemporary diversity of many populations, species and communities, which is characterized by marked climatic oscillations between glacial and interglacial periods. The origin and evolution of biodiversity in mountainous areas are highly dependent on historical orogenesis and associated climatic changes. The Chinese grouse Tetrastes sewerzowi is a forest-dwelling species endemic to the mountains to the east of the Qinghai–Tibet Plateau, which has been listed as Near Threatened with a decreasing trend by the IUCN because of ongoing deforestation and fragmentation of coniferous forests. It is important to place current population status into a broader ecological and evolutionary context to understand their demographic history. Results Analyses of the Chinese Grouse genome revealed fluctuations throughout the Pleistocene in effective population size. Populations decreased during early to middle Pleistocene but showed an expansion during late Pleistocene which was then followed by a sharp decline during the last glacial maximum (LGM). Ecological niche modeling indicated that a suitable habitat shift between high altitude regions to low altitude regions was due to a changing climate. This result parallels patterns of population size change in Chinese Grouse estimated from PSMC modelling, which suggested an expansion in population size from the last interglacial period (LIG) and then a peak and a bottleneck occurring at the last glacial maximum (LGM). Furthermore, the present-day distribution of Chinese Grouse is greatly reduced and fragmented. It will likely become even more fragmented in the future since coniferous forest cover is threatened in the region of their distribution and the availability of such habitat restricts their ecological niche. Conclusions The Chinese Grouse have experienced substantial population size changes from the beginning to the LIG and reached a peak before the LGM. A sharp decrease and bottleneck occurred during the LGM, when the coniferous forests were subjected to extensive loss. The results inferred from the whole genome sequencing and species distribution models both support historical population fluctuations. The distribution of the Chinese Grouse is strongly dependent on the coniferous forest cover. To protect the fragmented coniferous forests is an essential action to protect the Chinese Grouse.
Collapse
Affiliation(s)
- Kai Song
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden. .,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China.
| | - Bin Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Peter Halvarsson
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.,Unit of Parasitology, Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, PO Box 7036, 75007, Uppsala, Sweden
| | - Yun Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Ying-Xin Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China.
| | - Jacob Höglund
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| |
Collapse
|
19
|
Appenroth D, Melum VJ, West AC, Dardente H, Hazlerigg DG, Wagner GC. Photoperiodic induction without light-mediated circadian entrainment in a High Arctic resident bird. J Exp Biol 2020; 223:jeb220699. [PMID: 32587064 DOI: 10.1242/jeb.220699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/19/2020] [Indexed: 01/27/2023]
Abstract
Organisms use changes in photoperiod to anticipate and exploit favourable conditions in a seasonal environment. While species living at temperate latitudes receive day length information as a year-round input, species living in the Arctic may spend as much as two-thirds of the year without experiencing dawn or dusk. This suggests that specialised mechanisms may be required to maintain seasonal synchrony in polar regions. Svalbard ptarmigan (Lagopus muta hyperborea) are resident at 74-81°N latitude. They spend winter in constant darkness (DD) and summer in constant light (LL); extreme photoperiodic conditions under which they do not display overt circadian rhythms. Here, we explored how Arctic adaptation in circadian biology affects photoperiodic time measurement in captive Svalbard ptarmigan. For this purpose, DD-adapted birds, showing no circadian behaviour, either remained in prolonged DD, were transferred into a simulated natural photoperiod (SNP) or were transferred directly into LL. Birds transferred from DD to LL exhibited a strong photoperiodic response in terms of activation of the hypothalamic thyrotropin-mediated photoperiodic response pathway. This was assayed through expression of the Eya3, Tshβ and deiodinase genes, as well as gonadal development. While transfer to SNP established synchronous diurnal activity patterns, activity in birds transferred from DD to LL showed no evidence of circadian rhythmicity. These data show that the Svalbard ptarmigan does not require circadian entrainment to develop a photoperiodic response involving conserved molecular elements found in temperate species. Further studies are required to define how exactly Arctic adaptation modifies seasonal timer mechanisms.
Collapse
Affiliation(s)
- Daniel Appenroth
- Arctic Chronobiology and Physiology, University of Tromsø, 9019 Tromsø, Norway
| | - Vebjørn J Melum
- Arctic Chronobiology and Physiology, University of Tromsø, 9019 Tromsø, Norway
| | - Alexander C West
- Arctic Chronobiology and Physiology, University of Tromsø, 9019 Tromsø, Norway
| | - Hugues Dardente
- Physiologie de la Reproduction et des Comportements, INRA, CNRS, IFCE, Université de Tours, 37380 Nouzilly, France
| | - David G Hazlerigg
- Arctic Chronobiology and Physiology, University of Tromsø, 9019 Tromsø, Norway
| | - Gabriela C Wagner
- Arctic Chronobiology and Physiology, University of Tromsø, 9019 Tromsø, Norway
| |
Collapse
|
20
|
Sato Y, Ogden R, Kishida T, Nakajima N, Maeda T, Inoue-Murayama M. Population history of the golden eagle inferred from whole-genome sequencing of three of its subspecies. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe application of evolutionary genetic research to investigate the potential for endangered species to adapt to changing environments is important for conservation biology. Effective population size (Ne) is informative for understanding adaptive potential as it refers to the genetic variation in breeding individuals who have contributed to contemporary and historic population diversity. We reconstruct fluctuations in Ne in three golden eagle subspecies (Japanese, Scottish, North American) using the pairwise sequential Markovian coalescent (PSMC) model based on whole-genome sequence data. Our results indicate the timing of subspeciation events and suggest significant ongoing demographic reductions since the start of the Last Glacial Period. Importantly, we find evidence for gene flow from continental populations into the ancestral Japanese population resulting in a short, sharp recovery in genetic diversity. Timing agrees with the palaeogeographic estimates of land bridge connections between the Japanese archipelago and Asian continent and matches a similar Ne spike in the Scottish population, but not in the North American population. Given contemporary declines in isolated Japanese and UK island populations, our study highlights a concerning loss of local genetic diversity, but also indicates the likely response of populations to genetic reinforcement from neighbouring subspecies, increasing management options and encouraging a range-wide species conservation approach.
Collapse
Affiliation(s)
- Yu Sato
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, University of Edinburgh, UK
| | - Takushi Kishida
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Museum of Natural and Environmental History, Shizuoka, Japan
| | - Nobuyoshi Nakajima
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
| | - Taku Maeda
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health, Morioka, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
| |
Collapse
|
21
|
Bourgeois YXC, Bertrand JAM, Delahaie B, Holota H, Thébaud C, Milá B. Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage. Mol Ecol 2020; 29:1137-1153. [PMID: 32107807 DOI: 10.1111/mec.15396] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022]
Abstract
Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white-eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping-by-sequencing and pooled RAD-seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for investigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.
Collapse
Affiliation(s)
- Yann X C Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK.,Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Joris A M Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Laboratoire Génome & Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| |
Collapse
|
22
|
Loureiro LO, Engstrom MD, Lim BK. Comparative phylogeography of mainland and insular species of Neotropical molossid bats ( Molossus). Ecol Evol 2020; 10:389-409. [PMID: 31993120 PMCID: PMC6972955 DOI: 10.1002/ece3.5903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 01/01/2023] Open
Abstract
Historical events, habitat preferences, and geographic barriers might result in distinct genetic patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein, we use a genotype-by-sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes.
Collapse
Affiliation(s)
- Livia O. Loureiro
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Mark D. Engstrom
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Burton K. Lim
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
| |
Collapse
|
23
|
Chattopadhyay B, Garg KM, Ray R, Rheindt FE. Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity. Proc Biol Sci 2019; 286:20190304. [PMID: 31530139 PMCID: PMC6784725 DOI: 10.1098/rspb.2019.0304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/23/2019] [Indexed: 12/21/2022] Open
Abstract
Over the last approximately 2.6 Myr, Earth's climate has been dominated by cyclical ice ages that have profoundly affected species' population sizes, but the impact of impending anthropogenic climate change on species' extinction potential remains a worrying problem. We investigated 11 bat species from different taxonomic, ecological and geographical backgrounds using combined information from palaeoclimatic habitat reconstructions and genomes to analyse biotic impacts of historic climate change. We discover tightly correlated fluctuations between species' historic distribution and effective population size, identify frugivores as particularly susceptible to global warming, pinpoint large insectivores as having overall low effective population size and flag the onset of the Holocene (approx. 10-12 000 years ago) as the period with the generally lowest effective population sizes across the last approximately 1 Myr. Our study shows that combining genomic and palaeoclimatological approaches reveals effects of climatic shifts on genetic diversity and may help predict impacts of future climate change.
Collapse
Affiliation(s)
| | - Kritika M. Garg
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rajasri Ray
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, 560012 Karnataka, India
- Centre for Studies in Ethnobiology, Biodiversity and Sustainability (CEiBa), BG Road, Mokdumpur, Malda-732103 West Bengal, India
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
| |
Collapse
|
24
|
Sun L, Fu Y, Yang Y, Wang X, Cui W, Li D, Yuan X, Zhang Z, Fu Y, Li Y. Genomic Analyses Reveal Evidence of Independent Evolution, Demographic History, and Extreme Environment Adaptation of Tibetan Plateau Agaricus bisporus. Front Microbiol 2019; 10:1786. [PMID: 31456761 PMCID: PMC6700258 DOI: 10.3389/fmicb.2019.01786] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/18/2019] [Indexed: 12/30/2022] Open
Abstract
Agaricus bisporus distributed in the Tibetan Plateau of China has high-stress resistance that is valuable for breeding improvements. However, its evolutionary history, specialization, and adaptation to the extreme Tibetan Plateau environment are largely unknown. Here, we performed de novo genome sequencing of a representative Tibetan Plateau wild strain ABM and comparative genomic analysis with the reported European strain H97 and H39. The assembled ABM genome was 30.4 Mb in size, and comprised 8,562 protein-coding genes. The ABM genome shared highly conserved syntenic blocks and a few inversions with H97 and H39. The phylogenetic tree constructed by 1,276 single-copy orthologous genes in nine fungal species showed that the Tibetan Plateau and European A. bisporus diverged ∼5.5 million years ago. Population genomic analysis using genome resequencing of 29 strains revealed that the Tibetan Plateau population underwent significant differentiation from the European and American populations and evolved independently, and the global climate changes critically shaped the demographic history of the Tibetan Plateau population. Moreover, we identified key genes that are related to the cell wall and membrane system, and the development and defense systems regulated A. bisporus adapting to the harsh Tibetan Plateau environment. These findings highlight the value of genomic data in assessing the evolution and adaptation of mushrooms and will enhance future genetic improvements of A. bisporus.
Collapse
Affiliation(s)
- Lei Sun
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yuhua Fu
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Yang Yang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Xinxin Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Weijie Cui
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Dan Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Xiaohui Yuan
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, WA, United States
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| |
Collapse
|
25
|
Minias P, Dunn PO, Whittingham LA, Johnson JA, Oyler-McCance SJ. Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse. Sci Rep 2019; 9:6407. [PMID: 31015535 PMCID: PMC6478925 DOI: 10.1038/s41598-019-42885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/11/2019] [Indexed: 12/30/2022] Open
Abstract
The use of single nucleotide polymorphism (SNP) arrays to generate large SNP datasets for comparison purposes have recently become an attractive alternative to other genotyping methods. Although most SNP arrays were originally developed for domestic organisms, they can be effectively applied to wild relatives to obtain large panels of SNPs. In this study, we tested the cross-species application of the Affymetrix 600K Chicken SNP array in five species of North American prairie grouse (Centrocercus and Tympanuchus genera). Two individuals were genotyped per species for a total of ten samples. A high proportion (91%) of the total 580 961 SNPs were genotyped in at least one individual (73–76% SNPs genotyped per species). Principal component analysis with autosomal SNPs separated the two genera, but failed to clearly distinguish species within genera. Gene ontology analysis identified a set of genes related to morphogenesis and development (including genes involved in feather development), which may be primarily responsible for large phenotypic differences between Centrocercus and Tympanuchus grouse. Our study provided evidence for successful cross-species application of the chicken SNP array in grouse which diverged ca. 37 mya from the chicken lineage. As far as we are aware, this is the first reported application of a SNP array in non-passerine birds, and it demonstrates the feasibility of using commercial SNP arrays in research on non-model bird species.
Collapse
Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Peter O Dunn
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, Texas, USA
| | | |
Collapse
|
26
|
Kozma R, Rödin-Mörch P, Höglund J. Genomic regions of speciation and adaptation among three species of grouse. Sci Rep 2019; 9:812. [PMID: 30692562 PMCID: PMC6349846 DOI: 10.1038/s41598-018-36880-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 11/27/2018] [Indexed: 12/30/2022] Open
Abstract
Understanding the molecular basis of adaption is one of the central goals in evolutionary biology and when investigated across sister species it can provide detailed insight into the mechanisms of speciation. Here, we sequence the genomes of 34 individuals from three closely related grouse species in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show lineage specific signs of differential selection across the species. These genes are involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics reveal a strong signal of population expansion acting across the genomes. Additionally, we uncover a 3.5 Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating possible action of uniform selection in this region.
Collapse
Affiliation(s)
- Radoslav Kozma
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
| | - Patrik Rödin-Mörch
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden.
| |
Collapse
|
27
|
Kozma R, Lillie M, Benito BM, Svenning J, Höglund J. Past and potential future population dynamics of three grouse species using ecological and whole genome coalescent modeling. Ecol Evol 2018; 8:6671-6681. [PMID: 30038766 PMCID: PMC6053575 DOI: 10.1002/ece3.4163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 04/05/2018] [Accepted: 04/12/2018] [Indexed: 12/30/2022] Open
Abstract
Studying demographic history of species provides insight into how the past has shaped the current levels of overall biodiversity and genetic composition of species, but also how these species may react to future perturbations. Here we investigated the demographic history of the willow grouse (Lagopus lagopus), rock ptarmigan (Lagopus muta), and black grouse (Tetrao tetrix) through the Late Pleistocene using two complementary methods and whole genome data. Species distribution modeling (SDM) allowed us to estimate the total range size during the Last Interglacial (LIG) and Last Glacial Maximum (LGM) as well as to indicate potential population subdivisions. Pairwise Sequentially Markovian Coalescent (PSMC) allowed us to assess fluctuations in effective population size across the same period. Additionally, we used SDM to forecast the effect of future climate change on the three species over the next 50 years. We found that SDM predicts the largest range size for the cold-adapted willow grouse and rock ptarmigan during the LGM. PSMC captured intraspecific population dynamics within the last glacial period, such that the willow grouse and rock ptarmigan showed multiple bottlenecks signifying recolonization events following the termination of the LGM. We also see signals of population subdivision during the last glacial period in the black grouse, but more data are needed to strengthen this hypothesis. All three species are likely to experience range contractions under future warming, with the strongest effect on willow grouse and rock ptarmigan due to their limited potential for northward expansion. Overall, by combining these two modeling approaches, we have provided a multifaceted examination of the biogeography of these species and how they have responded to climate change in the past. These results help us understand how cold-adapted species may respond to future climate changes.
Collapse
Affiliation(s)
- Radoslav Kozma
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Mette Lillie
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
- Department of Biological and Environmental SciencesUniversity of GothenburgGöteborgSweden
| | - Blas M. Benito
- Department of BioscienceSection for Ecoinformatics and BiodiversityUniversity of AarhusAarhus CDenmark
| | - Jens‐Christian Svenning
- Department of BioscienceSection for Ecoinformatics and BiodiversityUniversity of AarhusAarhus CDenmark
| | - Jacob Höglund
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| |
Collapse
|
28
|
Bai WN, Yan PC, Zhang BW, Woeste KE, Lin K, Zhang DY. Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences. THE NEW PHYTOLOGIST 2018; 217:1726-1736. [PMID: 29178135 DOI: 10.1111/nph.14917] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/24/2017] [Indexed: 05/18/2023]
Abstract
Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable time periods. We applied the pairwise sequentially Markovian coalescent approach on the genomes of 11 temperate Juglans species to estimate trajectories of changes in effective population size (Ne ) and used a Bayesian-coalescent based approach that simultaneously considers multiple genomes (G-PhoCS) to estimate divergence times between lineages. Ne curves of all study species converged 1.0 million yr ago, probably reflecting the time when the walnut genus last shared a common ancestor. This estimate was confirmed by the G-PhoCS estimates of divergence times. But all species did not react similarly to the dramatic climatic oscillations following early Pleistocene cooling, so the timing and amplitude of changes in Ne differed among species and even among conspecific lineages. The population histories of temperate walnut species were not driven by extrinsic environmental changes alone, and a key role was probably played by species-specific factors such as coevolutionary interactions with specialized pathogens.
Collapse
Affiliation(s)
- Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Peng-Cheng Yan
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
- Beijing Key Laboratory of Cloud Computing Key Technology and Application, Beijing Computing Center, Beijing, 100094, China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Keith E Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
| | - Kui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| |
Collapse
|
29
|
First de novo whole genome sequencing and assembly of the pink-footed goose. Genomics 2018; 110:75-79. [DOI: 10.1016/j.ygeno.2017.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/24/2017] [Accepted: 08/26/2017] [Indexed: 11/17/2022]
|
30
|
Sveinsdóttir M, Magnússon KP. Complete mitochondrial genome and phylogenetic analysis of willow ptarmigan ( Lagopus lagopus) and rock ptarmigan ( Lagopus muta) (Galliformes: Phasianidae: Tetraoninae). Mitochondrial DNA B Resour 2017; 2:400-402. [PMID: 33473840 PMCID: PMC7800188 DOI: 10.1080/23802359.2017.1347834] [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] [Indexed: 11/12/2022] Open
Abstract
The complete mitochondrial genome sequences of the two sister species, Scandinavian willow ptarmigan Lagopus lagopus and Icelandic rock ptarmigan Lagopus muta, were characterized using next-generation sequencing. The mitogenome for willow ptarmigan was 16,677 bp long, with base composition of 30.3% A, 30.8% C, 13.3% G and 25.6% T, with a GC content of 44.1%, while for rock ptarmigan mitogenome was 16,687 bp long, with base composition of 30.2% A, 30.6% C, 13.4% G and 25.8% T, and a GC content of 44.0%. Like other Galliformes species, the mitogenomes comprised of 13 protein-coding genes, 22 tRNA, 2 rRNA and 2 non-coding regions; and control region (D-loop). All genes except ND6 and 8 tRNA were encoded on the + strand. All protein-coding genes started with ATG, except for COX1, where a GTG codon was present in both willow ptarmigan and rock ptarmigan. Phylogenetic analysis of the two novel mitogenomes with other Galliformes species demonstrates close relationship within the Tetraoninae subfamily.
Collapse
Affiliation(s)
- Máney Sveinsdóttir
- Faculty of Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
| | - Kristinn Pétur Magnússon
- Faculty of Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
- Collections and Systematics Department, Icelandic Institute of Natural History, Akureyri, Iceland
- Biomedical Center, University of Iceland, Reykjavik, Iceland
| |
Collapse
|
31
|
Pujolar JM, Dalén L, Hansen MM, Madsen J. Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age. Mol Ecol 2017; 26:6270-6283. [PMID: 28980346 DOI: 10.1111/mec.14374] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 02/06/2023]
Abstract
We investigated how population changes and fluctuations in the pink-footed goose might have been affected by climatic and anthropogenic factors. First, genomic data confirmed the existence of two separate populations: western (Iceland) and eastern (Svalbard/Denmark). Second, demographic inference suggests that the species survived the last glacial period as a single ancestral population with a low population size (100-1,000 individuals) that split into the current populations at the end of the last glacial maximum with Iceland being the most plausible glacial refuge. While population changes during the last glaciation were clearly environmental, we hypothesize that more recent demographic changes are human-related: (1) the inferred population increase in the Neolithic is due to deforestation to establish new lands for agriculture, increasing available habitat for pink-footed geese, (2) the decline inferred during the Middle Ages is due to human persecution, and (3) improved protection explains the increasing demographic trends during the 20th century. Our results suggest both environmental (during glacial cycles) and anthropogenic effects (more recent) can be a threat to species survival.
Collapse
Affiliation(s)
- J M Pujolar
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | - L Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - M M Hansen
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | - J Madsen
- Department of Bioscience-Kalø, Aarhus University, Rønde, Denmark
| |
Collapse
|
32
|
Kang J, Ma X, He S. Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq. Sci Rep 2017; 7:2813. [PMID: 28588195 PMCID: PMC5460224 DOI: 10.1038/s41598-017-02853-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Advances in genome scanning using high-throughput sequencing technologies has led to a revolution in studies of non-model organisms. The glyptosternoid fish Creteuchiloglanis macropterus, is widely distributed in the main stem and tributaries of the Nujiang River basin. Here, we analyzed IIB restriction-site-associated DNA (2b-RAD) sequences and mitochondrial DNA sequences, to assess the genomic signature of adaptation by detecting and estimating the degree of genetic differentiation among ten Creteuchiloglanis macropterus populations from the Nujiang River. The analyses revealed significant population differentiation among the up-tributaries, main stem, mid-tributary and low-tributary. Annotation of contigs containing outlier SNPs revealed that the candidate genes showed significant enrichment in several important biological process terms between up-tributaries and low-tributary, and exhibited prominent enrichment in the term macromolecular metabolic process between all tributaries and the main stem. Population dynamics analyses indicated that the Late Pleistocene glaciations strongly influenced the demographic history of C. macropterus. Our results provide strong evidence for the utility of RAD-seq in population genetics studies, and our generated SNP resource should provide a valuable tool for population genomics studies of C. macropterus in the future.
Collapse
Affiliation(s)
- Jingliang Kang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuhui Ma
- College of Animal Science, Guizhou University, Guizhou, 550025, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
| |
Collapse
|
33
|
Lagerholm VK, Sandoval-Castellanos E, Vaniscotte A, Potapova OR, Tomek T, Bochenski ZM, Shepherd P, Barton N, Van Dyck MC, Miller R, Höglund J, Yoccoz NG, Dalén L, Stewart JR. Range shifts or extinction? Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds. GLOBAL CHANGE BIOLOGY 2017; 23:1425-1435. [PMID: 27762483 DOI: 10.1111/gcb.13522] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/13/2016] [Indexed: 06/06/2023]
Abstract
Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long-term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back-casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum.
Collapse
Affiliation(s)
- Vendela K Lagerholm
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Edson Sandoval-Castellanos
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Amélie Vaniscotte
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Teresa Tomek
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Zbigniew M Bochenski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | | | - Nick Barton
- Institute of Archaeology, University of Oxford, Oxford, UK
| | - Marie-Claire Van Dyck
- Institute for the Analysis of Change in Contemporary and Historical Societies, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rebecca Miller
- Service of Prehistory, University of Liège, Liège, Belgium
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Nigel G Yoccoz
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - John R Stewart
- School of Applied Sciences, Bournemouth University, Dorset House, Talbot Campus, Poole, UK
| |
Collapse
|