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Cheek RG, McLaughlin JF, Gamboa MP, Marshall CA, Johnson BM, Silver DB, Mauro AA, Ghalambor CK. A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years. Evol Appl 2024; 17:e13637. [PMID: 38283609 PMCID: PMC10818135 DOI: 10.1111/eva.13637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/17/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950s, opossum shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Mysis were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity, test for genetic divergence between populations, and for evidence of adaptive evolution within the introduced populations in Colorado. We found very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that at least one undocumented introduction from an unknown source population hybridized with the population in Gross Reservoir. Despite the overall low genetic diversity we observed, F ST outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments. From an applied perspective, the observed patterns of divergence between populations suggest that genetic analysis can be a useful forensic tool to determine likely sources of invasive species.
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Affiliation(s)
- Rebecca G. Cheek
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Jessica F. McLaughlin
- Department of Environmental Science, Policy, and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Maybellene P. Gamboa
- Department of Organismal Biology and EcologyColorado CollegeColorado SpringsColoradoUSA
| | - Craig A. Marshall
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Council on Science and TechnologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Brett M. Johnson
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Douglas B. Silver
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Alexander A. Mauro
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of Biology, Centre for Biodiversity Dynamics (CBD)Norwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Cameron K. Ghalambor
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of Biology, Centre for Biodiversity Dynamics (CBD)Norwegian University of Science and Technology (NTNU)TrondheimNorway
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2
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Doniol-Valcroze P, Coiffard P, Alstrm P, Robb M, Dufour P, Crochet PA. Molecular and acoustic evidence support the species status of Anthus rubescens rubescens and Anthus [rubescens] japonicus (Passeriformes: Motacillidae). Zootaxa 2023; 5343:173-192. [PMID: 38221380 DOI: 10.11646/zootaxa.5343.2.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Indexed: 01/16/2024]
Abstract
The Buff-bellied Pipit Anthus rubescens comprises two allopatric subspecies groups: A. r. rubescens and A. r. alticola in North America and A. [r.] japonicus in north-east Asia. Despite their great morphological resemblance in breeding plumage, most individuals can be assigned to one or the other subspecies group in non-breeding plumage. Allopatric distributions, morphological differentiation and previously reported molecular divergence suggested the need for additional taxonomic study to assess the rank of these two populations. To resolve the taxonomy of the Buff-bellied Pipit species complex we analysed i) two mitochondrial DNA (mtDNA) loci and ii) nine bioacoustic parameters across 69 sound recordings (338 flight calls) recovered from public databases using principal component analysis and Euclidean distance measures. By comparing our mtDNA and call divergence measures with similar values measured between long-recognised species pairs of the genus, we show that the level of mitochondrial and acoustic divergence between the two Buff-bellied Pipit subspecies groups is typical of species-level divergence in the genus Anthus. Therefore, we recommend splitting the Buff-bellied Pipit species complex into two species: Anthus rubescens (American Pipit) and Anthus japonicus (Siberian Pipit). Our results also suggest that the Water Pipit A. spinoletta deserves taxonomic reassessment as its lineages are highly divergent in acoustics and mtDNA, while mtDNA relationships suggest paraphyly relative to the Rock Pipit A. petrosus. Our work highlights the crucial importance of integrative approaches in taxonomy and the usefulness of bioacoustics in studying cryptic diversity.
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Affiliation(s)
| | - Paul Coiffard
- LPO France; 1 rue Toufaire; 17300 Rochefort; France.
| | - Per Alstrm
- Animal Ecology; Department of Ecology and Genetics; Evolutionary Biology Centre; Uppsala University; Norbyvgen 18D; 752 36 Uppsala; Sweden; Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; China.
| | - Magnus Robb
- The Sound Approach; Carey House; Carey; Wareham; Dorset; BH20 7PG; United Kingdom.
| | - Paul Dufour
- CEFE; CNRS; Univ Montpellier; EPHE; IRD; Montpellier; France.
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3
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Winker K, Withrow JJ, Gibson DD, Pruett CL. Beringia as a high-latitude engine of avian speciation. Biol Rev Camb Philos Soc 2023; 98:1081-1099. [PMID: 36879465 DOI: 10.1111/brv.12945] [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: 04/23/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Beringia is a biogeographically dynamic region that extends from northeastern Asia into northwestern North America. This region has affected avian divergence and speciation in three important ways: (i) by serving as a route for intercontinental colonisation between Asia and the Americas; (ii) by cyclically splitting (and often reuniting) populations, subspecies, and species between these continents; and (iii) by providing isolated refugia through glacial cycles. The effects of these processes can be seen in taxonomic splits of shallow to increasing depths and in the presence of regional endemics. We review the taxa involved in the latter two processes (splitting-reuniting and isolation), with a focus on three research topics: avian diversity, time estimates of the generation of that diversity, and the regions within Beringia that might have been especially important. We find that these processes have generated substantial amounts of avian diversity, including 49 pairs of avian subspecies or species whose breeding distributions largely replace one another across the divide between the Old World and the New World in Beringia, and 103 avian species and subspecies endemic to this region. Among endemics, about one in three is recognised as a full biological species. Endemic taxa in the orders Charadriiformes (shorebirds, alcids, gulls, and terns) and Passeriformes (perching birds) are particularly well represented, although they show very different levels of diversity through evolutionary time. Endemic Beringian Charadriiformes have a 1.31:1 ratio of species to subspecies. In Passeriformes, endemic taxa have a 0.09:1 species-to-subspecies ratio, suggesting that passerine (and thus terrestrial) endemism might be more prone to long-term extinction in this region, although such 'losses' could occur through their being reconnected with wider continental populations during favourable climatic cycles (e.g. subspecies reintegration with other populations). Genetic evidence suggests that most Beringian avian taxa originated over the past 3 million years, confirming the importance of Quaternary processes. There seems to be no obvious clustering in their formation through time, although there might be temporal gaps with lower rates of diversity generation. For at least 62 species, taxonomically undifferentiated populations occupy this region, providing ample potential for future evolutionary diversification.
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Affiliation(s)
- Kevin Winker
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Jack J Withrow
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Daniel D Gibson
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Christin L Pruett
- Department of Biology, Ouachita Baptist University, 410 Ouachita St, Arkadelphia, AR, 71998, USA
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4
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Spaulding F, McLaughlin JF, Cheek RG, McCracken KG, Glenn TC, Winker K. Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex. Mol Phylogenet Evol 2023; 182:107733. [PMID: 36801373 PMCID: PMC10092703 DOI: 10.1016/j.ympev.2023.107733] [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: 08/19/2021] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023]
Abstract
The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca, A. c. nimia, and A. c. carolinensis) with a close relative, the yellow-billed teal (Anas flavirostris) from South America. A. c. crecca and A. c. carolinensis are seasonal migrants, while the other taxa are sedentary. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca, A. c. nimia, and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. This relationship can be summarized as (crecca, nimia, carolinensis)(flavirostris). However, whole mitogenomes revealed a different phylogeny: (crecca, nimia)(carolinensis, flavirostris). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts (crecca-nimia, crecca-carolinensis, and carolinensis-flavirostris). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (M ∼0.1-0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric (crecca-nimia), parapatric (crecca-carolinensis), and (mostly) allopatric (carolinensis-flavirostris). Our study shows that ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems with historically uncertain relationships and species limits.
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Affiliation(s)
- Fern Spaulding
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, USA; Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, USA.
| | - Jessica F McLaughlin
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Rebecca G Cheek
- Graduate Degree Program in Ecology, Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Kevin G McCracken
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, USA; Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, USA
| | - Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, USA; Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, USA
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5
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Wiens BJ, Combe FJ, Dickerson B, Divine LM, Padula VM, Sage GK, Talbot SL, Hope AG. Genetic drift drives rapid speciation of an Arctic insular endemic shrew (Sorex pribilofensis). Mol Ecol 2022; 31:5231-5248. [PMID: 35972323 DOI: 10.1111/mec.16658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 12/15/2022]
Abstract
Episodes of Quaternary environmental change shaped the genomes of extant species, influencing their response to contemporary environments, which are changing rapidly. Island endemics are among the most vulnerable to such change, accounting for a disproportionate number of recent extinctions. To prevent extinctions and conserve island biodiversity it is vital to combine knowledge of species' ecologies with their complex evolutionary histories. The Bering Sea has a history of cyclical island isolation and reconnection, coupled with modern rates of climate change that exceed global averages. The endangered Pribilof Island shrew (Sorex pribilofensis) is endemic to St. Paul Island, Alaska, which was isolated from mainland Beringia ~14,000 years ago by rising sea levels. Using ~11,000 single nucleotide polymorphisms, 17 microsatellites and mitochondrial sequence data, we test predictions about the evolutionary processes driving shrew speciation across Beringia. Our data show considerable differentiation of S. pribilofensis from mainland sibling species, relative to levels of divergence between mainland shrews. We also find a genome-wide loss of diversity and extremely low Ne for S. pribilofensis. We then show that intraspecific genetic diversity is significantly related to interspecific divergence, and that differentiation between S. pribilofensis and other Beringian shrews is highest across loci that are fixed in S. pribilofensis, indicating that strong drift has driven differentiation of this island species. Our findings show that drift as a consequence of Arctic climate cycling can rapidly reshape insular biodiversity. Arctic island species that lack genomic diversity and have evolved in response to past climate may have limited ability to respond to modern environmental changes.
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Affiliation(s)
- Ben J Wiens
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Fraser J Combe
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Lauren M Divine
- Aleut Community of St. Paul Island, Ecosystem Conservation Office, St. Paul, Alaska, USA
| | - Veronica M Padula
- Aleut Community of St. Paul Island, Ecosystem Conservation Office, St. Paul, Alaska, USA
| | - George K Sage
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Sandra L Talbot
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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6
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Spaulding F, McLaughlin JF, Glenn TC, Winker K. Estimating Movement Rates Between Eurasian and North American Birds That Are Vectors of Avian Influenza. Avian Dis 2022; 66:155-164. [PMID: 35510470 DOI: 10.1637/aviandiseases-d-21-00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/09/2021] [Indexed: 11/05/2022]
Abstract
Avian influenza (AI) is a zoonotic disease that will likely be involved in future pandemics. Because waterbird movements are difficult to quantify, determining the host-specific risk of Eurasian-origin AI movements into North America is challenging. We estimated relative rates of movements, based on long-term evolutionary averages of gene flow, between Eurasian and North American waterbird populations to obtain bidirectional baseline rates of the intercontinental movements of these AI hosts. We used population genomics and coalescent-based demographic models to obtain these gene-flow-based movement estimates. Inferred rates of movement between these continental populations varies greatly among species. Within dabbling ducks, gene flow, relative to effective population size, varies from ∼3 to 24 individuals/generation between Eurasian and American wigeons (Mareca penelope and Mareca americana) to ∼100-300 individuals/generation between continental populations of northern pintails (Anas acuta). These are evolutionary long-term averages and provide a solid foundation for understanding the relative risks of each of these host species in potential intercontinental AI movements. We scale these values to census size for evaluation in that context. In addition to being AI hosts, many of these bird species are also important in the subsistence diets of Alaskans, increasing the risk of direct bird-to-human exposure to Eurasian-origin AI virus. We contrast species-specific rates of intercontinental movements with the importance of each species in Alaskan diets to understand the relative risk of these taxa to humans. Assuming roughly equivalent AI infection rates among ducks, greater scaup (Aythya marila), mallard (Anas platyrhynchos), and northern pintail (Anas acuta) were the top three species presenting the highest risks for intercontinental AI movement both within the natural system and through exposure to subsistence hunters. Improved data on AI infection rates in this region could further refine these relative risk assessments. These directly comparable, species-based intercontinental movement rates and relative risk rankings should help in modeling, monitoring, and mitigating the impacts of intercontinental host and AI movements.
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Affiliation(s)
- Fern Spaulding
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK 99775, .,Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775
| | - Jessica F McLaughlin
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA 94720
| | - Travis C Glenn
- Department of Environmental Health Science and Institute of Bioinformatics, University of Georgia, Athens, GA 30602
| | - Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK 99775.,Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775
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7
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Conklin JR, Verkuil YI, Battley PF, Hassell CJ, Ten Horn J, Johnson JA, Tomkovich PS, Baker AJ, Piersma T, Fontaine MC. Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium. Mol Ecol 2022; 31:2124-2139. [PMID: 35106871 PMCID: PMC9545425 DOI: 10.1111/mec.16379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/13/2021] [Accepted: 01/14/2022] [Indexed: 11/30/2022]
Abstract
Present‐day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, Calidris canutus, is an arctic‐breeding, long‐distance migratory shorebird with six recognized subspecies defined by differences in morphology, migration behavior, and annual cycle phenology, in a global distribution thought to have arisen just since the last glacial maximum (LGM). We used nextRAD sequencing of 10,881 single‐nucleotide polymorphisms (SNPs) to assess the neutral genetic structure and phylogeographic history of 172 red knots representing all known global breeding populations. Using population genetics approaches, including model‐based scenario‐testing in an approximate Bayesian computation (ABC) framework, we infer that red knots derive from two main lineages that diverged ca. 34,000 years ago, and thus most probably persisted at the LGM in both Palearctic and Nearctic refugia, followed by at least two instances of secondary contact and admixture. Within two Beringian subspecies (C. c. roselaari and rogersi), we detected previously unknown genetic structure among sub‐populations sharing a migratory flyway, reflecting additional complexity in the phylogeographic history of the region. Conversely, we found very weak genetic differentiation between two Nearctic populations (rufa and islandica) with clearly divergent migratory phenotypes and little or no apparent contact throughout the annual cycle. Together, these results suggest that relative gene flow among migratory populations reflects a complex interplay of historical, geographical, and ecological factors.
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Affiliation(s)
- Jesse R Conklin
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Yvonne I Verkuil
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Phil F Battley
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Palmerston North, 4442, New Zealand
| | - Chris J Hassell
- Global Flyway Network, PO Box 3089, Broome, WA, 6725, Australia
| | - Job Ten Horn
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - James A Johnson
- U.S. Fish & Wildlife Service, Migratory Bird Management, 1011 E. Tudor Road, MS 201, Anchorage, Alaska, 99503, USA
| | - Pavel S Tomkovich
- Zoological Museum, Moscow MV Lomonosov State University, Bolshaya Nikitskaya Str. 6, Moscow, 125009, Russia
| | - Allan J Baker
- Department of Natural History, Royal Ontario Museum, 100 Queens Park, Toronto, ON, M5S 2C6, Canada
| | - Theunis Piersma
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.,Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Michaël C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.,MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France.,Montpellier Ecology and Evolution of Diseases Network (MEEDiN), Montpellier, France
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8
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Feng P, Zeng T, Yang H, Chen G, Du J, Chen L, Shen J, Tao Z, Wang P, Yang L, Lu L. Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China. BMC Genomics 2021; 22:401. [PMID: 34058976 PMCID: PMC8165772 DOI: 10.1186/s12864-021-07710-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 05/12/2021] [Indexed: 01/03/2023] Open
Abstract
Background Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures. Results Here, we report the resequencing of 60 ducks from Chinese spot-billed ducks (Anas zonorhyncha), mallards (Anas platyrhnchos), Fenghua ducks, Shaoxing ducks, Shanma ducks and Cherry Valley Pekin ducks of eastern China (ten from each population) at an average effective sequencing depth of ~ 6× per individual. The results of population and demographic analysis revealed a deep phylogenetic split between wild (Chinese spot-billed ducks and mallards) and domestic ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks. Conclusion Genetic structure analysis showed a close genetic relationship of Chinese spot-billed ducks and mallards, which supported that Chinese spot-billed ducks contributed to the breeding of domestic ducks. During the long history of artificial selection, domestic ducks have developed a complex biological adaptation to captivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07710-2.
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Affiliation(s)
- Peishi Feng
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China.,Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tao Zeng
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Yang
- Institute of Quality and Standards for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Science, Wuhan, China
| | - Li Chen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junda Shen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenrong Tao
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ping Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China.
| | - Lin Yang
- College of Animal Science, South China Agricultural University, Guangzhou, China.
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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9
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Leighton GM, Lu LJ, Holop E, Dobler J, Ligon RA. Sociality and migration predict hybridization across birds. Proc Biol Sci 2021; 288:20201946. [PMID: 33726589 DOI: 10.1098/rspb.2020.1946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hybridization represents a natural experiment that can provide insight into processes of speciation and diversification. Though considerable research has focused on hybrid zone dynamics, macroevolutionary investigations of the factors that influence hybridization are few. Here, we compile a database of avian hybrids and perform comparative analyses to determine whether several social and life-history variables influence broad patterns of hybridization. We perform three main analyses: phylogenetic logistic regression to examine variables that are associated with the presence of hybridization, phylogenetic Poisson regression of only those species exhibiting hybridization to determine which variables are associated with the extent of hybridization, and a phylogenetic logistic regression on a subset of data to assess potential pseudoreplication. After testing several social and life-history variables, we found that social bond duration is associated with the presence and extent of hybridization. Specifically, lengthy social bonds are negatively associated with the presence and extent of hybridization. In addition to social bond length, migration is positively linked with a greater likelihood of hybridization. The broad-scale correlations between species-specific traits and hybridization across diverse avian lineages suggest commonalities in the fine-scale processes involved in mating with heterospecifics, which in turn has implications for how we think about, study and understand hybridization processes and their influence on evolutionary trajectories.
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Affiliation(s)
- Gavin M Leighton
- Department of Biology, SUNY Buffalo State College, Buffalo, NY 14213, USA.,Department of Neurobiology & Behavior, Cornell Lab of Ornithology, Cornell University, 215 Tower Road, Ithaca, NY 14850, USA
| | - Lucy Jingyi Lu
- Department of Neurobiology & Behavior, Cornell Lab of Ornithology, Cornell University, 215 Tower Road, Ithaca, NY 14850, USA
| | - Eliot Holop
- Department of Neurobiology & Behavior, Cornell Lab of Ornithology, Cornell University, 215 Tower Road, Ithaca, NY 14850, USA
| | - Jessica Dobler
- Department of Neurobiology & Behavior, Cornell Lab of Ornithology, Cornell University, 215 Tower Road, Ithaca, NY 14850, USA
| | - Russell A Ligon
- Department of Neurobiology & Behavior, Cornell Lab of Ornithology, Cornell University, 215 Tower Road, Ithaca, NY 14850, USA
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10
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McLaughlin JF, Winker K. An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data. PeerJ 2020; 8:e9939. [PMID: 32995092 PMCID: PMC7501783 DOI: 10.7717/peerj.9939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022] Open
Abstract
Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. We used datasets from eight diverging bird lineages to make pairwise comparisons at different levels of taxonomic divergence (populations, subspecies, and species). Our data are from loci linked to ultraconserved elements and our analyses used one single nucleotide polymorphism per locus. All individuals were genotyped at all loci, effectively doubling sample size for coalescent analyses. We estimated population demographic parameters (effective population size, migration rate, and time since divergence) in a coalescent framework using Diffusion Approximation for Demographic Inference, an allele frequency spectrum method. Using divergence-with-gene-flow models optimized with full datasets, we subsampled at sequentially smaller sample sizes from full datasets of 6-8 diploid individuals per population (with both alleles called) down to 1:1, and then we compared estimates and their changes in accuracy. Accuracy was strongly affected by sample size, with considerable differences among estimated parameters and among lineages. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than three diploid individuals per population, or 6:6 haplotypes in coalescent terms). Migration (m) was fairly consistently estimated until <2 individuals per population, and no consistent trend of over-or underestimation was found in either time since divergence (T) or theta (Θ = 4N refμ). Lineages that were taxonomically recognized above the population level (subspecies and species pairs; that is, deeper divergences) tended to have lower variation in scaled root mean square error of parameter estimation at smaller sample sizes than population-level divergences, and many parameters were estimated accurately down to three diploid individuals per population. Shallower divergence levels (i.e., populations) often required at least five individuals per population for reliable demographic inferences using this approach. Although divergence levels might be unknown at the outset of study design, our results provide a framework for planning appropriate sampling and for interpreting results if smaller sample sizes must be used.
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Affiliation(s)
- Jessica F McLaughlin
- University of Alaska Museum & Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, USA.,Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Kevin Winker
- University of Alaska Museum & Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, USA
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