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Harkness BAS, Ibarguchi G, Poland VF, Friesen VL. Historical fragmentation and stepping-stone gene flow led to population genetic differentiation in a coastal seabird. Ecol Evol 2024; 14:e11204. [PMID: 38633521 PMCID: PMC11021922 DOI: 10.1002/ece3.11204] [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: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Understanding the forces that shape population genetic structure is fundamental both for understanding evolutionary trajectories and for conservation. Many factors can influence the geographic distribution of genetic variation, and the extent to which local populations differ can be especially difficult to predict in highly mobile organisms. For example, many species of seabirds are essentially panmictic, but some show strong structure. Pigeon Guillemots (Cepphus columba; Charadriiformes: Alcidae) breed in small colonies scattered along the North Pacific coastline and feed in shallow nearshore waters year-round. Given their distribution, gene flow is potentially lower and population genetic structure is stronger than in most other high-latitude Northern Hemisphere seabirds. We screened variation in the mitochondrial control region, four microsatellite loci, and two nuclear introns in 202 Pigeon Guillemots representing three of five subspecies. Mitochondrial sequences and nuclear loci both showed significant population differences, although structure was weaker for the nuclear loci. Genetic differentiation was correlated with geographic distance between sampling locations for both the mitochondrial and nuclear loci. Mitochondrial gene trees and demographic modeling both provided strong evidence for two refugial populations during the Pleistocene glaciations: one in the Aleutian Islands and one farther east and south. We conclude that historical fragmentation combined with a stepping-stone model of gene flow led to the relatively strong population differentiation in Pigeon Guillemots compared to other high-latitude Northern Hemisphere seabird species. Our study adds to growing evidence that Pleistocene glaciation events affected population genetic structure not only in terrestrial species but also in coastal marine animals.
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Affiliation(s)
- Bronwyn A. S. Harkness
- Department of BiologyQueen's UniversityKingstonOntarioCanada
- Present address:
Environment and Climate Change Canada, National Wildlife Research CentreOttawaOntarioCanada
| | - Gabriela Ibarguchi
- Department of BiologyQueen's UniversityKingstonOntarioCanada
- Present address:
Red Deer PolytechnicRed DeerAlbertaCanada
| | - Veronica F. Poland
- Department of BiologyQueen's UniversityKingstonOntarioCanada
- Present address:
KambahAustralian Capital TerritoryAustralia
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Kersten O, Star B, Krabberød AK, Atmore LM, Tørresen OK, Anker-Nilssen T, Descamps S, Strøm H, Johansson US, Sweet PR, Jakobsen KS, Boessenkool S. Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. SCIENCE ADVANCES 2023; 9:eadh1407. [PMID: 37801495 PMCID: PMC10558128 DOI: 10.1126/sciadv.adh1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.
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Affiliation(s)
- Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders K. Krabberød
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Hallvard Strøm
- Norwegian Polar Institute, Fram Centre, Langnes, Tromsø, Norway
| | | | - Paul R. Sweet
- American Museum of Natural History, New York, NY, USA
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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3
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Conservation genomics reveals low connectivity among populations of threatened roseate terns (Sterna dougallii) in the Atlantic Basin. CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01505-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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Kuklin VV. Biogeographical Aspects of Helminths Parasitizing Barents Sea Birds: Spatial Distribution and Host Preferences. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022090175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Sakurayama S, Nojima D, Yoshizawa M, Takeuchi T, Ito M, Kitano T. Genetic diversity of two populations of the tufted puffin Fratercula cirrhata (Pallas, 1769). Genes Genet Syst 2021; 96:119-128. [PMID: 34135205 DOI: 10.1266/ggs.20-00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The tufted puffin Fratercula cirrhata (Charadriiformes: Alcidae) is distributed throughout the boreal and low Arctic areas of the North Pacific, from California, USA to Hokkaido, Japan. Few studies have investigated the genetic diversity of this species. Therefore, we analyzed the genetic diversity of two captive populations using nucleotide sequences of two mitochondrial loci (COX1 and D-loop) and one nuclear locus (RHBG). We sequenced these loci for birds from Tokyo Sea Life Park (Kasai Rinkai Suizokuen), originally from Alaska, and birds from Aqua World Oarai, originally from far eastern Russia. We found five COX1 haplotypes and 17 D-loop haplotypes for the mitochondrial loci, and obtained 14 predicted haplotypes for the nuclear RHBG locus. The major haplotypes of all three loci occurred in individuals from both populations. Thus, there were no clear genetic differences between the populations with respect to these three loci. Although the breeding range of the tufted puffin covers the boreal and low Arctic from California to Hokkaido, our results suggest that the species has not genetically diverged within its breeding range.
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Affiliation(s)
| | | | | | | | | | - Takashi Kitano
- Graduate School of Science and Engineering, Ibaraki University
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6
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Hipfner JM, Prill MM, Studholme KR, Domalik AD, Tucker S, Jardine C, Maftei M, Wright KG, Beck JN, Bradley RW, Carle RD, Good TP, Hatch SA, Hodum PJ, Ito M, Pearson SF, Rojek NA, Slater L, Watanuki Y, Will AP, Bindoff AD, Crossin GT, Drever MC, Burg TM. Geolocator tagging links distributions in the non-breeding season to population genetic structure in a sentinel North Pacific seabird. PLoS One 2020; 15:e0240056. [PMID: 33166314 PMCID: PMC7652296 DOI: 10.1371/journal.pone.0240056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
We tested the hypothesis that segregation in wintering areas is associated with population differentiation in a sentinel North Pacific seabird, the rhinoceros auklet (Cerorhinca monocerata). We collected tissue samples for genetic analyses on five breeding colonies in the western Pacific Ocean (Japan) and on 13 colonies in the eastern Pacific Ocean (California to Alaska), and deployed light-level geolocator tags on 12 eastern Pacific colonies to delineate wintering areas. Geolocator tags were deployed previously on one colony in Japan. There was strong genetic differentiation between populations in the eastern vs. western Pacific Ocean, likely due to two factors. First, glaciation over the North Pacific in the late Pleistocene might have forced a southward range shift that historically isolated the eastern and western populations. And second, deep-ocean habitat along the northern continental shelf appears to act as a barrier to movement; abundant on both sides of the North Pacific, the rhinoceros auklet is virtually absent as a breeder in the Aleutian Islands and Bering Sea, and no tagged birds crossed the North Pacific in the non-breeding season. While genetic differentiation was strongest between the eastern vs. western Pacific, there was also extensive differentiation within both regional groups. In pairwise comparisons among the eastern Pacific colonies, the standardized measure of genetic differentiation (FꞌST) was negatively correlated with the extent of spatial overlap in wintering areas. That result supports the hypothesis that segregation in the non-breeding season is linked to genetic structure. Philopatry and a neritic foraging habit probably also contribute to the structuring. Widely distributed, vulnerable to anthropogenic stressors, and exhibiting extensive genetic structure, the rhinoceros auklet is fully indicative of the scope of the conservation challenges posed by seabirds.
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Affiliation(s)
- J. Mark Hipfner
- Wildlife Research Division, Environment and Climate Change Canada, Delta, British Columbia, Canada
- * E-mail:
| | - Marie M. Prill
- Department of Biology, University of Lethbridge, Lethbridge, Alberta, Canada
| | | | - Alice D. Domalik
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Strahan Tucker
- Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | | | - Mark Maftei
- Wildlife Research Division, Environment and Climate Change Canada, Delta, British Columbia, Canada
| | - Kenneth G. Wright
- Wildlife Research Division, Environment and Climate Change Canada, Delta, British Columbia, Canada
| | - Jessie N. Beck
- Oikonos Ecosystems Knowledge, Santa Cruz, California, United States of America
| | - Russell W. Bradley
- Point Blue Conservation Science, Petaluma, California, United States of America
| | - Ryan D. Carle
- Oikonos Ecosystems Knowledge, Santa Cruz, California, United States of America
| | - Thomas P. Good
- Northwest Fisheries Science Centre, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Scott A. Hatch
- Institute for Seabird Research and Conservation, Anchorage, Alaska, United States of America
| | - Peter J. Hodum
- Department of Biology, University of Puget Sound, Tacoma, Washington, United States of America
| | - Motohiro Ito
- Department of Applied Biosciences, Toyo University, Bunkyō-ku, Japan
| | - Scott F. Pearson
- Washington Department of Fish and Wildlife, Olympia, Washington, United States of America
| | - Nora A. Rojek
- United States Fish and Wildlife Service, Homer, Alaska, United States of America
| | - Leslie Slater
- United States Fish and Wildlife Service, Homer, Alaska, United States of America
| | - Yutaka Watanuki
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Alexis P. Will
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Aidan D. Bindoff
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, Tasmania, Australia
| | - Glenn T. Crossin
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Mark C. Drever
- Wildlife Research Division, Environment and Climate Change Canada, Delta, British Columbia, Canada
| | - Theresa M. Burg
- Department of Biology, University of Lethbridge, Lethbridge, Alberta, Canada
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7
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Lombal AJ, O'dwyer JE, Friesen V, Woehler EJ, Burridge CP. Identifying mechanisms of genetic differentiation among populations in vagile species: historical factors dominate genetic differentiation in seabirds. Biol Rev Camb Philos Soc 2020; 95:625-651. [PMID: 32022401 DOI: 10.1111/brv.12580] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 12/23/2019] [Accepted: 01/08/2020] [Indexed: 01/01/2023]
Abstract
Elucidating the factors underlying the origin and maintenance of genetic variation among populations is crucial for our understanding of their ecology and evolution, and also to help identify conservation priorities. While intrinsic movement has been hypothesized as the major determinant of population genetic structuring in abundant vagile species, growing evidence indicates that vagility does not always predict genetic differentiation. However, identifying the determinants of genetic structuring can be challenging, and these are largely unknown for most vagile species. Although, in principle, levels of gene flow can be inferred from neutral allele frequency divergence among populations, underlying assumptions may be unrealistic. Moreover, molecular studies have suggested that contemporary gene flow has often not overridden historical influences on population genetic structure, which indicates potential inadequacies of any interpretations that fail to consider the influence of history in shaping that structure. This exhaustive review of the theoretical and empirical literature investigates the determinants of population genetic differentiation using seabirds as a model system for vagile taxa. Seabirds provide a tractable group within which to identify the determinants of genetic differentiation, given their widespread distribution in marine habitats and an abundance of ecological and genetic studies conducted on this group. Herein we evaluate mitochondrial DNA (mtDNA) variation in 73 seabird species. Lack of mutation-drift equilibrium observed in 19% of species coincided with lower estimates of genetic differentiation, suggesting that dynamic demographic histories can often lead to erroneous interpretations of contemporary gene flow, even in vagile species. Presence of land across the species sampling range, or sampling of breeding colonies representing ice-free Pleistocene refuge zones, appear to be associated with genetic differentiation in Tropical and Southern Temperate species, respectively, indicating that long-term barriers and persistence of populations are important for their genetic structuring. Conversely, biotic factors commonly considered to influence population genetic structure, such as spatial segregation during foraging, were inconsistently associated with population genetic differentiation. In light of these results, we recommend that genetic studies should consider potential historical events when identifying determinants of genetic differentiation among populations to avoid overestimating the role of contemporary factors, even for highly vagile taxa.
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Affiliation(s)
- Anicee J Lombal
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - James E O'dwyer
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Vicki Friesen
- Department of Biology, Queen's University, 99 University Avenue, Kingston, OL, K7L 3N6, Canada
| | - Eric J Woehler
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Hobart, TAS, 7004, Australia
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
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8
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Thomas JE, Carvalho GR, Haile J, Rawlence NJ, Martin MD, Ho SYW, Sigfússon AÞ, Jósefsson VA, Frederiksen M, Linnebjerg JF, Samaniego Castruita JA, Niemann J, Sinding MHS, Sandoval-Velasco M, Soares AER, Lacy R, Barilaro C, Best J, Brandis D, Cavallo C, Elorza M, Garrett KL, Groot M, Johansson F, Lifjeld JT, Nilson G, Serjeanston D, Sweet P, Fuller E, Hufthammer AK, Meldgaard M, Fjeldså J, Shapiro B, Hofreiter M, Stewart JR, Gilbert MTP, Knapp M. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. eLife 2019; 8:e47509. [PMID: 31767056 PMCID: PMC6879203 DOI: 10.7554/elife.47509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/22/2019] [Indexed: 01/23/2023] Open
Abstract
The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
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Affiliation(s)
- Jessica E Thomas
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
| | - James Haile
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Michael D Martin
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Simon YW Ho
- School of Life and Environmental SciencesUniversity of SydneySydneyAustralia
| | | | | | | | | | | | - Jonas Niemann
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Mikkel-Holger S Sinding
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Greenland Institute of Natural ResourcesNuukGreenland
| | | | - André ER Soares
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Robert Lacy
- Department of Conservation ScienceChicago Zoological SocietyBrookfieldUnited States
| | | | - Juila Best
- Department of Archaeology, Anthropology and Forensic Science, Faculty of Science and TechnologyBournemouth UniversityPooleUnited Kingdom
- School of History, Archaeology and ReligionCardiff UniversityCardiffUnited Kingdom
| | | | - Chiara Cavallo
- Amsterdam Centre for Ancient Studies and ArchaeologyUniversity of AmsterdamAmsterdamNetherlands
| | - Mikelo Elorza
- Arqueología PrehistóricaSociedad de Ciencias AranzadiSan SebastiánSpain
| | - Kimball L Garrett
- Natural History Museum of Los Angeles CountyLos AngelesUnited States
| | - Maaike Groot
- Institut für Prähistorische ArchäologieFreie Universität BerlinBerlinGermany
| | | | | | - Göran Nilson
- Gothenburg Museum of Natural HistoryGothenburgSweden
| | - Dale Serjeanston
- Humanities ArchaeologyUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Paul Sweet
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkUnited States
| | | | | | | | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural SciencesUniversity of PotsdamPotsdamGermany
| | - John R Stewart
- Faculty of Science and TechnologyBournemouth UniversityDorsetUnited Kingdom
| | - M Thomas P Gilbert
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Michael Knapp
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
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10
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Tigano A, Sackton TB, Friesen VL. Assembly and RNA-free annotation of highly heterozygous genomes: The case of the thick-billed murre (Uria lomvia). Mol Ecol Resour 2017; 18:79-90. [PMID: 28815912 DOI: 10.1111/1755-0998.12712] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 08/02/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
Abstract
Thanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick-billed murre (Uria lomvia), an arctic colonial seabird. In this study, we tested the performance of three genome assemblers, ray/sscape, soapdenovo2 and platanus, in assembling the highly heterozygous genome of the thick-billed murre. Our results show that platanus, an assembler specifically designed for heterozygous genomes, outperforms the other two approaches and produces a highly contiguous (N50 = 15.8 Mb) and complete genome assembly (93% presence of genes from the Benchmarking Universal Single Copy Ortholog [BUSCO] gene set). Additionally, we annotated the thick-billed murre genome using a homology-based approach that takes advantage of the genomic resources available for birds and other taxa. Our study will be useful for those researchers who are approaching assembly and annotation of highly heterozygous genomes, or genomes of species of conservation concern, and/or who have limited financial resources.
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Affiliation(s)
- Anna Tigano
- Department of Biology, Queen's University, Kingston, ON, Canada
| | | | - Vicki L Friesen
- Department of Biology, Queen's University, Kingston, ON, Canada
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11
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Tigano A, Shultz AJ, Edwards SV, Robertson GJ, Friesen VL. Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird. Ecol Evol 2017; 7:2370-2381. [PMID: 28405300 PMCID: PMC5383466 DOI: 10.1002/ece3.2819] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/11/2017] [Accepted: 01/29/2017] [Indexed: 12/29/2022] Open
Abstract
Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick‐billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick‐billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome‐wide markers mapped to a newly assembled thick‐billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non‐breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.
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Affiliation(s)
- Anna Tigano
- Department of Biology Queen's University Kingston ON Canada
| | - Allison J Shultz
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology Harvard University Cambridge MA USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology Harvard University Cambridge MA USA
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12
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Thanou E, Sponza S, Nelson EJ, Perry A, Wanless S, Daunt F, Cavers S. Genetic structure in the European endemic seabird, Phalacrocorax aristotelis, shaped by a complex interaction of historical and contemporary, physical and nonphysical drivers. Mol Ecol 2016; 26:2796-2811. [PMID: 28028864 DOI: 10.1111/mec.13996] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 11/30/2022]
Abstract
Geographically separated populations tend to be less connected by gene flow, as a result of physical or nonphysical barriers preventing dispersal, and this can lead to genetic structure. In this context, highly mobile organisms such as seabirds are interesting because the small effect of physical barriers means nonphysical ones may be relatively more important. Here, we use microsatellite and mitochondrial data to explore the genetic structure and phylogeography of Atlantic and Mediterranean populations of a European endemic seabird, the European shag, Phalacrocorax aristotelis, and identify the primary drivers of their diversification. Analyses of mitochondrial markers revealed three phylogenetic lineages grouping the North Atlantic, Spanish/Corsican and eastern Mediterranean populations, apparently arising from fragmentation during the Pleistocene followed by range expansion. These traces of historical fragmentation were also evident in the genetic structure estimated by microsatellite markers, despite significant contemporary gene flow among adjacent populations. Stronger genetic structure, probably promoted by landscape, philopatry and local adaptation, was found among distant populations and those separated by physical and ecological barriers. This study highlights the enduring effect of Pleistocene climatic changes on shag populations, especially within the Mediterranean Basin, and suggests a role for cryptic northern refugia, as well as known southern refugia, on the genetic structure of European seabirds. Finally, it outlines how contemporary ecological barriers and behavioural traits may maintain population divergence, despite long-distance dispersal triggered by extreme environmental conditions (e.g. population crashes).
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Affiliation(s)
- Evanthia Thanou
- Section of Animal Biology, Department of Biology, University of Patras, Patras, GR-26504, Greece.,Centre for Ecology & Hydrology, Penicuik, EH26 0QB, UK
| | - Stefano Sponza
- Department of Mathematics and Geosciences, University of Trieste, I-34127, Trieste, Italy
| | - Emily J Nelson
- Centre for Ecology & Hydrology, Penicuik, EH26 0QB, UK.,Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Annika Perry
- Centre for Ecology & Hydrology, Penicuik, EH26 0QB, UK
| | - Sarah Wanless
- Centre for Ecology & Hydrology, Penicuik, EH26 0QB, UK
| | - Francis Daunt
- Centre for Ecology & Hydrology, Penicuik, EH26 0QB, UK
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