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Mello AC, Leao D, Dias L, Colombelli F, Recamonde-Mendoza M, Turchetto-Zolet AC, Matte U. Broken silence: 22,841 predicted deleterious synonymous variants identified in the human exome through computational analysis. Genet Mol Biol 2024; 46:e20230125. [PMID: 38259032 PMCID: PMC10804382 DOI: 10.1590/1678-4685-gmb-2023-0125] [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: 05/03/2023] [Accepted: 12/10/2023] [Indexed: 01/24/2024] Open
Abstract
Synonymous single nucleotide variants (sSNVs) do not alter the primary structure of a protein, thus it was previously accepted that they were neutral. Recently, several studies demonstrated their significance to a range of diseases. Still, variant prioritization strategies lack focus on sSNVs. Here, we identified 22,841 deleterious synonymous variants in 125,748 human exomes using two in silico predictors (SilVA and CADD). While 98.2% of synonymous variants are classified as neutral, 1.8% are predicted to be deleterious, yielding an average of 9.82 neutral and 0.18 deleterious sSNVs per exome. Further investigation of prediction features via Heterogeneous Ensemble Feature Selection revealed that impact on amino acid sequence and conservation carry the most weight for a deleterious prediction. Thirty nine detrimental sSNVs are not rare and are located on disease associated genes. Ten distinct putatively non-deleterious sSNVs are likely to be under positive selection in the North-Western European and East Asian populations. Taken together our analysis gives voice to the so-called silent mutations as we propose a robust framework for evaluating the deleteriousness of sSNVs in variant prioritization studies.
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Affiliation(s)
- Ana Carolina Mello
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa
Experimental, Laboratório de Células, Tecidos e Genes, Porto Alegre, RS,
Brazil
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Delva Leao
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Ciências Biológicas: Bioquímica, Porto Alegre, RS, Brazil
| | - Luis Dias
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa
Experimental, Laboratório de Células, Tecidos e Genes, Porto Alegre, RS,
Brazil
| | - Felipe Colombelli
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de
Informática, Porto Alegre, RS, Brazil
| | - Mariana Recamonde-Mendoza
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de
Informática, Porto Alegre, RS, Brazil
| | - Andreia Carina Turchetto-Zolet
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de
Genética, Porto Alegre, RS, Brazil
| | - Ursula Matte
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa
Experimental, Laboratório de Células, Tecidos e Genes, Porto Alegre, RS,
Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de
Genética, Porto Alegre, RS, Brazil
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2
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Farleigh K, Ascanio A, Farleigh ME, Schield DR, Card DC, Leal M, Castoe TA, Jezkova T, Rodríguez-Robles JA. Signals of differential introgression in the genome of natural hybrids of Caribbean anoles. Mol Ecol 2023; 32:6000-6017. [PMID: 37861454 DOI: 10.1111/mec.17170] [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: 12/28/2021] [Revised: 08/30/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023]
Abstract
Hybridization facilitates recombination between divergent genetic lineages and can be shaped by both neutral and selective processes. Upon hybridization, loci with no net fitness effects introgress randomly from parental species into the genomes of hybrid individuals. Conversely, alleles from one parental species at some loci may provide a selective advantage to hybrids, resulting in patterns of introgression that do not conform to random expectations. We investigated genomic patterns of differential introgression in natural hybrids of two species of Caribbean anoles, Anolis pulchellus and A. krugi in Puerto Rico. Hybrids exhibit A. pulchellus phenotypes but possess A. krugi mitochondrial DNA, originated from multiple, independent hybridization events, and appear to have replaced pure A. pulchellus across a large area in western Puerto Rico. Combining genome-wide SNP datasets with bioinformatic methods to identify signals of differential introgression in hybrids, we demonstrate that the genomes of hybrids are dominated by pulchellus-derived alleles and show only 10%-20% A. krugi ancestry. The majority of A. krugi loci in hybrids exhibit a signal of non-random differential introgression and include loci linked to genes involved in development and immune function. Three of these genes (delta like canonical notch ligand 1, jagged1 and notch receptor 1) affect cell differentiation and growth and interact with mitochondrial function. Our results suggest that differential non-random introgression for a subset of loci may be driven by selection favouring the inheritance of compatible mitochondrial and nuclear-encoded genes in hybrids.
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Affiliation(s)
- Keaka Farleigh
- Department of Biology, Miami University, Oxford, Ohio, USA
| | | | | | - Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Manuel Leal
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Todd A Castoe
- Department of Biology, University of Texas, Arlington, Arlington, Texas, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, Oxford, Ohio, USA
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3
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Jansson E, Faust E, Bekkevold D, Quintela M, Durif C, Halvorsen KT, Dahle G, Pampoulie C, Kennedy J, Whittaker B, Unneland L, Post S, André C, Glover KA. Global, regional, and cryptic population structure in a high gene-flow transatlantic fish. PLoS One 2023; 18:e0283351. [PMID: 36940210 PMCID: PMC10027230 DOI: 10.1371/journal.pone.0283351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/07/2023] [Indexed: 03/21/2023] Open
Abstract
Lumpfish (Cyclopterus lumpus) is a transatlantic marine fish displaying large population sizes and a high potential for dispersal and gene-flow. These features are expected to result in weak population structure. Here, we investigated population genetic structure of lumpfish throughout its natural distribution in the North Atlantic using two approaches: I) 4,393 genome wide SNPs and 95 individuals from 10 locations, and II) 139 discriminatory SNPs and 1,669 individuals from 40 locations. Both approaches identified extensive population genetic structuring with a major split between the East and West Atlantic and a distinct Baltic Sea population, as well as further differentiation of lumpfish from the English Channel, Iceland, and Greenland. The discriminatory loci displayed ~2-5 times higher divergence than the genome wide approach, revealing further evidence of local population substructures. Lumpfish from Isfjorden in Svalbard were highly distinct but resembled most fish from Greenland. The Kattegat area in the Baltic transition zone, formed a previously undescribed distinct genetic group. Also, further subdivision was detected within North America, Iceland, West Greenland, Barents Sea, and Norway. Although lumpfish have considerable potential for dispersal and gene-flow, the observed high levels of population structuring throughout the Atlantic suggests that this species may have a natal homing behavior and local populations with adaptive differences. This fine-scale population structure calls for consideration when defining management units for exploitation of lumpfish stocks and in decisions related to sourcing and moving lumpfish for cleaner fish use in salmonid aquaculture.
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Affiliation(s)
- Eeva Jansson
- Institute of Marine Research, Nordnes, Bergen, Norway
| | - Ellika Faust
- Department of Marine Sciences - Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Dorte Bekkevold
- DTU-Aqua National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Caroline Durif
- Institute of Marine Research, Austevoll Research Station, Storebø, Norway
| | | | - Geir Dahle
- Institute of Marine Research, Nordnes, Bergen, Norway
| | | | - James Kennedy
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | - Benjamin Whittaker
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, United Kingdom
| | | | - Søren Post
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Carl André
- Department of Marine Sciences - Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
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4
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Hernandez-Castro LE, Villacís AG, Jacobs A, Cheaib B, Day CC, Ocaña-Mayorga S, Yumiseva CA, Bacigalupo A, Andersson B, Matthews L, Landguth EL, Costales JA, Llewellyn MS, Grijalva MJ. Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting. PLoS Genet 2022; 18:e1010019. [PMID: 35120121 PMCID: PMC8849464 DOI: 10.1371/journal.pgen.1010019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 02/16/2022] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
Accurate prediction of vectors dispersal, as well as identification of adaptations that allow blood-feeding vectors to thrive in built environments, are a basis for effective disease control. Here we adopted a landscape genomics approach to assay gene flow, possible local adaptation, and drivers of population structure in Rhodnius ecuadoriensis, an important vector of Chagas disease. We used a reduced-representation sequencing technique (2b-RADseq) to obtain 2,552 SNP markers across 272 R. ecuadoriensis samples from 25 collection sites in southern Ecuador. Evidence of high and directional gene flow between seven wild and domestic population pairs across our study site indicates insecticide-based control will be hindered by repeated re-infestation of houses from the forest. Preliminary genome scans across multiple population pairs revealed shared outlier loci potentially consistent with local adaptation to the domestic setting, which we mapped to genes involved with embryogenesis and saliva production. Landscape genomic models showed elevation is a key barrier to R. ecuadoriensis dispersal. Together our results shed early light on the genomic adaptation in triatomine vectors and facilitate vector control by predicting that spatially-targeted, proactive interventions would be more efficacious than current, reactive approaches. Re-infestation of recently insecticide-treated houses by wild/secondary triatomine, their potential adaptation to this new environment and capabilities to geographically disperse across multiple human communities jeopardise sustainable Chagas disease control. This is the first study in Chagas disease vectors that identifies genomic regions possibly linked to adaptations to the built environment and describes landscape drivers for accurate prediction of geographic dispersal. We sampled multiple domestic and wild Rhodnius ecuadoriensis population pairs across a mountainous terrain in southern Ecuador. We evidenced that triatomine movement from forest to built enviroments does occur at a high rate. In these highly connected population pairs we detected loci possibly linked to local adaptation among the genomic makers we evaluated and in doing so we pave the way for future triatomine genomic research. We highlighted that current haphazardous vector control in the zone will be hindered by reinfestation of triatomines from the forest. Instead, we recommend frequent and spatially-targeted vector control and provided a landacape genomic model that identifies highly connected and isolated triatomine populations to facilitate efficient vector control.
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Affiliation(s)
- Luis E. Hernandez-Castro
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- The Epidemiology, Economics and Risk Assessment Group, The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Midlothian, United Kingdom
- * E-mail: (LEH-C); (MSL)
| | - Anita G. Villacís
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, United States of America
| | - Bachar Cheaib
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Casey C. Day
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, United States of America
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Cesar A. Yumiseva
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Antonella Bacigalupo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Louise Matthews
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Erin L. Landguth
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, United States of America
- Center for Population Health Research, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, United States of America
| | - Jaime A. Costales
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Martin S. Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (LEH-C); (MSL)
| | - Mario J. Grijalva
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Infectious and Tropical Disease Institute, Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, United States of America
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5
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Llanos‐Garrido A, Pérez‐Tris J, Díaz JA. Low genome-wide divergence between two lizard populations with high adaptive phenotypic differentiation. Ecol Evol 2021; 11:18055-18065. [PMID: 35003657 PMCID: PMC8717303 DOI: 10.1002/ece3.8403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/14/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Usually, adaptive phenotypic differentiation is paralleled by genetic divergence between locally adapted populations. However, adaptation can also happen in a scenario of nonsignificant genetic divergence due to intense gene flow and/or recent differentiation. While this phenomenon is rarely published, findings on incipient ecologically driven divergence or isolation by adaptation are relatively common, which could confound our understanding about the frequency at which they actually occur in nature. Here, we explore genome-wide traces of divergence between two populations of the lacertid lizard Psammodromus algirus separated by a 600 m elevational gradient. These populations seem to be differentially adapted to their environments despite showing low levels of genetic differentiation (according to previously studies of mtDNA and microsatellite data). We performed a search for outliers (i.e., loci subject to selection) trying to identify specific loci with FST statistics significantly higher than those expected on the basis of overall, genome-wide estimates of genetic divergence. We find that local phenotypic adaptation (in terms of a wide diversity of characters) was not accompanied by genome-wide differentiation, even when we maximized the chances of unveiling such differentiation at particular loci with FST-based outlier detection tests. Instead, our analyses confirmed the lack of genome-wide differentiation on the basis of more than 70,000 SNPs, which is concordant with a scenario of local adaptation without isolation by environment. Our results add evidence to previous studies in which local adaptation does not lead to any kind of isolation (or early stages of ecological speciation), but maintains phenotypic divergence despite the lack of a differentiated genomic background.
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Affiliation(s)
- Alejandro Llanos‐Garrido
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
- Department of Biodiversity, Ecology and EvolutionUCMMadridSpain
| | | | - José A. Díaz
- Department of Biodiversity, Ecology and EvolutionUCMMadridSpain
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6
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Complex population structure of the Atlantic puffin revealed by whole genome analyses. Commun Biol 2021; 4:922. [PMID: 34326442 PMCID: PMC8322098 DOI: 10.1038/s42003-021-02415-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
The factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.
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7
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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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8
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Mussmann SM, Douglas MR, Oakey DD, Douglas ME. Defining relictual biodiversity: Conservation units in speckled dace (Leuciscidae: Rhinichthys osculus) of the Greater Death Valley ecosystem. Ecol Evol 2020; 10:10798-10817. [PMID: 33072297 PMCID: PMC7548178 DOI: 10.1002/ece3.6736] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/19/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species-population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates this approach in speckled dace (Leuciscidae: Rhinichthys osculus) endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem. These fish persist in the Mojave Desert as isolated Plio-Pleistocene relicts and are of conservation concern, but lack formal taxonomic descriptions/designations. Double digest RAD (ddRAD) methods identified 14,355 SNP loci across 10 populations (N = 140). Species delimitation analyses [multispecies coalescent (MSC) and unsupervised machine learning (UML)] delineated four putative ESUs. F ST outlier loci (N = 106) were juxtaposed to uncover the potential for localized adaptations. We detected one hybrid population that resulted from upstream reconnection of habitat following contemporary pluvial periods, whereas remaining populations represent relics of ancient tectonism within geographically isolated springs and groundwater-fed streams. Our study offers three salient conclusions: a blueprint for a multifaceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically endangered Death Valley ecosystem fishes.
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Affiliation(s)
- Steven M. Mussmann
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - David D. Oakey
- School of Life SciencesArizona State UniversityTempeAZUSA
- Present address:
Arizona State Veteran HomePhoenixAZUSA
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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9
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Vu NTT, Zenger KR, Guppy JL, Sellars MJ, Silva CNS, Kjeldsen SR, Jerry DR. Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis. BMC Genomics 2020; 21:669. [PMID: 32993495 PMCID: PMC7526253 DOI: 10.1186/s12864-020-07084-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 09/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Restrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely distributed throughout the Indian and Pacific Oceans including along the western, northern and eastern coastline of Australia, where it is an important aquaculture and fishery species. Understanding the genetic structure and the influence of environmental factors leading to adaptive differences among populations of this species is important for farm genetic improvement programs and sustainable fisheries management. RESULTS Based on 278 individuals obtained from seven geographically disparate Australian locations, 10,624 high-quality SNP loci were used to characterize genetic diversity, population structure, genetic connectivity, and adaptive divergence. Significant population structure and differentiation were revealed among wild populations (average FST = 0.001-0.107; p < 0.05). Eighty-nine putatively outlier SNPs were identified to be potentially associated with environmental variables by using both population differentiation (BayeScan and PCAdapt) and environmental association (redundancy analysis and latent factor mixed model) analysis methods. Clear population structure with similar spatial patterns were observed in both neutral and outlier markers with three genetically distinct groups identified (north Queensland, Northern Territory, and Western Australia). Redundancy, partial redundancy, and multiple regression on distance matrices analyses revealed that both geographical distance and environmental factors interact to generate the structure observed across Australian P. monodon populations. CONCLUSION This study provides new insights on genetic population structure of Australian P. monodon in the face of environmental changes, which can be used to advance sustainable fisheries management and aquaculture breeding programs.
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Affiliation(s)
- Nga T T Vu
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia. .,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.
| | - Kyall R Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Jarrod L Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Melony J Sellars
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,CSIRO Agriculture & Food, Integrated Sustainable Aquaculture Production Program, Queensland Bioscience Precinct, St Lucia, 4067, Australia.,Present address: Genics Pty Ltd, Level 5, Gehrmann Building. 60 Research Road, St Lucia, QLD, 4067, Australia
| | - Catarina N S Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Shannon R Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Dean R Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.,Tropical Futures Institute, James Cook University, Singapore, Singapore
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10
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Colston-Nepali L, Provencher JF, Mallory ML, Franckowiak RP, Sun Z, Robertson GJ, Friesen VL. Using genomic tools to inform management of the Atlantic northern fulmar. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01309-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Levis NA, Reed EMX, Pfennig DW, Burford Reiskind MO. Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads. Ecol Evol 2020; 10:8976-8988. [PMID: 32884672 PMCID: PMC7452772 DOI: 10.1002/ece3.6602] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 12/24/2022] Open
Abstract
Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases-especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an "omnivore" morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a "carnivore" morph that is favored in ephemeral, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with each morph (carnivores vs. omnivores) and loci associated with adaptive phenotypic plasticity (adaptive vs. maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might mediate adaptive plasticity.
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Affiliation(s)
| | - Emily M. X. Reed
- Department of Biological SciencesNorth Carolina State UniversityRaleighNCUSA
| | - David W. Pfennig
- Department of BiologyUniversity of North CarolinaChapel HillNCUSA
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12
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Antaky CC, Conklin EE, Toonen RJ, Knapp IS, Price MR. Unexpectedly high genetic diversity in a rare and endangered seabird in the Hawaiian Archipelago. PeerJ 2020; 8:e8463. [PMID: 32071808 PMCID: PMC7007978 DOI: 10.7717/peerj.8463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/26/2019] [Indexed: 11/20/2022] Open
Abstract
Seabirds in the order of Procellariiformes have one of the highest proportions of threatened species of any avian order. Species undergoing recovery may be predicted to have a genetic signature of a bottleneck, low genetic diversity, or higher rates of inbreeding. The Hawaiian Band-rumped Storm Petrel ('Akē'akē; Hydrobates castro), a long-lived philopatric seabird, suffered massive population declines resulting in its listing under the Endangered Species Act in 2016 as federally Endangered. We used high-throughput sequencing to assess patterns of genetic diversity and potential for inbreeding in remaining populations in the Hawaiian Islands. We compared a total of 24 individuals, including both historical and modern samples, collected from breeding colonies or downed individuals found on the islands of Kaua'i, O'ahu, Maui, and the Big Island of Hawai'i. Genetic analyses revealed little differentiation between breeding colonies on Kaua'i and the Big Island colonies. Although small sample sizes limit inferences regarding other island colonies, downed individuals from O'ahu and Maui did not assign to known breeding colonies, suggesting the existence of an additional distinct breeding population. The maintenance of genetic diversity in future generations is an important consideration for conservation management. This study provides a baseline of population structure for the remaining nesting colonies that could inform potential translocations of the Endangered H. castro.
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Affiliation(s)
- Carmen C. Antaky
- Department of Natural Resources and Environmental Management, University of Hawai‘i at Mānoa, Honolulu, HI, USA
| | - Emily E. Conklin
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Robert J. Toonen
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Ingrid S.S. Knapp
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Melissa R. Price
- Department of Natural Resources and Environmental Management, University of Hawai‘i at Mānoa, Honolulu, HI, USA
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13
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Cullingham CI, Peery RM, Fortier CE, Mahon EL, Cooke JEK, Coltman DW. Linking genotype to phenotype to identify genetic variation relating to host susceptibility in the mountain pine beetle system. Evol Appl 2020; 13:48-61. [PMID: 31892943 PMCID: PMC6935584 DOI: 10.1111/eva.12773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/24/2022] Open
Abstract
Identifying genetic variants responsible for phenotypic variation under selective pressure has the potential to enable productive gains in natural resource conservation and management. Despite this potential, identifying adaptive candidate loci is not trivial, and linking genotype to phenotype is a major challenge in contemporary genetics. Many of the population genetic approaches commonly used to identify adaptive candidates will simultaneously detect false positives, particularly in nonmodel species, where experimental evidence is seldom provided for putative roles of the adaptive candidates identified by outlier approaches. In this study, we use outcomes from population genetics, phenotype association, and gene expression analyses as multiple lines of evidence to validate candidate genes. Using lodgepole and jack pine as our nonmodel study species, we analyzed 17 adaptive candidate loci together with 78 putatively neutral loci at 58 locations across Canada (N > 800) to determine whether relationships could be established between these candidate loci and phenotype related to mountain pine beetle susceptibility. We identified two candidate loci that were significant across all population genetic tests, and demonstrated significant changes in transcript abundance in trees subjected to wounding or inoculation with the mountain pine beetle fungal associate Grosmannia clavigera. Both candidates are involved in central physiological processes that are likely to be invoked in a trees response to stress. One of these two candidate loci showed a significant association with mountain pine beetle attack status in lodgepole pine. The spatial distribution of the attack-associated allele further coincides with other indicators of susceptibility in lodgepole pine. These analyses, in which population genetics was combined with laboratory and field experimental validation approaches, represent first steps toward linking genetic variation to the phenotype of mountain pine beetle susceptibility in lodgepole and jack pine, and provide a roadmap for more comprehensive analyses.
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Affiliation(s)
| | - Rhiannon M. Peery
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Colleen E. Fortier
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Elizabeth L. Mahon
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Department of Wood ScienceUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Janice E. K. Cooke
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - David W. Coltman
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
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14
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Llanos‐Garrido A, Pérez‐Tris J, Díaz JA. The combined use of raw and phylogenetically independent methods of outlier detection uncovers genome-wide dynamics of local adaptation in a lizard. Ecol Evol 2019; 9:14356-14367. [PMID: 31938524 PMCID: PMC6953648 DOI: 10.1002/ece3.5872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023] Open
Abstract
Local adaptation is a dynamic process by which different allele combinations are selected in different populations at different times, and whose genetic signature can be inferred by genome-wide outlier analyses. We combined gene flow estimates with two methods of outlier detection, one of them independent of population coancestry (CIOA) and the other one not (ROA), to identify genetic variants favored when ecology promotes phenotypic convergence. We analyzed genotyping-by-sequencing data from five populations of a lizard distributed over an environmentally heterogeneous range that has been changing since the split of eastern and western lineages ca. 3 mya. Overall, western lizards inhabit forest habitat and are unstriped, whereas eastern ones inhabit shrublands and are striped. However, one population (Lerma) has unstriped phenotype despite its eastern ancestry. The analysis of 73,291 SNPs confirmed the east-west division and identified nonoverlapping sets of outliers (12 identified by ROA and 9 by CIOA). ROA revealed ancestral adaptive variation in the uncovered outliers that were subject to divergent selection and differently fixed for eastern and western populations at the extremes of the environmental gradient. Interestingly, such variation was maintained in Lerma, where we found high levels of heterozygosity for ROA outliers, whereas CIOA uncovered innovative variants that were selected only there. Overall, it seems that both the maintenance of ancestral variation and asymmetric migration have counterbalanced adaptive lineage splitting in our model species. This scenario, which is likely promoted by a changing and heterogeneous environment, could hamper ecological speciation of locally adapted populations despite strong genetic structure between lineages.
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Affiliation(s)
- Alejandro Llanos‐Garrido
- Informatics GroupFaculty of Arts and SciencesHarvard UniversityCambridgeMAUSA
- Departamento de BiodiversidadUniversidad Complutense de MadridMadridSpain
| | - Javier Pérez‐Tris
- Departamento de BiodiversidadUniversidad Complutense de MadridMadridSpain
| | - José A. Díaz
- Departamento de BiodiversidadUniversidad Complutense de MadridMadridSpain
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15
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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.
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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
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16
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Yin M, Wang X, Ma X, Gießler S, Petrusek A, Griebel J, Hu W, Wolinska J. Cytonuclear diversity and shared mitochondrial haplotypes among Daphnia galeata populations separated by seven thousand kilometres. BMC Evol Biol 2018; 18:130. [PMID: 30176793 PMCID: PMC6122193 DOI: 10.1186/s12862-018-1256-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 08/27/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The zooplanktonic cladocerans Daphnia, present in a wide range of water bodies, are an important component of freshwater ecosystems. In contrast to their high dispersal capacity through diapausing eggs carried by waterfowl, Daphnia often exhibit strong population genetic differentiation. Here, to test for common patterns in the population genetic structure of a widespread Holarctic species, D. galeata, we genotyped two sets of populations collected from geographically distant areas: across 13 lakes in Eastern China and 14 lakes in Central Europe. The majority of these populations were genotyped at two types of markers: a mitochondrial gene (for 12S rRNA) and 15 nuclear microsatellite loci. RESULTS Mitochondrial DNA demonstrated relatively shallow divergence within D. galeata, with distinct haplotype compositions in the two study regions but one widely distributed haplotype shared between several of the Chinese as well as European populations. At microsatellite markers, clear separation was observed at both large (between China and Europe) and small (within Europe) geographical scales, as demonstrated by Factorial Correspondence Analyses, Bayesian assignment and a clustering method based on genetic distances. Genetic diversity was comparable between the sets of Chinese and European D. galeata populations for both types of markers. Interestingly, we observed a significant association between genetic distance and geographical distance for D. galeata populations in China but not in Europe. CONCLUSIONS Our results indicate relatively recent spread of D. galeata across wide expanses of the Palaearctic, with one mtDNA lineage of D. galeata successfully establishing over large distances. Despite a clear differentiation of Chinese and European D. galeata at a nuclear level, the pattern of genetic variation is nevertheless similar between both regions. Overall, our findings provide insights into the genetic population structure of a cladoceran species with extremely wide geographical range.
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Affiliation(s)
- Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China.
| | - Xiaoyu Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China
| | - Xiaolin Ma
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China
| | - Sabine Gießler
- Department Biologie II, Aquatic Evolutionary Ecology, Ludwig-Maximilians-Universität, Großhaderner Str. 2, 82152 Planegg-, Martinsried, Germany
| | - Adam Petrusek
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, 12844, Prague, Czechia
| | - Johanna Griebel
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecosystem Research, Mueggelseedamm 301, 12587, Berlin, Germany
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China
| | - Justyna Wolinska
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecosystem Research, Mueggelseedamm 301, 12587, Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Konigin-Luise-Str. 1-3, 14195, Berlin, Germany
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17
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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18
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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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19
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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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