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Caccavo JA, Arantes LS, Celemín E, Mbedi S, Sparmann S, Mazzoni CJ. Whole-genome resequencing improves the utility of otoliths as a critical source of DNA for fish stock research and monitoring. Mol Ecol Resour 2024; 24:e14013. [PMID: 39233613 DOI: 10.1111/1755-0998.14013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 07/23/2024] [Accepted: 08/15/2024] [Indexed: 09/06/2024]
Abstract
Fish ear bones, known as otoliths, are often collected in fisheries to assist in management, and are a common sample type in museum and national archives. Beyond their utility for ageing, morphological and trace element analysis, otoliths are a repository of valuable genomic information. Previous work has shown that DNA can be extracted from the trace quantities of tissue remaining on the surface of otoliths, despite the fact that they are often stored dry at room temperature. However, much of this work has used reduced representation sequencing methods in clean lab conditions, to achieve adequate yields of DNA, libraries and ultimately single-nucleotide polymorphisms (SNPs). Here, we pioneer the use of small-scale (spike-in) sequencing to screen contemporary otolith samples prepared in regular molecular biology (in contrast to clean) laboratories for contamination and quality levels, submitting for whole-genome resequencing only samples above a defined endogenous DNA threshold. Despite the typically low quality and quantity of DNA extracted from otoliths, we are able to produce whole-genome libraries and ultimately sets of filtered, unlinked and even putatively adaptive SNPs of ample numbers for downstream uses in population, climate and conservation genomics. By comparing with a set of tissue samples from the same species, we are able to highlight the quality and efficacy of otolith samples from DNA extraction and library preparation, to bioinformatic preprocessing and SNP calling. We provide detailed schematics, protocols and scripts of our approach, such that it can be adopted widely by the community, improving the use of otoliths as a source of valuable genomic data.
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Affiliation(s)
- Jilda Alicia Caccavo
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Department of Evolutionary Genetics, Leibniz-Institut für Zoo- und Wildtierforschung, IZW, Berlin, Germany
| | - Larissa S Arantes
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Department of Evolutionary Genetics, Leibniz-Institut für Zoo- und Wildtierforschung, IZW, Berlin, Germany
| | - Enrique Celemín
- Institute of Biochemistry and Biology, Evolutionary Biology & Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Susan Mbedi
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Museum für Naturkunde, Berlin, Germany
| | - Sarah Sparmann
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Leibniz-Institut für Gewässerökologie und Binnenfischerei (IGB), Berlin, Germany
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Department of Evolutionary Genetics, Leibniz-Institut für Zoo- und Wildtierforschung, IZW, Berlin, Germany
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2
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Escuer P, Guirao-Rico S, Arnedo MA, Sánchez-Gracia A, Rozas J. Population Genomics of Adaptive Radiations: Exceptionally High Levels of Genetic Diversity and Recombination in an Endemic Spider From the Canary Islands. Mol Ecol 2024:e17547. [PMID: 39400446 DOI: 10.1111/mec.17547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/26/2024] [Accepted: 09/24/2024] [Indexed: 10/15/2024]
Abstract
The spider genus Dysdera has undergone a remarkable diversification in the oceanic archipelago of the Canary Islands, with ~60 endemic species having originated during the 20 million years since the origin of the archipelago. This evolutionary radiation has been accompanied by substantial dietary shifts, often characterised by phenotypic modifications encompassing morphological, metabolic and behavioural changes. Hence, these endemic spiders represent an excellent model for understanding the evolutionary drivers and to pinpoint the genomic determinants underlying adaptive radiations. Recently, we achieved the first chromosome-level genome assembly of one of the endemic species, D. silvatica, providing a high-quality reference sequence for evolutionary genomics studies. Here, we conducted a low coverage-based resequencing study of a natural population of D. silvatica from La Gomera island. Taking advantage of the new high-quality genome, we characterised genome-wide levels of nucleotide polymorphism, divergence and linkage disequilibrium, and inferred the demographic history of this population. We also performed comprehensive genome-wide scans for recent positive selection. Our findings uncovered exceptionally high levels of nucleotide diversity and recombination in this geographically restricted endemic species, indicative of large historical effective population sizes. We also identified several candidate genomic regions that are potentially under positive selection, highlighting relevant biological processes, such as vision and nitrogen extraction as potential adaptation targets. These processes may ultimately drive species diversification in this genus. This pioneering study of spiders that are endemic to an oceanic archipelago lays the groundwork for broader population genomics analyses aimed at understanding the genetic mechanisms driving adaptive radiation in island ecosystems.
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Affiliation(s)
- Paula Escuer
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Sara Guirao-Rico
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Miquel A Arnedo
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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3
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Prochotta D, Winter S, Fennessy J, Janke A. Population genomics reveals mito-nuclear discordance and admixed populations in southern giraffe. Mol Phylogenet Evol 2024:108198. [PMID: 39276822 DOI: 10.1016/j.ympev.2024.108198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 07/30/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
Studying wildlife taxonomic diversity and identifying distinct populations has traditionally been largely based on morphology and geographic origin. More recently, this method has been supplemented by genetic data from the mitochondrial genome. However, this is limited as only maternally inherited and may not reflect the true nature of a population's genetics. Within the giraffe (Giraffa spp.), subspecies and unique populations were successfully characterized using both mitochondrial and genomic DNA studies, which led to new insights and, in some cases, unexpected results that required further verification. Here, we sequenced the genomes of 85 southern giraffe (G. giraffa) individuals from ten populations across southern Africa for a detailed investigation into the genetic diversity and history of its two subspecies, the Angolan (G. g. angolensis) and the South African (G. g. giraffa) giraffe. While the overall genotypes show low levels of runs of homozygosity compared to other mammals, the degree of heterozygosity is limited despite the large population size of South African giraffe. The nuclear genotype is largely congruent with the mitochondrial genotype. However, we have identified that the distribution of the Angolan giraffe is not as far east as indicated in an earlier mitochondrial DNA study. Botswana's Central Kalahari Game Reserve giraffe are unique, with a clear admixture of Angolan and South African giraffe populations. However, the enigmatic desert-dwelling giraffe of northwest Namibia is locally distinct from other Angolan giraffe yet exhibits intra-subspecies signs of admixture resulting from a recent introduction of individuals from Namibia's Etosha National Park. Whole genome sequencing is an invaluable and nearly indispensable tool for wildlife management to uncover genetic diversity that is undetectable through mitogenomic, geographical, and morphological means.
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Affiliation(s)
- David Prochotta
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany; Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria.
| | - Julian Fennessy
- Giraffe Conservation Foundation, PO Box 86099, Eros, Windhoek, Namibia; School of Biology and Environmental Science, University College Dublin, Ireland.
| | - Axel Janke
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany.
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4
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Blommaert J, Sandoval-Castillo J, Beheregaray LB, Wellenreuther M. Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper. Genomics 2024; 116:110929. [PMID: 39216708 DOI: 10.1016/j.ygeno.2024.110929] [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: 05/05/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Even before genome sequencing, genetic resources have supported species management and breeding programs. Current technologies, such as long-read sequencing, resolve complex genomic regions, like those rich in repeats or high in GC content. Improved genome contiguity enhances accuracy in identifying structural variants (SVs) and transposable elements (TEs). We present an improved genome assembly and SV catalogue for the Australasian snapper (Chrysophrys auratus). The new assembly is more contiguous, allowing for putative identification of 14 centromeres and transfer of 26,115 gene annotations from yellowfin seabream. Compared to the previous assembly, 35,000 additional SVs, including larger and more complex rearrangements, were annotated. SVs and TEs exhibit a distribution pattern skewed towards chromosome ends, likely influenced by recombination. Some SVs overlap with growth-related genes, underscoring their significance. This upgraded genome serves as a foundation for studying natural and artificial selection, offers a reference for related species, and sheds light on genome dynamics shaped by evolution.
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Affiliation(s)
- Julie Blommaert
- The New Zealand Institute for Plant and Food Research, Nelson, New Zealand.
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research, Nelson, New Zealand; School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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5
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Kwait R, Pinsky ML, Gignoux‐Wolfsohn S, Eskew EA, Kerwin K, Maslo B. Impact of putatively beneficial genomic loci on gene expression in little brown bats ( Myotis lucifugus, Le Conte, 1831) affected by white-nose syndrome. Evol Appl 2024; 17:e13748. [PMID: 39310794 PMCID: PMC11413065 DOI: 10.1111/eva.13748] [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: 08/06/2023] [Revised: 06/06/2024] [Accepted: 06/19/2024] [Indexed: 09/25/2024] Open
Abstract
Genome-wide scans for selection have become a popular tool for investigating evolutionary responses in wildlife to emerging diseases. However, genome scans are susceptible to false positives and do little to demonstrate specific mechanisms by which loci impact survival. Linking putatively resistant genotypes to observable phenotypes increases confidence in genome scan results and provides evidence of survival mechanisms that can guide conservation and management efforts. Here we used an expression quantitative trait loci (eQTL) analysis to uncover relationships between gene expression and alleles associated with the survival of little brown bats (Myotis lucifugus) despite infection with the causative agent of white-nose syndrome. We found that 25 of the 63 single-nucleotide polymorphisms (SNPs) associated with survival were related to gene expression in wing tissue. The differentially expressed genes have functional annotations associated with the innate immune system, metabolism, circadian rhythms, and the cellular response to stress. In addition, we observed differential expression of multiple genes with survival implications related to loci in linkage disequilibrium with focal SNPs. Together, these findings support the selective function of these loci and suggest that part of the mechanism driving survival may be the alteration of immune and other responses in epithelial tissue.
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Affiliation(s)
- Robert Kwait
- Department of Ecology, Evolution and Natural ResourcesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Malin L. Pinsky
- Department of Ecology, Evolution and Natural ResourcesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCaliforniaUSA
| | | | - Evan A. Eskew
- Institute for Interdisciplinary Data SciencesUniversity of IdahoMoscowIdahoUSA
| | - Kathleen Kerwin
- Department of Ecology, Evolution and Natural ResourcesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Brooke Maslo
- Department of Ecology, Evolution and Natural ResourcesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
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Vourlaki IT, Ramos-Onsins SE, Pérez-Enciso M, Castanera R. Evaluation of deep learning for predicting rice traits using structural and single-nucleotide genomic variants. PLANT METHODS 2024; 20:121. [PMID: 39127715 DOI: 10.1186/s13007-024-01250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Structural genomic variants (SVs) are prevalent in plant genomes and have played an important role in evolution and domestication, as they constitute a significant source of genomic and phenotypic variability. Nevertheless, most methods in quantitative genetics focusing on crop improvement, such as genomic prediction, consider only Single Nucleotide Polymorphisms (SNPs). Deep Learning (DL) is a promising strategy for genomic prediction, but its performance using SVs and SNPs as genetic markers remains unknown. RESULTS We used rice to investigate whether combining SVs and SNPs can result in better trait prediction over SNPs alone and examine the potential advantage of Deep Learning (DL) networks over Bayesian Linear models. Specifically, the performances of BayesC (considering additive effects) and a Bayesian Reproducible Kernel Hilbert space (RKHS) regression (considering both additive and non-additive effects) were compared to those of two different DL architectures, the Multilayer Perceptron, and the Convolution Neural Network, to explore their prediction ability by using various marker input strategies. We found that exploiting structural and nucleotide variation slightly improved prediction ability on complex traits in 87% of the cases. DL models outperformed Bayesian models in 75% of the studied cases, considering the four traits and the two validation strategies used. Finally, DL systematically improved prediction ability of binary traits against the Bayesian models. CONCLUSIONS Our study reveals that the use of structural genomic variants can improve trait prediction in rice, independently of the methodology used. Also, our results suggest that Deep Learning (DL) networks can perform better than Bayesian models in the prediction of binary traits, and in quantitative traits when the training and target sets are not closely related. This highlights the potential of DL to enhance crop improvement in specific scenarios and the importance to consider SVs in addition to SNPs in genomic selection.
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Affiliation(s)
- Ioanna-Theoni Vourlaki
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, 08193, Barcelona, Spain.
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Caldes de Montbui, 08140, Barcelona, Spain.
| | - Sebastián E Ramos-Onsins
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, 08193, Barcelona, Spain
| | - Miguel Pérez-Enciso
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, 08193, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
- Universitat Autónoma de Barcelona, 08193, Barcelona, Spain
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, 08193, Barcelona, Spain.
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Caldes de Montbui, 08140, Barcelona, Spain.
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Wagner I, Smolina I, Koop MEL, Bal T, Lizano AM, Choo LQ, Hofreiter M, Gennari E, de Sabata E, Shivji MS, Noble LR, Jones CS, Hoarau G. Genome analysis reveals three distinct lineages of the cosmopolitan white shark. Curr Biol 2024; 34:3582-3590.e4. [PMID: 39047735 DOI: 10.1016/j.cub.2024.06.076] [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: 12/18/2023] [Revised: 03/22/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
The white shark (Carcharodon carcharias) (Linnaeus, 1758), an iconic apex predator occurring in all oceans,1,2 is classified as Vulnerable globally3-with global abundance having dropped to 63% of 1970s estimates,4-and as Critically Endangered in Europe.5 Identification of evolutionary significant units and their management are crucial for conservation,6 especially as the white shark is facing various but often region-specific anthropogenic threats.7,8,9,10,11 Assessing connectivity in a cosmopolitan marine species requires worldwide sampling and high-resolution genetic markers.12 Both are lacking for the white shark, with studies to date typified by numerous but geographically limited sampling, and analyses relying largely on relatively small numbers of nuclear microsatellites,13,14,15,16,17,18,19 which can be plagued by various genotyping artefacts and thus require cautious interpretation.20 Sequencing and computational advances are finally allowing genomes21,22,23 to be leveraged into population studies,24,25,26,27 with datasets comprising thousands of single-nucleotide polymorphisms (SNPs). Here, combining target gene capture (TGC)28 sequencing (89 individuals, 4,000 SNPs) and whole-genome re-sequencing (17 individuals, 391,000 SNPs) with worldwide sampling across most of the distributional range, we identify three genetically distinct allopatric lineages (North Atlantic, Indo-Pacific, and North Pacific). These diverged 100,000-200,000 years ago during the Penultimate Glaciation, when low sea levels, different ocean currents, and water temperatures produced significant biogeographic barriers. Our results show that without high-resolution genomic analyses of samples representative of a species' range,12 the true extent of diversity, presence of past and contemporary barriers to gene flow, subsequent speciation, and local evolutionary events will remain enigmatic.
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Affiliation(s)
- Isabel Wagner
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Irina Smolina
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Martina E L Koop
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Thijs Bal
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Apollo M Lizano
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; Marine Science Institute, University of the Philippines, Diliman Quezon City 1101, Philippines
| | - Le Qin Choo
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Enrico Gennari
- Oceans Research Institute, Mossel Bay 6500, South Africa
| | | | - Mahmood S Shivji
- Save Our Seas Shark Foundation Research Center and Guy Harvey Research Institute, Nova Southeastern University, Dania Beach, FL 33004, USA
| | - Leslie R Noble
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2TZ, UK.
| | - Catherine S Jones
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2TZ, UK.
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
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Bruxaux J, Zhao W, Hall D, Curtu AL, Androsiuk P, Drouzas AD, Gailing O, Konrad H, Sullivan AR, Semerikov V, Wang XR. Scots pine - panmixia and the elusive signal of genetic adaptation. THE NEW PHYTOLOGIST 2024; 243:1231-1246. [PMID: 38308133 DOI: 10.1111/nph.19563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/14/2024] [Indexed: 02/04/2024]
Abstract
Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.
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Affiliation(s)
- Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - David Hall
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
- Forestry Research Institute of Sweden (Skogforsk), 918 21, Sävar, Sweden
| | | | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany
| | - Heino Konrad
- Department of Forest Biodiversity and Nature Conservation, Unit of Ecological Genetics, Austrian Research Centre for Forests (BFW), 1140, Vienna, Austria
| | - Alexis R Sullivan
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology, Ural Division of Russian Academy of Sciences, 620144, Ekaterinburg, Russia
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
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Capblancq T, Sękiewicz K, Dering M. Forest genomics in the Caucasus through the lens of its dominant tree species - Fagus orientalis. Mol Ecol 2024; 33:e17475. [PMID: 39021282 DOI: 10.1111/mec.17475] [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: 01/11/2024] [Revised: 05/29/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024]
Abstract
The last glacial period is known to have greatly influenced the demographic history of temperate forest trees, with important range contractions and post-glacial expansions that led to the formation of multiple genetic lineages and secondary contact zones in the Northern Hemisphere. These dynamics have been extensively studied for European and North American species but are still poorly understood in other temperate regions of rich biodiversity such as the Caucasus. Our study helps filling that gap by deciphering the genomic landscapes of F. orientalis across the South Caucasus. The use of genome-wide data confirmed a past demographic history strongly influenced by the Last Glacial Maximum, revealing two disjunct glacial refugia in the Colchis and Hyrcanian regions. The resulting patterns of genetic diversity, load and differentiation are not always concordant across the region, with genetic load pinpointing the location of the glacial refugia more efficiently than genetic diversity alone. The Hyrcanian forests show depleted genetic diversity and substantial isolation, even if long-distance gene flow is still present with the main centre of diversity in the Greater Caucasus. Finally, we characterize a strong heterogeneity of genetic diversity and differentiation along the species chromosomes, with noticeably a first chromosome showing low diversity and weak differentiation.
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Affiliation(s)
- Thibaut Capblancq
- Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, Laboratoire d'Écologie Alpine, Grenoble, France
| | | | - Monika Dering
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
- Department of Silviculture, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Poznań, Poland
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10
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Zhang J, Schneller NM, Field MA, Chan CX, Miller DJ, Strugnell JM, Riginos C, Bay L, Cooke I. Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef. Mol Ecol 2024; 33:e17468. [PMID: 39046252 DOI: 10.1111/mec.17468] [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: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024]
Abstract
The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to assist evolutionary processes in corals require a comprehensive understanding of the distribution and structure of standing variation, however, efforts to map genomic variation in corals have so far focussed almost exclusively on SNPs, overlooking structural variants that have been shown to drive adaptive processes in other taxa. Here, we show that the reef-building coral, Acropora kenti, harbours at least five large, highly polymorphic structural variants, all of which exhibit signatures of strongly suppressed recombination in heterokaryotypes, a feature commonly associated with chromosomal inversions. Based on their high minor allele frequency, uniform distribution across habitats and elevated genetic load, we propose that these inversions in A. kenti are likely to be under balancing selection. An excess of SNPs with high impact on protein-coding genes within these loci elevates their importance both as potential targets for adaptive selection and as contributors to genetic decline if coral populations become fragmented or inbred in future.
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Affiliation(s)
- Jia Zhang
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Nadja M Schneller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Matt A Field
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Miller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Jan M Strugnell
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Line Bay
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Ira Cooke
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
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11
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Ciezarek AG, Mehta TK, Man A, Ford AGP, Kavembe GD, Kasozi N, Ngatunga BP, Shechonge AH, Tamatamah R, Nyingi DW, Cnaani A, Ndiwa TC, Di Palma F, Turner GF, Genner MJ, Haerty W. Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes. Mol Biol Evol 2024; 41:msae116. [PMID: 38865496 PMCID: PMC11221657 DOI: 10.1093/molbev/msae116] [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: 09/21/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.
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Affiliation(s)
- Adam G Ciezarek
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Centre of Environment, Fisheries and Aquaculture Science (Cefas), Scientific Advice for Fisheries Management Team (SAFM), Lowestoft NR33 0H5, UK
| | - Tarang K Mehta
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Angela Man
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Antonia G P Ford
- School of Life and Health Sciences, Whitelands College, University of Roehampton, London SW15 4NA, UK
| | | | - Nasser Kasozi
- National Agricultural Research Organisation, Buginyanya Zonal Agricultural Research and Development Institute, Mbale, Uganda
| | | | | | | | | | - Avner Cnaani
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion 7528809, Israel
| | - Titus C Ndiwa
- Department of Clinical Studies, University of Nairobi, Nairobi, Kenya
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - George F Turner
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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12
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Vandewege MW, Gutierrez J, Davis DR, Forstner MRJ, Mali I. Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system. J Hered 2024; 115:253-261. [PMID: 38373252 PMCID: PMC11081133 DOI: 10.1093/jhered/esae011] [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: 04/30/2023] [Accepted: 02/15/2024] [Indexed: 02/21/2024] Open
Abstract
The lower Rio Grande and Pecos River of the southwest United States have been heavily modified by human activities, profoundly impacting the integrity of their aquatic wildlife. In this context, we focused our study on the population genomics of the Rio Grande Cooter (Pseudemys gorzugi), a freshwater turtle of increasing conservation concern, residing in these two rivers and their tributaries. The genetic data revealed two distinct populations: one in the Pecos and Black Rivers of New Mexico and another in the Rio Grande and Devils River of Texas, with admixed individuals identified at the confluence of the Rio Grande and Pecos River. In addition to having a smaller geographic range, we found lower observed heterozygosity, reduced nucleotide diversity, and a smaller effective population size (Ne) in New Mexico population. Our results depict a significant isolation-by-distance pattern across their distribution, with migration being notably infrequent at river confluences. These findings are pivotal for future conservation and restoration strategies, emphasizing the need to recognize the unique needs of each population.
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Affiliation(s)
- Michael W Vandewege
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Javier Gutierrez
- Biomedical Forensic Sciences, Anatomy and Neurobiology Department, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Drew R Davis
- Department of Biology, Eastern New Mexico University, Portales, NM, USA
- Biodiversity Collections, Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | | | - Ivana Mali
- Fisheries, Wildlife, and Conservation Biology Program, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
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13
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Caizergues AE, Santangelo JS, Ness RW, Angeoletto F, Anstett DN, Anstett J, Baena-Diaz F, Carlen EJ, Chaves JA, Comerford MS, Dyson K, Falahati-Anbaran M, Fellowes MDE, Hodgins KA, Hood GR, Iñiguez-Armijos C, Kooyers NJ, Lázaro-Lobo A, Moles AT, Munshi-South J, Paule J, Porth IM, Santiago-Rosario LY, Whitney KS, Tack AJM, Johnson MTJ. Does urbanisation lead to parallel demographic shifts across the world in a cosmopolitan plant? Mol Ecol 2024; 33:e17311. [PMID: 38468155 DOI: 10.1111/mec.17311] [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: 08/15/2023] [Revised: 12/08/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024]
Abstract
Urbanisation is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the 'urban facilitation model' suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the GLobal Urban Evolution project (GLUE), to study the effects of urbanisation on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of reduced Ne linked to urbanisation. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides the largest comprehensive test of the demographic effects of urbanisation. Our results contrast with the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.
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Affiliation(s)
- Aude E Caizergues
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - James S Santangelo
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - Rob W Ness
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Fabio Angeoletto
- Programa de Pós-Graduação em Gestão e Tecnologia Ambiental da Universidade Federal de Rondonópolis, Rondonópolis, Brasil
| | - Daniel N Anstett
- Department of Plant Biology, Department of Entomology, Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Julia Anstett
- Genomic Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Elizabeth J Carlen
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jaime A Chaves
- Universidad San Francisco de Quito, Ecuador, Quito
- San Francisco State University, San Francisco, California, USA
| | - Mattheau S Comerford
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, USA
| | | | | | | | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Glen Ray Hood
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Carlos Iñiguez-Armijos
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | - Adrián Lázaro-Lobo
- Biodiversity Research Institute (IMIB), CSIC-University of Oviedo-Principality of Asturias, Mieres, Spain
| | - Angela T Moles
- Evolution & Ecology Research Centre, UNSW-University of New South Wales, Sydney, New South Wales, Australia
| | - Jason Munshi-South
- Department of Biology and Louis Calder Center, Fordham University, New York City, New York, USA
| | - Juraj Paule
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Ilga M Porth
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Luis Y Santiago-Rosario
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Kaitlin Stack Whitney
- Science, Technology & Society Department, Rochester Institute of Technology, Rochester, New York, USA
| | - Ayko J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Marc T J Johnson
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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14
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Dalapicolla J, Weir JT, Vilaça ST, Quaresma TF, Schneider MPC, Vasconcelos ATR, Aleixo A. Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary. Ecol Evol 2024; 14:e11250. [PMID: 38660467 PMCID: PMC11040105 DOI: 10.1002/ece3.11250] [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: 09/26/2023] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
The "Amazon tipping point" is a global change scenario resulting in replacement of upland terra-firme forests by large-scale "savannization" of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra-firme inhabiting species should have experienced reductions in population size as drier habitats expanded. Here, we use whole-genomes of an Amazonian endemic organism (Scale-backed antbirds - Willisornis spp.) sampled from nine populations across the region to test this historical demography scenario. Populations from southeastern Amazonia and close to the Amazon-Cerrado ecotone exhibited a wide range of demographic patterns, while most of those from northern and western Amazonia experienced uniform expansions between 400 kya and 80-60 kya, with gradual declines toward 20 kya. Southeastern populations of Willisornis were the last to diversify and showed smaller heterozygosity and higher runs of homozygosity values than western and northern populations. These patterns support historical population declines throughout the Amazon that affected more strongly lineages in the southern and eastern areas, where historical "tipping point" conditions existed due to the widespread replacement of humid forest by drier and open vegetation during the LGM.
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Affiliation(s)
- Jeronymo Dalapicolla
- Instituto Tecnológico ValeBelémParáBrazil
- Departamento de Sistemática e EcologiaUniversidade Federal da Paraíba, João PessoaParaíbaBrazil
| | - Jason T. Weir
- Department of Biological SciencesUniversity of Toronto ScarboroughTorontoOntarioCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Natural History, Royal Ontario MuseumTorontoOntarioCanada
| | | | | | - Maria P. C. Schneider
- Laboratório de Genômica e BiotecnologiaInstituto de Ciências Biológicas, UFPABelémBrazil
| | - Ana Tereza R. Vasconcelos
- Laboratório de BioinformáticaLaboratório Nacional de Computação Científica, PetrópolisRio de JaneiroBrazil
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15
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Gose MA, Humble E, Brownlow A, Wall D, Rogan E, Sigurðsson GM, Kiszka JJ, Thøstesen CB, IJsseldijk LL, Ten Doeschate M, Davison NJ, Øien N, Deaville R, Siebert U, Ogden R. Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): Implications for conservation amid climate-driven range shifts. Heredity (Edinb) 2024; 132:192-201. [PMID: 38302666 PMCID: PMC10997624 DOI: 10.1038/s41437-024-00672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate species such as the white-beaked dolphin (Lagenorhynchus albirostris) face pressures from habitat shifts due to rising sea surface temperatures in addition to other direct anthropogenic threats. Unravelling the genetic connectivity between white-beaked dolphins across their range is needed to understand the extent to which climate change and anthropogenic pressures may impact species-wide genetic diversity and identify ways to protect remaining habitat. We address this by performing a population genomic assessment of white-beaked dolphins using samples from much of their contemporary range. We show that the species displays significant population structure across the North Atlantic at multiple scales. Analysis of contemporary migration rates suggests a remarkably high connectivity between populations in the western North Atlantic, Iceland and the Barents Sea, while two regional populations in the North Sea and adjacent UK and Irish waters are highly differentiated from all other clades. Our results have important implications for the conservation of white-beaked dolphins by providing guidance for the delineation of more appropriate management units and highlighting the risk that local extirpation may have on species-wide genetic diversity. In a broader context, this study highlights the importance of understanding genetic structure of all species threatened with climate change-driven range shifts to assess the risk of loss of species-wide genetic diversity.
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Affiliation(s)
- Marc-Alexander Gose
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.
| | - Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Dave Wall
- Irish Whale and Dolphin Group (IWDG), Kilrush, Ireland
| | - Emer Rogan
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | | | - Jeremy J Kiszka
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, FL, USA
| | | | - Lonneke L IJsseldijk
- Division of Pathology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Mariel Ten Doeschate
- Scottish Marine Animal Stranding Scheme, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Nils Øien
- Institute of Marine Research (IMR), Bergen, Norway
| | - Rob Deaville
- Institute of Zoology, Zoological Society of London, London, UK
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
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16
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Howe NS, Hale MC, Waters CD, Schaal SM, Shedd KR, Larson WA. Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha. Evol Appl 2024; 17:e13656. [PMID: 38357359 PMCID: PMC10866082 DOI: 10.1111/eva.13656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery-wild population pairs. In this study, we used low-coverage whole-genome sequencing to investigate signals of domestication selection in three separate hatchery populations of Chinook salmon, Oncorhynchus tshawytscha, after approximately seven generations of divergence from their corresponding wild progenitor populations. We sequenced 192 individuals from populations across Southeast Alaska and estimated genotype likelihoods at over six million loci. We discovered a total of 14 outlier peaks displaying high genetic differentiation (F ST) between hatchery-wild pairs, although no peaks were shared across the three comparisons. Peaks were small (53 kb on average) and often displayed elevated absolute genetic divergence (D xy) and linkage disequilibrium, suggesting some level of domestication selection has occurred. Our study provides evidence that domestication selection can lead to genetic differences between hatchery and wild populations in only a few generations. Additionally, our data suggest that population-specific adaptation to hatchery environments likely occurs through different genetic pathways, even for populations with similar standing genetic variation. These results highlight the need to collect paired genotype-phenotype data to understand how domestication may be affecting fitness and to identify potential management practices that may mitigate genetic risks despite multiple pathways of domestication.
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Affiliation(s)
- Natasha S. Howe
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Matthew C. Hale
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Charles D. Waters
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Sara M. Schaal
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Kyle R. Shedd
- Alaska Department of Fish and Game, Division of Commercial FisheriesGene Conservation LaboratoryAnchorageAlaskaUSA
| | - Wesley A. Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
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17
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Moran PA, Bosse M, Mariën J, Halfwerk W. Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity. Mol Ecol 2024; 33:e17258. [PMID: 38153193 DOI: 10.1111/mec.17258] [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: 03/06/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed that predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival, or reproduction. Here, we a priori examined the genomic impact of urbanisation on the Neotropical túngara frog (Engystomops pustulosus), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared with forest populations, and genomic variation was best explained by geographic distance rather than environmental factors. Adopting an a posteriori approach, we additionally found both urban and forest populations to have undergone population declines. The timing of these declines appears to coincide with extensive human activity around the Panama Canal during the last few centuries rather than recent urbanisation. Our study highlights the long-lasting legacy of past anthropogenic disturbances in the genome and the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact nonurban areas on both recent and older timescales.
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Affiliation(s)
- Peter A Moran
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mirte Bosse
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Janine Mariën
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wouter Halfwerk
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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18
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da Fonseca RR, Campos PF, Rey-Iglesia A, Barroso GV, Bergeron LA, Nande M, Tuya F, Abidli S, Pérez M, Riveiro I, Carrera P, Jurado-Ruzafa A, G. Santamaría MT, Faria R, Machado AM, Fonseca MM, Froufe E, C. Castro LF. Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia. Genes (Basel) 2024; 15:170. [PMID: 38397160 PMCID: PMC10888339 DOI: 10.3390/genes15020170] [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: 11/27/2023] [Revised: 01/08/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that whole genome data from 108 individuals from 16 sampling areas across 5000 km of the species' distribution range (from the Eastern Mediterranean to the archipelago of Azores) support at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution, including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear to belong to the Mediterranean cluster. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.
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Affiliation(s)
- Rute R. da Fonseca
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Paula F. Campos
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark;
| | - Gustavo V. Barroso
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA;
| | - Lucie A. Bergeron
- Section for Ecology and Evolution, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Manuel Nande
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Fernando Tuya
- Grupo en Biodiversidad y Conservación, IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, 35017 Las Palmas, Spain;
| | - Sami Abidli
- Laboratory of Environment Bio-Monitoring, Faculty of Sciences of Bizerte, University of Carthage, Bizerte 7021, Tunisia;
| | - Montse Pérez
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, IEO-CSIC, 36390 Vigo, Spain; (M.P.); (I.R.); (P.C.)
| | - Isabel Riveiro
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, IEO-CSIC, 36390 Vigo, Spain; (M.P.); (I.R.); (P.C.)
| | - Pablo Carrera
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, IEO-CSIC, 36390 Vigo, Spain; (M.P.); (I.R.); (P.C.)
| | - Alba Jurado-Ruzafa
- Centro Oceanográfico de Canarias, Instituto Español de Oceanografía, IEO-CSIC, 38180 Santa Cruz de Tenerife, Spain; (A.J.-R.); (M.T.G.S.)
| | - M. Teresa G. Santamaría
- Centro Oceanográfico de Canarias, Instituto Español de Oceanografía, IEO-CSIC, 38180 Santa Cruz de Tenerife, Spain; (A.J.-R.); (M.T.G.S.)
| | - Rui Faria
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - André M. Machado
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Miguel M. Fonseca
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Elsa Froufe
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - L. Filipe C. Castro
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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19
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Waples RS. Practical application of the linkage disequilibrium method for estimating contemporary effective population size: A review. Mol Ecol Resour 2024; 24:e13879. [PMID: 37873672 DOI: 10.1111/1755-0998.13879] [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: 06/22/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023]
Abstract
The method to estimate contemporary effective population size (Ne ) based on patterns of linkage disequilibrium (LD) at unlinked loci has been widely applied to natural and managed populations. The underlying model makes many simplifying assumptions, most of which have been evaluated in numerous studies published over the last two decades. Here, these performance evaluations are reviewed and summarized, with a focus on information that facilitates practical application to real populations in nature. Potential sources of bias that are discussed include calculation of r2 (a measure of LD), adjustments for sampling error, physical linkage, age structure, migration and spatial structure, mutation and selection, mating systems, changes in abundance, rare alleles, missing data, genotyping errors, data filtering choices and methods for combining multiple Ne estimates. Factors that affect precision are reviewed, including pseudoreplication that limits the information gained from large genomics datasets, constraints imposed by small samples of individuals, and the challenges in obtaining robust estimates for large populations. Topics that merit further research include the potential to weight r2 values by allele frequency, lump samples of individuals, use genotypic likelihoods rather than called genotypes, prune large LD values and apply the method to species practising partial monogamy.
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Affiliation(s)
- Robin S Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
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20
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Brinker P, Chen F, Chehida YB, Beukeboom LW, Fontaine MC, Salles JF. Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia. Mol Ecol 2023; 32:6644-6658. [PMID: 36125236 DOI: 10.1111/mec.16699] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022]
Abstract
The microbial community composition is crucial for diverse life-history traits in many organisms. However, we still lack a sufficient understanding of how the host microbiome is acquired and maintained, a pressing issue in times of global environmental change. Here we investigated to what extent host genotype, environmental conditions, and the endosymbiont Wolbachia influence the bacterial communities in the parasitic wasp Asobara japonica. We sampled multiple wasp populations across 10 locations in their natural distribution range in Japan and sequenced the host genome (whole genome sequencing) and microbiome (16S rRNA gene). We compared the host population structure and bacterial community composition of wasps that reproduce sexually and are uninfected with Wolbachia with wasps that reproduce asexually and carry Wolbachia. The bacterial communities in asexual wasps were highly similar due to a strong effect of Wolbachia rather than host genomic structure. In contrast, in sexual wasps, bacterial communities appear primarily shaped by a combination of population structure and environmental conditions. Our research highlights that multiple factors shape the bacterial communities of an organism and that the presence of a single endosymbiont can strongly alter their compositions. This information is crucial to understanding how organisms and their associated microbiome will react in the face of environmental change.
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Affiliation(s)
- Pina Brinker
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Fangying Chen
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, UK
- Department of Biology, University of York, York, UK
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES), Montpellier, France
| | - Joana Falcao Salles
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
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21
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Willis S, Micheletti S, Andrews KR, Narum S. PoolParty2: An integrated pipeline for analysing pooled or indexed low-coverage whole-genome sequencing data to discover the genetic basis of diversity. Mol Ecol Resour 2023. [PMID: 37921673 DOI: 10.1111/1755-0998.13888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 09/29/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
Whole-genome sequencing data allow survey of variation from across the genome, reducing the constraint of balancing genome sub-sampling with estimating recombination rates and linkage between sampled markers and target loci. As sequencing costs decrease, low-coverage whole-genome sequencing of pooled or indexed-individual samples is commonly utilized to identify loci associated with phenotypes or environmental axes in non-model organisms. There are, however, relatively few publicly available bioinformatic pipelines designed explicitly to analyse these types of data, and fewer still that process the raw sequencing data, provide useful metrics of quality control and then execute analyses. Here, we present an updated version of a bioinformatics pipeline called PoolParty2 that can effectively handle either pooled or indexed DNA samples and includes new features to improve computational efficiency. Using simulated data, we demonstrate the ability of our pipeline to recover segregating variants, estimate their allele frequencies accurately, and identify genomic regions harbouring loci under selection. Based on the simulated data set, we benchmark the efficacy of our pipeline with another bioinformatic suite, angsd, and illustrate the compatibility and complementarity of these suites using angsd to generate genotype likelihoods as input for identifying linkage outlier regions using alignment files and variants provided by PoolParty2. Finally, we apply our updated pipeline to an empirical dataset of low-coverage whole genomic data from population samples of Columbia River steelhead trout (Oncorhynchus mykiss), results from which demonstrate the genomic impacts of decades of artificial selection in a prominent hatchery stock. Thus, we not only demonstrate the utility of PoolParty2 for genomic studies that combine sequencing data from multiple individuals, but also illustrate how it compliments other bioinformatics resources such as angsd.
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Affiliation(s)
- Stuart Willis
- Hagerman Genetics Lab, Columbia River Inter-Tribal Fish Commission, Hagerman, Idaho, USA
| | - Steven Micheletti
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kimberly R Andrews
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
| | - Shawn Narum
- Hagerman Genetics Lab, Columbia River Inter-Tribal Fish Commission, Hagerman, Idaho, USA
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22
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Coimbra RTF, Winter S, Muneza A, Fennessy S, Otiende M, Mijele D, Masiaine S, Stacy-Dawes J, Fennessy J, Janke A. Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biol 2023; 21:215. [PMID: 37833744 PMCID: PMC10576358 DOI: 10.1186/s12915-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. RESULTS We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. CONCLUSIONS Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
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Affiliation(s)
- Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | | | | | | | | | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek, Namibia
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
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23
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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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24
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Preckler-Quisquater S, Kierepka EM, Reding DM, Piaggio AJ, Sacks BN. Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages? Mol Ecol 2023; 32:5323-5337. [PMID: 37632719 DOI: 10.1111/mec.17105] [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: 01/12/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500-3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70-200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today's contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms.
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Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Elizabeth M Kierepka
- North Carolina Museum of Natural Sciences, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Dawn M Reding
- Department of Biology, Luther College, Decorah, Iowa, USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services, National Wildlife Research Center, Wildlife Genetics Lab, Fort Collins, Colorado, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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25
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Saarman NP, Son JH, Zhao H, Cosme LV, Kong Y, Li M, Wang S, Weiss BL, Echodu R, Opiro R, Aksoy S, Caccone A. Genomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 114:105501. [PMID: 37709241 PMCID: PMC10593118 DOI: 10.1016/j.meegid.2023.105501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The primary vector of the trypanosome parasite causing human and animal African trypanosomiasis in Uganda is the riverine tsetse fly Glossina fuscipes fuscipes (Gff). Our study improved the Gff genome assembly with whole genome 10× Chromium sequencing of a lab reared pupae, identified autosomal versus sex-chromosomal regions of the genome with ddRAD-seq data from 627 field caught Gff, and identified SNPs associated with trypanosome infection with genome-wide association (GWA) analysis in a subset of 351 flies. Results from 10× Chromium sequencing greatly improved Gff genome assembly metrics and assigned a full third of the genome to the sex chromosome. Results from ddRAD-seq suggested possible sex-chromosome aneuploidy in Gff and identified a single autosomal SNP to be highly associated with trypanosome infection. The top associated SNP was ∼1100 bp upstream of the gene lecithin cholesterol acyltransferase (LCAT), an important component of the molecular pathway that initiates trypanosome lysis and protection in mammals. Results suggest that there may be naturally occurring genetic variation in Gff in genomic regions in linkage disequilibrium with LCAT that can protect against trypanosome infection, thereby paving the way for targeted research into novel vector control strategies that can promote parasite resistance in natural populations.
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Affiliation(s)
| | - Jae Hak Son
- Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Hongyu Zhao
- Yale School of Public Health, New Haven, CT, USA.
| | | | - Yong Kong
- Yale School of Public Health, New Haven, CT, USA.
| | - Mo Li
- Yale School of Public Health, New Haven, CT, USA
| | | | | | | | | | - Serap Aksoy
- Yale School of Public Health, New Haven, CT, USA.
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26
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Laine VN, Sävilammi T, Wahlberg N, Meramo K, Ossa G, Johnson JS, Blomberg AS, Yeszhanov AB, Yung V, Paterson S, Lilley TM. Whole-genome Analysis Reveals Contrasting Relationships Among Nuclear and Mitochondrial Genomes Between Three Sympatric Bat Species. Genome Biol Evol 2022; 15:6955983. [PMID: 36546695 PMCID: PMC9825270 DOI: 10.1093/gbe/evac175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 11/30/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Understanding mechanisms involved in speciation can be challenging, especially when hybridization or introgression blurs species boundaries. In bats, resolving relationships of some closely related groups has proved difficult due subtle interspecific variation both in morphometrics and molecular data sets. The endemic South American Histiotus bats, currently considered a subgenus of Eptesicus, harbor unresolved phylogenetic relationships and of those is a trio consisting of two closely related species: Eptesicus (Histiotus) macrotus and Eptesicus (Histiotus) montanus, and their relationship with a third, Eptesicus (Histiotus) magellanicus. The three sympatric species bear marked resemblance to each other, but can be differentiated morphologically. Furthermore, previous studies have been unable to differentiate the species from each other at a molecular level. In order to disentangle the phylogenetic relationships of these species, we examined the differentiation patterns and evolutionary history of the three Eptesicus (H.) species at the whole-genome level. The nuclear DNA statistics between the species suggest strong gene flow and recent hybridization between E. (H.) montanus and E. (H.) macrotus, whereas E. (H.) magellanicus shows a higher degree of isolation. In contrast, mitochondrial DNA shows a closer relationship between E. (H.) magellanicus and E. (H.) montanus. Opposing patterns in mtDNA and nuclear markers are often due to differences in dispersal, and here it could be both as a result of isolation in refugia during the last glacial maximum and female philopatry and male-biased dispersal. In conclusion, this study shows the importance of both the nuclear and mitochondrial DNA in resolving phylogenetic relationships and species histories.
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Affiliation(s)
- Veronika N Laine
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Tiina Sävilammi
- Department of Biology, University of Turku, Turku, Finland,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | | | - Katarina Meramo
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Gonzalo Ossa
- ConserBat EIRL, San Fabian, Chile,Asociación Murciélagos de Chile Pinüike, Santiago, Chile
| | - Joseph S Johnson
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | | | - Aidyn B Yeszhanov
- Institute of Zoology of the Ministry of Science and Education of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Veronica Yung
- Departamento Laboratorio Biomédico, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Steve Paterson
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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27
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Deng X, Frandsen PB, Dikow RB, Favre A, Shah DN, Shah RDT, Schneider JV, Heckenhauer J, Pauls SU. The impact of sequencing depth and relatedness of the reference genome in population genomic studies: A case study with two caddisfly species (Trichoptera, Rhyacophilidae, Himalopsyche). Ecol Evol 2022; 12:e9583. [PMID: 36523526 PMCID: PMC9745013 DOI: 10.1002/ece3.9583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/10/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Whole genome sequencing for generating SNP data is increasingly used in population genetic studies. However, obtaining genomes for massive numbers of samples is still not within the budgets of many researchers. It is thus imperative to select an appropriate reference genome and sequencing depth to ensure the accuracy of the results for a specific research question, while balancing cost and feasibility. To evaluate the effect of the choice of the reference genome and sequencing depth on downstream analyses, we used five confamilial reference genomes of variable relatedness and three levels of sequencing depth (3.5×, 7.5× and 12×) in a population genomic study on two caddisfly species: Himalopsyche digitata and H. tibetana. Using these 30 datasets (five reference genomes × three depths × two target species), we estimated population genetic indices (inbreeding coefficient, nucleotide diversity, pairwise F ST, and genome-wide distribution of F ST) based on variants and population structure (PCA and admixture) based on genotype likelihood estimates. The results showed that both distantly related reference genomes and lower sequencing depth lead to degradation of resolution. In addition, choosing a more closely related reference genome may significantly remedy the defects caused by low depth. Therefore, we conclude that population genetic studies would benefit from closely related reference genomes, especially as the costs of obtaining a high-quality reference genome continue to decrease. However, to determine a cost-efficient strategy for a specific population genomic study, a trade-off between reference genome relatedness and sequencing depth can be considered.
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Affiliation(s)
- Xi‐Ling Deng
- Senckenberg Research Institute and Natural History MuseumFrankfurt/MainGermany
- Institute of Insect BiotechnologyJustus‐Liebig‐University GießenGießenGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt/MainGermany
| | - Paul B. Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt/MainGermany
- Department of Plant & Wildlife SciencesBrigham Young UniversityProvoUtahUSA
- Data Science Lab, Office of the Chief Information OfficerSmithsonian InstitutionWashingtonDCUSA
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information OfficerSmithsonian InstitutionWashingtonDCUSA
| | - Adrien Favre
- Senckenberg Research Institute and Natural History MuseumFrankfurt/MainGermany
- Regional Nature Park of the Trient ValleySalvanSwitzerland
| | - Deep Narayan Shah
- Central Department of Environmental ScienceTribhuvan UniversityKirtipurNepal
| | - Ram Devi Tachamo Shah
- Aquatic Ecology Centre, School of ScienceKathmandu UniversityDhulikhelNepal
- Department of Life SciencesSchool of Science, Kathmandu UniversityDhulikhelNepal
| | - Julio V. Schneider
- Senckenberg Research Institute and Natural History MuseumFrankfurt/MainGermany
| | - Jacqueline Heckenhauer
- Senckenberg Research Institute and Natural History MuseumFrankfurt/MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt/MainGermany
| | - Steffen U. Pauls
- Senckenberg Research Institute and Natural History MuseumFrankfurt/MainGermany
- Institute of Insect BiotechnologyJustus‐Liebig‐University GießenGießenGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt/MainGermany
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28
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Wang Z, Chen L, Li Q, Zhang H, Shan Y, Qi L, Wang H, Chen Y. Association between single-nucleotide polymorphism rs145497186 related to NDUFV2 and lumbar disc degeneration: a pilot case–control study. J Orthop Surg Res 2022; 17:473. [PMID: 36309697 PMCID: PMC9618206 DOI: 10.1186/s13018-022-03368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/23/2022] [Indexed: 11/10/2022] Open
Abstract
Objective The association between the single-nucleotide polymorphisms (SNPs) rs28742109, rs12955018, rs987850, rs8093805, rs12965084 and rs145497186 related to gene named NADH dehydrogenase [ubiquinone] flavoprotein 2 (NDUFV2) and lumbar disc degeneration (LDD) was preliminary investigated in a small sample size.
Methods A total of 46 patients with LDD and 45 controls were recruited at Qilu Hospital of Shandong University, and each participant provided 5 mL peripheral venous blood. NA was extracted from the blood of each participant for further genotyping. The frequency of different genotypes in the case group and control group was determined, and analysis of the risk of LDD associated with different SNP genotypes was performed. The visual analogue scale (VAS) scores of the patients’ degree of chronic low back pain were calculated, and the relationship between VAS scores and SNPs was analysed.
Results After excluding the influence of sex, age, height, and weight on LDD, a significant association between SNP rs145497186 related to NDUFV2 and LDD persisted (P = 0.006). Simultaneously, rs145497186 was found to be associated with chronic low back pain in LDD populations.
Conclusion NDUFV2 rs145497186 SNP could be associated with susceptibility to LDD and the degree of chronic low back pain. Supplementary Information The online version contains supplementary material available at 10.1186/s13018-022-03368-y.
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29
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Çilingir FG, A'Bear L, Hansen D, Davis LR, Bunbury N, Ozgul A, Croll D, Grossen C. Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population. Gigascience 2022; 11:giac090. [PMID: 36251273 PMCID: PMC9553416 DOI: 10.1093/gigascience/giac090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/22/2022] [Accepted: 09/12/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is listed as Vulnerable on the International Union for Conservation of Nature Red List (v2.3) due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts for both wild and ex situpopulations. A high-quality genome would also open avenues to investigate the genetic basis of the species' exceptionally long life span. FINDINGS We produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture. We produced a 2.37-Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNA sequencing-assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. To assess the utility of the high-quality assembly for species conservation, we performed a low-coverage resequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. We further identified putatively deleterious mutations to be monitored. CONCLUSIONS We establish a high-quality chromosome-level reference genome for A. gigantea and one of the most complete turtle genomes available. We show that low-coverage whole-genome resequencing, for which alignment to the reference genome is a necessity, is a powerful tool to assess the population structure of the wild population and reveal the geographic origins of ex situ individuals relevant for genetic diversity management and rewilding efforts.
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Affiliation(s)
- F Gözde Çilingir
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Luke A'Bear
- Seychelles Islands Foundation, Victoria, Republic of Seychelles
| | - Dennis Hansen
- Zoological Museum, University of Zurich, Zurich 8006, Switzerland
- Indian Ocean Tortoise Alliance, Ile Cerf, Victoria, Republic of Seychelles
| | | | - Nancy Bunbury
- Seychelles Islands Foundation, Victoria, Republic of Seychelles
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Arpat Ozgul
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Daniel Croll
- Institute of Biology, University of Neuchâtel, Neuchâtel 2000, Switzerland
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
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Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level. Curr Biol 2022; 32:4360-4371.e6. [PMID: 36087578 DOI: 10.1016/j.cub.2022.08.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022]
Abstract
Supergenes govern multi-trait-balanced polymorphisms in a wide range of systems; however, our understanding of their origins and evolution remains incomplete. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown whether hemizygosity is pervasive among distyly S-loci. As hemizygosity has major consequences for supergene evolution and loss, clarifying whether this genetic architecture is shared among distylous species is critical. Here, we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes, provide a counterexample to classic inversion-based supergenes, and shed new light on the origin and maintenance of an iconic floral polymorphism.
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Jin L, Li Z, Wang C, Wang Y, Li X, Yang J, Zhao Y, Guo B. Contrasting population differentiation in two sympatric Triplophysa loaches on the Qinghai-Tibet Plateau. Front Genet 2022; 13:958076. [PMID: 36092882 PMCID: PMC9452750 DOI: 10.3389/fgene.2022.958076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Genetic differentiation in aquatic organisms is usually shaped by drainage connectivity. Sympatric aquatic species are thus expected to show similar population differentiation patterns and similar genetic responses to their habitats. Water bodies on the Qinghai-Tibet Plateau (QTP) have recently experienced dramatic physicochemical changes, threatening the biodiversity of aquatic organisms on the "roof of the world." To uncover ecological genetics in Tibetan loaches (Triplophysa)-the largest component of the QTP ichthyofauna-we characterized population differentiation patterns and adaptive mechanisms to salinity change in two sympatric and phylogenetically closely related Tibetan loaches, T. stewarti and T. stenura, by integrating population genomic, transcriptomic, and electron probe microanalysis approaches. Based on millions of genome-wide SNPs, the two Tibetan loach species show contrasting population differentiation patterns, with highly geographically structured and clear genetic differentiation among T. stewarti populations, whereas there is no such observation in T. stenura, which is also supported by otolith microchemistry mapping. While limited genetic signals of parallel adaption to salinity changes between the two species are found from either genetic or gene expression variation perspective, a catalog of genes involved in ion transport, energy metabolism, structural reorganization, immune response, detoxification, and signal transduction is identified to be related to adaptation to salinity change in Triplophysa loaches. Together, our findings broaden our understanding of the population characteristics and adaptive mechanisms in sympatric Tibetan loach species and would contribute to biodiversity conservation and management of aquatic organisms on the QTP.
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Affiliation(s)
- Ling Jin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zitong Li
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Chongnv Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yingnan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jian Yang
- Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Yahui Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
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Limited domestic introgression in a final refuge of the wild pigeon. iScience 2022; 25:104620. [PMID: 35880028 PMCID: PMC9308148 DOI: 10.1016/j.isci.2022.104620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 05/27/2022] [Accepted: 06/10/2022] [Indexed: 01/07/2023] Open
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Mas-Sandoval A, Pope NS, Nielsen KN, Altinkaya I, Fumagalli M, Korneliussen TS. Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data. Gigascience 2022; 11:giac032. [PMID: 35579549 PMCID: PMC9112775 DOI: 10.1093/gigascience/giac032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/16/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The site frequency spectrum summarizes the distribution of allele frequencies throughout the genome, and it is widely used as a summary statistic to infer demographic parameters and to detect signals of natural selection. The use of high-throughput low-coverage DNA sequencing data can lead to biased estimates of the site frequency spectrum due to high levels of uncertainty in genotyping. RESULTS Here we design and implement a method to efficiently and accurately estimate the multidimensional joint site frequency spectrum for large numbers of haploid or diploid individuals across an arbitrary number of populations, using low-coverage sequencing data. The method maximizes a likelihood function that represents the probability of the sequencing data observed given a multidimensional site frequency spectrum using genotype likelihoods. Notably, it uses an advanced binning heuristic paired with an accelerated expectation-maximization algorithm for a fast and memory-efficient computation, and can generate both unfolded and folded spectra and bootstrapped replicates for haploid and diploid genomes. On the basis of extensive simulations, we show that the new method requires remarkably less storage and is faster than previous implementations whilst retaining the same accuracy. When applied to low-coverage sequencing data from the fungal pathogen Neonectria neomacrospora, results recapitulate the patterns of population differentiation generated using the original high-coverage data. CONCLUSION The new implementation allows for accurate estimation of population genetic parameters from arbitrarily large, low-coverage datasets, thus facilitating cost-effective sequencing experiments in model and non-model organisms.
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Affiliation(s)
- Alex Mas-Sandoval
- Department of Life Sciences, Silwood Park campus, Imperial College London, SL5 7PY, Ascot, UK
| | - Nathaniel S Pope
- Department of Entomology, The Pennsylvania State University, 201 Old Main, University Park, PA 16802, USA
| | - Knud Nor Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Isin Altinkaya
- GLOBE, Section for Geogenetics, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park campus, Imperial College London, SL5 7PY, Ascot, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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Thomas L, Underwood JN, Rose NH, Fuller ZL, Richards ZT, Dugal L, Grimaldi CM, Cooke IR, Palumbi SR, Gilmour JP. Spatially varying selection between habitats drives physiological shifts and local adaptation in a broadcast spawning coral on a remote atoll in Western Australia. SCIENCE ADVANCES 2022; 8:eabl9185. [PMID: 35476443 PMCID: PMC9045720 DOI: 10.1126/sciadv.abl9185] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterizing the mechanisms of coral resilience to climate change. To explore these mechanisms in the reef coral Acropora tenuis, we collected samples from lagoon and reef slope habitats and combined whole-genome sequencing, ITS2 metabarcoding, experimental heat stress, and transcriptomics. Despite high gene flow across the atoll, we identified clear shifts in allele frequencies between habitats at relatively small linked genomic islands. Common garden heat stress assays showed corals from the lagoon to be more resistant to bleaching, and RNA sequencing revealed marked differences in baseline levels of gene expression between habitats. Our results provide new insight into the complex mechanisms of coral resilience to climate change and highlight the potential for spatially varying selection across complex coral reef seascapes to drive pronounced ecological divergence in climate-related traits.
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Affiliation(s)
- Luke Thomas
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
- UWA Oceans Institute, Oceans Graduate School, The University of Western Australia, Crawley, Australia
- Corresponding author.
| | - Jim N. Underwood
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
| | - Noah H. Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Zachary L. Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Zoe T. Richards
- Coral Conservation and Research Group, School of Molecular and Life Sciences, Curtin University, Perth, Australia
- Collections and Research, Western Australian Museum, Welshpool, Australia
| | - Laurence Dugal
- UWA Oceans Institute, Oceans Graduate School, The University of Western Australia, Crawley, Australia
| | - Camille M. Grimaldi
- UWA Oceans Institute, Oceans Graduate School, The University of Western Australia, Crawley, Australia
| | - Ira R. Cooke
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Stephen R. Palumbi
- Hopkins Marine Station, Biology Department, Stanford University, Pacific Grove, CA, USA
| | - James P. Gilmour
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
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Çilingir FG, Hansen D, Bunbury N, Postma E, Baxter R, Turnbull L, Ozgul A, Grossen C. Low-coverage reduced representation sequencing reveals subtle within-island genetic structure in Aldabra giant tortoises. Ecol Evol 2022; 12:e8739. [PMID: 35342600 PMCID: PMC8931707 DOI: 10.1002/ece3.8739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/01/2023] Open
Abstract
Aldabrachelys gigantea (Aldabra giant tortoise) is one of only two giant tortoise species left in the world and survives as a single wild population of over 100,000 individuals on Aldabra Atoll, Seychelles. Despite this large current population size, the species faces an uncertain future because of its extremely restricted distribution range and high vulnerability to the projected consequences of climate change. Captive-bred A. gigantea are increasingly used in rewilding programs across the region, where they are introduced to replace extinct giant tortoises in an attempt to functionally resurrect degraded island ecosystems. However, there has been little consideration of the current levels of genetic variation and differentiation within and among the islands on Aldabra. As previous microsatellite studies were inconclusive, we combined low-coverage and double-digest restriction-associated DNA (ddRAD) sequencing to analyze samples from 33 tortoises (11 from each main island). Using 5426 variant sites within the tortoise genome, we detected patterns of within-island population structure, but no differentiation between the islands. These unexpected results highlight the importance of using genome-wide genetic markers to capture higher-resolution genetic structure to inform future management plans, even in a seemingly panmictic population. We show that low-coverage ddRAD sequencing provides an affordable alternative approach to conservation genomic projects of non-model species with large genomes.
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Affiliation(s)
- F. Gözde Çilingir
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Dennis Hansen
- Zoological MuseumUniversity of ZurichZurichSwitzerland
- Indian Ocean Tortoise AllianceVictoriaSeychelles
| | - Nancy Bunbury
- Seychelles Islands FoundationVictoriaSeychelles
- Centre for Ecology and ConservationCollege of Life and Environmental SciencesUniversity of ExeterPenrynUK
| | - Erik Postma
- Centre for Ecology and ConservationCollege of Life and Environmental SciencesUniversity of ExeterPenrynUK
| | | | | | - Arpat Ozgul
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
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Severson AL, Korneliussen TS, Moltke I. LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data. Bioinformatics 2022; 38:1159-1161. [PMID: 34718411 PMCID: PMC8796377 DOI: 10.1093/bioinformatics/btab732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/28/2021] [Accepted: 10/24/2021] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION Inference of identity-by-descent (IBD) sharing along the genome between pairs of individuals has important uses. But all existing inference methods are based on genotypes, which is not ideal for low-depth Next Generation Sequencing (NGS) data from which genotypes can only be called with high uncertainty. RESULTS We present a new probabilistic software tool, LocalNgsRelate, for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data. Its inference is based on genotype likelihoods instead of genotypes, and thereby it takes the uncertainty of the genotype calling into account. Using real data from the 1000 Genomes project, we show that LocalNgsRelate provides more accurate IBD inference for low-depth NGS data than two state-of-the-art genotype-based methods, Albrechtsen et al. (2009) and hap-IBD. We also show that the method works well for NGS data down to a depth of 2×. AVAILABILITY AND IMPLEMENTATION LocalNgsRelate is freely available at https://github.com/idamoltke/LocalNgsRelate. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alissa L Severson
- Department of Genetics, Stanford University, Stanford, CA 94305-5020, USA
| | | | - Ida Moltke
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
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37
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Conservation Genomics of Two Threatened Subspecies of Northern Giraffe: The West African and the Kordofan Giraffe. Genes (Basel) 2022; 13:genes13020221. [PMID: 35205265 PMCID: PMC8872558 DOI: 10.3390/genes13020221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 11/17/2022] Open
Abstract
Three of the four species of giraffe are threatened, particularly the northern giraffe (Giraffa camelopardalis), which collectively have the smallest known wild population estimates. Among the three subspecies of the northern giraffe, the West African giraffe (Giraffa camelopardalis peralta) had declined to 49 individuals by 1996 and only recovered due to conservation efforts undertaken in the past 25 years, while the Kordofan giraffe (Giraffa camelopardalis antiquorum) remains at <2300 individuals distributed in small, isolated populations over a large geographical range in Central Africa. These combined factors could lead to genetically depauperated populations. We analyzed 119 mitochondrial sequences and 26 whole genomes of northern giraffe individuals to investigate their population structure and assess the recent demographic history and current genomic diversity of West African and Kordofan giraffe. Phylogenetic and population structure analyses separate the three subspecies of northern giraffe and suggest genetic differentiation between populations from eastern and western areas of the Kordofan giraffe’s range. Both West African and Kordofan giraffe show a gradual decline in effective population size over the last 10 ka and have moderate genome-wide heterozygosity compared to other giraffe species. Recent inbreeding levels are higher in the West African giraffe and in Kordofan giraffe from Garamba National Park, Democratic Republic of Congo. Although numbers for both West African and some populations of Kordofan giraffe have increased in recent years, the threat of habitat loss, climate change impacts, and illegal hunting persists. Thus, future conservation actions should consider close genetic monitoring of populations to detect and, where practical, counteract negative trends that might develop.
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Guzmán NV, Kemppainen P, Monti D, Castillo ERD, Rodriguero MS, Sánchez-Restrepo AF, Cigliano MM, Confalonieri VA. Stable inversion clines in a grasshopper species group despite complex geographical history. Mol Ecol 2021; 31:1196-1215. [PMID: 34862997 DOI: 10.1111/mec.16305] [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: 05/21/2020] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022]
Abstract
Chromosomal inversions are known to play roles in adaptation and differentiation in many species. They involve clusters of correlated genes (i.e., loci in linkage disequilibrium, LD) possibly associated with environmental variables. The grasshopper "species complex" Trimerotropis pallidipennis comprises several genetic lineages distributed from North to South America in arid and semi-arid high-altitude environments. The southernmost lineage, Trimerotropis sp., segregates for four to seven putative inversions that display clinal variation, possibly through adaptation to temperate environments. We analysed chromosomal, mitochondrial and genome-wide single nucleotide polymorphism data in 19 Trimerotropis sp. populations mainly distributed along two altitudinal gradients (MS and Ju). Populations across Argentina comprise two main chromosomally and genetically differentiated lineages: one distributed across the southernmost border of the "Andes Centrales," adding evidence for a differentiation hotspot in this area; and the other widely distributed in Argentina. Within the latter, network analytical approaches to LD found three clusters of correlated loci (LD-clusters), with inversion karyotypes explaining >79% of the genetic variation. Outlier loci associated with environmental variables mapped to two of these LD-clusters. Furthermore, despite the complex geographical history indicated by population genetic analyses, the clines in inversion karyotypes have remained stable for more than 20 generations, implicating their role in adaptation and differentiation within this lineage. We hypothesize that these clines could be the consequence of a coupling between extrinsic postzygotic barriers and spatially varying selection along environmental gradients resulting in a hybrid zone. These results provide a framework for future investigations about candidate genes implicated in rapid adaptation to new environments.
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Affiliation(s)
- Noelia V Guzmán
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Daniela Monti
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
| | - Elio R D Castillo
- Laboratorio de Genética Evolutiva "Dr. Claudio J. Bidau", FCEQyN, Universidad Nacional de Misiones (UNaM), Instituto de Biología Subtropical (IBS) (CONICET/UNaM), LQH, Posadas, Misiones, Argentina
| | - Marcela S Rodriguero
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
| | - Andrés F Sánchez-Restrepo
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina.,Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina
| | - Maria Marta Cigliano
- Museo de La Plata, Centro de Estudios Parasitológicos y de Vectores (CEPAVE- CONICET/UNLP), Universidad Nacional de la Plata, Buenos Aires, Argentina
| | - Viviana A Confalonieri
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
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Dahms C, Kemppainen P, Zanella LN, Zanella D, Carosi A, Merilä J, Momigliano P. Cast away in the Adriatic: Low degree of parallel genetic differentiation in three-spined sticklebacks. Mol Ecol 2021; 31:1234-1253. [PMID: 34843145 DOI: 10.1111/mec.16295] [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] [Received: 07/28/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
The three-spined stickleback (Gasterosteus aculeatus) has repeatedly and independently adapted to freshwater habitats from standing genetic variation (SGV) following colonization from the sea. However, in the Mediterranean Sea G. aculeatus is believed to have gone extinct, and thus the spread of locally adapted alleles between different freshwater populations via the sea since then has been highly unlikely. This is expected to limit parallel evolution, that is the extent to which phylogenetically related alleles can be shared among independently colonized freshwater populations. Using whole genome and 2b-RAD sequencing data, we compared levels of genetic differentiation and genetic parallelism of 15 Adriatic stickleback populations to 19 Pacific, Atlantic and Caspian populations, where gene flow between freshwater populations across extant marine populations is still possible. Our findings support previous studies suggesting that Adriatic populations are highly differentiated (average FST ≈ 0.45), of low genetic diversity and connectivity, and likely to stem from multiple independent colonizations during the Pleistocene. Linkage disequilibrium network analyses in combination with linear mixed models nevertheless revealed several parallel marine-freshwater differentiated genomic regions, although still not to the extent observed elsewhere in the world. We hypothesize that current levels of genetic parallelism in the Adriatic lineages are a relic of freshwater adaptation from SGV prior to the extinction of marine sticklebacks in the Mediterranean that has persisted despite substantial genetic drift experienced by the Adriatic stickleback isolates.
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Affiliation(s)
- Carolin Dahms
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Linda N Zanella
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Davor Zanella
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Antonella Carosi
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Perugia, Italy
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Division for Ecology and Biodiversity, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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Lou RN, Therkildsen NO. Batch effects in population genomic studies with low-coverage whole genome sequencing data: Causes, detection and mitigation. Mol Ecol Resour 2021; 22:1678-1692. [PMID: 34825778 DOI: 10.1111/1755-0998.13559] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 01/04/2023]
Abstract
Over the past few decades, there has been an explosion in the amount of publicly available sequencing data. This opens new opportunities for combining data sets to achieve unprecedented sample sizes, spatial coverage or temporal replication in population genomic studies. However, a common concern is that nonbiological differences between data sets may generate patterns of variation in the data that can confound real biological patterns, a problem known as batch effects. In this paper, we compare two batches of low-coverage whole genome sequencing (lcWGS) data generated from the same populations of Atlantic cod (Gadus morhua). First, we show that with a "batch-effect-naive" bioinformatic pipeline, batch effects systematically biased our genetic diversity estimates, population structure inference and selection scans. We then demonstrate that these batch effects resulted from multiple technical differences between our data sets, including the sequencing chemistry (four-channel vs. two-channel), sequencing run, read type (single-end vs. paired-end), read length (125 vs. 150 bp), DNA degradation level (degraded vs. well preserved) and sequencing depth (0.8× vs. 0.3× on average). Lastly, we illustrate that a set of simple bioinformatic strategies (such as different read trimming and single nucleotide polymorphism filtering) can be used to detect batch effects in our data and substantially mitigate their impact. We conclude that combining data sets remains a powerful approach as long as batch effects are explicitly accounted for. We focus on lcWGS data in this paper, which may be particularly vulnerable to certain causes of batch effects, but many of our conclusions also apply to other sequencing strategies.
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Ferchaud AL, Mérot C, Normandeau E, Ragoussis J, Babin C, Djambazian H, Bérubé P, Audet C, Treble M, Walkusz W, Bernatchez L. Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (Reinhardtius hippoglossoides). G3-GENES GENOMES GENETICS 2021; 12:6428537. [PMID: 34791178 DOI: 10.1093/g3journal/jkab376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022]
Abstract
Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that, similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex-determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.
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Affiliation(s)
- Anne-Laure Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Charles Babin
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Haig Djambazian
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Pierre Bérubé
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Margaret Treble
- Fisheries and Oceans Canada, Winnipeg Department, Arctic Aquatic Research Division, Freshwater Institute Winnipeg, Manitoba, R3T2N6, Canada
| | - Wocjciech Walkusz
- Fisheries and Oceans Canada, Winnipeg Department, Arctic Aquatic Research Division, Freshwater Institute Winnipeg, Manitoba, R3T2N6, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
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42
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Louis M, Galimberti M, Archer F, Berrow S, Brownlow A, Fallon R, Nykänen M, O'Brien J, Roberston KM, Rosel PE, Simon-Bouhet B, Wegmann D, Fontaine MC, Foote AD, Gaggiotti OE. Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. SCIENCE ADVANCES 2021; 7:eabg1245. [PMID: 34705499 PMCID: PMC8550227 DOI: 10.1126/sciadv.abg1245] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 09/08/2021] [Indexed: 05/27/2023]
Abstract
Studying repeated adaptation can provide insights into the mechanisms allowing species to adapt to novel environments. Here, we investigate repeated evolution driven by habitat specialization in the common bottlenose dolphin. Parapatric pelagic and coastal ecotypes of common bottlenose dolphins have repeatedly formed across the oceans. Analyzing whole genomes of 57 individuals, we find that ecotype evolution involved a complex reticulated evolutionary history. We find parallel linked selection acted upon ancient alleles in geographically distant coastal populations, which were present as standing genetic variation in the pelagic populations. Candidate loci evolving under parallel linked selection were found in ancient tracts, suggesting recurrent bouts of selection through time. Therefore, despite the constraints of small effective population size and long generation time on the efficacy of selection, repeated adaptation in long-lived social species can be driven by a combination of ecological opportunities and selection acting on ancestral standing genetic variation.
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Affiliation(s)
- Marie Louis
- Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews KY16 8LB, Scotland, UK
- Centre d'Etudes Biologiques de Chize, La Rochelle Université, 17000 La Rochelle, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
- Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350 Copenhagen, Denmark
| | - Marco Galimberti
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Frederick Archer
- National Marine Fisheries Service, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA
- Scripps Institution of Oceanography, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Galway-Mayo Institute of Technology, Dublin Road, H91 T8NW Galway, Ireland
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ramon Fallon
- School of Medicine, University of St Andrews, North Haugh, St Andrews, Fife KY16 9TF, Scotland, UK
| | | | - Joanne O'Brien
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Galway-Mayo Institute of Technology, Dublin Road, H91 T8NW Galway, Ireland
| | - Kelly M Roberston
- National Marine Fisheries Service, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA
| | - Patricia E Rosel
- National Marine Fisheries Service, Southeast Fisheries Science Center, NOAA, 646 Cajundome Boulevard, Lafayette, LA 70506, USA
| | - Benoit Simon-Bouhet
- Centre d'Etudes Biologiques de Chize, La Rochelle Université, 17000 La Rochelle, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES), Montpellier, France
| | - Andrew D Foote
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, UK
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim 7012, Norway
| | - Oscar E Gaggiotti
- Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews KY16 8LB, Scotland, UK
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43
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Lewald KM, Abrieux A, Wilson DA, Lee Y, Conner WR, Andreazza F, Beers EH, Burrack HJ, Daane KM, Diepenbrock L, Drummond FA, Fanning PD, Gaffney MT, Hesler SP, Ioriatti C, Isaacs R, Little BA, Loeb GM, Miller B, Nava DE, Rendon D, Sial AA, da Silva CSB, Stockton DG, Van Timmeren S, Wallingford A, Walton VM, Wang X, Zhao B, Zalom FG, Chiu JC. Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental United States. G3-GENES GENOMES GENETICS 2021; 11:6380432. [PMID: 34599814 PMCID: PMC8664444 DOI: 10.1093/g3journal/jkab343] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/10/2021] [Indexed: 11/14/2022]
Abstract
Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. In this study, we sequenced whole genomes of 237 individual flies collected across the continental United States, as well as several sites in Europe, Brazil, and Asia, to identify and analyze hundreds of thousands of genetic markers. We observed strong population structure between Western and Eastern US populations, but no evidence of any population structure between different latitudes within the continental United States, suggesting that there are no broad-scale adaptations occurring in response to differences in winter climates. We detect admixture from Hawaii to the Western United States and from the Eastern United States to Europe, in agreement with previously identified introduction routes inferred from microsatellite analysis. We also detect potential signals of admixture from the Western United States back to Asia, which could have important implications for shipping and quarantine policies for exported agriculture. We anticipate this large genomic dataset will spur future research into the genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.
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Affiliation(s)
- Kyle M Lewald
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Antoine Abrieux
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Derek A Wilson
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Yoosook Lee
- Florida Medical Entomology Laboratory, University of Florida Institute of Food and Agricultural Sciences, Vero Beach, FL 32603, USA
| | - William R Conner
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Felipe Andreazza
- Laboratory of Entomology, Embrapa Clima Temperado, BR 392 Km 78, Caixa Postal 403, Pelotas, RS 96010-971, Brazil
| | - Elizabeth H Beers
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA 99164, USA
| | - Hannah J Burrack
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27601, USA
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Lauren Diepenbrock
- UF IFAS Citrus Research and Education Center, University of Florida, Lake Alfred, FL 32603, USA
| | - Francis A Drummond
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Philip D Fanning
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Michael T Gaffney
- Horticultural Development Department, Teagasc, Ashtown, Dublin 15, Ireland
| | - Stephen P Hesler
- Department of Entomology, Cornell AgriTech, Cornell University, Geneva, NY 14850, USA
| | - Claudio Ioriatti
- Technology Transfer Centre, Fondazione Edmund Mach, Via E. Mach, 1, 38010 San Michele all'Adige (TN), Italy
| | - Rufus Isaacs
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Brian A Little
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Gregory M Loeb
- Department of Entomology, Cornell AgriTech, Cornell University, Geneva, NY 14850, USA
| | - Betsey Miller
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Dori E Nava
- Laboratory of Entomology, Embrapa Clima Temperado, BR 392 Km 78, Caixa Postal 403, Pelotas, RS 96010-971, Brazil
| | - Dalila Rendon
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Ashfaq A Sial
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | | | - Dara G Stockton
- Department of Entomology, Cornell AgriTech, Cornell University, Geneva, NY 14850, USA.,USDA-ARS, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Steven Van Timmeren
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Anna Wallingford
- Department of Entomology, Cornell AgriTech, Cornell University, Geneva, NY 14850, USA.,Department of Agriculture, Nutrition & Food Systems, University of New Hampshire, Durham, NH 03824, USA
| | - Vaughn M Walton
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Xingeng Wang
- USDA Agricultural Research Service, Beneficial Insects Introduction Research Unit, Newark, DE 19713, USA
| | - Bo Zhao
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27601, USA
| | - Frank G Zalom
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
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Gerard D. Scalable bias-corrected linkage disequilibrium estimation under genotype uncertainty. Heredity (Edinb) 2021; 127:357-362. [PMID: 34373594 PMCID: PMC8479074 DOI: 10.1038/s41437-021-00462-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023] Open
Abstract
Linkage disequilibrium (LD) estimates are often calculated genome-wide for use in many tasks, such as SNP pruning and LD decay estimation. However, in the presence of genotype uncertainty, naive approaches to calculating LD have extreme attenuation biases, incorrectly suggesting that SNPs are less dependent than in reality. These biases are particularly strong in polyploid organisms, which often exhibit greater levels of genotype uncertainty than diploids. A principled approach using maximum likelihood estimation with genotype likelihoods can reduce this bias, but is prohibitively slow for genome-wide applications. Here, we present scalable moment-based adjustments to LD estimates based on the marginal posterior distributions of the genotypes. We demonstrate, on both simulated and real data, that these moment-based estimators are as accurate as maximum likelihood estimators, but are almost as fast as naive approaches based only on posterior mean genotypes. This opens up bias-corrected LD estimation to genome-wide applications. In addition, we provide standard errors for these moment-based estimators. All methods discussed in this manuscript are implemented in the ldsep package, available on the Comprehensive R Archive Network ( https://cran.r-project.org/package=ldsep ).
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, DC, USA.
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45
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Mérot C, Berdan EL, Cayuela H, Djambazian H, Ferchaud AL, Laporte M, Normandeau E, Ragoussis J, Wellenreuther M, Bernatchez L. Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly. Mol Biol Evol 2021; 38:3953-3971. [PMID: 33963409 PMCID: PMC8382925 DOI: 10.1093/molbev/msab143] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed fly Coelopa frigida along a bioclimatic gradient stretching across 10° of latitude, a salinity gradient, and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyze 1,446 low-coverage whole genomes collected along those gradients. We found several large nonrecombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low-recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.
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Affiliation(s)
- Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Hugo Cayuela
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Anne-Laure Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Martin Laporte
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | | | - Maren Wellenreuther
- Seafood Research Unit, Plant & Food Research, Port Nelson, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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46
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Lou RN, Jacobs A, Wilder A, Therkildsen NO. A beginner's guide to low-coverage whole genome sequencing for population genomics. Mol Ecol 2021; 30:5966-5993. [PMID: 34250668 DOI: 10.1111/mec.16077] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/26/2022]
Abstract
Low-coverage whole genome sequencing (lcWGS) has emerged as a powerful and cost-effective approach for population genomic studies in both model and non-model species. However, with read depths too low to confidently call individual genotypes, lcWGS requires specialized analysis tools that explicitly account for genotype uncertainty. A growing number of such tools have become available, but it can be difficult to get an overview of what types of analyses can be performed reliably with lcWGS data, and how the distribution of sequencing effort between the number of samples analyzed and per-sample sequencing depths affects inference accuracy. In this introductory guide to lcWGS, we first illustrate how the per-sample cost for lcWGS is now comparable to RAD-seq and Pool-seq in many systems. We then provide an overview of software packages that explicitly account for genotype uncertainty in different types of population genomic inference. Next, we use both simulated and empirical data to assess the accuracy of allele frequency and genetic diversity estimation, detection of population structure, and selection scans under different sequencing strategies. Our results show that spreading a given amount of sequencing effort across more samples with lower depth per sample consistently improves the accuracy of most types of inference, with a few notable exceptions. Finally, we assess the potential for using imputation to bolster inference from lcWGS data in non-model species, and discuss current limitations and future perspectives for lcWGS-based population genomics research. With this overview, we hope to make lcWGS more approachable and stimulate its broader adoption.
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Affiliation(s)
- Runyang Nicolas Lou
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA
| | - Arne Jacobs
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Aryn Wilder
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA
| | - Nina O Therkildsen
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA
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47
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Castanera R, Vendrell-Mir P, Bardil A, Carpentier MC, Panaud O, Casacuberta JM. Amplification dynamics of miniature inverted-repeat transposable elements and their impact on rice trait variability. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:118-135. [PMID: 33866641 DOI: 10.1111/tpj.15277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Transposable elements (TEs) are a rich source of genetic variability. Among TEs, miniature inverted-repeat TEs (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latter through a typical cut-and-paste mechanism. However, MITEs are typically present at much higher copy numbers than class II transposons. We present here an analysis of 103 109 transposon insertion polymorphisms (TIPs) in 738 Oryza sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with its domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP-genome-wide association studies (TIP-GWAS) to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than single nucleotide polymorphisms (SNPs) on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidence of the replicative amplification of MITEs.
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Affiliation(s)
- Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Pol Vendrell-Mir
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Amélie Bardil
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex, 66860, France
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex, 66860, France
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
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48
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Rippe JP, Dixon G, Fuller ZL, Liao Y, Matz M. Environmental specialization and cryptic genetic divergence in two massive coral species from the Florida Keys Reef Tract. Mol Ecol 2021; 30:3468-3484. [PMID: 33894013 DOI: 10.1111/mec.15931] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/22/2021] [Accepted: 04/14/2021] [Indexed: 01/02/2023]
Abstract
Broadcast-spawning coral species have wide geographical ranges spanning strong environmental gradients, but it is unclear how much spatially varying selection these gradients actually impose. Strong divergent selection might present a considerable barrier for demographic exchange between disparate reef habitats. We investigated whether the cross-shelf gradient is associated with spatially varying selection in two common coral species, Montastraea cavernosa and Siderastrea siderea, in the Florida Keys. To this end, we generated a de novo genome assembly for M. cavernosa and used 2bRAD to genotype 20 juveniles and 20 adults of both species from each of the three reef zones to identify signatures of selection occurring within a single generation. Unexpectedly, each species was found to be composed of four genetically distinct lineages, with gene flow between them still ongoing but highly reduced in 13.0%-54.7% of the genome. Each species includes two sympatric lineages that are only found in the deep (20 m) habitat, while the other lineages are found almost exclusively on the shallower reefs (3-10 m). The two "shallow" lineages of M. cavernosa are also specialized for either nearshore or offshore: comparison between adult and juvenile cohorts indicates that cross-shelf migrants are more than twice as likely to die before reaching adulthood than local recruits. S. siderea and M. cavernosa are among the most ecologically successful species on the Florida Keys Reef Tract, and this work offers important insight into the genomic background of divergent selection and environmental specialization that may in part explain their resilience and broad environmental range.
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Affiliation(s)
- John P Rippe
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Groves Dixon
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Zachary L Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Yi Liao
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Mikhail Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Fang B, Kemppainen P, Momigliano P, Merilä J. Population structure limits parallel evolution in sticklebacks. Mol Biol Evol 2021; 38:4205-4221. [PMID: 33956140 PMCID: PMC8476136 DOI: 10.1093/molbev/msab144] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Population genetic theory predicts that small effective population sizes (Ne) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e., parallel evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically codistributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius). We found that P. pungitius harbors less genetic diversity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic parallelism across freshwater populations than P. pungitius: 2,996 versus 379 single nucleotide polymorphisms located within 26 versus 9 genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius, respectively. Most regions involved in parallel evolution in G. aculeatus showed increased levels of divergence, suggestive of selection on ancient haplotypes. In contrast, haplotypes involved in freshwater adaptation in P. pungitius were younger. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population subdivision limits local adaptation and therefore also the likelihood of parallel evolution.
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Affiliation(s)
- Bohao Fang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland.,Research Division of Ecology and Biodiversity, Faculty of Science, Kadoorie Building, The University of Hong Kong, Hong Kong SAR
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Coimbra RTF, Winter S, Kumar V, Koepfli KP, Gooley RM, Dobrynin P, Fennessy J, Janke A. Whole-genome analysis of giraffe supports four distinct species. Curr Biol 2021; 31:2929-2938.e5. [PMID: 33957077 DOI: 10.1016/j.cub.2021.04.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 01/06/2021] [Accepted: 04/14/2021] [Indexed: 12/24/2022]
Abstract
Species is the fundamental taxonomic unit in biology and its delimitation has implications for conservation. In giraffe (Giraffa spp.), multiple taxonomic classifications have been proposed since the early 1900s.1 However, one species with nine subspecies has been generally accepted,2 likely due to limited in-depth assessments, subspecies hybridizing in captivity,3,4 and anecdotal reports of hybrids in the wild.5 Giraffe taxonomy received new attention after population genetic studies using traditional genetic markers suggested at least four species.6,7 This view has been met with controversy,8 setting the stage for debate.9,10 Genomics is significantly enhancing our understanding of biodiversity and speciation relative to traditional genetic approaches and thus has important implications for species delineation and conservation.11 We present a high-quality de novo genome assembly of the critically endangered Kordofan giraffe (G. camelopardalis antiquorum)12 and a comprehensive whole-genome analysis of 50 giraffe representing all traditionally recognized subspecies. Population structure and phylogenomic analyses support four separately evolving giraffe lineages, which diverged 230-370 ka ago. These lineages underwent distinct demographic histories and show different levels of heterozygosity and inbreeding. Our results strengthen previous findings of limited gene flow and admixture among putative giraffe species6,7,9 and establish a genomic foundation for recognizing four species and seven subspecies, the latter of which should be considered as evolutionary significant units. Achieving a consensus over the number of species and subspecies in giraffe is essential for adequately assessing their threat level and will improve conservation efforts for these iconic taxa.
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Affiliation(s)
- Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany
| | - Vikas Kumar
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, VA, 22630, USA; Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Rebecca M Gooley
- Smithsonian-Mason School of Conservation, Front Royal, VA, 22630, USA; Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Pavel Dobrynin
- Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr., Saint Petersburg 197101, Russia
| | - Julian Fennessy
- Giraffe Conservation Foundation, PO Box 86099, Eros, Windhoek, Namibia
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
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