101
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Klingler KB, Jahner JP, Parchman TL, Ray C, Peacock MM. Genomic variation in the American pika: signatures of geographic isolation and implications for conservation. BMC Ecol Evol 2021; 21:2. [PMID: 33514306 PMCID: PMC7853312 DOI: 10.1186/s12862-020-01739-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/17/2020] [Indexed: 01/12/2023] Open
Abstract
Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.
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Affiliation(s)
| | - Joshua P Jahner
- Department of Biology, University of Nevada, Reno, 89557, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, 89557, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
| | - Chris Ray
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309-0334, USA
| | - Mary M Peacock
- Department of Biology, University of Nevada, Reno, 89557, USA. .,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.
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102
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Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results? Mol Genet Genomics 2021; 296:457-471. [PMID: 33469716 DOI: 10.1007/s00438-020-01756-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.
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103
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Shryock DF, Washburn LK, DeFalco LA, Esque TC. Harnessing landscape genomics to identify future climate resilient genotypes in a desert annual. Mol Ecol 2021; 30:698-717. [PMID: 33007116 DOI: 10.1111/mec.15672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/16/2022]
Abstract
Local adaptation features critically in shaping species responses to changing environments, complicating efforts to revegetate degraded areas. Rapid climate change poses an additional challenge that could reduce fitness of even locally sourced seeds in restoration. Predictive restoration strategies that apply seeds with favourable adaptations to future climate may promote long-term resilience. Landscape genomics is increasingly used to assess spatial patterns in local adaption and may represent a cost-efficient approach for identifying future-adapted genotypes. To demonstrate such an approach, we genotyped 760 plants from 64 Mojave Desert populations of the desert annual Plantago ovata. Genome scans on 5,960 SNPs identified 184 potentially adaptive loci related to climate and satellite vegetation metrics. Causal modelling indicated that variation in potentially adaptive loci was not confounded by isolation by distance or isolation by habitat resistance. A generalized dissimilarity model (GDM) attributed spatial turnover in potentially adaptive loci to temperature, precipitation and NDVI amplitude, a measure of vegetation green-up potential. By integrating a species distribution model (SDM), we find evidence that summer maximum temperature may both constrain the range of P. ovata and drive adaptive divergence in populations exposed to higher temperatures. Within the species' current range, warm-adapted genotypes are predicted to experience a fivefold expansion in climate niche by midcentury and could harbour key adaptations to cope with future climate. We recommend eight seed transfer zones and project each zone into its relative position in future climate. Prioritizing seed collection efforts on genotypes with expanding future habitat represents a promising strategy for restoration practitioners to address rapidly changing climates.
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Affiliation(s)
- Daniel F Shryock
- U.S. Geological Survey, Western Ecological Research Center, Henderson, NV, USA
| | | | - Lesley A DeFalco
- U.S. Geological Survey, Western Ecological Research Center, Henderson, NV, USA
| | - Todd C Esque
- U.S. Geological Survey, Western Ecological Research Center, Henderson, NV, USA
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104
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Elizabeth Alter S, Tariq L, Creed JK, Megafu E. Evolutionary responses of marine organisms to urbanized seascapes. Evol Appl 2021; 14:210-232. [PMID: 33519966 PMCID: PMC7819572 DOI: 10.1111/eva.13048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/19/2022] Open
Abstract
Many of the world's major cities are located in coastal zones, resulting in urban and industrial impacts on adjacent marine ecosystems. These pressures, which include pollutants, sewage, runoff and debris, temperature increases, hardened shorelines/structures, and light and acoustic pollution, have resulted in new evolutionary landscapes for coastal marine organisms. Marine environmental changes influenced by urbanization may create new selective regimes or may influence neutral evolution via impacts on gene flow or partitioning of genetic diversity across seascapes. While some urban selective pressures, such as hardened surfaces, are similar to those experienced by terrestrial species, others, such as oxidative stress, are specific to aquatic environments. Moreover, spatial and temporal scales of evolutionary responses may differ in the ocean due to the spatial extent of selective pressures and greater capacity for dispersal/gene flow. Here, we present a conceptual framework and synthesis of current research on evolutionary responses of marine organisms to urban pressures. We review urban impacts on genetic diversity and gene flow and examine evidence that marine species are adapting, or are predicted to adapt, to urbanization over rapid evolutionary time frames. Our findings indicate that in the majority of studies, urban stressors are correlated with reduced genetic diversity. Genetic structure is often increased in urbanized settings, but artificial structures can also act as stepping stones for some hard-surface specialists, promoting range expansion. Most evidence for rapid adaptation to urban stressors comes from studies of heritable tolerance to pollutants in a relatively small number of species; however, the majority of marine ecotoxicology studies do not test directly for heritability. Finally, we highlight current gaps in our understanding of evolutionary processes in marine urban environments and present a framework for future research to address these gaps.
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Affiliation(s)
- S. Elizabeth Alter
- Department of Biology & ChemistryCalifornia State University, Monterey BayChapman Academic Science CenterSeasideCAUSA
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
- Department of IchthyologyAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Laraib Tariq
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
| | - James Keanu Creed
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
- Department of IchthyologyAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Emmanuel Megafu
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
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105
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Rugiu L, de Wit P, Kostian I, Jormalainen V. Climate change driven hyposalinity as a selective agent in the littoral mesoherbivore Idotea balthica. MARINE ENVIRONMENTAL RESEARCH 2021; 163:105216. [PMID: 33227618 DOI: 10.1016/j.marenvres.2020.105216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/29/2020] [Accepted: 11/15/2020] [Indexed: 06/11/2023]
Abstract
Climate change will include a decrease in seawater salinity in the Baltic Sea. We quantified the effects of the projected future desalination on survival of the early life stage of the littoral herbivore Idotea balthica. We collected egg-bearing Idotea from three range-margin Baltic Sea populations, we exposed half of each brood to either current (6‰) or future salinity (3.5‰). We genotyped a subsample of each brood to analyse patterns of allelic change and to identify genomic regions targeted by selection. The survival was overall reduced by hyposalinity and broods varied in response to hyposalinity implying genetic variation in tolerance, with a stronger decrease in genetic diversity in future salinity. Finally, we identified proteins with crucial roles in basic cellular functions. This study indicates that projected future northern Baltic Sea hyposalinity will not just hamper I. balthica survival, but its selective pressure may also affect genetic diversity and cell physiology.
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Affiliation(s)
- Luca Rugiu
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden.
| | - Pierre de Wit
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Iita Kostian
- Section of Ecology, Department of Biology, University of Turku, Finland
| | - Veijo Jormalainen
- Section of Ecology, Department of Biology, University of Turku, Finland
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106
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Adaptive Evolution in Cities: Progress and Misconceptions. Trends Ecol Evol 2020; 36:239-257. [PMID: 33342595 DOI: 10.1016/j.tree.2020.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022]
Abstract
Current narratives suggest that urban adaptation - the adaptive evolution of organisms to cities - is pervasive across taxa and cities. However, in reviewing hundreds of studies, we find only six comprehensive examples of species adaptively evolving to urbanization. We discuss the utility and shortcomings of methods for studying urban adaptation. We then review diverse systems offering preliminary evidence for urban adaptation and outline a research program for advancing its study. Urban environments constitute diverse, interacting selective agents that test the limits of adaptation. Understanding urban adaptation therefore offers unique opportunities for addressing fundamental questions in evolutionary biology and for better conserving biodiversity in cities. However, capitalizing on these opportunities requires appropriate research methods and dissemination of accurate narratives.
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107
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Gugger PF, Fitz-Gibbon ST, Albarrán-Lara A, Wright JW, Sork VL. Landscape genomics of Quercus lobata reveals genes involved in local climate adaptation at multiple spatial scales. Mol Ecol 2020; 30:406-423. [PMID: 33179370 DOI: 10.1111/mec.15731] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 10/19/2020] [Accepted: 11/06/2020] [Indexed: 12/29/2022]
Abstract
Understanding how the environment shapes genetic variation provides critical insight about the evolution of local adaptation in natural populations. At multiple spatial scales and multiple geographic contexts within a single species, such information could address a number of fundamental questions about the scale of local adaptation and whether or not the same loci are involved at different spatial scales or geographic contexts. We used landscape genomic approaches from three local elevational transects and rangewide sampling to (a) identify genetic variation underlying local adaptation to environmental gradients in the California endemic oak, Quercus lobata; (b) examine whether putatively adaptive SNPs show signatures of selection at multiple spatial scales; and (c) map putatively adaptive variation to assess the scale and pattern of local adaptation. Of over 10 k single-nucleotide polymorphisms (SNPs) generated with genotyping-by-sequencing, we found signatures of natural selection by climate or local environment at over 600 SNPs (536 loci), some at multiple spatial scales across multiple analyses. Candidate SNPs identified with gene-environment tests (LFMM) at the rangewide scale also showed elevated associations with climate variables compared to the background at both rangewide and elevational transect scales with gradient forest analysis. Some loci overlap with those detected in other oak species, raising the question of whether the same loci might be involved in local climate adaptation in different congeneric species that inhabit different geographic contexts. Mapping landscape patterns of adaptive versus background genetic variation identified regions of marked local adaptation and suggests nonlinear association of candidate SNPs and environmental variables. Taken together, our results offer robust evidence for novel candidate genes for local climate adaptation at multiple spatial scales.
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Affiliation(s)
- Paul F Gugger
- Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, USA
| | - Sorel T Fitz-Gibbon
- Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Ana Albarrán-Lara
- Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Jessica W Wright
- USDA Forest Service, Pacific Southwest Research Station, Davis, CA, USA
| | - Victoria L Sork
- Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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108
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Chen Z, Narum SR. Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout. Mol Ecol 2020; 30:162-174. [PMID: 33135227 DOI: 10.1111/mec.15717] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022]
Abstract
Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. Here, we used low coverage whole-genome resequencing (lcWGR) on individuals to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts. This study includes allele frequency-based analyses for selective sweeps among populations, followed by multiple association tests for specific sets of phenotypes measured under thermal stress (acute and chronic survival/mortality; high or low cardiac performance groups). Depending on the groups in each set of analyses, sequencing reads covered 43%-75% of the genome at ≥15× and each analysis included millions of SNPs across the genome. In tests for selective sweeps among populations, a total of six chromosomal regions were significant. The further association tests for specific phenotypes revealed that the region on chromosome 4 was consistently the most significant and contains the cerk gene (ceramide kinase). This study provides insight into a potential genetic mechanism of local thermal adaptation and suggests cerk may be an important candidate gene. However, further validation of this cerk gene is necessary to determine if the association with cardiac performance results in a functional role to influence thermal performance when exposed to high water temperatures and hypoxic conditions.
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Affiliation(s)
- Zhongqi Chen
- Aquaculture Research Institute, University of Idaho, Hagerman, ID, USA
| | - Shawn R Narum
- Aquaculture Research Institute, University of Idaho, Hagerman, ID, USA.,Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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109
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A comparative genomics multitool for scientific discovery and conservation. Nature 2020; 587:240-245. [PMID: 33177664 PMCID: PMC7759459 DOI: 10.1038/s41586-020-2876-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
Abstract
The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity. A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal—including 131 previously uncharacterized species—from the Zoonomia Project provides data that support biological discovery, medical research and conservation.
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110
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Reid BN, Moran RL, Kopack CJ, Fitzpatrick SW. Rapture-ready darters: Choice of reference genome and genotyping method (whole-genome or sequence capture) influence population genomic inference in Etheostoma. Mol Ecol Resour 2020; 21:404-420. [PMID: 33058399 DOI: 10.1111/1755-0998.13275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/17/2020] [Accepted: 10/01/2020] [Indexed: 11/26/2022]
Abstract
Researchers studying nonmodel organisms have an increasing number of methods available for generating genomic data. However, the applicability of different methods across species, as well as the effect of reference genome choice on population genomic inference, remain difficult to predict in many cases. We evaluated the impact of data type (whole-genome vs. reduced representation) and reference genome choice on data quality and on population genomic and phylogenomic inference across several species of darters (subfamily Etheostomatinae), a highly diverse radiation of freshwater fish. We generated a high-quality reference genome and developed a hybrid RADseq/sequence capture (Rapture) protocol for the Arkansas darter (Etheostoma cragini). Rapture data from 1,900 individuals spanning four darter species showed recovery of most loci across darter species at high depth and consistent estimates of heterozygosity regardless of reference genome choice. Loci with baits spanning both sides of the restriction enzyme cut site performed especially well across species. For low-coverage whole-genome data, choice of reference genome affected read depth and inferred heterozygosity. For similar amounts of sequence data, Rapture performed better at identifying fine-scale genetic structure compared to whole-genome sequencing. Rapture loci also recovered an accurate phylogeny for the study species and demonstrated high phylogenetic informativeness across the evolutionary history of the genus Etheostoma. Low cost and high cross-species effectiveness regardless of reference genome suggest that Rapture and similar sequence capture methods may be worthwhile choices for studies of diverse species radiations.
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Affiliation(s)
- Brendan N Reid
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Rachel L Moran
- Department of Evolution, Ecology, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | | | - Sarah W Fitzpatrick
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA.,Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
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111
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Capblancq T, Fitzpatrick MC, Bay RA, Exposito-Alonso M, Keller SR. Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-020720-042553] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Signals of local adaptation have been found in many plants and animals, highlighting the heterogeneity in the distribution of adaptive genetic variation throughout species ranges. In the coming decades, global climate change is expected to induce shifts in the selective pressures that shape this adaptive variation. These changes in selective pressures will likely result in varying degrees of local climate maladaptation and spatial reshuffling of the underlying distributions of adaptive alleles. There is a growing interest in using population genomic data to help predict future disruptions to locally adaptive gene-environment associations. One motivation behind such work is to better understand how the effects of changing climate on populations’ short-term fitness could vary spatially across species ranges. Here we review the current use of genomic data to predict the disruption of local adaptation across current and future climates. After assessing goals and motivationsunderlying the approach, we review the main steps and associated statistical methods currently in use and explore our current understanding of the limits and future potential of using genomics to predict climate change (mal)adaptation.
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Affiliation(s)
- Thibaut Capblancq
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405, USA
| | - Matthew C. Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland 21532, USA
| | - Rachael A. Bay
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Stephen R. Keller
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405, USA
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112
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Jung H, Ventura T, Chung JS, Kim WJ, Nam BH, Kong HJ, Kim YO, Jeon MS, Eyun SI. Twelve quick steps for genome assembly and annotation in the classroom. PLoS Comput Biol 2020; 16:e1008325. [PMID: 33180771 PMCID: PMC7660529 DOI: 10.1371/journal.pcbi.1008325] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.
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Affiliation(s)
- Hyungtaek Jung
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Tomer Ventura
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - J. Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Woo-Jin Kim
- Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje, Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Seong-il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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113
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Dissanayake DSB, Holleley CE, Hill LK, O'Meally D, Deakin JE, Georges A. Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction. BMC Genomics 2020; 21:667. [PMID: 32993477 PMCID: PMC7526180 DOI: 10.1186/s12864-020-07071-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.
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Affiliation(s)
- Duminda Sampath Bandara Dissanayake
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia
| | - Clare Ellen Holleley
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia
| | - Laura Kate Hill
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Present Address: Centre for Gene Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Janine Eileen Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
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114
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Structure and Sequence of the Sex Determining Locus in Two Wild Populations of Nile Tilapia. Genes (Basel) 2020; 11:genes11091017. [PMID: 32872430 PMCID: PMC7563666 DOI: 10.3390/genes11091017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/15/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.
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115
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Langa J, Estonba A, Conklin D. EXFI: Exon and splice graph prediction without a reference genome. Ecol Evol 2020; 10:8880-8893. [PMID: 32884664 PMCID: PMC7452765 DOI: 10.1002/ece3.6587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 11/19/2022] Open
Abstract
For population genetic studies in nonmodel organisms, it is important to use every single source of genomic information. This paper presents EXFI, a Python pipeline that predicts the splice graph and exon sequences using an assembled transcriptome and raw whole-genome sequencing reads. The main algorithm uses Bloom filters to remove reads that are not part of the transcriptome, to predict the intron-exon boundaries, to then proceed to call exons from the assembly, and to generate the underlying splice graph. The results are returned in GFA1 format, which encodes both the predicted exon sequences and how they are connected to form transcripts. EXFI is written in Python, tested on Linux platforms, and the source code is available under the MIT License at https://github.com/jlanga/exfi.
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Affiliation(s)
- Jorge Langa
- Department of Genetics, Physical Anthropology and Animal PhysiologyFaculty of Science and TechnologyUniversity of the Basque CountryLeioaSpain
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal PhysiologyFaculty of Science and TechnologyUniversity of the Basque CountryLeioaSpain
| | - Darrell Conklin
- Department of Computer Science and Artificial Intelligence, Faculty of Computer ScienceUniversity of the Basque Country UPV/EHUSan SebastiánSpain
- IKERBASQUE, Basque Foundation for ScienceBilbaoSpain
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116
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Wright BR, Farquharson KA, McLennan EA, Belov K, Hogg CJ, Grueber CE. A demonstration of conservation genomics for threatened species management. Mol Ecol Resour 2020; 20:1526-1541. [DOI: 10.1111/1755-0998.13211] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Belinda R. Wright
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
| | - Katherine A. Farquharson
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
| | - Elspeth A. McLennan
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
| | - Katherine Belov
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
| | - Catherine E. Grueber
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
- San Diego Zoo Global San Diego CA USA
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117
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Waldvogel AM, Schreiber D, Pfenninger M, Feldmeyer B. Climate Change Genomics Calls for Standardized Data Reporting. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00242] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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118
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Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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119
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Torres-Dowdall J, Rometsch SJ, Kautt AF, Aguilera G, Meyer A. The direction of genital asymmetry is expressed stochastically in internally fertilizing anablepid fishes. Proc Biol Sci 2020; 287:20200969. [PMID: 32635868 DOI: 10.1098/rspb.2020.0969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Animal genitalia vary considerably across taxa, with divergence in many morphological traits, including striking departures from symmetry. Different mechanisms have been proposed to explain this diversity, mostly assuming that at least some of the phenotypic variation is heritable. However, heritability of the direction of genital asymmetry has been rarely determined. Anablepidae are internally fertilizing fish where the anal fin of males has been modified into an intromittent organ that transfers sperm into the gonopore of females. Males of anablepid fishes exhibit asymmetric genitalia, and both left- and right-sided individuals are commonly found at similar proportions within populations (i.e. antisymmetry). Although this polymorphism was described over a century ago, there have been no attempts to determine if genital asymmetry has a genetic basis and whether the different morphs are accumulating genetic differences, as might be expected since in some species females have also asymmetric gonopores and thereby can only be fertilized by compatible asymmetric males. We address this issue by combining breeding experiments with genome-wide data (ddRAD markers) in representative species of the two anablepid genera with asymmetric genitalia: Anableps and Jenynsia. Breeding experiments showed that all offspring were asymmetric, but their morphotype (i.e. right- or left-sided) was independent of parental morphotype, implying that the direction of asymmetry does not have a strong genetic component. Consistent with this conclusion, association analyses based on approximately 25 000 SNPs did not identify markers significantly associated with the direction of genital asymmetry and there was no evidence of population structure between left- and right-sided individuals. These results suggest that the direction of genital asymmetry in anablepid fishes might be stochastic, a commonly observed pattern in species with antisymmetry in morphological traits.
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Affiliation(s)
- Julián Torres-Dowdall
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Sina J Rometsch
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Andreas F Kautt
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Gastón Aguilera
- Unidad Ejecutora Lillo (CONICET), Fundación Miguel Lillo, Tucumán, Argentina
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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120
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Cayuela H, Rougemont Q, Laporte M, Mérot C, Normandeau E, Dorant Y, Tørresen OK, Hoff SNK, Jentoft S, Sirois P, Castonguay M, Jansen T, Praebel K, Clément M, Bernatchez L. Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish. Mol Ecol 2020; 29:2379-2398. [DOI: 10.1111/mec.15499] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Siv Nam Khang Hoff
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Pascal Sirois
- Département des sciences fondamentales Université du Québec à Chicoutimi Chicoutimi QC Canada
| | - Martin Castonguay
- Fisheries and Oceans Canada Institut Maurice‐Lamontagne Mont‐Joli QC Canada
| | - Teunis Jansen
- GINR‐Greenland Institute of Natural Resources Nuuk Greenland
- DTU Aqua‐National Institute of Aquatic Resources Technical University of Denmark Charlottenlund Castle, Charlottenlund Denmark
| | - Kim Praebel
- Norwegian College of Fishery Science Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Marie Clément
- Center for Fisheries Ecosystems Research Fisheries and Marine Institute of Memorial University of Newfoundland St. John's NL Canada
- Labrador Institute of Memorial University of Newfoundland Happy Valley‐Goose Bay NL Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
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121
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Carvalho CS, Forester BR, Mitre SK, Alves R, Imperatriz-Fonseca VL, Ramos SJ, Resende-Moreira LC, Siqueira JO, Trevelin LC, Caldeira CF, Gastauer M, Jaffé R. Combining genotype, phenotype, and environmental data to delineate site-adjusted provenance strategies for ecological restoration. Mol Ecol Resour 2020; 21:44-58. [PMID: 32419278 DOI: 10.1111/1755-0998.13191] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 12/29/2022]
Abstract
Despite the importance of climate-adjusted provenancing to mitigate the effects of environmental change, climatic considerations alone are insufficient when restoring highly degraded sites. Here we propose a comprehensive landscape genomic approach to assist the restoration of moderately disturbed and highly degraded sites. To illustrate it we employ genomic data sets comprising thousands of single nucleotide polymorphisms from two plant species suitable for the restoration of iron-rich Amazonian Savannas. We first use a subset of neutral loci to assess genetic structure and determine the genetic neighbourhood size. We then identify genotype-phenotype-environment associations, map adaptive genetic variation, and predict adaptive genotypes for restoration sites. Whereas local provenances were found optimal to restore a moderately disturbed site, a mixture of genotypes seemed the most promising strategy to recover a highly degraded mining site. We discuss how our results can help define site-adjusted provenancing strategies, and argue that our methods can be more broadly applied to assist other restoration initiatives.
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Affiliation(s)
- Carolina S Carvalho
- Instituto Tecnológico Vale, Belém, Pará, Brazil.,Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | - José O Siqueira
- Instituto Tecnológico Vale, Belém, Pará, Brazil.,Departamento de Ciência do Solo, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | | | | | | | - Rodolfo Jaffé
- Instituto Tecnológico Vale, Belém, Pará, Brazil.,Departamento de Ecologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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122
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Fraik AK, Margres MJ, Epstein B, Barbosa S, Jones M, Hendricks S, Schönfeld B, Stahlke AR, Veillet A, Hamede R, McCallum H, Lopez-Contreras E, Kallinen SJ, Hohenlohe PA, Kelley JL, Storfer A. Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. Evolution 2020; 74:1392-1408. [PMID: 32445281 DOI: 10.1111/evo.14023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022]
Abstract
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors (i.e., disease). The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species' extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment (i.e., climatic variables, elevation, vegetation cover) and/or DFTD. We employ genetic-environment association analyses using 6886 SNPs from 3287 individuals sampled pre- and post-disease arrival across the devil's geographic range. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD are not detected post-DFTD arrival. Several post-DFTD candidate loci are associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by strong selection resulting from the rapid onset of DFTD.
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Affiliation(s)
- Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Mark J Margres
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164.,Plant Biology, University of Minnesota, Minneapolis, Minnesota, 55455
| | - Soraia Barbosa
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Menna Jones
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Sarah Hendricks
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Barbara Schönfeld
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Amanda R Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Anne Veillet
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Rodrigo Hamede
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Hamish McCallum
- School of Environment, Griffith University Nathan, Nathan, QLD, 4111, Australia
| | - Elisa Lopez-Contreras
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Samantha J Kallinen
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
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123
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Li YL, Xing TF, Liu JX. Genome-wide association analyses based on whole-genome sequencing of Protosalanx hyalocranius provide insights into sex determination of Salangid fishes. Mol Ecol Resour 2020; 20:1038-1049. [PMID: 32315505 DOI: 10.1111/1755-0998.13172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 03/28/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022]
Abstract
Identification of sex determination system and sex-determining genes have important implications in conservation, ecology and evolution. However, much remains to be discovered about the evolution of different sexual determination systems in teleost fishes, of which the mechanisms of sex determination are remarkably variable. In the present study, the whole genomes of 20 males and 20 females of a Salangid fish, Protosalanx hyalocranius, were sequenced and genome wide association analyses were conducted to uncover its sex determination system and putative sex-determining genes. A total of 150 SNPs were significantly associated with sex, which showed high differentiation between sexes (FST ranged from 0.245 to 0.556). Of the 150 sex-associated SNPs, 76 SNPs displayed sex specificity with even coverage of depth and were female heterogametic, which suggested a ZZ/ZW sex determination system. Interestingly, one scaffold containing sex-specific SNPs displayed synteny to the sex chromosome of medaka. Annotations of sex-associated loci suggested that both transcriptional regulators (e.g., FOX genes) and secreted hormones and their receptors might be involved in the sex determination/differentiation of P. hyalocranius. More strikingly, we found a nonsense mutation in one copy of GALNT homology gene of all females, which suggested that "Z dosage" effect might play a vital role in the processes of sex determination/differentiation. These sex-specific loci could be a valuable resource for further research on sex determination of Salangid fishes and the results could contribute to the understanding of sex determination mechanisms and the evolution of sex chromosome in teleost fishes.
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Affiliation(s)
- Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Teng-Fei Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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124
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Rivera-Colón AG, Rochette NC, Catchen JM. Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data. Mol Ecol Resour 2020; 21:363-378. [PMID: 32275349 DOI: 10.1111/1755-0998.13163] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/25/2020] [Indexed: 12/20/2022]
Abstract
Restriction-site associated DNA sequencing (RADseq) has become a powerful and versatile tool in modern population genomics, enabling large-scale evolutionary and genomic analyses in otherwise inaccessible biological systems. With its widespread use, different variants on the protocol have been developed to suit specific experimental needs. Researchers face the challenge of choosing the optimal molecular and sequencing protocols for their reduced representation experimental design, an often-complicated process. Strategic errors can lead to biased data generation that has reduced power to answer biological questions. Here, we present RADinitio, simulation software for the selection and optimization of RADseq experiments via the generation of sequencing data that behave similarly to empirical sources. RADinitio provides an evolutionary simulation of populations, implementation of various RADseq protocols with customizable parameters, and thorough assessment of missing data. We test the efficacy of the software using different RAD protocols across several organisms, highlighting the importance of protocol selection on the magnitude and quality of data acquired. Additionally, we test the effects of RAD library preparation and sequencing on allelic dropout, observing that library preparation and sequencing often contributes more to missing alleles than population-level variation.
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Affiliation(s)
- Angel G Rivera-Colón
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, USA
| | - Nicolas C Rochette
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, USA
| | - Julian M Catchen
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, USA
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125
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de Jong MJ, Li Z, Qin Y, Quéméré E, Baker K, Wang W, Hoelzel AR. Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene. Mol Ecol 2020; 29:2777-2792. [PMID: 32306438 DOI: 10.1111/mec.15450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/25/2020] [Accepted: 04/03/2020] [Indexed: 01/13/2023]
Abstract
Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus Capreolus, speciation within this genus during the Quaternary and during divergence among European roe deer (C. capreolus) populations. Our analyses were facilitated by the generation of a new high-coverage reference genome for the Siberian roe deer (C. pygargus). We find progressive reductions in effective population size (Ne ), despite very large census sizes in modern C. capreolus populations and show that low Ne has impacted the C. capreolus genome, reducing diversity and increasing linkage disequilibrium. Even so, we find evidence for natural selection shared among C. capreolus populations, including a historically documented founder population that has been through a severe bottleneck. During each phylogenetic transition there is evidence for selection (from dN/dS and nucleotide diversity tests), including at loci associated with diapause (delayed embryonic development), a phenotype restricted to this genus among the even-toed ungulates. Together these data allow us to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change.
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Affiliation(s)
- Menno J de Jong
- Molecular Ecology Group, Department of Biosciences, Durham University, Durham, UK
| | - Zhipeng Li
- Department of Special Animal nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun City, China
| | - Yanli Qin
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Erwan Quéméré
- Comportement et Ecologie de la Faune Sauvage (CEFS), INRA, Université de Toulouse, Castanet-Tolosan, France.,Ecology and Ecosystems Health, Ouest, INRAE, Rennes, France
| | - Karis Baker
- Molecular Ecology Group, Department of Biosciences, Durham University, Durham, UK
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - A Rus Hoelzel
- Molecular Ecology Group, Department of Biosciences, Durham University, Durham, UK
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126
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127
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Within-Generation Polygenic Selection Shapes Fitness-Related Traits across Environments in Juvenile Sea Bream. Genes (Basel) 2020; 11:genes11040398. [PMID: 32272597 PMCID: PMC7231164 DOI: 10.3390/genes11040398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding the genetic underpinnings of fitness trade-offs across spatially variable environments remains a major challenge in evolutionary biology. In Mediterranean gilthead sea bream, first-year juveniles use various marine and brackish lagoon nursery habitats characterized by a trade-off between food availability and environmental disturbance. Phenotypic differences among juveniles foraging in different habitats rapidly appear after larval settlement, but the relative role of local selection and plasticity in phenotypic variation remains unclear. Here, we combine phenotypic and genetic data to address this question. We first report correlations of opposite signs between growth and condition depending on juvenile habitat type. Then, we use single nucleotide polymorphism (SNP) data obtained by Restriction Associated DNA (RAD) sequencing to search for allele frequency changes caused by a single generation of spatially varying selection between habitats. We found evidence for moderate selection operating at multiple loci showing subtle allele frequency shifts between groups of marine and brackish juveniles. We identified subsets of candidate outlier SNPs that, in interaction with habitat type, additively explain up to 3.8% of the variance in juvenile growth and 8.7% in juvenile condition; these SNPs also explained significant fraction of growth rate in an independent larval sample. Our results indicate that selective mortality across environments during early-life stages involves complex trade-offs between alternative growth strategies.
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128
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Liberles DA, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kaçar B, Meyer M, Murphy W, Posada D, Storfer A. Emerging Frontiers in the Study of Molecular Evolution. J Mol Evol 2020; 88:211-226. [PMID: 32060574 PMCID: PMC7386396 DOI: 10.1007/s00239-020-09932-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genomes and proteins, macromolecular and functional evolution, evolutionary cell biology, genome evolution, molecular evolutionary ecology, viral phylodynamics, theoretical population genomics, somatic cell molecular evolution, and directed evolution. While our effort is not meant to be exhaustive, it reflects research questions and problems in the field of molecular evolution that are exciting to our editors.
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Affiliation(s)
- David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
| | - Belinda Chang
- Department of Ecology and Evolutionary Biology and Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Aaron Goldman
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, 119 Woodland Street, Oberlin, OH, 44074, USA
| | - Jody Hey
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michelle Meyer
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - David Posada
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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129
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Balao F, Lorenzo MT, Sánchez-Robles JM, Paun O, García-Castaño JL, Terrab A. Early diversification and permeable species boundaries in the Mediterranean firs. ANNALS OF BOTANY 2020; 125:495-507. [PMID: 31730195 PMCID: PMC7061173 DOI: 10.1093/aob/mcz186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/14/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. METHODS We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. KEY RESULTS Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene-Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. CONCLUSIONS Our phylogenomic results contribute to shed light on conifers' diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.
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Affiliation(s)
- Francisco Balao
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
- For correspondence. E-mail
| | - María Teresa Lorenzo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - José Manuel Sánchez-Robles
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Juan Luis García-Castaño
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - Anass Terrab
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
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130
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Sivalingam J, Vineeth MR, Surya T, Singh K, Dixit SP, Niranjan SK, Tantia MS, Gupta ID, Ravikumar D. Genomic divergence reveals unique populations among Indian Yaks. Sci Rep 2020; 10:3636. [PMID: 32108137 PMCID: PMC7046631 DOI: 10.1038/s41598-020-59887-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/28/2019] [Indexed: 11/09/2022] Open
Abstract
The present study focused upon identification of genome-wide SNPs through the reduced representation approach and to study the genomic divergence of the Indian yak populations. A total of 80 samples belonging to Arunachali yak (N = 20), Himachali yak (N = 20), Ladakhi yak (N = 20) and Sikkimi yak (N = 20) of India were used in the study. The results of the study revealed a total of 579575 high quality SNPs along with 50319 INDELs in the Indian yaks. The observed heterozygosity was found to be high in Himachali yak, followed by Arunachali yak, Ladakhi yak and Sikkimi yaks. The Sikkimi yaks was found to be genetically distant, followed by Ladakhi yaks which was observed to have some few individuals from Arunachali and Himachali yaks. Arunachali and Himachali yaks are found to get clustered together and are genetically similar. The study provides evidence about the genomic diversity in the Indian yak populations and information generated in the present study may help to formulate a suitable breeding plan for endangered Indian yaks. Moreover, the unique yak populations identified in the study will further help to focus attention for future characterization and prioritization of the animals for conservation purposes through the ddRAD approach.
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Affiliation(s)
| | - M R Vineeth
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - T Surya
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Karanveer Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - S P Dixit
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - S K Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - M S Tantia
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - I D Gupta
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - D Ravikumar
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
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131
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Jackson JM, Pimsler ML, Oyen KJ, Strange JP, Dillon ME, Lozier JD. Local adaptation across a complex bioclimatic landscape in two montane bumble bee species. Mol Ecol 2020; 29:920-939. [PMID: 32031739 DOI: 10.1111/mec.15376] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 01/21/2020] [Accepted: 02/02/2020] [Indexed: 12/21/2022]
Abstract
Understanding evolutionary responses to variation in temperature and precipitation across species ranges is of fundamental interest given ongoing climate change. The importance of temperature and precipitation for multiple aspects of bumble bee (Bombus) biology, combined with large geographic ranges that expose populations to diverse environmental pressures, make these insects well-suited for studying local adaptation. Here, we analyzed genome-wide sequence data from two widespread bumble bees, Bombus vosnesenskii and Bombus vancouverensis, using multiple environmental association analysis methods to investigate climate adaptation across latitude and altitude. The strongest signatures of selection were observed in B. vancouverensis, but despite unique responses between species for most loci, we detected several shared responses. Genes relating to neural and neuromuscular function and ion transport were especially evident with respect to temperature variables, while genes relating to cuticle formation, tracheal and respiratory system development, and homeostasis were associated with precipitation variables. Our data thus suggest that adaptive responses for tolerating abiotic variation are likely to be complex, but that several parallels among species can emerge even for these complex traits and landscapes. Results provide the framework for future work into mechanisms of thermal and desiccation tolerance in bumble bees and a set of genomic targets that might be monitored for future conservation efforts.
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Affiliation(s)
- Jason M Jackson
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| | - Meaghan L Pimsler
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| | - Kennan J Oyen
- Department of Zoology & Physiology and Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - James P Strange
- Department of Entomology, The Ohio State University, Columbus, OH, USA
| | - Michael E Dillon
- Department of Zoology & Physiology and Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
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132
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Marrano A, Palmer AE, Moyers BT. Stacking up RADSeq assembly programs: From complete hit to completely abysmal. Mol Ecol Resour 2020; 20:357-359. [PMID: 32012467 DOI: 10.1111/1755-0998.13140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/06/2020] [Accepted: 01/30/2020] [Indexed: 11/29/2022]
Abstract
Decreasing sequencing costs have driven a rapid expansion of novel genotyping methods. One of these methods is the exploitation of restriction enzyme cut sites to generate genome-wide but reduced representation sequencing libraries (RRLs), alternatively termed genotyping by sequencing or restriction-site associated DNA sequencing. Without a reference genome, the resulting short sequence reads must be assembled de novo. There are many possible assembly programs, most not explicitly developed for RRL data, and we know little of their effectiveness. In this issue of Molecular Ecology Resources, LaCava et al. (2020) systematically evaluate six commonly used programs and two commonly varied parameters for complete and accurate assembly of RRLs, using simulated double digests of Homo sapiens and Arabidopsis thaliana genomes with varied mutation rates and types. The authors find substantial variation in performance across assembly programs. The most consistently high-performing assembler is infrequently used in their literature survey (CD-HIT; Li and Godzik, 2006), while several others fail to produce complete, accurate assemblies under many conditions. LaCava et al. additionally recommend best practices in parameter choice and evaluation of future assembly programs-advice that molecular ecologists working to assemble sequences of all kinds should take to heart.
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Affiliation(s)
- Annarita Marrano
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Alice E Palmer
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Brook T Moyers
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
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133
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Waldvogel A, Feldmeyer B, Rolshausen G, Exposito‐Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, Savolainen O, Bergland A, Flatt T, Guillaume F, Pfenninger M. Evolutionary genomics can improve prediction of species' responses to climate change. Evol Lett 2020; 4:4-18. [PMID: 32055407 PMCID: PMC7006467 DOI: 10.1002/evl3.154] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/31/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023] Open
Abstract
Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco-evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large-scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco-evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available resources more effectively, to implement mitigation measures before species go extinct and ecosystems lose important functions.
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Affiliation(s)
- Ann‐Marie Waldvogel
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | | | | | - Robert Kofler
- Institute of Population GeneticsVetmeduni ViennaAustria
| | - Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwichUnited Kingdom
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population GeneticsUniversity of HohenheimStuttgartGermany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute of Ecology, Evolution and DiversityGoethe‐UniversityFrankfurt am MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
| | | | | | - Alan Bergland
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia
| | - Thomas Flatt
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Frederic Guillaume
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZürichSwitzerland
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Institute for Organismic and Molecular EvolutionJohannes Gutenberg UniversityMainzGermany
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134
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Lavretsky P, McInerney NR, Mohl JE, Brown JI, James HF, McCracken KG, Fleischer RC. Assessing changes in genomic divergence following a century of human-mediated secondary contact among wild and captive-bred ducks. Mol Ecol 2020; 29:578-595. [PMID: 31872482 DOI: 10.1111/mec.15343] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022]
Abstract
Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.
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Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Nancy Rotzel McInerney
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | - Jonathon E Mohl
- Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, USA
| | - Joshua I Brown
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Helen F James
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Kevin G McCracken
- Department of Biology, University of Miami, Coral Gables, FL, USA.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, USA.,Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Institute of Arctic Biology, University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
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135
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Royer AM, Waite-Himmelwright J, Smith CI. Strong Selection Against Early Generation Hybrids in Joshua Tree Hybrid Zone Not Explained by Pollinators Alone. FRONTIERS IN PLANT SCIENCE 2020; 11:640. [PMID: 32528500 PMCID: PMC7264850 DOI: 10.3389/fpls.2020.00640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/24/2020] [Indexed: 05/07/2023]
Abstract
Coevolution frequently plays an important role in diversification, but the role of obligate pollination mutualisms in the maintenance of hybrid zones has rarely been investigated. Like most members of the genus Yucca, the two species of Joshua tree (Yucca brevifolia and Yucca jaegeriana) are involved in a tightly coevolved mutualism with yucca moths. There is strong evidence of a history of coevolution between Joshua trees and their moth pollinators. We use a geographic clines approach in the Joshua tree hybrid zone to ask if selection by the moths may currently contribute to maintaining separation between these species. We compare genomic, phenotypic, and pollinator frequency clines to test whether pollinators maintain the hybrid zone or follow it as passive participants. The results reveal dramatic overlapping genomic and pollinator clines, consistent with a narrow hybrid zone maintained by strong selection. Wider phenotypic clines and a chloroplast genomic cline displaced opposite the expected direction suggest that pollinators are not the main source of selection maintaining the hybrid zone. Rather, it seems that high levels of reproductive isolation, likely acting through multiple barriers and involving many parts of the genome, keep the hybrid zone narrow.
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Affiliation(s)
- Anne M. Royer
- Biology Department, The University of Scranton, Scranton, PA, United States
- *Correspondence: Anne M. Royer,
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136
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Borrell JS, Zohren J, Nichols RA, Buggs RJA. Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow. Evol Appl 2020; 13:161-175. [PMID: 31892950 PMCID: PMC6935589 DOI: 10.1111/eva.12883] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022] Open
Abstract
When populations of a rare species are small, isolated and declining under climate change, some populations may become locally maladapted. Detecting this maladaptation may allow effective rapid conservation interventions, even if based on incomplete knowledge. Population maladaptation may be estimated by finding genome-environment associations (GEA) between allele frequencies and environmental variables across a local species range, and identifying populations whose allele frequencies do not fit with these trends. We can then design assisted gene flow strategies for maladapted populations, to adjust their allele frequencies, entailing lower levels of intervention than with undirected conservation action. Here, we investigate this strategy in Scottish populations of the montane plant dwarf birch (Betula nana). In genome-wide restriction site-associated single nucleotide polymorphism (SNP) data, we found 267 significant associations between SNP loci and environmental variables. We ranked populations by maladaptation estimated using allele frequency deviation from the general trends at these loci; this gave a different prioritization for conservation action than the Shapely Index, which seeks to preserve rare neutral variation. Populations estimated to be maladapted in their allele frequencies at loci associated with annual mean temperature were found to have reduced catkin production. Using an environmental niche modelling (ENM) approach, we found annual mean temperature (35%), and mean diurnal range (15%), to be important predictors of the dwarf birch distribution. Intriguingly, there was a significant correlation between the number of loci associated with each environmental variable in the GEA and the importance of that variable in the ENM. Together, these results suggest that the same environmental variables determine both adaptive genetic variation and species range in Scottish dwarf birch. We suggest an assisted gene flow strategy that aims to maximize the local adaptation of dwarf birch populations under climate change by matching allele frequencies to current and future environments.
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Affiliation(s)
| | - Jasmin Zohren
- Sex Chromosome Biology LabThe Francis Crick InstituteLondonUK
| | - Richard A. Nichols
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Richard J. A. Buggs
- Jodrell LaboratoryRoyal Botanic Gardens, KewSurreyUK
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
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137
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Hines HM, Rahman SR. Evolutionary genetics in insect phenotypic radiations: the value of a comparative genomic approach. CURRENT OPINION IN INSECT SCIENCE 2019; 36:90-95. [PMID: 31541856 DOI: 10.1016/j.cois.2019.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Expanding genome sequencing and transgenic technologies are enabling the discovery of genes driving phenotypic diversity across insect taxa. Limitations in downstream functional genetic approaches, however, have been an obstacle for developing non-model systems for evolutionary genetics. Phenotypically diverse radiations, such as those exhibiting convergence and divergence as a result of mimicry, are ideal for evolutionary genetics as they can lead to insights using comparative genomic approaches alone. The varied and repeated instances of phenotypes in highly polymorphic systems allow assessment of whether similar loci are repeatedly targeted by selection and can inform how alleles sort across lineages. Comparative genomics of these taxa can be used to decipher components of gene regulatory networks, dissect regulatory regions, and validate genes.
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Affiliation(s)
- Heather M Hines
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA.
| | - Sarthok Rasique Rahman
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
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138
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Murray KD, Janes JK, Jones A, Bothwell HM, Andrew RL, Borevitz JO. Landscape drivers of genomic diversity and divergence in woodland Eucalyptus. Mol Ecol 2019; 28:5232-5247. [PMID: 31647597 PMCID: PMC7065176 DOI: 10.1111/mec.15287] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/23/2019] [Indexed: 01/03/2023]
Abstract
Spatial genetic patterns are influenced by numerous factors, and they can vary even among coexisting, closely related species due to differences in dispersal and selection. Eucalyptus (L'Héritier 1789; the "eucalypts") are foundation tree species that provide essential habitat and modulate ecosystem services throughout Australia. Here we present a study of landscape genomic variation in two woodland eucalypt species, using whole-genome sequencing of 388 individuals of Eucalyptus albens and Eucalyptus sideroxylon. We found exceptionally high genetic diversity (π ≈ 0.05) and low genome-wide, interspecific differentiation (FST = 0.15) and intraspecific differentiation between localities (FST ≈ 0.01-0.02). We found no support for strong, discrete population structure, but found substantial support for isolation by geographic distance (IBD) in both species. Using generalized dissimilarity modelling, we identified additional isolation by environment (IBE). Eucalyptus albens showed moderate IBD, and environmental variables have a small but significant amount of additional predictive power (i.e. IBE). Eucalyptus sideroxylon showed much stronger IBD and moderate IBE. These results highlight the vast adaptive potential of these species and set the stage for testing evolutionary hypotheses of interspecific adaptive differentiation across environments.
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Affiliation(s)
| | - Jasmine K Janes
- University of New EnglandArmidaleNSWAustralia
- Vancouver Island University,NanaimoBCCanada
| | - Ashley Jones
- Australian National UniversityCanberraACTAustralia
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139
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Rincon-Sandoval M, Betancur-R R, Maldonado-Ocampo JA. Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers. Mol Ecol 2019; 28:1096-1115. [PMID: 30714250 DOI: 10.1111/mec.15036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/17/2019] [Accepted: 01/23/2019] [Indexed: 01/06/2023]
Abstract
The Neotropical region represents one of the greatest biodiversity hot spots on earth. Despite its unparalleled biodiversity, regional comparative phylogeographic studies are still scarce, with most focusing on model clades (e.g. birds) and typically examining a handful of loci. Here, we apply a genome-wide comparative phylogeographic approach to test hypotheses of codiversification of freshwater fishes in the trans-Andean region. Using target capture methods, we examined exon data for over 1,000 loci combined with complete mitochondrial genomes to study the phylogeographic history of five primary fish species (>150 individuals) collected from eight major river basins in Northwestern South America and Lower Central America. To assess their patterns of genetic structure, we inferred genealogical concordance taking into account all major aspects of phylogeography (within loci, across multiple genes, across species and among biogeographic provinces). Based on phylogeographic concordance factors, we tested four a priori biogeographic hypotheses, finding support for three of them and uncovering a novel, unexpected pattern of codiversification. The four emerging inter-riverine patterns are as follows: (a) Tuira + Atrato, (b) Ranchería + Catatumbo, (c) Magdalena system and (d) Sinú + Atrato. These patterns are interpreted as shared responses to the complex uplifting and orogenic processes that modified or sundered watersheds, allowing codiversification and speciation over geological time. We also find evidence of cryptic speciation in one of the species examined and instances of mitochondrial introgression in others. These results help further our knowledge of the historical geographic factors shaping the outstanding biodiversity of the Neotropics.
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Affiliation(s)
- Melissa Rincon-Sandoval
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.,Department of Biology, University of Puerto Rico, San Juan, Puerto Rico
| | - Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, San Juan, Puerto Rico.,Department of Biology, The University of Oklahoma, Norman, Oklahoma
| | - Javier A Maldonado-Ocampo
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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140
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LaCava MEF, Aikens EO, Megna LC, Randolph G, Hubbard C, Buerkle CA. Accuracy of de novo assembly of DNA sequences from double-digest libraries varies substantially among software. Mol Ecol Resour 2019; 20:360-370. [PMID: 31665547 DOI: 10.1111/1755-0998.13108] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 11/29/2022]
Abstract
Advances in DNA sequencing have made it feasible to gather genomic data for non-model organisms and large sets of individuals, often using methods for sequencing subsets of the genome. Several of these methods sequence DNA associated with endonuclease restriction sites (various RAD and GBS methods). For use in taxa without a reference genome, these methods rely on de novo assembly of fragments in the sequencing library. Many of the software options available for this application were originally developed for other assembly types and we do not know their accuracy for reduced representation libraries. To address this important knowledge gap, we simulated data from the Arabidopsis thaliana and Homo sapiens genomes and compared de novo assemblies by six software programs that are commonly used or promising for this purpose (ABySS, CD-HIT, Stacks, Stacks2, Velvet and VSEARCH). We simulated different mutation rates and types of mutations, and then applied the six assemblers to the simulated data sets, varying assembly parameters. We found substantial variation in software performance across simulations and parameter settings. ABySS failed to recover any true genome fragments, and Velvet and VSEARCH performed poorly for most simulations. Stacks and Stacks2 produced accurate assemblies of simulations containing SNPs, but the addition of insertion and deletion mutations decreased their performance. CD-HIT was the only assembler that consistently recovered a high proportion of true genome fragments. Here, we demonstrate the substantial difference in the accuracy of assemblies from different software programs and the importance of comparing assemblies that result from different parameter settings.
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Affiliation(s)
- Melanie E F LaCava
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Ellen O Aikens
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Libby C Megna
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Gregg Randolph
- Genome Technologies Lab, University of Wyoming, Laramie, WY, USA
| | - Charley Hubbard
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Botany, University of Wyoming, Laramie, WY, USA
| | - C Alex Buerkle
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Botany, University of Wyoming, Laramie, WY, USA
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141
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Mynhardt S, Bennett NC, Bloomer P. New insights from RADseq data on differentiation in the Hottentot golden mole species complex from South Africa. Mol Phylogenet Evol 2019; 143:106667. [PMID: 31676418 DOI: 10.1016/j.ympev.2019.106667] [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: 03/15/2019] [Revised: 10/28/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022]
Abstract
Golden moles (Family Chrysochloridae) are small subterranean mammals, endemic to sub-Saharan Africa, and many of the 21 species are listed as threatened on the IUCN Red List. Most species have highly restricted ranges; however two species, the Hottentot golden mole (Amblysomus hottentotus) and the Cape golden mole (Chrysochloris asiatica) have relatively wide ranges. We recently uncovered cryptic diversity within A. hottentotus, through a phylogeographic analysis of this taxon using two mitochondrial gene regions and a nuclear intron. To further investigate this cryptic diversity, we generated nuclear SNP data from across the genome of A. hottentotus, by means of double-digest restriction-site associated DNA sequencing (ddRADSeq), and mapped reads to the Cape golden mole genome. We conducted a phylogenetic analysis and investigated population differentiation. Our results support the distinctiveness of A. h. meesteri. Furthermore, we provide evidence from nuclear SNPs in support of our previous finding that Central coastal samples represent a unique cryptic lineage that is highly divergent from A. h. pondoliae farther south. Although mtDNA suggests that Umtata may represent a unique lineage sister to A. h. longiceps, mito-nuclear discordance from our RADseq data indicate that these samples may instead be closer to A. h. pondoliae, and therefore may not represent a distinct lineage. We stress the importance of recognizing that understudied populations, such as that of Umtata, may represent populations or ESUs under threat and in need of conservation attention. We present a high-quality filtered SNP dataset, comprising thousands of SNPs, which may serve as a useful resource for future golden mole studies. We have thus added to the growing body of research demonstrating the power and utility of RADseq to investigate population differentiation.
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Affiliation(s)
- Samantha Mynhardt
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
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142
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Palmer DH, Rogers TF, Dean R, Wright AE. How to identify sex chromosomes and their turnover. Mol Ecol 2019; 28:4709-4724. [PMID: 31538682 PMCID: PMC6900093 DOI: 10.1111/mec.15245] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Although sex is a fundamental component of eukaryotic reproduction, the genetic systems that control sex determination are highly variable. In many organisms the presence of sex chromosomes is associated with female or male development. Although certain groups possess stable and conserved sex chromosomes, others exhibit rapid sex chromosome evolution, including transitions between male and female heterogamety, and turnover in the chromosome pair recruited to determine sex. These turnover events have important consequences for multiple facets of evolution, as sex chromosomes are predicted to play a central role in adaptation, sexual dimorphism, and speciation. However, our understanding of the processes driving the formation and turnover of sex chromosome systems is limited, in part because we lack a complete understanding of interspecific variation in the mechanisms by which sex is determined. New bioinformatic methods are making it possible to identify and characterize sex chromosomes in a diverse array of non-model species, rapidly filling in the numerous gaps in our knowledge of sex chromosome systems across the tree of life. In turn, this growing data set is facilitating and fueling efforts to address many of the unanswered questions in sex chromosome evolution. Here, we synthesize the available bioinformatic approaches to produce a guide for characterizing sex chromosome system and identity simultaneously across clades of organisms. Furthermore, we survey our current understanding of the processes driving sex chromosome turnover, and highlight important avenues for future research.
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Affiliation(s)
- Daniela H. Palmer
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Thea F. Rogers
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Rebecca Dean
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | - Alison E. Wright
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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143
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Semenov GA, Safran RJ, Smith CC, Turbek SP, Mullen SP, Flaxman SM. Unifying Theoretical and Empirical Perspectives on Genomic Differentiation. Trends Ecol Evol 2019; 34:987-995. [DOI: 10.1016/j.tree.2019.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 01/17/2023]
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144
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Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P, Pompanon F. An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity. Mol Ecol Resour 2019; 19:1497-1515. [PMID: 31359622 PMCID: PMC7115901 DOI: 10.1111/1755-0998.13070] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 06/30/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.
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Affiliation(s)
- Badr Benjelloun
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Frédéric Boyer
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Wahid Zamani
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, 46417-76489 Noor, Mazandaran, Iran
| | - Stefan Engelen
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Adriana Alberti
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Florian J. Alberto
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Mohamed BenBati
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Mustapha Ibnelbachyr
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Mouad Chentouf
- National Institute of Agronomic Research (INRA Maroc), CRRA Tangier, 90010 Tangier, Morocco
| | - Abdelmajid Bechchari
- National Institute of Agronomic Research (INRA Maroc), CRRA Oujda, 60000 Oujda, Morocco
| | - Hamid R. Rezaei
- Department of Environmental Sci, Gorgan University of Agricultural Sciences & Natural Resources, 41996-13776 Gorgan, Iran
| | - Saeid Naderi
- Environmental Sciences Department, Natural Resources Faculty, University of Guilan, 49138-15749 Guilan, Iran
| | - Alessandra Stella
- PTP Science Park, Bioinformatics Unit, Via Einstein-Loc. Cascina Codazza, 26900 Lodi, Italy
| | - Abdelkader Chikhi
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pierre Taberlet
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - François Pompanon
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
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145
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Fraik AK, Quackenbush C, Margres MJ, Comte S, Hamilton DG, Kozakiewicz CP, Jones M, Hamede R, Hohenlohe PA, Storfer A, Kelley JL. Transcriptomics of Tasmanian Devil ( Sarcophilus Harrisii) Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape. Genes (Basel) 2019; 10:E801. [PMID: 31614864 PMCID: PMC6826840 DOI: 10.3390/genes10100801] [Citation(s) in RCA: 5] [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: 08/30/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023] Open
Abstract
In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized gene expression differences among populations experiencing divergent environmental conditions in a wide variety of taxa. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. Herein, we aim to identify environmental and sex-driven patterns of gene expression in the Tasmanian devil (Sarcophilus harrisii), a critically endangered species that occupies a heterogeneous environment. We performed RNA-sequencing on ear tissue biopsies from adult male and female devils from three populations at the extremes of their geographic range. There were no transcriptome-wide patterns of differential gene expression that would be suggestive of significant, environmentally-driven transcriptomic responses. The general lack of transcriptome-wide variation in gene expression levels across the devil's geographic range is consistent with previous studies that documented low levels of genetic variation in the species. However, genes previously implicated in local adaptation to abiotic environment in devils were enriched for differentially expressed genes. Additionally, three modules of co-expressed genes were significantly associated with either population of origin or sex.
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Affiliation(s)
- Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
| | - Corey Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
| | - Mark J Margres
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA.
| | - Sebastien Comte
- School of Natural Sciences, Hobart, TAS 7001, Australia.
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, 1447 Forest Road, Orange, NSW 2800, Australia.
| | | | | | - Menna Jones
- School of Natural Sciences, Hobart, TAS 7001, Australia.
| | - Rodrigo Hamede
- School of Natural Sciences, Hobart, TAS 7001, Australia.
| | - Paul A Hohenlohe
- Department of Biological Sciences, University of Idaho, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, USA.
| | - Andrew Storfer
- Department of Biological Sciences, University of Idaho, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, USA.
| | - Joanna L Kelley
- Department of Biological Sciences, University of Idaho, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, USA.
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146
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Homola JJ, Loftin CS, Cammen KM, Helbing CC, Birol I, Schultz TF, Kinnison MT. Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs. J Hered 2019; 110:707-719. [PMID: 31278891 PMCID: PMC6785938 DOI: 10.1093/jhered/esz041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs (Lithobates sylvaticus). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an FST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 FST outlier loci. Discriminant analysis of principal components using the 37 FST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 FST outlier loci mapped to the American bullfrog (Rana [Lithobates] catesbeiana) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.
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Affiliation(s)
- Jared J Homola
- School of Biology and Ecology, University of Maine, Orono, ME
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI
| | - Cynthia S Loftin
- the US Geological Survey, Maine Cooperative Fish and Wildlife Research Unit, Orono, ME
| | | | - Caren C Helbing
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Inanc Birol
- the Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Thomas F Schultz
- the Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC
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147
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Euclide PT, McKinney GJ, Bootsma M, Tarsa C, Meek MH, Larson WA. Attack of the PCR clones: Rates of clonality have little effect on RAD‐seq genotype calls. Mol Ecol Resour 2019; 20:66-78. [DOI: 10.1111/1755-0998.13087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/12/2019] [Accepted: 08/16/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Peter T. Euclide
- Wisconsin Cooperative Fishery Research Unit College of Natural Resources University of Wisconsin‐Stevens Point Stevens Point WI USA
| | - Garrett J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - Matthew Bootsma
- Wisconsin Cooperative Fishery Research Unit College of Natural Resources University of Wisconsin‐Stevens Point Stevens Point WI USA
| | - Charlene Tarsa
- Department of Integrative Biology and AgBio Research Michigan State University East Lansing MI USA
| | - Mariah H. Meek
- Department of Integrative Biology and AgBio Research Michigan State University East Lansing MI USA
| | - Wesley A. Larson
- U.S. Geological Survey Wisconsin Cooperative Fishery Research Unit College of Natural Resources University of Wisconsin‐Stevens Point Stevens Point WI USA
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148
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Kess T, Boulding EG. Genome-wide association analyses reveal polygenic genomic architecture underlying divergent shell morphology in Spanish Littorina saxatilis ecotypes. Ecol Evol 2019; 9:9427-9441. [PMID: 31534666 PMCID: PMC6745682 DOI: 10.1002/ece3.5378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 12/18/2022] Open
Abstract
Gene flow between diverging populations experiencing dissimilar ecological conditions can theoretically constrain adaptive evolution. To minimize the effect of gene flow, alleles underlying traits essential for local adaptation are predicted to be located in linked genome regions with reduced recombination. Local reduction in gene flow caused by selection is expected to produce elevated divergence in these regions. The highly divergent crab-adapted and wave-adapted ecotypes of the marine snail Littorina saxatilis present a model system to test these predictions. We used genome-wide association (GWA) analysis of geometric morphometric shell traits associated with microgeographic divergence between the two L. saxatilis ecotypes within three separate sampling sites. A total of 477 snails that had individual geometric morphometric data and individual genotypes at 4,066 single nucleotide polymorphisms (SNPs) were analyzed using GWA methods that corrected for population structure among the three sites. This approach allowed dissection of the genomic architecture of shell shape divergence between ecotypes across a wide geographic range, spanning two glacial lineages. GWA revealed 216 quantitative trait loci (QTL) with shell size or shape differences between ecotypes, with most loci explaining a small proportion of phenotypic variation. We found that QTL were evenly distributed across 17 linkage groups, and exhibited elevated interchromosomal linkage, suggesting a genome-wide response to divergent selection on shell shape between the two ecotypes. Shell shape trait-associated loci showed partial overlap with previously identified outlier loci under divergent selection between the two ecotypes, supporting the hypothesis of diversifying selection on these genomic regions. These results suggest that divergence in shell shape between the crab-adapted and wave-adapted ecotypes is produced predominantly by a polygenic genomic architecture with positive linkage disequilibrium among loci of small effect.
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Affiliation(s)
- Tony Kess
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
- Present address:
Fisheries and Oceans CanadaSt. John'sNLCanada
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149
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Bourgeois Y, Boissinot S. Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer. Mol Ecol 2019; 28:3523-3543. [PMID: 31233650 DOI: 10.1111/mec.15162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
What makes a species able to colonize novel environments? This question is key to understand the dynamics of adaptive radiations and ecological niche shifts, but the mechanisms that underlie expansion into novel habitats remain poorly understood at a genomic scale. Lizards from the genus Anolis are typically tropical, and the green anole (Anolis carolinensis) constitutes an exception since it expanded into temperate North America from subtropical Florida. Thus, we used the green anole as a model to investigate signatures of selection associated with colonization of a new environment, namely temperate North America. To this end, we analysed 29 whole-genome sequences, covering the entire native range of the species. We used a combination of recent methods to quantify both positive and balancing selection in northern populations, including FST outlier methods, machine learning and ancestral recombination graphs. We naively scanned for genes of interest and assessed the overlap between multiple tests. Strikingly, we identified many genes involved in behaviour, suggesting that the recent successful colonization of northern environments may have been linked to behavioural shifts as well as physiological adaptation. Using a candidate genes strategy, we determined that genes involved in response to cold or behaviour displayed more frequently signals of selection, while controlling for local recombination rate, gene clustering and gene length. In addition, we found signatures of balancing selection at immune genes in all investigated genetic groups, but also at genes involved in neuronal and anatomical development.
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Affiliation(s)
- Yann Bourgeois
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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150
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Papadopulos AST, Igea J, Dunning LT, Osborne OG, Quan X, Pellicer J, Turnbull C, Hutton I, Baker WJ, Butlin RK, Savolainen V. Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea. Evolution 2019; 73:1986-1995. [PMID: 31298414 DOI: 10.1111/evo.13796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/24/2019] [Indexed: 12/18/2022]
Abstract
Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction site-associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, four of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.
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Affiliation(s)
- Alexander S T Papadopulos
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom.,Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, School of Biological Sciences, Bangor University, Bangor, LL57 2UW, United Kingdom
| | - Javier Igea
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom.,Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Luke T Dunning
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Owen G Osborne
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom
| | - Xueping Quan
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, United Kingdom
| | - Colin Turnbull
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom
| | - Ian Hutton
- Lord Howe Island Museum, Lord Howe Island, NSW, 2898, Australia
| | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, United Kingdom
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Department of Marine Sciences, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom.,Royal Botanic Gardens, Kew, Richmond, TW9 3AB, United Kingdom
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