1
|
Pontarp M, Lundberg P, Ripa J. The succession of ecological divergence and reproductive isolation in adaptive radiations. J Theor Biol 2024; 587:111819. [PMID: 38589008 DOI: 10.1016/j.jtbi.2024.111819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
Adaptive radiation is a major source of biodiversity but the way in which known components of ecological opportunity, ecological differentiation, and reproductive isolation underpin such biodiversity patterns remains elusive. Much is known about the evolution of ecological differentiation and reproductive isolation during single speciation events, but exactly how those processes scale up to complete adaptive radiations is less understood. Do we expect complete reproductive barriers between newly formed species before the ecological differentiation continues, or does proper species formation occur much later, long after the ecological diversification? Our goal is to improve our mechanistic understanding of adaptive radiations by analyzing an individual-based model that includes a suite of mechanisms that are known to contribute to biodiversity. The model includes variable biogeographic settings, ecological opportunities, and types of mate choice, which makes several different scenarios of an adaptive radiation possible. We find that evolving clades tend to exploit ecological opportunities early whereas reproductive barriers evolve later, demonstrating a decoupling of ecological differentiation and species formation. In many cases, we also find a long-term trend where assortative mating associated with ecological traits is replaced by sexual selection of neutral display traits as the primary mechanism for reproductive isolation. Our results propose that reticulate phylogenies are likely common and stem from initially low reproductive barriers, rather than the previously suggested idea of repeated hybridization events between well-separated species.
Collapse
Affiliation(s)
- Mikael Pontarp
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden.
| | - Per Lundberg
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden
| | - Jörgen Ripa
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden
| |
Collapse
|
2
|
Luo J, Cai Y, Xie Y, Jin X, Yu J, Xu M, Liu X, Li J. Genetic assessment of eight zoo populations of golden snub-nosed monkey ( Rhinopithecus roxellana) implication to the conservation management of captive populations. Evol Appl 2024; 17:e13726. [PMID: 38832080 PMCID: PMC11146145 DOI: 10.1111/eva.13726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/06/2024] [Accepted: 05/17/2024] [Indexed: 06/05/2024] Open
Abstract
Captive breeding programs play an important role in preserving the genetic diversity of endangered species. It is of utmost importance to conduct genetic assessment for captive populations in order to develop scientific breeding plans and conservation management strategies. Here, we genotyped 10 microsatellite loci and sequenced 368 bp of mitochondrial DNA control region for the golden snub-nosed monkey (Rhinopithecus roxellana) from eight captive populations in China, and compared the genetic indices of captive populations with a wild population. Meanwhile, we performed paternity tests to verify the genealogical records and established genetic lineages. A total of 157 individuals were identified from 161 fecal samples, including 135 captive individuals (approximately 25% of captive individuals in China). Microsatellite analysis showed that the nine populations had moderate levels of genetic diversity, with polymorphism information content (PIC) ranging from 0.43 to 0.542; the genetic diversity of captive populations (average PIC: 0.503) was slightly higher than that of the wild population (PIC: 0.438). The Structure analysis indicated that individuals of the eight captive populations contained two different genetic components. We conducted either single-blind or double-blind paternity testing on 40 offspring of captive individuals and found that five offspring from two zoos (Nanjing Hongshan Forest Zoo and Shanghai Wild Animal Park) showed discrepant kinships from their pedigree records, probably due to the inaccuracies in pedigree records. By constructing genetic pedigrees, inbred offspring were found in Beijing Zoo, Shanghai Zoo, Hangzhou Zoo, and Chengdu Zoo. Analysis based on mitochondrial DNA showed a high level of genetic diversity in the eight captive populations (mean nucleotide diversity: 0.047). However, no nucleotide diversity was found in the wild population. This study conducted a genetic survey for captive golden snub-nosed monkeys and will significantly benefit the genetic conservation management for captive populations in the future.
Collapse
Affiliation(s)
- Jinxia Luo
- Key Laboratory of Bio‐Resources and Eco‐Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
| | - Yansen Cai
- Key Laboratory of Bio‐Resources and Eco‐Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
- Department of Cell Biology and Genetic, School of Basic Medical SciencesSouthwest Medical UniversityLuzhouChina
| | - Yuchen Xie
- Key Laboratory of Bio‐Resources and Eco‐Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
| | - Xianlin Jin
- Key Laboratory of Bio‐Resources and Eco‐Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
| | - Jianqiu Yu
- Chengdu Zoo, Chengdu Research Institute of WildlifeChengduChina
| | - Mei Xu
- Chengdu Zoo, Chengdu Research Institute of WildlifeChengduChina
| | - Xuanzhen Liu
- Chengdu Zoo, Chengdu Research Institute of WildlifeChengduChina
| | - Jing Li
- Key Laboratory of Bio‐Resources and Eco‐Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
| |
Collapse
|
3
|
Fenton S, Jacobs A, Bean CW, Adams CE, Elmer KR. Genomic underpinnings of head and body shape in Arctic charr ecomorph pairs. Mol Ecol 2024; 33:e17305. [PMID: 38421099 DOI: 10.1111/mec.17305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Across its Holarctic range, Arctic charr (Salvelinus alpinus) populations have diverged into distinct trophic specialists across independent replicate lakes. The major aspect of divergence between ecomorphs is in head shape and body shape, which are ecomorphological traits reflecting niche use. However, whether the genomic underpinnings of these parallel divergences are consistent across replicates was unknown but key for resolving the substrate of parallel evolution. We investigated the genomic basis of head shape and body shape morphology across four benthivore-planktivore ecomorph pairs of Arctic charr in Scotland. Through genome-wide association analyses, we found genomic regions associated with head shape (89 SNPs) or body shape (180 SNPs) separately and 50 of these SNPs were strongly associated with both body and head shape morphology. For each trait separately, only a small number of SNPs were shared across all ecomorph pairs (3 SNPs for head shape and 10 SNPs for body shape). Signs of selection on the associated genomic regions varied across pairs, consistent with evolutionary demography differing considerably across lakes. Using a comprehensive database of salmonid QTLs newly augmented and mapped to a charr genome, we found several of the head- and body-shape-associated SNPs were within or near morphology QTLs from other salmonid species, reflecting a shared genetic basis for these phenotypes across species. Overall, our results demonstrate how parallel ecotype divergences can have both population-specific and deeply shared genomic underpinnings across replicates, influenced by differences in their environments and demographic histories.
Collapse
Affiliation(s)
- Sam Fenton
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Arne Jacobs
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Colin W Bean
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
- NatureScot, Clydebank, UK
| | - Colin E Adams
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| |
Collapse
|
4
|
Howe NS, Hale MC, Waters CD, Schaal SM, Shedd KR, Larson WA. Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha. Evol Appl 2024; 17:e13656. [PMID: 38357359 PMCID: PMC10866082 DOI: 10.1111/eva.13656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery-wild population pairs. In this study, we used low-coverage whole-genome sequencing to investigate signals of domestication selection in three separate hatchery populations of Chinook salmon, Oncorhynchus tshawytscha, after approximately seven generations of divergence from their corresponding wild progenitor populations. We sequenced 192 individuals from populations across Southeast Alaska and estimated genotype likelihoods at over six million loci. We discovered a total of 14 outlier peaks displaying high genetic differentiation (F ST) between hatchery-wild pairs, although no peaks were shared across the three comparisons. Peaks were small (53 kb on average) and often displayed elevated absolute genetic divergence (D xy) and linkage disequilibrium, suggesting some level of domestication selection has occurred. Our study provides evidence that domestication selection can lead to genetic differences between hatchery and wild populations in only a few generations. Additionally, our data suggest that population-specific adaptation to hatchery environments likely occurs through different genetic pathways, even for populations with similar standing genetic variation. These results highlight the need to collect paired genotype-phenotype data to understand how domestication may be affecting fitness and to identify potential management practices that may mitigate genetic risks despite multiple pathways of domestication.
Collapse
Affiliation(s)
- Natasha S. Howe
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Matthew C. Hale
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
| | - Charles D. Waters
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Sara M. Schaal
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| | - Kyle R. Shedd
- Alaska Department of Fish and Game, Division of Commercial FisheriesGene Conservation LaboratoryAnchorageAlaskaUSA
| | - Wesley A. Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries ServiceAlaska Fisheries Science Center, Auke Bay LaboratoriesJuneauAlaskaUSA
| |
Collapse
|
5
|
Carvalho J, Morales HE, Faria R, Butlin RK, Sousa VC. Integrating Pool-seq uncertainties into demographic inference. Mol Ecol Resour 2023; 23:1737-1755. [PMID: 37475177 DOI: 10.1111/1755-0998.13834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool-seq sources of error. By jointly modelling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole-genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod Littorina saxatilis, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.
Collapse
Affiliation(s)
- João Carvalho
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Portugal
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui Faria
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Roger K Butlin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Vítor C Sousa
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Portugal
| |
Collapse
|
6
|
Cerca J. Understanding natural selection and similarity: Convergent, parallel and repeated evolution. Mol Ecol 2023; 32:5451-5462. [PMID: 37724599 DOI: 10.1111/mec.17132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Parallel and convergent evolution offer some of the most compelling evidence for the significance of natural selection in evolution, as the emergence of similar adaptive solutions is unlikely to occur by random chance alone. However, these terms are often employed inconsistently, leading to misinterpretation and confusion, and recently proposed definitions have unintentionally diminished the emphasis on the evolution of similar adaptive solutions. Here, I examine various conceptual frameworks and definitions related to parallel and convergent evolution and propose a consolidated framework that enhances our comprehension of these evolutionary patterns. The primary aim of this framework is to harmonize the concepts of parallel and convergent evolution together with natural selection and the idea of similarity. Both concepts involve the evolution of similar adaptive solutions as a result of environmental challenges. The distinction lies in ancestral phenotypes. Parallel evolution takes place when the ancestral phenotypes (before selection) of the lineages are similar. Convergent evolution happens when the lineages have distinct ancestral phenotypes (before selection). Because an ancestral-based distinction will inevitably lead to cases where uncertainty in the distinction may arise, the framework includes a general term, repeated evolution, which can be used as a term applying to the evolution of similar phenotypes and genotypes as well as similar responses to environmental pressures. Based on the argument that genetic similarity may frequently arise without selection, the framework posits that the similarity of genetic sequences is not of great interest unless linked to the actions of natural selection or to the origins (mutation, standing genetic variation, gene flow) and locations of the similar sequences.
Collapse
Affiliation(s)
- José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
7
|
Szukala A, Lovegrove‐Walsh J, Luqman H, Fior S, Wolfe TM, Frajman B, Schönswetter P, Paun O. Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae). Mol Ecol 2023; 32:1832-1847. [PMID: 35152499 PMCID: PMC10946620 DOI: 10.1111/mec.16393] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/29/2021] [Accepted: 02/02/2022] [Indexed: 11/28/2022]
Abstract
Understanding how organisms adapt to the environment is a major goal of modern biology. Parallel evolution-the independent evolution of similar phenotypes in different populations-provides a powerful framework to investigate the evolutionary potential of populations, the constraints of evolution, its repeatability and therefore its predictability. Here, we quantified the degree of gene expression and functional parallelism across replicated ecotype formation in Heliosperma pusillum (Caryophyllaceae), and gained insights into the architecture of adaptive traits. Population structure analyses and demographic modelling support a previously formulated hypothesis of parallel polytopic divergence of montane and alpine ecotypes. We detect a large proportion of differentially expressed genes (DEGs) underlying divergence within each replicate ecotype pair, with a strikingly low number of shared DEGs across pairs. Functional enrichment of DEGs reveals that the traits affected by significant expression divergence are largely consistent across ecotype pairs, in strong contrast to the nonshared genetic basis. The remarkable redundancy of differential gene expression indicates a polygenic architecture for the diverged adaptive traits. We conclude that polygenic traits appear key to opening multiple routes for adaptation, widening the adaptive potential of organisms.
Collapse
Affiliation(s)
- Aglaia Szukala
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | | | - Hirzi Luqman
- Department of Environmental System ScienceETH ZürichZürichSwitzerland
| | - Simone Fior
- Department of Environmental System ScienceETH ZürichZürichSwitzerland
| | - Thomas M. Wolfe
- Institute for Forest EntomologyForest Pathology and Forest Protection, BOKUViennaAustria
| | - Božo Frajman
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | | | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| |
Collapse
|
8
|
He Y, Cooney CR, Maddock S, Thomas GH. Using pose estimation to identify regions and points on natural history specimens. PLoS Comput Biol 2023; 19:e1010933. [PMID: 36812227 PMCID: PMC9987800 DOI: 10.1371/journal.pcbi.1010933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 03/06/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
A key challenge in mobilising growing numbers of digitised biological specimens for scientific research is finding high-throughput methods to extract phenotypic measurements on these datasets. In this paper, we test a pose estimation approach based on Deep Learning capable of accurately placing point labels to identify key locations on specimen images. We then apply the approach to two distinct challenges that each requires identification of key features in a 2D image: (i) identifying body region-specific plumage colouration on avian specimens and (ii) measuring morphometric shape variation in Littorina snail shells. For the avian dataset, 95% of images are correctly labelled and colour measurements derived from these predicted points are highly correlated with human-based measurements. For the Littorina dataset, more than 95% of landmarks were accurately placed relative to expert-labelled landmarks and predicted landmarks reliably captured shape variation between two distinct shell ecotypes ('crab' vs 'wave'). Overall, our study shows that pose estimation based on Deep Learning can generate high-quality and high-throughput point-based measurements for digitised image-based biodiversity datasets and could mark a step change in the mobilisation of such data. We also provide general guidelines for using pose estimation methods on large-scale biological datasets.
Collapse
Affiliation(s)
- Yichen He
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield; Alfred Denny Building, University of Sheffield, Sheffield, United Kingdom
| | - Christopher R. Cooney
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield; Alfred Denny Building, University of Sheffield, Sheffield, United Kingdom
| | - Steve Maddock
- Department of Computer Science, University of Sheffield; Regent Court, University of Sheffield, Sheffield, United Kingdom
| | - Gavin H. Thomas
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield; Alfred Denny Building, University of Sheffield, Sheffield, United Kingdom
- Bird Group, Department of Life Sciences, The Natural History Museum at Tring; Tring, United Kingdom
| |
Collapse
|
9
|
Westram AM, Butlin R. Professor Kerstin Johannesson-winner of the 2022 Molecular Ecology Prize. Mol Ecol 2023; 32:26-29. [PMID: 36443277 DOI: 10.1111/mec.16779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/09/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Anja Marie Westram
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.,Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Roger Butlin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, Strömstad, Sweden
| |
Collapse
|
10
|
Weist P, Jentoft S, Tørresen OK, Schade FM, Pampoulie C, Krumme U, Hanel R. The role of genomic signatures of directional selection and demographic history in the population structure of a marine teleost with high gene flow. Ecol Evol 2022; 12:e9602. [PMID: 36514551 PMCID: PMC9731920 DOI: 10.1002/ece3.9602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Recent studies have uncovered patterns of genomic divergence in marine teleosts where panmixia due to high gene flow has been the general paradigm. These signatures of divergent selection are often impacted by structural variants, acting as "supergenes" facilitating local adaptation. The highly dispersing European plaice (Pleuronectes platessa)-in which putative structural variants (i.e., inversions) have been identified-has successfully colonized the brackish water ecosystem of the Baltic Sea. Thus, the species represents an ideal opportunity to investigate how the interplay of gene flow, structural variants, natural selection, past demographic history, and gene flow impacts on population (sub)structuring in marine systems. Here, we report on the generation of an annotated draft plaice genome assembly in combination with population sequencing data-following the salinity gradient from the Baltic Sea into the North Sea together with samples from Icelandic waters-to illuminate genome-wide patterns of divergence. Neutral markers pointed at large-scale panmixia across the European continental shelf associated with high gene flow and a common postglacial colonization history of shelf populations. However, based on genome-wide outlier loci, we uncovered signatures of population substructuring among the European continental shelf populations, i.e., suggesting signs of ongoing selection. Genome-wide selection analyses (xp-EHH) and the identification of genes within genomic regions of recent selective sweeps-overlapping with the outlier loci-suggest that these represent the signs of divergent selection. Our findings provide support for genomic divergence driven by local adaptation in the face of high gene flow and elucidate the relative importance of demographic history versus adaptive divergence in shaping the contemporary population genetic structure of a marine teleost. The role of the putative inversion(s) in the substructuring-and potentially ongoing adaptation-was seemingly not substantial.
Collapse
Affiliation(s)
- Peggy Weist
- Thünen Institute of Fisheries EcologyBremerhavenGermany
| | - Sissel Jentoft
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - Ole K. Tørresen
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | | | | | - Uwe Krumme
- Thünen Institute of Baltic Sea FisheriesRostockGermany
| | | |
Collapse
|
11
|
Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Evolution 2022; 76:2332-2346. [PMID: 35994296 PMCID: PMC9826283 DOI: 10.1111/evo.14602] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/24/2022] [Accepted: 07/23/2022] [Indexed: 01/22/2023]
Abstract
Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.
Collapse
Affiliation(s)
- Eva L. Koch
- School of BiosciencesUniversity of SheffieldSheffieldUK,Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Mark Ravinet
- School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Anja M. Westram
- Institute of Science and Technology Austria (ISTA)KlosterneuburgAustria,Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Kerstin Johannesson
- Marine Science, Tjärnö Marine LaboratoryUniversity of GothenburgGothenburgSweden
| | - Roger K. Butlin
- School of BiosciencesUniversity of SheffieldSheffieldUK,Marine Science, Tjärnö Marine LaboratoryUniversity of GothenburgGothenburgSweden
| |
Collapse
|
12
|
Bracamonte SE, Hofmann MJ, Lozano-Martín C, Eizaguirre C, Barluenga M. Divergent and non-parallel evolution of MHC IIB in the Neotropical Midas cichlid species complex. BMC Ecol Evol 2022; 22:41. [PMID: 35365100 PMCID: PMC8974093 DOI: 10.1186/s12862-022-01997-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/21/2022] [Indexed: 01/09/2023] Open
Abstract
Background Ecological diversification is the result of divergent natural selection by contrasting habitat characteristics that favours the evolution of distinct phenotypes. This process can happen in sympatry and in allopatry. Habitat-specific parasite communities have the potential to drive diversification among host populations by imposing selective pressures on their host's immune system. In particular, the hyperdiverse genes of the major histocompatibility complex (MHC) are implicated in parasite-mediated host divergence. Here, we studied the extent of divergence at MHC, and discuss how it may have contributed to the Nicaraguan Midas cichlid species complex diversification, one of the most convincing examples of rapid sympatric parallel speciation. Results We genotyped the MHC IIB for individuals from six sympatric Midas cichlid assemblages, each containing species that have adapted to exploit similar habitats. We recovered large allelic and functional diversity within the species complex. While most alleles were rare, functional groups of alleles (supertypes) were common, suggesting that they are key to survival and that they were maintained during colonization and subsequent radiations. We identified lake-specific and habitat-specific signatures for both allelic and functional diversity, but no clear pattern of parallel divergence among ecomorphologically similar phenotypes. Conclusions Colonization and demographic effects of the fish could have contributed to MHC evolution in the Midas cichlid in conjunction with habitat-specific selective pressures, such as parasites associated to alternative preys or environmental features. Additional ecological data will help evaluating the role of host–parasite interactions in the Midas cichlid radiations and aid in elucidating the potential role of non-parallel features differentiating crater lake species assemblages. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01997-9.
Collapse
Affiliation(s)
- Seraina E Bracamonte
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Melinda J Hofmann
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Carlos Lozano-Martín
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Marta Barluenga
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| |
Collapse
|
13
|
Hagberg L, Celemín E, Irisarri I, Hawlitschek O, Bella JL, Mott T, Pereira RJ. Extensive introgression at late stages of species formation: Insights from grasshopper hybrid zones. Mol Ecol 2022; 31:2384-2399. [PMID: 35191134 DOI: 10.1111/mec.16406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
Abstract
The process of species formation is characterised by the accumulation of multiple reproductive barriers. The evolution of hybrid male sterility, or Haldane's rule, typically characterises later stages of species formation, when reproductive isolation is strongest. Yet, understanding how quickly reproductive barriers evolve and their consequences for maintaining genetic boundaries between emerging species remains a challenging task because it requires studying taxa that hybridise in nature. Here, we address these questions using the meadow grasshopper Pseudochorthippus parallelus, where populations that show multiple reproductive barriers, including hybrid male sterility, hybridise in two natural hybrid zones. Using mitochondrial data, we infer that such populations have diverged some 100,000 years ago, at the beginning of the last glacial cycle in Europe. Nuclear data shows that contractions at multiple glacial refugia, and post-glacial expansions have facilitated genetic differentiation between lineages that today interact in hybrid zones. We find extensive introgression throughout the sampled species range, irrespective of current strength of reproductive isolation. Populations exhibiting hybrid male sterility in two hybrid zones show repeatable patterns of genomic differentiation, consistent with shared genomic constraints affecting ancestral divergence or with the role of those regions in reproductive isolation. Together, our results suggest that reproductive barriers that characterise late stages of species formation can evolve relatively quickly, particularly when associated with strong demographic changes. Moreover, we show that such barriers persist in the face of extensive gene flow, allowing future studies to identify associated genomic regions.
Collapse
Affiliation(s)
- Linda Hagberg
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Enrique Celemín
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany.,Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077, Göttingen, Germany.,Campus Institute Data Science (CIDAS), Göttingen, Germany
| | - Oliver Hawlitschek
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.,Zoologische Staatssammlung (SNSB-ZSM), Münchhausenstr. 21, 81247, Munich, Germany
| | - José L Bella
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Tamí Mott
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, 57072-900, Maceió, Alagoas, Brazil
| | - Ricardo J Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| |
Collapse
|
14
|
Reeve J, Li Q, Lindtke D, Yeaman S. Comparing genome scans among species of the stickleback order reveals three different patterns of genetic diversity. Ecol Evol 2022; 12:e8502. [PMID: 35127027 PMCID: PMC8796908 DOI: 10.1002/ece3.8502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/03/2022] Open
Abstract
Comparing genome scans among species is a powerful approach for investigating the patterns left by evolutionary processes. In particular, this offers a way to detect candidate genes that drive convergent evolution. We compared genome scan results to investigate if patterns of genetic diversity and divergence are shared among divergent species within the stickleback order (Gasterosteiformes): the threespine stickleback (Gasterosteus aculeatus), ninespine stickleback (Pungitius pungitus), and tubesnout (Aulorhynchus flavidus). Populations were sampled from the southern and northern edges of each species' range, to identify patterns associated with latitudinal changes in genetic diversity. Weak correlations in genetic diversity (F ST and expected heterozygosity) and three different patterns in the genomic landscape were found among these species. Additionally, no candidate genes for convergent evolution were detected. This is a counterexample to the growing number of studies that have shown overlapping genetic patterns, demonstrating that genome scan comparisons can be noisy due to the effects of several interacting evolutionary forces.
Collapse
Affiliation(s)
- James Reeve
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Present address:
Tjärnö Marina LaboratoriumGöteborgs UniversitetStrömstadSweden
| | - Qiushi Li
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Present address:
Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Dorothea Lindtke
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Present address:
Institute of Plant SciencesUniversity of BernBernSwitzerland
| | - Samuel Yeaman
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| |
Collapse
|
15
|
de Aranzamendi MC, Martínez JJ, Held C, Sahade R. Parallel shape divergence between ecotypes of the limpet Nacella concinna along the Antarctic Peninsula: a new model species for parallel evolution? ZOOLOGY 2021; 150:125983. [PMID: 34915245 DOI: 10.1016/j.zool.2021.125983] [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: 06/01/2021] [Revised: 09/23/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022]
Abstract
Parallel phenotypic divergence is the independent differentiation between phenotypes of the same lineage or species occupying ecologically similar environments in different populations. We tested in the Antarctic limpet Nacella concinna the extent of parallel morphological divergence in littoral and sublittoral ecotypes throughout its distribution range. These ecotypes differ in morphological, behavioural and physiological characteristics. We studied the lateral and dorsal outlines of shells and the genetic variation of the mitochondrial gene Cytochrome Oxidase subunit I from both ecotypes in 17 sample sites along more than 2,000 km. The genetic data indicate that both ecotypes belong to a single evolutionary lineage. The magnitude and direction of phenotypic variation differ between ecotypes across sample sites; completely parallel ecotype-pairs (i.e., they diverge in the same magnitude and in the same direction) were detected in 84.85% of lateral and 65.15% in dorsal view comparisons. Besides, specific traits (relative shell height, position of shell apex, and elliptical/pear-shape outline variation) showed high parallelism. We observed weak morphological covariation between the two shape shell views, indicating that distinct evolutionary forces and environmental pressures could be acting on this limpet shell shape. Our results demonstrate there is a strong parallel morphological divergence pattern in N. concinna along its distribution, making this Antarctic species a suitable model for the study of different evolutionary forces shaping the shell evolution of this limpet.
Collapse
Affiliation(s)
- María Carla de Aranzamendi
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Cátedra de Ecología Marina, Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Ecosistemas Marinos y Polares (ECOMARES), Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina.
| | - Juan José Martínez
- Laboratorio de Ecología Evolutiva y Biogeografía, Instituto de Ecorregiones Andinas (INECOA), CONICET and Universidad Nacional de Jujuy, C. Gorriti 237, San Salvador de Jujuy, 4600, Argentina.
| | - Christoph Held
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany.
| | - Ricardo Sahade
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Cátedra de Ecología Marina, Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Ecosistemas Marinos y Polares (ECOMARES), Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina.
| |
Collapse
|
16
|
Saha A, Andersson A, Kurland S, Keehnen NLP, Kutschera VE, Hössjer O, Ekman D, Karlsson S, Kardos M, Ståhl G, Allendorf FW, Ryman N, Laikre L. Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes. Mol Ecol 2021; 31:498-511. [PMID: 34699656 DOI: 10.1111/mec.16252] [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: 12/18/2020] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022]
Abstract
The sympatric existence of genetically distinguishable populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verified the existence of the two coexisting demes using a 96-SNP fluidigm array. We then applied whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome-wide FST ≈ 0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene-copies for LDH-A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.
Collapse
Affiliation(s)
- Atal Saha
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Anastasia Andersson
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sara Kurland
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Naomi L P Keehnen
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Ola Hössjer
- Department of Mathematics, Stockholm University, Stockholm, Sweden
| | - Diana Ekman
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Marty Kardos
- Flathead Lake Biological Station, University of Montana, Montana, USA.,National Marine Fisheries Service, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | | | - Fred W Allendorf
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Nils Ryman
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Linda Laikre
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| |
Collapse
|
17
|
Papadopulos AST, Helmstetter AJ, Osborne OG, Comeault AA, Wood DP, Straw EA, Mason L, Fay MF, Parker J, Dunning LT, Foote AD, Smith RJ, Lighten J. Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution. Mol Biol Evol 2021; 38:3724-3736. [PMID: 33950261 PMCID: PMC8382892 DOI: 10.1093/molbev/msab141] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, capacity of species to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonized isolated, disused mines with phytotoxic, zinc-contaminated soils. To test whether rapid, parallel adaptation to anthropogenic pollution has taken place, we used reduced representation sequencing (ddRAD) to reconstruct the evolutionary history of geographically proximate mine and coastal population pairs and found largely independent colonization of mines from different coastal sites. Furthermore, our results show that parallel evolution of zinc tolerance has occurred without gene flow spreading adaptive alleles between mine populations. In genomic regions where signatures of selection were detected across multiple mine-coast pairs, we identified genes with functions linked to physiological differences between the putative ecotypes, although genetic differentiation at specific loci is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities (and other environmental challenges) may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.
Collapse
Affiliation(s)
- Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Andrew J Helmstetter
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- FRB-CESAB, Institut Bouisson Bertrand, Rue de l'École de Médecine, Montpellier, France
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Aaron A Comeault
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Daniel P Wood
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Edward A Straw
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Ecology, Evolution & Behaviour, Department of Biological Sciences, School for Life Sciences and the Environment, Royal Holloway University of London, Egham, United Kingdom
| | | | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - Joe Parker
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- National Biofilms Innovation Centre, Department of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Andrew D Foote
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Department of Natural History, Norwegian University of Science and Technology, NTNU University Museum, Trondheim, Norway
| | - Rhian J Smith
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jackie Lighten
- Biosciences, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
18
|
Campbell MA, Anderson EC, Garza JC, Pearse DE. Polygenic basis and the role of genome duplication in adaptation to similar selective environments. J Hered 2021; 112:614-625. [PMID: 34420047 DOI: 10.1093/jhered/esab049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/20/2021] [Indexed: 02/02/2023] Open
Abstract
Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean access and compared them to each other and to an anadromous below-barrier population representing their ancestral source to search for signatures of both parallel and non-parallel adaptation. All landlocked populations displayed an increased frequency of a large inversion on chromosome Omy05, while three of the four populations exhibited elevated frequencies of another inversion located on chromosome Omy20. In addition, we identified numerous regions outside these two inversions that also show significant shifts in allele frequencies consistent with adaptive evolution. However, there was little concordance among above-barrier populations in these specific genomic regions under selection. In part, the lack of concordance appears to arise from ancestral autopolyploidy in rainbow trout that provides duplicate genomic regions of similar functional composition for selection to act upon. Thus, while selection acting on landlocked populations universally favors the resident ecotype, outside of the major chromosomal inversions, the resulting genetic changes are largely distinct among populations. Our results indicate that selection on standing genetic variation is likely the primary mode of rapid adaptation, and that both supergene complexes and individual loci contribute to adaptive evolution, further highlighting the diversity of adaptive genomic variation involved in complex phenotypic evolution.
Collapse
Affiliation(s)
- Matthew A Campbell
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Eric C Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - John Carlos Garza
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| |
Collapse
|
19
|
Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, Schön I. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 2021; 22:625. [PMID: 34418978 PMCID: PMC8380342 DOI: 10.1186/s12864-021-07917-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
Collapse
Affiliation(s)
- Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.
| | - Franz M Heindler
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Quentin Jossart
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Henri Robert
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Marie Verheye
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Bruno Danis
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Camille Moreau
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Université de Bourgogne Franche-Comté (UBFC) UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Tasnim Patel
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Anton P Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Isa Schön
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| |
Collapse
|
20
|
Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles. Nat Commun 2021; 12:4979. [PMID: 34404804 PMCID: PMC8370997 DOI: 10.1038/s41467-021-25256-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/21/2021] [Indexed: 01/26/2023] Open
Abstract
Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms. Relative contributions of pre-existing versus de novo genomic variation to adaptation remain unclear. Here, the authors address this problem by examining the adaptation of autotetraploid Arabidopsis arenosa to serpentine soils and find that both types of variations contribute to rapid adaptation.
Collapse
|
21
|
Maltseva AL, Varfolomeeva MA, Ayanka RV, Gafarova ER, Repkin EA, Pavlova PA, Shavarda AL, Mikhailova NA, Granovitch AI. Linking ecology, morphology, and metabolism: Niche differentiation in sympatric populations of closely related species of the genus Littorina ( Neritrema). Ecol Evol 2021; 11:11134-11154. [PMID: 34429908 PMCID: PMC8366845 DOI: 10.1002/ece3.7901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 05/08/2021] [Accepted: 06/22/2021] [Indexed: 12/03/2022] Open
Abstract
Divergence of ecological niches in phylogenetically closely related species indicates the importance of ecology in speciation, especially for sympatric species are considered. Such ecological diversification provides an advantage of alleviating interspecies competition and promotes more efficient exploitation of environmental resources, thus being a basis for ecological speciation. We analyzed a group of closely related species from the subgenus Neritrema (genus Littorina, Caenogastropoda) from the gravel-bouldery shores. In two distant sites at the Barents and Norwegian Sea, we examined the patterns of snail distribution during low tide (quantitative sampling stratified by intertidal level, presence of macrophytes, macrophyte species, and position on them), shell shape and its variability (geometric morphometrics), and metabolic characteristics (metabolomic profiling). The studied species diversified microbiotopes, which imply an important role of ecological specification in the recent evolution of this group. The only exception to this trend was the species pair L. arcana / L. saxatilis, which is specifically discussed. The ecological divergence was accompanied by differences in shell shape and metabolomic characteristics. Significant differences were found between L. obtusata versus L. fabalis and L. saxatilis / L. arcana versus L. compressa both in shell morphology and in metabolomes. L. saxatilis demonstrated a clear variability depending on intertidal level which corresponds to a shift in conditions within the occupied microhabitat. Interestingly, the differences between L. arcana (inhabiting the upper intertidal level) and L. compressa (inhabiting the lower one) were analogous to those between the upper and lower fractions of L. saxatilis. No significant level-dependent changes were found between the upper and lower fractions of L. obtusata, most probably due to habitat amelioration by fucoid macroalgae. All these results are discussed in the contexts of the role of ecology in speciation, ecological niche dynamics and conservatism, and evolutionary history of the Neritrema species.
Collapse
Affiliation(s)
- Arina L Maltseva
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Marina A Varfolomeeva
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Roman V Ayanka
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Elizaveta R Gafarova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Egor A Repkin
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Polina A Pavlova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Alexei L Shavarda
- Department of Analytical Phytochemistry Komarov Botanical Institute St. Petersburg Russia
- Research Park Centre for Molecular and Cell Technologies St. Petersburg State University St. Petersburg Russia
| | - Natalia A Mikhailova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
- Centre of Cell Technologies Institute of Cytology Russian Academy of Sciences St. Petersburg Russia
| | - Andrei I Granovitch
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| |
Collapse
|
22
|
Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Mol Ecol 2021; 30:3797-3814. [PMID: 33638231 DOI: 10.1111/mec.15861] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/12/2021] [Indexed: 12/28/2022]
Abstract
Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder-rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones.
Collapse
Affiliation(s)
- Anja M Westram
- IST Austria, Klosterneuburg, Austria.,Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Rui Faria
- Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
| | - Kerstin Johannesson
- Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Roger Butlin
- Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| |
Collapse
|
23
|
Magota K, Sakaguchi S, Lee JS, Yamamoto M, Takahashi D, Nagano AJ, Setoguchi H. Phylogeographic analysis of Saxifraga fortunei complex (Saxifragaceae) reveals multiple origins of morphological and ecological variations in the Japanese Archipelago. Mol Phylogenet Evol 2021; 163:107230. [PMID: 34133947 DOI: 10.1016/j.ympev.2021.107230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
Phenotypic polymorphism within a species is a notable phenomenon in evolutionary biology to understand the process of adaptive speciation and other historical events. The Saxifraga fortunei complex is a widespread herb found in East Asia. It includes several ecotypic taxa corresponding to their habitat environments. The distribution of the various ecotypes in a limited area of the Japanese Archipelago makes the species a suitable model to investigate the impact of population demographic history and natural selection on lineage diversification. Here, Sanger-based sequencing was used to estimate the divergence timeframe between populations of the Eurasian continent and Japan. Genome-wide SNPs obtained by ddRAD sequencing were used to investigate the phylogeographic origins of ecotypic taxa. The phylogenetic analyses revealed the divergence of the Japanese population from the continental population in the late Miocene. Two distinct regional clades of North and South Japan were identified; phenotypic diversification was evident only in the southern clade. The South Japan clades displayed a historical distribution expansion from north to south. The phenotypic variations appeared to have generated during the expansion. The ecotypic boundaries were incongruent with the genetic grouping. We propose that morphological and ecological specialization in Japanese populations was repeatedly generated by local natural selection.
Collapse
Affiliation(s)
- Kana Magota
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan.
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Jung-Sim Lee
- Korean National Arboretum, 415 Gwangneung Sumokwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-Province 11186, Republic of Korea
| | - Masaya Yamamoto
- Hyogo University of Teacher Education, 942-1 Shimokume, Kato, Hyogo 673-1494, Japan
| | - Daiki Takahashi
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| |
Collapse
|
24
|
Bakovic V, Martin Cerezo ML, Höglund A, Fogelholm J, Henriksen R, Hargeby A, Wright D. The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes. Mol Ecol 2021; 30:3530-3547. [PMID: 34002902 DOI: 10.1111/mec.15987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022]
Abstract
Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave vs. surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark-pigmented "reed" and light-pigmented "stonewort" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a quantitative trait locus (QTL) mapping study using a laboratory bred F2 and F4 cave × surface intercross. We identified genomic regions associated with body pigmentation, antennae length and body size. Furthermore, we compared genome-wide differentiation between natural populations and found several genes potentially associated with these habitats. The assessment of the cave QTL regions in the light-dark comparison of lake populations suggests that the regions associated with cave adaptation are also involved with genomic differentiation in the lake ecotypes. These demonstrate how troglomorphic adaptations can be used as a model for related ecotype formation.
Collapse
Affiliation(s)
- Vid Bakovic
- IFM Biology, University of Linköping, Linköping, Sweden
| | | | | | | | - Rie Henriksen
- IFM Biology, University of Linköping, Linköping, Sweden
| | | | | |
Collapse
|
25
|
Davison A, Neiman M. Pearls of wisdom-a Theo Murphy issue on molluscan genomics. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200151. [PMID: 33813890 PMCID: PMC8059963 DOI: 10.1098/rstb.2020.0151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 12/16/2022] Open
Affiliation(s)
- Angus Davison
- School of Life Sciences, University of Nottingham, Nottingham, Nottinghamshire NG7 2RD, UK
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| |
Collapse
|
26
|
Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evol Lett 2021; 5:196-213. [PMID: 34136269 PMCID: PMC8190449 DOI: 10.1002/evl3.227] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/06/2021] [Accepted: 03/29/2021] [Indexed: 01/11/2023] Open
Abstract
Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.
Collapse
Affiliation(s)
- Eva L Koch
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Hernán E Morales
- Evolutionary Genetics Section Globe Institute University of Copenhagen Copenhagen Denmark.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Jenny Larsson
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Anja M Westram
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,IST Austria Klosterneuburg Austria
| | - Rui Faria
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee Florida FL 32306-4120
| | - E Moriarty Lemmon
- Department of Biological Science Florida State University Tallahassee Florida FL 32306-4295
| | - Kerstin Johannesson
- Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Roger K Butlin
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| |
Collapse
|
27
|
Santos CA, Sonoda GG, Cortez T, Coutinho LL, Andrade SCS. Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation. Genome Biol Evol 2021; 13:6171147. [PMID: 33720344 PMCID: PMC8070887 DOI: 10.1093/gbe/evab050] [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: 11/04/2020] [Revised: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
Understanding how selection shapes population differentiation and local adaptation in marine species remains one of the greatest challenges in the field of evolutionary biology. The selection of genes in response to environment-specific factors and microenvironmental variation often results in chaotic genetic patchiness, which is commonly observed in rocky shore organisms. To identify these genes, the expression profile of the marine gastropod Littoraria flava collected from four Southeast Brazilian locations in ten rocky shore sites was analyzed. In this first L. flava transcriptome, 250,641 unigenes were generated, and 24% returned hits after functional annotation. Independent paired comparisons between 1) transects, 2) sites within transects, and 3) sites from different transects were performed for differential expression, detecting 8,622 unique differentially expressed genes. Araçá (AR) and São João (SJ) transect comparisons showed the most divergent gene products. For local adaptation, fitness-related differentially expressed genes were chosen for selection tests. Nine and 24 genes under adaptative and purifying selection, respectively, were most related to biomineralization in AR and chaperones in SJ. The biomineralization-genes perlucin and gigasin-6 were positively selected exclusively in the site toward the open ocean in AR, with sequence variants leading to pronounced protein structure changes. Despite an intense gene flow among L. flava populations due to its planktonic larva, gene expression patterns within transects may be the result of selective pressures. Our findings represent the first step in understanding how microenvironmental genetic variation is maintained in rocky shore populations and the mechanisms underlying local adaptation in marine species.
Collapse
Affiliation(s)
- Camilla A Santos
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gabriel G Sonoda
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luiz L Coutinho
- Departamento de Ciência Animal, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, São Paulo, SP, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| |
Collapse
|
28
|
Flanagan SP, Rose E, Jones AG. The population genomics of repeated freshwater colonizations by Gulf pipefish. Mol Ecol 2021; 30:1672-1687. [PMID: 33580570 DOI: 10.1111/mec.15841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/30/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022]
Abstract
How organisms adapt to the novel challenges imposed by the colonization of a new habitat has long been a central question in evolutionary biology. When multiple populations of the same species independently adapt to similar environmental challenges, the question becomes whether the populations have arrived at their adaptations through the same genetic mechanisms. In recent years, genetic techniques have been used to tackle these questions by investigating the genome-level changes underlying local adaptation. Here, we present a genomic analysis of colonization of freshwater habitats by a primarily marine fish, the Gulf pipefish (Syngnathus scovelli). We sample pipefish from four geographically distinct freshwater locations and use double-digest restriction site associated DNA sequencing to compare them to 12 previously studied saltwater populations. The two most geographically distant and isolated freshwater populations are the most genetically distinct, although demographic analysis suggests that these populations are experiencing ongoing migration with their saltwater neighbours. Additionally, outlier regions were found genome-wide, showing parallelism across ecotype pairs. We conclude that these multiple freshwater colonizations involve similar genomic regions, despite the large geographical distances and different underlying mechanisms. These similar patterns are probably facilitated by the interacting effects of intrinsic barriers, gene flow among populations and ecological selection in the Gulf pipefish.
Collapse
Affiliation(s)
- Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emily Rose
- Department of Biology, Valdosta State University, Valdosta, GA, USA
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| |
Collapse
|
29
|
Cerca J, Maurstad MF, Rochette NC, Rivera‐Colón AG, Rayamajhi N, Catchen JM, Struck TH. Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13562] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- José Cerca
- Frontiers in Evolutionary Zoology Natural History MuseumUniversity of Oslo Oslo Norway
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
- Department of Natural History NTNU University MuseumNorwegian University of Science and Technology Trondheim Norway
| | - Marius F. Maurstad
- Frontiers in Evolutionary Zoology Natural History MuseumUniversity of Oslo Oslo Norway
- Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
| | - Nicolas C. Rochette
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - Angel G. Rivera‐Colón
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
| | - Niraj Rayamajhi
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
| | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
| | - Torsten H. Struck
- Frontiers in Evolutionary Zoology Natural History MuseumUniversity of Oslo Oslo Norway
| |
Collapse
|
30
|
Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 2021; 10:e63167. [PMID: 33599612 PMCID: PMC7963486 DOI: 10.7554/elife.63167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.
Collapse
Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Nico L Avenant
- National Museum and Centre for Environmental Management, University of the Free StateBloemfonteinSouth Africa
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums ScotlandEdinburghUnited Kingdom
| | - Erwan Corre
- CNRS, Sorbonne Université, CNRS, ABiMS, Station Biologique de RoscoffRoscoffFrance
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| |
Collapse
|
31
|
Huang K, Huber G, Ritland K, Dunn DW, Li B. Performing parentage analysis for polysomic inheritances based on allelic phenotypes. G3-GENES GENOMES GENETICS 2021; 11:6080682. [PMID: 33585871 PMCID: PMC8022955 DOI: 10.1093/g3journal/jkaa064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/09/2020] [Indexed: 11/26/2022]
Abstract
Polyploidy poses several problems for parentage analysis. We present a new polysomic inheritance model for parentage analysis based on genotypes or allelic phenotypes to solve these problems. The effects of five factors are simultaneously accommodated in this model: (1) double-reduction, (2) null alleles, (3) negative amplification, (4) genotyping errors and (5) self-fertilization. To solve genotyping ambiguity (unknown allele dosage), we developed a new method to establish the likelihood formulas for allelic phenotype data and to simultaneously include the effects of our five chosen factors. We then evaluated and compared the performance of our new method with three established methods by using both simulated data and empirical data from the cultivated blueberry (Vaccinium corymbosum). We also developed and compared the performance of two additional estimators to estimate the genotyping error rate and the sample rate. We make our new methods freely available in the software package polygene, at http://github.com/huangkang1987/polygene.
Collapse
Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China.,Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Gwendolyn Huber
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Kermit Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| |
Collapse
|
32
|
Härer A, Bolnick DI, Rennison DJ. The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback. Mol Ecol 2020; 30:451-463. [PMID: 33222348 DOI: 10.1111/mec.15746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/21/2020] [Accepted: 11/09/2020] [Indexed: 12/23/2022]
Abstract
The repeated occurrence of similar phenotypes in independent lineages (i.e., parallel evolution) in response to similar ecological conditions can provide compelling insights into the process of adaptive evolution. An intriguing question is to what extent repeated phenotypic changes are underlain by repeated changes at the genomic level and whether patterns of genomic divergence differ with the geographic context in which populations evolve. Here, we combined genomic, morphological and ecological data sets to investigate the genomic signatures of divergence across populations of threespine stickleback (Gasterosteus aculeatus) that adapted to contrasting ecological niches (benthic or limnetic) in either sympatry or allopatry. We found that genome-wide differentiation (FST ) was an order of magnitude higher and substantially more repeatable for sympatric benthic and limnetic specialists compared to allopatric populations with similar levels of ecological divergence. We identified genomic regions consistently differentiated between sympatric ecotypes that were also differentiated between or associated with benthic vs. limnetic niche in allopatric populations. These candidate regions were enriched on three chromosomes known to be involved in the benthic-limnetic divergence of threespine stickleback. Some candidate regions overlapped with QTL for body shape and trophic traits such as gill raker number, traits that strongly differ between benthic and limnetic ecotypes. In summary, our study shows that magnitude and repeatability of genomic signatures of ecological divergence in threespine stickleback highly depend on the geographic context. The identified candidate regions provide starting points to identify functionally important genes for the adaptation to benthic and limnetic niches.
Collapse
Affiliation(s)
- Andreas Härer
- Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, USA
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Diana J Rennison
- Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
33
|
Knotek A, Konečná V, Wos G, Požárová D, Šrámková G, Bohutínská M, Zeisek V, Marhold K, Kolář F. Parallel Alpine Differentiation in Arabidopsis arenosa. FRONTIERS IN PLANT SCIENCE 2020; 11:561526. [PMID: 33363550 PMCID: PMC7753741 DOI: 10.3389/fpls.2020.561526] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/16/2020] [Indexed: 05/14/2023]
Abstract
Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbor the alpine ecotype and used SNP genotyping to test for repeated alpine colonization. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makes A. arenosa a promising candidate for studying genomic basis of adaptation.
Collapse
Affiliation(s)
- Adam Knotek
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Veronika Konečná
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Guillaume Wos
- Department of Botany, Charles University, Prague, Czechia
| | | | | | - Magdalena Bohutínská
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Vojtěch Zeisek
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Karol Marhold
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Filip Kolář
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
34
|
Zueva KJ, Lumme J, Veselov AE, Primmer CR, Pritchard VL. Population genomics reveals repeated signals of adaptive divergence in the Atlantic salmon of north‐eastern Europe. J Evol Biol 2020; 34:866-878. [DOI: 10.1111/jeb.13732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Affiliation(s)
| | - Jaakko Lumme
- Department of Biology University of Oulu Oulu Finland
| | | | - Craig R. Primmer
- Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland
- Institute of Biotechnology University of Helsinki Helsinki Finland
| | - Victoria L. Pritchard
- Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland
- Rivers and Lochs Institute Inverness College University of Highlands and Islands Inverness UK
| |
Collapse
|
35
|
Kess T, Brachmann M, Boulding EG. Putative chromosomal rearrangements are associated primarily with ecotype divergence rather than geographic separation in an intertidal, poorly dispersing snail. J Evol Biol 2020; 34:193-207. [PMID: 33108001 DOI: 10.1111/jeb.13724] [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: 10/29/2019] [Revised: 09/29/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022]
Abstract
Littorina saxatilis is becoming a model system for understanding the genomic basis of ecological speciation. The parallel formation of crab-adapted ecotypes that exhibit partial reproductive isolation from wave-adapted ecotypes has enabled genomic investigation of conspicuous shell traits. Recent genomic studies suggest that chromosomal rearrangements may enable ecotype divergence by reducing gene flow. However, the genomic architecture of traits that are divergent between ecotypes remains poorly understood. Here, we use 11,504 single nucleotide polymorphism (SNP) markers called using the recently released L. saxatilis genome to genotype 462 crab ecotype, wave ecotype and phenotypically intermediate Spanish L. saxatilis individuals with scored phenotypes. We used redundancy analysis to study the genetic architecture of loci associated with shell shape, shape corrected for size, shell size and shell ornamentation, and to compare levels of co-association among different traits. We discovered 341 SNPs associated with shell traits. Loci associated with trait divergence between ecotypes were often located inside putative chromosomal rearrangements recently characterized in Swedish L. saxatilis. In contrast, we found that shell shape corrected for size varied primarily by geographic site rather than by ecotype and showed little association with these putative rearrangements. We conclude that genomic regions of elevated divergence inside putative rearrangements were associated with divergence of L. saxatilis ecotypes along steep environmental axes-consistent with models of adaptation with gene flow-but were not associated with divergence among the three geographical sites. Our findings support predictions from models indicating the importance of genomic regions of reduced recombination allowing co-association of loci during ecological speciation with ongoing gene flow.
Collapse
Affiliation(s)
- Tony Kess
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Matthew Brachmann
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | | |
Collapse
|
36
|
Nielsen ES, Henriques R, Beger M, Toonen RJ, von der Heyden S. Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species. BMC Evol Biol 2020; 20:121. [PMID: 32938400 PMCID: PMC7493327 DOI: 10.1186/s12862-020-01679-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species' potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). RESULTS Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. CONCLUSION The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.
Collapse
Affiliation(s)
- Erica S Nielsen
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Romina Henriques
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.,Technical University of Denmark, National Institute of Aquatic Resources, Section for Marine Living Resources, Velsøvej 39, 8600, Silkeborg, Denmark
| | - Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
| |
Collapse
|
37
|
Cornwell BH. Gene flow in the anemone
Anthopleura elegantissima
limits signatures of local adaptation across an extensive geographic range. Mol Ecol 2020; 29:2550-2566. [DOI: 10.1111/mec.15506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/22/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
|
38
|
Haase M, Meng S, Horsák M. Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abstract
Changing environmental conditions force species either to disperse or to adapt locally either genetically or via phenotypic plasticity. Although limits of plasticity can be experimentally tested, the predictability of genetic adaptation is restricted due to its stochastic nature. Nevertheless, our understanding of evolutionary adaptation has been improving in particular through studies of parallel adaptation. Based on molecular phylogenetic inferences and morphological investigations of both recent and fossil shells we tracked the morphological changes in three land snails, Pupilla alpicola, Pupilla loessica and Pupilla muscorum. These species differ in habitat requirements as well as historical and extant distributions with P. alpicola and P. loessica being more similar to each other than to P. muscorum. Therefore, we hypothesized, that the three species reacted independently and individually to the conditions changing throughout the Pleistocene, but expected that changes within P. alpicola and P. loessica would be more similar compared to P. muscorum. Indeed, intraspecific shell shape differences across time were similar in P. alpicola and P. loessica, suggesting that similar niche shifts have led to similar transformations in parallel. In contrast, extant P. muscorum populations were practically identical in shape to their ancestors. They have probably tracked their ecological niches through time.
Collapse
Affiliation(s)
- Martin Haase
- AG Vogelwarte, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Stefan Meng
- Institute of Geography and Geology, University of Greifswald, Greifswald, Germany
| | - Michal Horsák
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| |
Collapse
|
39
|
Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution 2020; 74:1482-1497. [PMID: 32472616 DOI: 10.1111/evo.14027] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/07/2020] [Accepted: 05/21/2020] [Indexed: 01/01/2023]
Abstract
When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.
Collapse
Affiliation(s)
- Samuel Perini
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, 45296, Sweden
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, 40530, Sweden
| | | | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, 45296, Sweden
| | - Roger K Butlin
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, 45296, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S102TN, United Kingdom
| |
Collapse
|
40
|
Lapègue S, Heurtebise S, Cornette F, Guichoux E, Gagnaire PA. Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels. Genes (Basel) 2020; 11:E451. [PMID: 32326303 PMCID: PMC7230726 DOI: 10.3390/genes11040451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/07/2020] [Accepted: 04/15/2020] [Indexed: 11/16/2022] Open
Abstract
The Pacific oyster, Crassostrea gigas, was voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry, following a severe disease outbreak. Since then, the two species have been in contact in southern Europe and, therefore, have the potential to exchange genes. Recent evolutionary genomic works have provided empirical evidence that C. gigas and C. angulata exhibit partial reproductive isolation. Although hybridization occurs in nature, the rate of interspecific gene flow varies across the genome, resulting in highly heterogeneous genome divergence. Taking this biological property into account is important to characterize genetic ancestry and population structure in oysters. Here, we identified a subset of ancestry-informative makers from the most differentiated regions of the genome using existing genomic resources. We developed two different panels in order to (i) easily differentiate C. gigas and C. angulata, and (ii) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic populations. Our results confirm high genetic homogeneity among Pacific cupped oyster populations in France and reveal several cases of introgressions between Portuguese and Japanese oysters in France and Portugal.
Collapse
Affiliation(s)
- Sylvie Lapègue
- Ifremer, SG2M-LGPMM, 17390 La Tremblade, France; (S.H.); (F.C.)
| | | | | | - Erwan Guichoux
- BIOGECO, INRAE, University Bordeaux, F-33610 Cestas, France;
| | | |
Collapse
|
41
|
Jacobs A, Carruthers M, Yurchenko A, Gordeeva NV, Alekseyev SS, Hooker O, Leong JS, Minkley DR, Rondeau EB, Koop BF, Adams CE, Elmer KR. Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish. PLoS Genet 2020; 16:e1008658. [PMID: 32302300 PMCID: PMC7164584 DOI: 10.1371/journal.pgen.1008658] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 02/06/2020] [Indexed: 01/05/2023] Open
Abstract
Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.
Collapse
Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Madeleine Carruthers
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Andrey Yurchenko
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Natalia V. Gordeeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey S. Alekseyev
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Oliver Hooker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Loch Lomond, Glasgow, United Kingdom
| | - Jong S. Leong
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - David R. Minkley
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Eric B. Rondeau
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Ben F. Koop
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Colin E. Adams
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Loch Lomond, Glasgow, United Kingdom
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
42
|
Sunde J, Yıldırım Y, Tibblin P, Forsman A. Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike ( Esox lucius) and a Synthesis of Previous Studies. Front Genet 2020; 11:218. [PMID: 32231687 PMCID: PMC7082332 DOI: 10.3389/fgene.2020.00218] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/24/2020] [Indexed: 01/06/2023] Open
Abstract
Population genetic studies reveal biodiversity patterns and inform about drivers of evolutionary differentiation and adaptation, including gene flow, drift and selection. This can advance our understanding and aid decision making regarding management and conservation efforts. Microsatellites have long been used in population genetic studies. Thanks to the development of newer techniques, sequencing approaches such as restriction site associated DNA sequencing (RADseq) are on their way to replace microsatellites for some applications. However, the performance of these two marker types in population genetics have rarely been systematically compared. We utilized three neutrally and adaptively differentiated populations of anadromous pike (Esox lucius) to assess the relative performance of microsatellites and RADseq with respect to resolution and conclusiveness of estimates of population differentiation and genetic structure. To this end, the same set of individuals (N = 64) were genotyped with both RADseq and microsatellite markers. To assess effects of sample size, the same subset of 10 randomly chosen individuals from each population (N = 30 in total) were also genotyped with both methods. Comparisons of estimated genetic diversity and structure showed that both markers were able to uncover genetic structuring. The full RADseq dataset provided the clearest detection of the finer scaled genetic structuring, and the other three datasets (full and subset microsatellite, and subset RADseq) provided comparable results. A search for outlier loci performed on the full SNP dataset pointed to signs of selection potentially associated with salinity and temperature, exemplifying the utility of RADseq to inform about the importance of different environmental factors. To evaluate whether performance differences between the markers are general or context specific, the results of previous studies that have investigated population structure using both marker types were synthesized. The synthesis revealed that RADseq performed as well as, or better than microsatellites in detecting genetic structuring in the included studies. The differences in the ability to detect population structure, both in the present and the previous studies, are likely explained by the higher number of loci typically utilized in RADseq compared to microsatellite analysis, as increasing the number of markers will (regardless of the marker type) increase power and allow for clearer detection and higher resolution of genetic structure.
Collapse
Affiliation(s)
- Johanna Sunde
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar, Sweden
| | | | | | | |
Collapse
|
43
|
Wadsworth CB, Okada Y, Dopman EB. Phenology-dependent cold exposure and thermal performance of Ostrinia nubilalis ecotypes. BMC Evol Biol 2020; 20:34. [PMID: 32138649 PMCID: PMC7059338 DOI: 10.1186/s12862-020-1598-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/26/2020] [Indexed: 01/28/2023] Open
Abstract
Background Understanding adaptation involves establishing connections between selective agents and beneficial population responses. However, relatively little attention has been paid to seasonal adaptation, in part, because it requires complex and integrative knowledge about seasonally fluctuating environmental factors, the effects of variable phenology on exposure to those factors, and evidence for temporal specialization. In the European corn borer moth, Ostrinia nubilalis, sympatric pheromone strains exploit the same host plant (Zea mays) but may genetically differ in phenology and be reproductively “isolated by time.” Z strain populations in eastern North America have been shown to have a prolonged larval diapause and produce one annual mating flight (July), whereas E strain populations complete an earlier (June) and a later (August) mating flight by shortening diapause duration. Here, we find evidence consistent with seasonal “adaptation by time” between these ecotypes. Results We use 12 years of field observation of adult seasonal abundance to estimate phenology of ecotype life cycles and to quantify life-stage specific climatic conditions. We find that the observed reduction of diapause duration in the E strain leads their non-diapausing, active life stages to experience a ~ 4 °C colder environment compared to the equivalent life stages in the Z strain. For a representative pair of populations under controlled laboratory conditions, we compare life-stage specific cold tolerance and find non-diapausing, active life stages in the E strain have as much as a 60% greater capacity to survive rapid cold shock. Enhanced cold hardiness appears unrelated to life-stage specific changes in the temperature at which tissues freeze. Conclusions Our results suggest that isolation by time and adaptation by time may both contribute to population divergence, and they argue for expanded study in this species of allochronic populations in nature experiencing the full spectrum of seasonal environments. Cyclical selective pressures are inherent properties of seasonal habitats. Diverse fluctuating selective agents across each year (temperature, predation, competition, precipitation, etc.) may therefore be underappreciated drivers of biological diversity.
Collapse
Affiliation(s)
- Crista B Wadsworth
- Department of Biology, Tufts University, 200 Boston Ave, Suite 4700, Medford, MA, 02155, USA. .,Current Affiliation: Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, 85 Lomb Memorial Drive, Rochester, NY, 14623, USA.
| | - Yuta Okada
- Department of Biology, Tufts University, 200 Boston Ave, Suite 4700, Medford, MA, 02155, USA
| | - Erik B Dopman
- Department of Biology, Tufts University, 200 Boston Ave, Suite 4700, Medford, MA, 02155, USA.
| |
Collapse
|
44
|
Rojas D, Lima AP, Momigliano P, Simões PI, Dudaniec RY, de Avila-Pires TCS, Hoogmoed MS, da Cunha Bitar YO, Kaefer IL, Amézquita A, Stow A. The evolution of polymorphism in the warning coloration of the Amazonian poison frog Adelphobates galactonotus. Heredity (Edinb) 2020; 124:439-456. [PMID: 31712747 PMCID: PMC7028985 DOI: 10.1038/s41437-019-0281-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/25/2019] [Accepted: 10/26/2019] [Indexed: 11/09/2022] Open
Abstract
While intraspecific variation in aposematic signals can be selected for by different predatory responses, their evolution is also contingent on other processes shaping genetic variation. We evaluate the relative contributions of selection, geographic isolation, and random genetic drift to the evolution of aposematic color polymorphism in the poison frog Adelphobates galactonotus, distributed throughout eastern Brazilian Amazonia. Dorsal coloration was measured for 111 individuals and genetic data were obtained from 220 individuals at two mitochondrial genes (mtDNA) and 7963 Single Nucleotide Polymorphisms (SNPs). Four color categories were described (brown, blue, yellow, orange) and our models of frog and bird visual systems indicated that each color was distinguishable for these taxa. Using outlier and correlative analyses we found no compelling genetic evidence for color being under divergent selection. A time-calibrated mtDNA tree suggests that the present distribution of dorsal coloration resulted from processes occurring during the Pleistocene. Separate phylogenies based on SNPs and mtDNA resolved the same well supported clades, each containing different colored populations. Ancestral character state analysis provided some evidence for evolutionary transitions in color type. Genetic structure was more strongly associated with geographic features, than color category, suggesting that the distribution of color is explained by localized processes. Evidence for geographic isolation together with estimates of low effective population size implicates drift as playing a key role in color diversification. Our results highlight the relevance of considering the neutral processes involved with the evolution of traits with important fitness consequences.
Collapse
Affiliation(s)
- Diana Rojas
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, P.O. Box 2223, Manaus, AM, 69011-970, Brazil
- Universidade Federal do Amazonas, Instituto de Natureza e Cultura, Rua 1º de Maio 05, Benjamin Constant, AM, 69630-000, Brazil
| | - Albertina P Lima
- Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Manaus, AM, 69011-970, Brazil
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Pedro Ivo Simões
- Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Manaus, AM, 69011-970, Brazil
- Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof Moraes 1235, Recife, 50670-901, Brazil
| | - Rachael Y Dudaniec
- Department of Biological Sciences, Macquarie University, Balaclava Road, North Ryde, Sydney, NSW, 2109, Australia
| | | | - Marinus S Hoogmoed
- Museu Paraense Emilío Goeldi, Caixa Postal 399, Belém, PA, 66017-970, Brazil
| | - Youszef Oliveira da Cunha Bitar
- Programa de Pós-Graduação em Zoologia UFPA/Museu Paraense Emilio Goeldi, Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, PA, Brazil
| | - Igor L Kaefer
- Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Av. Rodrigo Octávio 6200, Manaus, AM, 69077-000, Brazil
| | - Adolfo Amézquita
- Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Adam Stow
- Department of Biological Sciences, Macquarie University, Balaclava Road, North Ryde, Sydney, NSW, 2109, Australia.
| |
Collapse
|
45
|
Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. J R Soc Interface 2020. [PMCID: PMC7061706 DOI: 10.1098/rsif.2019.0721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.
Collapse
Affiliation(s)
- J. Larsson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - S. Bengmark
- Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - T. Lundh
- Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - R. K. Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Department of Marine Sciences, University of Gothenburg, Stömstad, Sweden
| |
Collapse
|
46
|
Whiting JR, Fraser BA. Contingent Convergence: The Ability To Detect Convergent Genomic Evolution Is Dependent on Population Size and Migration. G3 (BETHESDA, MD.) 2020; 10:677-693. [PMID: 31871215 PMCID: PMC7003088 DOI: 10.1534/g3.119.400970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/19/2019] [Indexed: 12/02/2022]
Abstract
Outlier scans, in which the genome is scanned for signatures of selection, have become a prominent tool in studies of local adaptation, and more recently studies of genetic convergence in natural populations. However, such methods have the potential to be confounded by features of demographic history, such as population size and migration, which are considerably varied across natural populations. In this study, we use forward-simulations to investigate and illustrate how several measures of genetic differentiation commonly used in outlier scans (FST, DXY and Δπ) are influenced by demographic variation across multiple sampling generations. In a factorial design with 16 treatments, we manipulate the presence/absence of founding bottlenecks (N of founding individuals), prolonged bottlenecks (proportional size of diverging population) and migration rate between two populations with ancestral and diverged phenotypic optima. Our results illustrate known constraints of individual measures associated with reduced population size and a lack of migration; but notably we demonstrate how relationships between measures are similarly dependent on these features of demography. We find that false-positive signals of convergent evolution (the same simulated outliers detected in independent treatments) are attainable as a product of similar population size and migration treatments (particularly for DXY), and that outliers across different measures (for e.g., FST and DXY) can occur with little influence of selection. Taken together, we show how underappreciated, yet quantifiable measures of demographic history can influence commonly employed methods for detecting selection.
Collapse
Affiliation(s)
- James R Whiting
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD
| | - Bonnie A Fraser
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD
| |
Collapse
|
47
|
Rennison DJ, Delmore KE, Samuk K, Owens GL, Miller SE. Shared Patterns of Genome-Wide Differentiation Are More Strongly Predicted by Geography Than by Ecology. Am Nat 2020; 195:192-200. [DOI: 10.1086/706476] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
48
|
Johannesson K, Zagrodzka Z, Faria R, Marie Westram A, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? J Evol Biol 2019; 33:342-351. [PMID: 31724256 PMCID: PMC7079066 DOI: 10.1111/jeb.13570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022]
Abstract
Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.
Collapse
Affiliation(s)
- Kerstin Johannesson
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Zuzanna Zagrodzka
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Rui Faria
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | | | - Roger K Butlin
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| |
Collapse
|
49
|
Cryptic ecological and geographic diversification in coral-associated nudibranchs. Mol Phylogenet Evol 2019; 144:106698. [PMID: 31812568 DOI: 10.1016/j.ympev.2019.106698] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/03/2019] [Accepted: 11/30/2019] [Indexed: 12/18/2022]
Abstract
Coral reefs are among the most biologically diverse ecosystems of the world, yet little is known about the processes creating and maintaining their diversity. Ecologically, corallivory in nudibranchs resembles phytophagy in insects- a process that for decades has served as a model for ecological speciation via host shifting. This study uses extensive field collections, DNA sequencing, and phylogenetic analyses to reconstruct the evolutionary history of coral-associated nudibranchs and assess the relative roles that host shifting and geography may have played in their diversification. We find that the number of species is three times higher than the number previously known to science, with evidence for both allopatric and ecological divergence through host shifting and host specialization. Results contribute to growing support for the importance of ecological diversification in marine environments and provide evidence for new species in the genus Tenellia.
Collapse
|
50
|
Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. SCIENCE ADVANCES 2019; 5:eaav9963. [PMID: 31840052 PMCID: PMC6892616 DOI: 10.1126/sciadv.aav9963] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.
Collapse
Affiliation(s)
- Hernán E. Morales
- Centre for Marine Evolutionary Biology, Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Rui Faria
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Kerstin Johannesson
- Centre for Marine Evolutionary Biology, Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Tomas Larsson
- Centre for Marine Evolutionary Biology, Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, SE-752 37 Uppsala, Sweden
| | - Marina Panova
- Centre for Marine Evolutionary Biology, Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Anja M. Westram
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Roger K. Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Centre for Marine Evolutionary Biology, Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden
| |
Collapse
|