1
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Jeffery NW, Vercaemer B, Stanley RRE, Kess T, Dufresne F, Noisette F, O'Connor MI, Wong MC. Variation in genomic vulnerability to climate change across temperate populations of eelgrass ( Zostera marina). Evol Appl 2024; 17:e13671. [PMID: 38650965 PMCID: PMC11033490 DOI: 10.1111/eva.13671] [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: 01/20/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 04/25/2024] Open
Abstract
A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilization and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. In Canada, eelgrass is managed as a single phylogroup despite occurring across three oceans and a range of ocean temperatures and salinity gradients. Previous research has focused on applying relatively few markers to reveal population structure of eelgrass, whereas a whole-genome approach is warranted to investigate cryptic structure among populations inhabiting different ocean basins and localized environmental conditions. We used a pooled whole-genome re-sequencing approach to characterize population structure, gene flow and environmental associations of 23 eelgrass populations ranging from the Northeast United States to Atlantic, subarctic and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome-level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise F ST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the subarctic, consistent with colonization of the Arctic and Atlantic oceans from the Pacific less than 300 kya. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are predicted to be potentially more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should thus ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require additional mitigation measures given their potential susceptibility to a rapidly changing climate.
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Affiliation(s)
- Nicholas W. Jeffery
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Benedikte Vercaemer
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Ryan R. E. Stanley
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries CentreSt. John'sNewfoundland and LabradorCanada
| | - France Dufresne
- Département de BiologieUniversité du Québec à RimouskiRimouskiQuebecCanada
| | - Fanny Noisette
- Institut des Sciences de la mer, Université du Québec à RimouskiRimouskiQuebecCanada
| | - Mary I. O'Connor
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Melisa C. Wong
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
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2
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Brown RP, Sun H, Jin Y, Meloro C. Habitat-associated Genomic Variation in a Wall Lizard from an Oceanic Island. Genome Biol Evol 2023; 15:evad193. [PMID: 37862140 PMCID: PMC10637050 DOI: 10.1093/gbe/evad193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/30/2023] [Accepted: 10/02/2023] [Indexed: 10/22/2023] Open
Abstract
The lizard Teira dugesii exhibits morphological divergence between beach and inland habitats in the face of gene flow, within the volcanic island of Madeira, Portugal. Here, we analyzed genomic data obtained by genotyping-by-sequencing, which provided 16,378 single nucleotide polymorphisms (SNPs) from 94 individuals sampled from 15 sites across Madeira. Ancient within-island divergence in allopatry appears to have mediated divergence in similar species within other Atlantic islands, but this hypothesis was not supported for T. dugesii. Across all samples, a total of 168 SNPs were classified as statistical outliers using pcadapt and OutFLANK. Redundancy analysis (RDA) revealed that 17 of these outliers were associated with beach/inland habitats. The SNPs were located within 16 sequence tags and 15 of these were homologous with sequences in a 31 Mb region on chromosome 3 of a reference wall lizard genome (the remaining tag could not be associated with any chromosome). We further investigated outliers through contingency analyses of allele frequencies at each of four pairs of adjacent beach-inland sites. The majority of the outliers detected by the RDA were confirmed at two pairs of these matched sites. These analyses also suggested some parallel divergence at different localities. Six other outliers were associated with site elevation, four of which were located on chromosome 5 of the reference genome. Our study lends support to a previous hypothesis that divergent selection between gray shingle beaches and inland regions overcomes gene flow and leads to the observed morphological divergence between populations in these adjacent habitats.
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Affiliation(s)
- Richard P Brown
- College of Life Sciences, China Jiliang University, Hangzhou, P.R. China
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Hui Sun
- College of Life Sciences, China Jiliang University, Hangzhou, P.R. China
| | - Yuanting Jin
- College of Life Sciences, China Jiliang University, Hangzhou, P.R. China
| | - Carlo Meloro
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
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3
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Shen Y, Gan Y, Xiao Q, Huang Z, Liu J, Gong S, Wang Y, Yu W, Luo X, Ke C, You W. Divergent Carry-Over Effects of Hypoxia during the Early Development of Abalone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17836-17848. [PMID: 36479946 DOI: 10.1021/acs.est.2c04975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
After being exposed to environmental stimuli during early developmental stages, some organisms may gain or weaken physiological regulating abilities, which would have long-lasting effects on their performance. Environmental hypoxia events can have significant effects on marine organisms, but for breeding programs and other practical applications, it is important to further explore the long-term physiological effects of early hypoxia exposure in economically significant species. In this study, the Pacific abalone Haliotis discus hannai was exposed to moderate hypoxia (∼4 mg/L) from zygote to trochophora, and the assessments of hypoxia tolerance were conducted on the grow-out stage. The results revealed that juvenile abalones exposed to hypoxia at the early development stages were more hypoxia-tolerant but with slower weight growth, a phenomenon called the trade-off between growth and survival. These phenotypic effects driven by the hypoxia exposure were explained by strong selection of genes involved in signal transduction, autophagy, apoptosis, and hormone regulation. Moreover, long non-coding RNA regulation plays an important role modulating carry-over effects by controlling DNA replication and repair, signal transduction, myocardial activity, and hormone regulation. This study revealed that the ability to create favorable phenotypic differentiation through genetic selection and/or epigenetic regulation is important for the survival and development of aquatic animals in the face of rapidly changing environmental conditions.
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Affiliation(s)
- Yawei Shen
- State Key Laboratory of Marine Environmental Science, College of the Environmental and Ecology, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
- Fujian Institute for Sustainable Oceans, Xiamen University, Xiamen361102, China
| | - Yang Gan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Qizhen Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of the Environmental and Ecology, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Junyu Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Shihai Gong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Yi Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Wenchao Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
- Fujian Institute for Sustainable Oceans, Xiamen University, Xiamen361102, China
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4
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Arnqvist G, Sayadi A. A possible genomic footprint of polygenic adaptation on population divergence in seed beetles? Ecol Evol 2022; 12:e9440. [PMID: 36311399 PMCID: PMC9608792 DOI: 10.1002/ece3.9440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 09/14/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022] Open
Abstract
Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome‐wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate‐dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean FST = 0.23–0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's DNS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (dXY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome‐wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden
| | - Ahmed Sayadi
- Animal Ecology, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden,Rheumatology, Department of Medical SciencesUppsala UniversityUppsalaSweden
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5
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Nedoluzhko A, Orlova SY, Kurnosov DS, Orlov AM, Galindo-Villegas J, Rastorguev SM. Genomic Signatures of Freshwater Adaptation in Pacific Herring ( Clupea pallasii). Genes (Basel) 2022; 13:genes13101856. [PMID: 36292743 PMCID: PMC9601299 DOI: 10.3390/genes13101856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as “genomic islands of divergence”. Moreover, the Tajima’s D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait—osmoregulation.
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Affiliation(s)
- Artem Nedoluzhko
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint Petersburg, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
| | - Svetlana Yu. Orlova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 107140 Moscow, Russia
- Laboratory of Genetic Basis of Identification, Vavilov Institute of General Genetics of the Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
| | - Denis S. Kurnosov
- Research Group of Intraspecific Differentiation, Russian Federal Research Institute of Fisheries and Oceanography, Pacific Branch (TINRO), 690091 Vladivostok, Russia
| | - Alexei M. Orlov
- Laboratory of Oceanic Ichthyofauna, Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117218 Moscow, Russia
- Laboratory of Behavior of Lower Vertebrates, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Ichthyology, Dagestan State University, 367000 Makhachkala, Russia
- Department of Ichthyology and Hydrobiology, Tomsk State University, 634050 Tomsk, Russia
- Laboratory of Marine Biology, Caspian Institute of Biological Resources, Russian Academy of Sciences, 367000 Makhachkala, Russia
| | - Jorge Galindo-Villegas
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
| | - Sergey M. Rastorguev
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
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6
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Spies I, Tarpey C, Kristiansen T, Fisher M, Rohan S, Hauser L. Genomic differentiation in Pacific cod using
P
ool‐
S
eq. Evol Appl 2022; 15:1907-1924. [PMID: 36426128 PMCID: PMC9679252 DOI: 10.1111/eva.13488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/05/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022] Open
Abstract
Patterns of genetic differentiation across the genome can provide insight into selective forces driving adaptation. We used pooled whole genome sequencing, gene annotation, and environmental covariates to evaluate patterns of genomic differentiation and to investigate mechanisms responsible for divergence among proximate Pacific cod (Gadus macrocephalus) populations from the Bering Sea and Aleutian Islands and more distant Washington Coast cod. Samples were taken from eight spawning locations, three of which were replicated to estimate consistency in allele frequency estimation. A kernel smoothing moving weighted average of relative divergence (FST) identified 11 genomic islands of differentiation between the Aleutian Islands and Bering Sea samples. In some islands of differentiation, there was also elevated absolute divergence (dXY) and evidence for selection, despite proximity and potential for gene flow. Similar levels of absolute divergence (dXY) but roughly double the relative divergence (FST) were observed between the distant Bering Sea and Washington Coast samples. Islands of differentiation were much smaller than the four large inversions among Atlantic cod ecotypes. Islands of differentiation between the Bering Sea and Aleutian Island were associated with SNPs from five vision system genes, which can be associated with feeding, predator avoidance, orientation, and socialization. We hypothesize that islands of differentiation between Pacific cod from the Bering Sea and Aleutian Islands provide evidence for adaptive differentiation despite gene flow in this commercially important marine species.
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Affiliation(s)
- Ingrid Spies
- Resource Ecology and Fisheries Management Division Alaska Fisheries Science Center Seattle Washington USA
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | | | - Mary Fisher
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Sean Rohan
- Resource Assessment and Conservation Engineering Division Alaska Fisheries Science Center Seattle Washington USA
| | - Lorenz Hauser
- Resource Ecology and Fisheries Management Division Alaska Fisheries Science Center Seattle Washington USA
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7
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Genetic structure and diversity of amphidromous sculpin in Shiretoko, a mountainous peninsula in Japan. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01472-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Liu S, Wilson JM, Taylor EB, Richards JG. Freshwater adaptation in prickly sculpin (Pisces: Cottidae): intraspecific comparisons reveal evidence for water pH and Na+ concentration driving diversity in gill H+-ATPase and ionoregulation. J Exp Biol 2022; 225:276687. [PMID: 36062522 DOI: 10.1242/jeb.243500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 08/26/2022] [Indexed: 11/20/2022]
Abstract
Phenotypic divergence is a hallmark of adaptive radiation. One example involves differentiation in physiological traits involved in ion regulation among species with contrasting life-styles and living in distinct environments. Differentiation in ion regulation and its ecological implications among populations within species are, however, less well understood. To address this knowledge gap, we collected prickly sculpin (Cottus asper) from distinct habitat types including coastal rivers connected to estuaries, coastal lakes, and interior lakes, all from British Columbia, Canada. We tested for differences in plasma Na+ and Cl-, gill Na+/K+-ATPase and H+-ATPase activities and protein abundance as well as changes in body mass, and arterial blood pH in fish sampled from the field and acclimated to two different freshwater conditions in the laboratory including artificial lake water (ALW) and ion-poor water (IPW). We also tested for associations between environmental water chemistry and the physiological characteristics associated with ion regulation. Transfer to IPW resulted upregulation in gill Na+/K+-ATPase and H+-ATPase activities as well as increases in gill H+-ATPase protein expression level in each habitat compared with the common ALW treatment. Despite the presence of population-within-habitat type differences, significant habitat-type effects were revealed in most of the ion regulation characteristics examined under different acclimation conditions. Significantly lower plasma Cl- was detected in fish from coastal rivers compared to fish from the other two habitat types during the IPW treatment, which was also significantly lower compared with ALW. Similarly, gill Na+/K+-ATPase activity was lower in the coastal river populations in IPW than in fish from coastal and interior lakes, which was not in accordance with the protein expressed in the gill. For gill H+-ATPase, fish from interior lake populations had the highest level of activity across all habitat types under all conditions, which was related to the protein levels in the gill. The activity of gill H+-ATPase was positively correlated with the combined effect of water Na+ and pH under the ALW treatment. Our results suggest that variation in habitat may be an important factor driving differences in gill Na+/K+-ATPase and H+-ATPase activities across populations of C. asper. Further, the combined effect of water Na+ and pH may have played a key role in physiological adaptation in C. asper during post-glacial freshwater colonization and dispersal.
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Affiliation(s)
- Shuang Liu
- Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Jonathan M Wilson
- Department of Biology, Wilfrid Laurier University, 75 University Ave., Waterloo, ON N2L 3C5, Canada
| | - Eric B Taylor
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Jeffrey G Richards
- Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
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9
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Olivares‐Zambrano D, Daane J, Hyde J, Sandel MW, Aguilar A. Speciation genomics and the role of depth in the divergence of rockfishes (
Sebastes
) revealed through Pool‐seq analysis of enriched sequences. Ecol Evol 2022; 12:e9341. [PMID: 36188524 PMCID: PMC9502067 DOI: 10.1002/ece3.9341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 11/07/2022] Open
Abstract
Speciation in the marine environment is challenged by the wide geographic distribution of many taxa and potential for high rates of gene flow through larval dispersal mechanisms. Depth has recently been proposed as a potential driver of ecological divergence in fishes, and yet it is unclear how adaptation along these gradients' shapes genomic divergence. The genus Sebastes contains numerous species pairs that are depth‐segregated and can provide a better understanding of the mode and tempo of genomic diversification. Here, we present exome data on two species pairs of rockfishes that are depth‐segregated and have different degrees of divergence: S. chlorostictus–S. rosenblatti and S. crocotulus–S. miniatus. We were able to reliably identify “islands of divergence” in the species pair with more recent divergence (S. chlorostictus–S. rosenblatti) and discovered a number of genes associated with neurosensory function, suggesting a role for this pathway in the early speciation process. We also reconstructed demographic histories of divergence and found the best supported model was isolation followed by asymmetric secondary contact for both species pairs. These results suggest past ecological/geographic isolation followed by asymmetric secondary contact of deep to shallow species. Our results provide another example of using rockfish as a model for studying speciation and support the role of depth as an important mechanism for diversification in the marine environment.
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Affiliation(s)
- Daniel Olivares‐Zambrano
- Department of Biological SciencesCalifornia State University Los AngelesLos AngelesCaliforniaUSA
- Present address:
Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Jacob Daane
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexasUSA
| | - John Hyde
- National Oceanic and Atmospheric Administration, National Marine Fisheries ServiceNational Marine Fisheries ServiceSouthwest Fisheries Science CenterLa JollaCaliforniaUSA
| | - Michael W. Sandel
- Biological and Environmental SciencesUniversity of West AlabamaLivingstonAlabamaUSA
- Department of WIldlifeFisheries, and Aquaculture, Mississippi State UniversityMississippi StateMississippiUSA
| | - Andres Aguilar
- Department of Biological SciencesCalifornia State University Los AngelesLos AngelesCaliforniaUSA
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10
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Evolutionary Divergence and Radula Diversification in Two Ecomorphs from an Adaptive Radiation of Freshwater Snails. Genes (Basel) 2022; 13:genes13061029. [PMID: 35741791 PMCID: PMC9222583 DOI: 10.3390/genes13061029] [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: 05/14/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
(1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (3) Results: We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin’s finches. (4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.
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11
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Velotta JP, McCormick SD, Whitehead A, Durso CS, Schultz ET. Repeated Genetic Targets of Natural Selection Underlying Adaptation of Fishes to Changing Salinity. Integr Comp Biol 2022; 62:357-375. [PMID: 35661215 DOI: 10.1093/icb/icac072] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/16/2022] [Accepted: 05/05/2022] [Indexed: 11/12/2022] Open
Abstract
Ecological transitions across salinity boundaries have led to some of the most important diversification events in the animal kingdom, especially among fishes. Adaptations accompanying such transitions include changes in morphology, diet, whole-organism performance, and osmoregulatory function, which may be particularly prominent since divergent salinity regimes make opposing demands on systems that maintain ion and water balance. Research in the last decade has focused on the genetic targets underlying such adaptations, most notably by comparing populations of species that are distributed across salinity boundaries. Here, we synthesize research on the targets of natural selection using whole-genome approaches, with a particular emphasis on the osmoregulatory system. Given the complex, integrated and polygenic nature of this system, we expected that signatures of natural selection would span numerous genes across functional levels of osmoregulation, especially salinity sensing, hormonal control, and cellular ion exchange mechanisms. We find support for this prediction: genes coding for V-type, Ca2+, and Na+/K+-ATPases, which are key cellular ion exchange enzymes, are especially common targets of selection in species from six orders of fishes. This indicates that while polygenic selection contributes to adaptation across salinity boundaries, changes in ATPase enzymes may be of particular importance in supporting such transitions.
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Affiliation(s)
- Jonathan P Velotta
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
| | - Stephen D McCormick
- USGS, Eastern Ecological Science Center, Conte Anadromous Fish Research Center, Turners Falls, MA 01376, USA.,Department of Biology, University of Massachusetts, Amherst, MA, 01003USA
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California, Davis, Davis, CA 95616, USA
| | - Catherine S Durso
- Department of Computer Science, University of Denver, Denver, CO 80210, USA
| | - Eric T Schultz
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
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12
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Brookes B, Jeon H, Derry AM, Post JR, Rogers SM, Humphries S, Fraser DJ. Neutral and adaptive drivers of genomic change in introduced brook trout ( Salvelinus fontinalis) populations revealed by pooled sequencing. Ecol Evol 2022; 12:e8584. [PMID: 35154655 PMCID: PMC8820109 DOI: 10.1002/ece3.8584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/07/2022] [Indexed: 12/22/2022] Open
Abstract
Understanding the drivers of successful species invasions is important for conserving native biodiversity and for mitigating the economic impacts of introduced species. However, whole-genome resolution investigations of the underlying contributions of neutral and adaptive genetic variation in successful introductions are rare. Increased propagule pressure should result in greater neutral genetic variation, while environmental differences should elicit selective pressures on introduced populations, leading to adaptive differentiation. We investigated neutral and adaptive variation among nine introduced brook trout (Salvelinus fontinalis) populations using whole-genome pooled sequencing. The populations inhabit isolated alpine lakes in western Canada and descend from a common source, with an average of ~19 (range of 7-41) generations since introduction. We found some evidence of bottlenecks without recovery, no strong evidence of purifying selection, and little support that varying propagule pressure or differences in local environments shaped observed neutral genetic variation differences. Putative adaptive loci analysis revealed nonconvergent patterns of adaptive differentiation among lakes with minimal putatively adaptive loci (0.001%-0.15%) that did not correspond with tested environmental variables. Our results suggest that (i) introduction success is not always strongly influenced by genetic load; (ii) observed differentiation among introduced populations can be idiosyncratic, population-specific, or stochastic; and (iii) conservatively, in some introduced species, colonization barriers may be overcome by support through one aspect of propagule pressure or benign environmental conditions.
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Affiliation(s)
- Brent Brookes
- Department of BiologyConcordia UniversityMontréalQCCanada
| | - Hyung‐Bae Jeon
- Department of BiologyConcordia UniversityMontréalQCCanada
| | - Alison M. Derry
- Département des sciences biologiquesUniversité du Québec à MontréalMontréalQCCanada
| | - John R. Post
- Department of BiologyUniversity of CalgaryCalgaryABCanada
| | - Sean M. Rogers
- Department of BiologyUniversity of CalgaryCalgaryABCanada
| | - Shelley Humphries
- Parks CanadaNatural Resource Management BranchRadium Hot SpringsBCCanada
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13
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Koot E, Arnst E, Taane M, Goldsmith K, Thrimawithana A, Reihana K, González-Martínez SC, Goldsmith V, Houliston G, Chagné D. Genome-wide patterns of genetic diversity, population structure and demographic history in mānuka (Leptospermum scoparium) growing on indigenous Māori land. HORTICULTURE RESEARCH 2022; 9:uhab012. [PMID: 35039864 PMCID: PMC8771449 DOI: 10.1093/hr/uhab012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/09/2021] [Accepted: 09/02/2021] [Indexed: 06/14/2023]
Abstract
Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9-12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.
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Affiliation(s)
- Emily Koot
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
| | - Elise Arnst
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | - Melissa Taane
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
| | | | | | - Kiri Reihana
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | | | | | - Gary Houliston
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
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14
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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.
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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
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15
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Mauro AA, Torres-Dowdall J, Marshall CA, Ghalambor CK. A genetically based ecological trade-off contributes to setting a geographic range limit. Ecol Lett 2021; 24:2739-2749. [PMID: 34636129 DOI: 10.1111/ele.13900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/07/2021] [Accepted: 09/14/2021] [Indexed: 12/19/2022]
Abstract
Understanding the ecological factors that shape geographic range limits and the evolutionary constraints that prevent populations from adaptively evolving beyond these limits is an unresolved question. Here, we investigated why the euryhaline fish, Poecila reticulata, is confined to freshwater within its native range, despite being tolerant of brackish water. We hypothesised that competitive interactions with a close relative, Poecilia picta, in brackish water prevents P. reticulata from colonising brackish water. Using a combination of field transplant, common garden breeding, and laboratory behaviour experiments, we find support for this hypothesis, as P. reticulata are behaviourally subordinate and have lower survival in brackish water with P. picta. We also found a negative genetic correlation between P. reticulata growth in brackish water versus freshwater in the presence of P. picta, suggesting a genetically based trade-off between salinity tolerance and competitive ability could constrain adaptive evolution at the range limit.
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Affiliation(s)
- Alexander A Mauro
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Craig A Marshall
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Cameron K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA.,Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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16
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Mugula BB, Kiboi SK, Kanya JI, Egeru A, Okullo P, Curto M, Meimberg H. Knowledge Gaps in Taxonomy, Ecology, Population Distribution Drivers and Genetic Diversity of African Sandalwood ( Osyris lanceolata Hochst. & Steud.): A Scoping Review for Conservation. PLANTS 2021; 10:plants10091780. [PMID: 34579313 PMCID: PMC8465005 DOI: 10.3390/plants10091780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 11/26/2022]
Abstract
The increasing demand for ornamental, cosmetic and pharmaceutical products is driving exploitation of plant species globally. Sub-Saharan Africa harbours unique and valuable plant resources and is now a target of plant resource depletion. African Sandalwood (Osyris lanceolata), a multi-purpose and drought-tolerant species, has seen increased exploitation for the last thirty years and is now declared endangered. Initiatives to conserve O. lanceolata are not yet successful in Africa due to poor understanding of the species. This review surveys relevant research on the ecology, taxonomy, population dynamics, genetic diversity and ethnobotany of O. lanceolata, and highlights gaps in the literature for further research. A scoping review of grey literature, scholarly papers and reports was applied with pre-determined criteria to screen relevant information. Review findings indicate O. lanceolata is a globally distributed species with no identified center of origin. In Africa, it ranges from Algeria to Ethiopia and south to South Africa; in Europe it occurs in the Iberian Peninsula and Balearic Islands; in Asia from India to China, and also on Socotra. The species has a confusing taxonomy, with unresolved issues in nomenclature, country range distribution, extensive synonymisation and variation in growth form (shrub or tree). The species population is reported to be declining in Africa, but information on population dynamics across its entire range of distribution is anecdotal. Additionally, ecological factors influencing spatial distribution and survival of the species remain unknown. A variety of uses are reported for O. lanceolata globally, including: cultural; medicinal and food; dye; perfumery; timber; ethnoveterinary and phytoremediation. Key research areas and implications for conservation of O. lanceolata in Sub-Saharan Africa are proposed.
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Affiliation(s)
- Ben Belden Mugula
- School of Biological Sciences, College of Biological and Physical Sciences, University of Nairobi, Nairobi P.O. Box 30197-00100, Kenya; (S.K.K.); (J.I.K.)
- Department of Life and Physical Sciences, School of Natural Sciences, Bugema University, Kampala P.O. Box 6529, Uganda
- Correspondence:
| | - Samuel Kuria Kiboi
- School of Biological Sciences, College of Biological and Physical Sciences, University of Nairobi, Nairobi P.O. Box 30197-00100, Kenya; (S.K.K.); (J.I.K.)
| | - James Ireri Kanya
- School of Biological Sciences, College of Biological and Physical Sciences, University of Nairobi, Nairobi P.O. Box 30197-00100, Kenya; (S.K.K.); (J.I.K.)
| | - Anthony Egeru
- College of Environmental and Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Paul Okullo
- National Agricultural Research Organization (NARO), Entebbe P.O. Box 295, Uganda;
| | - Manuel Curto
- Department of Integrative Biology and Biodiversity Research, Institute of Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, Gregor Mendel-Straße 33, A-1180 Vienna, Austria; (M.C.); (H.M.)
- MARE-Marine and Environmental Sciences Centre, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal
| | - Harald Meimberg
- Department of Integrative Biology and Biodiversity Research, Institute of Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, Gregor Mendel-Straße 33, A-1180 Vienna, Austria; (M.C.); (H.M.)
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17
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Garcia-Elfring A, Paccard A, Thurman TJ, Wasserman BA, Palkovacs EP, Hendry AP, Barrett RDH. Using seasonal genomic changes to understand historical adaptation to new environments: Parallel selection on stickleback in highly-variable estuaries. Mol Ecol 2021; 30:2054-2064. [PMID: 33713378 DOI: 10.1111/mec.15879] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/21/2022]
Abstract
Parallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing to track seasonal allele frequency changes in six of these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.
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Affiliation(s)
- Alan Garcia-Elfring
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
| | - Antoine Paccard
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada.,McGill University Genome Center, McGill University, Montreal, QC, Canada
| | - Timothy J Thurman
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
| | - Ben A Wasserman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Eric P Palkovacs
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Andrew P Hendry
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
| | - Rowan D H Barrett
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
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18
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Bal TMP, Llanos-Garrido A, Chaturvedi A, Verdonck I, Hellemans B, Raeymaekers JAM. Adaptive Divergence under Gene Flow along an Environmental Gradient in Two Coexisting Stickleback Species. Genes (Basel) 2021; 12:435. [PMID: 33803820 PMCID: PMC8003309 DOI: 10.3390/genes12030435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address this, we studied the population genetic structure and morphological differentiation of sympatric three-spined and nine-spined stickleback. We conducted genotyping-by-sequencing and morphological trait characterisation using 24 individuals of each species from four lowland brackish water (LBW), four lowland freshwater (LFW) and three upland freshwater (UFW) sites in Belgium and the Netherlands. This combination of sites allowed us to contrast populations from isolated but environmentally similar locations (LFW vs. UFW), isolated but environmentally heterogeneous locations (LBW vs. UFW), and well-connected but environmentally heterogenous locations (LBW vs. LFW). Overall, both species showed comparable levels of genetic diversity and neutral genetic differentiation. However, for all three spatial scales, signatures of morphological and genomic adaptive divergence were substantially stronger among populations of the three-spined stickleback than among populations of the nine-spined stickleback. Furthermore, most outlier SNPs in the two species were associated with local freshwater sites. The few outlier SNPs that were associated with the split between brackish water and freshwater populations were located on one linkage group in three-spined stickleback and two linkage groups in nine-spined stickleback. We conclude that while both species show congruent evolutionary and genomic patterns of divergent selection, both species differ in the magnitude of their response to selection regardless of the geographical and environmental context.
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Affiliation(s)
- Thijs M. P. Bal
- Faculty of Biosciences and Aquaculture, Nord University, N-8049 Bodø, Norway;
| | | | - Anurag Chaturvedi
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland;
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
| | - Io Verdonck
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
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19
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Thia JA, McGuigan K, Liggins L, Figueira WF, Bird CE, Mather A, Evans JL, Riginos C. Genetic and phenotypic variation exhibit both predictable and stochastic patterns across an intertidal fish metapopulation. Mol Ecol 2021; 30:4392-4414. [PMID: 33544414 DOI: 10.1111/mec.15829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/12/2021] [Accepted: 01/28/2021] [Indexed: 11/28/2022]
Abstract
Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We sampled juvenile and adult life stages, at three sites, over three years. Genome-wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak-but-significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially divergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments.
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Affiliation(s)
- Joshua A Thia
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia.,School of BioSciences, The University of Melbourne, Melbourne, VIC., Australia
| | - Katrina McGuigan
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
| | - Libby Liggins
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Will F Figueira
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Christopher E Bird
- Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, TX, USA
| | - Andrew Mather
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
| | - Jennifer L Evans
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
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20
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Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
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Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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21
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Delgado ML, Manosalva A, Urbina MA, Habit E, Link O, Ruzzante DE. Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments. Mol Ecol 2020; 29:4857-4870. [PMID: 33048403 DOI: 10.1111/mec.15686] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022]
Abstract
Diadromy is known for having major effects on the distribution and richness of aquatic species, and so does its loss. The loss of diadromy has led to the diversification of many species, yet research focusing on understanding its molecular basis and consequences are limited. This is particularly true for amphidromous species despite being the most abundant group of diadromous species. Galaxias maculatus, an amphidromous species and one of the most widely distributed fishes in the Southern Hemisphere, exhibits many instances of nonmigratory or resident populations. The existence of naturally replicated resident populations in Patagonia can serve as an ideal system for the study of the mechanisms that lead to the loss of the diadromy and its ecological and evolutionary consequences. Here, we studied two adjacent river systems in which resident populations are genetically differentiated yet derived from the same diadromous population. By combining a reciprocal transplant experiment with genomic data, we showed that the two resident populations followed different evolutionary pathways by exhibiting a differential response in their capacity to survive in salt water. While one resident population was able to survive salt water, the other was not. Genomic analyses provided insights into the genes that distinguished (a) migratory from nonmigratory populations; (b) populations that can vs those that cannot survive a saltwater environment; and (c) between these resident populations. This study demonstrates that the loss of diadromy can be achieved by different pathways and that environmental (selection) and random (genetic drift) forces shape this dynamic evolutionary process.
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Affiliation(s)
| | - Aliro Manosalva
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Mauricio A Urbina
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Oscar Link
- Departamento de Ingeniería Civil, Facultad de Ingeniería, Universidad de Concepción, Concepción, Chile
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22
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Jansson E, Besnier F, Malde K, André C, Dahle G, Glover KA. Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations. BMC Genet 2020; 21:118. [PMID: 33036553 PMCID: PMC7547435 DOI: 10.1186/s12863-020-00921-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
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Affiliation(s)
- Eeva Jansson
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Francois Besnier
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Ketil Malde
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Geir Dahle
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.,Institute of Biology, University of Bergen, P. O. Box 7803, 5020, Bergen, Norway
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23
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Stanford BC, Clake DJ, Morris MR, Rogers SM. The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors. Evol Appl 2020; 13:1166-1182. [PMID: 32684953 PMCID: PMC7359838 DOI: 10.1111/eva.12935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
Rapid environmental changes impact the global distribution and abundance of species, highlighting the urgency to understand and predict how populations will respond. The analysis of differentially expressed genes has elucidated areas of the genome involved in adaptive divergence to past and present environmental change. Such studies however have been hampered by large numbers of differentially expressed genes and limited knowledge of how these genes work in conjunction with each other. Recent methods (broadly termed "pathway analyses") have emerged that aim to group genes that behave in a coordinated fashion to a factor of interest. These methods aid in functional annotation and uncovering biological pathways, thereby collapsing complex datasets into more manageable units, providing more nuanced understandings of both the organism-level effects of modified gene expression, and the targets of adaptive divergence. Here, we reanalyze a dataset that investigated temperature-induced changes in gene expression in marine-adapted and freshwater-adapted threespine stickleback (Gasterosteus aculeatus), using Weighted Gene Co-expression Network Analysis (WGCNA) with PANTHER Gene Ontology (GO)-Slim overrepresentation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Six modules exhibited a conserved response and six a divergent response between marine and freshwater stickleback when acclimated to 7°C or 22°C. One divergent module showed freshwater-specific response to temperature, and the remaining divergent modules showed differences in height of reaction norms. PPARAa, a transcription factor that regulates fatty acid metabolism and has been implicated in adaptive divergence, was located in a module that had higher expression at 7°C and in freshwater stickleback. This updated methodology revealed patterns that were not found in the original publication. Although such methods hold promise toward predicting population response to environmental stressors, many limitations remain, particularly with regard to module expression representation, database resources, and cross-database integration.
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Affiliation(s)
| | - Danielle J. Clake
- Department of Biological SciencesUniversity of CalgaryCalgaryABCanada
| | | | - Sean M. Rogers
- Department of Biological SciencesUniversity of CalgaryCalgaryABCanada
- Bamfield Marine Sciences CentreBamfieldBCCanada
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24
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Transcriptomic Analysis of Gill and Kidney from Asian Seabass ( Lates calcarifer) Acclimated to Different Salinities Reveals Pathways Involved with Euryhalinity. Genes (Basel) 2020; 11:genes11070733. [PMID: 32630108 PMCID: PMC7397140 DOI: 10.3390/genes11070733] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 12/13/2022] Open
Abstract
Asian seabass (or commonly known as barramundi), Lates calcarifer, is a bony euryhaline teleost from the Family Latidae, inhabiting nearshore, estuarine, and marine connected freshwaters throughout the tropical Indo-West Pacific region. The species is catadromous, whereby adults spawn in salinities between 28 and 34 ppt at the mouth of estuaries, with resultant juveniles usually moving into brackish and freshwater systems to mature, before returning to the sea to spawn again as adults. The species lives in both marine and freshwater habitats and can move quickly between the two; thus, the species' ability to tolerate changes in salinity makes it a good candidate for studying the salinity acclimation response in teleosts. In this study, the transcriptome of two major osmoregulatory organs (gills and kidneys) of young juvenile Asian seabass reared in freshwater and seawater were compared. The euryhaline nature of Asian seabass was found to be highly pliable and the moldability of the trait was further confirmed by histological analyses of gills and kidneys. Differences in major expression pathways were observed, with differentially expressed genes including those related to osmoregulation, tissue/organ morphogenesis, and cell volume regulation as central to the osmo-adaptive response. Additionally, genes coding for mucins were upregulated specifically under saline conditions, whereas several genes important for growth and development, as well as circadian entrainment were specifically enriched in fish reared in freshwater. Routing of the circadian rhythm mediated by salinity changes could be the initial step in salinity acclimation and possibly migration in euryhaline fish species such as the Asian seabass.
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25
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Schneider K, Adams CE, Elmer KR. Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids. BMC Genomics 2019; 20:1010. [PMID: 31870285 PMCID: PMC6929470 DOI: 10.1186/s12864-019-6361-2] [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: 06/18/2019] [Accepted: 12/01/2019] [Indexed: 12/11/2022] Open
Abstract
Background Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup. Results All selection analyses are based on Coregonus and Salvelinus compared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such as ap1m2, involved in immunity and development, and slc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genes syn3, with a role in neural processes, and ctsk, involved in bone remodelling. Conclusions Our approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.
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Affiliation(s)
- Kevin Schneider
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, G63 0AW, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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26
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Delgado ML, Górski K, Habit E, Ruzzante DE. The effects of diadromy and its loss on genomic divergence: The case of amphidromous
Galaxias maculatus
populations. Mol Ecol 2019; 28:5217-5231. [DOI: 10.1111/mec.15290] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/16/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Konrad Górski
- Departamento de Ecología Facultad de Ciencias y Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS) Universidad Católica de la Santísima Concepción Concepción Chile
| | - Evelyn Habit
- Centro de Ciencias Ambientales EULA Universidad de Concepción Concepción Chile
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27
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Titus BM, Blischak PD, Daly M. Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria). Mol Ecol 2019; 28:3572-3586. [PMID: 31233641 DOI: 10.1111/mec.15157] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 05/21/2019] [Accepted: 06/04/2019] [Indexed: 12/23/2022]
Abstract
Sympatric diversification is recognized to have played an important role in the evolution of biodiversity. However, an in situ sympatric origin for codistributed taxa is difficult to demonstrate because different evolutionary processes can lead to similar biogeographic outcomes, especially in ecosystems that can readily facilitate secondary contact due to a lack of hard barriers to dispersal. Here we use a genomic (ddRADseq), model-based approach to delimit a species complex of tropical sea anemones that are codistributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 and ordinary differential equations in Moments to test competing diversification scenarios that span the allopatric-sympatric continuum. Our results suggest that the corkscrew sea anemone Bartholomea annulata is a cryptic species complex whose members are codistributed throughout their range. Simulation and model selection analyses from both approaches suggest these lineages experienced historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model receives appreciable model support in fastsimcoal2. Leveraging the genome of the closely related Exaiptasia diaphana, we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan and the first range-wide molecular study of a tropical sea anemone, underscoring that anemone diversity is under-described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.
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Affiliation(s)
- Benjamin M Titus
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Paul D Blischak
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, USA
| | - Marymegan Daly
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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28
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Jeffries KM, Connon RE, Verhille CE, Dabruzzi TF, Britton MT, Durbin‐Johnson BP, Fangue NA. Divergent transcriptomic signatures in response to salinity exposure in two populations of an estuarine fish. Evol Appl 2019; 12:1212-1226. [PMID: 31293632 PMCID: PMC6597873 DOI: 10.1111/eva.12799] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In estuary and coastal systems, human demand for freshwater, climate change-driven precipitation variability, and extreme weather impact salinity levels, reducing connectivity between mesohaline coastal fish populations and potentially contributing to genomic divergence. We examined gill transcriptome responses to salinity in wild-caught juveniles from two populations of Sacramento splittail (Pogonichthys macrolepidotus), a species of conservation concern that is endemic to the San Francisco Estuary, USA, and the lower reaches of its tributaries. Recent extreme droughts have led to salinities above the tolerance limits for this species, creating a migration barrier between these populations, which potentially contributed to population divergence. We identified transcripts involved in a conserved response to salinity; however, the more salinity-tolerant San Pablo population had greater transcriptome plasticity (3.6-fold more transcripts responded than the Central Valley population) and a response consistent with gill remodeling after 168 hr of exposure to elevated salinity. The reorganization of the gill in response to changing osmotic gradients is a process critical for acclimation and would facilitate enhanced salinity tolerance. We detected an upregulation of receptors that control the Wnt (wingless-type) cell signaling pathway that may be required for an adaptive response to increases in salinity, patterns not observed in the relatively salinity-sensitive Central Valley population. We detected 62 single nucleotide polymorphisms (SNPs) in coding regions of 26 transcripts that differed between the populations. Eight transcripts that contained SNPs were associated with immune responses, highlighting the importance of diversity in immune gene sequences as a defining characteristic of genomic divergence between these populations. Our data demonstrate that these populations have divergent transcriptomic responses to salinity, which is consistent with observed physiological differences in salinity tolerance.
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Affiliation(s)
- Ken M. Jeffries
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
- Anatomy, Physiology & Cell Biology, School of Veterinary MedicineUniversity of CaliforniaDavisCalifornia
- Wildlife, Fish & Conservation BiologyUniversity of CaliforniaDavisCalifornia
| | - Richard E. Connon
- Anatomy, Physiology & Cell Biology, School of Veterinary MedicineUniversity of CaliforniaDavisCalifornia
| | - Christine E. Verhille
- Wildlife, Fish & Conservation BiologyUniversity of CaliforniaDavisCalifornia
- Present address:
Department of EcologyMontana State UniversityBozemanMontana
| | - Theresa F. Dabruzzi
- Wildlife, Fish & Conservation BiologyUniversity of CaliforniaDavisCalifornia
- Present address:
Biology DepartmentSaint Anselm CollegeManchesterNew Hampshire
| | - Monica T. Britton
- Bioinformatics Core Facility, Genome CenterUniversity of CaliforniaDavisCalifornia
| | | | - Nann A. Fangue
- Wildlife, Fish & Conservation BiologyUniversity of CaliforniaDavisCalifornia
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29
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Phair NL, Toonen RJ, Knapp I, von der Heyden S. Shared genomic outliers across two divergent population clusters of a highly threatened seagrass. PeerJ 2019; 7:e6806. [PMID: 31106053 PMCID: PMC6497040 DOI: 10.7717/peerj.6806] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/18/2019] [Indexed: 12/15/2022] Open
Abstract
The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.
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Affiliation(s)
- Nikki Leanne Phair
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Robert John Toonen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, Hawai’i, United States of America
| | - Ingrid Knapp
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, Hawai’i, United States of America
| | - Sophie von der Heyden
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
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30
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Yang M, Xu C, Duchesne P, Ma Q, Yin G, Fang Y, Lu F, Zhang W. Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries. Ecol Evol 2019; 9:3059-3074. [PMID: 30962881 PMCID: PMC6434575 DOI: 10.1002/ece3.4793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/31/2018] [Accepted: 11/12/2018] [Indexed: 12/22/2022] Open
Abstract
Estuarine organisms grow in highly heterogeneous habitats, and their genetic differentiation is driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and its adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate-high level of genetic differentiation among populations (range F ST: 0.0310-0.3325) was showed despite large ongoing dispersal. FLOCK assigned all individuals to 13 clusters and revealed a complex genetic structure. Some genetic clusters were limited in peripheries compared with very mixing constitution in center populations, suggesting local adaptation was more likely to occur in peripheral populations. 21 candidate outliers under positive selection were detected, and further, the differentiation patterns correlated with geographic distance, salinity difference, and colonization history were analyzed with or without the outliers. Combined results of AMOVA and IBD based on different dataset, it was found that the effects of geographic distance and population colonization history on isolation seemed to be promoted by divergent selection. However, none-liner IBE pattern indicates the effects of salinity were overwhelmed by spatial distance or other ecological processes in certain areas and also suggests that salinity was not the only selective factor driving population differentiation. These results together indicate that geographic distance, salinity difference, and colonization history co-contributed in shaping the genetic structure of S. mariqueter and that their relative importance was correlated with spatial scale and environment gradient.
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Affiliation(s)
- Mei Yang
- College of AgricultureYangtze UniversityJingzhouChina
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Chengyuan Xu
- School of Health, Medical and Applied SciencesCentral Queensland UniversityBundabergQueenslandAustralia
| | | | - Qiang Ma
- Shanghai Chongming Dongtan National Nature ReserveShanghaiChina
| | - Ganqiang Yin
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Yang Fang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Fan Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
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31
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Prates I, Penna A, Rodrigues MT, Carnaval AC. Local adaptation in mainland anole lizards: Integrating population history and genome-environment associations. Ecol Evol 2018; 8:11932-11944. [PMID: 30598788 PMCID: PMC6303772 DOI: 10.1002/ece3.4650] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 09/22/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
Environmental gradients constrain physiological performance and thus species' ranges, suggesting that species occurrence in diverse environments may be associated with local adaptation. Genome-environment association analyses (GEAA) have become central for studies of local adaptation, yet they are sensitive to the spatial orientation of historical range expansions relative to landscape gradients. To test whether potentially adaptive genotypes occur in varied climates in wide-ranged species, we implemented GEAA on the basis of genomewide data from the anole lizards Anolis ortonii and Anolis punctatus, which expanded from Amazonia, presently dominated by warm and wet settings, into the cooler and less rainy Atlantic Forest. To examine whether local adaptation has been constrained by population structure and history, we estimated effective population sizes, divergence times, and gene flow under a coalescent framework. In both species, divergence between Amazonian and Atlantic Forest populations dates back to the mid-Pleistocene, with subsequent gene flow. We recovered eleven candidate genes involved with metabolism, immunity, development, and cell signaling in A. punctatus and found no loci whose frequency is associated with environmental gradients in A. ortonii. Distinct signatures of adaptation between these species are not associated with historical constraints or distinct climatic space occupancies. Similar patterns of spatial structure between selected and neutral SNPs along the climatic gradient, as supported by patterns of genetic clustering in A. punctatus, may have led to conservative GEAA performance. This study illustrates how tests of local adaptation can benefit from knowledge about species histories to support hypothesis formulation, sampling design, and landscape gradient characterization.
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Affiliation(s)
- Ivan Prates
- Department of Vertebrate ZoologyNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Department of Biology, City College of New York and Graduate CenterCity University of New YorkNew YorkNew York
| | - Anna Penna
- Department of AnthropologyUniversity of Texas at San AntonioSan AntonioTexas
| | | | - Ana Carolina Carnaval
- Department of Biology, City College of New York and Graduate CenterCity University of New YorkNew YorkNew York
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32
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Walsh J, Kovach AI, Olsen BJ, Shriver WG, Lovette IJ. Bidirectional adaptive introgression between two ecologically divergent sparrow species. Evolution 2018; 72:2076-2089. [PMID: 30101975 DOI: 10.1111/evo.13581] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 07/10/2018] [Accepted: 07/31/2018] [Indexed: 12/24/2022]
Abstract
Natural hybrid zones can be used to dissect the mechanisms driving key evolutionary processes by allowing us to identify genomic regions important for establishing reproductive isolation and that allow for transfer of adaptive variation. We leverage whole-genome data in a system where two bird species, the saltmarsh (Ammospiza caudacuta) and Nelson's (A. nelsoni) sparrow, hybridize despite their relatively high background genetic differentiation and past ecological divergence. Adaptive introgression is plausible in this system because Nelson's sparrows are recent colonists of saltwater marshes, compared to the specialized saltmarsh sparrow that has a longer history of saltmarsh adaptation. Comparisons among whole-genome sequences of 34 individuals from allopatric and sympatric populations show that ongoing gene flow is shaping the genomic landscape, with allopatric populations exhibiting genome-wide FST estimates close to double of that observed in sympatry. We characterized patterns of introgression across the genome and identify regions that exhibit biased introgression into hybrids from one parental species. These regions offer compelling candidates for genes related to tidal marsh adaptations suggesting that adaptive introgression may be an important consequence of hybridization. These findings highlight the value of considering the landscapes of both genome-wide introgression and divergence when characterizing the evolutionary forces that drive speciation.
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Affiliation(s)
- Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, New York 14850.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire 03824
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - W Gregory Shriver
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware 19716
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, New York 14850.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853
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33
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Measuring Genetic Differentiation from Pool-seq Data. Genetics 2018; 210:315-330. [PMID: 30061425 DOI: 10.1534/genetics.118.300900] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/21/2018] [Indexed: 12/26/2022] Open
Abstract
The advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many nonmodel species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator of [Formula: see text] for Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Finally, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpin Cottus asper, we show how the use of an unbiased [Formula: see text] estimator may question the interpretation of population structure inferred from previous analyses.
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34
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Morris MRJ, Bowles E, Allen BE, Jamniczky HA, Rogers SM. Contemporary ancestor? Adaptive divergence from standing genetic variation in Pacific marine threespine stickleback. BMC Evol Biol 2018; 18:113. [PMID: 30021523 PMCID: PMC6052716 DOI: 10.1186/s12862-018-1228-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 07/03/2018] [Indexed: 11/25/2022] Open
Abstract
Background Populations that have repeatedly colonized novel environments are useful for studying the role of ecology in adaptive divergence – particularly if some individuals persist in the ancestral habitat. Such “contemporary ancestors” can be used to demonstrate the effects of selection by comparing phenotypic and genetic divergence between the derived population and their extant ancestors. However, evolution and demography in these “contemporary ancestors” can complicate inferences about the source (standing genetic variation, de novo mutation) and pace of adaptive divergence. Marine threespine stickleback (Gasterosteus aculeatus) have colonized freshwater environments along the Pacific coast of North America, but have also persisted in the marine environment. To what extent are marine stickleback good proxies of the ancestral condition? Results We sequenced > 5800 variant loci in over 250 marine stickleback from eight locations extending from Alaska to California, and phenotyped them for platedness and body shape. Pairwise FST varied from 0.02 to 0.18. Stickleback were divided into five genetic clusters, with a single cluster comprising stickleback from Washington to Alaska. Plate number, Eda, body shape, and candidate loci showed evidence of being under selection in the marine environment. Comparisons to a freshwater population demonstrated that candidate loci for freshwater adaptation varied depending on the choice of marine populations. Conclusions Marine stickleback are structured into phenotypically and genetically distinct populations that have been evolving as freshwater stickleback evolved. This variation complicates their usefulness as proxies of the ancestors of freshwater populations. Lessons from stickleback may be applied to other “contemporary ancestor”-derived population studies. Electronic supplementary material The online version of this article (10.1186/s12862-018-1228-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew R J Morris
- Department of Biology, Ambrose University, 150 Ambrose Circle SW, Calgary, AB, T3H 0L5, Canada.
| | - Ella Bowles
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Brandon E Allen
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Heather A Jamniczky
- McCaig Institute for Bone and Joint Health, Department of Cell Biology & Anatomy, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N 4Z6, Canada
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
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35
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Lucek K, Keller I, Nolte AW, Seehausen O. Distinct colonization waves underlie the diversification of the freshwater sculpin (Cottus gobio
) in the Central European Alpine region. J Evol Biol 2018; 31:1254-1267. [DOI: 10.1111/jeb.13339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/07/2018] [Accepted: 06/19/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Kay Lucek
- Department of Environmental Sciences; University of Basel; Basel Switzerland
- Department of Aquatic Ecology and Macroevolution; Institute of Ecology and Evolution; University of Bern; Bern Switzerland
- Department of Fish Ecology and Evolution; EAWAG Swiss Federal Institute of Aquatic Science and Technology; Center of Ecology, Evolution and Biochemistry; Kastanienbaum Switzerland
| | - Irene Keller
- Department of BioMedical Research and Swiss Institute of Bioinformatics; University of Bern; Bern Switzerland
| | - Arne W. Nolte
- Institute for Biology; Carl von Ossietzky University Oldenburg; Oldenburg Germany
- Department for Evolutionary Genetics; Max-Planck Institute for Evolutionary Biology; Plön Germany
| | - Ole Seehausen
- Department of Aquatic Ecology and Macroevolution; Institute of Ecology and Evolution; University of Bern; Bern Switzerland
- Department of Fish Ecology and Evolution; EAWAG Swiss Federal Institute of Aquatic Science and Technology; Center of Ecology, Evolution and Biochemistry; Kastanienbaum Switzerland
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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Dalongeville A, Benestan L, Mouillot D, Lobreaux S, Manel S. Combining six genome scan methods to detect candidate genes to salinity in the Mediterranean striped red mullet (Mullus surmuletus). BMC Genomics 2018; 19:217. [PMID: 29580201 PMCID: PMC5870821 DOI: 10.1186/s12864-018-4579-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/02/2018] [Indexed: 12/24/2022] Open
Abstract
Background Adaptive genomics may help predicting how a species will respond to future environmental changes. Genomic signatures of local adaptation in marine organisms are often driven by environmental selective agents impacting the physiology of organisms. With one of the highest salinity level, the Mediterranean Sea provides an excellent model to investigate adaptive genomic divergence underlying salinity adaptation. In the present study, we combined six genome scan methods to detect potential genomic signal of selection in the striped red mullet (Mullus surmuletus) populations distributed across a wide salinity gradient. We then blasted these outlier sequences on published fish genomic resources in order to identify relevant potential candidate genes for salinity adaptation in this species. Results Altogether, the six genome scan methods found 173 outliers out of 1153 SNPs. Using a blast approach, we discovered four candidate SNPs belonging to three genes potentially implicated in adaptation of M. surmuletus to salinity. The allele frequency at one of these SNPs significantly increases with salinity independently from the effect of longitude. The gene associated to this SNP, SOCS2, encodes for an inhibitor of cytokine and has previously been shown to be expressed under osmotic pressure in other marine organisms. Additionally, our results showed that genome scan methods not correcting for spatial structure can still be an efficient strategy to detect potential footprints of selection, when the spatial and environmental variation are confounded, and then, correcting for spatial structure in a second step represents a conservative method. Conclusion The present outcomes bring evidences of potential genomic footprint of selection, which suggest an adaptive response of M. surmuletus to salinity conditions in the Mediterranean Sea. Additional genomic data such as sequencing of a full-genome and transcriptome analyses of gene expression would provide new insights regarding the possibility that some striped red mullet populations are locally adapted to their saline environment. Electronic supplementary material The online version of this article (10.1186/s12864-018-4579-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alicia Dalongeville
- CEFE UMR 5175, EPHE, PSL Research University, CNRS, UM, SupAgro, IRD, INRA, 34293, Montpellier, France. .,MARBEC UMR 9190, CNRS - IRD - Université Montpellier - Ifremer, 34095, Montpellier, France.
| | - Laura Benestan
- Departement de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - David Mouillot
- MARBEC UMR 9190, CNRS - IRD - Université Montpellier - Ifremer, 34095, Montpellier, France
| | - Stephane Lobreaux
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, BP53 38041, Grenoble, France
| | - Stéphanie Manel
- CEFE UMR 5175, EPHE, PSL Research University, CNRS, UM, SupAgro, IRD, INRA, 34293, Montpellier, France
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Zhao Y, Peng W, Guo H, Chen B, Zhou Z, Xu J, Zhang D, Xu P. Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:45-59. [PMID: 29256104 DOI: 10.1007/s10126-017-9786-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/21/2017] [Indexed: 06/07/2023]
Abstract
The marine species usually show high dispersal capabilities accompanied by high levels of gene flow. On the other hand, many physical barriers distribute along the continental marginal seas and may prevent dispersals and increase population divergence. These complexities along the continental margin generate serious challenges to population genetic studies of marine species. Chinese sea bass Lateolabrax maculatus distributes broad latitudinal gradient spanning from the tropical to the mid-temperate zones in the continental margin seas of the Northwest Pacific Ocean. Using the double digest restriction-site-associated DNA tag sequencing (ddRAD) approach, we genotyped 10,297 SNPs for 219 Chinese seabass individuals of 12 populations along the Chinese coast in the Northwest Pacific region. Genetic divergence among these populations was evaluated, and population structure was established. The results suggested that geographically distant populations in the Bohai Gulf and the Beibu Gulf retain significant genetic divergence, which are connected by a series of intermediate populations in between. The results also suggested that Leizhou Peninsula, Hainan Island, and Shandong Peninsula are major physical barriers and substantially block gene flow and genetic admixture of L. maculatus. We also investigated the potential genetic basis of local adaptation correlating with population differentiation of L. maculatus. The sea surface temperature is a significantly differentiated environmental factor for the distribution of L. maculatus. The correlation of water temperature and genetic variations in extensively distributed populations was investigated with Bayesian-based approaches. The candidate genes underlying the local selection in geographically divergent populations were identified and annotated, providing clues to understand the potential mechanisms of adaptive evolution. Overall, our genome scale population genetic analysis provided insight into population divergence and local adaptation of Chinese sea bass in the continental marginal seas along Chinese coast.
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Affiliation(s)
- Yunfeng Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing, Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
| | - Wenzhu Peng
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Huayang Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Baohua Chen
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Zhixiong Zhou
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Jian Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing, Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Dianchang Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
| | - Peng Xu
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian, 352103, China.
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Veale AJ, Russello MA. Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka). Genome Biol Evol 2017; 9:2921-2939. [PMID: 29045601 PMCID: PMC5737441 DOI: 10.1093/gbe/evx215] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 12/12/2022] Open
Abstract
Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.
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Affiliation(s)
- Andrew J. Veale
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
- Present address: Department of Environmental and Animal Sciences, Unitec, 139 Carrington Rd, Auckland, New Zealand
| | - Michael A. Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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Fuentes-Pardo AP, Ruzzante DE. Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations. Mol Ecol 2017; 26:5369-5406. [PMID: 28746784 DOI: 10.1111/mec.14264] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.
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Rogers SM, Xu S, Schlüter PM. Introduction: integrative molecular ecology is rapidly advancing the study of adaptation and speciation. Mol Ecol 2017; 26:1-6. [DOI: 10.1111/mec.13947] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 11/30/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Sean M. Rogers
- Department of Biological Sciences; University of Calgary; Calgary Alberta Canada T3L 2R9
| | - Shuqing Xu
- Max Planck Institute for Chemical Ecology; Hans-Knöll-Straße 8 D-07745 Jena Germany
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
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