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Coll-Costa C, Dahms C, Kemppainen P, Alexandre CM, Ribeiro F, Zanella D, Zanella L, Merilä J, Momigliano P. Parallel evolution despite low genetic diversity in three-spined sticklebacks. Proc Biol Sci 2024; 291:20232617. [PMID: 38593844 PMCID: PMC11003780 DOI: 10.1098/rspb.2023.2617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
When populations repeatedly adapt to similar environments they can evolve similar phenotypes based on shared genetic mechanisms (parallel evolution). The likelihood of parallel evolution is affected by demographic history, as it depends on the standing genetic variation of the source population. The three-spined stickleback (Gasterosteus aculeatus) repeatedly colonized and adapted to brackish and freshwater. Most parallel evolution studies in G. aculeatus were conducted at high latitudes, where freshwater populations maintain connectivity to the source marine populations. Here, we analysed southern and northern European marine and freshwater populations to test two hypotheses. First, that southern European freshwater populations (which currently lack connection to marine populations) lost genetic diversity due to bottlenecks and inbreeding compared to their northern counterparts. Second, that the degree of genetic parallelism is higher among northern than southern European freshwater populations, as the latter have been subjected to strong drift due to isolation. The results show that southern populations exhibit lower genetic diversity but a higher degree of genetic parallelism than northern populations. Hence, they confirm the hypothesis that southern populations have lost genetic diversity, but this loss probably happened after they had already adapted to freshwater conditions, explaining the high degree of genetic parallelism in the south.
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Affiliation(s)
- Carla Coll-Costa
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, FI-00014, Finland
| | - Carolin Dahms
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Petri Kemppainen
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Carlos M. Alexandre
- MARE—Marine and Environmental Sciences Centre, Universidade de Évora, Évora, 7004-516, Portugal
| | - Filipe Ribeiro
- MARE—Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Davor Zanella
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, 10000, Croatia
| | - Linda Zanella
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, 10000, Croatia
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, FI-00014, Finland
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Paolo Momigliano
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
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2
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Ehemann NR, Meyer A, Hulsey CD. Morphological description of spontaneous pelvic fin loss in a neotropical cichlid fish. J Morphol 2024; 285:e21663. [PMID: 38100744 DOI: 10.1002/jmor.21663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
Pelvic fins are a characteristic structure of the vertebrate Bauplan. Yet, pelvic fin loss has occurred repeatedly across a wide diversity of other lineages of tetrapods and at least 48 times in teleost fishes. This pelvic finless condition is often associated with other morphological features such as body elongation, loss of additional structures, and bilateral asymmetry. However, despite the remarkable diversity in the several thousand cichlid fish species, none of them are characterized by the complete absence of pelvic fins. Here, we examined the musculoskeletal structure and associated bilateral asymmetry in Midas cichlids (Amphilophus cf. citrinellus) that lost their pelvic fins spontaneously in the laboratory. Due to this apparent mutational loss of the pelvic girdle and fins, the external and internal anatomy are described in a series of "normal" Midas individuals and their pelvic finless sibling tankmates. First, other traits associated with teleost pelvic fin loss, the genetic basis of pelvic fin loss, and the potential for pleiotropic effects of these genes on other traits in teleosts were all reviewed. Using these traits as a guide, we investigated whether other morphological differences were associated with the pelvic girdle/fin loss. The mean values of the masses of muscle of the pectoral fin, fin ray numbers in the unpaired fins, and oral jaw tooth numbers did not differ between the two pelvic fin morphotypes. However, significant differences in meristic values of the paired traits assessed were observed for the same side of the body between morphotypes. Notably, bilateral asymmetry was found exclusively for the posterior lateral line scales. Finally, we found limited evidence of pleiotropic effects, such as lateral line scale numbers and fluctuating asymmetry between the Midas pelvic fin morphotypes. The fast and relatively isolated changes in the Midas cichlids suggest minor but interesting pleiotropic effects could accompany loss of cichlid pelvic fins.
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Affiliation(s)
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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3
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Layton-Matthews K, Vriend SJG, Grøtan V, Loonen MJJE, Sæther BE, Fuglei E, Hansen BB. Extreme events, trophic chain reactions, and shifts in phenotypic selection. Sci Rep 2023; 13:15181. [PMID: 37704641 PMCID: PMC10499831 DOI: 10.1038/s41598-023-41940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023] Open
Abstract
Demographic consequences of rapid environmental change and extreme climatic events (ECEs) can cascade across trophic levels with evolutionary implications that have rarely been explored. Here, we show how an ECE in high Arctic Svalbard triggered a trophic chain reaction, directly or indirectly affecting the demography of both overwintering and migratory vertebrates, ultimately inducing a shift in density-dependent phenotypic selection in migratory geese. A record-breaking rain-on-snow event and ice-locked pastures led to reindeer mass starvation and a population crash, followed by a period of low mortality and population recovery. This caused lagged, long-lasting reductions in reindeer carrion numbers and resultant low abundances of Arctic foxes, a scavenger on reindeer and predator of migratory birds. The associated decrease in Arctic fox predation of goose offspring allowed for a rapid increase in barnacle goose densities. As expected according to r- and K-selection theory, the goose body condition (affecting reproduction and post-fledging survival) maximising Malthusian fitness increased with this shift in population density. Thus, the winter ECE acting on reindeer and their scavenger, the Arctic fox, indirectly selected for higher body condition in migratory geese. This high Arctic study provides rare empirical evidence of links between ECEs, community dynamics and evolution, with implications for our understanding of indirect eco-evolutionary impacts of global change.
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Affiliation(s)
- Kate Layton-Matthews
- Department of Biology, Centre for Biodiversity Dynamics, NTNU, Trondheim, Norway.
- Norwegian Institute for Nature Research, NINA, Tromsø, Norway.
| | - Stefan J G Vriend
- Department of Biology, Centre for Biodiversity Dynamics, NTNU, Trondheim, Norway
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Vidar Grøtan
- Department of Biology, Centre for Biodiversity Dynamics, NTNU, Trondheim, Norway
| | | | - Bernt-Erik Sæther
- Department of Biology, Centre for Biodiversity Dynamics, NTNU, Trondheim, Norway
| | - Eva Fuglei
- Norwegian Polar Institute, Tromsø, Norway
| | - Brage Bremset Hansen
- Department of Biology, Centre for Biodiversity Dynamics, NTNU, Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research, NINA, Trondheim, Norway
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4
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Dean LL, Magalhaes IS, D’Agostino D, Hohenlohe P, MacColl ADC. On the Origins of Phenotypic Parallelism in Benthic and Limnetic Stickleback. Mol Biol Evol 2023; 40:msad191. [PMID: 37652053 PMCID: PMC10490448 DOI: 10.1093/molbev/msad191] [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: 03/02/2023] [Revised: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Rapid evolution of similar phenotypes in similar environments, giving rise to in situ parallel adaptation, is an important hallmark of ecological speciation. However, what appears to be in situ adaptation can also arise by dispersal of divergent lineages from elsewhere. We test whether two contrasting phenotypes repeatedly evolved in parallel, or have a single origin, in an archetypal example of ecological adaptive radiation: benthic-limnetic three-spined stickleback (Gasterosteus aculeatus) across species pair and solitary lakes in British Columbia. We identify two genomic clusters across freshwater populations, which differ in benthic-limnetic divergent phenotypic traits and separate benthic from limnetic individuals in species pair lakes. Phylogenetic reconstruction and niche evolution modeling both suggest a single evolutionary origin for each of these clusters. We detected strong phylogenetic signal in benthic-limnetic divergent traits, suggesting that they are ancestrally retained. Accounting for ancestral state retention, we identify local adaptation of body armor due to the presence of an intraguild predator, the sculpin (Cottus asper), and environmental effects of lake depth and pH on body size. Taken together, our results imply a predominant role for retention of ancestral characteristics in driving trait distribution, with further selection imposed on some traits by environmental factors.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Isabel Santos Magalhaes
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- Department of Life Sciences, School of Health and Life Sciences, Whitelands College, University of Roehampton, London, UK
| | - Daniele D’Agostino
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- Water Research Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Paul Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Andrew D C MacColl
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
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5
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Seebacher F, Bamford SM, Le Roy A. Sex-specific transgenerational plasticity: developmental temperatures of mothers and fathers have different effects on sons and daughters. J Exp Biol 2023; 226:jeb245798. [PMID: 37293931 DOI: 10.1242/jeb.245798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Each parent can influence offspring phenotype via provisioning of the zygote or sex-specific DNA methylation. Transgenerational plasticity may therefore depend on the environmental conditions experienced by each parent. We tested this hypothesis by conducting a fully factorial experiment across three generations of guppies (Poecilia reticulata), determining the effects of warm (28°C) and cold (21°C) thermal backgrounds of mothers and fathers on mass and length, and thermal performance (sustained and sprint swimming speeds, citrate synthase and lactate dehydrogenase activities; 18, 24, 28, 32 and 36°C test temperatures) of sons and daughters. Offspring sex was significant for all traits except for sprint speed. Warmer mothers produced sons and daughters with reduced mass and length, and warmer fathers produced shorter sons. Sustained swimming speed (Ucrit) of male offspring was greatest when both parents were raised at 28°C, and warmer fathers produced daughters with greater Ucrit. Similarly, warmer fathers produced sons and daughters with greater metabolic capacity. We show that the thermal variation experienced by parents can modify offspring phenotype, and that predicting the impacts of environmental change on populations would require knowledge of the thermal background of each mother and father, particularly where sexes are spatially segregated.
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Affiliation(s)
- Frank Seebacher
- School of Life and Environmental Sciences, Heydon-Laurence Building A08, University of Sydney, Sydney, NSW 2006, Australia
| | - Stephanie M Bamford
- School of Life and Environmental Sciences, Heydon-Laurence Building A08, University of Sydney, Sydney, NSW 2006, Australia
| | - Amelie Le Roy
- School of Life and Environmental Sciences, Heydon-Laurence Building A08, University of Sydney, Sydney, NSW 2006, Australia
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6
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Seebacher F, Narayan E, Rummer JL, Tomlinson S, Cooke SJ. How can physiology best contribute to wildlife conservation in a warming world? CONSERVATION PHYSIOLOGY 2023; 11:coad038. [PMID: 37287992 PMCID: PMC10243909 DOI: 10.1093/conphys/coad038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 05/11/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Global warming is now predicted to exceed 1.5°C by 2033 and 2°C by the end of the 21st century. This level of warming and the associated environmental variability are already increasing pressure on natural and human systems. Here we emphasize the role of physiology in the light of the latest assessment of climate warming by the Intergovernmental Panel on Climate Change. We describe how physiology can contribute to contemporary conservation programmes. We focus on thermal responses of animals, but we acknowledge that the impacts of climate change are much broader phylogenetically and environmentally. A physiological contribution would encompass environmental monitoring, coupled with measuring individual sensitivities to temperature change and upscaling these to ecosystem level. The latest version of the widely accepted Conservation Standards designed by the Conservation Measures Partnership includes several explicit climate change considerations. We argue that physiology has a unique role to play in addressing these considerations. Moreover, physiology can be incorporated by institutions and organizations that range from international bodies to national governments and to local communities, and in doing so, it brings a mechanistic approach to conservation and the management of biological resources.
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Affiliation(s)
- Frank Seebacher
- School of Life and Environmental Sciences A08, University of Sydney, NSW 2006, Australia
| | - Edward Narayan
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia QLD4072, Australia
| | - Jodie L Rummer
- College of Science and Engineering and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville QLD 4810, Australia
| | - Sean Tomlinson
- School of Biological Sciences, University of Adelaide, SA 5000, Australia
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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7
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Janzen FH, Pérez-Rodríguez R, Domínguez-Domínguez O, Hendrickson DA, Sabaj MH, Blouin-Demers G. Phylogenetic relationships of the North American catfishes (Ictaluridae, Siluriformes): Investigating the origins and parallel evolution of the troglobitic species. Mol Phylogenet Evol 2023; 182:107746. [PMID: 36849094 DOI: 10.1016/j.ympev.2023.107746] [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: 11/02/2022] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Insular habitats have played an important role in developing evolutionary theory, including natural selection and island biogeography. Caves are insular habitats that place extreme selective pressures on organisms due to the absence of light and food scarcity. Therefore, cave organisms present an excellent opportunity for studying colonization and speciation in response to the unique abiotic conditions that require extreme adaptations. One vertebrate family, the North American catfishes (Ictaluridae), includes four troglobitic species that inhabit the karst region bordering the western Gulf of Mexico. The phylogenetic relationships of these species have been contentious, and conflicting hypotheses have been proposed to explain their origins. The purpose of our study was to construct a time-calibrated phylogeny of Ictaluridae using first-occurrence fossil data and the largest molecular dataset on the group to date. We test the hypothesis that troglobitic ictalurids have evolved in parallel, thus resulting from repeated cave colonization events. We found that Prietella lundbergi is sister to surface-dwelling Ictalurus and that Prietella phreatophila + Trogloglanis pattersoni are sister to surface-dwelling Ameiurus, suggesting that ictalurids colonized subterranean habitats at least twice in evolutionary history. The sister relationship between Prietella phreatophila and Trogloglanis pattersoni may indicate that these two species diverged from a common ancestor following a subterranean dispersal event between Texas and Coahuila aquifers. We recovered Prietella as a polyphyletic genus and recommend P. lundbergi be removed from this genus. With respect to Ameiurus, we found evidence for a potentially undescribed species sister to A. platycephalus, which warrants further investigation of Atlantic and Gulf slope Ameiurus species. In Ictalurus, we identified shallow divergence between I. dugesii and I. ochoterenai, I. australis and I. mexicanus, and I. furcatus and I. meridionalis, indicating a need to reexamine the validity of each species. Lastly, we propose minor revisions to the intrageneric classification of Noturus including the restriction of subgenus Schilbeodes to N. gyrinus (type species), N. lachneri, N. leptacanthus, and N. nocturnus.
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Affiliation(s)
- Francesco H Janzen
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | | | | | - Dean A Hendrickson
- Biodiversity Center, Texas Natural History Collections, University of Texas at Austin, Austin, TX 78758, United States
| | - Mark H Sabaj
- The Academy of Natural Sciences of Drexel University, Philadelphia, PA 19103, United States
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8
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Bruschini C, Edwards ED, Talavera G, Vaurasi VD, Latu GF, Dapporto L. A complete
COI
library of Samoan butterflies reveals layers of endemic diversity on oceanic islands. ZOOL SCR 2023. [DOI: 10.1111/zsc.12588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- Claudia Bruschini
- ZEN Lab, Dipartimento di Biologia Università degli Studi di Firenze Sesto Fiorentino Italia
| | - Eric D. Edwards
- Department of Conservation Conservation House Wellington New Zealand
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB) CSIC‐Ajuntament de Barcelona Barcelona Spain
| | - Varea D. Vaurasi
- Faculty of Science, National University of Samoa To'omatagi Samoa
| | | | - Leonardo Dapporto
- ZEN Lab, Dipartimento di Biologia Università degli Studi di Firenze Sesto Fiorentino Italia
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9
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Haines GE, Moisan L, Derry AM, Hendry AP. Dimensionality and Modularity of Adaptive Variation: Divergence in Threespine Stickleback from Diverse Environments. Am Nat 2023; 201:175-199. [PMID: 36724467 DOI: 10.1086/722483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractPopulations are subjected to diverse environmental conditions that affect fitness and induce evolutionary or plastic responses, resulting in phenotypic divergence. Some authors contend that such divergence is concentrated along a single major axis of trait covariance even if that axis does not lead populations directly toward a fitness optimum. Other authors argue that divergence can occur readily along many phenotype axes at the same time. We use populations of threespine stickleback (Gasterosteus aculeatus) from 14 lakes with contrasting ecological conditions to find some resolution along the continuum between these two extremes. Unlike many previous studies, we included several functional suites of traits (defensive, swimming, trophic) potentially subject to different sources of selection. We find that populations exhibit dimensionality of divergence that is high enough to preclude a history of constraint along a single axis-both for divergence in multivariate mean trait values and for the structure of trait covariances. Dimensionality varied among trait suites and were strongly influenced by the inclusion of specific traits, and integration of trait suites varied between populations. We leverage this variation into new insights about the process of divergence and suggest that similar analyses could increase understanding of other adaptive radiations.
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10
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Muir CD, Van Den Elzen CL, Angert AL. Selection on early survival does not explain germination rate clines in Mimulus cardinalis. AMERICAN JOURNAL OF BOTANY 2022; 109:1811-1821. [PMID: 36317645 DOI: 10.1002/ajb2.16076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Many traits covary with environmental gradients to form phenotypic clines. While local adaptation to the environment can generate phenotypic clines, other nonadaptive processes may also. If local adaptation causes phenotypic clines, then the direction of genotypic selection on traits should shift from one end of the cline to the other. Traditionally, genotypic selection on non-Gaussian traits like germination rate have been hampered because it is challenging to measure their genetic variance. METHODS Here we used quantitative genetics and reciprocal transplants to test whether a previously discovered cline in germination rate showed additional signatures of adaptation in the scarlet monkeyflower (Mimulus cardinalis). We measured genotypic and population level covariation between germination rate and early survival, a component of fitness. We developed a novel discrete log-normal model to estimate genetic variance in germination rate. RESULTS Contrary to our adaptive hypothesis, we found no evidence that genetic variation in germination rate contributed to variation in early survival. Across populations, southern populations in both gardens germinated earlier and survived more. CONCLUSIONS Southern populations have higher early survival but it is not caused by faster germination. This pattern is consistent with nonadaptive forces driving the phenotypic cline in germination rate, but future work will need to assess whether there is selection at other life stages. This statistical framework should help expand quantitative genetic analyses for other waiting-time traits.
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Affiliation(s)
- Christopher D Muir
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- School of Life Sciences, University of Hawai'i, Honolulu, HI, 96822, USA
| | - Courtney L Van Den Elzen
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Amy L Angert
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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11
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Taugbøl A, Solbakken MH, Jakobsen KS, Vøllestad LA. Salinity-induced transcriptome profiles in marine and freshwater threespine stickleback after an abrupt 6-hour exposure. Ecol Evol 2022; 12:e9395. [PMID: 36311407 PMCID: PMC9596333 DOI: 10.1002/ece3.9395] [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: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Saltwater and freshwater environments have opposing physiological challenges, yet, there are fish species that are able to enter both habitats during short time spans, and as individuals they must therefore adjust quickly to osmoregulatory contrasts. In this study, we conducted an experiment to test for plastic responses to abrupt salinity changes in two populations of threespine stickleback, Gasterosteus aculeatus, representing two ecotypes (freshwater and ancestral saltwater). We exposed both ecotypes to abrupt native (control treatment) and non‐native salinities (0‰ and 30‰) and sampled gill tissue for transcriptomic analyses after 6 h of exposure. To investigate genomic responses to salinity, we analyzed four different comparisons; one for each ecotype (in their control and exposure salinity; (1) and (2), one between ecotypes in their control salinity (3), and the fourth comparison included all transcripts identified in (3) that did not show any expressional changes within ecotype in either the control or the exposed salinity (4)). Abrupt salinity transfer affected the expression of 10 and 1530 transcripts for the saltwater and freshwater ecotype, respectively, and 1314 were differentially expressed between the controls, including 502 that were not affected by salinity within ecotype (fixed expression). In total, these results indicate that factors other than genomic expressional plasticity are important for osmoregulation in stickleback, due to the need for opposite physiological pathways to survive the abrupt change in salinity.
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Affiliation(s)
- Annette Taugbøl
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway,Norwegian Institute for Nature Research (NINA)LillehammerNorway
| | - Monica Hongrø Solbakken
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
| | - Kjetill S. Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
| | - Leif Asbjørn Vøllestad
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
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12
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Jackson N, Littleford-Colquhoun BL, Strickland K, Class B, Frere CH. Selection in the city: Rapid and fine-scale evolution of urban eastern water dragons. Evolution 2022; 76:2302-2314. [PMID: 35971751 DOI: 10.1111/evo.14596] [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: 12/06/2021] [Revised: 06/27/2022] [Accepted: 07/18/2022] [Indexed: 01/22/2023]
Abstract
Oceanic archipelagos have long been treated as a Petri dish for studies of evolutionary and ecological processes. Like archipelagos, cities exhibit similar patterns and processes, such as the rapid phenotypic divergence of a species between urban and nonurban environments. However, on a local scale, cities can be highly heterogenous, where geographically close populations can experience dramatically different environmental conditions. Nevertheless, we are yet to understand the evolutionary and ecological implications for populations spread across a heterogenous cityscape. To address this, we compared neutral genetic divergence to quantitative trait divergence within three native riparian and four city park populations of an iconic urban adapter, the eastern water dragon. We demonstrated that selection is likely acting to drive divergence of snout-vent length and jaw width across native riparian populations that are geographically isolated and across city park populations that are geographically close yet isolated by urbanization. City park populations as close as 0.9 km exhibited signs of selection-driven divergence to the same extent as native riparian populations isolated by up to 114.5 km. These findings suggest that local adaptation may be occurring over exceptionally small geographic and temporal scales within a single metropolis, demonstrating that city parks can act as archipelagos for the study of rapid evolution.
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Affiliation(s)
- Nicola Jackson
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Bethan L Littleford-Colquhoun
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, 02912, US.,Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, 02912, US
| | - Kasha Strickland
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,Department of Aquaculture and Fish Biology, Hólar University, Sauðarkrókur, 550, Iceland
| | - Barbara Class
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Celine H Frere
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Biological Sciences, University of Queensland, St. Lucia, QLD, 4072, Australia
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13
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Vaux F, Parvizi E, Craw D, Fraser CI, Waters J. Parallel recolonizations generate distinct genomic sectors in kelp following high-magnitude earthquake disturbance. Mol Ecol 2022; 31:4818-4831. [PMID: 35582778 PMCID: PMC9540901 DOI: 10.1111/mec.16535] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022]
Abstract
Large-scale disturbance events have the potential to drastically reshape biodiversity patterns. Notably, newly vacant habitat space cleared by disturbance can be colonized by multiple lineages, which can lead to the evolution of distinct spatial "sectors" of genetic diversity within a species. We test for disturbance-driven sectoring of genetic diversity in intertidal southern bull kelp, Durvillaea antarctica (Chamisso) Hariot, following the high-magnitude 1855 Wairarapa earthquake in New Zealand. Specifically, we use genotyping-by-sequencing (GBS) to analyse fine-scale population structure across the uplift zone and apply machine learning to assess the fit of alternative recolonizaton models. Our analysis reveals that specimens from the uplift zone carry distinctive genomic signatures potentially linked to post-earthquake recolonization processes. Specifically, our analysis identifies two parapatric spatial-genomic sectors of D. antarctica at Turakirae Head, which experienced the most dramatic uplift. Based on phylogeographical modelling, we infer that bull kelp in the Wellington region was probably a source for recolonization of the heavily uplifted Turakirae Head coastline, via two parallel, eastward recolonization events. By identifying multiple parapatric genotypic sectors within a recently recolonized coastal region, the current study provides support for the hypothesis that competing lineage expansions can generate striking spatial structuring of genetic diversity, even in highly dispersive taxa.
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Affiliation(s)
- Felix Vaux
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Elahe Parvizi
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Dave Craw
- Department of GeologyUniversity of OtagoDunedinNew Zealand
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14
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Fang B, Momigliano P, Kahilainen KK, Merilä J. Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation. Evolution 2022; 76:1905-1913. [PMID: 35797649 DOI: 10.1111/evo.14559] [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: 09/16/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 01/22/2023]
Abstract
The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here, we examine a whitefish population introduced to northern Finnish Lake Tsahkal in the late 1960s, where three divergent morphs (viz. littoral, pelagic, and profundal feeders) were found 10 generations after. Using demographic modeling based on genomic data, we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid sympatric divergence scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping, we identify five SNPs associated with gonad weight variation, a proxy for sexual maturity and spawning time. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.
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Affiliation(s)
- Bohao Fang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo, 36310, Spain
| | - Kimmo K Kahilainen
- Lammi Biological Station, University of Helsinki, Lammi, 16900, Finland.,Kilpisjärvi Biological Station, University of Helsinki, Kilpisjärvi, 99490, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
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15
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Roesti M, Gilbert KJ, Samuk K. Chromosomal inversions can limit adaptation to new environments. Mol Ecol 2022; 31:4435-4439. [PMID: 35810344 DOI: 10.1111/mec.16609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Abstract
Chromosomal inversions are often thought to facilitate local adaptation and population divergence because they can link multiple adaptive alleles into non-recombining genomic blocks. Selection should thus be more efficient in driving inversion-linked adaptive alleles to high frequency in a population, particularly in the face of maladaptive gene flow. But what if ecological conditions and hence selection on inversion-linked alleles change? Reduced recombination within inversions could then constrain the formation of optimal combinations of pre-existing alleles under these new ecological conditions. Here, we outline this idea of inversions limiting adaptation and divergence when ecological conditions change across time or space. We reason and use simulations to illustrate that the benefit of inversions for local adaptation and divergence under one set of ecological conditions can come with a concomitant constraint for adaptation to novel sets of ecological conditions. This limitation of inversions to adaptation may contribute to the maintenance of polymorphism within species.
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Affiliation(s)
- Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Kieran Samuk
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, USA
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16
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Aguirre WE, Reid K, Rivera J, Heins DC, Veeramah KR, Bell MA. Freshwater Colonization, Adaptation, and Genomic Divergence in Threespine Stickleback. Integr Comp Biol 2022; 62:388-405. [PMID: 35660873 PMCID: PMC9405723 DOI: 10.1093/icb/icac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/25/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
The Threespine Stickleback is ancestrally a marine fish, but many marine populations breed in fresh water (i.e., are anadromous), facilitating their colonization of isolated freshwater habitats a few years after they form. Repeated adaptation to fresh water during at least 10 My and continuing today has led to Threespine Stickleback becoming a premier system to study rapid adaptation. Anadromous and freshwater stickleback breed in sympatry and may hybridize, resulting in introgression of freshwater-adaptive alleles into anadromous populations, where they are maintained at low frequencies as ancient standing genetic variation. Anadromous stickleback have accumulated hundreds of freshwater-adaptive alleles that are disbursed as few loci per marine individual and provide the basis for adaptation when they colonize fresh water. Recent whole-lake experiments in lakes around Cook Inlet, Alaska have revealed how astonishingly rapid and repeatable this process is, with the frequency of 40% of the identified freshwater-adaptive alleles increasing from negligible (∼1%) in the marine founder to ≥50% within ten generations in fresh water, and freshwater phenotypes evolving accordingly. These high rates of genomic and phenotypic evolution imply very intense directional selection on phenotypes of heterozygotes. Sexual recombination rapidly assembles freshwater-adaptive alleles that originated in different founders into multilocus freshwater haplotypes, and regions important for adaptation to freshwater have suppressed recombination that keeps advantageous alleles linked within large haploblocks. These large haploblocks are also older and appear to have accumulated linked advantageous mutations. The contemporary evolution of Threespine Stickleback has provided broadly applicable insights into the mechanisms that facilitate rapid adaptation.
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Affiliation(s)
- Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL 60614, USA
| | - Kerry Reid
- School of Biological Sciences, Area of Ecology and Biodiversity, University of Hong Kong, Hong Kong, SAR, China.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jessica Rivera
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans 70118, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA 94720, USA
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17
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Laurentino TG, Boileau N, Ronco F, Berner D. The ectodysplasin-A receptor is a candidate gene for lateral plate number variation in stickleback fish. G3 GENES|GENOMES|GENETICS 2022; 12:6563190. [PMID: 35377433 PMCID: PMC9157104 DOI: 10.1093/g3journal/jkac077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/28/2022] [Indexed: 02/04/2023]
Abstract
Variation in lateral plating in stickleback fish represents a classical example of rapid and parallel adaptation in morphology. The underlying genetic architecture involves polymorphism at the ectodysplasin-A gene (EDA). However, lateral plate number is influenced by additional loci that remain poorly characterized. Here, we search for such loci by performing genome-wide differentiation mapping based on pooled whole-genome sequence data from a European stickleback population variable in the extent of lateral plating, while tightly controlling for the phenotypic effect of EDA. This suggests a new candidate locus, the EDA receptor gene (EDAR), for which additional support is obtained by individual-level targeted Sanger sequencing and by comparing allele frequencies among natural populations. Overall, our study illustrates the power of pooled whole-genome sequencing for searching phenotypically relevant loci and opens opportunities for exploring the population genetics and ecological significance of a new candidate locus for stickleback armor evolution.
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Affiliation(s)
- Telma G Laurentino
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Nicolas Boileau
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Fabrizia Ronco
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
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18
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Friis G, Atwell JW, Fudickar AM, Greives TJ, Yeh PJ, Price TD, Ketterson ED, Milá B. Rapid evolutionary divergence of a songbird population following recent colonization of an urban area. Mol Ecol 2022; 31:2625-2643. [DOI: 10.1111/mec.16422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/14/2022] [Accepted: 03/01/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Guillermo Friis
- National Museum of Natural Sciences Department of Biodiversity and Evolutionary Biology Spanish National Research Council (CSIC) Madrid 28006 Spain
| | | | - Adam M. Fudickar
- Department of Biology Indiana University Bloomington IN 47405 USA
| | - Timothy J. Greives
- Department of Biological Sciences North Dakota State University Fargo ND 58105 USA
| | - Pamela J. Yeh
- Department of Ecology and Evolutionary Biology University of California Los Angeles Los Angeles CA 90095 USA
| | - Trevor D. Price
- Department of Ecology and Evolution University of Chicago Chicago IL 60637 USA
| | | | - Borja Milá
- National Museum of Natural Sciences Department of Biodiversity and Evolutionary Biology Spanish National Research Council (CSIC) Madrid 28006 Spain
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19
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Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. Advancing human disease research with fish evolutionary mutant models. Trends Genet 2022; 38:22-44. [PMID: 34334238 PMCID: PMC8678158 DOI: 10.1016/j.tig.2021.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/03/2023]
Abstract
Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic the spectrum of disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease. EMMs complement traditional laboratory models by providing unique avenues to study gene-by-environment interactions, modular mutations in noncoding regions, and their evolved compensations. EMMs have improved our understanding of complex diseases, including cancer, diabetes, and aging, and illuminated mechanisms in many organs. Rapid advancements of sequencing and genome-editing technologies have catapulted the utility of EMMs, particularly in fish. Fish are the most diverse group of vertebrates, exhibiting a kaleidoscope of specialized phenotypes, many that would be pathogenic in humans but are adaptive in the species' specialized habitat. Importantly, evolved compensations can suggest avenues for novel disease therapies. This review summarizes current research using fish EMMs to advance our understanding of human disease.
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Affiliation(s)
- Emily A Beck
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Clayton M Small
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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20
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21
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Ramesh A, Groothuis TGG, Weissing FJ, Nicolaus M. Habitat fragmentation induces rapid divergence of migratory and isolated sticklebacks. Behav Ecol 2021. [DOI: 10.1093/beheco/arab121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Abstract
The adaptive capacity of many organisms is seriously challenged by human-imposed environmental change, which currently happens at unprecedented rates and magnitudes. For migratory fish, habitat fragmentation is a major challenge that can compromise their survival and reproduction. Therefore, it is important to study if fish populations can adapt to such modifications of their habitat. Here, we study whether originally anadromous three-spined stickleback populations (Gasterosteus aculeatus; “migrants”) changed in behavior and morphology in response to human-induced isolation. We made use of a natural field-experiment, where the construction of pumping stations and sluices in the 1970s unintendedly created replicates of land-locked stickleback populations (“resident”) in the Netherlands. For two years, we systematically tested populations of residents and migrants for differences in morphology and behavioral traits (activity, aggressiveness, exploration, boldness, and shoaling) in lab-based assays. We detected differences between migrant and resident populations in virtually all phenotypic traits studied: compared with the ancestral migrants, residents were smaller in size, had fewer and smaller plates and were significantly more active, aggressive, exploratory and bolder, and shoaled less. Despite large ecological differences between 2018 and 2019, results were largely consistent across the two years. Our study shows that human-induced environmental change has led to the rapid and consistent morphological and behavioral divergence of stickleback populations in about 50 generations. Such changes may be adaptive but this remains to be tested.
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Affiliation(s)
- Aparajitha Ramesh
- Theoretical Research in Evolutionary Life Sciences group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh, AG Groningen, The Netherlands
- Evolutionary Genetics, Development & Behaviour group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh, AG Groningen, The Netherlands
- Conservation Ecology group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh, AG Groningen, The Netherlands
| | - Ton G G Groothuis
- Evolutionary Genetics, Development & Behaviour group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh, AG Groningen, The Netherlands
- Theoretical Research in Evolutionary Life Sciences group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh, AG Groningen, The Netherlands
| | - Franz J Weissing
- Theoretical Research in Evolutionary Life Sciences group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh, AG Groningen, The Netherlands
- Theoretical Research in Evolutionary Life Sciences group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh, AG Groningen, The Netherlands
| | - Marion Nicolaus
- Conservation Ecology group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh, AG Groningen, The Netherlands
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22
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Haenel Q, Guerard L, MacColl ADC, Berner D. The maintenance of standing genetic variation: Gene flow vs. selective neutrality in Atlantic stickleback fish. Mol Ecol 2021; 31:811-821. [PMID: 34753205 PMCID: PMC9299253 DOI: 10.1111/mec.16269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022]
Abstract
Adaptation to derived habitats often occurs from standing genetic variation. The maintenance within ancestral populations of genetic variants favourable in derived habitats is commonly ascribed to long‐term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favoured in derived habitats are neutral in ancestral populations when their frequency is relatively low. To explore the latter, we first identify genetic variants important to the adaptation of threespine stickleback fish (Gasterosteus aculeatus) to a rare derived habitat—nutrient‐depleted acidic lakes—based on whole‐genome sequence data. Sequencing marine stickleback from six locations across the Atlantic Ocean then allows us to infer that the frequency of these derived variants in the ancestral habitat is unrelated to the likely opportunity for gene flow of these variants from acidic‐adapted populations. This result is consistent with the selective neutrality of derived variants within the ancestor. Our study thus supports an underappreciated explanation for the maintenance of standing genetic variation, and calls for a better understanding of the fitness consequences of adaptive variation across habitats and genomic backgrounds.
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Affiliation(s)
- Quiterie Haenel
- Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Laurent Guerard
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | | | - Daniel Berner
- Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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23
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Pita I, Mouillot D, Moullec F, Shin YJ. Contrasted patterns in climate change risk for Mediterranean fisheries. GLOBAL CHANGE BIOLOGY 2021; 27:5920-5933. [PMID: 34309958 DOI: 10.1111/gcb.15814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Climate change is rapidly becoming one of the biggest threats to marine life, and its impacts have the potential to strongly affect fisheries upon which millions of people rely. This is particularly crucial for the Mediterranean Sea, which is one of the world's biodiversity hotspots, one of the world's most overfished regions, and where temperatures are rising 25% faster than in the rest of the ocean on average. In this study, we calculated a vulnerability index for 100 species that compose 95% of the Mediterranean catches, through a trait-based approach. The Climate Risk Assessment (CRA) methodology was subsequently used to assess the risks due to climate change of Mediterranean fisheries. We found that the northern Mediterranean fisheries target more vulnerable species than their southern counterparts. However, when combining this catch-based vulnerability with a suite of socio-economic parameters, north African countries stand out as the most vulnerable to climate change impacts. Indeed, considering countries' exposure of the fisheries sector and their vulnerability to climate change, a sharp contrast between northern and southern Mediterranean appears, with Egypt and Tunisia scoring the highest risk. By integrating a trait-based approach on targeted marine species with socio-economic features, our analysis helps to better understand the ramifications of climate change consequences on Mediterranean fisheries and highlights the regions that could potentially be particularly affected.
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Affiliation(s)
- Ignacio Pita
- Marine Biodiversity, Exploitation and Conservation (MARBEC), Université Montpellier, Institut de Recherche pour le Développement (IRD), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), CNRS, Montpellier, France
| | - David Mouillot
- Marine Biodiversity, Exploitation and Conservation (MARBEC), Université Montpellier, Institut de Recherche pour le Développement (IRD), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), CNRS, Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Fabien Moullec
- Coastal Systems (COS), Royal Netherlands Institute for Sea Research, Den Burg, Noord-Holland, The Netherlands
| | - Yunne-Jai Shin
- Marine Biodiversity, Exploitation and Conservation (MARBEC), Université Montpellier, Institut de Recherche pour le Développement (IRD), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), CNRS, Montpellier, France
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24
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Abstract
The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host-microbiome and host-parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics.
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Affiliation(s)
- Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, California 94720, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
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25
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Papadopulos AST, Helmstetter AJ, Osborne OG, Comeault AA, Wood DP, Straw EA, Mason L, Fay MF, Parker J, Dunning LT, Foote AD, Smith RJ, Lighten J. Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution. Mol Biol Evol 2021; 38:3724-3736. [PMID: 33950261 PMCID: PMC8382892 DOI: 10.1093/molbev/msab141] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, capacity of species to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonized isolated, disused mines with phytotoxic, zinc-contaminated soils. To test whether rapid, parallel adaptation to anthropogenic pollution has taken place, we used reduced representation sequencing (ddRAD) to reconstruct the evolutionary history of geographically proximate mine and coastal population pairs and found largely independent colonization of mines from different coastal sites. Furthermore, our results show that parallel evolution of zinc tolerance has occurred without gene flow spreading adaptive alleles between mine populations. In genomic regions where signatures of selection were detected across multiple mine-coast pairs, we identified genes with functions linked to physiological differences between the putative ecotypes, although genetic differentiation at specific loci is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities (and other environmental challenges) may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.
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Affiliation(s)
- Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Andrew J Helmstetter
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- FRB-CESAB, Institut Bouisson Bertrand, Rue de l'École de Médecine, Montpellier, France
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Aaron A Comeault
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Daniel P Wood
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Edward A Straw
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Ecology, Evolution & Behaviour, Department of Biological Sciences, School for Life Sciences and the Environment, Royal Holloway University of London, Egham, United Kingdom
| | | | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - Joe Parker
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- National Biofilms Innovation Centre, Department of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Andrew D Foote
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Department of Natural History, Norwegian University of Science and Technology, NTNU University Museum, Trondheim, Norway
| | - Rhian J Smith
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jackie Lighten
- Biosciences, University of Exeter, Exeter, United Kingdom
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26
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Scott GR, Dalziel AC. Physiological insight into the evolution of complex phenotypes: aerobic performance and the O2 transport pathway of vertebrates. J Exp Biol 2021; 224:271829. [PMID: 34387318 DOI: 10.1242/jeb.210849] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Evolutionary physiology strives to understand how the function and integration of physiological systems influence the way in which organisms evolve. Studies of the O2 transport pathway - the integrated physiological system that transports O2 from the environment to mitochondria - are well suited to this endeavour. We consider the mechanistic underpinnings across the O2 pathway for the evolution of aerobic capacity, focusing on studies of artificial selection and naturally selected divergence among wild populations of mammals and fish. We show that evolved changes in aerobic capacity do not require concerted changes across the O2 pathway and can arise quickly from changes in one or a subset of pathway steps. Population divergence in aerobic capacity can be associated with the evolution of plasticity in response to environmental variation or activity. In some cases, initial evolutionary divergence of aerobic capacity arose exclusively from increased capacities for O2 diffusion and/or utilization in active O2-consuming tissues (muscle), which may often constitute first steps in adaptation. However, continued selection leading to greater divergence in aerobic capacity is often associated with increased capacities for circulatory and pulmonary O2 transport. Increases in tissue O2 diffusing capacity may augment the adaptive benefit of increasing circulatory O2 transport owing to their interactive influence on tissue O2 extraction. Theoretical modelling of the O2 pathway suggests that O2 pathway steps with a disproportionately large influence over aerobic capacity have been more likely to evolve, but more work is needed to appreciate the extent to which such physiological principles can predict evolutionary outcomes.
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Affiliation(s)
- Graham R Scott
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Anne C Dalziel
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, Nova Scotia, B3H 3C3, Canada
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27
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Zong SB, Li YL, Liu JX. Genomic Architecture of Rapid Parallel Adaptation to Fresh Water in a Wild Fish. Mol Biol Evol 2021; 38:1317-1329. [PMID: 33146383 PMCID: PMC8480189 DOI: 10.1093/molbev/msaa290] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. However, the genetic architecture underlying these adaptive changes is still poorly understood. Using population genomic approaches, we investigated the genomic architecture that underlies rapid parallel adaptation of Coilia nasus to fresh water by comparing four freshwater-resident populations with their ancestral anadromous population. Linkage disequilibrium network analysis and population genetic analyses revealed two putative large chromosome inversions on LG6 and LG22, which were enriched for outlier loci and exhibited parallel association with freshwater adaptation. Drastic frequency shifts and elevated genetic differentiation were observed for the two chromosome inversions among populations, suggesting that both inversions would undergo divergent selection between anadromous and resident ecotypes. Enrichment analysis of genes within chromosome inversions showed significant enrichment of genes involved in metabolic process, immunoregulation, growth, maturation, osmoregulation, and so forth, which probably underlay differences in morphology, physiology and behavior between the anadromous and freshwater-resident forms. The availability of beneficial standing genetic variation, large optimum shift between marine and freshwater habitats, and high efficiency of selection with large population size could lead to the observed rapid parallel adaptive genomic change. We propose that chromosomal inversions might have played an important role during the evolution of rapid parallel ecological divergence in the face of environmental heterogeneity in C. nasus. Our study provides insights into the genomic basis of rapid adaptation of complex traits in novel habitats and highlights the importance of structural genomic variants in analyses of ecological adaptation.
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Affiliation(s)
- Shao-Bing Zong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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28
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Waters JM, McCulloch GA. Reinventing the wheel? Reassessing the roles of gene flow, sorting and convergence in repeated evolution. Mol Ecol 2021; 30:4162-4172. [PMID: 34133810 DOI: 10.1111/mec.16018] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/31/2022]
Abstract
Biologists have long been intrigued by apparently predictable and repetitive evolutionary trajectories inferred across a variety of lineages and systems. In recent years, high-throughput sequencing analyses have started to transform our understanding of such repetitive shifts. While researchers have traditionally categorized such shifts as either "convergent" or "parallel," based on relatedness of the lineages involved, emerging genomic insights provide an opportunity to better describe the actual evolutionary mechanisms at play. A synthesis of recent genomic analyses confirms that convergence is the predominant driver of repetitive evolution among species, whereas repeated sorting of standing variation is the major driver of repeated shifts within species. However, emerging data reveal numerous notable exceptions to these expectations, with recent examples of de novo mutations underpinning convergent shifts among even very closely related lineages, while repetitive sorting processes have occurred among even deeply divergent taxa, sometimes via introgression. A number of very recent analyses have found evidence for both processes occurring on different scales within taxa. We suggest that the relative importance of convergent versus sorting processes depends on the interplay between gene flow among populations, and phylogenetic relatedness of the lineages involved.
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29
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Roberts Kingman GA, Vyas DN, Jones FC, Brady SD, Chen HI, Reid K, Milhaven M, Bertino TS, Aguirre WE, Heins DC, von Hippel FA, Park PJ, Kirch M, Absher DM, Myers RM, Di Palma F, Bell MA, Kingsley DM, Veeramah KR. Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. SCIENCE ADVANCES 2021; 7:7/25/eabg5285. [PMID: 34144992 PMCID: PMC8213234 DOI: 10.1126/sciadv.abg5285] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/05/2021] [Indexed: 05/30/2023]
Abstract
Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin's finches, suggesting that similar features are important for evolution across diverse taxa.
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Affiliation(s)
- Garrett A Roberts Kingman
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Deven N Vyas
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Mark Milhaven
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Thomas S Bertino
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL 60614-3207, USA
| | - David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Frank A von Hippel
- Department of Community, Environment and Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA
| | - Peter J Park
- Department of Biology, Farmingdale State College, Farmingdale, NY 11735-1021, USA
| | - Melanie Kirch
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Federica Di Palma
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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30
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Paccard A, Hanson D, Stuart YE, von Hippel FA, Kalbe M, Klepaker T, Skúlason S, Kristjánsson BK, Bolnick DI, Hendry AP, Barrett RDH. Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats. J Hered 2021; 111:43-56. [PMID: 31690947 DOI: 10.1093/jhered/esz056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
The repeatability of adaptive radiation is expected to be scale-dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation-their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.
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Affiliation(s)
- Antoine Paccard
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Dieta Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Frank A von Hippel
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tom Klepaker
- University of Bergen, Department of Biology, Bergen, Norway
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
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31
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Kirch M, Romundset A, Gilbert MTP, Jones FC, Foote AD. Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. Curr Biol 2021; 31:2027-2036.e8. [PMID: 33705715 DOI: 10.1016/j.cub.2021.02.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 10/21/2022]
Abstract
Adaptation is typically studied by comparing modern populations with contrasting environments. Individuals persisting in the ancestral habitat are typically used to represent the ancestral founding population; however, it has been questioned whether these individuals are good proxies for the actual ancestors.1 To address this, we applied a paleogenomics approach2 to directly access the ancestral genepool: partially sequencing the genomes of two 11- to 13,000-year-old stickleback recovered from the transitionary layer between marine and freshwater sediments of two Norwegian isolation lakes3 and comparing them with 30 modern stickleback genomes from the same lakes and adjacent marine fjord, in addition to a global dataset of 20 genomes.4 The ancient stickleback shared genome-wide ancestry with the modern fjord population, whereas modern lake populations have lost substantial ancestral variation following founder effects, and subsequent drift and selection. Freshwater-adaptive alleles found in one ancient stickleback genome have not risen to high frequency in the present-day population from the same lake. Comparison to the global dataset suggested incomplete adaptation to freshwater in our modern lake populations. Our findings reveal the impact of population bottlenecks in constraining adaptation due to reduced efficacy of selection on standing variation present in founder populations.
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Affiliation(s)
- Melanie Kirch
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, DK-1353 Copenhagen, Denmark; Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, 7491 Trondheim, Norway
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Andrew D Foote
- Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, 7491 Trondheim, Norway; Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, UK.
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32
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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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33
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Hu J, Wuitchik SJS, Barry TN, Jamniczky HA, Rogers SM, Barrett RDH. Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus). Genetics 2021; 217:1-15. [PMID: 33683369 PMCID: PMC8045681 DOI: 10.1093/genetics/iyab001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24-35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.
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Affiliation(s)
- Juntao Hu
- National Observation and Research Station for Yangtze Estuarine Wetland Ecosystems, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai 200438, China
- Redpath Museum and Department of Biology, McGill University, Montreal, QC H3A 0C4, Canada
| | - Sara J S Wuitchik
- Informatics Group, Harvard University, Cambridge, MA 02138, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Tegan N Barry
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Heather A Jamniczky
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, QC H3A 0C4, Canada
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34
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Rivera HE, Aichelman HE, Fifer JE, Kriefall NG, Wuitchik DM, Wuitchik SJS, Davies SW. A framework for understanding gene expression plasticity and its influence on stress tolerance. Mol Ecol 2021; 30:1381-1397. [PMID: 33503298 DOI: 10.1111/mec.15820] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/10/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
Phenotypic plasticity can serve as a stepping stone towards adaptation. Recently, studies have shown that gene expression contributes to emergent stress responses such as thermal tolerance, with tolerant and susceptible populations showing distinct transcriptional profiles. However, given the dynamic nature of gene expression, interpreting transcriptomic results in a way that elucidates the functional connection between gene expression and the observed stress response is challenging. Here, we present a conceptual framework to guide interpretation of gene expression reaction norms in the context of stress tolerance. We consider the evolutionary and adaptive potential of gene expression reaction norms and discuss the influence of sampling timing, transcriptomic resilience, as well as complexities related to life history when interpreting gene expression dynamics and how these patterns relate to host tolerance. We highlight corals as a case study to demonstrate the value of this framework for non-model systems. As species face rapidly changing environmental conditions, modulating gene expression can serve as a mechanistic link from genetic and cellular processes to the physiological responses that allow organisms to thrive under novel conditions. Interpreting how or whether a species can employ gene expression plasticity to ensure short-term survival will be critical for understanding the global impacts of climate change across diverse taxa.
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Affiliation(s)
- Hanny E Rivera
- Department of Biology, Boston University, Boston, MA, USA
| | | | - James E Fifer
- Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Sara J S Wuitchik
- Department of Biology, Boston University, Boston, MA, USA.,FAS Informatics, Harvard University, Cambridge, MA, USA
| | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA, USA
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35
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Hofmeister NR, Werner SJ, Lovette IJ. Environmental correlates of genetic variation in the invasive European starling in North America. Mol Ecol 2021; 30:1251-1263. [PMID: 33464634 DOI: 10.1111/mec.15806] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022]
Abstract
Populations of invasive species that colonize and spread in novel environments may differentiate both through demographic processes and local selection. European starlings (Sturnus vulgaris) were introduced to New York in 1890 and subsequently spread throughout North America, becoming one of the most widespread and numerous bird species on the continent. Genome-wide comparisons across starling individuals and populations can identify demographic and/or selective factors that facilitated this rapid and successful expansion. We investigated patterns of genomic diversity and differentiation using reduced-representation genome sequencing of 17 winter-season sampling sites. Consistent with this species' high dispersal rate and rapid expansion history, we found low geographical differentiation and few FST outliers even at a continental scale. Despite starting from a founding population of ~180 individuals, North American starlings show only a moderate genetic bottleneck, and models suggest a dramatic increase in effective population size since introduction. In genotype-environment associations we found that ~200 single-nucleotide polymorphisms are correlated with temperature and/or precipitation against a background of negligible genome- and range-wide divergence. Given this evidence, we suggest that local adaptation in North American starlings may have evolved rapidly even in this wide-ranging and evolutionarily young system. This survey of genomic signatures of expansion in North American starlings is the most comprehensive to date and complements ongoing studies of world-wide local adaptation in these highly dispersive and invasive birds.
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Affiliation(s)
- Natalie R Hofmeister
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Scott J Werner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | - Irby J Lovette
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
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36
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Quintela M, Richter‐Boix À, Bekkevold D, Kvamme C, Berg F, Jansson E, Dahle G, Besnier F, Nash RDM, Glover KA. Genetic response to human-induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway. Ecol Evol 2021; 11:1691-1718. [PMID: 33613998 PMCID: PMC7882954 DOI: 10.1002/ece3.7160] [Citation(s) in RCA: 3] [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: 12/07/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/21/2022] Open
Abstract
Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; that is, Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat, and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant F ST between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbor-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation (F ST) between marine and brackish sprat is larger in the comparison Norway-Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, that is, 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen.
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Affiliation(s)
| | - Àlex Richter‐Boix
- CREAFCampus de BellaterraAutonomous University of BarcelonaBarcelonaSpain
| | - Dorte Bekkevold
- DTU‐Aqua National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | | | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | | | - Richard D. M. Nash
- Centre for EnvironmentFisheries and Aquaculture Science (Cefas)LowestoftUK
| | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Institute of BiologyUniversity of BergenBergenNorway
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37
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Schluter D, Marchinko KB, Arnegard ME, Zhang H, Brady SD, Jones FC, Bell MA, Kingsley DM. Fitness maps to a large-effect locus in introduced stickleback populations. Proc Natl Acad Sci U S A 2021; 118:e1914889118. [PMID: 33414274 PMCID: PMC7826376 DOI: 10.1073/pnas.1914889118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A quantitative trait locus map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980s. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 y, yielding a similar estimate of selection, s = 0.49 ± 0.05, but a different degree of dominance. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.
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Affiliation(s)
- Dolph Schluter
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4;
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Kerry B Marchinko
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Matthew E Arnegard
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Haili Zhang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, CA 94720
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305;
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
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38
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Birrell JH, Shah AA, Hotaling S, Giersch JJ, Williamson CE, Jacobsen D, Woods HA. Insects in high-elevation streams: Life in extreme environments imperiled by climate change. GLOBAL CHANGE BIOLOGY 2020; 26:6667-6684. [PMID: 32931053 DOI: 10.1111/gcb.15356] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
Climate change is altering conditions in high-elevation streams worldwide, with largely unknown effects on resident communities of aquatic insects. Here, we review the challenges of climate change for high-elevation aquatic insects and how they may respond, focusing on current gaps in knowledge. Understanding current effects and predicting future impacts will depend on progress in three areas. First, we need better descriptions of the multivariate physical challenges and interactions among challenges in high-elevation streams, which include low but rising temperatures, low oxygen supply and increasing oxygen demand, high and rising exposure to ultraviolet radiation, low ionic strength, and variable but shifting flow regimes. These factors are often studied in isolation even though they covary in nature and interact in space and time. Second, we need a better mechanistic understanding of how physical conditions in streams drive the performance of individual insects. Environment-performance links are mediated by physiology and behavior, which are poorly known in high-elevation taxa. Third, we need to define the scope and importance of potential responses across levels of biological organization. Short-term responses are defined by the tolerances of individuals, their capacities to perform adequately across a range of conditions, and behaviors used to exploit local, fine-scale variation in abiotic factors. Longer term responses to climate change, however, may include individual plasticity and evolution of populations. Whether high-elevation aquatic insects can mitigate climatic risks via these pathways is largely unknown.
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Affiliation(s)
- Jackson H Birrell
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Alisha A Shah
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - J Joseph Giersch
- U.S. Geological Survey, Northern Rocky Mountain Science Center, West Glacier, MT, USA
| | | | - Dean Jacobsen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - H Arthur Woods
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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39
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Weeks BC, Naeem S, Winger BM, Cracraft J. The relationship between morphology and behavior in mixed-species flocks of island birds. Ecol Evol 2020; 10:10593-10606. [PMID: 33072282 PMCID: PMC7548193 DOI: 10.1002/ece3.6714] [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: 04/01/2020] [Revised: 07/15/2020] [Accepted: 07/29/2020] [Indexed: 12/28/2022] Open
Abstract
Understanding how co‐occurring species divide ecological space is a central issue in ecology. Functional traits have the potential to serve as a means for quantitatively assessing niche partitioning by different species based on their ecological attributes, such as morphology, behavior, or trophic habit. This enables testing ecological and evolutionary questions using functional traits at spatio‐temporal scales that are not feasible using traditional field methods. Both rapid evolutionary change and inter‐ and intraspecific competition, however, may limit the utility of morphological functional traits as indicators of how niches are partitioned. To address how behavior and morphology interact, we quantified foraging behavior of mixed‐species flocks of birds in the Solomon Islands to test whether behavior and morphology are correlated in these flocks. We find that foraging behavior is significantly correlated with morphological traits (p = .05), but this correlation breaks down after correcting for phylogenetic relatedness (p = .66). These results suggest that there are consistent correlations between aspects of behavior and morphology at large taxonomic scales (e.g., across genera), but the relationship between behavior and morphology depends largely on among‐clade differences and may be idiosyncratic at shallower scales (e.g., within genera). As a result, general relationships between behaviors and morphology may not be applicable when comparing close relatives.
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Affiliation(s)
- Brian C Weeks
- School for Environment and Sustainability University of Michigan Ann Arbor MI USA.,Department of Ecology, Evolution and Environmental Biology Columbia University New York NY USA.,Department of Ornithology American Museum of Natural History New York NY USA
| | - Shahid Naeem
- Department of Ecology, Evolution and Environmental Biology Columbia University New York NY USA
| | - Benjamin M Winger
- Museum of Zoology and Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Joel Cracraft
- Department of Ornithology American Museum of Natural History New York NY USA
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40
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Reznick D. The tree and the table: Darwin, Mendeleev and the meaning of 'theory'. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190309. [PMID: 32811366 DOI: 10.1098/rsta.2019.0309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/28/2020] [Indexed: 06/11/2023]
Abstract
Darwin and Mendeleev revolutionized their respective disciplines by organizing diverse facts into simple, pictorial representations-a tree and a table. Each representation provides a foundation for a scientific theory for two reasons. First, a successful theory unites diverse phenomena under a single explanatory framework. Second, it does so in a way that defines paths for future inquiry that extends its reach and tests its limits. For Mendeleev, this meant creating a table that accommodated the current understanding of the elements but also contained blanks that predicted the discovery of previously unknown elements. More importantly, the structure of the table helped shape future research to define the structure of matter. For Darwin, envisioning life as a tree meant defining the rules that govern the origin of adaptations, species and shape the constantly shifting diversity of life. At the same time, his theory inspired research into the laws of inheritance and created diverse new areas of research, like behaviour, sexual selection and biogeography. The shared property of Darwin and Mendeleev's contributions was to provide a unifying rational explanation for natural phenomena. This article is part of the theme issue 'Mendeleev and the periodic table'.
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Affiliation(s)
- David Reznick
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA 92521, USA
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41
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Leder EH, André C, Le Moan A, Töpel M, Blomberg A, Havenhand JN, Lindström K, Volckaert FAM, Kvarnemo C, Johannesson K, Svensson O. Post-glacial establishment of locally adapted fish populations over a steep salinity gradient. J Evol Biol 2020; 34:138-156. [PMID: 32573797 DOI: 10.1111/jeb.13668] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/04/2020] [Indexed: 12/21/2022]
Abstract
Studies of colonization of new habitats that appear from rapidly changing environments are interesting and highly relevant to our understanding of divergence and speciation. Here, we analyse phenotypic and genetic variation involved in the successful establishment of a marine fish (sand goby, Pomatoschistus minutus) over a steep salinity drop from 35 PSU in the North Sea (NE Atlantic) to two PSU in the inner parts of the post-glacial Baltic Sea. We first show that populations are adapted to local salinity in a key reproductive trait, the proportion of motile sperm. Thereafter, we show that genome variation at 22,190 single nucleotide polymorphisms (SNPs) shows strong differentiation among populations along the gradient. Sequences containing outlier SNPs and transcriptome sequences, mapped to a draft genome, reveal associations with genes with relevant functions for adaptation in this environment but without overall evidence of functional enrichment. The many contigs involved suggest polygenic differentiation. We trace the origin of this differentiation using demographic modelling and find the most likely scenario is that at least part of the genetic differentiation is older than the Baltic Sea and is a result of isolation of two lineages prior to the current contact over the North Sea-Baltic Sea transition zone.
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Affiliation(s)
- Erica H Leder
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.,Department of Biology, University of Turku, Turku, Finland.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Carl André
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.,Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Alan Le Moan
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.,Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Mats Töpel
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anders Blomberg
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jonathan N Havenhand
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.,Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Kai Lindström
- Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - Filip A M Volckaert
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Charlotta Kvarnemo
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Kerstin Johannesson
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.,Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Ola Svensson
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Department for Pre-School and School Teacher Education, University of Borås, Borås, Sweden
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42
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On the causes of geographically heterogeneous parallel evolution in sticklebacks. Nat Ecol Evol 2020; 4:1105-1115. [DOI: 10.1038/s41559-020-1222-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/14/2020] [Indexed: 12/22/2022]
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43
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Matz MV, Treml EA, Haller BC. Estimating the potential for coral adaptation to global warming across the Indo-West Pacific. GLOBAL CHANGE BIOLOGY 2020; 26:3473-3481. [PMID: 32285562 DOI: 10.1111/gcb.15060] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/18/2020] [Accepted: 02/23/2020] [Indexed: 06/11/2023]
Abstract
The potential of reef-building corals to adapt to increasing sea-surface temperatures is often debated but has rarely been comprehensively modeled on a region-wide scale. We used individual-based simulations to model adaptation to warming in a coral metapopulation comprising 680 reefs and representing the whole of the Central Indo-West Pacific. Encouragingly, some reefs-most notably Vietnam, Japan, Taiwan, New Caledonia and the southern half of the Great Barrier Reef-exhibited high capacity for adaptation and, in our model, maintained coral cover even under a rapid "business-as-usual" warming scenario throughout the modeled period (200 years). Higher resilience of these reefs was observed under all tested parameter settings except the models prohibiting selection and/or migration during warming. At the same time, the majority of reefs in the region tended to collapse within the first 100 years of warming. The adaptive potential (odds of maintaining high coral cover) of a given reef could be predicted based on two metrics: the reef's present-day temperature, and the proportion of recruits immigrating from warmer locations. The latter metric explains the most variation in adaptive potential, and significantly correlates with actual coral cover changes observed throughout the region between the 1970s and the early 2000s. These findings will help prioritize coral conservation efforts and plan assisted gene flow interventions to boost the adaptive potential of specific coral populations.
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Affiliation(s)
- Mikhail V Matz
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Eric A Treml
- Life and Environmental Sciences, Faculty of Science Engineering and Built Environment, Deakin University, Geelong, Vic., Australia
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45
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Laurentino TG, Moser D, Roesti M, Ammann M, Frey A, Ronco F, Kueng B, Berner D. Genomic release-recapture experiment in the wild reveals within-generation polygenic selection in stickleback fish. Nat Commun 2020; 11:1928. [PMID: 32317640 PMCID: PMC7174299 DOI: 10.1038/s41467-020-15657-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/19/2020] [Indexed: 11/29/2022] Open
Abstract
How rapidly natural selection sorts genome-wide standing genetic variation during adaptation remains largely unstudied experimentally. Here, we present a genomic release-recapture experiment using paired threespine stickleback fish populations adapted to selectively different lake and stream habitats. First, we use pooled whole-genome sequence data from the original populations to identify hundreds of candidate genome regions likely under divergent selection between these habitats. Next, we generate F2 hybrids from the same lake-stream population pair in the laboratory and release thousands of juveniles into a natural stream habitat. Comparing the individuals surviving one year of stream selection to a reference sample of F2 hybrids allows us to detect frequency shifts across the candidate regions toward the genetic variants typical of the stream population-an experimental outcome consistent with polygenic directional selection. Our study reveals that adaptation in nature can be detected as a genome-wide signal over just a single generation.
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Affiliation(s)
- Telma G Laurentino
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Dario Moser
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Marius Roesti
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Matthias Ammann
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Anja Frey
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Fabrizia Ronco
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Benjamin Kueng
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
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46
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Terekhanova NV, Barmintseva AE, Kondrashov AS, Bazykin GA, Mugue NS. Architecture of Parallel Adaptation in Ten Lacustrine Threespine Stickleback Populations from the White Sea Area. Genome Biol Evol 2020; 11:2605-2618. [PMID: 31406984 PMCID: PMC6761963 DOI: 10.1093/gbe/evz175] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2019] [Indexed: 12/20/2022] Open
Abstract
Adaptation of threespine stickleback to freshwater involves parallel recruitment of freshwater alleles in clusters of closely linked sites, or divergence islands (DIs). However, it remains unclear to what extent the DIs and the alleles that constitute them coincide between populations that underwent adaptation to freshwater independently. We examine threespine sticklebacks from ten freshwater lakes that emerged 500–1500 years ago in the White Sea basin, with the emphasis on repeatability of genomic patterns of adaptation among the lake populations and the role of local recombination rate in the distribution and structure of DIs. The 65 detected DIs are clustered in the genome, forming 12 aggregations, and this clustering cannot be explained by the variation of the recombination rate. Only 21 of the DIs are present in all the freshwater populations, likely being indispensable for successful colonization of freshwater environment by the ancestral marine population. Within most DIs, the same set of single nucleotide polymorphisms (SNPs) distinguish marine and freshwater haplotypes in all the lake populations; however, in some DIs, freshwater alleles differ between populations, suggesting that they could have been established by recruitment of different haplotypes in different populations.
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Affiliation(s)
- Nadezhda V Terekhanova
- Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
| | - Anna E Barmintseva
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, Moscow, Russia
| | - Alexey S Kondrashov
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan.,M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
| | - Nikolai S Mugue
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, Moscow, Russia.,N. K. Koltzov Institute of Developmental Biology RAS, Moscow, Russia
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47
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Asymmetric Isolation and the Evolution of Behaviors Influencing Dispersal: Rheotaxis of Guppies above Waterfalls. Genes (Basel) 2020; 11:genes11020180. [PMID: 32050464 PMCID: PMC7073897 DOI: 10.3390/genes11020180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 11/17/2022] Open
Abstract
Populations that are asymmetrically isolated, such as above waterfalls, can sometimes export emigrants in a direction from which they do not receive immigrants, and thus provide an excellent opportunity to study the evolution of dispersal traits. We investigated the rheotaxis of guppies above barrier waterfalls in the Aripo and Turure rivers in Trinidad-the later having been introduced in 1957 from a below-waterfall population in another drainage. We predicted that, as a result of strong selection against downstream emigration, both of these above-waterfall populations should show strong positive rheotaxis. Matching these expectations, both populations expressed high levels of positive rheotaxis, possibly reflecting contemporary (rapid) evolution in the introduced Turure population. However, the two populations used different behaviors to achieve the same performance of strong positive rheotaxis, as has been predicted in the case of multiple potential evolutionary solutions to the same functional challenge (i.e., "many-to-one mapping"). By contrast, we did not find any difference in rheotactic behavior above versus below waterfalls on a small scale within either river, suggesting constraints on adaptive divergence on such scales.
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48
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Abstract
Threespine stickleback populations provide a striking example of local adaptation to divergent habitats in populations that are connected by recurrent gene flow. These small fish occur in marine and freshwater habitats throughout the Northern Hemisphere, and in numerous cases the smaller freshwater populations have been established “de novo” from marine colonists. Independently evolved freshwater populations exhibit similar phenotypes that have been shown to derive largely from the same standing genetic variants. Geographic isolation prevents direct migration between the freshwater populations, strongly suggesting that these shared locally adaptive alleles are transported through the marine population. However it is still largely unknown how gene flow, recombination, and selection jointly impact the standing variation that might fuel this adaptation. Here we use individual-based, spatially explicit simulations to determine the levels of gene flow that best match observed patterns of allele sharing among habitats in stickleback. We aim to better understand how gene flow and local adaptation in large metapopulations determine the speed of adaptation and re-use of standing genetic variation. In our simulations we find that repeated adaptation uses a shared set of alleles that are maintained at low frequency by migration-selection balance in oceanic populations. This process occurs over a realistic range of intermediate levels of gene flow that match previous empirical population genomic studies in stickleback. Examining these simulations more deeply reveals how lower levels of gene flow leads to slow, independent adaptation to different habitats, whereas higher levels of gene flow leads to significant mutation load – but an increased probability of successful population genomic scans for locally adapted alleles. Surprisingly, we find that the genealogical origins of most freshwater adapted alleles can be traced back to the original generation of marine individuals that colonized the lakes, as opposed to subsequent migrants. These simulations provide deeper context for existing studies of stickleback evolutionary genomics, and guidance for future empirical studies in this model. More broadly, our results support existing theory of local adaptation but extend it by more completely documenting the genealogical history of adaptive alleles in a metapopulation.
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49
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Ord TJ, Garcia-Porta J, Querejeta M, Collar DC. Gliding Dragons and Flying Squirrels: Diversifying versus Stabilizing Selection on Morphology following the Evolution of an Innovation. Am Nat 2020; 195:E51-E66. [DOI: 10.1086/706305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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50
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Colautti DC, Miranda L, Gonzalez-Castro M, Villanova V, Strüssmann CA, Mancini M, Maiztegui T, Berasain G, Hattori R, Grosman F, Sanzano P, Lozano I, Vegh SL, Salinas V, Del Ponti O, Del Fresno P, Minotti P, Yamamoto Y, Baigún CRM. Evidence of a landlocked reproducing population of the marine pejerrey Odontesthes argentinensis (Actinopterygii; Atherinopsidae). JOURNAL OF FISH BIOLOGY 2020; 96:202-216. [PMID: 31729023 DOI: 10.1111/jfb.14207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In South America, the order Atheriniformes includes the monophyletic genus Odontesthes with 20 species that inhabit freshwater, estuarine and coastal environments. Pejerrey Odontesthes argentinensis is widely distributed in coastal and estuarine areas of the Atlantic Ocean and is known to foray into estuaries of river systems, particularly in conditions of elevated salinity. However, to our knowledge, a landlocked self-sustaining population has never been recorded. In this study, we examined the pejerrey population of Salada de Pedro Luro Lake (south-east of Buenos Aires Province, Argentina) to clarify its taxonomic identity. An integrative taxonomic analysis based on traditional meristic, landmark-based morphometrics and genetic techniques suggests that the Salada de Pedro Luro pejerrey population represents a novel case of physiological and morphological adaptation of a marine pejerrey species to a landlocked environment and emphasises the environmental plasticity of this group of fishes.
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Affiliation(s)
- Darío C Colautti
- Laboratorio de Ecología de Peces Instituto de Limnología 'Dr. Raúl A. Ringuelet' (ILPLA-CONICET), La Plata, Argentina
| | - Leandro Miranda
- Laboratorio de Ictiofisiología y Acuicultura IIB-INTECH (CONICET-UNSAM), Chascomús, Argentina
| | - Mariano Gonzalez-Castro
- Laboratorio de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras (IIMyC-CONICET), Mar del Plata, Argentina
| | - Vanina Villanova
- Laboratorio de Biotecnología Acuática (FCByF-UNR) Centro Científico, Tecnológico y Educativo Acuario del Río Paraná, Rosario, Argentina
- Centro Científico y Tecnológico Conicet Rosario (CCT-Conicet Rosario), Rosario, Argentina
| | - Carlos A Strüssmann
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Miguel Mancini
- Ecología & Acuicultura, Facultad de Agronomía y Veterinaria (UNRC), Río Cuarto, Argentina
| | - Tomas Maiztegui
- Laboratorio de Ecología de Peces Instituto de Limnología 'Dr. Raúl A. Ringuelet' (ILPLA-CONICET), La Plata, Argentina
| | - Gustavo Berasain
- Dirección Provincial de Pesca, Ministerio de agroindustria de la Provincia de Buenos Aires, Lastra y Juarez (7130), Chascomús, Buenos Aires, Argentina
| | - Ricardo Hattori
- São Paulo 31 Fisheries Institute (APTA/SAA), Campos do Jordão, 12460-000, Brazil
| | - Fabian Grosman
- Facultad de Ciencias Veterinarias, Instituto Ecosistemas (UNCPBA-CIC), Tandil, Argentina
| | - Pablo Sanzano
- Facultad de Ciencias Veterinarias, Instituto Ecosistemas (UNCPBA-CIC), Tandil, Argentina
| | - Ismael Lozano
- Laboratorio de Ecotoxicología Acuática, Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA-CONICET), Ciudad Universitaria, Buenos Aires, Argentina
| | - Sabina L Vegh
- Instituto de Investigaciones en Producción Animal (INPA-CONICET), Buenos Aires, Argentina
| | - Victor Salinas
- Ecología & Acuicultura, Facultad de Agronomía y Veterinaria (UNRC), Río Cuarto, Argentina
| | - Omar Del Ponti
- Departamento de Recursos Naturales, Facultad de Ciencias Exactas y Naturales (UNLPam), Santa Rosa, Argentina
| | - Pamela Del Fresno
- Laboratorio de Ictiofisiología y Acuicultura IIB-INTECH (CONICET-UNSAM), Chascomús, Argentina
| | - Priscila Minotti
- Laboratorio de Ecología, Teledetección y Ecoinformática3iA Instituto de Investigación e Ingeniería Ambiental Universidad Nacional de San Martín Campus Miguelete, Martín, Argentina
| | - Yoji Yamamoto
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Claudio R M Baigún
- Laboratorio de Ecología Pesquera Aplicada, Instituto de Investigación e Ingeniería Ambiental (UNSAM-CONICET), Buenos Aires, Argentina
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