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Sabolić I, Mira Ó, Brandt DYC, Lisičić D, Stapley J, Novosolov M, Bakarić R, Cizelj I, Glogoški M, Hudina T, Taverne M, Allentoft ME, Nielsen R, Herrel A, Štambuk A. Plastic and genomic change of a newly established lizard population following a founder event. Mol Ecol 2024; 33:e17255. [PMID: 38133599 DOI: 10.1111/mec.17255] [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: 07/14/2022] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
Understanding how phenotypic divergence arises among natural populations remains one of the major goals in evolutionary biology. As part of competitive exclusion experiment conducted in 1971, 10 individuals of Italian wall lizard (Podarcis siculus (Rafinesque-Schmaltz, 1810)) were transplanted from Pod Kopište Island to the nearby island of Pod Mrčaru (Adriatic Sea). Merely 35 years after the introduction, the newly established population on Pod Mrčaru Island had shifted their diet from predominantly insectivorous towards omnivorous and changed significantly in a range of morphological, behavioural, physiological and ecological characteristics. Here, we combine genomic and quantitative genetic approaches to determine the relative roles of genetic adaptation and phenotypic plasticity in driving this rapid phenotypic shift. Our results show genome-wide genetic differentiation between ancestral and transplanted population, with weak genetic erosion on Pod Mrčaru Island. Adaptive processes following the founder event are indicated by highly differentiated genomic loci associating with ecologically relevant phenotypic traits, and/or having a putatively adaptive role across multiple lizard populations. Diverged traits related to head size and shape or bite force showed moderate heritability in a crossing experiment, but between-population differences in these traits did not persist in a common garden environment. Our results confirm the existence of sufficient additive genetic variance for traits to evolve under selection while also demonstrating that phenotypic plasticity and/or genotype by environment interactions are the main drivers of population differentiation at this early evolutionary stage.
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Affiliation(s)
- Iva Sabolić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Óscar Mira
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Débora Y C Brandt
- Department of Integrative Biology, University of Berkeley, Berkeley, California, USA
| | - Duje Lisičić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Jessica Stapley
- Department of Environmental Sciences, ETH Zurich, Zurich, Switzerland
| | - Maria Novosolov
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert Bakarić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivan Cizelj
- Zoological Garden of Zagreb, Zagreb, Croatia
| | - Marko Glogoški
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Maxime Taverne
- C.N.R.S/M.N.H.N., Département d'Ecologie et de Gestion de la Biodiversité, Paris, France
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Rasmus Nielsen
- Department of Integrative Biology, University of Berkeley, Berkeley, California, USA
| | - Anthony Herrel
- C.N.R.S/M.N.H.N., Département d'Ecologie et de Gestion de la Biodiversité, Paris, France
- Department of Biology, Evolutionary Morphology of Vertebrates, Ghent University, Ghent, Belgium
- Department of Biology, University of Antwerp, Wilrijk, Belgium
- Naturhistorisches Museum Bern, Bern, Switzerland
| | - Anamaria Štambuk
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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Khan RH, Rhodes JS, Girard IA, Schwartz NE, Garland T. Does Behavior Evolve First? Correlated Responses to Selection for Voluntary Wheel-Running Behavior in House Mice. ECOLOGICAL AND EVOLUTIONARY PHYSIOLOGY 2024; 97:97-117. [PMID: 38728689 DOI: 10.1086/730153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
AbstractHow traits at multiple levels of biological organization evolve in a correlated fashion in response to directional selection is poorly understood, but two popular models are the very general "behavior evolves first" (BEF) hypothesis and the more specific "morphology-performance-behavior-fitness" (MPBF) paradigm. Both acknowledge that selection often acts relatively directly on behavior and that when behavior evolves, other traits will as well but most with some lag. However, this proposition is exceedingly difficult to test in nature. Therefore, we studied correlated responses in the high-runner (HR) mouse selection experiment, in which four replicate lines have been bred for voluntary wheel-running behavior and compared with four nonselected control (C) lines. We analyzed a wide range of traits measured at generations 20-24 (with a focus on new data from generation 22), coinciding with the point at which all HR lines were reaching selection limits (plateaus). Significance levels (226 P values) were compared across trait types by ANOVA, and we used the positive false discovery rate to control for multiple comparisons. This meta-analysis showed that, surprisingly, the measures of performance (including maximal oxygen consumption during forced exercise) showed no evidence of having diverged between the HR and C lines, nor did any of the life history traits (e.g., litter size), whereas body mass had responded (decreased) at least as strongly as wheel running. Overall, results suggest that the HR lines of mice had evolved primarily by changes in motivation rather than performance ability at the time they were reaching selection limits. In addition, neither the BEF model nor the MPBF model of hierarchical evolution provides a particularly good fit to the HR mouse selection experiment.
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Wang J, Cheng ZY, Dong YW. Demographic, physiological, and genetic factors linked to the poleward range expansion of the snail Nerita yoldii along the shoreline of China. Mol Ecol 2022; 31:4510-4526. [PMID: 35822322 DOI: 10.1111/mec.16610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 05/23/2022] [Accepted: 07/04/2022] [Indexed: 12/01/2022]
Abstract
Species range shift is one of the most significant consequences of climate change in the Anthropocene. A comprehensive study, including demographic, physiological, and genetic factors linked to poleward range expansion, is crucial for understanding how the expanding population occupies the new habitat. In the present study, we investigated the demographic, physiological, and genetic features of the intertidal gastropod Nerita yoldii, which has extended its northern limit by ~200 km over the former biogeographic break of the Yangtze River Estuary during recent decades. The neutral SNPs data showed that the new marginal populations formed a distinct cluster established by a few founders. Demographic modelling analysis revealed that the new marginal populations experienced a strong genetic bottleneck followed by recent demographic expansion. Successful expansion that overcame the founder effect might be attributed to its high capacity of rapid population growth and multiple introductions. According to the non-neutral SNPs under diversifying selection, there were high levels of heterozygosity in the new marginal populations, which might be beneficial for adapting to the novel thermal conditions. The common garden experiment showed that the new marginal populations have evolved divergent transcriptomic and physiological responses to heat stress, allowing them to occupy and survive in the novel environment. Lower transcriptional plasticity was observed in the new marginal populations. These results suggest a new biogeographic pattern of N. yoldii has formed with the occurrence of demographic, physiologic, and genetic changes, and emphasize the roles of adaptation of marginal populations during range expansion.
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Affiliation(s)
- Jie Wang
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, PR China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Zhi-Yuan Cheng
- State Key Laboratory of Marine Environmental Science, College of Marine and Earth Sciences, Xiamen University, Xiamen, PR China
| | - Yun-Wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, PR China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
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Fuller J, Ferchaud A, Laporte M, Le Luyer J, Davis TB, Côté SD, Bernatchez L. Absence of founder effect and evidence for adaptive divergence in a recently introduced insular population of white‐tailed deer (
Odocoileus virginianus
). Mol Ecol 2019; 29:86-104. [DOI: 10.1111/mec.15317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Jérémie Fuller
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Jérémy Le Luyer
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | | | - Steeve D. Côté
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
| | - Louis Bernatchez
- Département de Biologie Université Laval Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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Franks SJ. A harvest of weeds yields insight into a case of contemporary evolution. Mol Ecol 2019; 25:4421-3. [PMID: 27634049 DOI: 10.1111/mec.13791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/21/2016] [Indexed: 12/25/2022]
Abstract
When Charles Darwin was exploring the idea of evolution via natural selection, he looked to domesticated species, with the opening chapter of The Origin of Species titled 'Variation Under Domestication' (Darwin ). Domesticated species such as crops are a great example of artificial selection, which Darwin realized was analogous to natural selection. But growing among those carefully selected crop varieties are the unwelcome and unwanted plants we call weeds. Despite the importance of weeds and long-standing interest in their evolution (Baker ), we still know little about how agricultural weeds evolve, and we often fail to take evolution into account when attempting to manage them (Neve et al. ). Agricultural weeds are subjected to the unique conditions of farm fields, such as frequent soil disturbance and the addition of water and nutrients. They are also confronted with aggressive attempts at their removal via herbicides and mechanical means. As such, they are under intense demographic and selective pressure and can potentially rapidly evolve in response. In this issue of Molecular Ecology, Kuester and co-authors make a rare attempt to understand contemporary evolution in an agricultural weed (Kuester et al. ). They do so using the powerful resurrection approach of comparing ancestors and descendants under common conditions (Franks et al. ). They sampled multiple populations of the weedy plant Ipomoea purpurea at two points in time. A comparison of these greenhouse-grown ancestor and descendent populations showed that, over time, populations had lost significant levels of neutral genetic diversity, consistent with genetic bottlenecks. The authors also found a slight increase, on average, of resistance to the herbicide glyphosate, which is the active ingredient in Roundup(®) . This work is one of a growing number of studies demonstrating rapid evolution in natural populations (Thompson ) and also reveals evidence of both selection and drift in populations of an agricultural weed.
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Affiliation(s)
- Steven J Franks
- Department of Biological Sciences, Fordham University, 160 Larkin Hall, 441 E. Fordham Road, Bronx, NY, 10458, USA.
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Signor SA, New FN, Nuzhdin S. A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants. Genome Biol Evol 2018; 10:189-206. [PMID: 29228179 PMCID: PMC5767965 DOI: 10.1093/gbe/evx262] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 01/03/2023] Open
Abstract
The rapidly expanding availability of large NGS data sets provides an opportunity to investigate population genetics at an unprecedented scale. Drosophila simulans is the sister species of the model organism Drosophila melanogaster, and is often presumed to share similar demographic history. However, previous population genetic and ecological work suggests very different signatures of selection and demography. Here, we sequence a new panel of 170 inbred genotypes of a North American population of D. simulans, a valuable complement to the DGRP and other D. melanogaster panels. We find some unexpected signatures of demography, in the form of excess intermediate frequency polymorphisms. Simulations suggest that this is possibly due to a recent population contraction and selection. We examine the outliers in the D. simulans genome determined by a haplotype test to attempt to parse the contribution of demography and selection to the patterns observed in this population. Untangling the relative contribution of demography and selection to genomic patterns of variation is challenging, however, it is clear that although D. melanogaster was thought to share demographic history with D. simulans different forces are at work in shaping genomic variation in this population of D. simulans.
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Affiliation(s)
- Sarah A Signor
- Department of Molecular and Computational Biology, University of Southern California
| | - Felicia N New
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine
| | - Sergey Nuzhdin
- Department of Molecular and Computational Biology, University of Southern California
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Perrier C, Ferchaud AL, Sirois P, Thibault I, Bernatchez L. Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish. Mol Ecol 2017; 26:6317-6335. [PMID: 29024140 DOI: 10.1111/mec.14361] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 01/01/2023]
Abstract
Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated with lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated with inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated with inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.
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Affiliation(s)
- Charles Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Pascal Sirois
- Chaire de Recherche sur les Espèces Aquatiques Exploitées, Laboratoire des Sciences Aquatiques, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Isabel Thibault
- Direction de l'expertise sur la Faune Aquatique, Ministère des Forêts de la Faune et des Parcs du Québec, Québec, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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Convergent and divergent genetic changes in the genome of Chinese and European pigs. Sci Rep 2017; 7:8662. [PMID: 28819228 PMCID: PMC5561219 DOI: 10.1038/s41598-017-09061-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/20/2017] [Indexed: 01/17/2023] Open
Abstract
Since 10,000 BC, continuous human selection has led to intense genetic and phenotypic changes in pig (Sus scrofa) domestication. Through whole genome analysis of 257 individuals, we demonstrated artificial unidirectional and bidirectional selection as the primary force to shape the convergent and divergent changes between Chinese domestic pigs (CHD) and European domestic pigs (EUD). We identified 31 genes in unidirectional selection regions that might be related to fundamental domestication requirements in pigs. And these genes belong predominantly to categories related to the nervous system, muscle development, and especially to metabolic diseases. In addition, 35 genes, representing different breeding preference, were found under bidirectional selection for the distinct leanness and reproduction traits between CHD and EUD. The convergent genetic changes, contributing physical and morphological adaption, represent the common concerns on pig domestication. And the divergent genetic changes reflect distinct breeding goals between Chinese and European pigs. Using ITPR3, AHR and NMU as examples, we explored and validated how the genetic variations contribute to the phenotype changes.
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Hermes C, Döpper A, Schaefer HM, Segelbacher G. Effects of forest fragmentation on the morphological and genetic structure of a dispersal-limited, endangered bird species. NATURE CONSERVATION 2016. [DOI: 10.3897/natureconservation.16.10905] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Brauer CJ, Hammer MP, Beheregaray LB. Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin. Mol Ecol 2016; 25:5093-5113. [DOI: 10.1111/mec.13830] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory School of Biological Sciences Flinders University Adelaide SA 5042 Australia
| | - Michael P. Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory Darwin NT 0801 Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory School of Biological Sciences Flinders University Adelaide SA 5042 Australia
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