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Chaparro-Pedraza PC. Differential Stage-Specific Mortality as a Mechanism for Diversification. Am Nat 2024; 204:E28-E41. [PMID: 39008841 DOI: 10.1086/730446] [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] [Indexed: 07/17/2024]
Abstract
AbstractIndividual variability in mortality is widespread in nature. The general rule is that larger organisms have a greater chance of survival than smaller conspecifics. There is growing evidence that differential mortality between developmental stages has important consequences for the ecology and evolution of populations and communities. However, we know little about how it can influence diversification. Using an eco-evolutionary model of diversification that considers individual variability in mortality, I show that commonly observed differences in mortality between juveniles and adults can facilitate adaptive diversification. In particular, diversification is expected to be less restricted when mortality is more biased toward juveniles. Additionally, I find stage-specific differences in metabolic cost and foraging capacity to further facilitate diversification when adults are slightly superior competitors, due to either a lower metabolic cost or a higher foraging capacity, than juveniles. This is because by altering the population composition, differential stage-specific mortality and competitive ability can modulate the strength of intraspecific competition, which in turn determines the outcome of diversification. These results demonstrate the strong influence that ecological differences between developmental stages have on diversification and highlight the need for integrating developmental processes into diversification theory.
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2
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Keagy J, Hofmann HA, Boughman JW. Mate choice in the brain: species differ in how male traits 'turn on' gene expression in female brains. Proc Biol Sci 2024; 291:20240121. [PMID: 39079663 PMCID: PMC11288669 DOI: 10.1098/rspb.2024.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/21/2024] [Indexed: 08/03/2024] Open
Abstract
Mate choice plays a fundamental role in speciation, yet we know little about the molecular mechanisms that underpin this crucial decision-making process. Stickleback fish differentially adapted to limnetic and benthic habitats are reproductively isolated and females of each species use different male traits to evaluate prospective partners and reject heterospecific males. Here, we integrate behavioural data from a mate choice experiment with gene expression profiles from the brains of females actively deciding whether to mate. We find substantial gene expression variation between limnetic and benthic females, regardless of behavioural context, suggesting general divergence in constitutive gene expression patterns, corresponding to their genetic differentiation. Intriguingly, female gene co-expression modules covary with male display traits but in opposing directions for sympatric populations of the two species, suggesting male displays elicit a dynamic neurogenomic response that reflects known differences in female preferences. Furthermore, we confirm the role of numerous candidate genes previously implicated in female mate choice in other species, suggesting evolutionary tinkering with these conserved molecular processes to generate divergent mate preferences. Taken together, our study adds important new insights to our understanding of the molecular processes underlying female decision-making critical for generating sexual isolation and speciation.
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Affiliation(s)
- Jason Keagy
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Hans A. Hofmann
- Department of Integrative Biology, Institute for Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
| | - Janette W. Boughman
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
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3
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Pokrovac I, Rohner N, Pezer Ž. The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization. Mol Ecol 2024; 33:e17339. [PMID: 38556927 DOI: 10.1111/mec.17339] [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: 01/09/2024] [Revised: 03/16/2024] [Accepted: 03/22/2024] [Indexed: 04/02/2024]
Abstract
Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read-depth approach, we detected CNVs from previously re-sequenced genomes of 44 individuals belonging to two ancestral surfaces and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype-divergent CNVs are multiallelic and display copy number increases in cavefish compared to surface fish. Our findings suggest that multiallelic CNVs - including gene duplications - and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life.
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Affiliation(s)
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
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4
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DeHaan LM, Burns MD, Egan JP, Bloom DD. Diadromy Drives Elevated Rates of Trait Evolution and Ecomorphological Convergence in Clupeiformes (Herring, Shad, and Anchovies). Am Nat 2023; 202:830-850. [PMID: 38033182 DOI: 10.1086/726894] [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] [Indexed: 12/02/2023]
Abstract
AbstractMigration can have a profound influence on rates and patterns of phenotypic evolution. Diadromy is the migration between marine and freshwater habitats for feeding and reproduction that can require individuals to travel tens to thousands of kilometers. The high energetic demands of diadromy are predicted to select for ecomorphological traits that maximize swimming and locomotor efficiency. Intraspecific studies have shown repeated instances of divergence among diadromous and nondiadromous populations in locomotor and foraging traits, which suggests that at a macroevolutionary scale diadromous lineages may experience convergent evolution onto one or multiple adaptive optima. We tested for differences in rates and patterns of phenotypic evolution among diadromous and nondiadromous lineages in Clupeiformes, a clade that has evolved diadromy more than 10 times. Our results show that diadromous clupeiforms show convergent evolution for some locomotor traits and faster rates of evolution, which we propose are adaptive responses to the locomotor demands of migration. We also find evidence that diadromous lineages show convergence into multiple regions of multivariate trait space and suggest that these respective trait spaces are associated with differences in migration and trophic ecology. However, not all locomotor traits and no trophic traits show evidence of convergence or elevated rates of evolution associated with diadromy. Our results show that long-distance migration influences the tempo and patterns of phenotypic evolution at macroevolutionary scales, but there is not a single diadromous syndrome.
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5
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Wei M, Liu J, Wang S, Wang X, Liu H, Ma Q, Wang J, Shi W. Genetic Diversity and Phylogenetic Analysis of Zygophyllum loczyi in Northwest China's Deserts Based on the Resequencing of the Genome. Genes (Basel) 2023; 14:2152. [PMID: 38136974 PMCID: PMC10742952 DOI: 10.3390/genes14122152] [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: 10/01/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
In order to study the genetics of local adaptation in all main deserts of northwest China, whole genomes of 169 individuals were resequenced, which covers 20 populations of Zygophyllum loczyi (Zygophyllales: Zygophylaceae). We describe more than 15 million single nucleotide polymorphisms and numerous InDels. The expected heterozygosity and PIC values associated with local adaptation varied significantly across biogeographic regions. Variation in environmental factors contributes largely to the population genetic structure of Z. loczyi. Bayesian analysis performed with STRUCTURE defined four genetic clusters, while the results of principle component analysis were similar. Our results shows that the Qaidam Desert group appears to be diverging into two branches characterized by significant geographic separation and gene flow with two neighboring deserts. Geological data assume that it is possible that the Taklamakan Desert was the original distribution site, and Z. loczyi could have migrated later on and expanded within other desert areas. The above findings provide insights into the processes involved in biogeography, phylogeny, and differentiation within the northwest deserts of China.
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Affiliation(s)
- Mengmeng Wei
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingdian Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Suoming Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Xiyong Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
| | - Haisuang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Qing Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
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6
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Bellvert A, Adrián-Serrano S, Macías-Hernández N, Toft S, Kaliontzopoulou A, Arnedo MA. The Non-Dereliction in Evolution: Trophic Specialisation Drives Convergence in the Radiation of Red Devil Spiders (Araneae: Dysderidae) in the Canary Islands. Syst Biol 2023; 72:998-1012. [PMID: 37474131 DOI: 10.1093/sysbio/syad046] [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: 03/30/2022] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/22/2023] Open
Abstract
Natural selection plays a key role in deterministic evolution, as clearly illustrated by the multiple cases of repeated evolution of ecomorphological characters observed in adaptive radiations. Unlike most spiders, Dysdera species display a high variability of cheliceral morphologies, which has been suggested to reflect different levels of specialization to feed on isopods. In this study, we integrate geometric morphometrics and experimental trials with a fully resolved phylogeny of the highly diverse endemic species from the Canary Islands to 1) quantitatively delimit the different cheliceral morphotypes present in the archipelago, 2) test their association with trophic specialization, as reported for continental species, 3) reconstruct the evolution of these ecomorphs throughout the diversification of the group, 4) test the hypothesis of convergent evolution of the different morphotypes, and 5) examine whether specialization constitutes a case of evolutionary irreversibility in this group. We show the existence of 9 cheliceral morphotypes and uncovered their significance for trophic ecology. Further, we demonstrate that similar ecomorphs evolved multiple times in the archipelago, providing a novel study system to explain how convergent evolution and irreversibility due to specialization may be combined to shape phenotypic diversification in adaptive radiations.
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Affiliation(s)
- Adrià Bellvert
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Silvia Adrián-Serrano
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Nuria Macías-Hernández
- Department of Animal Biology, Edaphology and Geology, Universidad de La Laguna, Tenerife, Canary Islands, Spain
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, University of Helsinki, Finland
| | - Søren Toft
- Department of Biology, Aarhus University, Ny Munkegade 116, DK-8000 Århus C, Denmark
| | - Antigoni Kaliontzopoulou
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Miquel A Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal, 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
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Levin B, Komarova A, Simonov E, Tiunov A, Levina M, Golubtsov A, Kondrashov F, Meyer A. Speciation and repeated origins of hypertrophied lips in parallel adaptive radiations of cyprinid fish from East Africa. Ecol Evol 2023; 13:e10523. [PMID: 37711500 PMCID: PMC10497736 DOI: 10.1002/ece3.10523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
The evolution of convergent phenotypes is one of the most interesting phenomena of repeated adaptive radiations. Here, we examined the repeated patterns of thick-lipped or "rubberlip" phenotype of cyprinid fish of the genus Labeobarbus discovered in riverine environments of the Ethiopian Highlands, East Africa. To test the adaptive value of thickened lips, identify the ecological niche of the thick-lipped ecomorphs, and test whether these ecomorphs are the products of adaptive divergence, we studied six sympatric pairs of ecomorphs with hypertrophied lips and the normal lip structure from different riverine basins. Trophic morphology, diet, stable isotope (δ15N and δ13C) signatures, as well as mtDNA markers and genome-wide SNP variation, were analyzed. Our results show that thick-lipped ecomorphs partition trophic resources with generalized ecomorphs in only one-half of the examined sympatric pairs despite the pronounced divergence in lip structure. In these thick-lipped ecomorphs that were trophically diverged, the data on their diet along with the elevated 15N values suggest an invertivorous specialization different from the basal omnivorous-detritivouros feeding mode of the generalized ecomorphs. Genetic data confirmed an independent and parallel origin of all six lipped ecomorphs. Yet, only one of those six thick-lipped ecomorphs had a notable genetic divergence with sympatric non-lipped ecomorphs based on nuclear SNPs data (F ST = 0.21). Sympatric pairs can be sorted by combinations of phenotypic, ecological, and genetic divergence from an ecologically non-functional mouth polymorphism via ecologically functional polymorphism to a matured speciation stage via divergent evolution.
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Affiliation(s)
- Boris Levin
- Papanin Institute for Biology of Inland WatersRussian Academy of SciencesYaroslavlRussia
- Zoological Institute of Russian Academy of SciencesSaint‐PetersburgRussia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
| | - Aleksandra Komarova
- Papanin Institute for Biology of Inland WatersRussian Academy of SciencesYaroslavlRussia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
| | - Evgeniy Simonov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
| | - Alexei Tiunov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
| | - Marina Levina
- Papanin Institute for Biology of Inland WatersRussian Academy of SciencesYaroslavlRussia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
- Eco‐Analytical LaboratoryCherepovets State UniversityCherepovetsRussia
| | - Alexander Golubtsov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
| | | | - Axel Meyer
- Department of BiologyUniversity of KonstanzKonstanzGermany
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8
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Safian D, Ahmed M, van Kruistum H, Furness AI, Reznick DN, Wiegertjes GF, Pollux BJ. Repeated independent origins of the placenta reveal convergent and divergent organ evolution within a single fish family (Poeciliidae). SCIENCE ADVANCES 2023; 9:eadf3915. [PMID: 37611099 PMCID: PMC10446500 DOI: 10.1126/sciadv.adf3915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/24/2023] [Indexed: 08/25/2023]
Abstract
An outstanding question in biology is to what extent convergent evolution produces similar, but not necessarily identical, complex phenotypic solutions. The placenta is a complex organ that repeatedly evolved in the livebearing fish family Poeciliidae. Here, we apply comparative approaches to test whether evolution has produced similar or different placental phenotypes in the Poeciliidae and to what extent these phenotypes correlate with convergence at the molecular level. We show the existence of two placental phenotypes characterized by distinctly different anatomical adaptations (divergent evolution). Furthermore, each placental phenotype independently evolved multiple times across the family, providing evidence for repeated convergence. Moreover, our comparative genomic analysis revealed that the genomes of species with different placentas are evolving at a different pace. Last, we show that the two placental phenotypes correlate with two previously described contrasting life-history optima. Our results argue for high evolvability (both divergent and convergent) of the placenta within a group of closely related species in a single family.
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Affiliation(s)
- Diego Safian
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Evolutionary Developmental Biology Laboratory, The Francis Crick Institute, London, UK
| | - Marwa Ahmed
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Henri van Kruistum
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Animal Breeding and Genomics, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Andrew I. Furness
- U.S. Fish and Wildlife Service, Maryland Fish and Wildlife Conservation Office, Annapolis, MD, USA
| | - David N. Reznick
- Department of Biology, University of California, Riverside, Riverside, CA, USA
| | - Geert F. Wiegertjes
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Bart J.A. Pollux
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
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9
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Gonzalez ST, Alberto F, Molano G. Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs. Evolution 2023; 77:1354-1369. [PMID: 36929706 DOI: 10.1093/evolut/qpad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 02/14/2023] [Accepted: 03/23/2023] [Indexed: 03/18/2023]
Abstract
Giant kelp, Macrocystis pyrifera, exists as distinct morphological variants-or "ecomorphs"-in different populations, yet the mechanism for this variation is uncertain, and environmental drivers for either adaptive or plastic phenotypes have not been identified. The ecomorphs Macrocystis "pyrifera" and M. "integrifolia" are distributed throughout temperate waters of North and South America with almost no geographic overlap and exhibit an incongruous, non-mirrored, distribution across the equator. This study evaluates the degree of genetic divergence between M. "pyrifera" and M. "integrifolia" across 18 populations in Chile and California using whole-genome sequencing and single-nucleotide polymorphism markers. Our results based on a principal component analysis, admixture clustering by genetic similarity, and phylogenetic inference demonstrate that M. "pyrifera" and M. "integrifolia" are genetically distinguishable. Analyses reveal separation by Northern and Southern Hemispheres and between morphs within hemispheres, suggesting that the convergent "integrifolia" morphology arose separately in each hemisphere. This is the first study to use whole-genome sequencing to understand genetic divergence in giant kelp ecomorphs, identifying 83 potential genes under selection and providing novel insights about Macrocystis evolution that were not evident with previous genetic techniques. Future studies are needed to uncover the environmental forces driving local adaptation and presumed convergent evolution of these morphs.
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Affiliation(s)
- Sara T Gonzalez
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, CA, United States
| | - Filipe Alberto
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Gary Molano
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States
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10
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Venkataram S, Kryazhimskiy S. Evolutionary repeatability of emergent properties of ecological communities. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220047. [PMID: 37004728 PMCID: PMC10067272 DOI: 10.1098/rstb.2022.0047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/07/2022] [Indexed: 04/04/2023] Open
Abstract
Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Sandeep Venkataram
- Department of Ecology, Behavior and Evolution, UC San Diego, La Jolla, CA 92093, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, UC San Diego, La Jolla, CA 92093, USA
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11
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Ludt WB, Corbett EC, Kattawar J, Chakrabarty P, Faircloth BC. A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus). G3 (BETHESDA, MD.) 2023; 13:6997878. [PMID: 36683458 PMCID: PMC9997549 DOI: 10.1093/g3journal/jkad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/24/2023]
Abstract
North American sunfishes (Family Centrarchidae) are among the most popular sportfish throughout the United States and Canada. Despite the popularity of sunfishes, their ecological importance, and their extensive stocking and aquacultural history, few molecular studies have examined the evolutionary relationships and species boundaries among members of this group, many of which are known to hybridize. Here, we describe a chromosome-scale genome assembly representing Bluegill (Lepomis macrochirus), one of the most widespread centrarchid species. By combining long-read, Oxford Nanopore sequencing data with short-insert, whole-genome and HiC sequence reads, we produced an assembly (Lm_LA_1.1) having a total length of 889 Mb including 1,841 scaffolds and having a scaffold N50 of 36 Mb, L50 of 12, N90 of 29 Mb, and L90 of 22. We detected 99% (eukaryota_odb10) and 98% (actinopterygii_odb10) universal single-copy orthologs (BUSCOs), and ab initio gene prediction performed using this new assembly identified a set of 17,233 genes that were supported by external (OrthoDB v10) data. This new assembly provides an important addition to the growing set of assemblies already available for spiny-rayed fishes (Acanthomorpha), and it will serve as a resource for future studies that focus on the complex evolutionary history of centrarchids.
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Affiliation(s)
- William B Ludt
- Department of Ichthyology, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | - Eamon C Corbett
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jerry Kattawar
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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12
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Anderson SAS, Weir JT. The role of divergent ecological adaptation during allopatric speciation in vertebrates. Science 2022; 378:1214-1218. [PMID: 36520892 DOI: 10.1126/science.abo7719] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
After decades of debate, biologists today largely agree that most speciation events require an allopatric phase (that is, geographic separation), but the role of adaptive ecological divergence during this critical period is still unknown. Here, we show that relatively few allopatric pairs of birds, mammals, or amphibians exhibit trait differences consistent with models of divergent adaptation in each of many ecologically relevant traits. By fitting new evolutionary models to numerous sets of sister-pair trait differences, we find that speciating and recently speciated allopatric taxa seem to overwhelmingly evolve under similar rather than divergent macro-selective pressures. This contradicts the classical view of divergent adaptation as a prominent driver of the early stages of speciation and helps synthesize two historical controversies regarding the ecology and geography of species formation.
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Affiliation(s)
- Sean A S Anderson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto at Scarborough, Toronto, ON, Canada.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto at Scarborough, Toronto, ON, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
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13
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Anderson SAS, López-Fernández H, Weir JT. Ecology and the origin of non-ephemeral species. Am Nat 2022; 201:619-638. [PMID: 37130236 DOI: 10.1086/723763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractResearch over the past three decades has shown that ecology-based extrinsic reproductive barriers can rapidly arise to generate incipient species-but such barriers can also rapidly dissolve when environments change, resulting in incipient species collapse. Understanding the evolution of unconditional, "intrinsic" reproductive barriers is therefore important for understanding the longer-term buildup of biodiversity. In this article, we consider ecology's role in the evolution of intrinsic reproductive isolation. We suggest that this topic has fallen into a gap between disciplines: while evolutionary ecologists have traditionally focused on the rapid evolution of extrinsic isolation between co-occurring ecotypes, speciation geneticists studying intrinsic isolation in other taxa have devoted little attention to the ecological context in which it evolves. We argue that for evolutionary ecology to close this gap, the field will have to expand its focus beyond rapid adaptation and its traditional model systems. Synthesizing data from several subfields, we present circumstantial evidence for and against different forms of ecological adaptation as promoters of intrinsic isolation and discuss alternative forces that may be significant. We conclude by outlining complementary approaches that can better address the role of ecology in the evolution of nonephemeral reproductive barriers and, by extension, less ephemeral species.
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14
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Fraimout A, Päiviö E, Merilä J. Relaxed risk of predation drives parallel evolution of stickleback behavior. Evolution 2022; 76:2712-2723. [PMID: 36117280 PMCID: PMC9827860 DOI: 10.1111/evo.14631] [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: 01/07/2022] [Revised: 07/14/2022] [Accepted: 07/26/2022] [Indexed: 01/22/2023]
Abstract
The occurrence of similar phenotypes in multiple independent populations derived from common ancestral conditions (viz. parallel evolution) is a testimony of evolution by natural selection. Parallel evolution implies that populations share a common phenotypic response to a common selection pressure associated with habitat similarity. Examples of parallel evolution at genetic and phenotypic levels are fairly common, but the driving selective agents often remain elusive. Similarly, the role of phenotypic plasticity in facilitating early stages of parallel evolution is unclear. We investigated whether the relaxation of predation pressure associated with the colonization of freshwater ponds by nine-spined sticklebacks (Pungitius pungitius) likely explains the divergence in complex behaviors between marine and pond populations, and whether this divergence is parallel. Using laboratory-raised individuals exposed to different levels of perceived predation risk, we calculated vectors of phenotypic divergence for four behavioral traits between habitats and predation risk treatments. We found a significant correlation between the directions of evolutionary divergence and phenotypic plasticity, suggesting that divergence in behavior between habitats is aligned with the response to relaxation of predation pressure. Finally, we show alignment across multiple pairs of populations, and that relaxation of predation pressure has likely driven parallel evolution of behavior in this species.
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Affiliation(s)
- Antoine Fraimout
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinki00014Finland,Area of Ecology and Biodiversity, School of Biological SciencesThe University of Hong KongHong Kong SAR
| | - Elisa Päiviö
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinki00014Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinki00014Finland,Area of Ecology and Biodiversity, School of Biological SciencesThe University of Hong KongHong Kong SAR
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15
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Liu S, Wilson JM, Taylor EB, Richards JG. Freshwater adaptation in prickly sculpin (Pisces: Cottidae): intraspecific comparisons reveal evidence for water pH and Na+ concentration driving diversity in gill H+-ATPase and ionoregulation. J Exp Biol 2022; 225:276687. [PMID: 36062522 DOI: 10.1242/jeb.243500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 08/26/2022] [Indexed: 11/20/2022]
Abstract
Phenotypic divergence is a hallmark of adaptive radiation. One example involves differentiation in physiological traits involved in ion regulation among species with contrasting life-styles and living in distinct environments. Differentiation in ion regulation and its ecological implications among populations within species are, however, less well understood. To address this knowledge gap, we collected prickly sculpin (Cottus asper) from distinct habitat types including coastal rivers connected to estuaries, coastal lakes, and interior lakes, all from British Columbia, Canada. We tested for differences in plasma Na+ and Cl-, gill Na+/K+-ATPase and H+-ATPase activities and protein abundance as well as changes in body mass, and arterial blood pH in fish sampled from the field and acclimated to two different freshwater conditions in the laboratory including artificial lake water (ALW) and ion-poor water (IPW). We also tested for associations between environmental water chemistry and the physiological characteristics associated with ion regulation. Transfer to IPW resulted upregulation in gill Na+/K+-ATPase and H+-ATPase activities as well as increases in gill H+-ATPase protein expression level in each habitat compared with the common ALW treatment. Despite the presence of population-within-habitat type differences, significant habitat-type effects were revealed in most of the ion regulation characteristics examined under different acclimation conditions. Significantly lower plasma Cl- was detected in fish from coastal rivers compared to fish from the other two habitat types during the IPW treatment, which was also significantly lower compared with ALW. Similarly, gill Na+/K+-ATPase activity was lower in the coastal river populations in IPW than in fish from coastal and interior lakes, which was not in accordance with the protein expressed in the gill. For gill H+-ATPase, fish from interior lake populations had the highest level of activity across all habitat types under all conditions, which was related to the protein levels in the gill. The activity of gill H+-ATPase was positively correlated with the combined effect of water Na+ and pH under the ALW treatment. Our results suggest that variation in habitat may be an important factor driving differences in gill Na+/K+-ATPase and H+-ATPase activities across populations of C. asper. Further, the combined effect of water Na+ and pH may have played a key role in physiological adaptation in C. asper during post-glacial freshwater colonization and dispersal.
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Affiliation(s)
- Shuang Liu
- Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Jonathan M Wilson
- Department of Biology, Wilfrid Laurier University, 75 University Ave., Waterloo, ON N2L 3C5, Canada
| | - Eric B Taylor
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Jeffrey G Richards
- Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
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16
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Kennedy SR, Ying Lim J, Ashley Adams S, Krehenwinkel H, Gillespie RG. What is adaptive radiation? Many manifestations of the phenomenon in an iconic lineage of Hawaiian spiders. Mol Phylogenet Evol 2022; 175:107564. [PMID: 35787456 DOI: 10.1016/j.ympev.2022.107564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/27/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022]
Abstract
Adaptive radiation provides the ideal context for identifying and testing the processes that drive evolutionary diversification. However, different adaptive radiations show a variety of different patterns, making it difficult to come up with universal rules that characterize all such systems. Diversification may occur via several mechanisms including non-adaptive divergence, adaptation to novel environments, or character displacement driven by competition. Here, we characterize the ways these different drivers contribute to present-day diversity patterns, using the exemplary adaptive radiation of Hawaiian long-jawed orbweaver (Tetragnatha) spiders. We present the most taxonomically comprehensive phylogenetic hypothesis to date for this group, using 10 molecular markers and representatives from every known species across the archipelago. Among the lineages that make up this remarkable radiation, we find evidence for multiple diversification modalities. Several clades appear to have diversified in allopatry under a narrow range of ecological conditions, highlighting the role of niche conservatism in speciation. Others have shifted into new environments and evolved traits that appear to be adaptive in those environments. Still others show evidence for character displacement by close relatives, often resulting in convergent evolution of stereotyped ecomorphs. All of the above mechanisms seem to have played a role in giving rise to the exceptional diversity of morphological, ecological and behavioral traits represented among the many species of Hawaiian Tetragnatha. Taking all these processes into account, and testing how they operate in different systems, may allow us to identify universal principles underlying adaptive radiation.
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Affiliation(s)
| | - Jun Ying Lim
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Seira Ashley Adams
- Department of Environmental Science, Policy and Management, University of California Berkeley, USA
| | | | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California Berkeley, USA
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17
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Thompson KA, Schluter D. Heterosis counteracts hybrid breakdown to forestall speciation by parallel natural selection. Proc Biol Sci 2022; 289:20220422. [PMID: 35506223 PMCID: PMC9065978 DOI: 10.1098/rspb.2022.0422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In contrast to ecological speciation, where reproductive isolation evolves as a consequence of divergent natural selection, speciation by parallel natural selection has been less thoroughly studied. To test whether parallel evolution drives speciation, we leveraged the repeated evolution of benthic and limnetic ecotypes of threespine stickleback fish and estimated fitness for pure crosses and within-ecotype hybrids in semi-natural ponds and in laboratory aquaria. In ponds, we detected hybrid breakdown in both ecotypes but this was counterbalanced by heterosis and the strength of post-zygotic isolation was nil. In aquaria, we detected heterosis in limnetic crosses and breakdown in benthic crosses, which is suggestive of process- and ecotype-specific environment-dependence. In ponds, heterosis and breakdown were three times greater in limnetic crosses than in benthic crosses, contrasting the prediction that the fitness consequences of hybridization should be greater in crosses among more derived ecotypes. Consistent with a primary role for stochastic processes, patterns differed among crosses between populations from different lakes. Yet, the observation of qualitatively similar patterns of heterosis and hybrid breakdown for both ecotypes when averaging the lake pairs indicates that the outcome of hybridization is repeatable in a general sense.
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Affiliation(s)
- Ken A. Thompson
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dolph Schluter
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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18
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Masonick P, Meyer A, Hulsey CD. Phylogenomic analyses show repeated evolution of hypertrophied lips among Lake Malawi cichlid fishes. Genome Biol Evol 2022; 14:6568296. [PMID: 35417557 PMCID: PMC9017819 DOI: 10.1093/gbe/evac051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2022] [Indexed: 11/27/2022] Open
Abstract
Cichlid fishes have repeatedly evolved an astounding diversity of trophic morphologies. For example, hypertrophied lips have evolved multiple times in both African and Neotropical cichlids and could have even evolved convergently within single species assemblages such as African Lake Malawi cichlids. However, the extremely high diversification rate in Lake Malawi cichlids and extensive potential for hybridization has cast doubt on whether even genome-level phylogenetic reconstructions could delineate if these types of adaptations have evolved once or multiple times. To examine the evolution of this iconic trait using protein-coding and noncoding single nucleotide polymorphisms (SNPs), we analyzed the genomes of 86 Lake Malawi cichlid species, including 33 de novo resequenced genomes. Surprisingly, genome-wide protein-coding SNPs exhibited enough phylogenetic informativeness to reconstruct interspecific and intraspecific relationships of hypertrophied lip cichlids, although noncoding SNPs provided better support. However, thinning of noncoding SNPs indicated most discrepancies come from the relatively smaller number of protein-coding sites and not from fundamental differences in their phylogenetic informativeness. Both coding and noncoding reconstructions showed that several “sand-dwelling” hypertrophied lip species, sampled intraspecifically, form a clade interspersed with a few other nonhypertrophied lip lineages. We also recovered Abactochromis labrosus within the rock-dwelling “mbuna” lineage, starkly contrasting with the affinities of other hypertrophied lip taxa found in the largely sand-dwelling “nonmbuna” component of this radiation. Comparative analyses coupled with tests for introgression indicate there is no widespread introgression between the hypertrophied lip lineages and taken together suggest this trophic phenotype has likely evolved at least twice independently within-lake Malawi.
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Affiliation(s)
- Paul Masonick
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - C Darrin Hulsey
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany.,Current Address: School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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19
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Blain SA, Chavarie L, Kinney MH, Schluter D. A test of frequency‐dependent selection in the evolution of a generalist phenotype. Ecol Evol 2022; 12:e8831. [PMID: 35432932 PMCID: PMC9006234 DOI: 10.1002/ece3.8831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/30/2022] [Accepted: 02/04/2022] [Indexed: 11/14/2022] Open
Abstract
A solitary population of consumers frequently evolves to the middle of a resource gradient and an intermediate mean phenotype compared to a sympatric pair of competing species that diverge to either side via character displacement. The forces governing the distribution of phenotypes in these allopatric populations, however, are little investigated. Theory predicts that the intermediate mean phenotype of the generalist should be maintained by negative frequency‐dependent selection, whereby alternate extreme phenotypes are favored because they experience reduced competition for resources when rare. However, the theory makes assumptions that are not always met, and alternative explanations for an intermediate phenotype are possible. We provide a test of this prediction in a mesocosm experiment using threespine stickleback that are ecologically and phenotypically intermediate between the more specialized stickleback species that occur in pairs. We manipulated the frequency distribution of phenotypes in two treatments and then measured effects on a focal intermediate population. We found a slight frequency‐dependent effect on survival in the predicted direction but not on individual growth rates. This result suggests that frequency‐dependent selection might be a relatively weak force across the range of phenotypes within an intermediate population and we suggest several general reasons why this might be so. We propose that allopatric populations might often be maintained at an intermediate phenotype instead by stabilizing or fluctuating directional selection.
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Affiliation(s)
- Stephanie A. Blain
- Department of Zoology and Biodiversity Research Center University of British Columbia Vancouver British Columbia Canada
| | - Louise Chavarie
- Department of Zoology and Biodiversity Research Center University of British Columbia Vancouver British Columbia Canada
- Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Ås Norway
| | - Mackenzie H. Kinney
- Department of Zoology and Biodiversity Research Center University of British Columbia Vancouver British Columbia Canada
| | - Dolph Schluter
- Department of Zoology and Biodiversity Research Center University of British Columbia Vancouver British Columbia Canada
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20
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Wang Z, Jiang Y, Yang X, Bi H, Li J, Mao X, Ma Y, Ru D, Zhang C, Hao G, Wang J, Abbott RJ, Liu J. Molecular signatures of parallel adaptive divergence causing reproductive isolation and speciation across two genera. Innovation (N Y) 2022; 3:100247. [PMID: 35519515 PMCID: PMC9065898 DOI: 10.1016/j.xinn.2022.100247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/16/2022] [Indexed: 11/18/2022] Open
Abstract
Parallel evolution of reproductive isolation (PERI) provides strong evidence for natural selection playing a fundamental role in the origin of species. However, PERI has been rarely demonstrated for well established species drawn from different genera. In particular, parallel molecular signatures for the same genes in response to similar habitat divergence in such different lineages is lacking. Here, based on whole-genome sequencing data, we first explore the speciation process in two sister species of Carpinus (Betulaceae) in response to divergence for temperature and soil-iron concentration in habitats they occupy in northern and southwestern China, respectively. We then determine whether parallel molecular mutations occur during speciation in this pair of species and also in another sister-species pair of the related genus, Ostryopsis, which occupy similarly divergent habitats in China. We show that gene flow occurred during the origin of both pairs of sister species since approximately 9.8 or approximately 2 million years ago, implying strong natural selection during divergence. Also, in both species pairs we detected concurrent positive selection in a gene (LHY) for flowering time and in two paralogous genes (FRO4 and FRO7) of a gene family known to be important for iron tolerance. These changes were in addition to changes in other major genes related to these two traits. The different alleles of these particular candidate genes possessed by the sister species of Carpinus were functionally tested and indicated likely to alter flowering time and iron tolerance as previously demonstrated in the pair of Ostryopsis sister species. Allelic changes in these genes may have effectively resulted in high levels of prezygotic reproductive isolation to evolve between sister species of each pair. Our results show that PERI can occur in different genera at different timescales and involve similar signatures of molecular evolution at genes or paralogues of the same gene family, causing reproductive isolation as a consequence of adaptation to similarly divergent habitats. PERI provides strong evidence for natural selection playing a fundamental role in the origin of species PERI is rarely demonstrated for well-established species drawn from different genera We detected PERI across two genera (Carpinus and Ostryopsis) in the family Betulaceae PERI can occur in different genera at different timescales and involve molecular signatures at similar pathways
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Affiliation(s)
- Zefu Wang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xiaoyue Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hao Bi
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jialiang Li
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xingxing Mao
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yazhen Ma
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Cheng Zhang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Guoqian Hao
- Sichuan Tea College, Yibin University, Yibin 644000, China
| | - Jing Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | | | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Corresponding author
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21
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Gao W, Yu CX, Zhou WW, Zhang BL, Chambers EA, Dahn HA, Jin JQ, Murphy RW, Zhang YP, Che J. Species persistence with hybridization in toad-headed lizards driven by divergent selection and low recombination. Mol Biol Evol 2022; 39:6561330. [PMID: 35356979 PMCID: PMC9007161 DOI: 10.1093/molbev/msac064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Speciation plays a central role in evolutionary studies, and particularly how reproductive isolation (RI) evolves. The origins and persistence of RI are distinct processes that require separate evaluations. Treating them separately clarifies the drivers of speciation and then it is possible to link the processes to understand large-scale patterns of diversity. Recent genomic studies have focused predominantly on how species or RI originate. However, we know little about how species persist in face of gene flow. Here, we evaluate a contact zone of two closely related toad-headed lizards (Phrynocephalus) using a chromosome-level genome assembly and population genomics. To some extent, recent asymmetric introgression from Phrynocephalus putjatai to P. vlangalii reduces their genomic differences. However, their highly divergent regions (HDRs) have heterogeneous distributions across the genomes. Functional gene annotation indicates that many genes within HDRs are involved in reproduction and RI. Compared with allopatric populations, contact areas exhibit recent divergent selection on the HDRs and a lower population recombination rate. Taken together, this implies that divergent selection and low genetic recombination help maintain RI. This study provides insights into the genomic mechanisms that drive RI and two species persistence in the face of gene flow during the late stage of speciation.
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Affiliation(s)
- Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chuan-Xin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, University of Texas at Austin, Austin, USA.,Department of Environmental Science, Policy, and Management, Univerity of California, Berkeley, USA
| | - Hollis A Dahn
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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22
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Tolley KA, Tilbury CR, Burger M. Convergence and vicariance: speciation of chameleons in the Cape Fold Mountains, South Africa, and the description of three new species of Bradypodion Fitzinger, 1843. AFR J HERPETOL 2022. [DOI: 10.1080/21564574.2021.1998236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Krystal A Tolley
- South African National Biodiversity Institute, Claremont, Cape Town, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Colin R Tilbury
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - Marius Burger
- African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
- Flora Fauna & Man, Ecological Services Ltd., Tortola, British Virgin Islands
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23
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Thompson KA, Peichel CL, Rennison DJ, McGee MD, Albert AYK, Vines TH, Greenwood AK, Wark AR, Brandvain Y, Schumer M, Schluter D. Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent. PLoS Biol 2022; 20:e3001469. [PMID: 35007278 PMCID: PMC8746713 DOI: 10.1371/journal.pbio.3001469] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/04/2021] [Indexed: 12/25/2022] Open
Abstract
Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are "intrinsic," meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse-albeit indirect-signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.
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Affiliation(s)
- Ken A. Thompson
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
| | - Catherine L. Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diana J. Rennison
- Division of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Matthew D. McGee
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Timothy H. Vines
- DataSeer Research Data Services, Vancouver, British Columbia, Canada
| | | | - Abigail R. Wark
- Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Maryland, United States of America
| | - Dolph Schluter
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
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24
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Salisbury SJ, Ruzzante DE. Genetic Causes and Consequences of Sympatric Morph Divergence in Salmonidae: A Search for Mechanisms. Annu Rev Anim Biosci 2021; 10:81-106. [PMID: 34758272 DOI: 10.1146/annurev-animal-051021-080709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such morphs are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning speciation. Such insight is also critical for conserving salmonid diversity, the loss of which could have significant ecological and economic consequences. Our review suggests that genetic differentiation among sympatric morphs is largely nonparallel apart from a few key genes that may be critical for consistently driving morph differentiation. We discuss alternative levels of parallelism likely underlying consistent morph differentiation and identify several factors that may temper this incipient speciation between sympatric morphs, including glacial history and contemporary selective pressures. Our synthesis demonstrates that salmonids are useful for studying speciation and poses additional research questions to be answered by future study of this family. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- S J Salisbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
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Wood ZT, Lopez LK, Symons CC, Robinson RR, Palkovacs EP, Kinnison MT. Drivers and cascading ecological consequences of Gambusia affinis trait variation. Am Nat 2021; 199:E91-E110. [DOI: 10.1086/717866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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26
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Mehner T, Palm S, Delling B, Karjalainen J, Kiełpińska J, Vogt A, Freyhof J. Genetic relationships between sympatric and allopatric Coregonus ciscoes in North and Central Europe. BMC Ecol Evol 2021; 21:186. [PMID: 34615463 PMCID: PMC8496053 DOI: 10.1186/s12862-021-01920-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/29/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Sympatric speciation along ecological gradients has been studied repeatedly, in particular in freshwater fishes. Rapid post-glacial ecological divergence has resulted in numerous endemic species or ecologically distinct populations in lakes of the temperate zones. Here, we focus on the Baltic cisco (Coregonus albula) complex, to study the genetic similarity among two pairs of sympatric autumn- and spring-spawning populations from post-glacial German Lakes Stechlin and Breiter Luzin. For comparison, we included a similar pair of sympatric populations from the Swedish Lake Fegen. We wanted to explore potential genetic similarities between the three sympatric cisco population pairs in the three lakes, to evaluate whether the pairs may have emerged independently in the three lakes, or whether two different species may have colonized all three lakes independently. Furthermore, we considered allopatric C. albula populations from three Polish, three Finnish, and four Swedish locations, added one Siberian population of the sister species C. sardinella and a Swedish C. maraena (whitefish) population. By genotyping nine microsatellite markers in 655 individuals from these 18 populations, we wanted to elucidate how strongly the cisco populations differ across a larger geographical area within Europe. Finally, we compared the genetic differences between the spring- and autumn-spawning populations of ciscoes in the two German lakes to infer the potentially deteriorating effect of strong anthropogenic pressure on the lakes. RESULTS Dendrogram, Principal Coordinate Analysis and admixture analysis all indicated strong correspondence between population differentiation and geographical location for most cisco populations in Europe, including the Siberian population of C. sardinella. However, populations from some Swedish lakes deviated from this general pattern, by showing a distinct genetic structure. We found evidence for independent evolution of the three sympatric population pairs, because the populations co-occurring in the same lake were always most closely related. However, genetic differentiation was weak in the two German population pairs, but strong in the Swedish Lake Fegen, indicating that the weak differentiation in the German pairs reported earlier has eroded further. CONCLUSIONS Our results suggest that the genetic differentiation at neutral genetic markers among populations of the Baltic cisco complex has evolved (and is maintained) by random genetic drift in isolated populations. However, earlier studies on the Swedish populations combining mitochondrial DNA and microsatellite data indicate that also post-glacial immigration from separate glacial refugia has shaped the present genetic population structure. The low neutral differentiation of the German sympatric pairs in contrast to the Swedish pair suggests that recent anthropogenic effects on the lakes in Germany may put the endemic spring-spawners at risk to extinction.
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Affiliation(s)
- Thomas Mehner
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany.
| | - Stefan Palm
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | - Bo Delling
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Juha Karjalainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Jolanta Kiełpińska
- Department of Aquatic Bioengineering and Aquaculture, Faculty of Food Science and Fisheries, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Asja Vogt
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Jörg Freyhof
- Museum Für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
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27
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Willerth K, Franks E, Mee JA. Parallel and non-parallel divergence within polymorphic populations of brook stickleback, Culaea inconstans (Actinopterygii: Gasterosteidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Studying parallel evolution allows us to draw conclusions about the repeatability of adaptive evolution. Whereas populations likely experience similar selective pressures in similar environments, it is not clear if this will always result in parallel divergence of ecologically relevant traits. Our study investigates the extent of parallelism associated with the evolution of pelvic spine reduction in brook stickleback populations. We find that populations with parallel divergence in pelvic spine morphology do not exhibit parallel divergence in head and body morphology but do exhibit parallel divergence in diet. In addition, we compare these patterns associated with pelvic reduction in brook stickleback to well-studied patterns of divergence between spined and unspined threespine stickleback. Whereas spine reduction is associated with littoral habitats and a benthic diet in threespine stickleback, spine reduction in brook stickleback is associated with a planktonic diet. Hence, we find that pelvic spine divergence is associated with largely non-parallel ecological consequences across species.
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Affiliation(s)
- Kaitlyn Willerth
- Department of Biology, Mount Royal University, Calgary, AB, T3E 6K6, Canada
| | - Emily Franks
- Department of Biology, Mount Royal University, Calgary, AB, T3E 6K6, Canada
| | - Jonathan A Mee
- Department of Biology, Mount Royal University, Calgary, AB, T3E 6K6, Canada
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Zerebecki RA, Sotka EE, Hanley TC, Bell KL, Gehring C, Nice CC, Richards CL, Hughes AR. Repeated Genetic and Adaptive Phenotypic Divergence across Tidal Elevation in a Foundation Plant Species. Am Nat 2021; 198:E152-E169. [DOI: 10.1086/716512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Robyn A. Zerebecki
- Marine Science Center, Northeastern University, Nahant, Massachusetts 01908
- Dauphin Island Sea Lab, Dauphin Island, Alabama 36528
| | - Erik E. Sotka
- Department of Biology and Grice Marine Laboratory, College of Charleston, South Carolina 29412
| | - Torrance C. Hanley
- Marine Science Center, Northeastern University, Nahant, Massachusetts 01908
| | - Katherine L. Bell
- Department of Entomology, University of Maryland, College Park, Maryland 20742
| | - Catherine Gehring
- Department of Biological Science and Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, Arizona 86011
| | - Chris C. Nice
- Department of Biology, Texas State University, San Marcos, Texas 78666
| | - Christina L. Richards
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33617; and Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076 Tübingen, Germany
| | - A. Randall Hughes
- Marine Science Center, Northeastern University, Nahant, Massachusetts 01908
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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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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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31
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Huie JM, Prates I, Bell RC, de Queiroz K. Convergent patterns of adaptive radiation between island and mainland Anolis lizards. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab072] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Uncovering convergent and divergent patterns of diversification is a major goal of evolutionary biology. On four Greater Antillean islands, Anolis lizards have convergently evolved sets of species with similar ecologies and morphologies (ecomorphs). However, it is unclear whether closely related anoles from Central and South America exhibit similar patterns of diversification. We generated an extensive morphological data set to test whether mainland Draconura-clade anoles are assignable to the Caribbean ecomorphs. Based on a new classification framework that accounts for different degrees of morphological support, we found morphological evidence for mainland representatives of all six Caribbean ecomorphs and evidence that many ecomorphs have also evolved repeatedly on the mainland. We also found strong evidence that ground-dwelling anoles from both the Caribbean and the mainland constitute a new and distinct ecomorph class. Beyond the ecomorph concept, we show that the island and mainland anole faunas exhibit exceptional morphological convergence, suggesting that they are more similar than previously understood. However, the island and mainland radiations are not identical, indicating that regional differences and historical contingencies can lead to replicate yet variable radiations. More broadly, our findings suggest that replicated radiations occur beyond island settings more often than previously recognized.
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Affiliation(s)
- Jonathan M Huie
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Ivan Prates
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Herpetology Department, California Academy of Sciences, San Francisco, CA, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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32
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Colella JP, Tigano A, Dudchenko O, Omer AD, Khan R, Bochkov ID, Aiden EL, MacManes MD. Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice. J Hered 2021; 112:286-302. [PMID: 33686424 PMCID: PMC8141686 DOI: 10.1093/jhered/esab009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/27/2021] [Indexed: 01/14/2023] Open
Abstract
Warming climate and increasing desertification urge the identification of genes involved in heat and dehydration tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert-adapted species can highlight parallel or convergent patterns of genome evolution through the identification of shared signatures of selection. We generate a chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for a signature of parallel evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another congeneric desert specialist (Peromyscus eremicus) and a widely distributed habitat generalist (Peromyscus maniculatus), that may be locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of parallel evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in the P. crinitus genome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic tuning (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important for accommodating hot and dry environmental conditions.
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Affiliation(s)
- Jocelyn P Colella
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH.,Hubbard Genome Center, University of New Hampshire, Durham, NH.,Biodiversity Institute, University of Kansas, Lawrence, KS
| | - Anna Tigano
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH.,Hubbard Genome Center, University of New Hampshire, Durham, NH
| | - Olga Dudchenko
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Center for Theoretical and Biological Physics, Rice University, Houston, TX.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX
| | - Arina D Omer
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ruqayya Khan
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX
| | - Ivan D Bochkov
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX
| | - Erez L Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Center for Theoretical and Biological Physics, Rice University, Houston, TX.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.,School of Agriculture and Environment, University of Western Australia, Perth, WA, Australia
| | - Matthew D MacManes
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH.,Hubbard Genome Center, University of New Hampshire, Durham, NH
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33
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Sianta SA, Kay KM. Parallel evolution of phenological isolation across the speciation continuum in serpentine-adapted annual wildflowers. Proc Biol Sci 2021; 288:20203076. [PMID: 33849321 PMCID: PMC8059516 DOI: 10.1098/rspb.2020.3076] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/17/2021] [Indexed: 01/26/2023] Open
Abstract
Understanding the relative importance of reproductive isolating mechanisms across the speciation continuum remains an outstanding challenge in evolutionary biology. Here, we examine a common isolating mechanism, reproductive phenology, between plant sister taxa at different stages of adaptive divergence to gain insight into its relative importance during speciation. We study 17 plant taxa that have independently adapted to inhospitable serpentine soils, and contrast each with a nonserpentine sister taxon to form pairs at either ecotypic or species-level divergence. We use greenhouse-based reciprocal transplants in field soils to quantify how often flowering time (FT) shifts accompany serpentine adaptation, when FT shifts evolve during speciation, and the genetic versus plastic basis of these shifts. We find that genetically based shifts in FT in serpentine-adapted taxa are pervasive regardless of the stage of divergence. Although plasticity increases FT shifts in five of the pairs, the degree of plasticity does not differ when comparing ecotypic versus species-level divergence. FT shifts generally led to significant, but incomplete, reproductive isolation that did not vary in strength by stage of divergence. Our work shows that adaptation to a novel habitat may predictably drive phenological isolation early in the speciation process.
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Affiliation(s)
- Shelley A. Sianta
- Department of Ecology and Evolutionary Biology, University of California, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Kathleen M. Kay
- Department of Ecology and Evolutionary Biology, University of California, 130 McAllister Way, Santa Cruz, CA 95060, USA
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34
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Hudson CM, Lucek K, Marques DA, Alexander TJ, Moosmann M, Spaak P, Seehausen O, Matthews B. Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.611672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.
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35
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Profile of Dolph Schluter. Proc Natl Acad Sci U S A 2021; 118:2025630118. [PMID: 33431698 DOI: 10.1073/pnas.2025630118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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36
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Undin M, Lockhart PJ, Hills SFK, Castro I. Genetic Rescue and the Plight of Ponui Hybrids. FRONTIERS IN CONSERVATION SCIENCE 2021. [DOI: 10.3389/fcosc.2020.622191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Long-term sustainable and resilient populations is a key goal of conservation. How to best achieve this is controversial. There are, for instance, polarized views concerning the fitness and conservation value of hybrid populations founded through multi-origin translocations. A classic example concerns Apteryx (kiwi) in New Zealand. The A. mantelli of Ponui Island constitute a hybrid population where the birds are highly successful in their island habitat. A key dilemma for managers is understanding the reason for this success. Are the hybrid birds of Ponui Island of “no future conservation value” as recently asserted, or do they represent an outstanding example of genetic rescue and an important resource for future translocations? There has been a paradigm shift in scientific thinking concerning hybrids, but the ecological significance of admixed genomes remains difficult to assess. This limits what we can currently predict in conservation science. New understanding from genome science challenges the sufficiency of population genetic models to inform decision making and suggests instead that the contrasting outcomes of hybridization, “outbreeding depression” and “heterosis,” require understanding additional factors that modulate gene and protein expression and how these factors are influenced by the environment. We discuss these findings and the investigations that might help us to better understand the birds of Ponui, inform conservation management of kiwi and provide insight relevant for the future survival of Apteryx.
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37
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Rincon-Sandoval M, Duarte-Ribeiro E, Davis AM, Santaquiteria A, Hughes LC, Baldwin CC, Soto-Torres L, Acero P A, Walker HJ, Carpenter KE, Sheaves M, Ortí G, Arcila D, Betancur-R R. Evolutionary determinism and convergence associated with water-column transitions in marine fishes. Proc Natl Acad Sci U S A 2020; 117:33396-33403. [PMID: 33328271 PMCID: PMC7777220 DOI: 10.1073/pnas.2006511117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Repeatable, convergent outcomes are prima facie evidence for determinism in evolutionary processes. Among fishes, well-known examples include microevolutionary habitat transitions into the water column, where freshwater populations (e.g., sticklebacks, cichlids, and whitefishes) recurrently diverge toward slender-bodied pelagic forms and deep-bodied benthic forms. However, the consequences of such processes at deeper macroevolutionary scales in the marine environment are less clear. We applied a phylogenomics-based integrative, comparative approach to test hypotheses about the scope and strength of convergence in a marine fish clade with a worldwide distribution (snappers and fusiliers, family Lutjanidae) featuring multiple water-column transitions over the past 45 million years. We collected genome-wide exon data for 110 (∼80%) species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological and geological information. We also implemented approaches using genomic subsets to account for phylogenetic uncertainty in comparative analyses. Our results show independent incursions into the water column by ancestral benthic lineages in all major oceanic basins. These evolutionary transitions are persistently associated with convergent phenotypes, where deep-bodied benthic forms with truncate caudal fins repeatedly evolve into slender midwater species with furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. Convergent ecological and functional phenotypes along the benthic-pelagic axis are pervasive among different lineages and across vastly different evolutionary scales, achieving predictable high-fitness solutions for similar environmental challenges, ultimately demonstrating strong determinism in fish body-shape evolution.
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Affiliation(s)
- Melissa Rincon-Sandoval
- Department of Biology, The University of Oklahoma, Norman, OK 73019
- Universidad Nacional de Colombia sede Caribe, Centro de Estudios en Ciencias del Mar (CECIMAR), Santa Marta, Magdalena, Colombia
| | | | - Aaron M Davis
- Centre for Tropical Water and Aquatic Ecosystem Research, School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia
| | | | - Lily C Hughes
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Luisángely Soto-Torres
- Department of Biology, Universidad de Puerto Rico-Rio Piedras, San Juan Puerto Rico, 00931
| | - Arturo Acero P
- Universidad Nacional de Colombia sede Caribe, Centro de Estudios en Ciencias del Mar (CECIMAR), Santa Marta, Magdalena, Colombia
| | - H J Walker
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0244
| | | | - Marcus Sheaves
- Marine Data Technology Hub, James Cook University, Townsville, QLD 4811, Australia
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Dahiana Arcila
- Department of Biology, The University of Oklahoma, Norman, OK 73019
- Department of Ichthyology, Sam Noble Oklahoma Museum of Natural History, Norman, OK
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38
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Härer A, Bolnick DI, Rennison DJ. The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback. Mol Ecol 2020; 30:451-463. [PMID: 33222348 DOI: 10.1111/mec.15746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/21/2020] [Accepted: 11/09/2020] [Indexed: 12/23/2022]
Abstract
The repeated occurrence of similar phenotypes in independent lineages (i.e., parallel evolution) in response to similar ecological conditions can provide compelling insights into the process of adaptive evolution. An intriguing question is to what extent repeated phenotypic changes are underlain by repeated changes at the genomic level and whether patterns of genomic divergence differ with the geographic context in which populations evolve. Here, we combined genomic, morphological and ecological data sets to investigate the genomic signatures of divergence across populations of threespine stickleback (Gasterosteus aculeatus) that adapted to contrasting ecological niches (benthic or limnetic) in either sympatry or allopatry. We found that genome-wide differentiation (FST ) was an order of magnitude higher and substantially more repeatable for sympatric benthic and limnetic specialists compared to allopatric populations with similar levels of ecological divergence. We identified genomic regions consistently differentiated between sympatric ecotypes that were also differentiated between or associated with benthic vs. limnetic niche in allopatric populations. These candidate regions were enriched on three chromosomes known to be involved in the benthic-limnetic divergence of threespine stickleback. Some candidate regions overlapped with QTL for body shape and trophic traits such as gill raker number, traits that strongly differ between benthic and limnetic ecotypes. In summary, our study shows that magnitude and repeatability of genomic signatures of ecological divergence in threespine stickleback highly depend on the geographic context. The identified candidate regions provide starting points to identify functionally important genes for the adaptation to benthic and limnetic niches.
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Affiliation(s)
- Andreas Härer
- Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, USA
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Diana J Rennison
- Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, USA
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39
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Knotek A, Konečná V, Wos G, Požárová D, Šrámková G, Bohutínská M, Zeisek V, Marhold K, Kolář F. Parallel Alpine Differentiation in Arabidopsis arenosa. FRONTIERS IN PLANT SCIENCE 2020; 11:561526. [PMID: 33363550 PMCID: PMC7753741 DOI: 10.3389/fpls.2020.561526] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/16/2020] [Indexed: 05/14/2023]
Abstract
Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbor the alpine ecotype and used SNP genotyping to test for repeated alpine colonization. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makes A. arenosa a promising candidate for studying genomic basis of adaptation.
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Affiliation(s)
- Adam Knotek
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Veronika Konečná
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Guillaume Wos
- Department of Botany, Charles University, Prague, Czechia
| | | | | | - Magdalena Bohutínská
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Vojtěch Zeisek
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Karol Marhold
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Filip Kolář
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, University of Innsbruck, Innsbruck, Austria
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40
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Smolinský R, Baláž V, Nürnberger B. Tadpoles of hybridising fire-bellied toads (B. bombina and B. variegata) differ in their susceptibility to predation. PLoS One 2020; 15:e0231804. [PMID: 33285552 PMCID: PMC7721483 DOI: 10.1371/journal.pone.0231804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/17/2020] [Indexed: 12/02/2022] Open
Abstract
The role of adaptive divergence in the formation of new species has been the subject of much recent debate. The most direct evidence comes from traits that can be shown to have diverged under natural selection and that now contribute to reproductive isolation. Here, we investigate differential adaptation of two fire-bellied toads (Anura, Bombinatoridae) to two types of aquatic habitat. Bombina bombina and B. variegata are two anciently diverged taxa that now reproduce in predator-rich ponds and ephemeral aquatic sites, respectively. Nevertheless, they hybridise extensively wherever their distribution ranges adjoin. We show in laboratory experiments that, as expected, B. variegata tadpoles are at relatively greater risk of predation from dragonfly larvae, even when they display a predator-induced phenotype. These tadpoles spent relatively more time swimming and so prompted more attacks from the visually hunting predators. We argue in the discussion that genomic regions linked to high activity in B. variegata should be barred from introgression into the B. bombina gene pool and thus contribute to gene flow barriers that keep the two taxa from merging into one.
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Affiliation(s)
- Radovan Smolinský
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Vojtech Baláž
- Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Beate Nürnberger
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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41
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Kautt AF, Kratochwil CF, Nater A, Machado-Schiaffino G, Olave M, Henning F, Torres-Dowdall J, Härer A, Hulsey CD, Franchini P, Pippel M, Myers EW, Meyer A. Contrasting signatures of genomic divergence during sympatric speciation. Nature 2020; 588:106-111. [PMID: 33116308 PMCID: PMC7759464 DOI: 10.1038/s41586-020-2845-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/23/2020] [Indexed: 01/25/2023]
Abstract
The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin1,2. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process3. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs4, but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories5. Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.
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Affiliation(s)
- Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Alexander Nater
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gonzalo Machado-Schiaffino
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Functional Biology, Area of Genetics, University of Oviedo, Oviedo, Spain
| | - Melisa Olave
- Department of Biology, University of Konstanz, Konstanz, Germany
- Argentine Dryland Research Institute of the National Council for Scientific Research (IADIZA-CONICET), Mendoza, Argentina
| | - Frederico Henning
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Andreas Härer
- Department of Biology, University of Konstanz, Konstanz, Germany
- Division of Biological Sciences, Section of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, CA, USA
| | - C Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
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42
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Mas A, Lagadeuc Y, Vandenkoornhuyse P. Reflections on the Predictability of Evolution: Toward a Conceptual Framework. iScience 2020; 23:101736. [PMID: 33225244 PMCID: PMC7666346 DOI: 10.1016/j.isci.2020.101736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evolution is generally considered to be unpredictable because genetic variations are known to occur randomly. However, remarkable patterns of repeated convergent evolution are observed, for instance, loss of pigments by organisms living in caves. Analogous phenotypes appear in similar environments, sometimes in response to similar constraints. Alongside randomness, a certain evolutionary determinism also exists, for instance, the selection of particular phenotypes subjected to particular environmental constraints in the “evolutionary funnel.” We pursue the idea that eco-evolutionary specialization is in some way determinist. The conceptual framework of phenotypic changes entailing specialization presented in this essay explains how evolution can be predicted. We also discuss how the predictability of evolution could be tested using the case of metabolic specialization through gene losses. We also put forward that microorganisms could be key models to test and possibly make headway evolutionary predictions and knowledge about evolution.
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Affiliation(s)
- Alix Mas
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
| | - Yvan Lagadeuc
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
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43
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Singh R, Singh BN. Intra- and interspecific sexual isolation in two sibling species of Drosophila: D. ananassae and D. pallidosa. ETHOL ECOL EVOL 2020. [DOI: 10.1080/03949370.2020.1777210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Roshni Singh
- Genetics Laboratory, Institute of Science, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - Bashisth N. Singh
- Genetics Laboratory, Institute of Science, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
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44
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Rohner PT, Macagno ALM, Moczek AP. Evolution and plasticity of morph-specific integration in the bull-headed dung beetle Onthophagus taurus. Ecol Evol 2020; 10:10558-10570. [PMID: 33072280 PMCID: PMC7548182 DOI: 10.1002/ece3.6711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/18/2020] [Accepted: 08/04/2020] [Indexed: 01/01/2023] Open
Abstract
Developmental and evolutionary processes underlying phenotypic variation frequently target several traits simultaneously, thereby causing covariation, or integration, among phenotypes. While phenotypic integration can be neutral, correlational selection can drive adaptive covariation. Especially, the evolution and development of exaggerated secondary sexual traits may require the adjustment of other traits that support, compensate for, or otherwise function in a concerted manner. Although phenotypic integration is ubiquitous, the interplay between genetic, developmental, and ecological conditions in shaping integration and its evolution remains poorly understood. Here, we study the evolution and plasticity of trait integration in the bull-headed dung beetle Onthophagus taurus which is characterized by the polyphenic expression of horned ('major') and hornless ('minor') male morphs. By comparing populations subject to divergent intensities of mate competition, we tested whether mating system shifts affect integration of traits predicted to function in a morph-specific manner. We focussed on fore and hind tibia morphology as these appendages are used to stabilize major males during fights, and on wings, as they are thought to contribute to morph-based differences in dispersal behavior. We found phenotypic integration between fore and hind tibia length and horn length that was stronger in major males, suggesting phenotypic plasticity in integration and potentially secondary sexual trait compensation. Similarly, we observed that fore tibia shape was also integrated with relative horn length. However, although we found population differentiation in wing and tibia shape and allometry, populations did not differ in integration. Lastly, we detected little evidence for morph differences in integration in either tibia or wing shape, although wing allometries differed between morphs. This contrasts with previous studies documenting intraspecific differentiation in morphology, behavior, and allometry as a response to varying levels of mate competition across O. taurus populations. We discuss how sexual selection may shape morph-specific integration, compensation, and allometry across populations.
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45
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Anderson SAS, Weir JT. A Comparative Test for Divergent Adaptation: Inferring Speciation Drivers from Functional Trait Divergence. Am Nat 2020; 196:429-442. [PMID: 32970469 DOI: 10.1086/710338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractEcological differentiation between lineages is widely considered to be an important driver of speciation, but support for this hypothesis is mainly derived from the detailed study of a select set of model species pairs. Mounting evidence from nonmodel taxa, meanwhile, suggests that speciation often occurs with minimal differentiation in ecology or ecomorphology, calling into question the true contribution of divergent adaptation to species richness in nature. To better understand divergent ecological adaptation and its role in speciation generally, researchers require a comparative approach that can distinguish its signature from alternative processes, such as drift and parallel selection, in data sets containing many species pairs. Here we introduce new statistical models of divergent adaptation in the continuous traits of paired lineages. In these models, ecomorphological characters diverge as two lineages adapt toward alternative phenotypic optima following their departure from a common ancestor. The absolute distance between optima measures the extent of divergent selection and provides a basis for interpretation. We encode the models in the new R package diverge and extend them to allow the distance between optima to vary across continuous and categorical variables. We test model performance using simulation and demonstrate model application using published data sets of trait divergence in birds and mammals. Our framework provides the first explicit test for signatures of divergent selection in trait divergence data sets, and it will enable empiricists from a wide range of fields to better understand the dynamics of divergent adaptation and its prevalence in nature beyond just our best-studied model systems.
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46
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Merényi Z, Prasanna AN, Wang Z, Kovács K, Hegedüs B, Bálint B, Papp B, Townsend JP, Nagy LG. Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi. Mol Biol Evol 2020; 37:2228-2240. [PMID: 32191325 PMCID: PMC7403615 DOI: 10.1093/molbev/msaa077] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Convergent evolution is pervasive in nature, but it is poorly understood how various constraints and natural selection limit the diversity of evolvable phenotypes. Here, we analyze the transcriptome across fruiting body development to understand the independent evolution of complex multicellularity in the two largest clades of fungi-the Agarico- and Pezizomycotina. Despite >650 My of divergence between these clades, we find that very similar sets of genes have convergently been co-opted for complex multicellularity, followed by expansions of their gene families by duplications. Over 82% of shared multicellularity-related gene families were expanding in both clades, indicating a high prevalence of convergence also at the gene family level. This convergence is coupled with a rich inferred repertoire of multicellularity-related genes in the most recent common ancestor of the Agarico- and Pezizomycotina, consistent with the hypothesis that the coding capacity of ancestral fungal genomes might have promoted the repeated evolution of complex multicellularity. We interpret this repertoire as an indication of evolutionary predisposition of fungal ancestors for evolving complex multicellular fruiting bodies. Our work suggests that evolutionary convergence may happen not only when organisms are closely related or are under similar selection pressures, but also when ancestral genomic repertoires render certain evolutionary trajectories more likely than others, even across large phylogenetic distances.
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Affiliation(s)
- Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Arun N Prasanna
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Zheng Wang
- Department of Biostatistics, Yale University, New Haven, CT
| | - Károly Kovács
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
- Hungarian Centre of Excellence for Molecular Medicine, Metabolic Systems Biology Lab, Szeged, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
- Hungarian Centre of Excellence for Molecular Medicine, Metabolic Systems Biology Lab, Szeged, Hungary
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University, New Haven, CT
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
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47
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Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. The evolution of strong reproductive isolation between sympatric intertidal snails. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190545. [PMID: 32654639 DOI: 10.1098/rstb.2019.0545] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Anja M Westram
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Zuzanna B Zagrodzka
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Thomas Broquet
- CNRS and Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
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48
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Marin J, Achaz G, Crombach A, Lambert A. The genomic view of diversification. J Evol Biol 2020; 33:1387-1404. [PMID: 32654283 DOI: 10.1111/jeb.13677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/11/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022]
Abstract
The process of species diversification is traditionally summarized by a single tree, the species tree, whose reconstruction from molecular data is hindered by frequent conflicts between gene genealogies. Here, we argue that instead of seeing these conflicts as nuisances, we can exploit them to inform the diversification process itself. We adopt a gene-based view of diversification to model the ubiquitous presence of gene flow between diverging lineages, one of the most important processes explaining disagreements among gene trees. We propose a new framework for modelling the joint evolution of gene and species lineages relaxing the hierarchy between the species tree and gene trees inherent to the standard view, as embodied in a popular model known as the multispecies coalescent (MSC). We implement this framework in two alternative models called the gene-based diversification models (GBD): (a) GBD-forward following all evolving genomes through time and (b) GBD-backward based on coalescent theory. They feature four parameters tuning colonization, gene flow, genetic drift and genetic differentiation. We propose an inference method based on differences between gene trees. Applied to two empirical data sets prone to gene flow, we find better support for the GBD-backward model than for the MSC model. Along with the increasing awareness of the extent of gene flow, this work shows the importance of considering the richer signal contained in genomic histories, rather than in the mere species tree, to better apprehend the complex evolutionary history of species.
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Affiliation(s)
- Julie Marin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France
| | - Guillaume Achaz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Institut de Systématique, Évolution, Biodiversité (ISYEB), MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Université de Paris, Paris, France
| | - Anton Crombach
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Inria, Lyon Antenne La Doua, Villeurbanne, France.,INSA-Lyon, LIRIS, UMR 5205, Université de Lyon, Villeurbanne, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Laboratoire de Probabilités, Statistique et Modélisation (LPSM), CNRS UMR 8001, Sorbonne Université, Paris, France
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49
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Chen J, Yang L, Zhang R, Uebbing S, Zhang C, Jiang H, Lei Y, Lv W, Tian F, Zhao K, He S. Transcriptome-Wide Patterns of the Genetic and Expression Variations in Two Sympatric Schizothoracine Fishes in a Tibetan Plateau Glacier Lake. Genome Biol Evol 2020; 12:3725-3737. [PMID: 31917411 PMCID: PMC6978627 DOI: 10.1093/gbe/evz276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2019] [Indexed: 12/25/2022] Open
Abstract
Sympatric speciation remains a central focus of evolutionary biology. Although some evidence shows speciation occurring in this way, little is known about the gene expression evolution and the characteristics of population genetics as species diverge. Two closely related Gymnocypris fish (Gymnocypris chui and Gymnocypris scleracanthus), which come from a small glacier lake in the Tibetan Plateau, Lake Langcuo, exist a possible incipient sympatric adaptive ecological speciation. We generated large amounts of RNA-Seq data from multiple individuals and tissues from each of the two species and compared gene expression patterns and genetic polymorphisms between them. Ordination analysis separated samples by organ rather than by species. The degree of expression difference between organs within and between species was different. Phylogenetic analyses indicated that the two closely related taxa formed a monophyletic complex. Population structure analysis displayed two distinctly divergent clusters of G. chui and G. scleracanthus populations. By contrast, G. scleracanthus population genetic diversity is higher than that of G. chui. Considerable sites of the two populations were differentiated with a coefficient of FST = 0.25–0.50, implying that a small proportion of loci nevertheless exhibited deep divergence in two comparisons. Concomitantly, putatively selected genes during speciation revealed functional categories are enriched in bone morphogenesis, cell growth, neurogenetics, enzyme activity, and binding activity in G. chui population. In contrast, nutrition and localization were highlighted in G. scleracanthus. Collectively, morphological traits and dietary preference combine with genetic variation and expression variation, probably contributed to the incipient speciation of two sympatric populations.
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Affiliation(s)
- Juan Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Renyi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Severin Uebbing
- Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Cunfang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Öhlund G, Bodin M, Nilsson KA, Öhlund S, Mobley KB, Hudson AG, Peedu M, Brännström Å, Bartels P, Præbel K, Hein CL, Johansson P, Englund G. Ecological speciation in European whitefish is driven by a large-gaped predator. Evol Lett 2020; 4:243-256. [PMID: 32547784 PMCID: PMC7293097 DOI: 10.1002/evl3.167] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/21/2019] [Accepted: 02/02/2020] [Indexed: 12/15/2022] Open
Abstract
Lake-dwelling fish that form species pairs/flocks characterized by body size divergence are important model systems for speciation research. Although several sources of divergent selection have been identified in these systems, their importance for driving the speciation process remains elusive. A major problem is that in retrospect, we cannot distinguish selection pressures that initiated divergence from those acting later in the process. To address this issue, we studied the initial stages of speciation in European whitefish (Coregonus lavaretus) using data from 358 populations of varying age (26-10,000 years). We find that whitefish speciation is driven by a large-growing predator, the northern pike (Esox lucius). Pike initiates divergence by causing a largely plastic differentiation into benthic giants and pelagic dwarfs: ecotypes that will subsequently develop partial reproductive isolation and heritable differences in gill raker number. Using an eco-evolutionary model, we demonstrate how pike's habitat specificity and large gape size are critical for imposing a between-habitat trade-off, causing prey to mature in a safer place or at a safer size. Thereby, we propose a novel mechanism for how predators may cause dwarf/giant speciation in lake-dwelling fish species.
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Affiliation(s)
- Gunnar Öhlund
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
- Department of Business Administration, Technology, and Social SciencesLuleå University of TechnologyLuleåSE‐971 87Sweden
- Department of Wildlife, Fish, and Environmental StudiesSLUUmeåSE‐901 83Sweden
| | - Mats Bodin
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
- Department of Mathematics and Mathematical StatisticsUmeå UniversityUmeåSE‐901 87Sweden
| | - Karin A. Nilsson
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
- Department of Integrative BiologyUniversity of GuelphGuelphONN1G 2W1Canada
| | - Sven‐Ola Öhlund
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
| | - Kenyon B. Mobley
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
- Max Planck Institute for Evolutionary BiologyPlönD‐24302Germany
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinki00014Finland
| | - Alan G. Hudson
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
- School of Biological Sciences, Life Sciences BuildingUniversity of BristolBristolBS8 1TQUnited Kingdom
| | - Mikael Peedu
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
| | - Åke Brännström
- Department of Mathematics and Mathematical StatisticsUmeå UniversityUmeåSE‐901 87Sweden
- Evolution and Ecology ProgramInternational Institute for Applied Systems AnalysisLaxenburgA‐2361Austria
| | - Pia Bartels
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
| | - Kim Præbel
- Norwegian College of Fishery ScienceUiT The Arctic University of NorwayTromsøN‐9037Norway
| | - Catherine L. Hein
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
- Climate Impacts Research Centre (CIRC)Abisko Scientific Research StationAbiskoSE‐981 07Sweden
| | - Petter Johansson
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
| | - Göran Englund
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSE‐901 87Sweden
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