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Fouqueau L, Polechová J. Eco-evolutionary dynamics in changing environments: integrating theory with data. J Evol Biol 2024; 37:579-587. [PMID: 38941551 DOI: 10.1093/jeb/voae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/30/2024]
Affiliation(s)
- Louise Fouqueau
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Jitka Polechová
- Department of Mathematics, University of Vienna, Vienna, Austria
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2
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Wacker KS, Winger BM. An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates. Am Nat 2024; 203:362-381. [PMID: 38358813 DOI: 10.1086/728598] [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: 02/17/2024]
Abstract
AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.
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3
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Medina I, Dong C, Marquez R, Perez DM, Wang IJ, Stuart-Fox D. Anti-predator defences are linked with high levels of genetic differentiation in frogs. Proc Biol Sci 2024; 291:20232292. [PMID: 38264783 PMCID: PMC10806439 DOI: 10.1098/rspb.2023.2292] [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: 01/15/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
Predator-prey interactions have been suggested as drivers of diversity in different lineages, and the presence of anti-predator defences in some clades is linked to higher rates of diversification. Warning signals are some of the most widespread defences in the animal world, and there is evidence of higher diversification rates in aposematic lineages. The mechanisms behind such species richness, however, are still unclear. Here, we test whether lineages that use aposematism as anti-predator defence exhibit higher levels of genetic differentiation between populations, leading to increased opportunities for divergence. We collated from the literature more than 3000 pairwise genetic differentiation values across more than 700 populations from over 60 amphibian species. We find evidence that over short geographical distances, populations of species of aposematic lineages exhibit greater genetic divergence relative to species that are not aposematic. Our results support a scenario where the use of warning signals could restrict gene flow, and suggest that anti-predator defences could impact divergence between populations and potentially have effects at a macro-evolutionary scale.
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Affiliation(s)
- Iliana Medina
- School of BioSciences, University of Melbourne, Melbourne 3010, Australia
| | - Caroline Dong
- School of BioSciences, University of Melbourne, Melbourne 3010, Australia
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70115, USA
| | - Roberto Marquez
- Department of Ecology and Evolutionary Biology and Michigan Society of Fellows, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniela M. Perez
- Max Plank Institute of Animal Behaviour, 78464 Konstanz, Germany
| | - Ian J. Wang
- Department of Environmental Science, Policy, and Management, Rausser College of Natural Resources, University of California, Berkeley, CA 94720, USA
| | - Devi Stuart-Fox
- School of BioSciences, University of Melbourne, Melbourne 3010, Australia
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4
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Kalirad A, Burch CL, Azevedo RBR. Genetic drift promotes and recombination hinders speciation on holey fitness landscapes. PLoS Genet 2024; 20:e1011126. [PMID: 38252672 PMCID: PMC10833538 DOI: 10.1371/journal.pgen.1011126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 02/01/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Dobzhansky and Muller proposed a general mechanism through which microevolution, the substitution of alleles within populations, can cause the evolution of reproductive isolation between populations and, therefore, macroevolution. As allopatric populations diverge, many combinations of alleles differing between them have not been tested by natural selection and may thus be incompatible. Such genetic incompatibilities often cause low fitness in hybrids between species. Furthermore, the number of incompatibilities grows with the genetic distance between diverging populations. However, what determines the rate and pattern of accumulation of incompatibilities remains unclear. We investigate this question by simulating evolution on holey fitness landscapes on which genetic incompatibilities can be identified unambiguously. We find that genetic incompatibilities accumulate more slowly among genetically robust populations and identify two determinants of the accumulation rate: recombination rate and population size. In large populations with abundant genetic variation, recombination selects for increased genetic robustness and, consequently, incompatibilities accumulate more slowly. In small populations, genetic drift interferes with this process and promotes the accumulation of genetic incompatibilities. Our results suggest a novel mechanism by which genetic drift promotes and recombination hinders speciation.
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Affiliation(s)
- Ata Kalirad
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Christina L. Burch
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ricardo B. R. Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
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5
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Chen YS, Muellner-Riehl AN, Yang Y, Liu J, Dimitrov D, Luo A, Luo Y, Sun H, Wang ZH. Dispersal modes affect Rhamnaceae diversification rates in a differentiated manner. Proc Biol Sci 2023; 290:20231926. [PMID: 37989241 PMCID: PMC10688438 DOI: 10.1098/rspb.2023.1926] [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: 08/27/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
The evolution of dispersal modes has been proposed to promote the diversification of angiosperms. However, little is known about the relative impact of different dispersal modes on plant diversification. We test the association between dispersal modes and diversification rates using Rhamnaceae, the cosmopolitan buckthorn family, as a model. We found that species with diplochory have the highest diversification rates followed by those with myrmecochory and ballistic dispersal, while lineages dispersed by vertebrates and wind have relatively low diversification rates. The difference in diversification rates may be closely linked to the difference in dispersal distance and ecological interactions implied by each dispersal mode. Species which disperse over larger geographical distances may have much higher speciation rates due to the increased chance of establishing isolated populations due to geological barriers or habitat fragmentation. However, long-distance dispersal may also increase the chance of extinction. By contrast, species with short-distance dispersal modes may have low speciation rates. Complex interactions with the surrounding environment may, however, impact diversification rates positively by increasing plant survival and reproductive success.
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Affiliation(s)
- Yong-Sheng Chen
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Alexandra N. Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, 04013 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04013 Leipzig, Germany
| | - Yi Yang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, People's Republic of China
- Research Center of Ecological Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, People's Republic of China
| | - Jian Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen 7800, 5020, Norway
| | - Ao Luo
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yuan Luo
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Zhi-Heng Wang
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing 100871, People's Republic of China
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6
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Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution. Cold Spring Harb Perspect Biol 2023; 15:a041447. [PMID: 37604585 PMCID: PMC10626258 DOI: 10.1101/cshperspect.a041447] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics. While an important role for CRs in speciation has been suggested, evidence primarily stems from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at a macroevolutionary level has been supported by associations between species diversity and rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of CRs and taxa. Now that more broadly applicable and precise CR detection approaches have become available, we address the challenges in filling some of the conceptual and empirical gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.
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Affiliation(s)
- Kay Lucek
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier, France
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Nora Walden
- Centre for Organismal Studies, University of Heidelberg, 69117 Heidelberg, Germany
| | - Anja Marie Westram
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado;
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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7
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Yamaguchi R, Wiley B, Otto SP. The phoenix hypothesis of speciation. Proc Biol Sci 2022; 289:20221186. [PMID: 36382528 PMCID: PMC9667362 DOI: 10.1098/rspb.2022.1186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2023] Open
Abstract
Genetic divergence among allopatric populations builds reproductive isolation over time. This process is accelerated when populations face a changing environment that allows large-effect mutational differences to accumulate, but abrupt change also places populations at risk of extinction. Here we use simulations of Fisher's geometric model with explicit population dynamics to explore the genetic changes that occur in the face of environmental changes. Because evolutionary rescue leads to the fixation of mutations whose phenotypic effects are larger on average compared with populations not at risk of extinction, these mutations are thus more likely to lead to reproductive isolation. We refer to the formation of new species from the ashes of populations in decline as the phoenix hypothesis of speciation. The phoenix hypothesis predicts more substantial hybrid fitness breakdown among populations surviving a higher extinction risk. The hypothesis was supported when many loci underlie adaptation. With only a small number of potential rescue mutations, however, mutations that fixed in different populations were more likely to be identical, with such parallel changes reducing isolation. Consequently, reproductive isolation builds fastest in populations subject to an intermediate extinction risk, given a limited number of mutations available for adaptation.
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Affiliation(s)
- Ryo Yamaguchi
- Department of Advanced Transdisciplinary Science, Hokkaido University, Sapporo, Hokkaido 060-0808, Japan
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Bryn Wiley
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Sarah P. Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
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8
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Butlin RK. The language of isolation: a commentary on Westram et al., 2022. J Evol Biol 2022; 35:1195-1199. [PMID: 36063154 PMCID: PMC9543646 DOI: 10.1111/jeb.14029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 01/01/2023]
Affiliation(s)
- Roger K Butlin
- School of Biosciences, The University of Sheffield, Sheffield, UK.,Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
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9
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Stuckert AMM, Matute DR. Using neutral loci to quantify reproductive isolation and speciation: a commentary on Westram et al., 2022. J Evol Biol 2022; 35:1169-1174. [PMID: 36063155 DOI: 10.1111/jeb.14057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 01/23/2023]
Affiliation(s)
- Adam M M Stuckert
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, USA
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10
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Abstract
AbstractEvolvability is best addressed from a multi-level, macroevolutionary perspective through a comparative approach that tests for among-clade differences in phenotypic diversification in response to an opportunity, such as encountered after a mass extinction, entering a new adaptive zone, or entering a new geographic area. Analyzing the dynamics of clades under similar environmental conditions can (partially) factor out shared external drivers to recognize intrinsic differences in evolvability, aiming for a macroevolutionary analog of a common-garden experiment. Analyses will be most powerful when integrating neontological and paleontological data: determining differences among extant populations that can be hypothesized to generate large-scale, long-term contrasts in evolvability among clades; or observing large-scale differences among clade histories that can by hypothesized to reflect contrasts in genetics and development observed directly in extant populations. However, many comparative analyses can be informative on their own, as explored in this overview. Differences in clade-level evolvability can be visualized in diversity-disparity plots, which can quantify positive and negative departures of phenotypic productivity from stochastic expectations scaled to taxonomic diversification. Factors that evidently can promote evolvability include modularity—when selection aligns with modular structure or with morphological integration patterns; pronounced ontogenetic changes in morphology, as in allometry or multiphase life cycles; genome size; and a variety of evolutionary novelties, which can also be evaluated using macroevolutionary lags between the acquisition of a trait and phenotypic diversification, and dead-clade-walking patterns that may signal a loss of evolvability when extrinsic factors can be excluded. High speciation rates may indirectly foster phenotypic evolvability, and vice versa. Mechanisms are controversial, but clade evolvability may be higher in the Cambrian, and possibly early in the history of clades at other times; in the tropics; and, for marine organisms, in shallow-water disturbed habitats.
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11
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van Holstein LA, Foley RA. A process-based approach to hominin taxonomy provides new perspectives on hominin speciation. Evol Anthropol 2022; 31:166-174. [PMID: 35758550 DOI: 10.1002/evan.21946] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 02/02/2022] [Accepted: 04/29/2022] [Indexed: 11/11/2022]
Abstract
A longstanding debate in hominin taxonomy is that between "lumpers" and "splitters." We argue that both approaches assume an unrealistically static model of speciation. Speciation is an extended process, of which fossils provide a record. Fossils should be interpreted in a more dynamic framework than is the norm. We introduce the process-based approach (PBA), in which we suggest that "splitters" recognize and name units at an earlier stage of speciation than "lumpers" do. The "determinants" of speciation can control the rate at which population isolates form, or the rate at which these complete the speciation process, or both. Embedded in the PBA, differences between existing lumped and split taxonomies are a heuristic tool to study these processes. We apply the PBA to show that not all hominin populations reached later stages of the speciation process and that populations have a disproportionate likelihood of doing so from ∼3.1 to ∼1.5 Ma. We outline and discuss resulting new research questions.
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Affiliation(s)
- Laura A van Holstein
- Department of Archaeology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, UK
| | - Robert A Foley
- Department of Archaeology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, UK
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12
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Cogni R, Quental TB, Guimarães PR. Ehrlich and Raven escape and radiate coevolution hypothesis at different levels of organization: Past and future perspectives. Evolution 2022; 76:1108-1123. [PMID: 35262199 DOI: 10.1111/evo.14456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 01/21/2023]
Abstract
The classic paper by Ehrlich and Raven on coevolution will soon be 60 years old. Although they were not the first to develop the idea of coevolution, their thought-provoking paper certainly popularized this idea and inspired several generations of scientists interested in coevolution. Here, we describe some of their main contributions, quantitatively measure the impact of their seminal paper on different fields of research, and discuss how ideas related to their original paper might push the study of coevolution forward. To guide our discussion, we explore their original hypothesis into three research fields that are associated with distinct scales/levels of organization: (1) the genetic mechanisms underlying coevolutionary interactions; (2) the potential association between coevolutionary diversification and the organization of ecological networks; and (3) the micro- and macroevolutionary mechanisms and expected patterns under their hypothesis. By doing so, we discuss potentially overlooked aspects and future directions for the study of coevolutionary dynamics and diversification.
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Affiliation(s)
- Rodrigo Cogni
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Tiago B Quental
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Paulo R Guimarães
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
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13
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Burgin G, Hopkins R. A missing link: Connecting plant and pollinator population structure. AMERICAN JOURNAL OF BOTANY 2022; 109:668-671. [PMID: 35421258 DOI: 10.1002/ajb2.1844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Grace Burgin
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Arnold Arboretum of Harvard University, Boston, MA, 02131, USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Arnold Arboretum of Harvard University, Boston, MA, 02131, USA
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14
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Brown JI, Harrigan RJ, Lavretsky P. Evolutionary and Ecological Drivers of Local Adaptation and Speciation in a North American Avian Species Complex. Mol Ecol 2022; 31:2578-2593. [PMID: 35263000 DOI: 10.1111/mec.16423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Abstract
Throughout the speciation process, genomic divergence can be differentially impacted by selective pressures, as well as gene flow and genetic drift. Disentangling the effects of these evolutionary mechanisms remains challenging, especially for non-model organisms. Accounting for complex evolutionary histories and contemporary population structure often requires sufficient sample sizes, for which the expense of full genomes remains prohibitive. Here, we demonstrate the utility of partial-genome sequence data for range-wide samples to shed light into the divergence process of two closely related ducks, the Mexican duck (Anas diazi) and mallard (A. platyrhynchos). We determine the role of selective and neutral processes during speciation of Mexican ducks by integrating evolutionary and demographic modelling with genotype-environment and genotype-phenotype association testing. First, evolutionary models and demographic analyses support the hypothesis that Mexican ducks originally diverged ~300,000 years ago in a climate refugia arising during a glacial period in in a southwestern North America, and that subsequent environmental selective pressures played a key role in divergence. Mexican ducks then showed cyclical demographic patterns that likely reflected repeated range expansions and contractions, along with bouts of gene flow with mallards during glacial cycles. Finally, we provide evidence that sexual selection acted on several phenotypic traits as a co-evolutionary process, facilitating the development of reproductive barriers that initially arose due to strong ecological selection. More broadly, this work reveals that the genomic and phenotypic patterns observed across species complexes are the result of myriad factors that contribute in dynamic ways to the evolutionary trajectories of a lineage.
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Affiliation(s)
- Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
| | - Ryan J Harrigan
- Center for Tropical Research, University of California, Los Angeles, La Kretz Hall, Suite 300, Los Angeles, CA, 90095, U.S.A
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
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15
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Singhal S, Colli GR, Grundler MR, Costa GC, Prates I, Rabosky DL. No link between population isolation and speciation rate in squamate reptiles. Proc Natl Acad Sci U S A 2022; 119:e2113388119. [PMID: 35058358 PMCID: PMC8795558 DOI: 10.1073/pnas.2113388119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process-the propensity for population isolation-as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation-including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist-are likely to play a larger role than population isolation in controlling speciation rate variation in squamates.
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Affiliation(s)
- Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747;
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Maggie R Grundler
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109;
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
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16
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Freeman BG, Rolland J, Montgomery GA, Schluter D. Faster evolution of a premating reproductive barrier is not associated with faster speciation rates in New World passerine birds. Proc Biol Sci 2022; 289:20211514. [PMID: 34982949 PMCID: PMC8727149 DOI: 10.1098/rspb.2021.1514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 12/07/2021] [Indexed: 01/14/2023] Open
Abstract
Why are speciation rates so variable across the tree of life? One hypothesis is that this variation is explained by how rapidly reproductive barriers evolve. We tested this hypothesis by conducting a comparative study of the evolution of bird song, a premating barrier to reproduction. Speciation in birds is typically initiated when geographically isolated (allopatric) populations evolve reproductive barriers. We measured the strength of song as a premating barrier between closely related allopatric populations by conducting 2339 field experiments to measure song discrimination for 175 taxon pairs of allopatric or parapatric New World passerine birds, and estimated recent speciation rates from molecular phylogenies. We found evidence that song discrimination is indeed an important reproductive barrier: taxon pairs with high song discrimination in allopatry did not regularly interbreed in parapatry. However, evolutionary rates of song discrimination were not associated with recent speciation rates. Evolutionary rates of song discrimination were also unrelated to latitude or elevation, but species with innate song (suboscines) evolved song discrimination much faster than species with learned song (oscines). We conclude that song is a key premating reproductive barrier in birds, but faster evolution of this reproductive barrier between populations does not consistently result in faster diversification between species.
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Affiliation(s)
- Benjamin G. Freeman
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada V6T1Z4
- Department of Zoology, University of British Columbia, Vancouver, Canada V6T1Z4
| | - Jonathan Rolland
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada V6T1Z4
- Department of Zoology, University of British Columbia, Vancouver, Canada V6T1Z4
- CNRS, UMR5174, Laboratoire Evolution et Diversité Biologique, Université Toulouse 3 Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, Toulouse 31062, France
| | - Graham A. Montgomery
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA 90095, USA
| | - Dolph Schluter
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada V6T1Z4
- Department of Zoology, University of British Columbia, Vancouver, Canada V6T1Z4
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17
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Val P, Lyons NJ, Gasparini N, Willenbring JK, Albert JS. Landscape Evolution as a Diversification Driver in Freshwater Fishes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.788328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The exceptional concentration of vertebrate diversity in continental freshwaters has been termed the “freshwater fish paradox,” with > 15,000 fish species representing more than 20% of all vertebrate species compressed into tiny fractions of the Earth’s land surface area (<0.5%) or total aquatic habitat volume (<0.001%). This study asks if the fish species richness of the world’s river basins is explainable in terms of river captures using topographic metrics as proxies. The River Capture Hypothesis posits that drainage-network rearrangements have accelerated biotic diversification through their combined effects on dispersal, speciation, and extinction. Yet rates of river capture are poorly constrained at the basin scale worldwide. Here we assess correlations between fish species density (data for 14,953 obligate freshwater fish species) and basin-wide metrics of landscape evolution (data for 3,119 river basins), including: topography (elevation, average relief, slope, drainage area) and climate (average rainfall and air temperature). We assess the results in the context of both static landscapes (e.g., species-area and habitat heterogeneity relationships) and transient landscapes (e.g., river capture, tectonic activity, landscape disequilibrium). We also relax assumptions of functional neutrality of basins (tropical vs. extratropical, tectonically stable vs. active terrains). We found a disproportionate number of freshwater species in large, lowland river basins of tropical South America, Africa, and Southeast Asia, under predictable conditions of large geographic area, tropical climate, low topographic relief, and high habitat volume (i.e., high rainfall rates). However, our results show that these conditions are only necessary, but not fully sufficient, to explain the basins with the highest diversity. Basins with highest diversity are all located on tectonically stable regions, places where river capture is predicted to be most conducive to the formation of high fish species richness over evolutionary timescales. Our results are consistent with predictions of several landscape evolution models, including the River Capture Hypothesis, Mega Capture Hypothesis, and Intermediate Capture Rate Hypothesis, and support conclusions of numerical modeling studies indicating landscape transience as a mechanistic driver of net diversification in riverine and riparian organisms with widespread continental distributions.
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18
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Prates I, Singhal S, Marchán-Rivadeneira MR, Grundler MR, Moritz C, Donnellan SC, Rabosky DL. Genetic and Ecogeographic Controls on Species Cohesion in Australia’s Most Diverse Lizard Radiation. Am Nat 2022; 199:E57-E75. [DOI: 10.1086/717411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ivan Prates
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109
| | - Sonal Singhal
- Department of Biology, California State University–Dominguez Hills, Carson, California 90747
| | | | - Maggie R. Grundler
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720
| | - Craig Moritz
- Division of Ecology and Evolution and Centre for Biodiversity Analysis, Australian National University, Camberra, Australian Capital Territory, Australia
| | | | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109
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19
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Harmon LJ, Pennell MW, Henao-Diaz LF, Rolland J, Sipley BN, Uyeda JC. Causes and Consequences of Apparent Timescaling Across All Estimated Evolutionary Rates. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-011921-023644] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolutionary rates play a central role in connecting micro- and macroevolution. All evolutionary rate estimates, including rates of molecular evolution, trait evolution, and lineage diversification, share a similar scaling pattern with time: The highest rates are those measured over the shortest time interval. This creates a disconnect between micro- and macroevolution, although the pattern is the opposite of what some might expect: Patterns of change over short timescales predict that evolution has tremendous potential to create variation and that potential is barely tapped by macroevolution. In this review, we discuss this shared scaling pattern across evolutionary rates. We break down possible explanations for scaling into two categories, estimation error and model misspecification, and discuss how both apply to each type of rate. We also discuss the consequences of this ubiquitous pattern, which can lead to unexpected results when comparing ratesover different timescales. Finally, after addressing purely statistical concerns, we explore a few possibilities for a shared unifying explanation across the three types of rates that results from a failure to fully understand and account for how biological processes scale over time.
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Affiliation(s)
- Luke J. Harmon
- Institute for Bioinformatics and Evolutionary Studies (IBEST) and Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA
| | - Matthew W. Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - L. Francisco Henao-Diaz
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jonathan Rolland
- Laboratoire Evolution et Diversité Biologique, CNRS, UMR5174, Université Toulouse III–Paul Sabatier, 31062 Toulouse, France
| | - Breanna N. Sipley
- Program for Bioinformatics and Computational Biology, University of Idaho, Moscow, Idaho 83844, USA
| | - Josef C. Uyeda
- Department of Biological Sciences, Virginia Tech University, Blacksburg, Virginia 24061, USA
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20
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Ortego J, Knowles LL. Geographical isolation versus dispersal: Relictual alpine grasshoppers support a model of interglacial diversification with limited hybridization. Mol Ecol 2021; 31:296-312. [PMID: 34651368 DOI: 10.1111/mec.16225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/21/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023]
Abstract
Alpine biotas are paradigmatic of the countervailing roles of geographical isolation and dispersal during diversification. In temperate regions, repeated distributional shifts driven by Pleistocene climatic oscillations produced both recurrent pulses of population fragmentation and opportunities for gene flow during range expansions. Here, we test whether a model of divergence in isolation vs. with gene flow is more likely in the diversification of flightless alpine grasshoppers of the genus Podisma from the Iberian Peninsula. The answer to this question can also provide key insights about the pace of evolution. Specifically, if the data fit a divergence in isolation model, this suggests rapid evolution of reproductive isolation. Genomic data confirm a Pleistocene origin of the species complex, and multiple analytical approaches revealed limited asymmetric historical hybridization between two taxa. Genomic-based demographic reconstructions, spatial patterns of genetic structure and range shifts inferred from palaeodistribution modelling suggest severe range contraction accompanied by declines in effective population sizes during interglacials (i.e., contemporary populations confined to sky islands are relicts) and expansions during the coldest stages of the Pleistocene in each taxon. Although limited hybridization during secondary contact leads to phylogenetic uncertainty if gene flow is not accommodated when estimating evolutionary relationships, all species exhibit strong genetic cohesiveness. Our study lends support to the notion that the accumulation of incipient differences during periods of isolation were sufficient to lead to lineage persistence, but also that the demographic changes, dispersal constraints and spatial distribution of the sky islands themselves mediated species diversification in temperate alpine biotas.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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21
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Dool SE, Picker MD, Eberhard MJB. Limited dispersal and local adaptation promote allopatric speciation in a biodiversity hotspot. Mol Ecol 2021; 31:279-295. [PMID: 34643310 DOI: 10.1111/mec.16219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 01/20/2023]
Abstract
Recently diverged or diverging populations can offer unobstructed insights into early barriers to gene flow during the initial stages of speciation. The current study utilised a novel insect system (order Mantophasmatodea) to shed light on the early drivers of speciation. The members of this group have limited dispersal abilities, small allopatric distributions and strong habitat associations in the Cape Floristic Region biodiversity hotspot in South Africa. Sister taxa from the diverse family Austrophasmatidae were chosen as focal species (Karoophasma biedouwense, K. botterkloofense). Population genetics and Generalized Dissimilarity Modelling (GDM) were used to characterise spatial patterns of genetic variation and evaluate the contribution of environmental factors to population divergence and speciation. Extensive sampling confirmed the suspected allopatry of these taxa. However, hybrids were identified in a narrow region occurring between the species' distributions. Strong population structure was found over short geographic distances; particularly in K. biedouwense in which geographic distance accounted for 32% of genetic variation over a scale of 50 km (r = .56, p < .001). GDM explained 42%-78% of the deviance in observed genetic dissimilarities. Geographic distance was consistently indicated to be important for between species and within population differentiation, suggesting that limited dispersal ability may be an important neutral driver of divergence. Temperature, altitude, precipitation and vegetation were also indicated as important factors, suggesting the possible role of adaptation to local environmental conditions for species divergence. The discovery of the hybrid-zone, and the multiple allopatric species pairs in Austrophasmatidae support the idea that this could be a promising group to further our understanding of speciation modes.
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Affiliation(s)
- Serena E Dool
- General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany.,CBGP, INRAE, CIRAD, IRD, Institut Agro, University of Montpellier, Montpellier, France
| | - Mike D Picker
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Monika J B Eberhard
- General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
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22
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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23
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Edwards SV, Robin V, Ferrand N, Moritz C. The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. Genome Biol Evol 2021; 14:6339579. [PMID: 34347070 PMCID: PMC8743039 DOI: 10.1093/gbe/evab176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong “sense of place,” comparative phylogeography offers abundant “place-based” educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Vv Robin
- Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Tirupati, Andhra Pradesh, 517507, India
| | - Nuno Ferrand
- CIBIO/InBIO, Laboratório Associado, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Portugal
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
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24
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Miller EC. Comparing diversification rates in lakes, rivers, and the sea. Evolution 2021; 75:2055-2073. [PMID: 34181244 DOI: 10.1111/evo.14295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 05/29/2021] [Accepted: 06/06/2021] [Indexed: 12/23/2022]
Abstract
The diversity of species inhabiting freshwater relative to marine habitats is striking, given that freshwater habitats encompass <1% of Earth's water. The most commonly proposed explanation for this pattern is that freshwater habitats are more fragmented than marine habitats, allowing more opportunities for allopatric speciation and thus increased diversification rates in freshwater. However, speciation may be generally faster in sympatry than in allopatry, as illustrated by lacustrine radiations such as African cichlids. Such differences between rivers and lakes may be important to consider when comparing diversification broadly among freshwater and marine groups. Here I compared diversification rates of teleost fishes in marine, riverine and lacustrine habitats. I found that lakes had faster speciation and net diversification rates than other aquatic habitats. However, most freshwater diversity arose in rivers. Surprisingly, riverine and marine habitats had similar rates of net diversification on average. Biogeographic models suggest that lacustrine habitats are evolutionarily unstable, explaining the dearth of lacustrine species in spite of their rapid diversification. Collectively, these results suggest that strong diversification rate differences are unlikely to explain the freshwater paradox. Instead, this pattern may be attributable to the comparable amount of time spent in riverine and marine habitats over the 200-million-year history of teleosts.
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25
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Fenker J, McCulloch GA, Vasconcellos MM, Silva DC, Domingos FMCB. Digest: Dispersal reduction drives rapid diversification in alpine grasshoppers. Evolution 2021; 75:2132-2134. [PMID: 34189736 DOI: 10.1111/evo.14296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Dispersal-associated traits -such as flight ability- influence how species move across the landscape, and can dramatically impact their distributions and patterns of genetic structure. Ortego et al. examine genomic data from two recently diverged alpine grasshopper lineages with distinct wing sizes to assess the demographic impacts of flight loss. The authors showed that flight loss may lead to asymmetric introgression during speciation, and can significantly increase rates of intraspecific diversification.
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Affiliation(s)
- Jessica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia.,Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Daiana Cardoso Silva
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, Brazil
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26
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Fenker J, Tedeschi LG, Melville J, Moritz C. Predictors of phylogeographic structure among codistributed taxa across the complex Australian monsoonal tropics. Mol Ecol 2021; 30:4276-4291. [PMID: 34216506 DOI: 10.1111/mec.16057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/16/2021] [Accepted: 06/28/2021] [Indexed: 11/28/2022]
Abstract
Differences in the geographic scale and depth of phylogeographic structure across codistributed taxa can reveal how microevolutionary processes such as population isolation and persistence drive diversification. In turn, environmental heterogeneity, species' traits, and historical biogeographic barriers may influence the potential for isolation and persistence. Using extensive SNP data and a combination of population genetic summary statistics and landscape genomic analyses, we explored predictors of the scale and depth of phylogeographic structure in codistributed lizard taxa from the topographically and climatically complex monsoonal tropics (AMT) of Australia. We first resolved intraspecific lineages and then tested whether genetic divergence across space within lineages is related to isolation by distance, resistance and/or environment and whether these factors differ across genera or between rock-related versus habitat generalist taxa. We then tested whether microevolutionary processes within lineages explain differences in the geographic scale and depth of intraspecific phylogeographic lineages. The results indicated that landscape predictors of phylogeographic structure differ between taxa. Within lineages, there was prevalent isolation by distance, but the strength of isolation by distance is independent of the taxonomic family, habitat specialization, and climate. Isolation by environment is the strongest predictor of landscape-scale genetic divergence for all taxa, with both temperature and precipitation acting as limiting factors. The strength of isolation by distance does not predict the geographic scale of the phylogeographic structure. However, more localized lineages had higher mean individual heterozygosity and less negative Tajima's D. This result implies that finer-scale phylogeographic structuring within species is associated with larger and more stable populations and, hence, persistence.
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Affiliation(s)
- Jessica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Leonardo G Tedeschi
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jane Melville
- Department of Sciences, Museums Victoria, Melbourne, VIC, Australia.,School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
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27
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de Alencar LRV, Quental TB. Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale. Ecol Evol 2021; 11:5828-5843. [PMID: 34141187 PMCID: PMC8207422 DOI: 10.1002/ece3.7511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 11/05/2022] Open
Abstract
Although speciation dynamics have been described for several taxonomic groups in distinct geographic regions, most macroevolutionary studies still lack a detailed mechanistic view on how or why speciation rates change. To help partially fill this gap, we suggest that the interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales. Our framework is developed under different scenarios: when speciation is mediated by geographical or resource-partitioning opportunities, and when diversity is limited or not. We also discuss how organismal intrinsic properties and different overall geographical settings can influence the tempo and mode of speciation. We argue that specific conditions observed at the microscale might produce a pulse in speciation rates even without a pulse in either climate or physical barriers. We also propose a hypothesis to reconcile the apparent inconsistency between speciation measured at the microscale and macroscale, and emphasize that diversification rates are better seen as an emergent property. We hope to bring the reader's attention to interesting mechanisms to be further studied, to motivate the development of new theoretical models that connect microevolution and macroevolution, and to inspire new empirical and methodological approaches to more adequately investigate speciation dynamics either using neontological or paleontological data.
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Affiliation(s)
| | - Tiago Bosisio Quental
- Departamento de EcologiaInstituto de BiociênciasUniversidade de São PauloSão PauloBrazil
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28
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Freeman BG, Pennell MW. The latitudinal taxonomy gradient. Trends Ecol Evol 2021; 36:778-786. [PMID: 34074540 DOI: 10.1016/j.tree.2021.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
Emerging large-scale datasets coupled with statistical advances have provided new insights into the processes that generate the latitudinal diversity gradient (LDG). But many of these studies run into an old, if often underappreciated, problem: The interpretation of the data critically depends on the consistent application of criteria to define what constitutes a species. This is particularly pernicious for the LDG because good species have been easier to recognize in temperate than in tropical regions. We provide evidence that this latitudinal taxonomy gradient exists, discuss how this potentially impacts inferences about latitudinal variation in ecoevolutionary processes such as population differentiation and speciation, and provide a roadmap for how to mitigate taxonomic biases in the study of biodiversity patterns.
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Affiliation(s)
- Benjamin G Freeman
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada, V6T1Z4; Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada, V6T1Z4; Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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29
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Thompson CL, Alberti M, Barve S, Battistuzzi FU, Drake JL, Goncalves GC, Govaert L, Partridge C, Yang Y. Back to the future: Reintegrating biology to understand how past eco-evolutionary change can predict future outcomes. Integr Comp Biol 2021; 61:2218-2232. [PMID: 33964141 DOI: 10.1093/icb/icab068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
During the last few decades, biologists have made remarkable progress in understanding the fundamental processes that shape life. But despite the unprecedented level of knowledge now available, large gaps still remain in our understanding of the complex interplay of eco-evolutionary mechanisms across scales of life. Rapidly changing environments on Earth provide a pressing need to understand the potential implications of eco-evolutionary dynamics, which can be achieved by improving existing eco-evolutionary models and fostering convergence among the sub-fields of biology. We propose a new, data-driven approach that harnesses our knowledge of the functioning of biological systems to expand current conceptual frameworks and develop corresponding models that can more accurately represent and predict future eco-evolutionary outcomes. We suggest a roadmap toward achieving this goal. This long-term vision will move biology in a direction that can wield these predictive models for scientific applications that benefit humanity and increase the resilience of natural biological systems. We identify short, medium, and long-term key objectives to connect our current state of knowledge to this long-term vision, iteratively progressing across three stages: 1) utilizing knowledge of biological systems to better inform eco-evolutionary models, 2) generating models with more accurate predictions, and 3) applying predictive models to benefit the biosphere. Within each stage, we outline avenues of investigation and scientific applications related to the timescales over which evolution occurs, the parameter space of eco-evolutionary processes, and the dynamic interactions between these mechanisms. The ability to accurately model, monitor, and anticipate eco-evolutionary changes would be transformational to humanity's interaction with the global environment, providing novel tools to benefit human health, protect the natural world, and manage our planet's biosphere.
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Affiliation(s)
| | - Marina Alberti
- Department of Urban Design and Planning, University of Washington,
| | - Sahas Barve
- Smithsonian National Museum of Natural History,
| | | | - Jeana L Drake
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles,
| | | | - Lynn Govaert
- Department of Evolutionary Biology and Environmental Studies, University of Zurich; Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, URPP Global Change and Biodiversity, University of Zurich,
| | | | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota,
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30
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Landis JB, Miller CM, Broz AK, Bennett AA, Carrasquilla-Garcia N, Cook DR, Last RL, Bedinger PA, Moghe GD. Migration through a Major Andean Ecogeographic Disruption as a Driver of Genetic and Phenotypic Diversity in a Wild Tomato Species. Mol Biol Evol 2021; 38:3202-3219. [PMID: 33822137 PMCID: PMC8321546 DOI: 10.1093/molbev/msab092] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Evolutionary dynamics at the population level play a central role in creating the diversity of life on our planet. In this study, we sought to understand the origins of such population-level variation in mating systems and defensive acylsugar chemistry in Solanum habrochaites—a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-site-Associated-DNA-Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4–6 ancestral populations. Detailed characterization of mating systems of these clusters revealed emergence of multiple self-compatible (SC) groups from progenitor self-incompatible populations in the northern part of the species range. Emergence of these SC groups was also associated with fixation of deleterious alleles inactivating acylsugar acetylation. The Amotape-Huancabamba Zone—a geographical landmark in the Andes with high endemism and isolated microhabitats—was identified as a major driver of differentiation in the northern species range, whereas large geographical distances contributed to population structure and evolution of a novel SC group in the central and southern parts of the range, where the species was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating population differentiation, and enhance our understanding of the microevolutionary processes that create biological diversity.
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Affiliation(s)
- Jacob B Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.,Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Alexandra A Bennett
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | | | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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31
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Matute DR, Cooper BS. Comparative studies on speciation: 30 years since Coyne and Orr. Evolution 2021; 75:764-778. [PMID: 33491225 PMCID: PMC8247902 DOI: 10.1111/evo.14181] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/28/2022]
Abstract
Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly a hundred years evolutionary geneticists have characterized reproductive isolation (RI) mechanisms and specific barriers to gene flow required for species formation. The seminal work of Coyne and Orr provided the first comprehensive comparative analysis of speciation. By combining phylogenetic hypotheses and species range data with estimates of genetic divergence and multiple mechanisms of RI across Drosophila, Coyne and Orr's influential meta-analyses answered fundamental questions and motivated new analyses that continue to push the field forward today. Now 30 years later, we revisit the five questions addressed by Coyne and Orr, identifying results that remain well supported and others that seem less robust with new data. We then consider the future of speciation research, with emphasis on areas where novel methods and data motivate potential progress. While the literature remains biased towards Drosophila and other model systems, we are enthusiastic about the future of the field.
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Affiliation(s)
- Daniel R. Matute
- Biology DepartmentUniversity of North CarolinaChapel HillNorth Carolina27510
| | - Brandon S. Cooper
- Division of Biological SciencesUniversity of MontanaMissoulaMontana59812
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32
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SARS-CoV-2: Cross-scale Insights from Ecology and Evolution. Trends Microbiol 2021; 29:593-605. [PMID: 33893024 PMCID: PMC7997387 DOI: 10.1016/j.tim.2021.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/19/2022]
Abstract
Ecological and evolutionary processes govern the fitness, propagation, and interactions of organisms through space and time, and viruses are no exception. While coronavirus disease 2019 (COVID-19) research has primarily emphasized virological, clinical, and epidemiological perspectives, crucial aspects of the pandemic are fundamentally ecological or evolutionary. Here, we highlight five conceptual domains of ecology and evolution – invasion, consumer-resource interactions, spatial ecology, diversity, and adaptation – that illuminate (sometimes unexpectedly) the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We describe the applications of these concepts across levels of biological organization and spatial scales, including within individual hosts, host populations, and multispecies communities. Together, these perspectives illustrate the integrative power of ecological and evolutionary ideas and highlight the benefits of interdisciplinary thinking for understanding emerging viruses.
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33
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Ortego J, Gutiérrez-Rodríguez J, Noguerales V. Demographic consequences of dispersal-related trait shift in two recently diverged taxa of montane grasshoppers. Evolution 2021; 75:1998-2013. [PMID: 33646593 DOI: 10.1111/evo.14205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/03/2021] [Accepted: 02/17/2021] [Indexed: 12/19/2022]
Abstract
Although the pervasiveness of intraspecific wing-size polymorphism and transitions to flightlessness have long captivated biologists, the demographic outcomes of shifts in dispersal ability are not yet well understood and have been seldom studied at early stages of diversification. Here, we use genomic data to infer the consequences of dispersal-related trait variation in the taxonomically controversial short-winged (Chorthippus corsicus corsicus) and long-winged (Chorthippus corsicus pascuorum) Corsican grasshoppers. Our analyses revealed lack of contemporary hybridization between sympatric long- and short-winged forms and phylogenomic reconstructions supported their taxonomic distinctiveness, rejecting the hypothesis of intraspecific wing polymorphism. Statistical evaluation of alternative models of speciation strongly supported a scenario of Pleistocene divergence (<1.5 Ma) with ancestral gene flow. According to neutral expectations from differences in dispersal capacity, historical effective migration rates from the long- to the short-winged taxon were threefold higher than in the opposite direction. Although populations of the two taxa present a marked genetic structure and have experienced parallel demographic histories, our coalescent-based analyses suggest that reduced dispersal has fueled diversification in the short-winged C. c. corsicus. Collectively, our study illustrates how dispersal reduction can speed up geographical diversification and increase the opportunity for allopatric speciation in topographically complex landscapes.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Víctor Noguerales
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canarias, Spain
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34
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Wessinger CA. From pollen dispersal to plant diversification: genetic consequences of pollination mode. THE NEW PHYTOLOGIST 2021; 229:3125-3132. [PMID: 33159813 DOI: 10.1111/nph.17073] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/02/2020] [Indexed: 06/11/2023]
Abstract
Pollinators influence patterns of plant speciation, and one intuitive hypothesis is that pollinators affect rates of plant diversification through their effects on pollen dispersal. By specifying mating events and pollen flow across the landscape, distinct types of pollinators may cause different opportunities for allopatric speciation. This pollen dispersal-dependent speciation hypothesis predicts that pollination mode has effects on the spatial context of mating events that scale up to impact population structure and rates of species formation. Here I consider recent comparative studies, including genetic analyses of plant mating events, population structure and comparative phylogenetic analyses, to examine evidence for this model. These studies suggest that highly mobile pollinators conduct greater gene flow within and among populations, compared to less mobile pollinators. These differences influence patterns of population structure across the landscape. However, the effects of pollination mode on speciation rates is less predictable. In some contexts, the predicted effects of pollen dispersal are outweighed by other factors that govern speciation rates. A multiscale approach to examine effects of pollination mode on plant mating system, population structure and rates of diversification is key to determining the role of pollen dispersal on plant speciation for model clades.
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Affiliation(s)
- Carolyn A Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 27708, USA
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35
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Miller MJ, Bermingham E, Turner BL, Touchon JC, Johnson AB, Winker K. Demographic consequences of foraging ecology explain genetic diversification in Neotropical bird species. Ecol Lett 2021; 24:563-571. [PMID: 33389805 DOI: 10.1111/ele.13674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 11/30/2022]
Abstract
Despite evidence that species' traits affect rates of bird diversification, biogeographic studies tend to prioritise earth history in Neotropical bird speciation. Here we compare mitochondrial genetic differentiation among 56 co-distributed Neotropical bird species with varying ecologies. The trait 'diet' best predicted divergence, with plant-dependent species (mostly frugivores and nectivores) showing lower levels of genetic divergence than insectivores or mixed-diet species. We propose that the greater vagility and demographic instability of birds whose diets rely on fruit, seeds, or nectar known to vary in abundance seasonally and between years relative to birds that eat primarily insects, drives episodic re-unification of otherwise isolated populations, resetting the divergence 'clock'. Testing this prediction using coalescent simulations, we find that plant-dependent species show stronger signals of recent demographic expansion compared to insectivores or mixed-diet species, consistent with this hypothesis. Our study provides evidence that localised ecological phenomena scale up to generate larger macroevolutionary patterns.
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Affiliation(s)
- Matthew J Miller
- Department of Biology & Wildlife, University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775, USA.,Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama
| | - Eldredge Bermingham
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama.,Patricia and Phillip Frost Museum of Science, Miami, FL, 33129, USA
| | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama
| | - Justin C Touchon
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama.,Biology Department, Vassar College, 124 Raymond Ave., Poughkeepsie, NY, 12604, USA
| | - Andrew B Johnson
- Department of Biology & Wildlife, University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775, USA.,Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kevin Winker
- Department of Biology & Wildlife, University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775, USA
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36
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On the Origin of Coexisting Species. Trends Ecol Evol 2020; 36:284-293. [PMID: 33353727 DOI: 10.1016/j.tree.2020.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/07/2020] [Accepted: 11/13/2020] [Indexed: 11/22/2022]
Abstract
Speciation is frequently initiated but rarely completed, a phenomenon hypothesized to arise due to the failure of nascent lineages to persist. Although a failure to persist often has ecological causes, key gaps exist between ecological and evolutionary theories that, if filled, would clarify when and why speciation succeeds or fails. Here, we apply ecological coexistence theory to show how the alignment between different forms of niche opportunity and niche use shape the initiation, progression, and completion of speciation. Niche evolution may drive coexistence or competitive exclusion, and an ability to coexist ecologically may help or hinder speciation. Our perspective allows progress towards unifying the origin and maintenance of species diversity across the tree of life.
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37
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Miranda LS, Prestes BO, Aleixo A. Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa193] [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
Here we use an integrative approach, including coalescent-based methods, isolation–migration and species distribution models, to infer population structure, divergence times and diversification in the two species of the genus Cymbilaimus (Aves, Thamnophilidae). Our results support a recent and rapid diversification with both incomplete lineage sorting and gene flow shaping the evolutionary history of Cymbilaimus. The spatio-temporal pattern of cladogenesis suggests that Cymbilaimus originated in the north/western portion of cis-Andean South America and then diversified into the Brazilian Shield and Central America after consolidation of the modern Amazonian drainage and the Andean range. This evolutionary scenario is explained by cycles of range expansion and dispersal, followed by isolation, and recurrent gene flow, during the last 1.2 Myr. Our results agree with those recently reported for other closely related suboscine lineages, whereby the window of introgression between closely related taxa remains open for up to a few million years after their original split. In Cymbilaimus, introgression was recurrent between C. lineatus and C. sanctaemariae, even after they acquired vocal and ecological differentiation, supporting the claim that at least in Neotropical suboscines, full reproductive compatibility may take millions of years to evolve and cannot be interpreted as synonymous with a lack of speciation.
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Affiliation(s)
- Leonardo S Miranda
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
- Coordenação de Ciências da Terra e Ecologia, Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - Bernardo O Prestes
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - Alexandre Aleixo
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, PA, Brazil
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38
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Tobias JA, Ottenburghs J, Pigot AL. Avian Diversity: Speciation, Macroevolution, and Ecological Function. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-025023] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The origin, distribution, and function of biological diversity are fundamental themes of ecology and evolutionary biology. Research on birds has played a major role in the history and development of these ideas, yet progress was for many decades limited by a focus on patterns of current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from a recent wave of integrative studies combining comprehensive phylogenetic, environmental, and functional trait data at unprecedented scales. We review these empirical advances and describe how they are reshaping our understanding of global patterns of bird diversity and the processes by which it arises, with implications for avian biogeography and functional ecology. Further expansion and integration of data sets may help to resolve longstanding debates about the evolutionary origins of biodiversity and offer a framework for understanding and predicting the response of ecosystems to environmental change.
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Affiliation(s)
- Joseph A. Tobias
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot SL5 7PY, United Kingdom
| | - Jente Ottenburghs
- Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Alex L. Pigot
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
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39
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Balfour VL, Black D, Shuker DM. A single pleiotropic locus influences the rate of hybridization between two sibling species of Lygaeus bugs. Ecol Evol 2020; 10:12224-12232. [PMID: 33209283 PMCID: PMC7663077 DOI: 10.1002/ece3.6853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/08/2020] [Indexed: 11/21/2022] Open
Abstract
The evolution of reproductive isolation lies at the heart of understanding the process of speciation. Of particular interest is the relationship between pre- and postzygotic reproductive isolation, and the genetic architecture of traits that contribute to one or both forms of reproductive isolation. The sibling species of seed bug Lygaeus equestris and L. simulans show a classic pattern of asymmetric prezygotic reproductive isolation, with female L. equestris hybridizing with male L. simulans, but with no hybridization in the reciprocal direction. We have recently described a mutant pale color form of L. simulans, that inherits as a single Mendelian locus and is pleiotropic for a number of other life history and behavioral traits. Here, we tested whether this locus also influences pre- and postzygotic reproductive isolation. Two sets of experimental crosses revealed that behavioral isolation varied with mutant versus wild-type phenotype for male L. simulans, with the pale form less successful at mating with female L. equestris. In terms of trying to assess postzygotic isolation, levels of hybrid offspring production were uniformly low across the experiments. However, we did obtain, for the first time, hybrid offspring from a pairing between a female L. simulans and a male L. equestris. In this instance, the female was of the pale mutant genotype. Together with evidence for heterozygote advantage in terms of nymph survival, we consider our results in terms of possible mechanisms of reproductive isolation between this species pair, the role of the pale mutation, and the possible genetic architectures underlying the mutation, from a single gene to a supergene.
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40
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Prates I, Singhal S. Predicting speciation probability from replicated population histories. Mol Ecol 2020; 29:2954-2956. [PMID: 32745299 DOI: 10.1111/mec.15577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/27/2020] [Indexed: 11/30/2022]
Abstract
In this issue of Molecular Ecology, Yamasaki et al. (2020) use genetic data from extensive sampling of Rhinogobius goby fish across the Ryukyu Archipelago in Japan to demonstrate the parallel speciation of a freshwater form from an ancestral amphidromous form. They then show that ecosystem size strongly predicts the probability of speciation between the two forms across islands. In doing so, this study connects population-level processes (microevolution) to broad-scale biodiversity patterns (macroevolution), an important but understudied link in evolutionary biology. Moving forward, we can build on this research to (a) more directly determine how geographic, ecological and historical factors influence the different stages of the speciation process, and (b) understand whether mechanisms inferred from insular radiations extend to those on continents, where both demographic histories and environmental regimes are likely more complex.
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Affiliation(s)
- Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sonal Singhal
- Department of Biology, California State University Dominguez Hills, Carson, CA, USA
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41
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Gamba D, Muchhala N. Global patterns of population genetic differentiation in seed plants. Mol Ecol 2020; 29:3413-3428. [PMID: 32743850 DOI: 10.1111/mec.15575] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/06/2020] [Accepted: 07/23/2020] [Indexed: 01/07/2023]
Abstract
Evaluating the factors that drive patterns of population differentiation in plants is critical for understanding several biological processes such as local adaptation and incipient speciation. Previous studies have given conflicting results regarding the significance of pollination mode, seed dispersal mode, mating system, growth form and latitudinal region in shaping patterns of genetic structure, as estimated by FST values, and no study to date has tested their relative importance together across a broad scale. Here, we assembled a 337-species data set for seed plants from publications with data on FST from nuclear markers and species traits, including variables pertaining to the sampling scheme of each study. We used species traits, while accounting for sampling variables, to perform phylogenetic multiple regressions. Results demonstrated that FST values were higher for tropical, mixed-mating, non-woody species pollinated by small insects, indicating greater population differentiation, and lower for temperate, outcrossing trees pollinated by wind. Among the factors we tested, latitudinal region explained the largest portion of variance, followed by pollination mode, mating system and growth form, while seed dispersal mode did not significantly relate to FST . Our analyses provide the most robust and comprehensive evaluation to date of the main ecological factors predicted to drive population differentiation in seed plants, with important implications for understanding the basis of their genetic divergence. Our study supports previous findings showing greater population differentiation in tropical regions and is the first that we are aware of to robustly demonstrate greater population differentiation in species pollinated by small insects.
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Affiliation(s)
- Diana Gamba
- Biology Department, University of Missouri, Saint Louis, MO, USA
| | - Nathan Muchhala
- Biology Department, University of Missouri, Saint Louis, MO, USA
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42
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Ahmad SF, Singchat W, Jehangir M, Panthum T, Srikulnath K. Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution. Genes (Basel) 2020; 11:E827. [PMID: 32708239 PMCID: PMC7397244 DOI: 10.3390/genes11070827] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
Reptiles are notable for the extensive genomic diversity and species richness among amniote classes, but there is nevertheless a need for detailed genome-scale studies. Although the monophyletic amniotes have recently been a focus of attention through an increasing number of genome sequencing projects, the abundant repetitive portion of the genome, termed the "repeatome", remains poorly understood across different lineages. Consisting predominantly of transposable elements or mobile and satellite sequences, these repeat elements are considered crucial in causing chromosomal rearrangements that lead to genomic diversity and evolution. Here, we propose major repeat landscapes in representative reptilian species, highlighting their evolutionary dynamics and role in mediating chromosomal rearrangements. Distinct karyotype variability, which is typically a conspicuous feature of reptile genomes, is discussed, with a particular focus on rearrangements correlated with evolutionary reorganization of micro- and macrochromosomes and sex chromosomes. The exceptional karyotype variation and extreme genomic diversity of reptiles are used to test several hypotheses concerning genomic structure, function, and evolution.
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Affiliation(s)
- Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Integrative Genomics Lab-LGI, Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
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43
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Huang J. Is population subdivision different from speciation? From phylogeography to species delimitation. Ecol Evol 2020; 10:6890-6896. [PMID: 32760499 PMCID: PMC7391551 DOI: 10.1002/ece3.6524] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Species-level diversity and the underlying mechanisms that lead to the formation of new species, that is, speciation, have often been confounded with intraspecific diversity and population subdivision. The delineation between intraspecific and interspecific divergence processes has received much less attention than species delimitation. The ramifications of confounding speciation and population subdivision are that the term speciation has been used to describe many different biological divergence processes, rendering the results, or inferences, between studies incomparable. Phylogeographic studies have advanced our understanding of how spatial variation in the pattern of biodiversity can begin, become structured, and persist through time. Studies of species delimitation have further provided statistical and model-based approaches to determine the phylogeographic entities that merit species status. However, without a proper understanding and delineation between the processes that generate and maintain intraspecific and interspecific diversity in a study system, the delimitation of species may still not be biologically and evolutionarily relevant. I argue that variation in the continuity of the divergence process among biological systems could be a key factor leading to the enduring contention in delineating divergence patterns, or species delimitation, meriting future comparative studies to help us better understand the nature of biological species.
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Affiliation(s)
- Jen‐Pan Huang
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
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44
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Elgetany AH, Rensburg H, Hektoen M, Matthee C, Budaeva N, Simon CA, Struck TH. Species delineation in the speciation grey zone—The case of
Diopatra
(Annelida, Onuphidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12421] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Asmaa H. Elgetany
- Zoology Department Faculty of Science Damietta University New Damietta, Central Zone Egypt
- Natural History Museum University of Oslo Oslo Norway
| | - Hendré Rensburg
- Department of Botany and Zoology Stellenbosch University Stellenbosch South Africa
| | - Martin Hektoen
- NTNU University Museum Norwegian University of Science and Technology Trondheim Norway
| | - Conrad Matthee
- Department of Botany and Zoology Stellenbosch University Stellenbosch South Africa
| | - Nataliya Budaeva
- Department of Natural History University Museum of Bergen University of Bergen Bergen Norway
| | - Carol A Simon
- Department of Botany and Zoology Stellenbosch University Stellenbosch South Africa
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45
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Gagnaire PA. Comparative genomics approach to evolutionary process connectivity. Evol Appl 2020; 13:1320-1334. [PMID: 32684961 PMCID: PMC7359831 DOI: 10.1111/eva.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/01/2023] Open
Abstract
The influence of species life history traits and historical demography on contemporary connectivity is still poorly understood. However, these factors partly determine the evolutionary responses of species to anthropogenic landscape alterations. Genetic connectivity and its evolutionary outcomes depend on a variety of spatially dependent evolutionary processes, such as population structure, local adaptation, genetic admixture, and speciation. Over the last years, population genomic studies have been interrogating these processes with increasing resolution, revealing a large diversity of species responses to spatially structured landscapes. In parallel, multispecies meta-analyses usually based on low-genome coverage data have provided fundamental insights into the ecological determinants of genetic connectivity, such as the influence of key life history traits on population structure. However, comparative studies still lack a thorough integration of macro- and micro-evolutionary scales to fully realize their potential. Here, I present how a comparative genomics framework may provide a deeper understanding of evolutionary process connectivity. This framework relies on coupling the inference of long-term demographic and selective history with an assessment of the contemporary consequences of genetic connectivity. Standardizing this approach across several species occupying the same landscape should help understand how spatial environmental heterogeneity has shaped the diversity of historical and contemporary connectivity patterns in different taxa with contrasted life history traits. I will argue that a reasonable amount of genome sequence data can be sufficient to resolve and connect complex macro- and micro-evolutionary histories. Ultimately, implementing this framework in varied taxonomic groups is expected to improve scientific guidelines for conservation and management policies.
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Hedin M, Foldi S, Rajah-Boyer B. Evolutionary divergences mirror Pleistocene paleodrainages in a rapidly-evolving complex of oasis-dwelling jumping spiders (Salticidae, Habronattus tarsalis). Mol Phylogenet Evol 2020; 144:106696. [DOI: 10.1016/j.ympev.2019.106696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/14/2019] [Accepted: 11/27/2019] [Indexed: 10/25/2022]
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Bolte CE, Eckert AJ. Determining the when, where and how of conifer speciation: a challenge arising from the study 'Evolutionary history of a relict conifer Pseudotaxus chienii'. ANNALS OF BOTANY 2020; 125:v-vii. [PMID: 31913458 PMCID: PMC6948208 DOI: 10.1093/aob/mcz201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Constance E Bolte
- Integrative Life Sciences Doctoral Program, Virginia Commonwealth University, Richmond, VA, USA
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
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Alencar LRV, Quental TB. Exploring the drivers of population structure across desert snakes can help to link micro and macroevolution. Mol Ecol 2019; 28:4529-4532. [PMID: 31602718 DOI: 10.1111/mec.15247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/14/2022]
Abstract
To understand the underlying mechanisms generating population genetic divergence and structure is a critical step towards understanding how biodiversity evolves at both micro- and macroevolutionary scales. At the population-level, geographic isolation as well as adaptation to local environmental conditions can generate different patterns of spatial genetic variation among populations. Specific organismal traits as well as the characteristics of the environment might influence the process under which populations become spatially structured. In a From the Cover article in this issue of Molecular Ecology, Myers et al. (2019) present an integrative approach to investigate if the Cochise filter barrier (CFB), lying between the Sonoran and Chihuahuan Deserts, and the surrounding river networks were relevant in driving the population structure of 13 snake species. While local environmental conditions seem to predominantly contribute to lineage divergence, traditionally studied vicariant barriers seem to have played a minor role in shaping population structure across the studied species. This study brings insights into how population-level processes could contribute to the formation of incipient species, which ultimately might affect the speciation rates measured at macroevolutionary scales. Hence, Myers et al. (2019) not only represents an integrative study aiming to understand the drivers of population genetic divergence, but also a potentially important contribution to our ongoing challenge in linking micro- and macroevolution.
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Affiliation(s)
| | - Tiago B Quental
- Department of Ecology, University of São Paulo, São Paulo, Brazil
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