1
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Monjaraz-Ruedas R, Starrett J, Leavitt D, Hedin M. Broken Ring Speciation in California Mygalomorph Spiders (Nemesiidae, Calisoga). Am Nat 2024; 204:55-72. [PMID: 38857341 DOI: 10.1086/730262] [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: 06/12/2024]
Abstract
AbstractIdealized ring species, with approximately continuous gene flow around a geographic barrier but singular reproductive isolation at a ring terminus, are rare in nature. A broken ring species model preserves the geographic setting and fundamental features of an idealized model but accommodates varying degrees of gene flow restriction over complex landscapes through evolutionary time. Here we examine broken ring species dynamics in Calisoga spiders, which, like the classic ring species Ensatina salamanders, are distributed around the Central Valley of California. Using nuclear and mitogenomic data, we test key predictions of common ancestry, ringlike biogeography, biogeographic timing, population connectivity, and terminal overlap. We show that a ring complex of populations shares a single common ancestor, and from an ancestral area in the Sierra Nevada mountains, two distributional and phylogenomic arms encircle the Central Valley. Isolation by distance occurs along these distributional arms, although gene flow restriction is also evident. Where divergent lineages meet in the South Coast Ranges, we find rare lineage sympatry, without evidence for nuclear gene flow and with clear evidence for morphological and ecological divergence. We discuss general insights provided by broken ring species and how such a model could be explored and extended in other systems and future studies.
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2
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Seeholzer GF, Brumfield RT. Speciation-by-Extinction. Syst Biol 2023; 72:1433-1442. [PMID: 37542735 DOI: 10.1093/sysbio/syad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of "speciation-by-extinction" in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.
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Affiliation(s)
- Glenn F Seeholzer
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY, 14850, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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3
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Kauai F, Mortier F, Milosavljevic S, Van de Peer Y, Bonte D. Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems. Proc Biol Sci 2023; 290:20222456. [PMID: 36946113 PMCID: PMC10031433 DOI: 10.1098/rspb.2022.2456] [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: 12/08/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
Polyploidy, i.e. the occurrence of multiple sets of chromosomes, is regarded as an important phenomenon in plant ecology and evolution, with all flowering plants likely having a polyploid ancestry. Owing to genome shock, minority cytotype exclusion and reduced fertility, polyploids emerging in diploid populations are expected to face significant challenges to successful establishment. Their establishment and persistence are often explained by possible fitness or niche differences that would relieve the competitive pressure with diploid progenitors. Experimental evidence for such advantages is, however, not unambiguous, and considerable niche overlap exists among most polyploid species and their diploid counterparts. Here, we develop a neutral spatially explicit eco-evolutionary model to understand whether neutral processes can explain the eco-evolutionary patterns of polyploids. We present a general mechanism for polyploid establishment by showing that sexually reproducing organisms assemble in space in an iterative manner, reducing frequency-dependent mating disadvantages and overcoming potential reduced fertility issues. Moreover, we construct a mechanistic theoretical framework that allows us to understand the long-term evolution of mixed-ploidy populations and show that our model is remarkably consistent with recent phylogenomic estimates of species extinctions in the Brassicaceae family.
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Affiliation(s)
- Felipe Kauai
- Department of Biology, Terrestrial Ecology Unit, Ghent University, BE-9000 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, BE-9000 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Frederik Mortier
- Department of Biology, Terrestrial Ecology Unit, Ghent University, BE-9000 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, BE-9000 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Silvija Milosavljevic
- Department of Biology, Terrestrial Ecology Unit, Ghent University, BE-9000 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, BE-9000 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, BE-9000 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Dries Bonte
- Department of Biology, Terrestrial Ecology Unit, Ghent University, BE-9000 Ghent, Belgium
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4
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Princepe D, Czarnobai S, Pradella TM, Caetano RA, Marquitti FMD, de Aguiar MAM, Araujo SBL. Diversity patterns and speciation processes in a two-island system with continuous migration. Evolution 2022; 76:2260-2271. [PMID: 36036483 DOI: 10.1111/evo.14603] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/22/2022] [Indexed: 01/22/2023]
Abstract
Geographic isolation is a central mechanism of speciation, but perfect isolation of populations is rare. Although speciation can be hindered if gene flow is large, intermediate levels of migration can enhance speciation by introducing genetic novelty in the semi-isolated populations or founding small communities of migrants. Here, we consider a two-island neutral model of speciation with continuous migration and study diversity patterns as a function of the migration probability, population size, and number of genes involved in reproductive isolation (dubbed as genome size). For small genomes, low levels of migration induce speciation on the islands that otherwise would not occur. Diversity, however, drops sharply to a single species inhabiting both islands as the migration probability increases. For large genomes, sympatric speciation occurs even when the islands are strictly isolated. Then species richness per island increases with the probability of migration, but the total number of species decreases as they become cosmopolitan. For each genome size, there is an optimal migration intensity for each population size that maximizes the number of species. We discuss the observed modes of speciation induced by migration and how they increase species richness in the insular system while promoting asymmetry between the islands and hindering endemism.
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Affiliation(s)
- Débora Princepe
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brasil
| | - Simone Czarnobai
- Programa de Pós Graduação em Ecologia e Conservação, Universidade Federal do Paraná, Curitiba, Brasil
| | - Thiago M Pradella
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brasil
| | - Rodrigo A Caetano
- Departamento de Física, Universidade Federal do Paraná, Curitiba, Brasil
| | - Flavia M D Marquitti
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brasil.,Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brasil
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brasil
| | - Sabrina B L Araujo
- Departamento de Física, Universidade Federal do Paraná, Curitiba, Brasil
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5
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Dickens JK, Bitton PP, Bravo GA, Silveira LF. Species limits, patterns of secondary contact and a new species in the Trogon rufus complex (Aves: Trogonidae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The black-throated trogon, Trogon rufus, is a widespread, polytypic species-complex with a convoluted taxonomic history. Here, we integrated morphological, vocal and genetic datasets, including spectral data and digital quantification of barred plumage, to assess and redefine its species limits according to the foremost species concepts. We suggest the recognition of four named and one new species. Trogon tenellus and T. cupreicauda are divergent across Central and South America without geographic overlap or intermediates. Trogon chrysochloros in the Atlantic Forests of Brazil is phenotypically, genetically and ecologically distinct. In Amazonia, Trogon rufus consists of three phenotypically distinct subspecies intergrading with each other in a ring-like formation around central Amazonian rivers. Trogon rufus rufus in the Guiana Shield, Trogon rufus amazonicus in south-eastern Amazonia and Trogon rufus sulphureus in western Amazonia, with contact across the Lower Amazon and Madeira rivers, likely due to secondary contact between incompletely diverged lineages. The unique combination of song, morphology and mtDNA features of an unnamed, isolated population in the Atlantic Forest of north-eastern Brazil resulted in its description as a new species, known only from the type locality and considered here as Critically Endangered, requiring urgent conservation actions.
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Affiliation(s)
- Jeremy Kenneth Dickens
- Museu de Zoologia da Universidade de São Paulo, 481 Av. Nazaré, Ipiranga, São Paulo, Brazil
- Fundación Para La Tierra, 321 Mariscal José Félix Estigarribia, Pilar, 2800, Ñeembucú, Paraguay
| | - Pierre-Paul Bitton
- Department of Psychology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL, Canada
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Luís Fábio Silveira
- Museu de Zoologia da Universidade de São Paulo, 481 Av. Nazaré, Ipiranga, São Paulo, Brazil
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6
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Lipo CP, DiNapoli RJ, Madsen ME, Hunt TL. Population structure drives cultural diversity in finite populations: A hypothesis for localized community patterns on Rapa Nui (Easter Island, Chile). PLoS One 2021; 16:e0250690. [PMID: 33979335 PMCID: PMC8115772 DOI: 10.1371/journal.pone.0250690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/13/2021] [Indexed: 12/02/2022] Open
Abstract
Understanding how and why cultural diversity changes in human populations remains a central topic of debate in cultural evolutionary studies. Due to the effects of drift, small and isolated populations face evolutionary challenges in the retention of richness and diversity of cultural information. Such variation, however, can have significant fitness consequences, particularly when environmental conditions change unpredictably, such that knowledge about past environments may be key to long-term persistence. Factors that can shape the outcomes of drift within a population include the semantics of the traits as well as spatially structured social networks. Here, we use cultural transmission simulations to explore how social network structure and interaction affect the rate of trait retention and extinction. Using Rapa Nui (Easter Island, Chile) as an example, we develop a model-based hypothesis for how the structural constraints of communities living in small, isolated populations had dramatic effects and likely led to preventing the loss of cultural information in both community patterning and technology.
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Affiliation(s)
- Carl P. Lipo
- Department of Anthropology, Environmental Studies Program, Harpur College of Arts and Sciences, Binghamton University, Binghamton, NY, United States of America
| | - Robert J. DiNapoli
- Department of Anthropology, Environmental Studies Program, Harpur College of Arts and Sciences, Binghamton University, Binghamton, NY, United States of America
| | - Mark E. Madsen
- Department of Anthropology, University of Washington, Seattle, WA, United States of America
| | - Terry L. Hunt
- The Honors College and School of Anthropology, University of Arizona, Tucson, AZ, United States of America
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7
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Wang Y, Feijó A, Cheng J, Xia L, Wen Z, Ge D, Sun J, Lu L, Li S, Yang Q. Ring distribution patterns-diversification or speciation? Comparative phylogeography of two small mammals in the mountains surrounding the Sichuan Basin. Mol Ecol 2021; 30:2641-2658. [PMID: 33817880 DOI: 10.1111/mec.15913] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 01/26/2023]
Abstract
Studying the genetic differentiation in a unique geographical area contributes to understanding the process of speciation. Here, we explore the spatial genetic structure and underlying formation mechanism of two congeneric small mammal species (Apodemus draco and A. chevrieri), which are mainly distributed in the mountains surrounding the lowland Sichuan Basin, southwest China. We applied a set of comparative phylogeographical analyses to determine their genetic diversification patterns, combining mitochondrial (Cytb and COI) and nuclear (microsatellite loci) markers, with dense sampling throughout the range (411 A. draco from 21 sites and 191 A. chevrieri from 22 sites). Moreover, we performed three complementary statistical methods to investigate the correlation between genotype and geographical and environmental components, and predicted the potential suitable distributional range under the present and historical climate conditions. Our results suggest that both species have experienced allopatric differentiation and admixture in historical periods, resulting in a ring-shape diversification, under the barrier effect of the Sichuan Basin. We infer that the tectonic events of the Qinghai-Tibetan Plateau and climatic oscillations during the Quaternary played an important role on the genetic divergence of the two species by providing environmental heterogeneity and geographical variation. Our study reveals a case of two sympatric small mammals following a ring-shaped diversification pattern and provides insight into the process of differentiation.
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Affiliation(s)
- Yanqun Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,School of Animal Science, Xichang College, Xichang, Sichuan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jian Sun
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Liang Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Song Li
- Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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8
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Cianciarullo AM, Bonini-Domingos CR, Vizotto LD, Kobashi LS, Beçak ML, Beçak W. Whole-genome duplication and hemoglobin differentiation traits between allopatric populations of Brazilian Odontophrynus americanus species complex (Amphibia, Anura). Genet Mol Biol 2019; 42:436-444. [PMID: 31259358 PMCID: PMC6726162 DOI: 10.1590/1678-4685-gmb-2017-0260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 07/25/2018] [Indexed: 11/21/2022] Open
Abstract
Two allopatric populations of Brazilian diploid and tetraploid
Odontophrynus americanus species complex, both from São
Paulo state, had their blood hemoglobin biochemically analyzed. In addition,
these specimens were cytogenetically characterized. Biochemical characterization
of hemoglobin expression showed a distinct banding pattern between the
allopatric specimens. Besides this, two distinct phenotypes, not linked to
ploidy, sex, or age, were observed in adult animals of both populations.
Phenotype A exhibits dark-colored body with small papillae, ogival-shaped jaw
with reduced interpupillary distance and shorter hind limbs. Phenotype B shows
yellowish-colored body with larger papillae, arch-shaped jaw with broader
interpupillary distance and longer hind limbs. Intermediate phenotypes were also
found. Considering the geographical isolation of both populations, differences
in chromosomal secondary constrictions and distinct hemoglobins banding
patterns, these data indicate that 2n and 4n populations represent cryptic
species in the O. americanus species complex. The observed
phenotypic diversity can be interpreted as population genetic variability.
Eventually future data may indicate a probable beginning of speciation in these
Brazilian frogs. Such inter- and intrapopulational differentiation/speciation
process indicates that O. americanus species complex taxonomy
deserves further evaluation by genomics and metabarcoding communities, also
considering the pattern of hemoglobin expression, in South American frogs.
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Affiliation(s)
| | - Claudia R Bonini-Domingos
- Department of Biology, Laboratory of Hemoglobins and Genetics of the Hematological Diseases, Universidade Estadual Paulista "Julio de Mesquita Filho (UNESP), São José do Rio Preto, SP, Brazil
| | - Luiz D Vizotto
- Department of Zoology, Universidade Estadual Paulista "Julio de Mesquita Filho (UNESP), São José do Rio Preto, SP, Brazil
| | - Leonardo S Kobashi
- Laboratory of Ecology and Evolution, Instituto Butantan, São Paulo, SP, Brazil.,Universidade Paulista (UNIP) São Paulo, SP, Brazil
| | | | - Willy Beçak
- Laboratory of Genetics, Instituto Butantan, São Paulo, SP, Brazil
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9
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Cacho NI, Monteverde-Suárez MJ, McIntyre PJ. Convergent evolution in floral morphology in a plant ring species, the Caribbean Euphorbia tithymaloides. AMERICAN JOURNAL OF BOTANY 2019; 106:1032-1045. [PMID: 31281963 DOI: 10.1002/ajb2.1318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Ring species have long fascinated evolutionary biologists for their potential insights into lineage divergence and speciation across space. Few studies have investigated the potential for convergent or parallel evolution along the diverging fronts of ring species. We investigated a potential case of parallel floral variation in the Caribbean spurge Euphorbia tithymaloides, the only plant system with molecular support as a ring species. The terminal populations of each front, despite being the most divergent, exhibit such similar floral traits that they were originally considered each other's closest relative. METHODS We evaluated convergence in floral and leaf traits in relation to geography across 95 populations spanning the distribution of E. tithymaloides. We also reanalyzed available genetic data (from previous phylogenetic analyses) in an explicitly spatial framework. RESULTS Floral morphology appears to have shifted in a convergent fashion along both geographic fronts of E. tithymaloides, resulting in shorter and more compact inflorescences in Antillean populations compared to the typical elongate "slipper-like" cyathia characteristic of the area of origin. Patterns of spatial genetic variation were more consistent with a two-fronted invasion of the Caribbean than with a simpler model of isolation-by-distance. CONCLUSIONS Floral divergence in E. tithymaloides is consistent with convergent evolution along the two fronts of a ring species. We outline several (not mutually exclusive) mechanisms that could be driving patterns in morphology, including shifts toward generalized pollination with reduced reliance on hummingbirds, shifts in floral structure closely matching available hummingbird bill traits, and shifts toward increased selfing.
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Affiliation(s)
- N Ivalú Cacho
- Instituto de Biología, Universidad Nacional Autónoma de México, CDMX 04510, Mexico
| | | | - Patrick J McIntyre
- NatureServe, Western Regional Office, 1680 38th St., Suite 120, Boulder, Colorado, 80301, USA
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10
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Costa CLN, Lemos-Costa P, Marquitti FMD, Fernandes LD, Ramos MF, Schneider DM, Martins AB, de Aguiar MAM. Signatures of Microevolutionary Processes in Phylogenetic Patterns. Syst Biol 2018; 68:131-144. [PMID: 29939352 DOI: 10.1093/sysbio/syy049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/13/2018] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem, we analyzed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.
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Affiliation(s)
- Carolina L N Costa
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Paula Lemos-Costa
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Flavia M D Marquitti
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Lucas D Fernandes
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900 Piracicaba, SP, Brazil
| | - Marlon F Ramos
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - David M Schneider
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Ayana B Martins
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Department of Fish Ecology & Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
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11
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Vincenot L, Popa F, Laso F, Donges K, Rexer KH, Kost G, Yang ZL, Nara K, Selosse MA. Out of Asia: Biogeography of fungal populations reveals Asian origin of diversification of the Laccaria amethystina complex, and two new species of violet Laccaria. Fungal Biol 2017; 121:939-955. [DOI: 10.1016/j.funbio.2017.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/28/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022]
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12
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Muniz DG, Santos ESA, Guimarães PR, Nakagawa S, Machado G. A multinomial network method for the analysis of mate choice and assortative mating in spatially structured populations. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12798] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Danilo G. Muniz
- Postgraduate Programme in Ecology Department of Ecology Institute of Biosciences University of São Paulo São Paulo Brazil
- LAGE Lab Department of Ecology Institute of Biosciences University of São Paulo São Paulo Brazil
| | - Eduardo S. A. Santos
- LAGE Lab Department of Ecology Institute of Biosciences University of São Paulo São Paulo Brazil
- BECO Lab Department of Zoology Institute of Biosciences University of São Paulo São Paulo Brazil
| | - Paulo R. Guimarães
- LAGE Lab Department of Ecology Institute of Biosciences University of São Paulo São Paulo Brazil
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre, and School of Biological, Earth and Environmental Sciences University New South Wales Sydney NSW Australia
| | - Glauco Machado
- LAGE Lab Department of Ecology Institute of Biosciences University of São Paulo São Paulo Brazil
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13
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King DM, Scott AD, Bahar S. Multiple phase transitions in an agent-based evolutionary model with neutral fitness. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170005. [PMID: 28484629 PMCID: PMC5414266 DOI: 10.1098/rsos.170005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/17/2017] [Indexed: 06/07/2023]
Abstract
Null models are crucial for understanding evolutionary processes such as speciation and adaptive radiation. We analyse an agent-based null model, considering a case without selection-neutral evolution-in which organisms are defined only by phenotype. Universal dynamics has previously been demonstrated in a related model on a neutral fitness landscape, showing that this system belongs to the directed percolation (DP) universality class. The traditional null condition of neutral fitness (where fitness is defined as the number of offspring each organism produces) is extended here to include equal probability of death among organisms. We identify two types of phase transition: (i) a non-equilibrium DP transition through generational time (i.e. survival), and (ii) an equilibrium ordinary percolation transition through the phenotype space (based on links between mating organisms). Owing to the dynamical rules of the DP reaction-diffusion process, organisms can only sparsely fill the phenotype space, resulting in significant phenotypic diversity within a cluster of mating organisms. This highlights the necessity of understanding hierarchical evolutionary relationships, rather than merely developing taxonomies based on phenotypic similarity, in order to develop models that can explain phylogenetic patterns found in the fossil record or to make hypotheses for the incomplete fossil record of deep time.
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Affiliation(s)
- Dawn M. King
- Department of Physics and Astronomy and Center for Neurodynamics, University of Missouri at St Louis, St Louis, MO 63121, USA
| | - Adam D. Scott
- Division of Oncology, Department of Medicine, Washington University, St Louis, MO 63108, USA
- McDonnell Genome Institute, Department of Medicine, Washington University, St Louis, MO 63108, USA
| | - Sonya Bahar
- Department of Physics and Astronomy and Center for Neurodynamics, University of Missouri at St Louis, St Louis, MO 63121, USA
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14
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Rios VP, Kraenkel RA. Do I Know You? How Individual Recognition Affects Group Formation and Structure. PLoS One 2017; 12:e0170737. [PMID: 28125708 PMCID: PMC5268392 DOI: 10.1371/journal.pone.0170737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 12/09/2016] [Indexed: 11/21/2022] Open
Abstract
Groups in nature can be formed by interactions between individuals, or by external pressures like predation. It is reasonable to assume that groups formed by internal and external conditions have different dynamics and structures. We propose a computational model to investigate the effects of individual recognition on the formation and structure of animal groups. Our model is composed of agents that can recognize each other and remember previous interactions, without any external pressures, in order to isolate the effects of individual recognition. We show that individual recognition affects the number and size of groups, and the modularity of the social networks. This model can be used as a null model to investigate the effects of external factors on group formation and persistence.
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Affiliation(s)
- Vitor Passos Rios
- Programa de Pós-Graduação em Ecologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail:
| | - Roberto André Kraenkel
- Instituto de Física Teórica, Universidade Estadual Paulista, São Paulo, São Paulo, Brazil
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15
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Vijay N. Digest: Why are there no ring species?*. Evolution 2017; 71:501-502. [DOI: 10.1111/evo.13162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022]
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16
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de Brito Martins A, de Aguiar MAM. Barriers to gene flow and ring species formation. Evolution 2016; 71:442-448. [PMID: 27861800 DOI: 10.1111/evo.13121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/20/2016] [Indexed: 11/30/2022]
Abstract
Ring species are groups of organisms that dispersed along a ring-shaped region in such a way that the two ends of the population that meet after many generations are reproductively isolated. They provide a rare opportunity to understand the role of spatial structuring in speciation. Here, we simulate the evolution of ring species assuming that individuals become sexually isolated if the genetic distance between them is above a certain threshold. The model incorporates two forms of dispersal limitation: exogenous geographic barriers that limit the population range and endogenous barriers that result in genetic structuring within the population range. As expected, species' properties that reduce gene flow within the population range facilitate the evolution of reproductive isolation and ring species formation. However, if populations are confined to narrow ranges by geographic barriers, ring species formation increases when local mating is less spatially restricted. Ring species are most likely to form if a population expands while confined to a quasi-unidimensional range but preserving high mobility in the direction of the range expansion. These conditions are unlikely to be met or persist in real populations and may explain why ring species are rare.
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Affiliation(s)
- Ayana de Brito Martins
- Depto. de Física da Matéria Condensada, Inst. de Física "Gleb Wataghin", Universidade Estadual de Campinas, Campinas, SP, Brazil.,Depto. de Ecologia, Inst. de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, ZH, Switzerland
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17
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Dufresnes C, Litvinchuk SN, Leuenberger J, Ghali K, Zinenko O, Stöck M, Perrin N. Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis). Mol Ecol 2016; 25:4285-300. [PMID: 27220555 DOI: 10.1111/mec.13706] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 04/26/2016] [Accepted: 05/11/2016] [Indexed: 11/30/2022]
Abstract
Hotspots of intraspecific genetic diversity, which are of primary importance for the conservation of species, have been associated with glacial refugia, that is areas where species survived the Quaternary climatic oscillations. However, the proximate mechanisms generating these hotspots remain an open issue. Hotspots may reflect the long-term persistence of large refugial populations; alternatively, they may result from allopatric differentiation between small and isolated populations, that later admixed. Here, we test these two scenarios in a widely distributed species of tree frog, Hyla orientalis, which inhabits Asia Minor and southeastern Europe. We apply a fine-scale phylogeographic survey, combining fast-evolving mitochondrial and nuclear markers, with a dense sampling throughout the range, as well as ecological niche modelling, to understand what shaped the genetic variation of this species. We documented an important diversity centre around the Black Sea, composed of multiple allopatric and/or parapatric diversifications, likely driven by a combination of Pleistocene climatic fluctuations and complex regional topography. Remarkably, this diversification forms a ring around the Black Sea, from the Caucasus through Anatolia and eastern Europe, with terminal forms coming into contact and partially admixing in Crimea. Our results support the view that glacial refugia generate rather than host genetic diversity and can also function as evolutionary melting pots of biodiversity. Moreover, we report a new case of ring diversification, triggered by a large, yet cohesive dispersal barrier, a very rare situation in nature. Finally, we emphasize the Black Sea region as an important centre of intraspecific diversity in the Palearctic with implications for conservation.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg, 194064, Russia
| | - Julien Leuenberger
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Karim Ghali
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Oleksandr Zinenko
- The Museum of Nature, V. N. Karazin Kharkiv National University, Trinkler st. 8, Kharkiv, 61058, Ukraine
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, Berlin, D-12587, Germany
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
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18
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Schneider DM, Martins AB, de Aguiar MAM. The mutation-drift balance in spatially structured populations. J Theor Biol 2016; 402:9-17. [PMID: 27132184 DOI: 10.1016/j.jtbi.2016.04.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 02/22/2016] [Accepted: 04/18/2016] [Indexed: 11/17/2022]
Abstract
In finite populations the action of neutral mutations is balanced by genetic drift, leading to a stationary distribution of alleles that displays a transition between two different behaviors. For small mutation rates most individuals will carry the same allele at equilibrium, whereas for high mutation rates of the alleles will be randomly distributed with frequencies close to one half for a biallelic gene. For well-mixed haploid populations the mutation threshold is μc=1/2N, where N is the population size. In this paper we study how spatial structure affects this mutation threshold. Specifically, we study the stationary allele distribution for populations placed on regular networks where connected nodes represent potential mating partners. We show that the mutation threshold is sensitive to spatial structure only if the number of potential mates is very small. In this limit, the mutation threshold decreases substantially, increasing the diversity of the population at considerably low mutation rates. Defining kc as the degree of the network for which the mutation threshold drops to half of its value in well-mixed populations we show that kc grows slowly as a function of the population size, following a power law. Our calculations and simulations are based on the Moran model and on a mapping between the Moran model with mutations and the voter model with opinion makers.
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Affiliation(s)
- David M Schneider
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp 13083-970, Campinas, SP, Brazil
| | - Ayana B Martins
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp 13083-970, Campinas, SP, Brazil
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp 13083-970, Campinas, SP, Brazil
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19
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Pereira RJ, Wake DB. Ring species as demonstrations of the continuum of species formation. Mol Ecol 2016; 24:5312-4. [PMID: 26509692 DOI: 10.1111/mec.13412] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/02/2015] [Indexed: 11/28/2022]
Abstract
In the mid-20th century, Ernst Mayr (1942) and Theodosius Dobzhansky (1958) championed the significance of 'circular overlaps' or 'ring species' as the perfect demonstration of the gradual nature of species formation. As an ancestral species expands its range, wrapping around a geographic barrier, derived taxa within the ring display interactions typical of populations, such as genetic and morphological intergradation, while overlapping taxa at the terminus of the ring behave largely as sympatric, reproductively isolated species. Are ring species extremely rare or are they just difficult to detect? What conditions favour their formation? Modelling studies have attempted to address these knowledge gaps by estimating the biological parameters that result in stable ring species (Martins et al. 2013), and determining the necessary topographic parameters of the barriers encircled (Monahan et al. 2012). However, any generalization is undermined by a major limitation: only a handful of ring species are known to exist in nature. In addition, many of them have been broken into multiple species presumed to be evolving independently, usually obscuring the evolutionary dynamics that generate diversity. A paper in this issue of Molecular Ecology by Fuchs et al. (2015), focused on the entire genealogy of a bulbul (Alophoixus) species complex, offers key insights into the evolutionary processes underlying diversification of this Indo-Malayan bird. Their findings fulfil most of the criteria that can be expected for ring species (Fig. ): an ancestor has colonized the mainland from Sundaland, expanded along the forested habitat wrapping around Thailand's lowlands, adjacent taxa intergrade around the ring distribution, and terminal taxa overlap at the ring closure. Although it remains unclear whether ring divergence has resulted in restrictive gene flow relative to that observed around the ring, their results suggest that circular overlaps might be more common in nature than currently recognized in the literature. Most importantly, this work shows that the continuum of species formation that Mayr and Dobzhansky praised in circular overlaps is found in biological systems currently described as 'rings of species', in addition to the idealized 'ring species'.
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Affiliation(s)
- Ricardo J Pereira
- Faculty of Science, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - David B Wake
- Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USA
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20
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Wiland-szymańska J, Buczkowska K, Drapikowska M, Maślak M, Bączkiewicz A, Czylok A. Genetic structure and barcode identification of an endangered orchid species, Liparis loeselii, in Poland. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1153005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | - Katarzyna Buczkowska
- Department of Genetics, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Maria Drapikowska
- Department of Ecology and Environmental Protection, Poznan University of Life Sciences, Piątkowska 94C, 60-649 Poznań, Poland
| | | | - Alina Bączkiewicz
- Department of Genetics, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Andrzej Czylok
- Faculty of Earth Sciences, University of Silesia, Będzińska 60, 41-200 Sosnowiec, Poland
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21
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22
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Schneider DM, Baptestini EM, de Aguiar MAM. Diploid versus haploid models of neutral speciation. J Biol Phys 2016; 42:235-45. [PMID: 26755353 DOI: 10.1007/s10867-015-9404-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/15/2015] [Indexed: 11/28/2022] Open
Abstract
Neutral models of speciation based on isolation by distance and assortative mating, termed topopatric, have shown to be successful in describing abundance distributions and species-area relationships. Previous works have considered this type of process in the context of haploid genomes. Here we discuss the implementation of two schemes of dominance to analyze the effects of diploidy: a complete dominance model in which one allele dominates over the other and a perfect codominant model in which heterozygous genotypes give rise to a third phenotype. In the case of complete dominance, we observe that speciation requires stronger spatial inbreeding in comparison to the haploid model. For perfect codominance, instead, speciation demands stronger genetic assortativeness. Nevertheless, once speciation is established, the three models predict the same abundance distributions even at the quantitative level, revealing the robustness of the original mechanism to describe biodiversity features.
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Affiliation(s)
- David M Schneider
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-859, Campinas, SP, Brazil.
| | - Elizabeth M Baptestini
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-859, Campinas, SP, Brazil
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-859, Campinas, SP, Brazil
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23
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Fuchs J, Ericson PG, Bonillo C, Couloux A, Pasquet E. The complex phylogeography of the Indo-MalayanAlophoixusbulbuls with the description of a putative new ring species complex. Mol Ecol 2015. [DOI: 10.1111/mec.13337] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jérôme Fuchs
- Département Systématique et Evolution; UMR7205 Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle; CP 51, 57 rue Cuvier F-75231 Paris Cedex 05 France
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum National d'Histoire Naturelle; 57 rue Cuvier F-75231 Paris Cedex 05 France
| | - Per G.P. Ericson
- Department of Zoology; Swedish Museum of Natural History; P.O. Box 50007 SE-10405 Stockholm Sweden
| | - Céline Bonillo
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum National d'Histoire Naturelle; 57 rue Cuvier F-75231 Paris Cedex 05 France
| | - Arnaud Couloux
- Genoscope; Centre National de Séquençage; 2, rue Gaston Crémieux, CP5706 91057 Evry Cedex France
| | - Eric Pasquet
- Département Systématique et Evolution; UMR7205 Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle; CP 51, 57 rue Cuvier F-75231 Paris Cedex 05 France
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum National d'Histoire Naturelle; 57 rue Cuvier F-75231 Paris Cedex 05 France
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de Aguiar MAM, Schneider DM, do Carmo E, Campos PRA, Martins AB. Error catastrophe in populations under similarity-essential recombination. J Theor Biol 2015; 374:48-53. [PMID: 25843218 DOI: 10.1016/j.jtbi.2015.03.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/24/2015] [Accepted: 03/24/2015] [Indexed: 10/23/2022]
Abstract
Organisms are often more likely to exchange genetic information with others that are similar to themselves. One of the most widely accepted mechanisms of RNA virus recombination requires substantial sequence similarity between the parental RNAs and is termed similarity-essential recombination. This mechanism may be considered analogous to assortative mating, an important form of non-random mating that can be found in animals and plants. Here we study the dynamics of haplotype frequencies in populations evolving under similarity-essential recombination. Haplotypes are represented by a genome of B biallelic loci and the Hamming distance between individuals is used as a criterion for recombination. We derive the evolution equations for the haplotype frequencies assuming that recombination does not occur if the genetic distance is larger than a critical value G and that mutation occurs at a rate μ per locus. Additionally, uniform crossover is considered. Although no fitness is directly associated to the haplotypes, we show that frequency-dependent selection emerges dynamically and governs the haplotype distribution. A critical mutation rate μc can be identified as the error threshold transition, beyond which this selective information cannot be stored. For μ<μc the distribution consists of a dominant sequence surrounded by a cloud of closely related sequences, characterizing a quasispecies. For μ>μc the distribution becomes uniform, with all haplotypes having the same frequency. In the case of extreme assortativeness, where individuals only recombine with others identical to themselves (G=0), the error threshold results μc=1/4, independently of the genome size. For weak assortativity (G=B-1)μc=2(-(B+1)) and for the case of no assortativity (G=B) μc=0. We compute the mutation threshold for 0<G<B and show that, for large B, it depends only on the ratio G/B. We discuss the consequences of these results for recombination in viruses and for speciation.
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Affiliation(s)
- Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, 13083-970, Campinas, SP, Brazil.
| | - David M Schneider
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, 13083-970, Campinas, SP, Brazil
| | - Eduardo do Carmo
- Universidade Federal da Integração Latino Americana, 85867-970 Foz do Iguaçu, PR, Brazil
| | - Paulo R A Campos
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Ayana B Martins
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, 13083-970, Campinas, SP, Brazil; Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
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25
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Christie MR, Knowles LL. Habitat corridors facilitate genetic resilience irrespective of species dispersal abilities or population sizes. Evol Appl 2015; 8:454-63. [PMID: 26029259 PMCID: PMC4430769 DOI: 10.1111/eva.12255] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/16/2015] [Indexed: 01/16/2023] Open
Abstract
Corridors are frequently proposed to connect patches of habitat that have become isolated due to human-mediated alterations to the landscape. While it is understood that corridors can facilitate dispersal between patches, it remains unknown whether corridors can mitigate the negative genetic effects for entire communities modified by habitat fragmentation. These negative genetic effects, which include reduced genetic diversity, limit the potential for populations to respond to selective agents such as disease epidemics and global climate change. We provide clear evidence from a forward-time, agent-based model (ABM) that corridors can facilitate genetic resilience in fragmented habitats across a broad range of species dispersal abilities and population sizes. Our results demonstrate that even modest increases in corridor width decreased the genetic differentiation between patches and increased the genetic diversity and effective population size within patches. Furthermore, we document a trade-off between corridor quality and corridor design whereby populations connected by high-quality habitat (i.e., low corridor mortality) are more resilient to suboptimal corridor design (e.g., long and narrow corridors). The ABM also revealed that species interactions can play a greater role than corridor design in shaping the genetic responses of populations to corridors. These results demonstrate how corridors can provide long-term conservation benefits that extend beyond targeted taxa and scale up to entire communities irrespective of species dispersal abilities or population sizes.
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Affiliation(s)
- Mark R Christie
- Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA ; Department of Biological Sciences & Department of Forestry and Natural Resources, Purdue University West Lafayette, IN, USA
| | - L Lacey Knowles
- Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
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27
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Bard J. Generating anatomical variation through mutations in networks - implications for evolution. J Anat 2014; 225:123-31. [PMID: 24934180 DOI: 10.1111/joa.12205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2014] [Indexed: 12/01/2022] Open
Abstract
Genetic mutation leads to anatomical variation only indirectly because many proteins involved in generating anatomical structures in embryos operate cooperatively within molecular networks. These include gene-regulatory or control networks (CNs) for timing, signaling and patterning together with the process networks (PNs) for proliferation, apoptosis, differentiation and morphogenesis that they control. This paper argues that anatomical variation is achieved through a two-stage process: mutation alters the outputs of CNs and perhaps the proliferation network, and such changed outputs alter the ways that PNs construct tissues. This systems-biology approach has several implications: first, because networks contain many cooperating proteins, they amplify the effects of genetic variation so enabling mutation to generate a wider range of phenotypes than a single changed protein acting alone could. Second, this amplification helps explain how novel phenotypes can be produced relatively rapidly. Third, because even organisms with novel anatomical phenotypes derive from variants in standard networks, there is no genetic barrier to their producing viable offspring. This approach also clarifies a terminological difficulty: classical evolutionary genetics views genes in terms of phenotype heritability rather than as DNA sequences. This paper suggests that the molecular phenotype of the classical concept of a gene is often a protein network, with a mutation leading to an alteration in that network's dynamics.
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Affiliation(s)
- Jonathan Bard
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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28
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Alcaide M, Scordato ESC, Price TD, Irwin DE. Genomic divergence in a ring species complex. Nature 2014; 511:83-5. [DOI: 10.1038/nature13285] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/26/2014] [Indexed: 11/09/2022]
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29
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Conditions for neutral speciation via isolation by distance. J Theor Biol 2013; 335:51-6. [DOI: 10.1016/j.jtbi.2013.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 06/11/2013] [Indexed: 11/19/2022]
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