1
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Kimmitt AA, Pegan TM, Jones AW, Wacker KS, Brennan CL, Hudon J, Kirchman JJ, Ruegg K, Benz BW, Herman R, Winger BM. Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum. Proc Biol Sci 2023; 290:20221334. [PMID: 36695033 PMCID: PMC9874272 DOI: 10.1098/rspb.2022.1334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023] Open
Abstract
Pleistocene climate cycles are well documented to have shaped contemporary species distributions and genetic diversity. Northward range expansions in response to deglaciation following the Last Glacial Maximum (LGM; approximately 21 000 years ago) are surmised to have led to population size expansions in terrestrial taxa and changes in seasonal migratory behaviour. Recent findings, however, suggest that some northern temperate populations may have been more stable than expected through the LGM. We modelled the demographic history of 19 co-distributed boreal-breeding North American bird species from full mitochondrial gene sets and species-specific molecular rates. We used these demographic reconstructions to test how species with different migratory strategies were affected by glacial cycles. Our results suggest that effective population sizes increased in response to Pleistocene deglaciation earlier than the LGM, whereas genetic diversity was maintained throughout the LGM despite shifts in geographical range. We conclude that glacial cycles prior to the LGM have most strongly shaped contemporary genetic diversity in these species. We did not find a relationship between historic population dynamics and migratory strategy, contributing to growing evidence that major switches in migratory strategy during the LGM are unnecessary to explain contemporary migratory patterns.
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Affiliation(s)
- Abigail A. Kimmitt
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Teresa M. Pegan
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew W. Jones
- Department of Ornithology, Cleveland Museum of Natural History, Cleveland, OH 44106, USA
| | - Kristen S. Wacker
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Courtney L. Brennan
- Department of Ornithology, Cleveland Museum of Natural History, Cleveland, OH 44106, USA
| | - Jocelyn Hudon
- Royal Alberta Museum, Edmonton, Alberta Canada, T5J 0G2
| | | | - Kristen Ruegg
- Biology Department, Colorado State University, Fort Collins, CO 80521, USA
| | - Brett W. Benz
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rachael Herman
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Benjamin M. Winger
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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2
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Friis G, Atwell JW, Fudickar AM, Greives TJ, Yeh PJ, Price TD, Ketterson ED, Milá B. Rapid evolutionary divergence of a songbird population following recent colonization of an urban area. Mol Ecol 2022; 31:2625-2643. [DOI: 10.1111/mec.16422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/14/2022] [Accepted: 03/01/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Guillermo Friis
- National Museum of Natural Sciences Department of Biodiversity and Evolutionary Biology Spanish National Research Council (CSIC) Madrid 28006 Spain
| | | | - Adam M. Fudickar
- Department of Biology Indiana University Bloomington IN 47405 USA
| | - Timothy J. Greives
- Department of Biological Sciences North Dakota State University Fargo ND 58105 USA
| | - Pamela J. Yeh
- Department of Ecology and Evolutionary Biology University of California Los Angeles Los Angeles CA 90095 USA
| | - Trevor D. Price
- Department of Ecology and Evolution University of Chicago Chicago IL 60637 USA
| | | | - Borja Milá
- National Museum of Natural Sciences Department of Biodiversity and Evolutionary Biology Spanish National Research Council (CSIC) Madrid 28006 Spain
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3
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Vázquez-Miranda H, Zink RM, Pinto BJ. Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence. Mol Phylogenet Evol 2022; 171:107466. [DOI: 10.1016/j.ympev.2022.107466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/22/2022] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
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4
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McEntee JP, Zhelezov G, Werema C, Najar N, Peñalba JV, Mulungu E, Mbilinyi M, Karimi S, Chumakova L, Gordon Burleigh J, Bowie RCK. Punctuated evolution in the learned songs of African sunbirds. Proc Biol Sci 2021; 288:20212062. [PMID: 34784761 PMCID: PMC8595995 DOI: 10.1098/rspb.2021.2062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Learned traits are thought to be subject to different evolutionary dynamics than other phenotypes, but their evolutionary tempo and mode has received little attention. Learned bird song has been thought to be subject to rapid and constant evolution. However, we know little about the evolutionary modes of learned song divergence over long timescales. Here, we provide evidence that aspects of the territorial songs of Eastern Afromontane sky island sunbirds Cinnyris evolve in a punctuated fashion, with periods of stasis of the order of hundreds of thousands of years or more, broken up by evolutionary pulses. Stasis in learned songs is inconsistent with learned traits being subject to constant or frequent change, as would be expected if selection does not constrain song phenotypes over evolutionary timescales. Learned song may instead follow a process resembling peak shifts on adaptive landscapes. While much research has focused on the potential for rapid evolution in bird song, our results suggest that selection can tightly constrain the evolution of learned songs over long timescales. More broadly, these results demonstrate that some aspects of highly variable, plastic traits can exhibit punctuated evolution, with stasis over long time periods.
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Affiliation(s)
- Jay P McEntee
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.,Department of Biology, Missouri State University, Springfield, MO 65897, USA
| | - Gleb Zhelezov
- School of Mathematics, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - Chacha Werema
- Department of Zoology and Wildlife Conservation, University of Dar-es-salaam, PO Box 35064, Tanzania
| | - Nadje Najar
- School of Natural Resources, University of Nebraska, Lincoln, NE 68503, USA
| | - Joshua V Peñalba
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Invalidenstrasse 43, 10115 Berlin, Germany
| | | | | | | | - Lyubov Chumakova
- School of Mathematics, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - J Gordon Burleigh
- Biology Department, University of Florida, Gainesville, FL 32611, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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5
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Recuerda M, Carlos Illera J, Blanco G, Zardoya R, Milá B. Sequential colonization of oceanic archipelagos led to a species-level radiation in the common chaffinch complex (Aves: Fringilla coelebs). Mol Phylogenet Evol 2021; 164:107291. [PMID: 34384903 DOI: 10.1016/j.ympev.2021.107291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/28/2021] [Accepted: 08/05/2021] [Indexed: 11/25/2022]
Abstract
Oceanic archipelagos are excellent systems for studying speciation, yet inference of evolutionary process requires that the colonization history of island organisms be known with accuracy. Here, we used phylogenomics and patterns of genetic diversity to infer the sequence and timing of colonization of Macaronesia by mainland common chaffinches (Fringilla coelebs), and assessed whether colonization of the different archipelagos has resulted in a species-level radiation. To reconstruct the evolutionary history of the complex we generated a molecular phylogeny based on genome-wide SNP loci obtained from genotyping-by-sequencing, we ran ancestral range biogeographic analyses, and assessed fine-scale genetic structure between and within archipelagos using admixture analysis. To test for a species-level radiation, we applied a probabilistic tree-based species delimitation method (mPTP) and an integrative taxonomy approach including phenotypic differences. Results revealed a circuitous colonization pathway in Macaronesia, from the mainland to the Azores, followed by Madeira, and finally the Canary Islands. The Azores showed surprisingly high genetic diversity, similar to that found on the mainland, and the other archipelagos showed the expected sequential loss of genetic diversity. Species delimitation methods supported the existence of several species within the complex. We conclude that the common chaffinch underwent a rapid radiation across Macaronesia that was driven by the sequential colonization of the different archipelagos, resulting in phenotypically and genetically distinct, independent evolutionary lineages. We recommend a taxonomic revision of the complex that takes into account its genetic and phenotypic diversity.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC),Madrid 28006, Spain.
| | - Juan Carlos Illera
- Biodiversity Research Unit (UO-CSIC-PA), Oviedo University, 33600 Mieres, Asturias, Spain
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC),Madrid 28006, Spain
| | - Rafael Zardoya
- National Museum of Natural Sciences, Spanish National Research Council (CSIC),Madrid 28006, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC),Madrid 28006, Spain
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6
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Temperature heterogeneity correlates with intraspecific variation in physiological flexibility in a small endotherm. Nat Commun 2021; 12:4401. [PMID: 34285216 PMCID: PMC8292308 DOI: 10.1038/s41467-021-24588-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 06/24/2021] [Indexed: 02/06/2023] Open
Abstract
Phenotypic flexibility allows individuals to reversibly modify trait values and theory predicts an individual's relative degree of flexibility positively correlates with the environmental heterogeneity it experiences. We test this prediction by integrating surveys of population genetic and physiological variation with thermal acclimation experiments and indices of environmental heterogeneity in the Dark-eyed Junco (Junco hyemalis) and its congeners. We combine field measures of thermogenic capacity for 335 individuals, 22,006 single nucleotide polymorphisms genotyped in 181 individuals, and laboratory acclimations replicated on five populations. We show that Junco populations: (1) differ in their thermogenic responses to temperature variation in the field; (2) harbor allelic variation that also correlates with temperature heterogeneity; and (3) exhibit intra-specific variation in thermogenic flexibility in the laboratory that correlates with the heterogeneity of their native thermal environment. These results provide comprehensive support that phenotypic flexibility corresponds with environmental heterogeneity and highlight its importance for coping with environmental change.
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7
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Kimmitt AA. Females as the Gatekeepers to Seasonal Breeding: What We Can Learn by Studying Reproductive Mechanisms in Both Sexes. Integr Comp Biol 2021; 60:703-711. [PMID: 32617554 DOI: 10.1093/icb/icaa095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Seasonal reproduction is a widespread adaptation in vertebrates, such that individuals time their reproductive efforts to match peak resource abundance. Individuals rely on environmental cues to regulate hormonal mechanisms governing timing of breeding. Historically, studies on physiological mechanisms of seasonal reproduction, specifically in birds, have disproportionately focused on males compared to females. For this review, I conducted a literature search of the last decade of avian research and found a persistent sex bias in the field of physiological mechanisms of seasonal reproduction. Using work conducted with the dark-eyed junco (Junco hyemalis) as a case study, I present a possible solution to combat the sex bias: natural comparisons of populations that differ in reproductive timing to investigate mechanisms of reproduction in both sexes. Populations of dark-eyed juncos that differ in migratory behavior (i.e., migrant and resident) exhibit overlapping ranges during winter and early spring; residents begin breeding in early spring prior to the departure of migrants. This system, and others like it, provides an opportunity to compare mechanisms of reproduction in populations that differ in reproductive timing despite experiencing the same environmental conditions in early spring. In juncos, migrant and resident females and males exhibit similar patterns of hypothalamic regulation of reproduction in early spring, but sex differences in gonadal sensitivity between the populations could be an important distinction that partially explains sex differences in reproductive development. Comparing mechanisms of reproduction in free-living populations and in captivity can reveal important mechanisms that determine the onset of reproductive development, as well as potential sex differences in these mechanisms. Understanding the mechanisms of reproductive phenology has important implications for understanding how species will survive and reproduce in a changing climate.
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Affiliation(s)
- Abigail A Kimmitt
- Department of Biology, Texas A&M University, 3258 TAMU College Station, TX 77843, USA
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8
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Levin RA, Miller JS. Molecular signatures of long-distance oceanic dispersal and the colonization of Pacific islands in Lycium carolinianum. AMERICAN JOURNAL OF BOTANY 2021; 108:694-710. [PMID: 33811320 DOI: 10.1002/ajb2.1626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Long-distance dispersal has been important in explaining the present distributions of many plant species. Despite being infrequent, such dispersal events have considerable evolutionary consequences, because bottlenecks during colonization can result in reduced genetic diversity. We examined the phylogeographic history of Lycium carolinianum, a widespread taxon that ranges from southeastern North America to several Pacific islands, with intraspecific diversity in sexual and mating systems. METHODS We used Bayesian, likelihood, and coalescent approaches with nuclear and plastid sequence data and genome-wide single nucleotide polymorphisms to reconstruct the dispersal history of this species. We also compared patterns of genetic variation in mainland and island populations using single nucleotide polymorphisms and allelic diversity at the S-RNase mating system gene. RESULTS Lycium carolinianum is monophyletic and dispersed once from the North American mainland, colonizing the Pacific islands ca. 40,100 years ago. This dispersal was accompanied by a loss of genetic diversity in SNPs and the S-RNase locus due to a colonization bottleneck and the loss of self-incompatibility. Additionally, we documented at least two independent transitions to gynodioecy: once following the colonization of the Hawaiian Islands and loss of self-incompatibility, and a second time associated with polyploidy in the Yucatán region of Mexico. CONCLUSIONS Long-distance dispersal via fleshy, bird dispersed fruits best explains the unusually widespread distribution of L. carolinianum. The collapse of diversity at the S-RNase locus in island populations suggests that self-fertilization may have facilitated the subsequent colonization of Pacific islands following a single dispersal from mainland North America.
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Affiliation(s)
- Rachel A Levin
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
| | - Jill S Miller
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
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9
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Friis G, Milá B. Change in sexual signalling traits outruns morphological divergence across an ecological gradient in the post-glacial radiation of the songbird genus Junco. J Evol Biol 2020; 33:1276-1293. [PMID: 32603490 DOI: 10.1111/jeb.13671] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/30/2022]
Abstract
The relative roles of natural and sexual selection in promoting evolutionary lineage divergence remains controversial and difficult to assess in natural systems. Local adaptation through natural selection is known to play a central role in promoting evolutionary divergence, yet secondary sexual traits can vary widely among species in recent radiations, suggesting that sexual selection may also be important in the early stages of speciation. Here, we compare rates of divergence in ecologically relevant traits (morphology) and sexually selected signalling traits (coloration) relative to neutral structure in genome-wide molecular markers and examine patterns of variation in sexual dichromatism to explore the roles of natural and sexual selection in the diversification of the songbird genus Junco (Aves: Passerellidae). Juncos include divergent lineages in Central America and several dark-eyed junco (J. hyemalis) lineages that diversified recently as the group recolonized North America following the last glacial maximum (ca. 18,000 years ago). We found an accelerated rate of divergence in sexually selected characters relative to ecologically relevant traits. Moreover, sexual dichromatism measurements suggested a positive relationship between the degree of colour divergence and the strength of sexual selection when controlling for neutral genetic distance. We also found a positive correlation between dichromatism and latitude, which coincides with the geographic axis of decreasing lineage age in juncos but also with a steep ecological gradient. Finally, we found significant associations between genome-wide variants linked to functional genes and proxies of both sexual and natural selection. These results suggest that the joint effects of sexual and ecological selection have played a prominent role in the junco radiation.
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Affiliation(s)
- Guillermo Friis
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Borja Milá
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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10
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Ketterson ED. What Do Ecology, Evolution, and Behavior Have in Common? The Organism in the Middle. Am Nat 2020; 196:103-118. [PMID: 32673095 DOI: 10.1086/709699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Biologists who publish in The American Naturalist are drawn to its unifying mission of covering research in the fields of ecology, evolution, behavior, and integrative biology. Presented here is one scientist's attempt to straddle these fields by focusing on a single organism. It is also an account of how time spent in the field stimulates a naturalist to wonder "why did that animal just do that?" and how research is guided by chance and intention interacting with the scientific literature and the people one meets along the way. With respect to the science, the examples come from bird migration, hormones and their connection to phenotypic integration, sexual and natural selection, and urban ecology. They also come from research on the impact of environmental change on the timing of reproduction and the potential for allochrony in migratory species to influence population divergence.
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11
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Ham-Dueñas JG, Canales-del-Castillo R, Voelker G, Ruvalcaba-Ortega I, Aguirre-Calderón CE, González-Rojas JI. Adaptive genetic diversity and evidence of population genetic structure in the endangered Sierra Madre Sparrow (Xenospiza baileyi). PLoS One 2020; 15:e0232282. [PMID: 32352998 PMCID: PMC7192469 DOI: 10.1371/journal.pone.0232282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/10/2020] [Indexed: 12/13/2022] Open
Abstract
The magnitude and distribution of genetic diversity through space and time can provide useful information relating to evolutionary potential and conservation status in threatened species. In assessing genetic diversity in species that are of conservation concern, several studies have focused on the use of Toll-like receptors (TLRs). TLRs are innate immune genes related to pathogen resistance, and polymorphisms may reflect not only levels of functional diversity, but may also be used to assess genetic diversity within and among populations. Here, we combined four potentially adaptive markers (TLRs) with one mitochondrial (COI) marker to evaluate genetic variation in the endangered Sierra Madre Sparrow (Xenospiza baileyi). This species offers an ideal model to investigate population and evolutionary genetic processes that may be occurring in a habitat restricted endangered species with disjunct populations (Mexico City and Durango), the census sizes of which differ by an order of magnitude. TLRs diversity in the Sierra Madre Sparrow was relatively high, which was not expected given its two small, geographically isolated populations. Genetic diversity was different (but not significantly so) between the two populations, with less diversity seen in the smaller Durango population. Population genetic structure between populations was due to isolation and different selective forces acting on different TLRs; population structure was also evident in COI. Reduction of genetic diversity in COI was observed over 20 years in the Durango population, a result likely caused by habitat loss, a factor which may be the main cause of diversity decline generally. Our results provide information related to the ways in which adaptive variation can be altered by demographic changes due to human-mediated habitat alterations. Furthermore, our findings may help to guide conservation schemes for both populations and their restricted habitat.
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Affiliation(s)
- José G. Ham-Dueñas
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
| | - Ricardo Canales-del-Castillo
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
- * E-mail:
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Biodiversity Research and Teaching Collections, Texas A&M University, College Station, Texas, United States of America
| | - Irene Ruvalcaba-Ortega
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
| | | | - José I. González-Rojas
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
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12
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Valente L, Phillimore AB, Melo M, Warren BH, Clegg SM, Havenstein K, Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. A simple dynamic model explains the diversity of island birds worldwide. Nature 2020; 579:92-96. [PMID: 32076267 DOI: 10.1038/s41586-020-2022-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 01/22/2020] [Indexed: 12/17/2022]
Abstract
Colonization, speciation and extinction are dynamic processes that influence global patterns of species richness1-6. Island biogeography theory predicts that the contribution of these processes to the accumulation of species diversity depends on the area and isolation of the island7,8. Notably, there has been no robust global test of this prediction for islands where speciation cannot be ignored9, because neither the appropriate data nor the analytical tools have been available. Here we address both deficiencies to reveal, for island birds, the empirical shape of the general relationships that determine how colonization, extinction and speciation rates co-vary with the area and isolation of islands. We compiled a global molecular phylogenetic dataset of birds on islands, based on the terrestrial avifaunas of 41 oceanic archipelagos worldwide (including 596 avian taxa), and applied a new analysis method to estimate the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation). Our model predicts-with high explanatory power-several global relationships. We found a decline in colonization with isolation, a decline in extinction with area and an increase in speciation with area and isolation. Combining the theoretical foundations of island biogeography7,8 with the temporal information contained in molecular phylogenies10 proves a powerful approach to reveal the fundamental relationships that govern variation in biodiversity across the planet.
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Affiliation(s)
- Luis Valente
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany. .,Naturalis Biodiversity Center, Leiden, The Netherlands. .,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands. .,Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
| | | | - Martim Melo
- Museu de História Natural e da Ciência da Universidade do Porto, Porto, Portugal.,Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBio, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,FitzPatrick Institute, DST-NRF Centre of Excellence, University of Cape Town, Cape Town, South Africa
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
| | - Sonya M Clegg
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK.,Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, Australia
| | - Katja Havenstein
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Mieres, Spain
| | - Christophe Thébaud
- Unité Mixte de Recherche 5174, CNRS-IRD-Paul Sabatier University, Toulouse, France
| | - Tina Aschenbach
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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13
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Lipshutz SE, George EM, Bentz AB, Rosvall KA. Evaluating testosterone as a phenotypic integrator: From tissues to individuals to species. Mol Cell Endocrinol 2019; 496:110531. [PMID: 31376416 PMCID: PMC6731036 DOI: 10.1016/j.mce.2019.110531] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/14/2019] [Accepted: 07/30/2019] [Indexed: 12/19/2022]
Abstract
Hormones have the potential to bring about rapid phenotypic change; however, they are highly conserved over millions of years of evolution. Here, we examine the evolution of hormone-mediated phenotypes, and the extent to which regulation is achieved via independence or integration of the many components of endocrine systems. We focus on the sex steroid testosterone (T), its cognate receptor (androgen receptor) and related endocrine components. We pose predictions about the mechanisms underlying phenotypic integration, including coordinated sensitivity to T within and among tissues and along the HPG axis. We then assess these predictions with case studies from wild birds, asking whether gene expression related to androgenic signaling naturally co-varies among individuals in ways that would promote phenotypic integration. Finally, we review how mechanisms of integration and independence vary over developmental or evolutionary time, and we find limited support for integration.
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Affiliation(s)
- S E Lipshutz
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
| | - E M George
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA; Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA
| | - A B Bentz
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA; Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA
| | - K A Rosvall
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA; Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA
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14
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Kimmitt AA, Hardman JW, Stricker CA, Ketterson ED. Migratory strategy explains differences in timing of female reproductive development in seasonally sympatric songbirds. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13386] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Jack W. Hardman
- Department of Biology Indiana University Bloomington Indiana
| | | | - Ellen D. Ketterson
- Department of Biology Indiana University Bloomington Indiana
- Environmental Resilience Institute Indiana University Bloomington Indiana
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15
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Thanou E, Kornilios P, Lymberakis P, Leaché AD. Genomic and mitochondrial evidence of ancient isolations and extreme introgression in the four-lined snake. Curr Zool 2019; 66:99-111. [PMID: 32467710 PMCID: PMC7245017 DOI: 10.1093/cz/zoz018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/11/2019] [Indexed: 12/04/2022] Open
Abstract
Comparing mitochondrial and genomic phylogenies is an essential tool for investigating speciation processes, because each genome carries different inheritance properties and evolutionary characteristics. Furthermore, mitonuclear discordance may arise from ecological adaptation, historic isolation, population size changes, and sex-biased dispersal. Closely related taxa are expected to experience gene flow; however, this may not be true for insular populations or populations isolated in refugia. The four-lined snake Elaphe quatuorlineata has a fragmented distribution, separating populations of the Italian and Balkan Peninsulas, whereas several insular Aegean populations of significantly smaller body size (Cyclades island group and Skyros Island, Greece) are currently considered distinct subspecies. We constructed the species-tree phylogeny of this species utilizing genome-wide single nucleotide polymorphisms and a gene-tree based on complete cytochrome b sequences, aiming to detect convergence and discrepancies between biparentally and maternally inherited genomes. Population structuring, phylogenetic patterns and migration events among geographically defined lineages supported our hypothesis of isolation in multiple sub-refugia. Where biogeographical barriers did not restrict subsequent dispersal, extensive genetic exchange occurred between mainland Balkan populations. This process has led to the mitochondrial sweep of an ancestral mitolineage that survived only in peripheral (East Greece) and insular populations (North Cyclades and Skyros). The Central Cyclades represent an ancient lineage for both molecular markers that emerged almost 3.3 Mya. Considering their distinct morphology, insular E. quatuorlineata populations should be the future focus of an extensive sampling, especially since the mitonuclear discordance observed in this species could be related to ecological adaptations, such as the island-dwarfism phenomenon.
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Affiliation(s)
- Evanthia Thanou
- Department of Biology, University of Washington, Seattle, WA, USA.,The Molecular Ecology Backshop, Loutraki, Greece
| | - Panagiotis Kornilios
- Department of Biology, University of Washington, Seattle, WA, USA.,The Molecular Ecology Backshop, Loutraki, Greece.,Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Barcelona, Spain
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Greece
| | - Adam D Leaché
- Department of Biology, University of Washington, Seattle, WA, USA
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16
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Friis G, Fandos G, Zellmer AJ, McCormack JE, Faircloth BC, Milá B. Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird. Mol Ecol 2018; 27:5137-5153. [PMID: 30451354 DOI: 10.1111/mec.14946] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 09/26/2018] [Accepted: 10/15/2018] [Indexed: 12/25/2022]
Abstract
The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation-by-adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci.
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Affiliation(s)
- Guillermo Friis
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Guillermo Fandos
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Amanda J Zellmer
- Department of Biology, Occidental College, Los Angeles, California
| | - John E McCormack
- Department of Biology, Occidental College, Los Angeles, California.,Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, California
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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17
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Kimmitt AA, Dietz SL, Reichard DG, Ketterson ED. Male courtship preference during seasonal sympatry may maintain population divergence. Ecol Evol 2018; 8:11833-11841. [PMID: 30598780 PMCID: PMC6303717 DOI: 10.1002/ece3.4640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 01/15/2023] Open
Abstract
Animal migration can lead to a population distribution known as seasonal sympatry, in which closely-related migrant and resident populations of the same species co-occur in sympatry during part of the year, but are otherwise allopatric. During seasonal sympatry in early spring, residents may initiate reproduction before migrants depart, presenting an opportunity for gene flow. Differences in reproductive timing between migrant and resident populations may favor residents that exhibit preferences for potential mates of similar migratory behavior and reproductive timing, thus maintaining population divergence. We studied dark-eyed juncos (Junco hyemalis), a songbird that exhibits seasonal sympatry. We conducted simulated courtship interactions in which we presented free-living resident males with either a caged migrant or resident female and quantified courtship behavior prior to the departure of the migrants. We found that resident males preferred to court resident females: they sang more short-range songs and exhibited more visual displays associated with courtship when presented with resident females. We conclude that males distinguish between migrant and resident females during seasonal sympatry when the risk of interacting with non-reproductive, migrant females is high. Male mate choice in seasonal sympatry is likely adaptive for male reproductive success. As a secondary effect, male mating preference could act to maintain or promote divergence between populations that differ in migratory strategy.
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Affiliation(s)
| | - Samantha L. Dietz
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth Carolina
- Department of Biological ScienceFlorida State UniversityTallahasseeFlorida
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18
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Abolins-Abols M, Kornobis E, Ribeca P, Wakamatsu K, Peterson MP, Ketterson ED, Milá B. Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco (Junco hyemalis
). Mol Ecol 2018; 27:4501-4515. [DOI: 10.1111/mec.14878] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/22/2018] [Accepted: 09/07/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Mikus Abolins-Abols
- Department of Animal Biology; University of Illinois; Urbana Illinois
- Department of Biology; Indiana University; Bloomington Indiana
| | - Etienne Kornobis
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | | | - Kazumasa Wakamatsu
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | | | | | - Borja Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
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19
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Slowinski SP, Fudickar AM, Hughes AM, Mettler RD, Gorbatenko OV, Spellman GM, Ketterson ED, Atwell JW. Sedentary songbirds maintain higher prevalence of haemosporidian parasite infections than migratory conspecifics during seasonal sympatry. PLoS One 2018; 13:e0201563. [PMID: 30133475 PMCID: PMC6104930 DOI: 10.1371/journal.pone.0201563] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/17/2018] [Indexed: 01/01/2023] Open
Abstract
Long-distance migrations influence the physiology, behavior, and fitness of migratory animals throughout their annual cycles, and fundamentally alter their interactions with parasites. Several hypotheses relating migratory behavior to the likelihood of parasitism have entered the literature, making conflicting, testable predictions. To assess how migratory behavior of hosts is associated with parasitism, we compared haemosporidian parasite infections between two closely related populations of a common North American sparrow, the dark-eyed junco, that co-occur in shared habitats during the non-breeding season. One population is sedentary and winters and breeds in the Appalachian Mountains. The other population is migratory and is found in seasonal sympatry with the sedentary population from October through April, but then flies (≥ 900 km) northwards to breed. The populations were sampled in the wild on the shared montane habitat at the beginning of winter and again after confining them in a captive common environment until the spring. We found significantly higher prevalence of haemosporidian parasite infections in the sedentary population. Among infected juncos, we found no difference in parasite densities (parasitemias) between the sedentary and migrant populations and no evidence for winter dormancy of the parasites. Our results suggest that long-distance migration may reduce the prevalence of parasite infections at the population level. Our results are inconsistent with the migratory exposure hypothesis, which posits that long-distance migration increases exposure of hosts to diverse parasites, and with the migratory susceptibility hypothesis, which posits that trade-offs between immune function and migration increase host susceptibility to parasites. However, our results are consistent with the migratory culling hypothesis, which posits that heavily infected animals are less likely to survive long-distance migration, and with the migratory escape hypothesis, which posits that long-distance migration allows host populations to seasonally escape areas of high infection risk.
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Affiliation(s)
- Samuel P. Slowinski
- Department of Biology, Indiana University, Bloomington, IN, United States of America
- * E-mail:
| | - Adam M. Fudickar
- Environmental Resilience Institute, Indiana University, Bloomington, IN, United States of America
| | - Alex M. Hughes
- Department of Biology, Indiana University, Bloomington, IN, United States of America
| | - Raeann D. Mettler
- School of Natural Sciences, Black Hills State University, Spearfish, SD, United States of America
| | - Oxana V. Gorbatenko
- School of Natural Sciences, Black Hills State University, Spearfish, SD, United States of America
| | - Garth M. Spellman
- Zoology Department, Denver Museum of Nature and Science, Denver, CO, United States of America
| | - Ellen D. Ketterson
- Department of Biology, Indiana University, Bloomington, IN, United States of America
- Environmental Resilience Institute, Indiana University, Bloomington, IN, United States of America
| | - Jonathan W. Atwell
- Department of Biology, Indiana University, Bloomington, IN, United States of America
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20
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Buckley J, Holub EB, Koch MA, Vergeer P, Mable BK. Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection. BMC Genomics 2018; 19:496. [PMID: 29945543 PMCID: PMC6020377 DOI: 10.1186/s12864-018-4806-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 05/18/2018] [Indexed: 11/22/2022] Open
Abstract
Background Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is unclear whether high throughput genotyping approaches for identification of single nucleotide polymorphisms have sufficient power to detect modes of selection expected to result in reduced genetic differentiation among populations. In this study, we used Arabidopsis lyrata to investigate whether signatures of balancing selection can be detected based on genomic smoothing of Restriction Associated DNA sequencing (RAD-seq) data. We compared how different sampling approaches (both within and between subspecies) and different background levels of polymorphism (inbreeding or outcrossing populations) affected the ability to detect genomic regions showing key signatures of balancing selection, specifically elevated polymorphism, reduced differentiation and shifts towards intermediate allele frequencies. We then tested whether candidate genes associated with disease resistance (R-gene analogs) were detected more frequently in these regions compared to other regions of the genome. Results We found that genomic regions showing elevated polymorphism contained a significantly higher density of R-gene analogs predicted to be under pathogen-mediated selection than regions of non-elevated polymorphism, and that many of these also showed evidence for an intermediate site-frequency spectrum based on Tajima’s D. However, we found few genomic regions that showed both elevated polymorphism and reduced FST among populations, despite strong background levels of genetic differentiation among populations. This suggests either insufficient power to detect the reduced population structure predicted for genes under balancing selection using sparsely distributed RAD markers, or that other forms of diversifying selection are more common for the R-gene analogs tested. Conclusions Genome scans based on a small number of individuals sampled from a wide range of populations were sufficient to confirm the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts. Electronic supplementary material The online version of this article (10.1186/s12864-018-4806-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James Buckley
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. .,Adaptation to a Changing Environment, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Eric B Holub
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne, CV35 9EF, UK
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, D69120, Heidelberg, Germany
| | - Philippine Vergeer
- Plant Ecology and Nature Conservation Group, Wageningen University, P.O.Box 47, 6700, AA, Wageningen, The Netherlands
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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21
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McEntee JP, Tobias JA, Sheard C, Burleigh JG. Tempo and timing of ecological trait divergence in bird speciation. Nat Ecol Evol 2018; 2:1120-1127. [DOI: 10.1038/s41559-018-0570-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/02/2018] [Indexed: 01/23/2023]
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22
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23
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Delahaie B, Cornuault J, Masson C, Bertrand JAM, Bourgeois YXC, Milá B, Thébaud C. Narrow hybrid zones in spite of very low population differentiation in neutral markers in an island bird species complex. J Evol Biol 2017; 30:2132-2145. [DOI: 10.1111/jeb.13177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/26/2017] [Accepted: 09/07/2017] [Indexed: 02/06/2023]
Affiliation(s)
- B. Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
- Centre d'Ecologie Fonctionnelle et Evolutive; CNRS-UMR5175 CEFE; Montpellier France
| | - J. Cornuault
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - C. Masson
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - J. A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - Y. X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - B. Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | - C. Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
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