1
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Wacker KS, Winger BM. An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates. Am Nat 2024; 203:362-381. [PMID: 38358813 DOI: 10.1086/728598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.
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2
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Jiao X, Wu L, Zhang D, Wang H, Dong F, Yang L, Wang S, Amano HE, Zhang W, Jia C, Rheindt FE, Lei F, Song G. Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains. Mol Biol Evol 2024; 41:msae027. [PMID: 38318973 PMCID: PMC10919924 DOI: 10.1093/molbev/msae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.
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Affiliation(s)
- Xiaolu Jiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Le Yang
- Tibet Plateau Institute of Biology, Lhasa 850000, China
| | - Shangyu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Weiwei Zhang
- Center for Wildlife Resources Conservation Research, Jiangxi Agricultural University, Nanchang, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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3
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Singhal S, Derryberry GE, Bravo GA, Derryberry EP, Brumfield RT, Harvey MG. The dynamics of introgression across an avian radiation. Evol Lett 2021; 5:568-581. [PMID: 34917397 PMCID: PMC8645201 DOI: 10.1002/evl3.256] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/11/2021] [Accepted: 08/31/2021] [Indexed: 01/20/2023] Open
Abstract
Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson's D‐statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur.
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Affiliation(s)
- Sonal Singhal
- Department of Biology California State University, Dominguez Hills Carson California 90747
| | - Graham E Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts 02138.,Museum of Comparative Zoology Harvard University Cambridge Massachusetts 02138
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Robb T Brumfield
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana 70803.,Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Michael G Harvey
- Department of Biological Sciences The University of Texas at El Paso El Paso Texas 79968.,Biodiversity Collections The University of Texas at El Paso El Paso Texas 79968
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4
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Venegas PJ, Chávez G, García-Ayachi LA, Duran V, Torres-Carvajal O. A new species of wood lizard (Hoplocercinae, Enyalioides) from the Río Huallaga Basin in Central Peru. EVOLUTIONARY SYSTEMATICS 2021. [DOI: 10.3897/evolsyst.5.69227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report the discovery of a new species of Enyalioides from the premontane forest of the Río Huallaga basin in central Peru. The most similar and phylogenetically related species are E. binzayedi and E. rudolfarndti. However, the new species differs from E. binzayedi (state of character in parentheses) by having dorsal scales strongly keeled on paravertebral region and feebly keeled or smooth elsewhere (prominent medial keel on each dorsal scale), more dorsals in transverse row between dorsolateral crests at midbody 26–39, x̄ = 30.44 (22–31, x̄ = 27.57), and a conspicuous posteromedial black patch in the gular region of males (absent). Contrarily, adult males of the new species and E. rudolfarndti are readily distinguished by having a conspicuous posteromedial black patch in the gular region, absent in E. rudolfarndti, and by lacking a conspicuous orange blotch (faint if present) on the antehumeral region, as in E. rudolfarndti. We also present an updated molecular phylogenetic tree of hoplocercines, which strongly supports both referral of the newly discovered species to Enyalioides and its status as distinct from those recognized previously.
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5
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E Luzuriaga-Aveiga V, Ugarte M, Weir JT. Distinguishing genomic homogenization from parapatric speciation in an elevationally replacing pair of Ramphocelus tanagers. Mol Ecol 2021; 30:5517-5529. [PMID: 34403554 DOI: 10.1111/mec.16128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022]
Abstract
Geographically connected species pairs with weakly differentiated genomes could either represent cases of genomic homogenization in progress or of incipient parapatric speciation. Discriminating between these processes is difficult because intermediate stages of either may produce weakly differentiated genomes that diverge at few locations. We used coalescent modelling applied to a genome-wide sample of SNPs to discriminate between speciation with gene flow and genomic homogenization in two phenotypically distinct but genomically weakly diverged species of elevationally replacing Ramphocelus tanagers, forming a hybrid zone in the Andean foothills. We found overwhelming support for a model of genomic homogenization following secondary contact. Simulating under this model suggested that our species pair was differentiated (FST = 0.30) at secondary contact but that most of the genome has rapidly homogenized during 254 Ky of high gene flow towards the present (FST = 0.02). Despite extensive genome-wide homogenization, plumage remains distinctive with a narrower than expected geographic cline width, indicating divergent selection on colour. We found two SNPs significantly associated with plumage colour, which retain moderately high FST . We conclude that the majority of the genome has fused, but that divergent selection on select loci probably maintains the geographically structured colour differences between these incipient species.
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Affiliation(s)
- Vanessa E Luzuriaga-Aveiga
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Mauricio Ugarte
- Área de Ornitología, Universidad Nacional de San Agustín de Arequipa, Museo de Historia Natural Arequipa, Peru
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.,Department of Ornithology, Royal Ontario Museum, Toronto, Ontario, Canada
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6
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Raposo do Amaral F, Thom G, Lima-Ribeiro MS, Alvarado-Serrano DF, Montesanti JAC, Pellegrino KCM, Miyaki CY, Hickerson MJ, Maldonado-Coelho M. Rugged relief and climate promote isolation and divergence between two neotropical cold-associated birds. Evolution 2021; 75:2371-2387. [PMID: 34375460 DOI: 10.1111/evo.14318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 06/21/2021] [Accepted: 07/19/2021] [Indexed: 01/15/2023]
Abstract
The role of historical factors in establishing patterns of diversity in tropical mountains is of interest to understand the buildup of megadiverse biotas. In these regions, the historical processes of range fragmentation and contraction followed by dispersal are thought to be mediated by the interplay between rugged relief (complex topography) and climate fluctuations and likely explain most of the dynamics of diversification in plants and animals. Although empirical studies addressing the interaction between climate and topography have provided invaluable insights into population divergence and speciation patterns in tropical montane organisms, a more detailed and robust test of such processes in an explicit spatio-temporal framework is still lacking. Consequently, our ability to gain insights into historical range shifts over time and the genomic footprint left by them is limited. Here, we used niche modeling and subgenomic population-level datasets to explore the evolution of two species of warbling finches (genus Microspingus) disjunctly distributed across the Montane Atlantic Forest, a Neotropical region with complex geological and environmental histories. Population structure inferences suggest a scenario of three genetically differentiated populations, which are congruent with both geography and phenotypic variation. Demographic simulations support asynchronous isolation of these populations as recently as ∼40,000 years ago, relatively stable population sizes over recent time, and past gene flow subsequent to divergence. Throughout the last 800,000 years, niche models predicted extensive expansion into lowland areas with increasing overlap of species distributions during glacial periods, with prominent retractions and isolation into higher altitudes during interglacials, which are in line with signs of introgression of currently isolated populations. These results support a dual role of cyclical climatic changes: population divergence and persistence in mountain tops during warm periods followed by periods of expansion and admixture in lower elevations during cold periods. Our results underscore the role of the interplay between landscape and climate as an important mechanism in the evolution of the Neotropical montane biota.
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Affiliation(s)
- Fábio Raposo do Amaral
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil
| | - Gregory Thom
- Department of Ornithology, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024-5192, USA
| | - Matheus S Lima-Ribeiro
- Departamento de Ciências Biológicas, Universidade Federal de Jataí, CP 03, Jataí, GO, 75804-020, Brazil
| | - Diego F Alvarado-Serrano
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Life Sciences Building R219, Athens, OH, 45701, USA
| | - Julia A C Montesanti
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil
| | - Katia C M Pellegrino
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil
| | - Cristina Y Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
| | - Michael J Hickerson
- Department of Biology, City College of New York, 160, Convent Avenue, New York, NY, 10031, USA
| | - Marcos Maldonado-Coelho
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil.,Department of Biology, Lund University, Lund, SE-223 62, Sweden
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7
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Pulgarín-R PC, Olivera-Angel M, Ortíz L, Nanclares D, Velásquez-Restrepo S, Díaz-Nieto JF. DNA barcodes of birds from northern Colombia. Biodivers Data J 2021; 9:e64842. [PMID: 34084068 PMCID: PMC8163714 DOI: 10.3897/bdj.9.e64842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/02/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcode datasets are a useful tool for conservation and aid in taxonomic identification, particularly in megadiverse tropical countries seeking to document and describe its biota, which is dropping at an alarming rate during recent decades. Here we report the barcodes for several low elevation bird species from northern Colombia with the goal to provide tools for species identification in this region of South America. We blood-sampled birds in a lowland tropical forest with various degrees of intervention using standard 3 × 12 m mist-nets. We extracted DNA and sequenced the COI barcode gene using standard primers and laboratory methods. We obtained 26 COI sequences from 18 species, 10 families and three orders and found that barcodes largely matched (but not always) phenotypic identification (> 90%) and they also facilitated the identification of several challenging passerine species. Despite our reduced sampling, our study represents the first attempt to document COI barcodes for birds (from blood samples) in this part of Colombia, which fills a considerable gap of sampling in this part of South America.
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Affiliation(s)
- Paulo Cesar Pulgarín-R
- Facultad de Ciencias y Biotecnología, Universidad CES, Medellín, ColombiaFacultad de Ciencias y Biotecnología, Universidad CESMedellínColombia
| | - Martha Olivera-Angel
- Biogénesis, Facultad de Ciencias Agrarias, Universidad de Antioquia, Cl. 73 #73A-79, Medellín, ColombiaBiogénesis, Facultad de Ciencias Agrarias, Universidad de Antioquia, Cl. 73 #73A-79MedellínColombia
| | - Luisa Ortíz
- Biogénesis, Facultad de Ciencias Agrarias, Universidad de Antioquia, Cl. 73 #73A-79, Medellín, ColombiaBiogénesis, Facultad de Ciencias Agrarias, Universidad de Antioquia, Cl. 73 #73A-79MedellínColombia
| | - Duván Nanclares
- Biogénesis, Facultad de Ciencias Agrarias, Universidad de Antioquia, Cl. 73 #73A-79, Medellín, ColombiaBiogénesis, Facultad de Ciencias Agrarias, Universidad de Antioquia, Cl. 73 #73A-79MedellínColombia
| | - Sara Velásquez-Restrepo
- Grupo Biodiversidad, Evolución y Conservación (BEC), Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Carrera 49 No. 7 sur-50, Medellín, ColombiaGrupo Biodiversidad, Evolución y Conservación (BEC), Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Carrera 49 No. 7 sur-50MedellínColombia
| | - Juan Fernando Díaz-Nieto
- Grupo Biodiversidad, Evolución y Conservación (BEC), Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Carrera 49 No. 7 sur-50, Medellín, ColombiaGrupo Biodiversidad, Evolución y Conservación (BEC), Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Carrera 49 No. 7 sur-50MedellínColombia
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8
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Lim MCW, Bi K, Witt CC, Graham CH, Dávalos LM. Pervasive Genomic Signatures of Local Adaptation to Altitude Across Highland Specialist Andean Hummingbird Populations. J Hered 2021; 112:229-240. [PMID: 33631009 DOI: 10.1093/jhered/esab008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/23/2021] [Indexed: 01/28/2023] Open
Abstract
Populations along steep environmental gradients are subject to differentiating selection that can result in local adaptation, despite countervailing gene flow, and genetic drift. In montane systems, where species are often restricted to narrow ranges of elevation, it is unclear whether the selection is strong enough to influence functional differentiation of subpopulations differing by a few hundred meters in elevation. We used targeted capture of 12 501 exons from across the genome, including 271 genes previously implicated in altitude adaptation, to test for adaptation to local elevations for 2 highland hummingbird species, Coeligena violifer (n = 62) and Colibri coruscans (n = 101). For each species, we described population genetic structure across the complex geography of the Peruvian Andes and, while accounting for this structure, we tested whether elevational allele frequency clines in single nucleotide polymorphisms (SNPs) showed evidence for local adaptation to elevation. Although the 2 species exhibited contrasting population genetic structures, we found signatures of clinal genetic variation with shifts in elevation in both. The genes with SNP-elevation associations included candidate genes previously discovered for high-elevation adaptation as well as others not previously identified, with cellular functions related to hypoxia response, energy metabolism, and immune function, among others. Despite the homogenizing effects of gene flow and genetic drift, natural selection on parts of the genome evidently optimizes elevation-specific cellular function even within elevation range-restricted montane populations. Consequently, our results suggest local adaptation occurring in narrow elevation bands in tropical mountains, such as the Andes, may effectively make them "taller" biogeographic barriers.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, CA.,California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA (Bi)
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY.,Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY
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9
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Chávez G, García Ayachi LA, Catenazzi A. A new species of frog (Terrarana, Strabomantidae, Phrynopus) from the Peruvian Andean grasslands. PeerJ 2020; 8:e9433. [PMID: 32612895 PMCID: PMC7320723 DOI: 10.7717/peerj.9433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/06/2020] [Indexed: 11/28/2022] Open
Abstract
We describe a new, medium-sized species of terrestrial frog of the genus Phrynopus from a single locality in the central Andes of Peru (Departamento de Huánuco) at 3,730 meters of elevation. Phylogenetic analyses supported Phrynopus remotum sp. nov. as an independent lineage, sister to most of its congeners. The new species is morphologically distinguishable by the presence of small tubercles on upper eyelids and heels, an areolate venter, and the absence of dorsolateral folds or ridges. This species inhabits the highlands adjacent to the Marañón Dry valley. The only sympatric amphibian species recorded is the marsupial frog Gastrotheca peruana.
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Affiliation(s)
- Germán Chávez
- División de Herpetología, CORBIDI, Lima, Perú
- Instituto Peruano de Herpetología, Lima, Perú
| | | | - Alessandro Catenazzi
- División de Herpetología, CORBIDI, Lima, Perú
- Department of Biological Sciences, Florida International University, Miami, FL, United States of America
- Instituto Peruano de Herpetología, Lima, Perú
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10
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Musher LJ, Ferreira M, Auerbach AL, McKay J, Cracraft J. Why is Amazonia a 'source' of biodiversity? Climate-mediated dispersal and synchronous speciation across the Andes in an avian group (Tityrinae). Proc Biol Sci 2020; 286:20182343. [PMID: 30940057 DOI: 10.1098/rspb.2018.2343] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Amazonia is a 'source' of biodiversity for other Neotropical ecosystems, but which conditions trigger in situ speciation and emigration is contentious. Three hypotheses for how communities have assembled include (1) a stochastic model wherein chance dispersal events lead to gradual emigration and species accumulation, (2) diversity-dependence wherein successful dispersal events decline through time due to ecological limits, and (3) barrier displacement wherein environmental change facilitates dispersal to other biomes via transient habitat corridors. We sequenced thousands of molecular markers for the Neotropical Tityrinae (Aves) and applied a novel filtering protocol to identify loci with high utility for dated phylogenomics. We used these loci to estimate divergence times and model Tityrinae's evolutionary history. We detected a prominent role for speciation driven by barriers including synchronous speciation across the Andes and found that dispersal increased toward the present. Because diversification was continuous but dispersal was non-random over time, we show that barrier displacement better explains Tityrinae's history than stochasticity or diversity-dependence. We propose that Amazonia is a source of biodiversity because (1) it is a relic of a biome that was once more extensive, (2) environmentally mediated corridors facilitated emigration and (3) constant diversification is attributed to a spatially heterogeneous landscape that is perpetually dynamic through time.
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Affiliation(s)
- Lukas J Musher
- 1 Department of Ornithology, American Museum of Natural History , Central Park West @ 79th Street, New York, NY 10024 , USA.,2 The Richard Gilder Graduate School, American Museum of Natural History , Central Park West @ 79th Street, New York, NY 10024 , USA
| | - Mateus Ferreira
- 3 Programa Pós-Graduação em Genética, Conservação e Biologia Evolutiva, INPA , Manaus, AM , Brazil
| | - Anya L Auerbach
- 4 Department of Biological Sciences Collegiate Division, University of Chicago , 1101 East 57th Street, Chicago, IL 60637 , USA
| | - Jessica McKay
- 1 Department of Ornithology, American Museum of Natural History , Central Park West @ 79th Street, New York, NY 10024 , USA
| | - Joel Cracraft
- 1 Department of Ornithology, American Museum of Natural History , Central Park West @ 79th Street, New York, NY 10024 , USA
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11
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Hamlin JAP, Hibbins MS, Moyle LC. Assessing biological factors affecting postspeciation introgression. Evol Lett 2020; 4:137-154. [PMID: 32313689 PMCID: PMC7156103 DOI: 10.1002/evl3.159] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 11/26/2019] [Accepted: 01/12/2020] [Indexed: 12/14/2022] Open
Abstract
An increasing number of phylogenomic studies have documented a clear “footprint” of postspeciation introgression among closely related species. Nonetheless, systematic genome‐wide studies of factors that determine the likelihood of introgression remain rare. Here, we propose an a priori hypothesis‐testing framework that uses introgression statistics—including a new metric of estimated introgression, Dp—to evaluate general patterns of introgression prevalence and direction across multiple closely related species. We demonstrate this approach using whole genome sequences from 32 lineages in 11 wild tomato species to assess the effect of three factors on introgression—genetic relatedness, geographical proximity, and mating system differences—based on multiple trios within the “ABBA–BABA” test. Our analyses suggest each factor affects the prevalence of introgression, although our power to detect these is limited by the number of comparisons currently available. We find that of 14 species pairs with geographically “proximate” versus “distant” population comparisons, 13 showed evidence of introgression; in 10 of these cases, this was more prevalent between geographically closer populations. We also find modest evidence that introgression declines with increasing genetic divergence between lineages, is more prevalent between lineages that share the same mating system, and—when it does occur between mating systems—tends to involve gene flow from more inbreeding to more outbreeding lineages. Although our analysis indicates that recent postspeciation introgression is frequent in this group—detected in 15 of 17 tested trios—estimated levels of genetic exchange are modest (0.2–2.5% of the genome), so the relative importance of hybridization in shaping the evolutionary trajectories of these species could be limited. Regardless, similar clade‐wide analyses of genomic introgression would be valuable for disentangling the major ecological, reproductive, and historical determinants of postspeciation gene flow, and for assessing the relative contribution of introgression as a source of genetic variation.
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Affiliation(s)
| | - Mark S Hibbins
- Department of Biology Indiana University Bloomington Indiana 47405
| | - Leonie C Moyle
- Department of Biology Indiana University Bloomington Indiana 47405
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12
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Gutiérrez‐Pinto N, McCracken KG, Tubaro P, Kopuchian C, Astie A, Cadena CD. Molecular and morphological differentiation among Torrent Duck (
Merganetta armata
) populations in the Andes. ZOOL SCR 2019. [DOI: 10.1111/zsc.12367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Natalia Gutiérrez‐Pinto
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
- School of Biological Sciences University of Nebraska Lincoln Nebraska
| | - Kevin G. McCracken
- Department of Biology University of Miami Coral Gables Florida
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Sciences Miami Florida
- Institute of Arctic Biology University of Alaska Museum Fairbanks Alaska
- Department of Biology and Wildlife University of Alaska Fairbanks Fairbanks Alaska
| | - Pablo Tubaro
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN ‐ CONICET) Buenos Aires Argentina
| | - Cecilia Kopuchian
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN ‐ CONICET) Buenos Aires Argentina
- Centro de Ecología Aplicada del Litoral (CECOAL‐CONICET) Corrientes Argentina
| | - Andrea Astie
- Instituto Argentino de Investigaciones de las Zonas Áridas (CONICET‐CCT Mendoza) Mendoza Argentina
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
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13
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Linck E, Battey CJ. Minor allele frequency thresholds strongly affect population structure inference with genomic data sets. Mol Ecol Resour 2019; 19:639-647. [DOI: 10.1111/1755-0998.12995] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/14/2018] [Accepted: 01/04/2019] [Indexed: 01/25/2023]
Affiliation(s)
- Ethan Linck
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington Seattle Washington
| | - C. J. Battey
- Department of Biology and Institute of Ecology and Evolution University of Oregon Eugene Oregon
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14
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Cadena CD, Pérez-emán JL, Cuervo AM, Céspedes LN, Epperly KL, Klicka JT. Extreme genetic structure and dynamic range evolution in a montane passerine bird: implications for tropical diversification. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly207] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Jorge L Pérez-emán
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
- Colección Ornitológica Phelps, Caracas, Venezuela
| | - Andrés M Cuervo
- Louisiana State University Museum of Natural Science, Baton Rouge, LA, USA
- Instituto de Investigación en Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Laura N Céspedes
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Kevin L Epperly
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - John T Klicka
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
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15
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Beckman EJ, Benham PM, Cheviron ZA, Witt C. Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins. Mol Ecol 2018; 27:4350-4367. [DOI: 10.1111/mec.14795] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Elizabeth J. Beckman
- Division of Biological Sciences University of Montana Missoula Montana
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico
| | - Phred M. Benham
- Division of Biological Sciences University of Montana Missoula Montana
| | | | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico
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16
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On geographic barriers and Pleistocene glaciations: Tracing the diversification of the Russet-crowned Warbler (Myiothlypis coronata) along the Andes. PLoS One 2018. [PMID: 29522515 PMCID: PMC5844518 DOI: 10.1371/journal.pone.0191598] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We studied the phylogeography and plumage variation of the Russet-crowned Warbler (Myiothlypis coronata), from Venezuela to Bolivia, with focus on populations from Ecuador and northern Peru. We analyzed sequences of mitochondrial and nuclear genes, geographic distributions, as well as photographs of specimens deposited at museum collections. Phylogenetic analyses identified three major lineages formed by populations from: Venezuela and Colombia (M. c. regulus), Ecuador and northern Peru (M. elata, M. castaneiceps, M. orientalis, M. c. chapmani), and central Peru and Bolivia (M. c. coronata). We found further population structure within M. c. regulus and M. c. coronata, and population structure and complexity of plumage variation within the Ecuador-northern Peru lineage. Time-calibrated trees estimated that most intraspecific variation originated during the Pleistocene; however, this pattern may not be attributed to an increase in diversification rate during that period. We discuss these results in the context of the importance of geographic-ecological barriers in promoting lineage diversification along the Andes and put forward a preliminary taxonomic proposal for major lineages identified in this study.
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17
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18
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Tinghitella RM, Lackey ACR, Martin M, Dijkstra PD, Drury JP, Heathcote R, Keagy J, Scordato ESC, Tyers AM. On the role of male competition in speciation: a review and research agenda. Behav Ecol 2017. [DOI: 10.1093/beheco/arx151] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
| | - Alycia C R Lackey
- Department of Biological Sciences, Watershed Studies Institute, Murray State University, Murray, KY, USA
| | - Michael Martin
- Department of Biology, Oxford College of Emory University, Oxford, GA, USA
| | - Peter D Dijkstra
- Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Jonathan P Drury
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert Heathcote
- Centre for Research in Animal Behaviour, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Jason Keagy
- Department of Animal Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Elizabeth S C Scordato
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Alexandra M Tyers
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor, Gwynedd,, Wales, UK
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19
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Turissini DA, Matute DR. Fine scale mapping of genomic introgressions within the Drosophila yakuba clade. PLoS Genet 2017; 13:e1006971. [PMID: 28873409 PMCID: PMC5600410 DOI: 10.1371/journal.pgen.1006971] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 09/15/2017] [Accepted: 08/09/2017] [Indexed: 12/15/2022] Open
Abstract
The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of São Tomé, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.
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Affiliation(s)
- David A. Turissini
- Biology Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel R. Matute
- Biology Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
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20
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Turbek SP. Digest: For ecologically similar Andean birds, gene flow and plumage uniformity go hand in hand. Evolution 2017; 71:1911-1912. [PMID: 28489269 DOI: 10.1111/evo.13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/04/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Sheela P Turbek
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, Colorado, 80309
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