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Weir JT, Aleixo A, Pulido-Santacruz P. Amazonian rivers are leaky barriers to gene flow in forest understory birds. Proc Biol Sci 2024; 291:20240795. [PMID: 39226930 DOI: 10.1098/rspb.2024.0795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 09/05/2024] Open
Abstract
Ever since Alfred Russel Wallace's nineteenth-century observation that related terrestrial species are often separated on opposing riverbanks, major Amazonian rivers have been recognized as key drivers of speciation. However, rivers are dynamic entities whose widths and courses may vary through time. It thus remains unknown how effective rivers are at reducing gene flow and promoting speciation over long timescales. We fit demographic models to genomic sequences to reconstruct the history of gene flow in three pairs of avian taxa fully separated by different Amazonian rivers, and whose geographic ranges do not make contact in headwater regions where rivers may cease to be barriers. Models with gene flow were best fit but still supported an initial period without any gene flow, which ranged from 187 000 to over 959 000 years, suggesting that rivers are capable of initiating speciation through long stretches of allopatric divergence. Allopatry was followed by either bursts or prolonged episodes of gene flow that retarded genomic differentiation but did not fully homogenize populations. Our results support Amazonian rivers as key barriers that promoted speciation and the build-up of species richness, but they also suggest that river barriers are often leaky, with genomic divergence accumulating slowly owing to episodes of substantial gene flow.
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Affiliation(s)
- Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto , Toronto, Ontario M5S 3B2, Canada
- Department of Biological Sciences, University of Toronto Scarborough , Toronto, Ontario M1C 1A4, Canada
- Department of Ornithology, Royal Ontario Museum , Toronto, Ontario M5S 2C6, Canada
| | - Alexandre Aleixo
- Pós-graduação em Biodiversidade e Evolução, Museu Paraense Emílio Goeldi , Belém 66040-170, Brazil
- Vale Technology Institute-Sustainable Development (ITV-DS) , Belém 66055-090, Brazil
| | - Paola Pulido-Santacruz
- Department of Ecology and Evolutionary Biology, University of Toronto , Toronto, Ontario M5S 3B2, Canada
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario , Bogotá 111221, Colombia
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2
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Musher LJ, Del-Rio G, Marcondes RS, Brumfield RT, Bravo GA, Thom G. Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops). Syst Biol 2024; 73:36-52. [PMID: 37804132 DOI: 10.1093/sysbio/syad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023] Open
Abstract
Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.].
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Affiliation(s)
- Lukas J Musher
- Department of Ornithology, The Academy of Natural Sciences of Drexel University, Philadelphia, PA 19103, USA
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Glaucia Del-Rio
- Cornell Laboratory of Ornithology and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Rafael S Marcondes
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Robb T Brumfield
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Gustavo A Bravo
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá 111311, Colombia
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gregory Thom
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
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3
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Dalapicolla J, Weir JT, Vilaça ST, Quaresma TF, Schneider MPC, Vasconcelos ATR, Aleixo A. Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary. Ecol Evol 2024; 14:e11250. [PMID: 38660467 PMCID: PMC11040105 DOI: 10.1002/ece3.11250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
The "Amazon tipping point" is a global change scenario resulting in replacement of upland terra-firme forests by large-scale "savannization" of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra-firme inhabiting species should have experienced reductions in population size as drier habitats expanded. Here, we use whole-genomes of an Amazonian endemic organism (Scale-backed antbirds - Willisornis spp.) sampled from nine populations across the region to test this historical demography scenario. Populations from southeastern Amazonia and close to the Amazon-Cerrado ecotone exhibited a wide range of demographic patterns, while most of those from northern and western Amazonia experienced uniform expansions between 400 kya and 80-60 kya, with gradual declines toward 20 kya. Southeastern populations of Willisornis were the last to diversify and showed smaller heterozygosity and higher runs of homozygosity values than western and northern populations. These patterns support historical population declines throughout the Amazon that affected more strongly lineages in the southern and eastern areas, where historical "tipping point" conditions existed due to the widespread replacement of humid forest by drier and open vegetation during the LGM.
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Affiliation(s)
- Jeronymo Dalapicolla
- Instituto Tecnológico ValeBelémParáBrazil
- Departamento de Sistemática e EcologiaUniversidade Federal da Paraíba, João PessoaParaíbaBrazil
| | - Jason T. Weir
- Department of Biological SciencesUniversity of Toronto ScarboroughTorontoOntarioCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Natural History, Royal Ontario MuseumTorontoOntarioCanada
| | | | | | - Maria P. C. Schneider
- Laboratório de Genômica e BiotecnologiaInstituto de Ciências Biológicas, UFPABelémBrazil
| | - Ana Tereza R. Vasconcelos
- Laboratório de BioinformáticaLaboratório Nacional de Computação Científica, PetrópolisRio de JaneiroBrazil
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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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Thom G, Moreira LR, Batista R, Gehara M, Aleixo A, Smith BT. Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds. Genome Biol Evol 2024; 16:evae002. [PMID: 38236173 PMCID: PMC10823491 DOI: 10.1093/gbe/evae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.
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Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lucas Rocha Moreira
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Romina Batista
- Programa de Coleções Biológicas, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
- School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Department of Environmental Genomics, Instituto Tecnológico Vale, Belém, Brazil
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
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6
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Fecchio A, Batalha-Filho H, Dispoto JH, Bell JA, Weckstein JD. Distinct biogeographic processes and areas of endemism contributed differentially to Plasmodium and Parahaemoproteus community assembly on Marajó Island. Mol Phylogenet Evol 2023:107828. [PMID: 37247702 DOI: 10.1016/j.ympev.2023.107828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/16/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Amazonia is the primary source of haemosporidian diversity for South American biomes. Yet, our understanding of the contribution of each area of endemism and the biogeographical processes that generated such diversity in this group of vector transmitted parasites remains incomplete. For example, a recently formed fluvial island in the Amazon delta - Marajó Island, is composed of avian lineages from adjacent Amazonian areas of endemism, but also from open habitats, such as Cerrado. This raises the question: Is the parasite assemblage found in avian hosts on this island formed by parasite lineages from adjacent Amazonian areas of endemism or Cerrado? Here, we assessed the spatiotemporal evolution of Plasmodium and Parahaemoproteus parasites. Our biogeographic analysis showed that dispersal dominated Plasmodium diversification, whereas duplication was more frequent for the genus Parahaemoproteus. We show that the Inambari area of endemism was the primary source for Plasmodium diversity on Marajó Island, but that this island received more Parahaemoproteus lineages from Cerrado than any Amazonian area of endemism. The unique patterns of dispersal for each parasite genus coupled with their propensity to shift hosts locally may have facilitated their diversification across Amazonia, suggesting that differences in deep evolutionary history may have constrained their colonization of Marajó Island.
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Affiliation(s)
- Alan Fecchio
- Centro de Investigación Esquel de Montaña y Estepa Patagónica (CIEMEP), CONICET - Universidad Nacional de la Patagonia San Juan Bosco, Esquel, Chubut, Argentina
| | - Henrique Batalha-Filho
- Laboratório de Evolução e Biogeografia, Instituto de Biologia, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Janice H Dispoto
- Department of Ornithology, Academy of Natural Sciences of Drexel University, Philadelphia, PA, USA
| | - Jeffrey A Bell
- Department of Biology, University of North Dakota, Grand Forks, ND, USA
| | - Jason D Weckstein
- Department of Ornithology, Academy of Natural Sciences of Drexel University, Philadelphia, PA, USA; Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, Philadelphia, PA, USA
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7
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Snead AA, Clark RD. The Biological Hierarchy, Time, and Temporal 'Omics in Evolutionary Biology: A Perspective. Integr Comp Biol 2022; 62:1872-1886. [PMID: 36057775 DOI: 10.1093/icb/icac138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 01/05/2023] Open
Abstract
Sequencing data-genomics, transcriptomics, epigenomics, proteomics, and metabolomics-have revolutionized biological research, enabling a more detailed study of processes, ranging from subcellular to evolutionary, that drive biological organization. These processes, collectively, are responsible for generating patterns of phenotypic variation and can operate over dramatically different timescales (milliseconds to billions of years). While researchers often study phenotypic variation at specific levels of biological organization to isolate processes operating at that particular scale, the varying types of sequence data, or 'omics, can also provide complementary inferences to link molecular and phenotypic variation to produce an integrated view of evolutionary biology, ranging from molecular pathways to speciation. We briefly describe how 'omics has been used across biological levels and then demonstrate the utility of integrating different types of sequencing data across multiple biological levels within the same study to better understand biological phenomena. However, single-time-point studies cannot evaluate the temporal dynamics of these biological processes. Therefore, we put forward temporal 'omics as a framework that can better enable researchers to study the temporal dynamics of target processes. Temporal 'omics is not infallible, as the temporal sampling regime directly impacts inferential ability. Thus, we also discuss the role the temporal sampling regime plays in deriving inferences about the environmental conditions driving biological processes and provide examples that demonstrate the impact of the sampling regime on biological inference. Finally, we forecast the future of temporal 'omics by highlighting current methodological advancements that will enable temporal 'omics to be extended across species and timescales. We extend this discussion to using temporal multi-omics to integrate across the biological hierarchy to evaluate and link the temporal dynamics of processes that generate phenotypic variation.
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Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - René D Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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Anderson SAS, López-Fernández H, Weir JT. Ecology and the origin of non-ephemeral species. Am Nat 2022; 201:619-638. [PMID: 37130236 DOI: 10.1086/723763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractResearch over the past three decades has shown that ecology-based extrinsic reproductive barriers can rapidly arise to generate incipient species-but such barriers can also rapidly dissolve when environments change, resulting in incipient species collapse. Understanding the evolution of unconditional, "intrinsic" reproductive barriers is therefore important for understanding the longer-term buildup of biodiversity. In this article, we consider ecology's role in the evolution of intrinsic reproductive isolation. We suggest that this topic has fallen into a gap between disciplines: while evolutionary ecologists have traditionally focused on the rapid evolution of extrinsic isolation between co-occurring ecotypes, speciation geneticists studying intrinsic isolation in other taxa have devoted little attention to the ecological context in which it evolves. We argue that for evolutionary ecology to close this gap, the field will have to expand its focus beyond rapid adaptation and its traditional model systems. Synthesizing data from several subfields, we present circumstantial evidence for and against different forms of ecological adaptation as promoters of intrinsic isolation and discuss alternative forces that may be significant. We conclude by outlining complementary approaches that can better address the role of ecology in the evolution of nonephemeral reproductive barriers and, by extension, less ephemeral species.
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Toews DPL, Rhinehart TA, Mulvihill R, Galen S, Gosser SM, Johnson T, Williamson JL, Wood AW, Latta SC. Genetic confirmation of a hybrid between two highly divergent cardinalid species: A rose-breasted grosbeak ( Pheucticus ludovicianus) and a scarlet tanager ( Piranga olivacea). Ecol Evol 2022; 12:e9152. [PMID: 35928797 PMCID: PMC9343856 DOI: 10.1002/ece3.9152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 12/04/2022] Open
Abstract
Using low-coverage whole-genome sequencing, analysis of vocalizations, and inferences from natural history, we document a first-generation hybrid between a rose-breasted grosbeak (Pheucticus ludovicianus) and a scarlet tanager (Piranga olivacea). These two species occur sympatrically throughout much of eastern North America, although were not previously known to interbreed. Following the field identification of a putative hybrid, we use genetic and bioacoustic data to show that a rose-breasted grosbeak was the maternal parent and a scarlet tanager was the paternal parent of the hybrid, whose song was similar to the latter species. These two species diverged >10 million years ago, and thus it is surprising to find a hybrid formed under natural conditions in the wild. Notably, the hybrid has an exceptionally heterozygous genome, with a conservative estimate of a heterozygous base every 100 bp. The observation that this hybrid of such highly divergent parental taxa has survived until adulthood serves as another example of the capacity for hybrid birds to survive with an exceptionally divergent genomic composition.
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Affiliation(s)
- David P. L. Toews
- Department of Biology, 619 Mueller LaboratoryPennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Tessa A. Rhinehart
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Robert Mulvihill
- Department of Conservation and Field ResearchNational AviaryPittsburghPennsylvaniaUSA
| | - Spencer Galen
- Biology DepartmentUniversity of ScrantonScrantonPennsylvaniaUSA
| | | | - Tom Johnson
- The Academy of Natural Sciences of Drexel UniversityPhiladelphiaPennsylvaniaUSA
| | - Jessie L. Williamson
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Andrew W. Wood
- Department of Biology, 619 Mueller LaboratoryPennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Steven C. Latta
- Department of Conservation and Field ResearchNational AviaryPittsburghPennsylvaniaUSA
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Dornas T, Dantas SM, Araújo-Silva LE, Morais F, Aleixo A. Comparative Phylogeography of Birds Across the Tocantins–Araguaia Interfluve Reveals a New Biogeographic Suture in the Amazon Far East. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.826394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Few phylogeographic studies have focused on understanding the role of the Tocantins–Araguaia Interfluve (TAI) in the diversification of Amazonian biodiversity. Herein we evaluate the phylogeographic relationships of 14 avian lineages present in the TAI and its two neighboring Amazonian Areas of Endemism: the Xingu (XAE) and Belém (BAE). Four alternative scenarios coupling degree of genetic differentiation and area relationships were tested: (1) populations distributed in TAI, BAE, and XAE are not genetically differentiated from each other (assumed as the null hypothesis); (2) populations from TAI are more closely related to those from BAE; (3) populations from TAI are more closely related to those from XAE; and (4) TAI populations represent independent or endemic lineages not present in either the BAE or XAE. Molecular analyses considered Bayesian Inference methods and Bayesian Information Criterion (BIC) evolutionary models, haplotype sharing and genetic differentiation estimates. We found three distinct phylogeographic patterns: (i) four lineages presented no population structure across XAE, TAI and BAE; (ii) six lineages were represented in the TAI with distinct phylogroups replacing each other between XAE and BAE, but with varying degrees of contact and evidence of gene-flow within the TAI; and (iii) for four lineages, the Tocantins River acted as a barrier isolating BAE phylogroups from those inhabiting both TAI and XAE. These different patterns demonstrate a heterogeneous response to the barrier effects posed by both the Tocantins and Araguaia rivers on the local fauna. Historical geomorphological and hydromorphological factors, such as the presence and absence of paleochannels and anastomosed channel stretches and variations in sedimentation rates support a dynamic history for the Araguaia-Tocantins floodplains, likely accounting for the observed heterogeneity in species’ specific responses. Finally, the scenario of phylogeographic breaks and population subdivision recovered herein along the Tocantins and Araguaia rivers, associated with the existence of contact zones and the occurrence of gene flow, define the TAI as hitherto unknown biogeographic suture zone, localized in southeasternmost Amazonia.
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11
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Barrera-Guzmán AO, Aleixo A, Faccio M, de Melo Dantas S, Weir JT. Gene flow, genomic homogenization and the timeline to speciation in Amazonian manakins. Mol Ecol 2022; 31:4050-4066. [PMID: 35665558 DOI: 10.1111/mec.16562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/28/2022] [Accepted: 05/12/2022] [Indexed: 11/26/2022]
Abstract
Phylogeographic studies of the most species rich region of the planet - the Amazon basin - repeatedly uncover genetically distinctive, allopatric lineages within currently named species, but understanding whether such lineages are reproductively isolated species is challenging. Here we harness the power of genome-wide datasets together with detailed phylogeographic sampling to both characterize the number of unique lineages and infer levels of reproductive isolation for three parapatric manakin species that make up the genus Pipra. The mitochondrial and nuclear genomes both support six distinctive lineages. The youngest lineages are now highly admixed with each other across major portions of their geographic ranges with one lineage now extinct in a genomically unadmixed state. In contrast, the oldest sets of lineages - dated to 1.4 million years - exhibit narrow hybrid zones. By fitting demographic models to parapatric lineage pairs we found that levels of gene flow and genomic homogenization decline with increasing evolutionary age. Only lineages descending from the 1.4 Ma basal node in the genus experience negligible gene flow, possess genomes resistant to homogenization and are separated by narrow hybrid zones. We conclude that a million years or more were required for Pipra manakins to become reproductively isolated. We suggest the six lineages be reclassified as two or three reproductively isolated species. Our unique approach to quantifying reproductive isolation in parapatric lineages could be applied broadly to other phylogeographic studies and would help determine species classification of the plethora of newly identified lineages in the Amazon basin and other regions.
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Affiliation(s)
- Alfredo O Barrera-Guzmán
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.,Departamento de Biología Marina, Campus de Ciencias biológicas y Agropecuarias, Universidad Autónoma de Yucatán
| | - Alexandre Aleixo
- Pós-graduação em Biodiversidade e Evolução, Museu Paraense Emílio Goeldi, Belém, Brazil.,Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Maya Faccio
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Sidnei de Melo Dantas
- Pós-graduação em Biodiversidade e Evolução, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - 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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12
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Moncrieff AE, Faircloth BC, Brumfield RT. Systematics of Lepidothrix manakins (Aves: Passeriformes: Pipridae) using RADcap markers. Mol Phylogenet Evol 2022; 173:107525. [DOI: 10.1016/j.ympev.2022.107525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/06/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
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13
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Silva DC, Oliveira HFM, Zangrandi PL, Domingos FMCB. Flying Over Amazonian Waters: The Role of Rivers on the Distribution and Endemism Patterns of Neotropical Bats. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.774083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Amazon comprises many of the largest rivers in the planet and also houses some of the richest bat communities in the world. Rivers are important geographic barriers for the dispersal and distribution of different taxa worldwide and, particularly in the Amazon region, they form the conceptual and empirical bases for the recognition of the so-called Areas of Endemism of terrestrial vertebrates. Despite the vast literature on the role of rivers on vertebrate community structure in the Amazon Forest, this process has never been investigated using a comprehensive dataset of Neotropical bat communities in the region. In this study, we aimed at: (1) evaluating the patterns of bat endemism across the Amazon Forest; (2) testing for the relationship between the distribution of bat species in the Amazon and the interfluve Areas of Endemism as currently recognized, and; (3) analyzing the importance of major Amazonian rivers in bat beta-diversity (turnover and nestedness) in the Amazon. Our results indicate that rivers are not major barriers for the current distribution of most bat species, and bat community composition breaks were divided into two clusters separating the east and west regions, and a third cluster in northern Amazon. In addition, there was no significant overlap among species distribution limits and the interfluve Areas of Endemism. Interestingly, the geographic patterns that we found for bat communities composition breaks highly resembles the one recovered using bird communities, suggesting that similar ecological and historical drivers might be acting to determine the distribution of flying vertebrates in the Amazon. Moreover, Amazonian bat distribution and endemism patterns were likely shaped by factors other than rivers, such as species interactions and the current environmental conditions. In conclusion, our results highlight the importance of modern analytical approaches to investigate large scale ecological patterns in the Neotropical region, and also challenge the widely recognized role of rivers on the determination of community structure and endemism patterns in the Amazon Forest, at least for bats.
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14
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Musher LJ, Giakoumis M, Albert J, Del-Rio G, Rego M, Thom G, Aleixo A, Ribas CC, Brumfield RT, Smith BT, Cracraft J. River network rearrangements promote speciation in lowland Amazonian birds. SCIENCE ADVANCES 2022; 8:eabn1099. [PMID: 35394835 PMCID: PMC8993111 DOI: 10.1126/sciadv.abn1099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide markers to evaluate the histories of divergence and introgression in six Amazonian avian species complexes. We first tested the assumption that rivers are barriers for these taxa and found that even relatively small rivers facilitate divergence. We then tested whether species diverged with gene flow and recovered reticulate histories for all species, including one potential case of hybrid speciation. Our results support the hypothesis that river rearrangements promote speciation and reveal that many rainforest taxa are micro-endemic, unrecognized, and thus threatened with imminent extinction. We propose that Amazonian hyper-diversity originates partly from fine-scale barrier displacement processes-including river dynamics-which allow small populations to differentiate and disperse into secondary contact.
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Affiliation(s)
- Lukas J. Musher
- Department of Ornithology, The Academy of Natural
Sciences of Drexel University, Philadelphia, PA 19103, USA
- Department of Ornithology, American Museum of Natural
History, New York, NY 10028, USA
- Corresponding author.
| | - Melina Giakoumis
- Department of Biology, City College of New York, New
York, NY 10031, USA
- Graduate Center, City University of New York, New
York, NY 10016, USA
| | - James Albert
- Department of Biology, University of Louisiana at
Lafayette, Lafayette, LA 70503, USA
| | - Glaucia Del-Rio
- Department of Biological Sciences, Louisiana State
University, Baton Rouge, LA 70803, USA
- Museum of Natural Science, Louisiana State
University, Baton Rouge, LA 70803, USA
| | - Marco Rego
- Department of Biological Sciences, Louisiana State
University, Baton Rouge, LA 70803, USA
- Museum of Natural Science, Louisiana State
University, Baton Rouge, LA 70803, USA
| | - Gregory Thom
- Department of Ornithology, American Museum of Natural
History, New York, NY 10028, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History of Helsinki,
University of Helsinki, Helsinki, Finland
- Museu Paraense Emílio Goeldi, Belém,
Brazil
- Instituto Tecnológico Vale, Belém,
Brazil
| | - Camila C. Ribas
- Instituto Nacional de Pesquisas da
Amazônia, INPA, Manaus, Brazil
| | - Robb T. Brumfield
- Department of Biological Sciences, Louisiana State
University, Baton Rouge, LA 70803, USA
- Museum of Natural Science, Louisiana State
University, Baton Rouge, LA 70803, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural
History, New York, NY 10028, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural
History, New York, NY 10028, USA
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15
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The formation of avian montane diversity across barriers and along elevational gradients. Nat Commun 2022; 13:268. [PMID: 35022441 PMCID: PMC8755808 DOI: 10.1038/s41467-021-27858-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/15/2021] [Indexed: 01/25/2023] Open
Abstract
Tropical mountains harbor exceptional concentrations of Earth's biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species' altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.
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16
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17
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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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18
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Dickens JK, Bitton PP, Bravo GA, Silveira LF. Species limits, patterns of secondary contact and a new species in the Trogon rufus complex (Aves: Trogonidae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The black-throated trogon, Trogon rufus, is a widespread, polytypic species-complex with a convoluted taxonomic history. Here, we integrated morphological, vocal and genetic datasets, including spectral data and digital quantification of barred plumage, to assess and redefine its species limits according to the foremost species concepts. We suggest the recognition of four named and one new species. Trogon tenellus and T. cupreicauda are divergent across Central and South America without geographic overlap or intermediates. Trogon chrysochloros in the Atlantic Forests of Brazil is phenotypically, genetically and ecologically distinct. In Amazonia, Trogon rufus consists of three phenotypically distinct subspecies intergrading with each other in a ring-like formation around central Amazonian rivers. Trogon rufus rufus in the Guiana Shield, Trogon rufus amazonicus in south-eastern Amazonia and Trogon rufus sulphureus in western Amazonia, with contact across the Lower Amazon and Madeira rivers, likely due to secondary contact between incompletely diverged lineages. The unique combination of song, morphology and mtDNA features of an unnamed, isolated population in the Atlantic Forest of north-eastern Brazil resulted in its description as a new species, known only from the type locality and considered here as Critically Endangered, requiring urgent conservation actions.
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Affiliation(s)
- Jeremy Kenneth Dickens
- Museu de Zoologia da Universidade de São Paulo, 481 Av. Nazaré, Ipiranga, São Paulo, Brazil
- Fundación Para La Tierra, 321 Mariscal José Félix Estigarribia, Pilar, 2800, Ñeembucú, Paraguay
| | - Pierre-Paul Bitton
- Department of Psychology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL, Canada
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Luís Fábio Silveira
- Museu de Zoologia da Universidade de São Paulo, 481 Av. Nazaré, Ipiranga, São Paulo, Brazil
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19
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Dolby GA. Towards a unified framework to study causality in Earth-life systems. Mol Ecol 2021; 30:5628-5642. [PMID: 34427004 PMCID: PMC9292314 DOI: 10.1111/mec.16142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/17/2021] [Accepted: 08/20/2021] [Indexed: 01/04/2023]
Abstract
There is considerable interest in better understanding how earth processes shape the generation and distribution of life on Earth. This question, at its heart, is one of causation. In this article I propose that at a regional level, earth processes can be thought of as behaving somewhat deterministically and may have an organized effect on the diversification and distribution of species. However, the study of how landscape features shape biology is challenged by pseudocongruent or collinear variables. I demonstrate that causal structures can be used to depict the cause–effect relationships between earth processes and biological patterns using recent examples from the literature about speciation and species richness in montane settings. This application shows that causal diagrams can be used to better decipher the details of causal relationships by motivating new hypotheses. Additionally, the abstraction of this knowledge into structural equation metamodels can be used to formulate theory about relationships within Earth–life systems more broadly. Causal structures are a natural point of collaboration between biologists and Earth scientists, and their use can mitigate against the risk of misassigning causality within studies. My goal is that by applying causal theory through application of causal structures, we can build a systems‐level understanding of what landscape features or earth processes most shape the distribution and diversification of species, what types of organisms are most affected, and why.
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Affiliation(s)
- Greer A Dolby
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
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20
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Bennett KFP, Lim HC, Braun MJ. Sexual selection and introgression in avian hybrid zones: Spotlight on Manacus. Integr Comp Biol 2021; 61:1291-1309. [PMID: 34128981 DOI: 10.1093/icb/icab135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybrid zones offer a window into the processes and outcomes of evolution, from species formation or fusion to genomic underpinnings of specific traits and isolating mechanisms. Sexual selection is believed to be an important factor in speciation processes, and hybrid zones present special opportunities to probe its impact. The manakins (Aves, Pipridae) are a promising group in which to study the interplay of sexual selection and natural hybridization: they show substantial variation across the family in the strength of sexual selection they experience, they readily hybridize within and between genera, and they appear to have formed hybrid species, a rare event in birds. A hybrid zone between two manakins in the genus Manacus is unusual in that plumage and behavioral traits of one species have introgressed asymmetrically into populations of the second species through positive sexual selection, then apparently stalled at a river barrier. This is one of a handful of documented examples of asymmetric sexual trait introgression with a known selective mechanism. It offers opportunities to examine reproductive isolation, introgression, plumage color evolution, and natural factors enhancing or constraining the effects of sexual selection in real time. Here, we review previous work in this system, propose new hypotheses for observed patterns, and recommend approaches to test them.
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Affiliation(s)
- Kevin F P Bennett
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Haw Chuan Lim
- Department of Biology, George Mason University, Manassas, VA, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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21
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Buainain N, Maximiano MFA, Ferreira M, Aleixo A, Faircloth BC, Brumfield RT, Cracraft J, Ribas CC. Multiple species and deep genomic divergences despite little phenotypic differentiation in an ancient Neotropical songbird, Tunchiornis ochraceiceps (Sclater, 1860) (Aves: Vireonidae). Mol Phylogenet Evol 2021; 162:107206. [PMID: 34015447 DOI: 10.1016/j.ympev.2021.107206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 11/20/2022]
Abstract
Several bird taxa have been recently described or elevated to full species and almost twice as many bird species than are currently recognized may exist. Defining species is one of the most basic and important issues in biological science because unknown or poorly defined species hamper subsequent studies. Here, we evaluate the species limits and evolutionary history of Tunchiornis ochraceiceps-a widespread forest songbird that occurs in the lowlands of Central America, Chocó and Amazonia-using an integrative approach that includes plumage coloration, morphometrics, vocalization and genomic data. The species has a relatively old crown age (~9 Ma) and comprises several lineages with little, if any, evidence of gene flow among them. We propose a taxonomic arrangement composed of four species, three with a plumage coloration diagnosis and one deeply divergent cryptic species. Most of the remaining lineages have variable but unfixed phenotypic characters despite their relatively old origin. This decoupling of genomic and phenotypic differentiation reveals a remarkable case of phenotypic conservatism, possibly due to strict habitat association. Lineages are geographically delimited by the main Amazonian rivers and the Andes, a pattern observed in studies of other understory upland forest Neotropical birds, although phylogenetic relationships and divergence times among populations are idiosyncratic.
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Affiliation(s)
- Nelson Buainain
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil.
| | - Marina F A Maximiano
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Mateus Ferreira
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Av. Cap. Ene Garcez, 2413, Boa Vista, Roraima, RR 69304-000, Brazil
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Brant C Faircloth
- Louisiana State University, Department of Biological Sciences, Baton Rouge, LA 70803, USA; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Louisiana State University, Department of Biological Sciences, Baton Rouge, LA 70803, USA; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Joel Cracraft
- American Museum of Natural History, Department of Ornithology, New York, NY, USA
| | - Camila C Ribas
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo, 2936, Manaus, AM 69067-375, Brazil
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22
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Sherry TW. Sensitivity of Tropical Insectivorous Birds to the Anthropocene: A Review of Multiple Mechanisms and Conservation Implications. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.662873] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Epigraph: “The house is burning. We do not need a thermometer. We need a fire hose.” (P. 102, Janzen and Hallwachs, 2019). Insectivorous birds are declining widely, and for diverse reasons. Tropical insectivorous birds, more than 60% of all tropical birds, are particularly sensitive to human disturbances including habitat loss and fragmentation, intensive agriculture and pesticide use, and climate change; and the mechanisms are incompletely understood. This review addresses multiple, complementary and sometimes synergistic explanations for tropical insectivore declines, by categorizing explanations into ultimate vs. proximate, and direct versus indirect. Ultimate explanations are diverse human Anthropocene activities and the evolutionary history of these birds. This evolutionary history, synthesized by the Biotic Challenge Hypothesis (BCH), explains tropical insectivorous birds' vulnerabilities to many proximate threats as a function of both these birds' evolutionary feeding specialization and poor dispersal capacity. These traits were favored evolutionarily by both the diversity of insectivorous clades competing intensely for prey and co-evolution with arthropods over long evolutionary time periods. More proximate, ecological threats include bottom-up forces like declining insect populations, top-down forces like meso-predator increases, plus the Anthropocene activities underlying these factors, especially habitat loss and fragmentation, agricultural intensification, and climate change. All these conditions peak in the lowland, mainland Neotropics, where insectivorous bird declines have been repeatedly documented, but also occur in other tropical locales and continents. This multiplicity of interacting evolutionary and ecological factors informs conservation implications and recommendations for tropical insectivorous birds: (1) Why they are so sensitive to global change phenomena is no longer enigmatic, (2) distinguishing ultimate versus proximate stressors matters, (3) evolutionary life-histories predispose these birds to be particularly sensitive to the Anthropocene, (4) tropical regions and continents vary with respect to these birds' ecological sensitivity, (5) biodiversity concepts need stronger incorporation of species' evolutionary histories, (6) protecting these birds will require more, larger reserves for multiple reasons, and (7) these birds have greater value than generally recognized.
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23
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Ribas TFA, Pieczarka JC, Griffin DK, Kiazim LG, Nagamachi CY, O Brien PCM, Ferguson-Smith MA, Yang F, Aleixo A, O'Connor RE. Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype. BMC Ecol Evol 2021; 21:34. [PMID: 33653261 PMCID: PMC7927240 DOI: 10.1186/s12862-021-01768-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Thamnophilidae birds are the result of a monophyletic radiation of insectivorous Passeriformes. They are a diverse group of 225 species and 45 genera and occur in lowlands and lower montane forests of Neotropics. Despite the large degree of diversity seen in this family, just four species of Thamnophilidae have been karyotyped with a diploid number ranging from 76 to 82 chromosomes. The karyotypic relationships within and between Thamnophilidae and another Passeriformes therefore remain poorly understood. Recent studies have identified the occurrence of intrachromosomal rearrangements in Passeriformes using in silico data and molecular cytogenetic tools. These results demonstrate that intrachromosomal rearrangements are more common in birds than previously thought and are likely to contribute to speciation events. With this in mind, we investigate the apparently conserved karyotype of Willisornis vidua, the Xingu Scale-backed Antbird, using a combination of molecular cytogenetic techniques including chromosome painting with probes derived from Gallus gallus (chicken) and Burhinus oedicnemus (stone curlew), combined with Bacterial Artificial Chromosome (BAC) probes derived from the same species. The goal was to investigate the occurrence of rearrangements in an apparently conserved karyotype in order to understand the evolutionary history and taxonomy of this species. In total, 78 BAC probes from the Gallus gallus and Taeniopygia guttata (the Zebra Finch) BAC libraries were tested, of which 40 were derived from Gallus gallus macrochromosomes 1-8, and 38 from microchromosomes 9-28. RESULTS The karyotype is similar to typical Passeriformes karyotypes, with a diploid number of 2n = 80. Our chromosome painting results show that most of the Gallus gallus chromosomes are conserved, except GGA-1, 2 and 4, with some rearrangements identified among macro- and microchromosomes. BAC mapping revealed many intrachromosomal rearrangements, mainly inversions, when comparing Willisornis vidua karyotype with Gallus gallus, and corroborates the fissions revealed by chromosome painting. CONCLUSIONS Willisornis vidua presents multiple chromosomal rearrangements despite having a supposed conservative karyotype, demonstrating that our approach using a combination of FISH tools provides a higher resolution than previously obtained by chromosome painting alone. We also show that populations of Willisornis vidua appear conserved from a cytogenetic perspective, despite significant phylogeographic structure.
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Affiliation(s)
- Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- School of Biosciences, University of Kent, Canterbury, UK
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | - Lucas G Kiazim
- School of Biosciences, University of Kent, Canterbury, UK
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Patricia Caroline Mary O Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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24
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Miranda LS, Prestes BO, Aleixo A. Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Here we use an integrative approach, including coalescent-based methods, isolation–migration and species distribution models, to infer population structure, divergence times and diversification in the two species of the genus Cymbilaimus (Aves, Thamnophilidae). Our results support a recent and rapid diversification with both incomplete lineage sorting and gene flow shaping the evolutionary history of Cymbilaimus. The spatio-temporal pattern of cladogenesis suggests that Cymbilaimus originated in the north/western portion of cis-Andean South America and then diversified into the Brazilian Shield and Central America after consolidation of the modern Amazonian drainage and the Andean range. This evolutionary scenario is explained by cycles of range expansion and dispersal, followed by isolation, and recurrent gene flow, during the last 1.2 Myr. Our results agree with those recently reported for other closely related suboscine lineages, whereby the window of introgression between closely related taxa remains open for up to a few million years after their original split. In Cymbilaimus, introgression was recurrent between C. lineatus and C. sanctaemariae, even after they acquired vocal and ecological differentiation, supporting the claim that at least in Neotropical suboscines, full reproductive compatibility may take millions of years to evolve and cannot be interpreted as synonymous with a lack of speciation.
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Affiliation(s)
- Leonardo S Miranda
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
- Coordenação de Ciências da Terra e Ecologia, Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - Bernardo O Prestes
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - Alexandre Aleixo
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, PA, Brazil
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25
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Cronemberger ÁA, Aleixo A, Mikkelsen EK, Weir JT. Postzygotic isolation drives genomic speciation between highly crypticHypocnemisantbirds from Amazonia. Evolution 2020; 74:2512-2525. [DOI: 10.1111/evo.14103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 08/28/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Áurea A. Cronemberger
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Canada
- Pós‐graduação em Biodiversidade e Evolução Museu Paraense Emílio Goeldi Belém Brazil
| | - Alexandre Aleixo
- Pós‐graduação em Biodiversidade e Evolução Museu Paraense Emílio Goeldi Belém Brazil
- Finnish Museum of Natural History University of Helsinki Helsinki Finland
| | - Else K. Mikkelsen
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Canada
| | - Jason T. Weir
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Canada
- Department of Natural History Royal Ontario Museum Toronto Canada
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26
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Anderson SAS, Weir JT. A Comparative Test for Divergent Adaptation: Inferring Speciation Drivers from Functional Trait Divergence. Am Nat 2020; 196:429-442. [PMID: 32970469 DOI: 10.1086/710338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractEcological differentiation between lineages is widely considered to be an important driver of speciation, but support for this hypothesis is mainly derived from the detailed study of a select set of model species pairs. Mounting evidence from nonmodel taxa, meanwhile, suggests that speciation often occurs with minimal differentiation in ecology or ecomorphology, calling into question the true contribution of divergent adaptation to species richness in nature. To better understand divergent ecological adaptation and its role in speciation generally, researchers require a comparative approach that can distinguish its signature from alternative processes, such as drift and parallel selection, in data sets containing many species pairs. Here we introduce new statistical models of divergent adaptation in the continuous traits of paired lineages. In these models, ecomorphological characters diverge as two lineages adapt toward alternative phenotypic optima following their departure from a common ancestor. The absolute distance between optima measures the extent of divergent selection and provides a basis for interpretation. We encode the models in the new R package diverge and extend them to allow the distance between optima to vary across continuous and categorical variables. We test model performance using simulation and demonstrate model application using published data sets of trait divergence in birds and mammals. Our framework provides the first explicit test for signatures of divergent selection in trait divergence data sets, and it will enable empiricists from a wide range of fields to better understand the dynamics of divergent adaptation and its prevalence in nature beyond just our best-studied model systems.
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Buainain N, Canton R, Zuquim G, Tuomisto H, Hrbek T, Sato H, Ribas CC. Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus. Mol Ecol 2020; 29:2922-2939. [PMID: 32623766 DOI: 10.1111/mec.15534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 06/04/2020] [Accepted: 06/18/2020] [Indexed: 01/27/2023]
Abstract
Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally-dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modelling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380 to 166 kya, and expansion of the distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated with long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.
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Affiliation(s)
- Nelson Buainain
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
| | - Roberta Canton
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Gabriela Zuquim
- Department of Biology, University of Turku, Turun Yliopisto, Finland
| | - Hanna Tuomisto
- Department of Biology, University of Turku, Turun Yliopisto, Finland
| | - Tomas Hrbek
- Departmento de Genetica, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Hiromitsu Sato
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Camila C Ribas
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
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Maximiano MFDA, d'Horta FM, Tuomisto H, Zuquim G, Van doninck J, Ribas CC. The relative role of rivers, environmental heterogeneity and species traits in driving compositional changes in southeastern Amazonian bird assemblages. Biotropica 2020. [DOI: 10.1111/btp.12793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | - Hanna Tuomisto
- Amazon Research Team Department of Biology University of Turku Turku Finland
| | - Gabriela Zuquim
- Amazon Research Team Department of Biology University of Turku Turku Finland
- Department of Biology Aarhus University Denmark Europe
| | - Jasper Van doninck
- Amazon Research Team Department of Biology University of Turku Turku Finland
| | - Camila Cherem Ribas
- Biodiversity Section Instituto Nacional de Pesquisas da Amazônia (INPA) Manaus Brazil
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Ottenburghs J. Digest: Avian genomes are permeable to introgression for a few million years. Evolution 2020; 74:1010-1011. [PMID: 32246724 DOI: 10.1111/evo.13968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/25/2020] [Indexed: 11/30/2022]
Abstract
How wide is the time window for introgression after divergence? Pulido-Santacruz et al. addressed this question by studying the evolutionary history of the bird genus Dendrocincla. They found five introgression events that occurred between a few hundred thousand and around 2.5 million years after divergence. The introgressed genomic proportion declined exponentially with the age of the hybridizing taxa. Hence, this study suggests that species boundaries are permeable up to 2.5 million years after divergence.
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Affiliation(s)
- Jente Ottenburghs
- Department of Ecology and Genetics, Uppsala University, Uppsala, 75236, Sweden.,Wildlife Ecology and Conservation, Wageningen University and Research, Wageningen, 6708 PB, The Netherlands.,Forest Ecology and Forest Management, Wageningen University and Research, Wageningen, 6708 PB, The Netherlands
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Pulido‐Santacruz P, Aleixo A, Weir JT. Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation*. Evolution 2020; 74:842-858. [DOI: 10.1111/evo.13902] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 10/31/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Paola Pulido‐Santacruz
- Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Bogotá Colombia
- Current address: Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Calle 28A No. 15 – 09 Bogotá Colombia
| | | | - Jason T. Weir
- Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
- Department of Biological SciencesUniversity of Toronto Scarborough Toronto Canada
- Department of OrnithologyRoyal Ontario Museum Toronto Canada
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Schneiberg I, Boscolo D, Devoto M, Marcilio-Silva V, Dalmaso CA, Ribeiro JW, Ribeiro MC, de Camargo Guaraldo A, Niebuhr BB, Varassin IG. Urbanization homogenizes the interactions of plant-frugivore bird networks. Urban Ecosyst 2020. [DOI: 10.1007/s11252-020-00927-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Origin of Elevational Replacements in a Clade of Nearly Flightless Birds: Most Diversity in Tropical Mountains Accumulates via Secondary Contact Following Allopatric Speciation. NEOTROPICAL DIVERSIFICATION: PATTERNS AND PROCESSES 2020. [DOI: 10.1007/978-3-030-31167-4_23] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Loureiro LO, Engstrom MD, Lim BK. Comparative phylogeography of mainland and insular species of Neotropical molossid bats ( Molossus). Ecol Evol 2020; 10:389-409. [PMID: 31993120 PMCID: PMC6972955 DOI: 10.1002/ece3.5903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 01/01/2023] Open
Abstract
Historical events, habitat preferences, and geographic barriers might result in distinct genetic patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein, we use a genotype-by-sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes.
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Affiliation(s)
- Livia O. Loureiro
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Mark D. Engstrom
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Burton K. Lim
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
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Schultz ED, Pérez-Emán J, Aleixo A, Miyaki CY, Brumfield RT, Cracraft J, Ribas CC. Diversification history in the Dendrocincla fuliginosa complex (Aves: Dendrocolaptidae): Insights from broad geographic sampling. Mol Phylogenet Evol 2019; 140:106581. [DOI: 10.1016/j.ympev.2019.106581] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 07/17/2019] [Accepted: 08/12/2019] [Indexed: 02/08/2023]
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Weir JT, Price TD. Song playbacks demonstrate slower evolution of song discrimination in birds from Amazonia than from temperate North America. PLoS Biol 2019; 17:e3000478. [PMID: 31639139 PMCID: PMC6804960 DOI: 10.1371/journal.pbio.3000478] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/17/2019] [Indexed: 11/19/2022] Open
Abstract
Genetic data indicate differences in speciation rate across latitudes, but underlying causes have been difficult to assess because a critical phase of the speciation process is initiated in allopatry, in which, by definition, individuals from different taxa do not interact. We conducted song playback experiments between 109 related pairs of mostly allopatric bird species or subspecies in Amazonia and North America to compare the rate of evolution of male discrimination of songs. Relative to local controls, the number of flyovers and approach to the speaker were higher in Amazonia. We estimate that responses to songs of relatives are being lost about 6 times more slowly in Amazonia than in North America. The slow loss of response holds even after accounting for differences in song frequency and song length. Amazonian species with year-round territories are losing aggressive responses especially slowly. We suggest the presence of many species and extensive interspecific territoriality favors recognition of songs sung by sympatric heterospecifics, which results in a broader window of recognition and hence an ongoing response to novel similar songs. These aggressive responses should slow the establishment of sympatry between recently diverged forms. If male responses to novel allopatric taxa reflect female responses, then premating reproductive isolation is also evolving more slowly in Amazonia. The findings are consistent with previously demonstrated slower recent rates of expansion of sister taxa into sympatry, slower rates of evolution of traits important for premating isolation, and slower rates of speciation in general in Amazonia than in temperate North America.
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Affiliation(s)
- Jason T. Weir
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolutionary Biology and Department of Biological Sciences, University of Toronto, Toronto, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, Canada
- * E-mail:
| | - Trevor D. Price
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
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Ribas CC, Aleixo A. Diversity and evolution of Amazonian birds: implications for conservation and biogeography. AN ACAD BRAS CIENC 2019; 91:e20190218. [PMID: 31411243 DOI: 10.1590/0001-3765201920190218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/12/2019] [Indexed: 11/21/2022] Open
Abstract
Amazonia has been a focus of interest since the early days of biogeography as an intrinsically complex and extremely diverse region. This region comprises an intricate mosaic that includes diverse types of forest formations, flooded environments and open vegetation. Increased knowledge about the distribution of species in Amazonia has led to the recognition of complex biogeographic patterns. The confrontation of these biogeographic patterns with information on the geological and climatic history of the region has generated several hypotheses dedicated to explain the origin of the biological diversity. Genomic information, coupled with knowledge of Earth's history, especially the evolution of the Amazonian landscape, presents fascinating possibilities for understanding the mechanisms that govern the origin and maintenance of diversity patterns in one of the most diverse regions of the world. For this we will increasingly need more intense and coordinated interactions between researchers studying biotic diversification and the evolution of landscapes. From the interaction between these two fields of knowledge that are in full development, an increasingly detailed understanding of the historical mechanisms related to the origin of the species will surely arise.
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Affiliation(s)
- Camila C Ribas
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, 69060-001 Manaus, AM, Brazil
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014, Helsinki, Finland
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37
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Silva SM, Peterson AT, Carneiro L, Burlamaqui TCT, Ribas CC, Sousa-Neves T, Miranda LS, Fernandes AM, d'Horta FM, Araújo-Silva LE, Batista R, Bandeira CHMM, Dantas SM, Ferreira M, Martins DM, Oliveira J, Rocha TC, Sardelli CH, Thom G, Rêgo PS, Santos MP, Sequeira F, Vallinoto M, Aleixo A. A dynamic continental moisture gradient drove Amazonian bird diversification. SCIENCE ADVANCES 2019; 5:eaat5752. [PMID: 31281878 PMCID: PMC6609164 DOI: 10.1126/sciadv.aat5752] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/30/2019] [Indexed: 05/04/2023]
Abstract
The Amazon is the primary source of Neotropical diversity and a nexus for discussions on processes that drive biotic diversification. Biogeographers have focused on the roles of rivers and Pleistocene climate change in explaining high rates of speciation. We combine phylogeographic and niche-based paleodistributional projections for 23 upland terra firme forest bird lineages from across the Amazon to derive a new model of regional biological diversification. We found that climate-driven refugial dynamics interact with dynamic riverine barriers to produce a dominant pattern: Older lineages in the wetter western and northern parts of the Amazon gave rise to lineages in the drier southern and eastern parts. This climate/drainage basin evolution interaction links landscape dynamics with biotic diversification and explains the east-west diversity gradients across the Amazon.
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Affiliation(s)
- Sofia Marques Silva
- Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Caixa Postal 399, 66040-170 Belém, Pará, Brazil
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
- Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | | | - Lincoln Carneiro
- Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Caixa Postal 399, 66040-170 Belém, Pará, Brazil
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
- Faculdade de Educação do Campo, Universidade Federal do Pará, Cametá, Brazil
| | - Tibério César Tortola Burlamaqui
- Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Caixa Postal 399, 66040-170 Belém, Pará, Brazil
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
| | - Camila C. Ribas
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo, 2936, Manaus, Amazonas, Brazil
| | - Tiago Sousa-Neves
- Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Caixa Postal 399, 66040-170 Belém, Pará, Brazil
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
- Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Leonardo S. Miranda
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
- Instituto Tecnológico Vale, Belém, Pará, Brazil
| | - Alexandre M. Fernandes
- Universidade Federal Rural de Pernambuco, Fazenda Saco, BR 232, 56909-535 Serra Talhada, Pernambuco, Brazil
| | - Fernando M. d'Horta
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936 Manaus, Amazonas, Brazil
- Instituto de Biociências, Universidade de São Paulo, R. do Matão 277, 05508-090 São Paulo, São Paulo, Brazil
| | - Lucas Eduardo Araújo-Silva
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
| | - Romina Batista
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936 Manaus, Amazonas, Brazil
| | | | - Sidnei M. Dantas
- Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Caixa Postal 399, 66040-170 Belém, Pará, Brazil
| | - Mateus Ferreira
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936 Manaus, Amazonas, Brazil
| | - Denise M. Martins
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
| | - Joiciane Oliveira
- Universidade Federal do Pará, Alameda Leandro Ribeiro, 68600-000 Bragança, Pará, Brazil
| | - Tainá C. Rocha
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
| | - Carla H. Sardelli
- Instituto de Biociências, Universidade de São Paulo, R. do Matão 277, 05508-090 São Paulo, São Paulo, Brazil
| | - Gregory Thom
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
- Instituto de Biociências, Universidade de São Paulo, R. do Matão 277, 05508-090 São Paulo, São Paulo, Brazil
| | - Péricles Sena Rêgo
- Universidade Federal do Pará, Alameda Leandro Ribeiro, 68600-000 Bragança, Pará, Brazil
| | - Marcos Pérsio Santos
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Av. Perimetral 1901, 66077-830 Belém, Pará, Brazil
| | - Fernando Sequeira
- Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Marcelo Vallinoto
- Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- Universidade Federal do Pará, Alameda Leandro Ribeiro, 68600-000 Bragança, Pará, Brazil
| | - Alexandre Aleixo
- Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Caixa Postal 399, 66040-170 Belém, Pará, Brazil
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Corresponding author.
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Takenaka M, Tokiwa T, Tojo K. Concordance between molecular biogeography of Dipteromimus tipuliformis and geological history in the local fine scale (Ephemeroptera, Dipteromimidae). Mol Phylogenet Evol 2019; 139:106547. [PMID: 31260742 DOI: 10.1016/j.ympev.2019.106547] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 11/29/2022]
Abstract
Species distribution area is determined by both biotic and abiotic factors. In particular, significant geological events influence the biodiversity and the genetic structures of the organisms inhabiting the area. The establishment of physical barriers (e.g., mountains, rivers), drives species differentiation by their interference with biological dispersal or gene flow. The Japanese Islands have a high degree of biodiversity. This study focused on the Kii Peninsula, which stands out as a region of exhibiting particularly high biodiversity, and also exceptionally high endemism. The Kii Peninsula has experienced active mountain formation ever since the Quaternary period. In this study, we investigate the influence of geological events on the establishment of genetic diversity. We focused on the mayfly, Dipteromimus tipuliformis. Phylogenetic analyses were performed utilizing the mitochondrial DNA 16S rRNA and COI regions, and the nuclear DNA histone H3, PEPCK and 28S rRNA regions. As a result, it was shown that this mayfly exhibits a genetic structure that strongly reflects the geological history of the Kii Peninsula, and detected their dispersal process across the Median Tectonic Line. This is a unique and significant study, in that it clearly shows the relationship between the phylogenetic evolution of this mayfly and the corresponding geological history in surprisingly geographic fine scale.
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Affiliation(s)
- Masaki Takenaka
- Department of Mountain and Environmental Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Tetsuya Tokiwa
- Department of Geology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Koji Tojo
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan.
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Benning JW, Eckhart VM, Geber MA, Moeller DA. Biotic Interactions Contribute to the Geographic Range Limit of an Annual Plant: Herbivory and Phenology Mediate Fitness beyond a Range Margin. Am Nat 2019; 193:786-797. [DOI: 10.1086/703187] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Macedo G, Silva M, Amaral FRD, Maldonado-Coelho M. Symmetrical discrimination despite weak song differentiation in 2 suboscine bird sister species. Behav Ecol 2019. [DOI: 10.1093/beheco/arz066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Song mediates territorial competition and mate choice in birds and population divergence in this signal can have important evolutionary consequences. For example, divergent songs can act in specific recognition and limit gene flow and, hence, have a fundamental role on the origin and/or integrity of evolutionary lineages. Especially interesting systems to test the role of song in specific recognition are species pairs that present small structural differences in this signal. Here, we perform song play-back experiments on males of a long-diverged sister pair of Neotropical Suboscine species, the squamate antbird (Myrmoderus squamosus) and the white-bibbed antbird (Myrmoderus loricatus), which occur in parapatry in the Atlantic Forest and that overlap extensively in song variation. Previous evidence indicates that genetic introgression between these species is either absent or negligible, suggesting that vocal discrimination or other mechanisms function as effective barriers to gene flow. Our results show that responses to heterospecific songs were symmetrical and intermediary compared with responses to conspecific songs in both species. A stronger response to conspecific territorial songs suggests that conspecific individuals pose greater competitive threat than heterospecifics. An important implication of our study is that even small song differences can play an important role in specific recognition.
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Affiliation(s)
- Gabriel Macedo
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Marco Silva
- SAVE Brasil, BirdLife International, São Paulo, Brazil
| | - Fábio Raposo do Amaral
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Marcos Maldonado-Coelho
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
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Rampant introgressive hybridization in Pogoniulus tinkerbirds (Piciformes: Lybiidae) despite millions of years of divergence. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko. Mol Phylogenet Evol 2019; 133:54-66. [DOI: 10.1016/j.ympev.2018.12.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022]
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Luzuriaga-Aveiga VE, Weir JT. Elevational differentiation accelerates trait evolution but not speciation rates in Amazonian birds. Ecol Lett 2019; 22:624-633. [PMID: 30714311 DOI: 10.1111/ele.13229] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/15/2018] [Accepted: 01/04/2019] [Indexed: 01/21/2023]
Abstract
The importance of ecologically mediated divergent selection in accelerating trait evolution has been poorly studied in the most species-rich biome of the planet, the continental Neotropics. We performed macroevolutionary analyses of trait divergence and diversification rates across closely related pairs of Andean and Amazonian passerine birds, to assess whether the difference in elevational range separating species pairs - a proxy for the degree of ecological divergence - influences the speed of trait evolution and diversification rates. We found that elevational differentiation is associated with faster divergence of song frequency, a trait important for pre-mating isolation, and several morphological traits, which may contribute to extrinsic post-mating isolation. However, elevational differentiation did not increase recent speciation rates, possibly due to early bursts of diversification during the uplift of the eastern Andes followed by a slow-down in speciation rate. Our results suggest that ecological differentiation may speed up trait evolution, but not diversification of Neotropical birds.
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Affiliation(s)
- Vanessa E Luzuriaga-Aveiga
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M1C 1A4, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M1C 1A4, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada.,Department of Ornithology, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada
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Pulido-Santacruz P, Aleixo A, Weir JT. Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation. Proc Biol Sci 2019. [PMID: 29514967 DOI: 10.1098/rspb.2017.2081] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We possess limited understanding of how speciation unfolds in the most species-rich region of the planet-the Amazon basin. Hybrid zones provide valuable information on the evolution of reproductive isolation, but few studies of Amazonian vertebrate hybrid zones have rigorously examined the genome-wide underpinnings of reproductive isolation. We used genome-wide genetic datasets to show that two deeply diverged, but morphologically cryptic sister species of forest understorey birds show little evidence for prezygotic reproductive isolation, but substantial postzygotic isolation. Patterns of heterozygosity and hybrid index revealed that hybrid classes with heavily recombined genomes are rare and closely match simulations with high levels of selection against hybrids. Genomic and geographical clines exhibit a remarkable similarity across loci in cline centres, and have exceptionally narrow cline widths, suggesting that postzygotic isolation is driven by genetic incompatibilities at many loci, rather than a few loci of strong effect. We propose Amazonian understorey forest birds speciate slowly via gradual accumulation of postzygotic genetic incompatibilities, with prezygotic barriers playing a less important role. Our results suggest old, cryptic Amazonian taxa classified as subspecies could have substantial postzygotic isolation deserving species recognition and that species richness is likely to be substantially underestimated in Amazonia.
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Affiliation(s)
| | - Alexandre Aleixo
- Department of Zoology, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada .,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada
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Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae). Mol Phylogenet Evol 2018; 126:314-320. [DOI: 10.1016/j.ympev.2018.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 04/04/2018] [Accepted: 04/11/2018] [Indexed: 11/19/2022]
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Naka LN, Brumfield RT. The dual role of Amazonian rivers in the generation and maintenance of avian diversity. SCIENCE ADVANCES 2018; 4:eaar8575. [PMID: 30083603 PMCID: PMC6070317 DOI: 10.1126/sciadv.aar8575] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 06/19/2018] [Indexed: 05/04/2023]
Abstract
The Amazon River and its major tributaries delimit the distributions of hundreds of terrestrial taxa. It remains unclear whether river-bounded distributions and taxon replacements reflect the historical role of rivers in generating species diversity as vicariant forces, or are the result of their role as secondary barriers, maintaining current levels of species diversity by inhibiting gene flow and population introgression. We use a community-wide comparative phylogeographic and phylogenetic approach to address the roles that the Rio Negro and the Rio Branco play in the avian speciation process in the Guiana Shield. Examining 74 pairs of ecologically similar geographic replacements that turn over across the lower Negro, we found substantial variation in the levels of genetic divergence and the inferred timing of diversification among pairs, ranging from ~0.24 to over 8 million years (Ma ago). The breadth of this variation is inconsistent with a single, shared speciation event. Coalescent simulations also rejected a simultaneous divergence scenario for pairs divided by the Rio Branco but could not reject a single diversification pulse for a subset of 12 pairs of taxa divided by the upper Negro. These results are consistent with recent geomorphological hypotheses regarding the origins of these rivers. Phylogenetically, taxon pairs represent a blend of sister (~40%) and nonsister taxa (~60%), consistent with river-associated allopatric or peripatric speciation and secondary contact, respectively. Our data provide compelling evidence that species turnover across the Rio Negro basin encompasses a mixture of histories, supporting a dual role for Amazonian rivers in the generation and maintenance of biological diversity.
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Affiliation(s)
- Luciano N. Naka
- Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
- Corresponding author.
| | - Robb T. Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
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Gibbs HL, Sovic M, Amazonas D, Chalkidis H, Salazar-Valenzuela D, Moura-Da-Silva AM. Recent lineage diversification in a venomous snake through dispersal across the Amazon River. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx158] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, USA
- Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, OH, USA
| | - Michael Sovic
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Diana Amazonas
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo, Brazil
| | | | - David Salazar-Valenzuela
- Centro de Investigación de la Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, Quito, Ecuador
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Mason NA, Olvera‐Vital A, Lovette IJ, Navarro‐Sigüenza AG. Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White-collared Seedeater complex (Thraupidae: Sporophila torqueola). Ecol Evol 2018; 8:1867-1881. [PMID: 29435260 PMCID: PMC5792519 DOI: 10.1002/ece3.3799] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022] Open
Abstract
Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White-collared Seedeater (Sporophila torqueola) of Central America and Mexico. We combine measurements of morphology and plumage patterning with thousands of nuclear loci derived from ultraconserved elements (UCEs) and mitochondrial DNA to evaluate population differentiation. We find deep levels of molecular divergence between two S. torqueola lineages that are phenotypically diagnosable: One corresponds to S. t. torqueola along the Pacific coast of Mexico, and the other includes S. t. morelleti and S. t. sharpei from the Gulf Coast of Mexico and Central America. Surprisingly, these two lineages are strongly differentiated in both nuclear and mitochondrial markers, and each is more closely related to other Sporophila species than to one another. We infer low levels of gene flow between these two groups based on demographic models, suggesting multiple independent evolutionary lineages within S. torqueola have been obscured by coarse-scale similarity in plumage patterning. These findings improve our understanding of the biogeographic history of this lineage, which includes multiple dispersal events out of South America and across the Isthmus of Tehuantepec into Mesoamerica. Finally, the phenotypic and genetic distinctiveness of the range-restricted S. t. torqueola highlights the Pacific Coast of Mexico as an important region of endemism and conservation priority.
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Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
- Fuller Evolutionary Biology ProgramCornell Laboratory of OrnithologyIthacaNYUSA
| | | | - Irby J. Lovette
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
- Fuller Evolutionary Biology ProgramCornell Laboratory of OrnithologyIthacaNYUSA
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de Abreu FHT, Schietti J, Anciães M. Spatial and environmental correlates of intraspecific morphological variation in three species of passerine birds from the Purus–Madeira interfluvium, Central Amazonia. Evol Ecol 2018. [DOI: 10.1007/s10682-018-9929-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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50
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Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird. Proc Natl Acad Sci U S A 2017; 115:E218-E225. [PMID: 29279398 DOI: 10.1073/pnas.1717319115] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hybrid speciation is rare in vertebrates, and reproductive isolation arising from hybridization is infrequently demonstrated. Here, we present evidence supporting a hybrid-speciation event involving the genetic admixture of the snow-capped (Lepidothrix nattereri) and opal-crowned (Lepidothrix iris) manakins of the Amazon basin, leading to the formation of the hybrid species, the golden-crowned manakin (Lepidothrix vilasboasi). We used a genome-wide SNP dataset together with analysis of admixture, population structure, and coalescent modeling to demonstrate that the golden-crowned manakin is genetically an admixture of these species and does not represent a hybrid zone but instead formed through ancient genetic admixture. We used spectrophotometry to quantify the coloration of the species-specific male crown patches. Crown patches are highly reflective white (snow-capped manakin) or iridescent whitish-blue to pink (opal-crowned manakin) in parental species but are a much less reflective yellow in the hybrid species. The brilliant coloration of the parental species results from nanostructural organization of the keratin matrix feather barbs of the crown. However, using electron microscopy, we demonstrate that the structural organization of this matrix is different in the two parental species and that the hybrid species is intermediate. The intermediate nature of the crown barbs, resulting from past admixture appears to have rendered a duller structural coloration. To compensate for reduced brightness, selection apparently resulted in extensive thickening of the carotenoid-laden barb cortex, producing the yellow crown coloration. The evolution of this unique crown-color signal likely culminated in premating isolation of the hybrid species from both parental species.
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