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Fernandes AM, Cohn-Haft M, Fábio Silveira L, Aleixo A, Nascimento N, Olsson U. Speciation in savanna birds in South America: The case of the Least Nighthawk Chordeiles pusillus (Aves: Caprimulgidae) in and out of the Amazon. Mol Phylogenet Evol 2024; 198:108117. [PMID: 38852908 DOI: 10.1016/j.ympev.2024.108117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 05/19/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
The Least Nighthawk Chordeiles pusillus is widespread wherever there are savannas in the South American tropics, often in isolated patches, such as white-sands savannas in the Amazon rainforest realm. Here, we investigate genetic relationships between populations of the Least Nighthawk to understand historical processes leading to its diversification and to determine dispersal routes between northern and southern savannas by way of three hypothesized dispersal corridors by comparing samples from white-sand savannas to samples from other savannas outside of the Amazon rainforest region. We use 32 mtDNA samples from the range of C. pusillus to infer a dated phylogeny. In a subset of 17 samples, we use shotgun sequences to infer a distance-based phylogeny and to estimate individual admixture proportions. We calculate gene flow and shared alleles between white-sand and non-Amazonian populations using the ABBA-BABA test (D statistics), and Principal Component Analysis (PCA) to examine genetic structure within and between lineages. Finally, we use species distribution modelling (SDM) of conditions during the Last Glacial Maximum (LGM), currently, and in the future (2050-2080) to predict potential species occurrence under a climate change scenario. Two main clades (estimated to have diverged around 1.07 million years ago) were recovered with mtDNA sequences and Single Nucleotide Polymorphism (SNPs) and were supported by NGSadmix and PCA: one in the Amazon basin white-sand savannas, the other in the non-Amazonian savannas. Possible allele sharing between these clades was indicated by the D-statistics between northern non-Amazonian populations and the white-sand savanna population, but this was not corroborated by the admixture analyses. Dispersal among northern non-Amazonian populations may have occurred in a dry corridor between the Guianan and the Brazilian Shield, which has since moved eastward. Our data suggest that the lineages separated well before the Last Glacial Maximum, consequently dispersal could have happened at any earlier time during similar climatic conditions. Subsequently, non-Amazonian lineages became more divergent among themselves, possibly connecting and dispersing across the mouth of the Amazon River across Marajó island during favourable climatic conditions in the Pleistocene.
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Affiliation(s)
| | | | | | - Alexandre Aleixo
- Museu Paraense Emílio Goeldi, Belém, Brazil; Instituto Tecnológico Vale, Brazil
| | | | - Urban Olsson
- Department of Biology and Environmental Science, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
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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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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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Ocampo D, Winker K, Miller MJ, Sandoval L, Albert C. Uy J. Rapid diversification of the Variable Seedeater superspecies complex despite widespread gene flow. Mol Phylogenet Evol 2022; 173:107510. [DOI: 10.1016/j.ympev.2022.107510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/16/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022]
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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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7
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Ericson PGP, Irestedt M, Nylander JAA, Christidis L, Joseph L, Qu Y. Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics. Syst Biol 2021; 69:820-829. [PMID: 32415976 PMCID: PMC7440736 DOI: 10.1093/sysbio/syaa040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 12/02/2022] Open
Abstract
The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. [Adaptive radiation; bowerbirds; mating system, sexual selection; whole genome sequencing.]
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Affiliation(s)
- Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden
| | - Les Christidis
- School of Environment, Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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8
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Capurucho JMG, Ashley MV, Tsuru BR, Cooper JC, Bates JM. Dispersal ability correlates with range size in Amazonian habitat-restricted birds. Proc Biol Sci 2020; 287:20201450. [PMID: 33203330 DOI: 10.1098/rspb.2020.1450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding how species attain their geographical distributions and identifying traits correlated with range size are important objectives in biogeography, evolutionary biology and biodiversity conservation. Despite much effort, results have been varied and general trends have been slow to emerge. Studying species pools that occupy specific habitats, rather than clades or large groupings of species occupying diverse habitats, may better identify ranges size correlates and be more informative for conservation programmes in a rapidly changing world. We evaluated correlations between a set of organismal traits and range size in bird species from Amazonian white-sand ecosystems. We assessed if results are consistent when using different data sources for phylogenetic and range hypotheses. We found that dispersal ability, as measured by the hand-wing index, was correlated with range size in both white-sand birds and their non-white-sand sister taxa. White-sand birds had smaller ranges on average than their sister taxa. The results were similar and robust to the different data sources. Our results suggest that the patchiness of white-sand ecosystems limits species' ability to reach new habitat islands and establish new populations.
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Affiliation(s)
- João M G Capurucho
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA.,Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Mary V Ashley
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Brian R Tsuru
- Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Jacob C Cooper
- Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.,Committee on Evolutionary Biology, The University of Chicago, 1025 E 57th Street, Chicago, IL 60637, USA
| | - John M Bates
- Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
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9
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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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10
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Patterns and Processes of Diversification in Amazonian White Sand Ecosystems: Insights from Birds and Plants. NEOTROPICAL DIVERSIFICATION: PATTERNS AND PROCESSES 2020. [DOI: 10.1007/978-3-030-31167-4_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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11
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Rossetti DF, Moulatlet GM, Tuomisto H, Gribel R, Toledo PM, Valeriano MM, Ruokolainen K, Cohen MCL, Cordeiro CLO, Rennó CD, Coelho LS, Ferreira CAC. White sand vegetation in an Amazonian lowland under the perspective of a young geological history. AN ACAD BRAS CIENC 2019; 91:e20181337. [PMID: 31800703 DOI: 10.1590/0001-3765201920181337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/22/2019] [Indexed: 11/21/2022] Open
Abstract
What controls the formation of patchy substrates of white sand vegetation in the Amazonian lowlands is still unclear. This research integrated the geological history and plant inventories of a white sand vegetation patch confined to one large fan-shaped sandy substrate of northern Amazonia, which is related to a megafan environment. We examined floristic patterns to determine whether abundant species are more often generalists than the rarer one, by comparing the megafan environments and older basement rocks. We also investigated the pattern of species accumulation as a function of increasing sampling effort. All plant groups recorded a high proportion of generalist species on the megafan sediments compared to older basement rocks. The vegetation structure is controlled by topographic gradients resulting from the smooth slope of the megafan morphology and microreliefs imposed by various megafan subenvironments. Late Pleistocene-Holocene environmental disturbances caused by megafan sedimentary processes controlled the distribution of white sand vegetation over a large area of the Amazonian lowlands, and may have also been an important factor in species diversification during this period. The integration of geological and biological data may shed new light on the existence of many patches of white sand vegetation from the plains of northern Amazonia.
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Affiliation(s)
- Dilce F Rossetti
- Instituto Brasileiro de Pesquisas Espaciais/INPE, Coordenação Geral de Observação da Terra/CGOBT, Rua dos Astronautas, 1758, Jardim da Granja, 12245-970 São José dos Campos, SP, Brazil
| | - Gabriel M Moulatlet
- Universidad Regional Amazónica/IKIAM, Km 7, Vía Muyuna, Parroquia Muyuna, Tena, Napo, Ecuador
| | - Hanna Tuomisto
- University of Turku /UTU, Department of Biology, 20014, Turku, Finland
| | - Rogério Gribel
- Instituto Nacional de Pesquisas da Amazônia/ INPA, Coordenação de Biodiversidade, Av. André Araújo, 2936, 69067-375 Manaus, AM, Brazil
| | - Peter M Toledo
- Instituto Brasileiro de Pesquisas Espaciais/INPE, Coordenação Geral de Observação da Terra/CGOBT, Rua dos Astronautas, 1758, Jardim da Granja, 12245-970 São José dos Campos, SP, Brazil
| | - Márcio M Valeriano
- Instituto Brasileiro de Pesquisas Espaciais/INPE, Coordenação Geral de Observação da Terra/CGOBT, Rua dos Astronautas, 1758, Jardim da Granja, 12245-970 São José dos Campos, SP, Brazil
| | - Kalle Ruokolainen
- University of Turku/UTU, Department of Geography and Geology, 20014, Turku, Finland
| | - Marcelo C L Cohen
- Programa de Pós-Graduação em Geologia e Geoquímica, Universidade Federal do Pará/UFPA, Rua Augusto Correa 01, Guamá, 66075-110 Belém, PA, Brazil
| | - Carlos L O Cordeiro
- Instituto Brasileiro de Pesquisas Espaciais/INPE, Coordenação Geral de Observação da Terra/CGOBT, Rua dos Astronautas, 1758, Jardim da Granja, 12245-970 São José dos Campos, SP, Brazil
| | - Camilo D Rennó
- Instituto Brasileiro de Pesquisas Espaciais/INPE, Coordenação Geral de Observação da Terra/CGOBT, Rua dos Astronautas, 1758, Jardim da Granja, 12245-970 São José dos Campos, SP, Brazil
| | - Luiz S Coelho
- Instituto Nacional de Pesquisas da Amazônia/ INPA, Coordenação de Biodiversidade, Av. André Araújo, 2936, 69067-375 Manaus, AM, Brazil
| | - Carlos A C Ferreira
- Instituto Nacional de Pesquisas da Amazônia/ INPA, Coordenação de Biodiversidade, Av. André Araújo, 2936, 69067-375 Manaus, AM, Brazil
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12
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Reis CA, Dias C, Araripe J, Aleixo A, Anciães M, Sampaio I, Schneider H, Rêgo PS. Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance. ZOOL SCR 2019. [DOI: 10.1111/zsc.12395] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Camila Alves Reis
- Curso de Pós‐Graduação em Zoologia Universidade Federal do ParáMuseu Paraense Emílio Goeldi Belém Brazil
| | - Cleyssian Dias
- Curso de Pós‐Graduação em Zoologia Universidade Federal do ParáMuseu Paraense Emílio Goeldi Belém Brazil
| | - Juliana Araripe
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
| | - Alexandre Aleixo
- Finnish Museum of Natural History University of Helsinki Helsinki Finland
| | - Marina Anciães
- Laboratório de Evolução e Comportamento Animal COBIO Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
| | - Horacio Schneider
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
| | - Péricles Sena Rêgo
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
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Speciation, gene flow, and seasonal migration in Catharus thrushes (Aves:Turdidae). Mol Phylogenet Evol 2019; 139:106564. [PMID: 31330265 DOI: 10.1016/j.ympev.2019.106564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 10/26/2022]
Abstract
New World thrushes in the genus Catharus are small, insectivorous or omnivorous birds that have been used to explore several important questions in avian evolution, including the evolution of seasonal migration and plumage variation. Within Catharus, members of a clade of obligate long-distance migrants (C. fuscescens, C. minimus, and C. bicknelli) have also been used in the development of heteropatric speciation theory, a divergence process in which migratory lineages (which might occur in allopatry or sympatry during portions of their annual cycle) diverge despite low levels of gene flow. However, research on Catharus relationships has thus far been restricted to the use of small genetic datasets, which provide limited resolution of both phylogenetic and demographic histories. We used a large, multi-locus dataset from loci containing ultraconserved elements (UCEs) to study the demographic histories of the migratory C. fuscescens-minimus-bicknelli clade and to resolve the phylogeny of the migratory species of Catharus. Our dataset included more than 2000 loci and over 1700 variable genotyped sites, and analyses supported our prediction of divergence with gene flow in the fully migratory clade, with significant gene flow among all three species. Our phylogeny of the genus differs from past work in its placement of C. ustulatus, and further analyses suggest historic gene flow throughout the genus, producing genetically reticulate (or network) phylogenies. This raises questions about trait origins and suggests that seasonal migration and the resulting migratory condition of heteropatry is likely to promote hybridization not only during pairwise divergence and speciation, but also among non-sisters.
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Hill GE. Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression. Integr Comp Biol 2019; 59:912-924. [DOI: 10.1093/icb/icz019] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.
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Affiliation(s)
- Geoffrey E Hill
- Department of Biological Sciences, 331 Funchess Hall, Auburn University, Auburn, AL 36849-5414, USA
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