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Luna LW, Naka LN, Thom G, Knowles LL, Sawakuchi AO, Aleixo A, Ribas CC. Late Pleistocene landscape changes and habitat specialization as promoters of population genomic divergence in Amazonian floodplain birds. Mol Ecol 2023; 32:214-228. [PMID: 36261866 DOI: 10.1111/mec.16741] [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: 06/16/2022] [Revised: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022]
Abstract
Although vicariant processes are expected to leave similar genomic signatures among codistributed taxa, ecological traits such as habitat and stratum can influence genetic divergence within species. Here, we combined landscape history and habitat specialization to understand the historical and ecological factors responsible for current levels of genetic divergence in three species of birds specialized in seasonally flooded habitats in muddy rivers and which are widespread in the Amazon basin but have isolated populations in the Rio Branco. Populations of the white-bellied spinetail (Mazaria propinqua), lesser wagtail-tyrant (Stigmatura napensis) and bicolored conebill (Conirostrum bicolor) are currently isolated in the Rio Branco by the black-waters of the lower Rio Negro, offering a unique opportunity to test the effect of river colour as a barrier to gene flow. We used ultraconserved elements (UCEs) to test alternative hypotheses of population history in a comparative phylogeographical approach by modelling genetic structure, demographic history and testing for shared divergence time among codistributed taxa. Our analyses revealed that (i) all three populations from the Rio Branco floodplains are genetically distinct from other populations along the Amazon River floodplains; (ii) these divergences are the result of at least two distinct events, consistent with species habitat specialization; and (iii) the most likely model of population evolution includes lower population connectivity during the Late Pleistocene transition (~250,000 years ago), with gene flow being completely disrupted after the Last Glacial Maximum (~21,000 years ago). Our findings highlight how landscape evolution modulates population connectivity in habitat specialist species and how organisms can have different responses to the same historical processes of environmental change, depending on their habitat affinity.
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Affiliation(s)
- Leilton Willians Luna
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Zoology, Universidade Federal do Pará/Emílio Goeldi Museum, Belém, Brazil
| | - Luciano Nicolas Naka
- Laboratory of Avian Ecology and Evolution, Department of Zoology, Universidade Federal do Pernambuco, Recife, Brazil
| | - Gregory Thom
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Laura Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Alexandre Aleixo
- Department of Zoology, Universidade Federal do Pará/Emílio Goeldi Museum, Belém, Brazil.,Instituto Tecnológico Vale, Belém, Brazil.,Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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2
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French CM, Berezin CT, Overcast I, Méndez De La Cruz FR, Basu S, Martínez Bernal RL, Murphy RW, Hickerson MJ, Blair C. Forest cover and geographical distance influence fine-scale genetic structure of leaf-toed geckos in the tropical dry forests of western Mexico. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac118] [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]
Abstract
Abstract
The biodiversity within tropical dry forests (TDFs) is astounding and yet poorly catalogued due to inadequate sampling and the presence of cryptic species. In the Mexican TDF, endemic species are common, and the landscape has been continually altered by geological and anthropogenic changes. To understand how landscape and environmental variables have shaped the population structure of endemic species, we studied the recently described species of leaf-toed gecko, Phyllodactylus benedettii, in coastal western Mexico. Using double-digest restriction site-associated DNA sequencing data, we first explore population structure and estimate the number of ancestral populations. The results indicate a high degree of genetic structure with little admixture, and patterns corresponding to both latitudinal and altitudinal gradients. We find that genetic structure cannot be explained purely by geographical distance, and that ecological corridors may facilitate dispersal and gene flow. We then model the spatial distribution of P. benedettii in the TDF through time and find that the coastline has been climatically suitable for the species since the Last Glacial Maximum. Landscape genetic analyses suggest that the combination of isolation by distance (IBD) and isolation by resistance (IBR; forest cover) has influenced the spatial genetic structure of the species. Overall, our genomic data demonstrate fine-scale population structure in TDF habitat, a complex colonization history, and spatial patterns consistent with both IBD and other ecological factors. These results further highlight the Mexican TDF as a diversity hotspot and suggest that continued anthropogenic changes are likely to affect native fauna.
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Affiliation(s)
- Connor M French
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
| | - Casey-Tyler Berezin
- Department of Biology, City College of New York , 160 Convent Avenue, New York, NY 10031 , USA
| | - Isaac Overcast
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Institut de Biologie de l’Ecole Normale Superieure , 46 Rue d’Ulm, 75005 Paris , France
- Division of Vertebrate Zoology, American Museum of Natural History , 200 Central Park West, New York, NY 10024 , USA
| | | | - Saptarsi Basu
- Department of Biological Sciences, New York City College of Technology, The City University of New York , 285 Jay Street, Brooklyn, NY 11201 , USA
| | | | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum , 100 Queen’s Park, Toronto, ON M5S 2C6 , Canada
| | - Michael J Hickerson
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Department of Biology, City College of New York , 160 Convent Avenue, New York, NY 10031 , USA
| | - Christopher Blair
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Department of Biological Sciences, New York City College of Technology, The City University of New York , 285 Jay Street, Brooklyn, NY 11201 , USA
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3
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The tangled evolutionary history of a long-debated Mesoamerican taxon: the Velazquez Woodpecker (Melanerpes santacruzi, Aves: Picidae). Mol Phylogenet Evol 2022; 170:107445. [DOI: 10.1016/j.ympev.2022.107445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 11/19/2022]
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Stopiglia R, Barbosa W, Ferreira M, Raposo MA, Dubois A, Harvey MG, Kirwan GM, Forcato G, Bockmann FA, Ribas CC. Taxonomic challenges posed by discordant evolutionary scenarios supported by molecular and morphological data in the Amazonian Synallaxis rutilans group (Aves: Furnariidae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab076] [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]
Abstract
Abstract
Alpha taxonomy endeavours to propose a coherent vision of existing species and, simultaneously, to individualize the natural entities useful to understand evolutionary processes. This ideal is especially difficult when available data lack congruence. Here we address the polytypic species Synallaxis rutilans (ruddy spinetail), a suboscine passerine widely distributed in the Amazon Basin and whose taxonomy could, potentially, aid our understanding of processes shaping its biodiversity. Combining genetic [genomic ultraconserved elements (UCE) and mtDNA] and morphological data, we demonstrate that while delimitation of genetic lineages and their phylogenetic relationships are strongly associated with classic Amazonian geographic barriers, such as rivers, different coloration patterns appear to be more associated with local selection processes for phenotype. Employing an evolutionary approach, whereby the species is considered a taxonomic category, rather than a nomenclatural rank, we propose to recognize five species: S. amazonica, S. caquetensis, S. dissors, S. omissa and S. rutilans. The taxonomic arrangement proposed here permits better understanding of the similarities and differences among taxa from different areas of endemism, and represents patterns of genetic and morphological diversity resulting from distinct processes acting across certain time frames. This arrangement draws attention to the importance of understanding the evolutionary processes operating in the complex and constantly changing Amazonian landscape.
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Affiliation(s)
- Renata Stopiglia
- Museu de História Natural do Ceará Prof. Dias da Rocha, CCS, Universidade Estadual do Ceará, Av. Dr. Silas Munguba, 1700, Fortaleza, CE, 60714–903, Brazil
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristóvão, 20940-040, Rio de Janeiro, RJ, Brazil
- Laboratório de Ictiologia de Ribeirão Preto, FFCLRP, Universidade de São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP, Brazil
- Institut de Systématique, Évolution, Biodiversité, Muséum National d’Histoire Naturelle, Sorbonne Universités, 25 rue Cuvier, 75005, Paris, France
| | - Waleska Barbosa
- Programa de Pós-Graduação em Ecologia, INPA, Manaus, AM, Brazil
| | - Mateus Ferreira
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, INPA, Manaus, AM, Brazil
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Boa Vista, RR, 69310-000, Brazil
| | - Marcos A Raposo
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristóvão, 20940-040, Rio de Janeiro, RJ, Brazil
| | - Alain Dubois
- Institut de Systématique, Évolution, Biodiversité, Muséum National d’Histoire Naturelle, Sorbonne Universités, 25 rue Cuvier, 75005, Paris, France
| | - Michael G Harvey
- Department of Biological Sciences and Biodiversity Collections, The University of Texas at El Paso, 304 Biology Building, 500 West University Ave., El Paso, Texas 79968, USA
| | - Guy M Kirwan
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristóvão, 20940-040, Rio de Janeiro, RJ, Brazil
- Bird Group, Department of Life Sciences, Natural History Museum, Tring, Herts, UK
| | - Giovanna Forcato
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristóvão, 20940-040, Rio de Janeiro, RJ, Brazil
| | - Flavio A Bockmann
- Laboratório de Ictiologia de Ribeirão Preto, FFCLRP, Universidade de São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP, Brazil
- Programa de Pós-Graduação em Biologia Comparada, FFCLRP-USP, Ribeirão Preto, SP, Brazil
| | - Camila C Ribas
- Biodiversity Section and Zoological Collections, Instituto Nacional de Pesquisas da Amazônia, 69067–375, Manaus, AM, Brazil
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Sympatric and independently evolving lineages in the Thoropa miliaris - T. taophora species complex (Anura: Cycloramphidae). Mol Phylogenet Evol 2021; 166:107220. [PMID: 34481948 DOI: 10.1016/j.ympev.2021.107220] [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: 09/18/2020] [Revised: 04/28/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022]
Abstract
Species delimitation can be challenging and affected by subjectivity. Sibling lineages that occur in sympatry constitute good candidates for species delimitation regardless of the adopted species concept. The Thoropa miliaris + T. taophora species complex exhibits high genetic diversity distributed in several lineages that occur sympatrically in the southeastern Atlantic Forest of Brazil. We used 414 loci obtained by anchored hybrid enrichment to characterize genetic variation in the Thoropa miliaris species group (T. saxatilis, T megatympanum, T. miliaris, and T. taophora), combining assignment analyses with traditional and coalescent phylogeny reconstruction. We also investigated evolutionary independence in co-occurring lineages by estimating gene flow, and validated lineages under the multispecies coalescent. We recovered most previously described lineages as unique populations in assignment analyses; exceptions include two lineages within T. miliaris that are further substructured, and the merging of all T. taophora lineages. We found very low probabilities of gene flow between sympatric lineages, suggesting independent evolution. Species tree inferences and species delimitation yielded resolved relationships and indicate that all lineages constitute putative species that diverged during the Pliocene and Pleistocene, later than previously estimated.
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Raposo do Amaral F, Thom G, Lima-Ribeiro MS, Alvarado-Serrano DF, Montesanti JAC, Pellegrino KCM, Miyaki CY, Hickerson MJ, Maldonado-Coelho M. Rugged relief and climate promote isolation and divergence between two neotropical cold-associated birds. Evolution 2021; 75:2371-2387. [PMID: 34375460 DOI: 10.1111/evo.14318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 06/21/2021] [Accepted: 07/19/2021] [Indexed: 01/15/2023]
Abstract
The role of historical factors in establishing patterns of diversity in tropical mountains is of interest to understand the buildup of megadiverse biotas. In these regions, the historical processes of range fragmentation and contraction followed by dispersal are thought to be mediated by the interplay between rugged relief (complex topography) and climate fluctuations and likely explain most of the dynamics of diversification in plants and animals. Although empirical studies addressing the interaction between climate and topography have provided invaluable insights into population divergence and speciation patterns in tropical montane organisms, a more detailed and robust test of such processes in an explicit spatio-temporal framework is still lacking. Consequently, our ability to gain insights into historical range shifts over time and the genomic footprint left by them is limited. Here, we used niche modeling and subgenomic population-level datasets to explore the evolution of two species of warbling finches (genus Microspingus) disjunctly distributed across the Montane Atlantic Forest, a Neotropical region with complex geological and environmental histories. Population structure inferences suggest a scenario of three genetically differentiated populations, which are congruent with both geography and phenotypic variation. Demographic simulations support asynchronous isolation of these populations as recently as ∼40,000 years ago, relatively stable population sizes over recent time, and past gene flow subsequent to divergence. Throughout the last 800,000 years, niche models predicted extensive expansion into lowland areas with increasing overlap of species distributions during glacial periods, with prominent retractions and isolation into higher altitudes during interglacials, which are in line with signs of introgression of currently isolated populations. These results support a dual role of cyclical climatic changes: population divergence and persistence in mountain tops during warm periods followed by periods of expansion and admixture in lower elevations during cold periods. Our results underscore the role of the interplay between landscape and climate as an important mechanism in the evolution of the Neotropical montane biota.
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Affiliation(s)
- Fábio Raposo do Amaral
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil
| | - Gregory Thom
- Department of Ornithology, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024-5192, USA
| | - Matheus S Lima-Ribeiro
- Departamento de Ciências Biológicas, Universidade Federal de Jataí, CP 03, Jataí, GO, 75804-020, Brazil
| | - Diego F Alvarado-Serrano
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Life Sciences Building R219, Athens, OH, 45701, USA
| | - Julia A C Montesanti
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil
| | - Katia C M Pellegrino
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil
| | - Cristina Y Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
| | - Michael J Hickerson
- Department of Biology, City College of New York, 160, Convent Avenue, New York, NY, 10031, USA
| | - Marcos Maldonado-Coelho
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil.,Department of Biology, Lund University, Lund, SE-223 62, Sweden
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Bocalini F, Bolívar-Leguizamón SD, Silveira LF, Bravo GA. Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic Forest. Mol Phylogenet Evol 2020; 154:106973. [PMID: 33059067 DOI: 10.1016/j.ympev.2020.106973] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 09/08/2020] [Accepted: 09/28/2020] [Indexed: 11/30/2022]
Abstract
The Pernambuco Center of Endemism (PCE) is the northernmost strip of the Atlantic Forest (AF). Biogeographic affinities among avifaunas in the PCE, the southern-central Atlantic Forest (SCAF), and Amazonia (AM) have not been studied comprehensively, and current patterns of genetic diversity in the PCE remain unclear. The interplay between species' ecological attributes and historical processes, such as Pleistocene climate fluctuations or the appearance of rivers, may have affected population genetic structures in the PCE. Moreover, the role of past connections between the PCE and AM and the elevational distribution of species in assembling the PCE avifauna remain untested. Here, we investigated the biogeographic history of seven taxa endemic to the PCE within a comparative phylogeographic framework based on a mean of 3,618 independent single nucleotide polymorphisms (SNPs) extracted from flanking regions of ultraconserved elements (UCEs) and one mitochondrial gene. We found that PCE populations were more closely related to SCAF populations than they were to those in AM, regardless of their elevational range, with divergence times placed during the Mid-Pleistocene. These splits were consistent with a pattern of allopatric divergence with gene flow until the upper Pleistocene and no signal of rapid changes in population sizes. Our results support the existence of a Pleistocene refugium driving current genetic diversity in the PCE, thereby rejecting the role of the São Francisco River as a primary barrier for population divergence. Additionally, we found that connections with Amazonia also played a significant role in assembling the PCE avifauna through subsequent migration events.
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Affiliation(s)
- Fernanda Bocalini
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil; Departamento de Zoologia do Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil.
| | | | - Luís F Silveira
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil
| | - Gustavo A Bravo
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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da Silva Ribeiro T, Batalha-Filho H, Silveira LF, Miyaki CY, Maldonado-Coelho M. Life history and ecology might explain incongruent population structure in two co-distributed montane bird species of the Atlantic Forest. Mol Phylogenet Evol 2020; 153:106925. [PMID: 32771546 DOI: 10.1016/j.ympev.2020.106925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 07/03/2020] [Accepted: 08/03/2020] [Indexed: 11/16/2022]
Abstract
Comparative phylogeography is a powerful approach to investigate the role of historical and environmental processes in the evolution of biodiversity within a region. In this regard, comparative studies of species with similar habitat preferences are valuable to reduce the confounding influence of habitat association when interpreting phylogeographic patterns. In the Atlantic Forest of South America, phylogeographic studies of highland and lowland species have shown distinct population structure patterns so far, suggesting that such species have responded differently to Pleistocene glacial cycles. Herein, we performed a comparative analysis using molecular data and paleodistribution models of two Montane Atlantic Forest (MAF) co-distributed passerine birds with similar habitat requirements but with distinct life-history traits and ecologies: the frugivore lek-breeding Blue Manakin (Chiroxiphia caudata) and the insectivore and socially monogamous Drab-Breasted Bamboo Tyrant (Hemitriccus diops). We aimed to shed light on the role of contrasting life histories and ecologies onto the demography and population structure of MAF species. We sampled both species throughout most of their distribution range, sequenced a mitochondrial and a nuclear molecular marker, and used standard phylogeographic methods to investigate population structure and ecological niche modeling (ENM) to infer the species' paleodistributions. Our analyses recovered a phylogeographic break in H. diops in the region of the Doce River, but no genetic structure in C. caudata. We also found higher differentiation among subpopulations within each lineage of H. diops than among subpopulations of C. caudata. We suggest that these discrepancies in population structure might be due to distinct life-history traits and their impact on gene flow and generation time. For example, while H. diops is an insectivore species, C. caudata is a frugivore and the latter ecological aspect likely selects for a higher dispersion distance. Additionally, because C. caudata is a lek-breeding species, it has a longer generation time than H. diops. These traits could hinder genetic differentiation when populations become geographically isolated. Nonetheless, both species showed some common biological features, such as signatures of synchronous population expansion and larger distribution ranges during the Last Glacial Maximum, possibly due to similar cold tolerance.
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Affiliation(s)
- Tiago da Silva Ribeiro
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil.
| | - Henrique Batalha-Filho
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
| | - Luis Fábio Silveira
- Museu de Zoologia, Universidade de São Paulo, 04263-000 São Paulo, SP, Brazil
| | - Cristina Yumi Miyaki
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
| | - Marcos Maldonado-Coelho
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
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Mao X, Tsagkogeorga G, Thong VD, Rossiter SJ. Resolving evolutionary relationships among six closely related taxa of the horseshoe bats (Rhinolophus) with targeted resequencing data. Mol Phylogenet Evol 2019; 139:106551. [DOI: 10.1016/j.ympev.2019.106551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/11/2019] [Accepted: 07/01/2019] [Indexed: 01/04/2023]
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A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae). DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.
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