Phylogenomics and biogeography of the world's thrushes (Aves, Turdus) : new evidence for a more parsimonious evolutionary history

To elucidate the relationships and spatial range evolution across the world of the bird genus Turdus (Aves), we produced a large genomic dataset comprising ca 2 million nucleotides for ca 100 samples representing 53 species, including over 2000 loci. We estimated time-calibrated maximum-likelihood and multispecies coalescentphylogenies and carried out biogeographic analyses. Our results indicate that there have been considerably fewer trans-oceanic dispersals within the genus Turdus than previously suggested, such that the Palaearctic clade did not originate in America and the African clade was not involved in the colonization of the Americas. Instead, our findings suggest that dispersal from the Western Palaearctic via the Antilles to the Neotropics might have occurred in a single event, giving rise to the rich Neotropical diversity of Turdus observed today, with no reverse dispersals to thePalaearctic or Africa. Our large multilocus dataset, combined with dense species-level sampling and analysed under probabilistic methods, brings important insights into historical biogeography and systematics, even in a scenario of fast and spatially complex diversification.Peer reviewe

Divide to conquer: A complex pattern of biodiversity depicted by vertebrate components in the Brazilian Atlantic Forest

The identification of northern and southern components in different vertebrate species led researchers to accept a two-component hypothesis for the Brazilian Atlantic forest (BAF). Nevertheless, neither a formal proposal nor a meta-analysis to confirm this coincidence was ever made. Our main objective here was therefore to systematically test in how many vertebrate components the BAF could be divided by analysing existing empirical data. We used two approaches: (1) mapping and comparing the proposed areas of vertebrate endemism in the BAF and (2) analysing studies mentioning spatial subdivisions in distinct forest-dependent vertebrates within the biome, by the use of panbiogeography. The four large-scale endemism area components together with the six small-scale panbiogeographical ones allowed the definition of three BAF greater regions, subdivided into nine vertebrate components, latitudinally and longitudinally organized. Empirical time estimates of the diversification events within the BAF were also reviewed. Diversification of these vertebrates occurred not only in the Pleistocene but also throughout the Miocene. Our results confirm the BAF's complex history, both in space and time. We propose that future research should be small-scale and focused in the vertebrate components identified herein. Given the BAF's heterogeneity, studying via sections will be much more useful in identifying the BAF's historical biogeography. © 2012 The Linnean Society of London

Andean Tectonics and Mantle Dynamics as a Pervasive Influence on Amazonian Ecosystem

The Amazonian landscape evolution is the result of the combined effect of Andean tectonism, climate and the Earth’s interior dynamics. To reconstruct the landscape evolution and its influence on paleoenvironmental variations within Amazonia since the Oligocene, we conducted numerical experiments that incorporate different surface and geodynamic processes, reproducing many paleogeographic features as inferred from the sedimentary record. We show that the evolution of the drainage pattern gradually reduced the area of sedimentation derived from the Guiana and Brazilian shields while expanded the Andean derived deposits during the Miocene, affecting the nutrient availability. First order biotic habitats were inferred from these paleogeographical reconstructions, showing an eastward expansion of várzea and terra firme forests and consequent retraction of igapó forests, with a millennial-scale reconfiguration of a mosaic of habitats in the lowlands. We conclude that this dynamism probably guided the observed patterns of speciation in the most biodiverse biome on Earth. © 2019, The Author(s)

Impacts of a large hydroelectric dam on the Madeira River (Brazil) on floodplain avifauna

Hydroelectric dams represent an important threat to seasonally flooded environments in the Amazon basin. We aimed to evaluate how a dam in the Madeira River, one of the largest tributaries of the Amazonas River, affected floodplain avifauna. Bird occurrence was recorded through simultaneous passive acoustic monitoring in early successional vegetation and floodplain forest downstream from the dam and upstream in sites impacted by permanent flooding after dam reservoir filling. Species were identified through manual inspection and semi-automated classification of the recordings. To assess the similarity in vegetation between downstream and upstream sites, we used Landsat TM/ETM+ composite images from before (2009-2011) and after (2016-2018) reservoir filling. Downstream and upstream floodplain forest sites were similar before, but not after dam construction. Early successional vegetation sites were already different before dam construction. We recorded 195 bird species. While species richness did not differ between upstream and downstream sites, species composition differed significantly. Ten species were indicators of early successional vegetation upstream, and four downstream. Ten species were indicators of floodplain forest upstream, and 31 downstream. Seven of 24 floodplain specialist species were detected by the semi-automated classification only upstream. While we found some bird species characteristic of early successional vegetation in the upstream sites, we did not find most species characteristic of tall floodplain forest. Predominantly carnivorous, insectivorous, and nectarivorous species appear to have been replaced by generalist and widely distributed species.</p

Systematics and biogeography of the Automolus infuscatus complex (Aves; Furnariidae): Cryptic diversity reveals western Amazonia as the origin of a transcontinental radiation

A revision of the avian Neotropical genus Automolus and the Furnariidae family points to the paraphyly of A. infuscatus and reveals a species complex comprising A. infuscatus, A. ochrolaemus, A. paraensis, A. leucophthalmus, A. lammi and A. subulatus, the latter historically classified in the genus Hyloctistes. Detailed knowledge of the taxonomy, geographic distribution, phylogenetic relationship and divergence times of a taxon allows exploration of its evolutionary history and the testing of different scenarios of diversification. In this context, we studied the A. infuscatus complex using molecular data in order to unveil its cryptic diversity and reveal its evolutionary history. For that we sequenced two mitochondrial (ND2 and cytb) and three nuclear markers (G3PDH, ACO, Fib7) for 302 individuals belonging to all species in the complex and most described subspecies. Our analysis supports the paraphyly of A. infuscatus, indicating the existence of at least two distinct clades not closely related. The remaining species were all recovered as monophyletic. Notwithstanding, a well-structured intraspecific diversity was found with 19 lineages suggesting substantial cryptic diversity within the described species. A. subulatus was recovered within the complex, corroborating its position inside the genus. In spite of the high congruence between distributions of different lineages, with several sister lineages currently separated by the same barriers, the temporal incongruence between divergences over the same barriers reveals a complex evolutionary history. While older events might be related to the emergence of barriers such as the Andes and major Amazonian rivers, younger events suggest dispersal after the consolidation of those barriers. Our analysis suggests that the complex had its origin around 6 million years (Ma) and inhabited Western Amazonia in Late Miocene-Early Pliocene. Considering the riparian habit of species in its sister clade, the rise and early diversifications of the complex may be related to the establishment of terra firme forests as it changed from a floodplain to a fluvial system. The late Amazonian colonization by A. subulatus and A. ochrolaemus lineages may have been hampered by the previous existence of well established A. infuscatus lineages in the region. © 2016 Elsevier Inc

Combining phylogeography and landscape genetics of Xenopipo atronitens (Aves: Pipridae), a white sand campina specialist, to understand Pleistocene landscape evolution in Amazonia

Open vegetation (campinas and campinaranas) associated with white sand patches occurs in the form of islands in a forested matrix throughout the Amazon basin. Bird species restricted to these habitats have patchy distributions, although connectivity may have been influenced by past glacial cycles as a result of the substitution of forest by savanna. Because these landscape changes are a matter of debate in the history of Amazonia, we studied the diversification of Xenopipo atronitens, a white sand specialist, aiming to infer the effects of past climate changes. The split of Xenopipo atronitens from its sister species, Xenopipo uniformis, may be related to Tepuis erosion and retreat of escarpments during the Miocene, or to a dispersal event. Compared with birds from terra firme forest, X.atronitens has low genetic structure. Low levels of unidirectional gene flow were found from the Guyana Shield to adjacent areas. Demographic expansion starting approximately 25 kyr BP was detected for some populations and is probably related to the Last Glacial Maximum and subsequent climate improvement. Landscape genetic analyses indicate that the forested (terra firme) matrix acts as a barrier for the dispersal of X.atronitens. The results of the present study indicate that glacial cycles have deeply influenced Amazonian biogeographical history, demonstrating a complex interaction between forest and nonforest habitats during the Pleistocene. © 2013 The Linnean Society of London

Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian floodplain endemic species

Before populations become independent evolutionary lineages, the effects of micro evolutionary processes tend to generate complex scenarios of diversification that may affect phylogenetic reconstruction. Not accounting for gene flow in species tree estimates can directly impact topology, effective population sizes and branch lengths, and the resulting estimation errors are still poorly understood in wild populations. In this study, we used an integrative approach, including sequence capture of ultra-conserved elements (UCEs), mtDNA Sanger sequencing and morphological data to investigate species limits and phylogenetic relationships in face of gene flow in an Amazonian endemic species (Myrmoborus lugubris: Aves).We used commonly implemented species tree and model-based approaches to understand the potential effects of gene flow in phylogenetic reconstructions. The genetic structure observed was congruent with the four recognized subspecies of M. lugubris. Morphological and UCEs data supported the presence of a wide hybrid zone between M. l. femininus from the Madeira river and M. l. lugubris from the Middle and lower Amazon river, which were recovered as sister taxa by species tree methods. When fitting gene flowinto simulated demographic models with different topologies, the best-fit model indicated these two taxa as non-sister lineages, a finding that is in agreement with the results of mitochondrial and morphological analyses. Our results demonstrated that failing to account for gene flow when estimating phylogenies at shallow divergence levels can generate topological uncertainty, which can nevertheless be statistically well supported, and that model testing approaches using simulated data can be useful tools to test alternative phylogenetic hypotheses. © The Author(s) 2018

Towards integrative taxonomy in Neotropical botany: Disentangling the Pagamea guianensis species complex (Rubiaceae)

Species complexes are common in the Neotropical flora, and the Pagamea guianensis complex is one of the most widespread groups of species in the Amazonian white-sand flora. Previous analyses suggested the occurrence of ten species in this group, but species limits remained unclear due to poor sampling, morphological overlap and low molecular variation. Here we present the most comprehensive population and molecular sampling across the geographical distribution of the P. guianensis complex to date in order to test the monophyly of this group and to clarify species limits. Using a high-throughput DNA sequencing approach, we sequenced 431 loci (> 34 M bases) for 179 individuals. We applied phylogenetic and species tree analyses to resolve phylogenetic relationships among the sampled individuals. Species delimitation was inferred based on genomic data, and we tested whether hypothesized species could be differentiated using morphological, ecological and near-infrared spectroscopy data. We confirm the monophyly of the P. guianensis complex and accept 15 distinct and well-supported lineages, here proposed as 14 species and one subspecies. Our findings highlight the importance of multiple lines of evidence from independent datasets in the process of species delimitation and species discovery in species complexes in the Neotropics. © The Botanical Journal of the Linnean Society 2018

ATLANTIC ‐ PRIMATES : a dataset of communities and occurrences of primates in the Atlantic Forests of South America

Primates play an important role in ecosystem functioning and offer critical insights into human evolution, biology, behavior, and emerging infectious diseases. There are 26 primate species in the Atlantic Forests of South America, 19 of them endemic. We compiled a dataset of 5,472 georeferenced locations of 26 native and 1 introduced primate species, as hybrids in the genera Callithrix and Alouatta. The dataset includes 700 primate communities, 8,121 single species occurrences and 714 estimates of primate population sizes, covering most natural forest types of the tropical and subtropical Atlantic Forest of Brazil, Paraguay and Argentina and some other biomes. On average, primate communities of the Atlantic Forest harbor 2 ± 1 species (range = 1–6). However, about 40% of primate communities contain only one species. Alouatta guariba (N = 2,188 records) and Sapajus nigritus (N = 1,127) were the species with the most records. Callicebus barbarabrownae (N = 35), Leontopithecus caissara (N = 38), and Sapajus libidinosus (N = 41) were the species with the least records. Recorded primate densities varied from 0.004 individuals/km2 (Alouatta guariba at Fragmento do Bugre, Paraná, Brazil) to 400 individuals/km2 (Alouatta caraya in Santiago, Rio Grande do Sul, Brazil). Our dataset reflects disparity between the numerous primate census conducted in the Atlantic Forest, in contrast to the scarcity of estimates of population sizes and densities. With these data, researchers can develop different macroecological and regional level studies, focusing on communities, populations, species co‐occurrence and distribution patterns. Moreover, the data can also be used to assess the consequences of fragmentation, defaunation, and disease outbreaks on different ecological processes, such as trophic cascades, species invasion or extinction, and community dynamics. There are no copyright restrictions. Please cite this Data Paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.Fil: Culot, Laurence. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Pereira, Lucas Augusto. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Agostini, Ilaria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Centro de Investigaciones del Bosque Atlántico; ArgentinaFil: de Almeida, Marco Antônio Barreto. Pontificia Universidade Católica do Rio Grande do Sul; BrasilFil: Alves, Rafael Souza Cruz. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Baldovino, María Celia. Centro de Investigaciones del Bosque Atlántico; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Instituto Miguel Lillo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán; ArgentinaFil: Di Bitetti, Mario Santiago. Centro de Investigaciones del Bosque Atlántico; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; ArgentinaFil: Oklander, Luciana Inés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; ArgentinaFil: Holzmann, Ingrid. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Bio y Geociencias del NOA. Universidad Nacional de Salta. Facultad de Ciencias Naturales. Museo de Ciencias Naturales. Instituto de Bio y Geociencias del NOA; ArgentinaFil: Dums, Marcos. RUMO S.A. Licenciamento Ambiental; BrasilFil: Lombardi, Pryscilla Moura. RUMO S.A. Licenciamento Ambiental; BrasilFil: Bonikowski, Renata Twardowsky Ramalho. RUMO S.A. Licenciamento Ambiental; BrasilFil: Age, Stéfani Gabrieli. RUMO S.A. Licenciamento Ambiental; BrasilFil: Souza Alves, João Pedro. Universidade Federal de Pernambuco; BrasilFil: Chagas, Renata. Universidade Federal da Paraíba; BrasilFil: da Cunha, Rogério Grassetto Teixeira. Universidade Federal de Alfenas; BrasilFil: Valença Montenegro, Monica Mafra. Centro Nacional de Pesquisa e Conservaçao de Primates Brasileiros; BrasilFil: Ludwig, Gabriela. Centro Nacional de Pesquisa e Conservaçao de Primates Brasileiros; BrasilFil: Jerusalinsky, Leandro. Centro Nacional de Pesquisa e Conservaçao de Primates Brasileiros; BrasilFil: Buss, Gerson. Centro Nacional de Pesquisa e Conservaçao de Primates Brasileiros; BrasilFil: de Azevedo, Renata Bocorny. Centro Nacional de Pesquisa e Conservaçao de Primates Brasileiros; BrasilFil: Filho, Roberio Freire. Universidade Federal de Pernambuco; BrasilFil: Bufalo, Felipe. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Milhe, Louis. Université D'Avignon et des Pays du Vaucluse; FranciaFil: Santos, Mayara Mulato dos. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Sepulvida, Raíssa. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Ferraz, Daniel da Silva. Universidade do Estado de Minas Gerais; BrasilFil: Faria, Michel Barros. Universidade do Estado de Minas Gerais; BrasilFil: Ribeiro, Milton Cezar. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Galetti, Mauro. Universidade Estadual Paulista Julio de Mesquita Filho; Brasi

Brazilian legislation on genetic heritage harms biodiversity convention goals and threatens basic biology research and education

Univ Fed Rio de Janeiro, Museu Nacl, Dept Bot, Quinta Boa Vista S-N, BR-20940040 Rio de Janeiro, RJ, BrazilUniv Fed Rio de Janeiro, Museu Nacl, Dept Vertebrados, Quinta Boa Vista S-N, BR-20940040 Rio de Janeiro, RJ, BrazilInst Oswaldo Cruz, Fundacao Oswaldo Cruz, Ave Brasil 4365, BR-21040360 Rio De Janeiro, RJ, BrazilUniv Fed Rural Rio De Janeiro, Inst Biol, Dept Biol Anim, BR-23851970 Seropedica 74503, RJ, BrazilUniv Fed Rio de Janeiro, Museu Nacl, Dept Geol & Paleontol, Lab Sistemat & Tafon Vertebrados Fosseis, Quinta,Boa Vista S-N, BR-20940040 Rio de Janeiro, RJ, BrazilMuseu Paraense Emilio Goeldi, Coordenacao Zool, Av Magalhaes Barata 376, BR-66040170 Belem, PA, BrazilUniv Fed Paraiba, Ctr Ciencias Exatas & Nat, Dept Sistemat & Ecol, UFPB,CCEN, Campus 1, BR-58059900 Joao Pessoa, Paraiba, BrazilCtr Pesquisa Aggeu Magalhaes, Ctr Pesquisas Aggeu Magalhaes, Fundacao Oswaldo Cruz, Av Prof Moraes Rego S-N, BR-50670420 Recife, PE, BrazilInst Nacl de Pesquisas da Amazonia, Programa Colecoes & Acervos Cient, Av Andre Araujo 2936, BR-69060001 Manaus, AM, BrazilUniv Fed Rio de Janeiro, Dept Zool, UFRJ, CCS, Bloco A, BR-21941590 Rio De Janeiro, RJ, BrazilUniv Estado Rio de Janeiro, Inst Biol, Dept Ecol, Rua Sao Francisco Xavier 524, BR-20550019 Rio De Janeiro, RJ, BrazilUniv Sao Paulo, Museu Zool USP, Lab Diptera, Av Nazare 481,Sala 404, BR-04263000 Sao Paulo, SP, BrazilUniv Estadual Paulista, Dept Zool, 12, Av 24 A,1515, BR-13506900 Rio Claro, SP, BrazilUniv Estadual Paulista, Ctr Aquicultura, 12, Av 24 A,1515, BR-13506900 Rio Claro, SP, BrazilInst Nacl Canc, Coordenacao Pesquisa, Rua Andre Cavalcanti 37,4 Andar, BR-20231050 Rio De Janeiro, RJ, BrazilUniv Estadual Paulista, Lab Ecol & Comportamento Anuros, Dept Morfol & Fisiol Anim, Fac Ciencias Agr & Vet, Via Acesso Prof Paulo Donato Castellane Km 05, BR-14884900 Jaboticabal, SP, BrazilUniv Fed Fronteira Sul, Rua Jacob Reinaldo Haupenthal 1580, BR-97900000 Cerro Largo, RS, BrazilUniv Estadual Paulista, Dept Zool & Botan, Inst Biociencias Letras & Ciencias Exatas, BR-15054000 Sao Jose Do Rio Preto, SP, BrazilUniv Fed Minas Gerais, Inst Ciencias Biol, Dept Biol Geral, Av Antonio Carlos 6627,CP 486,Sala L3-244, BR-31270010 Belo Horizonte, MG, BrazilUniv Fed Juiz De Fora, Inst Ciencias Biol, Dept Bot, Campus Univ, BR-36036900 Juiz De Fora, MG, BrazilUniv Sao Paulo, FFCLRP, Dept Biol, Av Bandeirantes 3900, BR-14040901 Ribeirao Preto, SP, BrazilInst Butantan, Lab Especial Colecoes Zool, Av Dr Vital Brasil 1500, BR-05503900 Sao Paulo, SP, BrazilUniv Fed Vicosa, Ctr Ciencias Biol & Saude, Campus Univ S-N, BR-36570000 Vicosa, MG, BrazilUniv Brasilia, Dept Zool, Inst Ciencias Biol, BR-70910900 Brasilia, DF, BrazilInst Chico Mendes Conservacao Biodiversidade ICMB, Reserva Biol Guaribas, PB 071,Km 01 Estrada Jacarau, BR-58280000 Mamanguape, PB, BrazilFundacao Oswaldo Cruz, Estrada Rodrigues Caldas 3400, BR-22713375 Rio De Janeiro, RJ, BrazilUniv Fed Uberlandia, Pesquisa, Rua Ceara S-N, BR-38400902 Uberlandia, MG, BrazilUniv Estadual Campinas, Multiusuario Bioacust, Lab Hist Nat Anfibios Brasileiros, Dept Biol Anim,Inst Biol, BR-13083970 Campinas, SP, BrazilUniv Fed Rio Grande do Sul, Inst Biociencias, Soc Brasileira Ictiol, Dept Zool,Agron, Av Bento Goncalves 9500, BR-91501970 Porto Alegre, RS, BrazilUniv Fed Rio de Janeiro, Museu Nacl, Dept Entomol, Quinta,Boa Vista S-N, BR-20940040 Rio De Janeiro, RJ, BrazilUniv Sao Paulo, Inst Biociencias, Soc Brasileira Herpetol, Dept Ecol, Rua Matao,Trav 14, BR-05508090 Sao Paulo, BrazilUniv Fed Sao Joao Del Rei, Dept Ciencias Nat, Praca Dom Helvecio 74, BR-36301160 Sao Joao Del Rei, MG, BrazilUniv Sao Paulo, Museu Zool USP, Dept Vertebrados, Av Nazare 481,Caixa Postal 42494, BR-05422970 Sao Paulo, SP, BrazilUniv Estadual Santa Cruz, Dept Ciencias Biol, Km 16, BR-45662900 Ilheus, BA, BrazilInst Nacl Pesquisas Espaciais, Coordenacao Ciencia Sistema Terrestre, Ave Astronautas 1758, BR-12227010 Sao Jose Dos Campos, SP, BrazilPontificia Univ Catol Rio Grande Sul, Escola Ciencias, Av Ipiranga 6681,Predio 40,Sala 110, BR-90619900 Porto Alegre, RS, BrazilUniv Fed Goias, Inst Ciencias Biol, Lab Ecol & Comportamento Anim, Dept Ecol, BR-74000970 Goiania, Go, BrazilUniv Estadual Paulista, Dept Zool, 12, Av 24 A,1515, BR-13506900 Rio Claro, SP, BrazilUniv Estadual Paulista, Ctr Aquicultura, 12, Av 24 A,1515, BR-13506900 Rio Claro, SP, BrazilUniv Estadual Paulista, Lab Ecol & Comportamento Anuros, Dept Morfol & Fisiol Anim, Fac Ciencias Agr & Vet, Via Acesso Prof Paulo Donato Castellane Km 05, BR-14884900 Jaboticabal, SP, BrazilUniv Estadual Paulista, Dept Zool & Botan, Inst Biociencias Letras & Ciencias Exatas, BR-15054000 Sao Jose Do Rio Preto, SP, Brazi