Effects of Pleistocene climate changes on species ranges and evolutionary processes in the Neotropical Atlantic Forest

The effects of global glaciations on the distribution of organisms is an essential element of many diversification models. However, the empirical evidence supporting this idea is mixed, in particular with respect to explaining tropical forest evolution. In the present study, we evaluated the impacts of range shifts associated with Pleistocene global glacial cycles on the evolution of tropical forests. In particular, we tested the predictions: (1) that population genetic structure increases with fragmentation variation between the present and the Last Glacial Maximum (LGM) and also (2) with geographical range instability; and (3) that genetic diversity increases with range stability and (4) decreases with fragmentation variation between periods. To address our predictions, we studied population genetic structures and modelled present and past distributions of 15 Atlantic Forest (AF) endemic birds. Afterwards, we evaluated the relationship of population genetic parameters with metrics of species range shifts between the present and the LGM. We found that geographical ranges of AF birds changed in concert with Pleistocene glacial cycles but, unexpectedly, our findings suggest the novel idea that ranges during glacial maxima were slightly larger on average, as well as equally fragmented and displaced from the interglacial ranges. Our findings suggest that range shifts over the late Pleistocene impacted on the diversification of forest organisms, although they did not show that those range shifts had a strong effect. We found that a combination of fragmentation variation across time, small current range size, and range stability increased population genetic structure. However, neither fragmentation, nor range stability affected genetic diversity. Our study showed that evolutionary responses to range shifts across AF birds have a high variance, which could explain the mixed support given by single-species studies to the action of Pleistocene range shifts on population evolution.Fil: Cabanne, Gustavo Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Trujillo Arias, Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Flores, Pamela. Universidad Nacional de General Sarmiento; ArgentinaFil: Pessoa, Rodrigo. Universidade Estadual de Montes Claros; BrasilFil: d'Horta, Fernando M.. Instituto Nacional de Pesquisas da Amazônia; BrasilFil: Miyaki, Cristina Y.. Universidade de Sao Paulo; Brasi

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

GAUDY JUVENILE PLUMAGES OF CINEREOUS MOURNER (LANIOCERA HYPOPYRRA) AND BRAZILIAN LANIISOMA (LANIISOMA ELEGANS)

We describe the juvenile plumages of the Cinereous Mourner (Laniocera hypopyrra) and the Brazilian Laniisoma (Laniisoma elegans). Both L. hypopyrra and L. elegans possess a dramatically conspicuous plumage as juveniles in contrast to the generally cryptic plumage pattern exhibited by most juvenile birds. They are predominantly covered by cinnamon-orange feathers with black terminal spots, contrasting with the nest and the predominant colors of their environment. This colorful plumage presumably makes them more at risk from predation by visually oriented animals (e.g., raptors and primates), during one of the most vulnerable phases of their life, and strongly suggests these plumages function as a true, or false (mimicry), signal of 'unprofitability'. Previous knowledge concerning the phylogenetic relationships between these two genera, and the juvenile plumage patterns of other species placed in the Tityridae indicate this shared character in L. hypopyrra and L. elegans represents a synapomorphy within this clade, thereby providing additional evidence of their relationship. Received 13 December 2011. Accepted 1 May 2012

Plumage data Dendrocolaptes platyrostris

The plumage data is in the attached file (Plumage Dendrocolaptes platyrostris.txt). It is a spreadsheet in plain text containing for each population (n=38) median scores of each of the five studied plumage characters and a population total plumage score. The population total plumage score is equal to the sum of median scores of each of the five characters. The table also presents geographic location of each population. See section Material and Methods of the publication for further details

Data from: Evolution of Dendrocolaptes platyrostris (Aves: Furnariidae) between the South American open vegetation corridor and the Atlantic forest

The open vegetation corridor of South America is a region dominated by savanna biomes. It contains forests, i.e. riverine forests, that may act as corridors for rainforest specialist between the open vegetation corridor and its neighboring biomes, the Amazonian and Atlantic forests. A prediction for this scenario is that populations of rainforest specialists in the open vegetation corridor and in the forested biomes show no significant genetic divergence. We addressed this hypothesis by studying plumage and genetic variation of the Planalto woodcreeper Dendrocolaptes platyrostris Spix (1824) (Aves: Furnariidae), a forest specialist that occurs in both the open habitat and in the Atlantic forest. Our questions are: (1) is there any evidence of genetic continuity between populations of the open habitat and the Atlantic forest? and (2) is plumage variation congruent with patterns of neutral genetic structure or with ecological factors related to habitat type? We used cytochrome b and mtDNA control region sequences to show that D. platyrostris is monophyletic and that presents substantial intraspecific differentiation. We found two areas of plumage stability: one associated to Cerrado and the other associated to southern Atlantic Forest. Multiple Mantel tests showed that most of the plumage variation followed transition of habitats but not phylogeographic gaps, suggesting that selection may be related to the evolution of the species plumage. Results were not compatible with the idea that forest specialist in the open vegetation corridor and in the Atlantic forest are linked at the population level because birds from each region were not part of the same genetic unit. Divergence in the presence of gene flow across the ecotone between both regions might explain our results. Also, our findings indicate that the southern Atlantic forest may have been significantly affected by Pleistocene climatic alteration, but that those events did not cause local extinction of most taxa, as occurred in other regions of the globe where forests were significantly affected by global glaciations. Finally, our results neither supported subspecies nor regions of stability of plumage as species

Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rain forest understorey specialists

Aim To evaluate the role of historical processes in the evolution of Sclerurus leaftossers by integrating phylogenetic and phylogeographical approaches. Location Humid forests of the Neotropical region. Methods We reconstructed the evolutionary history of Sclerurus based on DNA sequences representing all species and 20 of the 26 recognized subspecies using one autosomal nuclear locus and three protein-coding mitochondrial gene sequences. Phylogenetic relationships were inferred using Bayesian and maximum-likelihood methods. We used Bayesian coalescent-based approaches to evaluate demographic changes through time, and to estimate the timing of diversification events. Based on these results, we examined the temporal accumulation of divergence events using lineage-through-time plots. Results The monophyly of all Sclerurus species was strongly supported except for Sclerurus mexicanus, which was paraphyletic in relation to Sclerurus rufigularis, and for the sister pair Sclerurus scansor-Sclerurus albigularis, which were not reciprocally monophyletic in the nuclear tree. We found remarkably deep phylogeographical structure within all Sclerurus species, and overall this structure was congruent with currently recognized subspecies and Neotropical areas of endemism. Diversification within Sclerurus has occurred at a relatively constant rate since the Middle Miocene. Main conclusions Our results strongly support the relevance of physiographical (e.g. Nicaragua Depression, Isthmus of Panama, Andean Cordillera, great rivers of Amazonia) and ecological barriers (open vegetation corridor) and ecological gradients (elevational zonation) to the diversification of Neotropical forest-dwelling organisms. Despite the high congruence among the spatial patterns identified, the variance in divergence times suggests multiple speciation events occurring independently across the same barrier, and a role for dispersal. The phylogenetic patterns and cryptic diversity uncovered in this study demonstrate that the current taxonomy of Sclerurus underestimates the number of species. © 2012 Blackwell Publishing Ltd

Plumage data Dendrocolaptes platyrostris

The plumage data is in the attached file (Plumage Dendrocolaptes platyrostris.txt). It is a spreadsheet in plain text containing for each population (n=38) median scores of each of the five studied plumage characters and a population total plumage score. The population total plumage score is equal to the sum of median scores of each of the five characters. The table also presents geographic location of each population. See section Material and Methods of the publication for further details

Uma abordagem integrada da história biogeográfica da avifauna Neotropical de terras baixas: combinando padrões de diversificação e evolução da paisagem

Abstract – The importance of landscape evolution as driver of biotic diversification in the Neotropical lowlands has long been appreciated, but no clear common mechanisms have been revealed. We suggest that three main issues have collaborated to this: (i) poor understanding of earth history; (ii) problems with testing diversification hypotheses; and (iii) poor representation of diversity by current taxonomy. Thus, in order to study diversification patterns, some basic steps need to be observed: (i) the units of biodiversity need to be properly recognized through taxonomic reviews, with good geographic sampling; (ii) diversification patterns need to be carefully confronted to new information on landscape history and (iii) hypotheses need to be evaluated against direct and unambiguous predictions from alternative historical scenarios. Here we show how studies that sample all evolutionary units and use integrative approaches that combine diversification analysis with detailed data on earth history can provide new insights on the role of historical factors on the diversification of Neotropical organisms. The results presented show that both paleogeographic and paleoclimatic processes may have had an important role in the diversification of lowland Neotropical avian groups during the Pleistocene and before.A importância da evolução da paisagem como agente causador da diversificacão biológica na região Neotropical é conhecida há tempo, mas mecanismos comuns até hoje não foram revelados. Sugerimos que três fatores principais contribuem para essa ausência de consenso: (i) pouco conhecimento da história da Terra, (ii) problemas com o teste de hipóteses de diversificação, e (iii) representação incompleta da diversidade pela taxonomia atual. Portanto, para estudar padrões de diversificacão alguns passos básicos têm que ser observados: (i) as unidades evolutivas têm que ser identificadas através de revisões taxonômicas, (ii) padrões de diversificacão precisam ser correlacionados a informações recentes sobre a história da Terra e (iii) hipóteses precisam ser avaliadas em relação a predições diretas e não ambíguas derivadas de cenários históricos alternativos. Neste artigo mostramos como estudos que amostram todas as unidades evolutivas e utilizam abordagens integrativas que combinam análise da diversificacão com dados detalhados sobre a história da Terra podem fornecer novas perspectivas sobre o papel dos fatores históricos na diversificação de organismos Neotropicais. Os resultados apresentados mostram que tanto mudanças paleoclimáticas quanto paleogeográficas podem ter sido importantes na diversificação de grupos de aves Neotropicais de terras baixas durante e antes do Pleistoceno.Fil: Ribas, Camila C.. Instituto Nacional de Pesquisas da Amazônia; BrasilFil: Maldonado Coelho, Marcos. Universidade de Sao Paulo; Brasil. University of Missouri; Estados UnidosFil: Smith, Brian Tilston. State University of Louisiana; Estados UnidosFil: Cabanne, Gustavo Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; ArgentinaFil: d'Horta, Fernando M.. Universidade de Sao Paulo; BrasilFil: Naka, Luciano N.. State University of Louisiana; Estados Unido

Avian malaria, ecological host traits and mosquito abundance in southeastern Amazonia

SUMMARY Avian malaria is a vector transmitted disease caused by Plasmodium and recent studies suggest that variation in its prevalence across avian hosts is correlated with a variety of ecological traits. Here we examine the relationship between prevalence and diversity of Plasmodium lineages in southeastern Amazonia and: (1) host ecological traits (nest location, nest type, flocking behaviour and diet); (2) density and diversity of avian hosts; (3) abundance and diversity of mosquitoes; and (4) season. We used molecular methods to detect Plasmodium in blood samples from 675 individual birds of 120 species. Based on cytochrome b sequences, we recovered 89 lineages of Plasmodium from 136 infected individuals sampled across seven localities. Plasmodium prevalence was homogeneous over time (dry season and flooding season) and space, but heterogeneous among 51 avian host species. Variation in prevalence among bird species was not explained by avian ecological traits, density of avian hosts, or mosquito abundance. However, Plasmodium lineage diversity was positively correlated with mosquito abundance. Interestingly, our results suggest that avian host traits are less important determinants of Plasmodium prevalence and diversity in southeastern Amazonia than in other regions in which they have been investigated. © Cambridge University Press 2017

The "Atlantis Forest hypothesis" does not explain Atlantic Forest phylogeography

Univ Fed Sao Paulo, Inst Ciencias Ambientais Quim & Farmaceut, BR-09972270 Diadema, SP, BrazilHarvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USAHarvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USAUniv Fed Parana, Ctr Politecn, Dept Zool, Setor Ciencias Biol, BR-81531 Curitiba, Parana, BrazilUniv Fed Rio de Janeiro, Museu Nacl, Dept Vertebrados, BR-20940040 Rio De Janeiro, RJ, BrazilUniv Sao Paulo, Dept Genet & Biol Evolut, BR-05508090 Sao Paulo, SP, Brazilnst Nacl de Pesquisas da Amazonia, Programa Posgrad Genet Conservacao & Biol Evolut, BR-69067375 Manaus, Amazonas, BrazilUniv Fed Sao Paulo, Inst Ciencias Ambientais Quim & Farmaceut, BR-09972270 Diadema, SP, BrazilWeb of Scienc