Matheus S. Lima-Ribeiro

A coupled phylogeographical and species distribution modelling approach recovers the demographical history of a Neotropical seasonally dry forest tree species

We investigated here the demographical history of Tabebuia impetiginosa (Bignoniaceae) to understand the dynamics of the disjunct geographical distribution of South American seasonally dry forests (SDFs), based on coupling an ensemble approach encompassing hindcasting species distribution modelling and statistical phylogeographical analysis. We sampled 17 populations (280 individuals) in central Brazil and analysed the polymorphisms at chloroplast (trnS‐trnG, psbA‐trnH, and ycf6‐trnC intergenic spacers) and nuclear (ITS nrDNA) genomes. Phylogenetic analyses based on median‐joining network showed no haplotype sharing among population but strong evidence of incomplete lineage sorting. Coalescent analyses showed historical constant populations size, negligible gene flow among populations, and an ancient time to most recent common ancestor dated from ~4.7 ± 1.1 Myr BP. Most divergences dated from the Lower Pleistocene, and no signal of important population size reduction was found in coalescent tree and tests of demographical expansion. Demographical scenarios were built based on past geographical range dynamic models, using two a priori biogeographical hypotheses (‘Pleistocene Arc’ and ‘Amazonian SDF expansion’) and on two additional hypotheses suggested by the palaeodistribution modelling built with several algorithms for distribution modelling and palaeoclimatic data. The simulation of these demographical scenarios showed that the pattern of diversity found so far for T. impetiginosa is in consonance with a palaeodistribution expansion during the last glacial maximum (LGM, 21 kyr BP), strongly suggesting that the current disjunct distribution of T. impetiginosa in SDFs may represent a climatic relict of a once more wide distribution.

A Short Guide to the Climatic Variables of the Last Glacial Maximum for Biogeographers

Ecological niche models are widely used for mapping the distribution of species during the last glacial maximum (LGM). Although the selection of the variables and General Circulation Models (GCMs) used for constructing those maps determine the model predictions, we still lack a discussion about which variables and which GCM should be included in the analysis and why. Here, we analyzed the climatic predictions for the LGM of 9 different GCMs in order to help biogeographers to select their GCMs and climatic layers for mapping the species ranges in the LGM. We 1) map the discrepancies between the climatic predictions of the nine GCMs available for the LGM, 2) analyze the similarities and differences between the GCMs and group them to help researchers choose the appropriate GCMs for calibrating and projecting their ecological niche models (ENM) during the LGM, and 3) quantify the agreement of the predictions for each bioclimatic variable to help researchers avoid the environmental variables with a poor consensus between models. Our results indicate that, in absolute values, GCMs have a strong disagreement in their temperature predictions for temperate areas, while the uncertainties for the precipitation variables are in the tropics. In spite of the discrepancies between model predictions, temperature variables (BIO1-BIO11) are highly correlated between models. Precipitation variables (BIO12- BIO19) show no correlation between models, and specifically, BIO14 (precipitation of the driest month) and BIO15 (Precipitation Seasonality (Coefficient of Variation)) show the highest level of discrepancy between GCMs. Following our results, we strongly recommend the use of different GCMs for constructing or projecting ENMs, particularly when predicting the distribution of species that inhabit the tropics and the temperate areas of the Northern and Southern Hemispheres, because climatic predictions for those areas vary greatly among GCMs. We also recommend the exclusion of BIO14 and BIO15 from ENMs because those variables show a high level of discrepancy between GCMs. Thus, by excluding them, we decrease the level of uncertainty of our predictions. All the climatic layers produced for this paper are freely available in http://ecoclimate.org/.

Efeitos de borda sobre a vegetação e estruturação populacional em fragmentos de Cerradão no Sudoeste Goiano, Brasil

Efeitos de borda sao modificacoes nos parâmetros fisicos, quimicos e biologicos observadas na area de contato do fragmento de vegetacao com a matriz circundante. O objetivo desse estudo foi testar a hipotese de que os efeitos de borda afetam alguns parâmetros vegetacionais e populacional em fragmentos de Cerradao no municipio de Caiaponia, Goias. Para isso, estudou-se a estrutura da vegetacao, o padrao de distribuicao espacial de Vernonia aurea Mart. ex DC. (Asteraceae) e as condicoes microclimaticas (temperatura do ar e do solo e umidade relativa do ar) em dois ambientes, borda e interior, de tres fragmentos de Cerradao com diferentes tamanhos (1,5 ha; 9 ha e 35 ha). Os resultados mostraram uma nitida influencia dos efeitos de borda em todos os parâmetros analisados, uma vez que a estrutura da vegetacao, o nivel de agregacao dos individuos de V. aurea e os parâmetros microclimaticos foram diferentes entre o interior e a borda dos fragmentos analisados. Esses dados corroboram com outros estudos realizados em diferentes ecossistemas, indicando que a fragmentacao dos habitats modifica a composicao e estrutura da vegetacao, a estrutura espacial e a dinâmica das populacoes vegetais e, consequentemente, animais, podendo levar a extincao de populacoes locais e reducao da diversidade biologica.

Relaxed random walk model coupled with ecological niche modeling unravel the dispersal dynamics of a Neotropical savanna tree species in the deeper Quaternary

Understanding the dispersal routes of Neotropical savanna tree species is an essential step to unravel the effects of past climate change on genetic patterns, species distribution and population demography. Here we reconstruct the demographic history and dispersal dynamics of the Neotropical savanna tree species Tabebuia aurea to understand the effects of Quaternary climate change on its current spatial patterns of genetic diversity. We sampled 285 individuals from 21 populations throughout Brazilian savannas and sequenced all individuals for three chloroplast intergenic spacers and ITS nrDNA. We analyzed data using a multi-model inference framework by coupling the relaxed random walk model (RRW), ecological niche modeling (ENM) and statistical phylogeography. The most recent common ancestor of T. aurea lineages dated from ~4.0 ± 2.5 Ma. T. aurea lineages cyclically dispersed from the West toward the Central-West Brazil, and from the Southeast toward the East and Northeast Brazil, following the paleodistribution dynamics shown by the ENMs through the last glacial cycle. A historical refugium through time may have allowed dispersal of lineages among populations of Central Brazil, overlapping with population expansion during interglacial periods and the diversification of new lineages. Range and population expansion through the Quaternary were, respectively, the most frequent prediction from ENMs and the most likely demographic scenario from coalescent simulations. Consistent phylogeographic patterns among multiple modeling inferences indicate a promising approach, allowing us to understand how cyclical climate changes through the Quaternary drove complex population dynamics and the current patterns of species distribution and genetic diversity.

Ecological niche and phylogeography elucidate complex biogeographic patterns in Loxosceles rufescens (Araneae, Sicariidae) in the Mediterranean Basin

BackgroundUnderstanding the evolutionary history of morphologically cryptic species complexes is difficult, and made even more challenging when geographic distributions have been modified by human-mediated dispersal. This situation is common in the Mediterranean Basin where, aside from the environmental heterogeneity of the region, protracted human presence has obscured the biogeographic processes that shaped current diversity. Loxosceles rufescens (Araneae, Sicariidae) is an ideal example: native to the Mediterranean, the species has dispersed worldwide via cohabitation with humans. A previous study revealed considerable molecular diversity, suggesting cryptic species, but relationships among lineages did not correspond to geographic location.ResultsDelimitation analyses on cytochrome c oxidase subunit I identified 11 different evolutionary lineages, presenting two contrasting phylogeographic patterns: (1) lineages with well-structured populations in Morocco and Iberia, and (2) lineages lacking geographic structure across the Mediterranean Basin. Dating analyses placed main diversification events in the Pleistocene, and multiple Pleistocene refugia, identified using ecological niche modeling (ENM), are compatible with allopatric differentiation of lineages. Human-mediated transportation appears to have complicated the current biogeography of this medically important and synanthropic spider.ConclusionsWe integrated ecological niche models with phylogeographic analyses to elucidate the evolutionary history of L. rufescens in the Mediterranean Basin, with emphasis on the origins of mtDNA diversity. We found support for the hypothesis that northern Africa was the center of origin for L. rufescens, and that current genetic diversity originated in allopatry, likely promoted by successive glaciations during the Pleistocene. We corroborated the scenario of multiple refugia within the Mediterranean, principally in northern Africa, combining results from eight atmosphere–ocean general circulation models (AOGCMs) with two different refugium-delimitation methodologies. ENM results were useful for providing general views of putative refugia, with fine-scale details depending on the level of stringency applied for agreement among models.

Recovering species demographic history from multi-model inference: the case of a Neotropical savanna tree species

BackgroundGlaciations were recurrent throughout the Quaternary and potentially shaped species genetic structure worldwide by affecting population dynamics. Here, we implemented a multi-model inference approach to recover the distribution dynamics and demographic history of a Neotropical savanna tree, Tabebuia aurea (Bignoniaceae). Exploring different algorithms and paleoclimatic simulations, we used ecological niche modelling to generate alternative hypotheses of potential demographic changes through the last glacial cycle and estimated genetic parameters using coalescent modelling.ResultsComparing predictions from demographic hypotheses with genetic parameters of modern populations, our findings revealed a likely scenario of population decline, with spatial displacement towards Northeast Brazil from the last glacial maximum to the mid-Holocene. Subsequently, populations expanded in response to the return of the climatically suitable conditions in Central-West Brazil. Nevertheless, a wide historical refugium across Central Brazil likely maintained large populations connected throughout time. The expected genetic signatures from such predicted distribution dynamics are also corroborated by spatial genetic structure observed in modern populations.ConclusionBy exploring uncertainties inherent in multiple working hypotheses, we have shown that multi-model inference is a fruitful and efficient approach to recover the nature, timing and geographical context of the Tabebuia aurea population dynamic in response to the Quaternary climate changes.

Multi-model inference in comparative phylogeography: an integrative approach based on multiple lines of evidence

Comparative phylogeography has its roots in classical biogeography and, historically, relies on a pattern-based approach. Here, we present a model-based framework for comparative phylogeography. Our framework was initially developed for statistical phylogeography based on a multi-model inference approach, by coupling ecological niche modeling, coalescent simulation and direct spatio-temporal reconstruction of lineage diffusion using a relaxed random walk model. This multi-model inference framework is particularly useful to investigate the complex dynamics and current patterns in genetic diversity in response to processes operating on multiple taxonomic levels in comparative phylogeography. In addition, because of the lack, or incompleteness of fossil record, the understanding of the role of biogeographical events (vicariance and dispersal routes) in most regions worldwide is barely known. Thus, we believe that the expansion of that framework for multiple species under a comparative approach may give clues on genetic legacies in response to Quaternary climate changes and other biogeographical processes.

A large historical refugium explains spatial patterns of genetic diversity in a Neotropical savanna tree species

Background and Aims The relative role of Pleistocene climate changes in driving the geographic distribution and genetic diversity of South American species is not well known, especially from open biomes such as the Cerrado, the most diverse tropical savanna, encompassing high levels of endemism. Here the effects of Quaternary climatic changes on demographic history, distribution dynamics and genetic diversity of Dimorphandra mollis, an endemic tree species widely distributed in the Cerrado, were investigated. Methods A total of 38 populations covering most of the distribution of D. mollis were analysed using internal transcribed spacer (ITS) sequences and nuclear microsatellite variation [simple sequence repeats (SSRs)]. The framework incorporated statistical phylogeography, coalescent analyses and ecological niche modelling (ENM). Key Results Different signatures of Quaternary climatic changes were found for ITS sequences and SSRs corresponding to different time slices. Coalescent analyses revealed large and constant effective population sizes, with high historical connectivity among the populations for ITS sequences and low effective population sizes and gene flow with recent population retraction for SSRs. ENMs indicated a slight geographical range retraction during the Last Glacial Maximum. A large historical refugium across central Brazil was predicted. Spatially explicit analyses showed a spatial cline pattern in genetic diversity related to the paleodistribution of D. mollis and to the centre of its historical refugium. Conclusions The complex genetic patterns found in D. mollis are the result of a slight geographical range retraction during the Last Glacial Maximum followed by population expansion to the east and south from a large refugium in the central part of the Cerrado. This historical refugium is coincident with an area predicted to be climatically stable under future climate scenarios. The identified refugium should be given high priority in conservation polices to safeguard the evolutionary potential of the species under predicted future climatic changes.

Conservation biogeography of the Cerrado's wild edible plants under climate change: Linking biotic stability with agricultural expansion.

UNLABELLED REMISE OF THE STUDY: Wild edible plants (WEPs) have an important cultural and economic role in human population worldwide. Human impacts are quickly converting natural habitats in agricultural, cattle ranch, and urbanized lands, putting native species on peril of risk of extinction, including some WEPs. Moreover, global climate changes also can pose another threat to species persistency. Here, we established conservation priorities for the Cerrado, a neotropical region in South America with high levels of plant endemism and vulnerability, aiming to assure long-term persistency of 16 most important WEPs. We evaluated these conservation priorities using a conservation biogeography framework using ecological patterns and process at a biogeographical scale to deal with species conservation features. METHODS We built ecological niche models for 16 WEPs from Cerrado in the neotropics using climate models for preindustrial, past (Last Glacial Maximum) and future (year 2080) time periods to establish climatically stable areas through time, finding refugias for these WEPs. We used a spatial prioritization algorithm based on the spatial pattern of irreplaceability across the neotropics, aiming to ensure the persistence of at least 25% of range size in climatically stable areas for each WEP, using agricultural models as constraints. KEY RESULTS The Southeast Cerrado was the most biotically stable and irreplaceable region for the WEPs compared with other areas across the neotropics. CONCLUSIONS Our findings strongly suggest that the Southeast Cerrado should be considered a conservation priority, with new protected areas to be sustainably managed and restored, to guarantee the supply of cultural and ecosystem services provided from the Cerrados WEPs.

Associação de Constrictotermes cyphergaster Silvestri (Isoptera: Termitidae) com espécies arbóreas do Cerrado brasileiro

Termites usually build nests differently shaped and characterized according to each species, to protect and keep society cohesion. Some species build nests in the ground, some prefer tree thunks or branches as support, whereas other dig galleries in the wood. The purpose of this study is to analyze the relationship between the occurrence of arboreal termites Constrictotermes cyphergaster Silvestri and tree species that support the nest of this species, in a Cerrado sensu strictu of the Serra de Caldas Novas, GO. Data suggest a association relationship between C. Cyphergaster and the tree species Qualea grandiflora Mart., Annona crassiflora Mart., Caryocar brasiliense Camb. and Plathymenia reticulata Benth., shown by high Qui-squared values (chi2 = 214.986, gl. = 20, P < 0.001). This relationship may be found among other termites and tree species, including Cerrado biome, and may be due to several factors, such as natural competitors and predators, toxin production by other tree species or benefits between associated species (facultative mutualism or facilitation).