Jose Alexandre Felizola Diniz-Filho

Federal University of Goiás | UFG · Departamento de Ecologia

Over two million species have been named so far, but many will be invalidated due to redundant descriptions. Undetected invalid species (i.e., synonyms) can impair inferences we make in biodiversity research and hamper the implementation of effective conservation strategies. However, the processes leading to the accumulation of invalid names remain...

Despite the urgency imposed by the current biodiversity crisis, many species remain undescribed, facing extinction before their formal recognition by science. Accelerating species descriptions is thus imperative. However, descriptions should be robust and based on good taxonomic practice, which may enhance long-term nomenclatural stability that is...

Aim In this study, we sought to understand how the Linnean shortfall (i.e., the lack of knowledge about species taxonomy) interacts with the Darwinian shortfall (i.e., the lack of knowledge about phylogenetic relationships among species), which potentially jeopardises geographical patterns in estimates of speciation rates. Location New World. Tax...

With the advancements in bioinformatics and ecoinformatics tools, it has become feasible to utilize vast amounts of biodiversity information to describe biological patterns and attempt to assess the ecological and evolutionary processes underlying them, as well as to establish more effective and comprehensive conservation actions. However, existing...

Ecological and evolutionary processes are recognized as the main factors generating and maintaining biodiversity. However, how biodiversity knowledge is collated, organized, and distributed worldwide influences our perceptions and inferences about biodiversity and the underlying processes. We demonstrated that name-bearing type specimens (NBT), the...

It is now widely recognized that broad-scale patterns in species richness, particularly the Latitudinal Diversity Gradients (LDGs), are driven by complex interactions among ecological, evolutionary, and historical processes. However, even if it is now possible to better evaluate evolutionary explanations for LDGs based on speciation and diversifica...

Most described species have not been explicitly included in phylogenetic trees—a problem named the Darwinian shortfall—owing to a lack of molecular and/or morphological data, thus hampering the explicit incorporation of evolution into large-scale biodiversity analyses. We investigate potential drivers of the Darwinian shortfall in tetrapods, a grou...

With the advancements in bioinformatics and ecoinformatics tools, it has become feasible to utilize vast amounts of biodiversity information to describe biological patterns and attempt to assess the ecological and evolutionary processes underlying them, as well as to establish more effective and comprehensive conservation actions. However, existing...

Ambotuy Favoring males’ specific sexual signals, female preferences play a major role in frogs’ evolutionary process by selecting traits linked to those signals. However, the factors constraining and determining those preferences are scarcely explored in an evolutionary background. Here, through a phylogenetic comparative approach we check whether...

There has been a continuous interest in understanding the patterns of genetic diversity in natural populations because of the role of intraspecific genetic diversity as the basis of all evolutionary change and thus, its potential effects on population persistence when facing environmental changes. Here, we provided the first description of genetic...

Climate’s effect on global biodiversity is typically viewed through the lens of temperature, humidity and resulting ecosystem productivity1,2,3,4,5,6. However, it is not known whether biodiversity depends solely on these climate conditions, or whether the size and fragmentation of these climates are also crucial. Here we shift the common perspectiv...

The imprint left by niche evolution on the variation of biological diversity across spatial and environmental gradients is still debated among ecologists. Furthermore, understanding to what extent dispersal limitation may reinforce or blur such imprint is still a gap in the ecological knowledge. In this article we introduce a simulation approach co...

Macroecology and biogeography have made significant strides in understanding the patterns and processes underlying biodiversity, yet the problem of underdetermination (the Duhem–Quine thesis) remains an ongoing challenge. Underdetermination arises when multiple explanations are consistent with the observed data, resulting in challenges in theory an...

Species are the currency of most biodiversity studies. However, many shortfalls and biases remain in our biodiversity estimates, preventing a comprehensive understanding of the eco-evolutionary processes that have shaped the biodiversity currently available on Earth. Biased biodiversity estimates also jeopardize the effective implementation of data...

By the end of this century, human-induced climate change and habitat loss may drastically reduce biodiversity, with expected effects on many amphibian lineages. One of these effects is the shift in the geographic distributions of species when tracking suitable climates. Here, we employ a macroecological approach to dynamically model geographic rang...

More than two million species have been described so far, but our knowledge on most taxa remains scarce or inexistent, and the available biodiversity data is often taxonomically, phylogenetically and spatially biased. Unevenness in research effort across species or regions can interact with data biases and compromise our ability to properly study a...

Although spatial analysis of population genetic structure has been one of the most important ways to infer microevolutionary processes, these studies are usually focused on neutral dynamics and limited dispersal, interpreted under the theoretical reasoning of isolation-by-distance. More recently, however, there has been a growing interest on how en...

A Correlação entre Diversidade Genética e Diversidade de Espécies (SGDC, sigla do inglês Species-Genetic Diversity Correlation) é uma abordagem de Genética de Comunidades que tem por finalidade investigar e quantificar a correlação entre a diversidade genética e a diversidade de espécies que, sob a influência de fatores ambientais, moldam os padrõe...

O surgimento de novas mutações em linha- gens do vírus SARS-CoV-2 ganhou grande repercussão na mídia e nas redes sociais no segundo ano da pandemia. O ponto central da questão é que algumas mutações em de- terminados genes dessas linhagens podem conferir a elas maior capacidade de infecção e, talvez, maior patogenicidade. Tendo em vista que o vírus...

The Tocantins-Araguaia Basin is one of the largest river systems in South America, located entirely within Brazilian territory. In the last decades, capital-concentrating activities such as agribusiness, mining, and hydropower promoted extensive changes in land cover, hydrology, and environmental conditions. These changes are jeopardizing the basin...

Biddick & Burns (2021) proposed a null/neutral model that reproduces the island rule as a product of random drift. We agree that it is unnecessary to assume adaptive processes driving island dwarfing or gigantism, but several flaws make their approach unrealistic and thus unsuitable as a stochastic model for evolutionary size changes.

Aim The Island Rule—that is, the tendency for body size to decrease in large mammals and increase in small mammals on islands has been commonly evaluated through macroecological or macroevolutionary, pattern-orientated approaches, which generally fail to model the microevolutionary processes driving either dwarfing or gigantism. Here, we seek to id...

At least six different Homo species populated the World during the latest Pliocene to the Pleistocene. The extinction of all but one of them is currently shrouded in mystery, and no consistent explanation has yet been advanced, despite the enormous importance of the matter. Here, we use a recently implemented past climate emulator and an extensive...

Homo sapiens is the only species alive able to take advantage of its cognitive abilities to inhabit almost all environments on Earth. Humans are able to culturally construct, rather than biologically inherit, their occupied climatic niche to a degree unparalleled within the animal kingdom. Precisely, when hominins acquired such an ability remains u...

Aim Studying species richness patterns by considering all species as equivalent units may prevent a deeper understanding of the origin and maintenance of biodiversity. Here, we deconstructed the species richness of Neotropical lianas by specific attributes of species to study richness–environment relationships. Location Neotropics. Taxon Tribe Bi...

The pandemic state of COVID-19 caused by the SARS CoV-2 put the world in quarantine, led to hundreds of thousands of deaths and is causing an unprecedented economic crisis. However, COVID-19 is spreading in different rates at different countries. Here, we tested the effect of three classes of predictors, i.e., socioeconomic, climatic and transport,...

A bstract The expansion of the new coronavirus disease (COVID-19) triggered a renewed interest in epidemiological models and on how parameters can be estimated from observed data. Here we investigated the relationship between average number of transmissions though time, the reproductive number Rt , and social distancing index as reported by mobile...

Caryocar brasiliense (Caryocaraceae) is a Neotropical tree species widely distributed in Brazilian Savannas. This species is very popular in central Brazil mainly by the use of its fruits in the local cuisine, and indeed it is one of the candidates, among Brazilian native plants, for fast track incorporation into cropping systems. Here we sequenced...

Phylogenetic niche conservatism can be investigated at multiple scales on an explicit geographical context. Haplotype-based comparative analyses of lineages occupying the same region, and thus subjected to similar environmental factors, allow decoupling shared evolutionary and ecological patterns, as well as multiple dimensions of adaptive diversif...

Conservation strategies aiming to safeguard species genetic diversity in the Cerrado are urgent. The biome is an agriculture frontier and lost at least 50% of its natural capital since the early 1950s, with the highest rate of vegetation clearing among all Brazilian biomes. Here we match information on geographic range shifts in response to climate...

Body size is one of the most influential traits affecting many ecological and physiological processes across animal and plant taxa. Studies of the environmental factors shaping body size patterns may evaluate either temporal or spatial dimensions. Here, we analyzed body size evolution in the radiation of Anolis lizards across both geographical and...

Aim Despite longstanding investigation, the gradients of species richness remain unknown for most taxa because of shortfalls in knowledge regarding the quantity and distribution of species. Here, we explore the ability of a geostatistical interpolation model, regression‐kriging, to recover geographical gradients of species richness. We examined the...

According to the island rule, small-bodied vertebrates will tend to evolve larger body size on islands, whereas the opposite happens to large-bodied species. This controversial pattern has been studied at the macroecological and biogeographical scales, but new developments in quantitative evolutionary genetics now allow studying the island rule fro...

Stryphnodendron adstringens is a medicinal plant belonging to the Leguminosae family, and it is commonly found in the southeastern savannas, endemic to the Cerrado biome. The goal of this study was to assemble and annotate the chloroplast genome of S. adstringens and to compare it with previously known genomes of the mimosoid clade within Leguminos...

The high diversity of plant species in the tropics has revealed complex phenological patterns and reproductive strategies occurring throughout the year. Describing and analysing tropical plant phenology, and detecting triggers, demands to consider the circular nature of recurrent life cycle events and the use of appropriated statistical metrics. He...

Aim Tall and structurally complex forests can provide ample habitat and niche space for climbing plants, supporting high liana species richness. We test to what extent canopy height (as a proxy of 3‐D habitat structure), climate and soil interact to determine species richness in the largest clade of Neotropical lianas. We expect that the effect of...

Ecological Niche Models (ENMs) have different performances in predicting potential geographic distributions. Here we meta-analyzed the likely effects of climate change on the potential geographic distribution of 1,205 bird species from the Neotropical region, modeled using eight ENMs and three Atmosphere-Ocean General Circulation Models (AOGCM). We...

Reptiles are highly susceptible to climate change, responding negatively to thermal and rainfall alterations mainly in relation to their reproductive processes. Based on that, we evaluated the effects of climate change on climatically suitable areas for the occurrence of snakes in the Atlantic Forest hotspot, considering the responses of distinct r...

Results from ecological niche models usually indicate a worrying scenario in terms of biodiversity loss. Continuous efforts to improve these models (e.g., allowing for dispersal limitation) have recently been updated to include the potential of species’ persistence, in otherwise unsuitable regions, due to natural selection (a process called evoluti...

The Hymenaea clade is a lineage of the subfamily Detarioideae of Leguminosae. The clade is currently composed of three genera: Guibourtia, Hymenaea, and Peltogyne. The genera Guibourtia and Hymenaea present an Amphi-Atlantic distribution, whereas Peltogyne is exclusively found in the Neotropics. Previous studies have focused on the phylogeny of the...

Expanding populations may loss genetic diversity because sequential founder events throughout a wave of demographic expansion may cause “allele surfing”, as the alleles of founder individuals may propagate rapidly through space. The spatial components of allele surfing have been studied by geneticists, but have never been investigate on dynamic and...

Aim To evaluate the effect of biogeographical history on climatic niche diversification. Location Simulated clades evolving in South America. Methods We modelled species evolution under neutral community dynamics and purposely assumed that climatic niche is an emergent property of species. This assumption allows us to better understand whether ph...

Despite the widespread use of Ecological Niche Models (ENMs) for predicting the responses of species to climate change, these models do not explicitly incorporate any population‐level mechanism. On the other hand, mechanistic models adding population processes (e.g., biotic interactions, dispersal and adaptive potential to abiotic constraints) are...

The world is passing through abrupt climate changes that are a threat for biodiversity. Stryphnodendron adstringens (Mart.) Coville (Fabaceae) is a tree species endemic to the “Cerrado” biome with a high economic potential. Its exploitation is done in an extractive way, which, coupled with climate changes and other landscape changes, can contribute...

One outstanding phenotypic character in Homo is its brain evolution. Pagel (Morphology, shape and phylogeny, CRC Press, Boca Raton, 2002) performed a phylogenetic analysis of the evolution of cranial capacity (as a surrogate of brain size) in fossil hominins, finding evidence for gradual evolutionary change with accelerating rate. Since Pagel’s pio...

Aim This study aims to evaluate phylogenetic structure of turtle communities and their potential correlates on a global scale. More specifically, we tested whether cold temperatures and low precipitation could act as potential environmental filters of turtle communities and whether the dispersal limitation caused by altitudinal range could generate...

Climate change threatens freshwater fish by severely modify water quality and hydrological dynamics, hence altering the species distribution. We assessed the climate change effects on the geographical distribution of Salminus brasiliensis, a keystone species of economic interest in the La Plata River basin. Using ecological niche models, we estimat...

Cave bears (Ursus spelaeus) are an iconic component of the European late Quaternary Ice Age megafauna. Recent demographic analyses based on cave bear mtDNA sequences and refined radiocarbon dating indicate that cave bear population size and genetic diversity started to decline some 50 kilo years ago (kya). Hence, neither the coldest phase of the la...

Species co-occurrence in local assemblages is shaped by different processes at different spatial and temporal scales. Here we focus on historical explanations and examine the phylogenetic structure of local assemblages of the Furnariides clade (Aves: Passeriformes), assessing the influence of diversification rates on the assembly and species co-occ...

The idea that simplicity of explanation is important in science is as old as science itself. However, scientists often assume that parsimonious theories, hypothesis and models are more plausible than complex ones, forgetting that there is no empirical evidence to connect parsimony with credibility. The justification for the parsimony principle is s...

South American coralsnakes are characterized by inconspicuous and poorly known species, which are potentially very sensitive to climate change. Here, we assess the impact of future climate change on the distributions of the Micrurus lemniscatus species complex after addressing the Wallacean shortfalls and refining the knowledge about their current...

List of museums. List of museums from which specimens were examined. (PDF)

Number of occurrence records. Number of occurrence records from museum collections and after mapping over the South American grid. (PDF)

Ecological niche modeling methods. Ecological niche modeling methods used to estimate species potential distributions. (PDF)

Habitat suitability maps. Consensus maps of habitat suitability derived from 12 niche modeling methods and 5 climate models. Hot colors indicate high habitat suitability; cool colors, low habitat suitability. Black dots indicate presence records used in the modeling processes; A) Micrurus l. lemniscatus, B) Micrurus l. carvalhoi, C) Micrurus diutiu...

Results of ENM for M. l. carvalhoi. Results of ENM and analyses for M. l. carvalhoi after controlling for spatial aggregation in occurrence records. (PDF)

List of occurrence records. List of occurrence records with the collection IDs. Collection abbreviations correspond to the museums listed in the S1 Appendix above. (PDF)

Climatic models. Details of the climatic simulations (AOGCMs) used in the ecological niche modeling. (PDF)

Output for factorial analysis. Loadings of the bioclimatic variables in the first five axes of varimax rotated factor analysis, based on the CCSM AOGCM. Numbers in bold highlight the highest loading of the selected variable in each factor. (PDF)

Habitat suitability map for M. l. cavalhoi. Consensus maps of habitat suitability from ENMs for M. l. cavalhoi for A) present, and B) future after controlling for spatial autocorrelation in occurrence records. Black dots are the most equidistant records select in the environmental space. (PDF)

Terrestrial ecoregions. Delimitation of the terrestrial ecoregions used to assess the level of species representation in protected areas. For each taxon, the selection of these areas was done by overlapping the map of habitat suitability (after applying specific decision thresholds) with the map of South American ecoregions. An ecoregion was select...

Output of model evalution. The mean true skill statistics (TSS) values across five AOGCMs (CCSM, CNRM, GISS, MIROC and MRI) for each ENM method. (PDF)