Phylogenetic diversity, habitat loss and conservation in South American pitvipers (Crotalinae: Bothrops and Bothrocophias )

Total-evidence phylogeny and evolutionary morphology of New World pitvipers (Serpentes: Viperidae: Crotalinae)

Crotalines (pitvipers) in the Americas are distributed from southern Canada to southern Argentina, and are represented by 13 genera and 163 species that constitute a monophyletic group. Their phylogenetic relationships have been assessed mostly based on DNA sequences, while morphological data have scarcely been used for phylogenetic inquiry. We present a total-evidence phylogeny of New World pitvipers, the most taxon/character comprehensive phylogeny to date. Our analysis includes all genera, morphological data from external morphology, cranial osteology and hemipenial morphology, and DNA sequences from mitochondrial and nuclear genes. We performed analyses with parsimony as an optimality criterion, using different schemes for character weighting. We evaluated the contribution of the different sources of characters to the phylogeny through analyses of reduced datasets and calculation of weighted homoplasy and retention indexes. We performed a morphological character analysis to identify synapomorphies for the main clades. In terms of biogeography, our results support a single colonization event of the Americas by pitvipers, and a cladogenetic event into a Neotropical clade and a North American/Neotropical clade. The results also shed light on the previously unstable position of some taxa, although they could not sufficiently resolve the position of Bothrops lojanus, which may lead to the paraphyly of either Bothrops or Bothrocophias. The morphological character analyses demonstrated that an important phylogenetic signal is contained in characters related to head scalation, the jaws and the dorsum of the skull, and allowed us to detect morphological convergences in external morphology associated with arboreality.

Functional diversity regulates the effects of habitat degradation on biocrust phylogenetic and taxonomic diversities

Biocrusts are major contributors to dryland diversity, functioning, and services. However, little is known about how habitat degradation will impact multiple facets of biocrust diversity and measurable functional traits. We evaluated changes in taxonomic, functional, and phylogenetic diversity of biocrust-forming lichens along a habitat degradation gradient related to the presence of linear infrastructure (i.e., a road) and a profound agricultural driven transformation. To do so, we selected 50 remnants of a Mediterranean shrubland. We considered several surrogates of habitat quality and causal disturbance on the various diversity facets of biocrusts by using structural equation modeling, hypothesizing that habitat degradation primarily affects functional diversity, which in turn regulates changes in taxonomic and phylogenetic diversities, and also that taxonomic and phylogenetic diversities are coupled. Fragment connectivity, distance to linear infrastructure (i.e., a road) and, particularly, soil fertility (i.e., soil P concentration), had mostly negative effects on biocrust functional diversity, which in turn affected both taxonomic and phylogenetic diversities. However, we found no direct effects of habitat degradation variables on the taxonomic and phylogenetic diversities. We also found that increases in phylogenetic diversity had a positive effect on taxonomic diversity along the habitat degradation gradient. Our results indicate that functional diversity of biocrusts is strongly affected by habitat degradation, which may profoundly alter their contribution to ecosystem functioning and services. Furthermore, functional diversity regulates the response of biocrust taxonomic and phylogenetic diversity to habitat degradation. These findings indicate that habitat degradation alters and simplifies the diversity of functional traits of biocrust-forming lichens, leading to biodiversity loss, with important consequences for the conservation of global drylands biodiversity.

Habitat Specificity Modulates the Response of Small Mammals to Habitat Fragmentation, Loss, and Quality in a Neotropical Savanna

Landscape conversion of natural environments into agriculture and pasture are driving a marked biodiversity decline in the tropics. Consequences of fragmentation might depend upon habitat amount in the landscape, while the quality of remnants can also affect some species. These factors have been poorly studied in relation to different spatial scales. Furthermore, the impacts of these human-driven alterations may go beyond species loss, possibly causing a loss of ecosystem function and services. In this study, we investigated how changes in landscape configuration (patch size and isolation), habitat loss (considering a landscape gradient of 10, 25, and 40% of remnant forest cover), and habitat quality (forest structure) affect small mammal abundance, richness, taxonomic/functional diversity, and species composition in fragmented landscapes of semideciduous forests in the Brazilian Cerrado. Analyses were performed separately for habitat generalists and forest specialists. We live-trapped small mammals and measured habitat quality descriptors four times in 36 forest patches over the years 2018 and 2019, encompassing both rainy and dry seasons, with a total capture effort of 45,120 trap-nights. Regression analyses indicated that the effect of landscape configuration was not dependent on the proportion of habitat amount in the landscape to determine small mammal assemblages. However, both patch size and habitat loss impacted different aspects of the assemblages in distinct ways. Smaller patches were mainly linked to an overall increase in small mammal abundance, while the abundance of habitat generalists was also negatively affected by habitat amount. Generalist species richness was determined by the proportion of habitat amount in the landscape. Specialist richness was influenced by patch forest quality only, suggesting that species with more demanding habitat requirements might respond to fragmentation and habitat loss at finer scales. Taxonomic or functional diversity were not influenced by landscape structure or habitat quality. However, patch size and habitat amount in the landscape were the major drivers of change in small mammal species composition in semideciduous forests in the Brazilian savanna.

Environmental Drivers of Diversification and Hybridization in Neotropical Butterflies

Studying how the environment shapes current biodiversity patterns in species rich regions is a fundamental issue in biogeography, ecology, and conservation. However, in the Neotropics, the study of the forces driving species distribution and richness, is mostly based on vertebrates and plants. In this study, we used 54,392 georeferenced records for 46 species and 1,012 georeferenced records for 38 interspecific hybrids of the Neotropical Heliconius butterflies to investigate the role of the environment in shaping their distribution and richness, as well as their geographic patterns of phylogenetic diversity and phylogenetic endemism. We also evaluated whether niche similarity promotes hybridization in Heliconius. We found that these insects display five general distribution patterns mostly explained by precipitation and isothermality, and to a lesser extent, by altitude. Interestingly, altitude plays a major role as a predictor of species richness and phylogenetic diversity, while precipitation explains patterns of phylogenetic endemism. We did not find evidence supporting the role of the environment in facilitating hybridization because hybridizing species do not necessarily share the same climatic niche despite some of them having largely overlapping geographic distributions. Overall, we confirmed that, as in other organisms, high annual temperature, a constant supply of water, and spatio-topographic complexity are the main predictors of diversity in Heliconius. However, future studies at large scale need to investigate the effect of microclimate variables and ecological interactions.

Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.

BioDinamica: a toolkit for analyses of biodiversity and biogeography on the Dinamica-EGO modelling platform

Biogeography and macroecology are at the heart of the debate on ecology and evolution. We have developed the BioDinamica package, a suite of user-friendly graphical programs for analysing spatial patterns of biogeography and macroecology. BioDinamica includes analyses of beta-diversity, species richness, endemicity, phylo-diversity, species distribution models, predictive models of biodiversity patterns, and several tools for spatial biodiversity analysis. BioDinamica consists of a sub-library of Dinamica-EGO operators developed by integrating EGO native functions with R scripts. The BioDinamica operators can be assembled to create complex analytical and simulation models through the EGO graphical programming interface. In addition, we make available “Wizard” tutorials for end users. BioDinamica can be downloaded free of charge from the Dinamica EGO submodel store. The tools made available in BioDinamica not only facilitate complex biodiversity analyses, they also help develop state-of-the-art spatial models for biogeography and macroecology studies.

Phylogenetically informed spatial planning as a tool to prioritise areas for threatened plant conservation within a Mediterranean biodiversity hotspot

Global plant diversity is at risk due to anthropogenic changes to ecosystems, but given severely limited conservation resources, a reliable prioritisation strategy for species and sites is needed. Our objective was to identify key areas for conserving the phylogenetic diversity (PD) of threatened vascular plants in Italy, one of the most species-rich regions in the Mediterranean Basin. We used spatial data and the conservation status of 995 threatened vascular plants and applied a phylogenetically informed spatial planning to minimize conservation costs. We then determined the degree of overlap with existing protected areas and evaluated whether this PD-based prioritisation of areas provides adequate protection for threatened phylogenetically distinctive species (EDGE). The cost-effective procedure identified as priority for conservation 12% of the study territory, while achieving over 90% of conservation targets (total PD). We showed that priority areas and protected areas are moderately spatially mismatched. We also showed that not all top-EDGE species were met by the procedure applied, hence we conclude that the PD-based model indicated key areas for protection, but nevertheless additional attention is needed to protect top-EDGE species. This study represents one of the most comprehensive analyses, to date, for the conservation of the native flora in the Mediterranean, incorporating both spatial distribution and evolutionary relationships. Our work on the prioritisation of threatened plant species across Italy can serve as a guide for future conservation applications.

Conceptual and empirical advances in Neotropical biodiversity research

The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.

Patterns, biases and prospects in the distribution and diversity of Neotropical snakes

MOTIVATION

We generated a novel database of Neotropical snakes (one of the world's richest herpetofauna) combining the most comprehensive, manually compiled distribution dataset with publicly available data. We assess, for the first time, the diversity patterns for all Neotropical snakes as well as sampling density and sampling biases.

MAIN TYPES OF VARIABLES CONTAINED

We compiled three databases of species occurrences: a dataset downloaded from the Global Biodiversity Information Facility (GBIF), a verified dataset built through taxonomic work and specialized literature, and a combined dataset comprising a cleaned version of the GBIF dataset merged with the verified dataset.

SPATIAL LOCATION AND GRAIN

Neotropics, Behrmann projection equivalent to 1° × 1°.

TIME PERIOD

Specimens housed in museums during the last 150 years.

MAJOR TAXA STUDIED

Squamata: Serpentes.

SOFTWARE FORMAT

Geographical information system (GIS).

RESULTS

The combined dataset provides the most comprehensive distribution database for Neotropical snakes to date. It contains 147,515 records for 886 species across 12 families, representing 74% of all species of snakes, spanning 27 countries in the Americas. Species richness and phylogenetic diversity show overall similar patterns. Amazonia is the least sampled Neotropical region, whereas most well-sampled sites are located near large universities and scientific collections. We provide a list and updated maps of geographical distribution of all snake species surveyed.

MAIN CONCLUSIONS

The biodiversity metrics of Neotropical snakes reflect patterns previously documented for other vertebrates, suggesting that similar factors may determine the diversity of both ectothermic and endothermic animals. We suggest conservation strategies for high-diversity areas and sampling efforts be directed towards Amazonia and poorly known species.

Morphometric and phylogenetic analyses of Serpentirhabdias viperidicus n. sp. (Nematoda: Rhabdiasidae) from the lancehead snake Bothrops moojeni Hoge, 1966 (Reptilia: Serpentes: Viperidae) in Brazil

Serpentirhabdias viperidicus n. sp. (Nematoda: Rhabdiasidae) is described from the lungs of the ‘Brazilian lancehead’ Bothrops moojeni (Hoge, 1966) from the savannah in São Paulo State, Brazil. The new species is the eighth species of Serpentirhabdias described in the Neotropical region, and differs from other species mainly by a combination of characters: lips slightly notable, presence of fine striations at posterior ends, presence of two parallel lines with intercalated pores, a pore-shaped phasmid situated at the level of the anal aperture and another two in the posterior half of the tail. It is the first species of Serpentirhabdias reported in this snake host and the second species of this genus found parasitizing South American viperidian snakes. Molecular phylogenetic analysis using ribosomal (ITS and 28S partial) genes confirms Serpentirhabdias viperidicus n. sp. as a new species that clustered in the Serpentirhabdias clade, sister taxon to Serpentirhabdias fuscovenosa and Serpentirhabdias elaphe. This is the first description of Serpentirhabdias species from Brazil using molecular approaches and morphological characters to confirm the monophyly of this recent genus.

Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador

Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

Ontogenetic Variation in Biological Activities of Venoms from Hybrids between Bothrops erythromelas and Bothrops neuwiedi Snakes

Lance-headed snakes are found in Central and South America, and they account for most snakebites in Brazil. The phylogeny of South American pitvipers has been reviewed, and the presence of natural and non-natural hybrids between different species of Bothrops snakes demonstrates that reproductive isolation of several species is still incomplete. The present study aimed to analyze the biological features, particularly the thrombin-like activity, of venoms from hybrids born in captivity, from the mating of a female Bothrops erythromelas and a male Bothrops neuwiedi, two species whose venoms are known to display ontogenetic variation. Proteolytic activity on azocoll and amidolytic activity on N-benzoyl-DL-arginine-p-nitroanilide hydrochloride (BAPNA) were lowest when hybrids were 3 months old, and increased over body growth, reaching values similar to those of the father when hybrids were 12 months old. The clotting activity on plasma diminished as hybrids grew; venoms from 3- and 6-months old hybrids showed low clotting activity on fibrinogen (i.e., thrombin-like activity), like the mother venom, and such activity was detected only when hybrids were older than 1 year of age. Altogether, these results point out that venom features in hybrid snakes are genetically controlled during the ontogenetic development. Despite the presence of the thrombin-like enzyme gene(s) in hybrid snakes, they are silenced during the first six months of life.