The South American Dry Diagonal, also called the Diagonal of Open Formations, is a large region of seasonally dry vegetation extending from northeastern Brazil to northern Argentina, comprising the Caatinga, Cerrado, and Chaco subregions. A growing body of phylogeography literature has determined that a complex history of climatic changes coupled with more ancient geological events has produced a diverse and endemic-rich Dry Diagonal biota. However, the exact drivers are still under investigation, and their relative strengths and effects are controversial. Pleistocene climatic fluctuations structured lineages via vegetation shifts, refugium formation, and corridors between the Amazon and Atlantic forests. In some taxa, older geological events, such as the reconfiguration of the São Francisco River, uplift of the Central Brazilian Plateau, or the Miocene inundation of the Chaco by marine incursions, were more important. Here, we review the Dry Diagonal phylogeography literature, discussing each hypothesized driver of diversification and assessing degree of support. Few studies statistically test these hypotheses, with most support drawn from associating encountered phylogeographic patterns such as population structure with the timing of ancient geoclimatic events. Across statistical studies, most hypotheses are well supported, with the exception of the Pleistocene Arc Hypothesis. However, taxonomic and regional biases persist, such as a proportional overabundance of herpetofauna studies, and the under-representation of Chaco studies. Overall, both Pleistocene climate change and Neogene geological events shaped the evolution of the Dry Diagonal biota, though the precise effects are regionally and taxonomically varied. We encourage further use of model-based analyses to test evolutionary scenarios, as well as interdisciplinary collaborations to progress the field beyond its current focus on the traditional set of geoclimatic hypotheses.
A Diagonal de Formações Abertas da América do Sul, também chamada de Diagonal Seca é uma grande região de vegetação sazonalmente seca que se estende do Nordeste do Brasil até o Norte da Argentina, composta pelas subregiões Caatinga, Cerrado e Chaco. Uma crescente literatura em filogeografia tem demonstrado que a diversa e endêmica biota Diagonal de Formações Abertas é produto de uma história complexa de mudanças climáticas, em conjunto com eventos geológicos mais antigos. Entretanto, os fatores específicos que geram essa diversidade e endemismo continuam sendo investigados, e há controvérsias em relação à importância relativa de cada um deles. Flutuações climáticas durante o Pleistoceno estruturaram linhagens através de mudanças na vegetação, formação de refúgios, e corredores entre a Floresta Amazônica e Mata Atlântica. Para alguns grupos taxonômicos, eventos geológicos durante o Neogeno, tal como a mudança no curso do São Francisco, o soerguimento do Planalto Central no Brasil, ou eventos durante o Mioceneo como a inundação do Chaco devido a incursões marinhas, foram mais importantes. No presente trabalho, nós revisamos a literatura sobre filogeografia na Diagonal de Formações Abertas, levantamos as hipóteses de diversificação sugeridas, e avaliamos seu grau de suporte. Poucos estudos testaram hipóteses estatisticamente, com maior parte do suporte atribuído aos padrões filogeográficos encontrados. Dentre os estudos que usaram uma abordagem estatística, a maioria das hipóteses são bem suportadas, exceto a hipótese dos arcos Pleistocênicos. Entretanto, vieses taxonômicos e regionais persistem, tal como a relativa prevalência de estudos herpetológicos e a falta de estudos sobre o Chaco. De forma geral, tanto as mudanças climáticas no Pleistoceno, quanto mudanças geológicas no Neogeno moldaram a evolução da Diagonal de Formações Abertas, apesar do efeito exato de cada um desses fatores variar dependendo da região e grupo taxonômico. Nós recomendamos o uso de análises baseadas em teste de modelos para testar cenários evolutivos, assim como colaborações interdisciplinares incluindo biólogos, geólogos e climatólogos para expandir o campo de estudo para além do seu atual foco atrelado às tradicionais hipóteses geoclimáticas mencionadas acima.

Despite extensive research on biodiversity in Neotropical forests, biodiversity in seasonally dry, open biomes in South America has been underestimated until recently. We leverage a widespread group, Boana albopunctata, to uncover cryptic lineages and investigate the timing of diversification in Neotropical anurans with a focus on dry diagonal biomes (Cerrado, Caatinga and Chaco) and the ecotone between Amazonia and the Cerrado. We inferred a multilocus phylogeny of the B. albopunctata species group that includes 15 of 18 described species, recovered two cryptic species, and reconstructed the timing of diversification among species distributed across multiple South American biomes. One new potential species (B. aff. steinbachi), sampled in the Amazonian state of Acre, clustered within the B. calcara-fasciata species complex and is close to B. steinbachi. A second putative new species (B. aff. multifasciata), sampled in the Amazonia-Cerrado ecotone, is closely related to B. multifasciata. Lastly, we place a recently identified Cerrado lineage (B. aff. albopuncata) into the B. albopunctata species group phylogeny for the first time. Our ancestral range reconstruction showed that species in the B. albopuctata group likely dispersed from Amazonia-Cerrado into the dry-diagonal and Atlantic Forest. Intraspecies demography showed, for both B. raniceps and B. albopunctata, signs of rapid expansion across the dry diagonal. Similarly, for one clade of B. multifasciata, our analyses support an invasion of the Cerrado from Amazonia, followed by a rapid expansion across the open diagonal biomes. Thus, our study recovers several recent divergences along the Amazonia-Cerrado ecotone in northern Brazil. Tectonic uplift and erosion in the late Miocene and climate oscillations in the Pleistocene corresponded with estimated divergence times in the dry diagonal and Amazonia-Cerrado ecotone. Our study highlights the importance of these threatened open formations in the generation of biodiversity in the Neotropics.

Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.

The genus Isoëtes is globally distributed. Within the Neotropics, Isoëtes occurs in various habitats and ecosystems, making it an interesting case study to address phylogenetic and biogeographic questions. We sequenced and assembled plastomes and ribosomal DNA (rDNA) sequences to reconstruct phylogenetic relationships in Isoëtes from tropical regions in the Neotropics. The ploidy level of nine taxa was established to address the potential source of phylogenetic incongruence in the genus. Node ages were estimated using MCMCTree. The ancestral range estimates were conducted in BioGeoBEARS. Plastome-based phylogenies were congruent throughout distinct matrices and partition schemes, exhibiting high support for almost all nodes. Whereas, we found incongruences between the rDNA and plastome datasets. Chromosome counts identified three diploids, five tetraploids and one likely hexaploid among Neotropical species. Plastome-based node age estimates showed that the radiation of the crown Isoëtes group occurred at 20 Ma, with the diversification of the tropical American (TAA) clade taking place in the Pleistocene at 1.7 Ma. Ancestral range estimates showed that the ancestor of the TAA clade may have evolved first in the dry diagonal area in South America before reaching more humid regions. In addition, the colonization of the Brazilian semiarid region occurred three times, while the occupation of the Cerrado and Amazon regions occurred twice and once, respectively. Our study showed a large unobserved diversity within the genus in warm-dry regions in the Neotropics. Plastomes provided sufficient genomic information to establish a robust phylogenetic framework to answer evolutionary questions in Isoëtes from the Neotropics.

Phylogenetic niche conservatism (PNC) shapes the distribution of organisms by constraining lineages to particular climatic conditions. Conversely, if areas with similar climates are geographically isolated, diversification may also be limited by dispersal. Neotropical xeric habitats provide an ideal system to test the relative roles of climate and geography on diversification, as they occur in disjunct areas with similar biotas. Sicariinae sand spiders are intimately associated with these xeric environments, particularly seasonally dry tropical forests (SDTFs) and subtropical deserts/scrublands in Africa (Hexophthalma) and the Neotropics (Sicarius). We explore the role of PNC, geography and biome shifts in their evolution and timing of diversification. We estimated a time-calibrated, total-evidence phylogeny of Sicariinae, and used published distribution records to estimate climatic niche and biome occupancy. Topologies were used for estimating ancestral niches and biome shifts. We used variation partitioning methods to test the relative importance of climate and spatially autocorrelated factors in explaining the spatial variation in phylogenetic structure of Sicarius across the Neotropics. Neotropical Sicarius are ancient and split from their African sister-group around 90 (57-131) million years ago. Most speciation events took place in the Miocene. Sicariinae records can be separated in two groups corresponding to temperate/dry and tropical/seasonally dry climates. The ancestral climatic niche of Sicariinae are temperate/dry areas, with 2-3 shifts to tropical/seasonally dry areas in Sicarius. Similarly, ancestral biomes occupied by the group are temperate and dry (deserts, Mediterranean scrub, temperate grasslands), with 2-3 shifts to tropical, seasonally dry forests and grasslands. Most of the variation in phylogenetic structure is explained by long-distance dispersal limitation that is independent of the measured climatic conditions. Sicariinae have an ancient association to arid lands, suggesting that PNC prevented them from colonizing mesic habitats. However, niches are labile at a smaller scale, with several shifts from deserts to SDTFs. This suggests that PNC and long-distance dispersal limitation played major roles in confining lineages to isolated areas of SDTF/desert over evolutionary history, although shifts between xeric biomes occurred whenever geographical opportunities were presented.

We undertook a comprehensive, critical review of literature concerning the distribution, conservation status, and taxonomy of species of mammals endemic to the Cerrado and the Caatinga, the two largest biomes of the South American Dry-Diagonal. We present species accounts and lists of species, which we built with criteria that, in our opinion, yielded results with increased scientific rigor relative to previously published lists - e.g., excluding nominal taxa whose statuses as species have been claimed only on the basis of unpublished data, incomplete taxonomic work, or weak evidence. For various taxa, we provided arguments regarding species distributions, conservation and taxonomic statuses previously lacking in the literature. Two major findings are worth highlighting. First, we unveil the existence of a group of species endemic to both the Cerrado and the Caatinga (i.e., present in both biomes and absent in all other biomes). From the biogeographic point of view, this group, herein referred to as Caatinga-Cerrado endemics, deserves attention as a unit - just as in case of the Caatinga-only and the Cerrado-only endemics. We present preliminary hypotheses on the origin of these three endemic faunas (Cerrado-only, Caatinga-only, and Caatinga-Cerrado endemics). Secondly, we discovered that a substantial portion of the endemic mammalian faunas of the Caatinga and the Cerrado faces risks of extinction that are unrecognized in the highly influential Red List of Threatened Species published by the International Union for Conservation of Nature (IUCN). \"Data deficient\" is a category that misrepresents the real risks of extinction of these species considering that (a) some of these species are known only from a handful of specimens collected in a single or a few localities long ago; (b) the Cerrado and the Caatinga have been sufficiently sampled to guarantee collection of additional specimens of these species if they were abundant; (c) natural habitats of the Cerrado and the Caatinga have been substantially altered or lost in recent decades. Failures either in the design of the IUCN criteria or in their application to assign categories of extinction risks represent an additional important threat to these endemic faunas because their real risks of extinctions become hidden. It is imperative to correct this situation, particularly considering that these species are associated to habitats that are experiencing fast transformation into areas for agriculture, at an unbearable cost for biodiversity.