Comparative Phylogeography of Birds Across the Tocantins–Araguaia Interfluve Reveals a New Biogeographic Suture in the Amazon Far East

Few phylogeographic studies have focused on understanding the role of the Tocantins–Araguaia Interfluve (TAI) in the diversification of Amazonian biodiversity. Herein we evaluate the phylogeographic relationships of 14 avian lineages present in the TAI and its two neighboring Amazonian Areas of Endemism: the Xingu (XAE) and Belém (BAE). Four alternative scenarios coupling degree of genetic differentiation and area relationships were tested: (1) populations distributed in TAI, BAE, and XAE are not genetically differentiated from each other (assumed as the null hypothesis); (2) populations from TAI are more closely related to those from BAE; (3) populations from TAI are more closely related to those from XAE; and (4) TAI populations represent independent or endemic lineages not present in either the BAE or XAE. Molecular analyses considered Bayesian Inference methods and Bayesian Information Criterion (BIC) evolutionary models, haplotype sharing and genetic differentiation estimates. We found three distinct phylogeographic patterns: (i) four lineages presented no population structure across XAE, TAI and BAE; (ii) six lineages were represented in the TAI with distinct phylogroups replacing each other between XAE and BAE, but with varying degrees of contact and evidence of gene-flow within the TAI; and (iii) for four lineages, the Tocantins River acted as a barrier isolating BAE phylogroups from those inhabiting both TAI and XAE. These different patterns demonstrate a heterogeneous response to the barrier effects posed by both the Tocantins and Araguaia rivers on the local fauna. Historical geomorphological and hydromorphological factors, such as the presence and absence of paleochannels and anastomosed channel stretches and variations in sedimentation rates support a dynamic history for the Araguaia-Tocantins floodplains, likely accounting for the observed heterogeneity in species’ specific responses. Finally, the scenario of phylogeographic breaks and population subdivision recovered herein along the Tocantins and Araguaia rivers, associated with the existence of contact zones and the occurrence of gene flow, define the TAI as hitherto unknown biogeographic suture zone, localized in southeasternmost Amazonia.

Molecular Phylogeny of Cryptonanus (Didelphidae: Thylamyini): Evidence for a recent and complex diversification in South American open biomes

Systematic revisions of South American marsupials have contributed to our knowledge about genus and species diversity in the last decades, including studies of the most recently described genus Cryptonanus (Didelphidae), currently comprising four recognized species. Herein we provide the first phylogeny for these mouse opossums based on comprehensive sampling, including representatives from all nominal taxa, encompassing most of the geographic distribution of the genus while also extending its known range. The taxonomic status of Cryptonanus species was explored by analyses of multiple mitochondrial and nuclear DNA markers to assess phylogenetic relationships and to provide divergence time estimates, species delimitations and biogeographical hypotheses. Cryptonanus monophyly remained highly supported despite the inclusion of abundant new data from more than a hundred specimens, comprising 10 independent evolutionary lineages. Species-complexes within valid nominal taxa reveal higher species richness in the genus. Based on divergence estimates from a dated phylogeny, we suggest that Cryptonanus diversified along the Quaternary, with speciation events occurring well into the Pleistocene. The best supported biogeographical hypothesis endorses speciation by vicariance and subset speciation across open formations in shaping the evolutionary history of this didelphid genus, strongly associated with dry tropical landscapes of South America.

A morphological and molecular study of Hydrodynastes gigas (Serpentes, Dipsadidae), a widespread species from South America

BACKGROUND

Studies with integrative approaches (based on different lines of evidence) are fundamental for understanding the diversity of organisms. Different data sources can improve the understanding of the taxonomy and evolution of snakes. We used this integrative approach to verify the taxonomic status of Hydrodynastes gigas (Duméril, Bibron & Duméril, 1854), given its wide distribution throughout South America, including the validity of the recently described Hydrodynastes melanogigas Franco, Fernandes & Bentim, 2007.

METHODS

We performed a phylogenetic analysis of Bayesian Inference with mtDNA 16S and Cytb, and nuDNA Cmos and NT3 concatenated (1,902 bp). In addition, we performed traditional morphometric analyses, meristic, hemipenis morphology and coloration pattern of H. gigas and H. melanogigas.

RESULTS

According to molecular and morphological characters, H. gigas is widely distributed throughout South America. We found no evidence to support that H. gigas and H. melanogigas species are distinct lineages, therefore, H. melanogigas is a junior synonym of H. gigas. Thus, the melanic pattern of H. melanogigas is the result of a polymorphism of H. gigas. Melanic populations of H. gigas can be found in the Tocantins-Araguaia basin.

Effect of river size on Amazonian primate community structure: A biogeographic analysis using updated taxonomic assessments

The mechanisms that underlie the diversification of Neotropical primates remain contested. One mechanism that has found support is the riverine barrier hypothesis (RBH), which postulates that large rivers impede gene flow between populations on opposite riverbanks and promote allopatric speciation. Ayres and Clutton-Brock (1992) demonstrated that larger Amazonian rivers acted as barriers, delineating the distribution limits of primate species. However, profound changes in taxonomy and species concepts have led to the proliferation of Neotropical primate taxa, which may have reduced support for their results. Using the most recent taxonomic assessments and distribution maps, we tested the effect of increasing river size on the similarity of opposite riverbank primate communities in the Amazon. First, we conducted a literature review of primate taxonomy and developed a comprehensive spatial database, then applied geographical information system to query mapped primate ranges against the riverine geography of the Amazon watershed to produce a similarity index for opposite riverbank communities. Finally, we ran models to test how measures of river size predicted levels of similarity. We found that, almost without exception, similarity scores were lower than scores from Ayres and Clutton-Brock (1992) for the same rivers. Our model showed a significant negative relationship between streamflow and similarity in all tests, and found river width significant for the segmented Amazon, but not for multiple Amazon watershed rivers. Our results support the RBH insofar as they provide evidence for the prediction that rivers with higher streamflow act as more substantial barriers to dispersal, and accordingly exhibit greater variation in community composition between riverbanks.

Dwarf geckos and giant rivers: the role of the São Francisco River in the evolution of Lygodactylus klugei (Squamata: Gekkonidae) in the semi-arid Caatinga of north-eastern Brazil

Species diversification can be strongly influenced by geomorphological features, such as mountains, valleys and rivers. Rivers can act as hard or soft barriers to gene flow depending on their size, speed of flow, historical dynamics and regional topographical characteristics. The São Francisco River (SFR) is the largest perennial river in the Caatinga biome in north-eastern Brazil and has been considered a barrier to gene flow and dispersal. Herein, we evaluated the role of the SFR on the evolution of Lygodactylus klugei, a small gecko from the Caatinga. Using a single-locus species delimitation method (generalized mixed Yule coalescent), we defined lineages (haploclades). Subsequently, we evaluated the role of the SFR in structuring genetic diversity in this species using a multilocus approach to quantify migration across margins. We also evaluated genetic structure based on nuclear markers, testing the number of populations found through an assignment test (STRUCTURE) across the species distribution. We recovered two mitochondrial lineages structured with respect to the SFR, but only a single population was inferred from nuclear markers. Given that we detected an influence of the SFR only on mitochondrial markers, we suggest that the current river course has acted as a relatively recent geographical barrier for L. klugei, for ~450 000 years.

Species diversity of Marmosa subgenus Micoureus (Didelphimorphia, Didelphidae) and taxonomic evaluation of the white-bellied woolly mouse opossum, Marmosa constantiae

Marmosa subgenus Micoureus contains six currently recognized species, distributed from southern Belize to northern Argentina. Although recent studies have demonstrated the monophyly of the subgenus, the species have not been recently revised. Except for M. phaea, we evaluated the species diversity in this subgenus of mouse opossums using integrated morphological, morphometric and molecular data, with emphasis on M. constantiae. We used a total of 700 specimens for morphological and morphometric analyses. For phylogenetic, species delimitation, molecular variance and population structuring analyses (the latter two only for M. constantiae), we used the mitochondrial cytochrome b gene. Morphometric variation patterns were evaluated through Principal Component Analysis and Discriminant Function Analysis. Our results indicate that there are seven species in our samples. Among the species analysed morphologically, some can be discriminated by craniodental measurements and all can be discriminated through morphology. Marmosa constantiae is polyphyletic, composed of two lineages, one of which is correctly named M. budini. Marmosa constantiae (s.s.) has a well-known genetic structure, with no clear geographic structure and no consistent morphological patterns. Several records of M. demerarae in the literature correspond to M. constantiae. Marmosa demerarae may thus represent a complex formed of at least two species.

The role of Pleistocene climate change in the genetic variability, distribution and demography of Proechimys cuvieri and P. guyannensis (Rodentia: Echimyidae) in northeastern Amazonia

The spiny rats, genus Proechimys, have the highest species richness within the Echimyidae family, as well as species with high genetic variability. The genus distribution includes tropical South America and Central America south to Honduras. In this study, we evaluate the phylogeographic histories of Proechimys guyannensis and P. cuvieri using cytochrome b, in a densely sampled area in northeastern Amazon where both species are found in sympatry in different environments. For each species, Bayesian and Maximum Likelihood phylogenetic analysis were congruent and recovered similar clades in the studied area. Bayesian phylogenetic analysis using a relaxed molecular clock showed that these clusters of haplotypes diversified during Pleistocene for both species. Apparently, the large rivers of the region did not act as barriers, as some clades include specimens collected from opposite banks of Oiapoque, Araguari and Jari rivers. Bayesian skyline plot analysis showed recent demographic expansion in both species. The Pleistocene climatic changes in concert with the geologic changes in the Amazon fan probably acted as drivers in the diversification that we detected in these two spiny rats. Proechimys cuvieri and P. guyannensis show genetic structure in the eastern part of the Guiana region. Greater genetic distances observed in P. guyannensis, associated with highly structured groups, suggest that more detailed studies of systematics and ecology should be directed to this species.

Genetic variability of populations of the white-eared opossum, Didelphis albiventris Lund 1840 (Didelphimorphia; Didelphidae) in Brazil

Didelphis albiventris are found throughout Northeast and Central Brazil to central-southern Uruguay and it was subject of few studies in a population level. Given this, the present study investigated the genetic variability of the species using the mitochondrial molecular marker cytochrome oxidase c subunit I. We analyzed samples from the different biomes within three Brazilian regions: Northeast (Caatinga , Cerrado, and Atlantic Forest), Southeast (Cerrado , Atlantic Forest, Cerrado/Atlantic Forest, and Cerrado/Caatinga ecotones) and South (Pampa and Atlantic Forest). Software BAPs retrieved five distinct demes: dm 1, dm 2, and dm 5 that occurs in South, Northeast and Southeast regions respectively and the dm 3 and dm 4 are wide distributed in Northeast and Southeast. Population analysis performed with AMOVA, haplotype network and Mantel test estimated the veracity of the demes. The FST shows structuring for the five demes, with dm 1 (South region) isolated from the others, however the other analysis showed the Northeast/Southeast demes (dm 2-5) united, diagnosing gene flow between them, mainly at the transitional zones, in areas as far away as areas with similar latitude interval (Southeast vs South) that was not detected gene flow. In the haplotype network, the mutational steps was conclusive in split dm1 from dm 2-5 with 15 mutational steps and the Mantel test was moderated, which is explained by genetic similarity despite the great geographic distances (Northeast/Southeast). Thus, our analysis recognized two different lineages (South and Northeast/Southeast) and indicate that the biomes were not decisive in their isolation. The sharing of demes at the transitional zones and in areas with high latitudinal intervals reflects a recent ancestral polymorphism for D. albiventris. The plasticity in the occupation of the space by this species contributes in its wide dispersion capability, that is, geographical distribution. Our results revealed important implications for the management of D. albiventris in these transitional zones areas where demes were shared.