Multilocus phylogeny and historical biogeography of Hypostomus shed light on the processes of fish diversification in La Plata Basin

Distribution history of the widespread Neotropical genus Hypostomus was studied to shed light on the processes that shaped species diversity. We inferred a calibrated phylogeny, ancestral habitat preference, ancestral areas distribution, and the history of dispersal and vicariance events of this genus. The phylogenetic and distribution analyses indicate that Hypostomus species inhabiting La Plata Basin do not form a monophyletic clade, suggesting that several unrelated ancestral species colonized this basin in the Miocene. Dispersal to other rivers of La Plata Basin started about 8 Mya, followed by habitat shifts and an increased rate of cladogenesis. Amazonian Hypostomus species colonized La Plata Basin several times in the Middle Miocene, probably via the Upper Paraná and the Paraguay rivers that acted as dispersal corridors. During the Miocene, La Plata Basin experienced marine incursions, and geomorphological and climatic changes that reconfigured its drainage pattern, driving dispersal and diversification of Hypostomus. The Miocene marine incursion was a strong barrier and its retraction triggered Hypostomus dispersal, increased speciation rate and ecological diversification. The timing of hydrogeological changes in La Plata Basin coincides well with Hypostomus cladogenetic events, indicating that the history of this basin has acted on the diversification of its biota.

Diversification of Neotropical Freshwater Fishes

Neotropical freshwater fishes (NFFs) constitute the most diverse continental vertebrate fauna on Earth, with more than 6,200 named species compressed into an aquatic footprint <0.5% of the total regional land-surface area and representing the greatest phenotypic disparity and functional diversity of any continental ichthyofauna. Data from the fossil record and time-calibrated molecular phylogenies indicate that most higher taxa (e.g., genera, families) diversified relatively continuously through the Cenozoic, across broad geographic ranges of the South American platform. Biodiversity data for most NFF clades support a model of continental radiation rather than adaptive radiation, in which speciation occurs mainly in allopatry, and speciation and adaptation are largely decoupled. These radiations occurred under the perennial influence of river capture and sea-level oscillations, which episodically fragmented and merged portions of adjacent river networks. The future of the NFF fauna into the Anthropocene is uncertain, facing numerous threats at local, regional, and continental scales.

Biogeographical Network Analysis of Cretaceous Terrestrial Tetrapods: A Phylogeny-Based Approach

Network methods are widely used to represent and analyze biogeography. It is difficult, however, to convert occurrence data of fossil vertebrates to a biogeographical network, as most species were known from a single locality. A new method for creating a biogeographical network that can incorporate phylogenetic information is proposed in this study, which increases the number of edges in the network of fossil vertebrates and enables the application of various network methods. Using ancestral state reconstruction via maximum parsimony, the method first estimates the biogeographical regions of all internal nodes of a given phylogeny using biogeographical information on the terminal taxa. Then, each internal node in the phylogenetic tree is converted to an edge in the biogeographical network that connects the region(s), if unambiguously estimated, of its two descendants. The new method was applied to phylogenetic trees generated by a birth-death model. Under all conditions tested, an average of $CDATA[$CDATA[$>$$70% of the internal nodes in phylogenetic trees were converted into edges. Three network indices-link density, average link weight, and endemism index (EI)-were evaluated for their usefulness in comparing different biogeographical networks. The EI reflects the rate of dispersal; the other indices reflect nonbiogeographical parameters, the number of taxa and regions, which highlights the importance of evaluating network indices before applying them to biogeographical studies. Multiple Cretaceous biogeographical networks were constructed from the phylogenies of five tetrapod taxa: terrestrial crocodyliforms, terrestrial turtles, nonavian dinosaurs, avians, and pterosaurs. The networks of avians and pterosaurs showed similar topologies and a strong correlation, and unexpectedly high endemism indices. These similarities were probably a result of shared taphonomic biases (i.e., the Lagerstätten effect) for volant taxa with fragile skeletons. The crocodyliform network was partitioned into the Gondwanan and Laurasian continents. The dinosaur network was partitioned into three groups of continents: 1) North America, Asia, and Australia; 2) Europe and Africa; and 3) India, Madagascar, and South America. When Early and Late Cretaceous dinosaurs were analyzed separately, the dinosaur networks were divided into 1) North America, Asia, and Australia; and 2) Europe, Africa, India, and South America for the Early Cretaceous and 1) North America, Asia, and Europe; and 2) India, Madagascar, and South America for the Late Cretaceous. This partitioning of dinosaur and crocodyliform networks corroborates the results of previous biogeographical studies and indicates that the method introduced here can retrieve biogeographical signals from a source phylogeny when sufficient data are available for most targeted biogeographical regions.

The changing course of the Amazon River in the Neogene: center stage for Neotropical diversification

ABSTRACT We review geological evidence on the origin of the modern transcontinental Amazon River, and the paleogeographic history of riverine connections among the principal sedimentary basins of northern South America through the Neogene. Data are reviewed from new geochronological datasets using radiogenic and stable isotopes, and from traditional geochronological methods, including sedimentology, structural mapping, sonic and seismic logging, and biostratigraphy. The modern Amazon River and the continental-scale Amazon drainage basin were assembled during the late Miocene and Pliocene, via some of the largest purported river capture events in Earth history. Andean sediments are first recorded in the Amazon Fan at about 10.1-9.4 Ma, with a large increase in sedimentation at about 4.5 Ma. The transcontinental Amazon River therefore formed over a period of about 4.9-5.6 million years, by means of several river capture events. The origins of the modern Amazon River are hypothesized to be linked with that of mega-wetland landscapes of tropical South America (e.g. várzeas, pantanals, seasonally flooded savannahs). Mega-wetlands have persisted over about 10% northern South America under different configurations for >15 million years. Although the paleogeographic reconstructions presented are simplistic and coarse-grained, they are offered to inspire the collection and analysis of new sedimentological and geochronological datasets.