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Species discovery methods utilizing coalescent-based approaches are powerful tools for detecting cryptic lineages within morphological conservative groups, thus being an important methodology of in...

River capture is a geological process of potentially great importance in shaping the genetic diversity, distributions, and community composition of freshwater taxa. Using phylogeographic analyses of ddRAD-seq data from suckermouth armored catfish (Hypostomussp. 2) populations, we tested for predicted genetic effects of headwater river capture events in central Brazil, previously supported by geological and community ecological data. We analyzed 227 ddRAD tags (3829 SNP loci) across 42 samples. Molecular results strongly supported sixHypostomusgenetic clusters/lineages, with the deepest divergence ∼1.25 million years ago in the early Pleistocene between a clade from the Upper Paraná and Upper São Francisco river basins versus all other lineages. Consistent with the ‘Paraná Capture Hypothesis’, several lines of evidence supported mid-Pleistocene colonization and vicariant isolation ofHypostomuspopulations from an ancestral Upper Paraná population, including: (1) significant phylogeographic structure, with predicted phylogenetic patterns, (2) higher Paraná lineage diversity, (3) ancestral geographic locations reconstructed in the Paraná basin, and (4) non-random interdrainage dispersal and vicariance events, indicating river captures primarily into the Tocantins and Upper São Francisco basinsc.∼220,000–145,500 years ago. Phylogeographic inference was complicated by lack of lineage monophyly across loci and lineages distributed in multiple basins, the latter of which lent support to the non-mutually exclusive ‘Frequent Interdrainage Dispersal Hypothesis’. However, species tree and demographic modeling results suggested these were artefacts of incomplete sorting of alleles in large ancestral populations over a geologically recent timeframe of divergence. Qualitative and quantitative sensitivity analyses demonstrated that our downstream genetic results were robust to effects of varying ddRAD-seq assembly parameters, which heavily influenced the number of output loci. We predict that codistributed freshwater taxa in Central Brazil may not exhibit phylogeographic patterns similar toHypostomussp. 2 due to complex patterns of superimposed river capture events, or if smaller ancestral population sizes have allowed more complete lineage sorting in other taxa.

Biogeography is an area of study dedicated to understanding the evolutionary processes that resulted in current organismal distribution patterns. In general, exclusively terrestrial and exclusively aquatic vertebrates have well-studied and defined biogeographic patterns in the New World, but the biogeography of semiaquatic organisms is still poorly understood. In this chapter we discuss the biogeographic patterns and processes of New-World crocodylians. Although dispersal was probably an important process for the diversification of the ancestors of this group, the species/lineages—especially those of the South Americans—have their geographic distributions delimited by natural geographical barriers such as watershed divides, waterfalls and rapids, and captured watersheds, but also ecological specialization and competitive exclusions. The species/lineages occupying these areas show nearly identical divergence times, pointing to common historical processes that drove the evolution and divergence of these species/lineages. Recent studies have shown that widely distributed species have diversified into a significant number of independent evolutionary lineages. Knowing the biogeographic patterns of this group is of fundamental importance for conservation, since in the Anthropocene the effects of changes caused by man are devastating, destroying in a short period of time what nature took thousands/millions of years to build.

We developed forensic nuclear SNPs for the side-necked turtle, Phrynops geoffroanus, using next-generation sequencing-based genotyping. We created a reduced-representation library for 23 individuals representing four previously identified lineages of P. geoffroanus using the ddRAD methodology for sequencing on the IonTorrent PGM. We analyzed the sequence data using the Stacks pipeline. We found 811 loci containing 1380 private SNPs. Of these, 473 were fixed in lineages 1, 2 and 3, or with frequency >0.91 in lineage 4. Seventy-three SNPs could be useful for forensics purpose (assignment of individuals to lineage of origin) using traditional PCR-based genotyping methods.

We isolated and characterized 10 new microsatellites loci for Paleosuchus trigonatus using ION TORRENT Sequencing Technology. We tested the transferability of these loci to three related species of the subfamily Caimaninae, and used these bi-parental markers to test population structure and genetic diversity of two populations of P. trigonatus impacted by hydroelectric dam construction on the Madeira (N = 16) and Xingu (N = 16) rivers. We also investigated the transferability of these markers to three related species: Paleosuchus palpebrosus (N = 5), Caiman crocodilus (N = 6) and Melanosuchus niger (N = 6). The genetic diversity of P. trigonatus was low in both the Madeira (He: 0.535 ± 0.148) and Xingu (He: 0.381 ± 0.222) populations, but the loci were sufficiently polymorphic to be used in system of mating and kinship studies in P. trigonatus. DAPC analysis with our set of microsatellites loci was able to separate the four species of Caimaninae studied and to detect a shallow genetic structure between Madeira and Xingu populations of P. trigonatus. AMOVA and STRUCTURE analyses using locprior model corroborate this shallow genetic structure. These novel molecular markers will be also useful in conservation genetics and phylogeographic studies of P. trigonatus, since they improve our ability to monitor the putative effects of dams on the loss of genetic diversity and allow us to investigate population dynamics and microevolutionary processes that occurred in the species.