Biology subjects

Reinales, S.

Publications and source records attributed to Reinales, S..

3 recordsLinked to original sources

bioRxiv2026

Integrating lineage-specific and universal genomic probes illuminates phylogenetic relationships and molecular evolution in Sauvagesieae (Ochnaceae)

Obtaining large and well-resolved phylogenetic trees for neotropical clades is challenging, as many species inhabit remote regions, and sampling often relies on herbarium specimens with highly degraded DNA. Target capture provides an effective solution for retrieving molecular data from fragmentary material. However, data processing using tools generally designed for diploid organisms and single-copy loci is also challenging, particularly when events such as genome duplication and hybridisation have shaped the lineage evolution. We used dual-hybridisation to integrate Ochnaceae-specific and universal probes to reconstruct the phylogenetic relationships of Sauvagesieae, a pantropical clade with ca. 90 species mainly distributed in the northern Andes, the Brazilian Espinhaco Range, and the Amazon-Guyana region. We tested different filtering strategies involving missing data and paralogs to assess probable sources of tree discordance and topological uncertainty. We found no significant benefit in reducing tree discordance after removing entire genes due to the presence of paralogs or a high amount of missing data. Removing fragmentary sequences instead improved alignments and increased branch support of gene trees. By quantifying the proportion of SNPs, analysing the distribution of the allele frequencies, and gene-tree quartet frequencies, we found evidence of polyploidisation and hybridisation, which could reduce resolution at internal nodes, particularly in mountain clades. Our results underscore the importance of exploring the complexities of target-capture data, not only to improve phylogenetic resolution but also to understand the sources of phylogenetic conflict and the underlying molecular evolutionary processes.

genomics↗

bioRxiv2024

Fossil Freshwater Fishes from the Pliocene of northern Colombia and the Palaeogeography of northern South America

1Freshwater fishes from northern Colombia are reported from the Sincelejo and Ware formations, of Pliocene age. A total of ten taxa have been identified comprising two orders, five families, and nine genera. Characters from dental morphology, fin spines, and cranial bones are provided as taxonomic tools for the study of fossil fishes. All of the taxa are members of groups currently restricted to drainages east of the Andes, suggesting that physical drainage connection was still present by the Pliocene between the Amazon-Orinoco and trans-Andean drainages such as the Magdalena-Cauca, or that these groups persisted in the trans-Andean region at least until Pliocene times. The genera Hemidoras, Serrasalmus, and Trachely-opterichthys are new records for the fossil fish fauna of South America. The genus Zungaro represents a new record for the trans-Andean region, whereas the genus Platysilurus is for the first time in Colombia. Most of these occurrences also represent the youngest occurrences in the fossil record. Literature records are reidentified as Pygocentrus from the La Venta fauna and the earily Oligocene in Peru. These assemblages suggest that the Sincelejo and Ware formations were deposited in rivers of large size that were part of a large drainage network connected to the Amazon-Orinoco despite being currently located west of the Andes. These findings suggest that the Cordillera Oriental and the Merida Andes were not dividing yet the drainage network in northern South America by the middle to late Miocene.

paleontology↗

bioRxiv2024

tbea: tools for pre- and post-processing in Bayesian evolutionary analyses

Estimating phylogenies in which branch lengths are expressed in units of absolute time is crucial for testing hypotheses in evolutionary biology. However, bioinformatic tools to pre- and post-process data from Bayesian divergence time estimation analyses are often not easily interoperable, and documenting methodological choices is not a generalized practice. The R package tbea is a tool-set to integrate biological, geological and palaeontological information to optimize the specification of models, their parameters and prior distributions in divergence times estimation analyses. tbea implements statistical models to (i) better translate time information in dating sources into the specified calibration densities, (ii) improve comparisons between prior and posterior distributions for parameters of interest, (iii) carry out inference on origination times for a set of distributions, (iv) summarise different distributions into a single one, and (v) improve the reproducibility of divergence time estimation analyses allowing users to document methodological choices. We illustrate the package functionalities by carrying out two worked examples. One on the phylogenetic relationships and divergence time estimation of South American Cynodontidae, and another one on the separation time of drainages East and West of the Andes in South America. It is expected that the tools herein available will be key when estimating events in time from sets of point estimates, as well as the combination of different posterior densities from the same parameter are useful to justifying the selection of secondary calibration points, or discussing the timing of biogeographic events when multiple sources are available.

evolutionary biology↗