Biology subjects

Alda, F.

Publications and source records attributed to Alda, F..

5 recordsLinked to original sources

bioRxiv2026

Diversifying the Northern Neotropics: Phylogenomics and Evolutionary History of the Early-Diverging Herichthyine Cichlids Thorichthys and Trichromis

Among Neotropical cichlids the tribe Heroini exhibits substantial ecological diversity and is one of the dominant fish groups across northern Neotropical riverscapes. The majority of studies on heroine cichlids have focused on macroevolutionary patterns but the role of geological and ecological factors shaping lineage diversification within the tribe remains poorly understood. Here we used ultraconserved elements (UCEs) to infer a taxonomically complete and geographically comprehensive phylogenomic framework of the early-diverging herichthyine sister genera Thorichthys and Trichromis and to comparatively investigate their evolutionary and biogeographic histories. All our phylogenomic hypotheses support the monophyly of both genera and two species subgroups within Thorichthys. Our results provide evidence of a) unrecognized diversity within Trichromis salvini, b) uncertainty in species boundaries in Thorichthys, and c) the first report of ghost introgression in fishes of the northern Neotropics. Additionally, our results demonstrate the importance of the Papaloapan and Coatzacoalcos watersheds for fish diversification in the region. Finally, we show patterns consistent with ecological divergence during the evolution of this group, particularly among sympatric species. Altogether, these patterns suggest that lineage diversification in northern Neotropical cichlids has been driven by the interaction of geological restructuring, climatic and sea-level oscillations, and heterogeneous ecological pressures.

evolutionary biology↗

bioRxiv2024

Geography is a stronger predictor of diversification of monogenean parasites (Platyhelminthes) than host relatedness in characid fishes of Middle America

Host-parasite associations have historically been considered compelling examples of coevolution and useful in examining cospeciation. However, modern molecular methods have revealed more complex dynamics than previously assumed, with host-switching events appearing commonly across taxa and challenging traditional views of strict coevolution in host-parasite relationships. Monogenean parasites are considered highly host-specific and have long served as models for probing evolution of host-parasite associations, particularly in differentiating geographic and phylogenetic patterns of parasite diversification. We investigated the phylogeographic patterns of monogenean ectoparasites associated with four species of characid fishes across Panama, Nicaragua, and Mexico. Our hypothesis posited that parasite diversity and community structure would be more strongly correlated with host species (suggesting cospeciation) than with geographic location (indicative of allopatric speciation). We found high genetic differentiation among parasites and their hosts across different locations. However, while geography explained the genetic structure of both host fishes and parasites, the observed patterns were neither congruent nor parallel. Parasite community structure and genetic similarity were consistently better explained by geographic location than by host species, although both factors played a significant role. Contrary to our predictions, we found no evidence of cospeciation. Instead, the diversification of these monogenean parasites appears to be primarily driven by their ability to switch hosts. At this taxonomical scale, host-switching is mediated by the geographical proximity of potential hosts, underscoring the importance of spatial factors in parasite evolution.

evolutionary biology↗

bioRxiv2024

Complete mitochondrial genomes of riverine Lamprologus (Actinopterygii, Cichlidae) with an emphasis on the blind cichlid L. lethops

Lamprologine cichlids are a diverse group of fishes distributed in Lake Tanganyika and the Congo River. Nine species of Lamprologus occur in the Congo River basin including the only blind cichlid Lamprologus lethops, but little is known about the natural history and evolution of this enigmatic species. To alleviate this knowledge gap, we characterized the complete mitochondrial genomes of L. lethops and its riverine congeners and provided a phylogenetic hypothesis based on these data. We recovered complete mitochondrial genomes from eleven specimens of eight species of Lamprologus. Mitogenomes were identical in the number and order of genes and similar in size (16,579-16,587 bp). In contrast to previous phylogenomic studies, riverine Lamprologus were recovered in two non-sister mitochondrial lineages that were more closely related to other genera of Lake Tanganyika lamprologines than to each other. In the first lineage, most relationships were not highly supported. In the second lineage, L. lethops was recovered as the sister species of L. markerti, L. mocquardi and L. tigripictilis. Interestingly, sequences from L. mocquardi were found in the two mitochondrial lineages. Our results hint at multiple events of past introgression and highlight the importance of increasing taxonomic and genomic sampling to study complex evolutionary histories.

evolutionary biology↗

bioRxiv2022

Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 and colonization patterns of Middle America

Hyphessobrycon is one of the most species rich and widely distributed genera in the family Characidae, with more than 160 species ranging from Veracruz, Mexico to Argentina. The majority of the diversity of Hyphessobrycon shows a cis-Andean distribution; only nine species are trans-Andean including H. compressus (Meek 1908). It is well established that Hyphessobrycon is not monophyletic but has been suggested that natural groups can be identified within the larger Hyphessobrycon species group. In this study, we test the monophyly of trans-Andean species of Hyphessobrycon and investigate the placement of H. compressus. We have inferred the first phylogenomic hypothesis of trans-Andean Hyphessobrycon that includes nearly complete taxonomic sampling (eight of nine valid species) using ultraconserved elements (UCEs). We analyzed 75% (1682 UCEs), 90% (1258 UCEs), and 95% (838 UCEs) complete data matrices, and inferred phylogenomic hypotheses under concatenation and coalescent approaches. In all cases, we recovered the monophyly of trans-Andean Hyphessobrycon inclusive of H. compressus, and strong support for three species groups and evidence of cryptic diversity within the widespread H. compressus and H. condotensis. We used our phylogenomic hypothesis to investigate the biogeographic history of Hyphessobrycon in Middle America. Our ancestral range estimation analysis suggests a single event of cis- to trans-Andean colonization followed by stepwise colonization from the Pacific slope of northwestern South America (Choco block) to northern Middle America (Maya block). Our work supports the recognition of the trans-Andean species as Hyphessobrycon sensu stricto and provides a robust evolutionary template to examine morphological characters that will allow us to better understand the diversity of Hyphessobrycon in Middle America.

evolutionary biology↗

bioRxiv2018

A target enrichment bait set for studying relationships among ostariophysan fishes

O_LITarget enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (>1000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian superorder.\nC_LIO_LIIn this manuscript, we describe how we designed a bait set to enrich 2,708 ultraconserved nuclear loci from ostariophysan fishes by combining an existing genome assembly with low coverage sequence data collected from two ostariophysan lineages.\nC_LIO_LIWe perform a series of enrichment experiments using this bait set across the ostariophysan Tree of Life, from the deepest splits among the major groups (>150 MYA) to more recent divergence events that have occured during the last 50 million years.\nC_LIO_LIOur results demonstrate that the bait set we designed is useful for addressing phylogenetic questions from the origin of crown ostariophysans to more recent divergence events, and our in silico results suggest that this bait set may be useful for addressing evolutionary questions in closely related groups of fishes, like Clupeiformes.\nC_LI

evolutionary biology↗