Biology subjects

Arroyave, J.

Publications and source records attributed to Arroyave, J..

4 recordsLinked to original sources

bioRxiv2026

African origin and Late Cretaceous divergence of the Middle American catfish Lacantunia enigmatica corroborated by a global mitogenome phylogeny

Two decades ago, the new siluriform family Lacantuniidae was erected to accommodate its sole known extant representative, Lacantunia enigmatica, a morphologically aberrant catfish restricted to the Middle Usumacinta River basin along the Guatemala-Mexico border. While its discovery was unexpected, its proposed phylogenetic placement--nested within a large clade of exclusively African-endemic families rather than closely related to regionally sympatric North American or Neotropical lineages--was baffling. To test this counterintuitive phylogenetic and biogeographic hypothesis, we collected new specimens of L. enigmatica and sequenced, assembled, and annotated for the first time its complete mitochondrial genome. We then constructed the most taxonomically comprehensive mitochondrial data matrix of catfishes to date by including published mitochondrial genomes representing the majority of siluriform families. Using Bayesian co-estimation of phylogeny and divergence times, we inferred the evolutionary position of the puzzling L. enigmatica within a time-scaled global catfish phylogeny. Our results offer improved resolution and understanding of higher-level siluriform relationships and refine the timescale of catfish evolution. Crucially, our findings corroborate the hypothesis that L. enigmatica is sister to the African family Claroteidae and represents a relict lineage that originated in Africa during the Late Cretaceous (74.99 Ma; 95% HPD=68.58-81.39) and eventually culminated in Middle America. Our results therefore uphold the necessity of transoceanic dispersal--as opposed to Gondwanan vicariance--to explain this otherwise puzzling biogeographic pattern.

evolutionary biology↗

bioRxiv2025

Parallel and non-parallel features of adaptive radiation in Yucatan pupfishes

Understanding the extent of parallelism across adaptive radiations remains a central problem in evolutionary biology. We used whole-genome resequencing of 123 individuals to compare the adaptive radiation of Cyprinodon pupfishes in Lake Chichancanab, Mexico, to an independent radiation of San Salvador Island (SSI) pupfishes in the Bahamas, and assess the repeatability of adaptive genetic architecture, sources of adaptive variation, and stages of selection. Despite rapid craniofacial divergence of trophic specialists within 8-15 kya, only two candidate genes (0.5%; 2/426) were shared between Caribbean radiations. Although adaptive introgression played a major role in SSI, we found minimal evidence of adaptive introgression in Chichancanab, likely due to the geographic isolation of this inland lake. Instead, de novo mutations provided a substantial source of adaptive variation (30.6%) for the endemic zooplanktivore, 15 times higher than the endemic scale-eater on SSI. However, in parallel with SSI, we found strong evidence that adaptive divergence occurred in stages, first on regulatory and standing genetic variation, then on de novo and nonsynonymous mutations. Consistent with adaptive variants near opsin and spermatogenesis genes, functional categories unique to Chichancanab, we found greater visual acuity and divergent sperm morphology in lab-reared zooplanktivores relative to generalists using laboratory assays. Consistent with extensive adaptive de novo mutations in WNT10A and rapid diversification of tooth size in the zooplanktivore, we found that experimental inhibition of the Wnt pathway in generalists resulted in narrower oral teeth. We conclude that de novo mutations, not introgression, can drive rapid adaptive radiations in isolated environments.

evolutionary biology↗

bioRxiv2025

Adaptive radiation along ecological and morphological lines of least resistance in Cyprinodon pupfishes

Adaptive radiation results in part from ecological opportunity in a new environment, but it is unclear how pre-existing constraints in the founding population may limit this process. Genetic lines of least resistance, and by proxy morphological variance, are known to limit adaptive divergence, but ecological variance is rarely investigated. Here we test whether ecological or morphological lines of least resistance in generalist populations may have constrained the directions of species divergence in two independent Caribbean adaptive radiations of Cyprinodon pupfishes. We find almost universal congruence between the major multivariate dimensions of intraspecific craniofacial and dietary variance within generalist populations and the major axes of interspecific divergence within each adaptive radiation. This is surprising given that we document unique trophic specialists within each radiation, including a bivalve-specialist, zooplanktivore, molluscivore/ostracod-specialist, and scale-eating specialist, while nearly all generalist populations were observed to feed rarely on these same resources. We conclude that pre-existing genetic constraints within each founding generalist population, resulting in dimensions of greater ecological and morphological variance, may partially constrain and predict the directions of species divergence and dietary specialization during adaptive radiation. We also provide a new framework for examining ecological lines of least resistance.

evolutionary biology↗

bioRxiv2023

Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments

Gene loss is an important mechanism for evolution in low-light or cave environments where visual adaptations often involve a reduction or loss of eyesight. The plaat gene family are phospholipases essential for the degradation of organelles in the lens of the eye. They translocate to damaged organelle membranes, inducing them to rupture. This rupture is required for lens transparency and is essential for developing a functioning eye. Plaat3 is thought to be responsible for this role in mammals, while plaat1 is thought to be responsible in other vertebrates. We used a macroevolutionary approach and comparative genomics to examine the origin, loss, synteny, and selection of plaat1 across bony fishes and tetrapods. We show that plaat1 (likely ancestral to all bony fish + tetrapods) has been lost in squamates and is significantly degraded in lineages of low-visual acuity and blind mammals and fish. Our findings suggest that plaat1 is important for visual acuity across bony vertebrates, and that its loss through relaxed selection and pseudogenization may have played a role in the repeated evolution of visual systems in low-light-environments. Our study sheds light on the importance of gene-loss in trait evolution and provides insights into the mechanisms underlying visual acuity in low-light environments.

evolutionary biology↗