Biology subjects

Santaquiteria, A.

Publications and source records attributed to Santaquiteria, A..

6 recordsLinked to original sources

bioRxiv2026

A single freshwater invasion gave rise to the world's dominant freshwater fish group

The ultraspeciose clade Otophysa - catfishes, carps, minnows, tetras, and their kin - accounts for most vertebrate diversity in modern freshwater ecosystems. However, a controversial assemblage of largely-fragmentary marine fossils has led some authors, most recently Liu et al., to advocate parallel freshwater invasions for this otherwise inland lineage. Here, we test this hypothesis under multiple sources of uncertainty. We provide the first phylogenetic analysis of the recently-named marine fossil genus Sooinichthys, resolving it as sister to all modern otophysans. We also find that Santanichthys, long treated as an early marine otophysan, lacks a Weberian apparatus and plausibly belongs outside Ostariophysi entirely. When increasing the taxon and marker sampling of Liu et al.'s genomic dataset, standardizing their ecological coding, accounting for alternative interpretations of important morphological characters, and applying a suite of biogeographic models, we find a marine origin in only 6 of 132 analyses, and only when enforcing fossil placements inconsistent with our own phylogenetic results. We contend that the parallel freshwater invasion hypothesis of otophysan diversification is an artifact of sparse taxon sampling, taphonomic biases, model selection errors, and fossil overinterpretation. The result is a cautionary case for inferences about the cradle of any ancient freshwater clade.

evolutionary biology↗

bioRxiv2026

Convergent evolution of extreme snout elongation in deep-sea fishes reveals constrained trajectories

Phenotypic extremes are scattered across the Tree of Life, suggesting that evolutionary constraints often limit their emergence. Yet striking departures from standard body plans, such as elongate snouts, have evolved convergently across deep time. We investigate extreme morphologies in two distantly related deep-sea fish clades: spikefishes (pufferfish relatives) and snipefishes (seahorse relatives). Using spikefishes as a study system, including all 24 living and fossil species, we integrated genome-wide phylogenomic data with a fossil and extant morphological character matrix, skull shape and dentition analyses from 64 CT scans, phenotypic and divergence matrices from >200 X-rays, functional manipulations of freshly collected and cleared-and-stained specimens, and formal convergence test across 300 percomorph species. We show that snout elongation evolved independently twice within spikefishes, reaching intermediate and extreme conditions along one predictable, ordered trajectory of additive skeletal rearrangements. Snout bones form a highly integrated, semi-autonomous module that channels evolutionary change along intrinsic lines of least resistance, coinciding with accelerated cranial evolution and expanded morphospaces in a clade with enhanced cranial mobility. Snipefishes converge on the same body plan through largely non-homologous elements and distinct linkage mechanics, except for near-identical vomer convergence. Extreme morphologies can emerge when phenotypic integration aligns with functional innovation, guiding evolution along repeatable trajectories.

evolutionary biology↗

bioRxiv2026

Ecological axes of skull diversification in a massive 1 vertebrate radiation

Eupercarian spiny-rayed fishes are one of the largest vertebrate radiations, rivaling mammals and occupying nearly every aquatic habitat. We present a densely sampled, time-calibrated phylogenomic framework for Eupercaria, supporting a revised classification, combined with the largest cranial phenomics dataset for fishes. Habitat and trophic ecology make independent, complementary contributions to skull shape. Most species cluster around a conserved generalized architecture, the Percomorph Pile, from which one clade of pufferfishes, anglerfishes, butterflyfishes, and surgeonfishes repeatedly invaded novel morphospace; exceptionally high rates on its deep branches indicate that rapid skull evolution arose early in this clade. Freshwater lineages converge on the ancestral condition, reflecting late arrival into systems occupied by older otophysans, whereas durophages show the greatest disparity and converge on derived forms. Cranial diversity was partitioned among subclades during the Cretaceous and later within them across the Cenozoic, showing that clade-level differences in evolutionary rates and ecological opportunity jointly shaped skull diversification.

evolutionary biology↗

bioRxiv2026

REPEATED MARINE-TO-FRESHWATER FISH TRANSITIONS REVEAL PALEOENVIRONMENTAL MODULATION OF ADAPTIVE RADIATION

Tropical rivers in Australia and New Guinea (Sahul) provide a rare natural experiment in vertebrate evolution: unlike other continental systems, their freshwater ichthyofaunas are composed almost entirely of marine-derived lineages rather than primary freshwater fishes. This unique biogeographic setting enables replicated tests of why some marine-to-freshwater transitions give rise to extensive adaptive radiations whereas others remain species-poor, and whether these outcomes reflect ecological opportunity or temporally structured paleoenvironmental constraints. Using a densely sampled, time-calibrated phylogenomic framework spanning 2,303 teleost species, we identified a likely range of 27-34 marine-to-freshwater transitions during the Cenozoic, including a pronounced Middle Miocene peak (16-11 Ma). Although ecological opportunity in Sahul rivers enabled repeated colonization in the absence of dominant primary freshwater incumbents, younger freshwater lineages nevertheless diversify faster than older ones, contradicting the expectation that early arrivers should undergo elevated diversification when accessing vacant niche space. Although some colonizations coincide with bursts of speciation consistent with adaptive radiation, many yielded few species despite long residence times. Functional trait analyses likewise revealed no consistent relationship between colonization timing, ecological breadth, or diversification rate, although expanded functional space characterizes previously proposed Sahul adaptive radiations. Comparisons with paleoenvironmental curves indicate that colonization success correlates with sea-level minima and low-oxygen conditions, suggesting that Earth history dynamics modulated when ecological opportunity was accessible. Our results show that although ecological opportunity enabled repeated freshwater invasions into the Sahul region, diversification outcomes are governed by the interaction of paleoenvironmental dynamics and possibly lineage-specific traits, generating stark asymmetries in freshwater radiations. Significance statementTropical rivers in Australia and New Guinea host one of the most unusual continental freshwater fish assemblages on Earth, composed almost entirely of marine-derived lineages. This system allows asking why some colonizing lineages diversify dramatically while others remain species-poor on a continental scale. Using large-scale phylogenomic and functional trait data, we show that early arrival alone does not predict diversification success. Instead, the lineages that radiate most successfully are those whose arrival coincides with windows of paleoenvironmental opportunity created by sea-level and oxygen fluctuations. These results reveal that the fates of colonizing lineages are shaped not only by ecological opportunity, but also by Earth-history dynamics that govern when, where, and how species can invade and diversify.

evolutionary biology↗

bioRxiv2023

Phylogenomics reveals the deep ocean as an accelerator for evolutionary diversification in anglerfishes

Colonization of a novel habitat is often followed by radiation in the wake of ecological opportunity. Alternatively, some habitats should be inherently more constraining than others if the challenges of that environment have few evolutionary solutions. We examined the push-and-pull of these factors on evolution following habitat transitions, using anglerfishes (Lophiiformes) as a model. Deep-sea fishes are notoriously difficult to study, and poor sampling has limited progress thus far. Here we present a new phylogeny of anglerfishes with unprecedented taxonomic sampling (1,092 loci and 40% of species), combined with three-dimensional phenotypic data from museum specimens obtained with micro-CT scanning. We use these datasets to examine the tempo and mode of phenotypic and lineage diversification using phylogenetic comparative methods, comparing lineages in shallow and deep benthic versus bathypelagic habitats. Our results show that anglerfishes represent a surprising case where the bathypelagic lineage has greater taxonomic and phenotypic diversity than coastal benthic relatives. This defies expectations based on ecological principles since the bathypelagic zone is the most homogeneous habitat on Earth. Deep-sea anglerfishes experienced rapid lineage diversification concomitant with colonization of the bathypelagic zone from a continental slope ancestor. They display the highest body, skull and jaw shape disparity across lophiiforms. In contrast, reef-associated taxa show strong constraints on shape and low evolutionary rates, contradicting patterns suggested by other shallow marine fishes. We found that Lophiiformes as a whole evolved under an early burst model with subclades occupying distinct body shapes. We further discuss to what extent the bathypelagic clade is a secondary adaptive radiation, or if its diversity can be explained by non-adaptive processes.

evolutionary biology↗

bioRxiv2023

Non-linear phylogenetic regression using regularized kernels

O_LIPhylogenetic regression is a type of Generalized Least Squares (GLS) method that incorporates a covariance matrix based on the evolutionary relationships between species (i.e., phylogenetic relationships). While this method has found widespread use in hypothesis testing via comparative phylogenetic methods, such as phylogenetic ANOVA, its ability to account for non-linear relationships has received little attention. C_LIO_LITo address this issue, we utilized GLS in a high-dimensional feature space, employing linear combinations of transformed data to account for non-linearity, a common approach in kernel regression. We analyzed two biological datasets using both Radial Basis Function (RBF) and linear kernel transformations. The first dataset contained morphometric data, while the second dataset comprised discrete trait data and diversification rates as labels. Hyperparameter tuning of the model was achieved through cross-validation rounds in the training set. C_LIO_LIIn the tested biological datasets, regularized kernels reduced the error rate (as measured by RMSE) by around 20% compared to linear-based regression when data did not exhibit linear relationships. In simulated datasets, the error rate decreased almost exponentially with the level of non-linearity. C_LIO_LIThese results show that introducing kernels into phylogenetic regression analysis presents a novel and promising tool for complementing phylogenetic comparative methods. We have integrated this method into Python package named phyloKRR, which is freely available at: https://github.com/Ulises-Rosas/phylokrr. C_LI

evolutionary biology↗