Biology subjects

Arcila, D.

Publications and source records attributed to Arcila, D..

At least 19 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

Independent origins of fish endothermy converge on a developmental regulatory signature

Why independent origins of the same complex physiological trait repeatedly produce similar body forms and physiological changes remains central in evolutionary biology. Endothermy, the internal production and retention of metabolic heat, evolved at least four times in ray-finned fishes, providing natural replicates for convergent genomic signatures. We present a chromosome-scale analysis of three transitions (opah, tunas, and swordfish), including a new chromosome-level genome of the rare, charismatic Pacific oarfish, analyzed with 31 other teleost genomes. The strongest signal is regulatory: of 253,680 conserved noncoding elements, 577 are rate-accelerated in endothermic lineages, with 67 accelerated in all three, exceeding matched ectothermic controls and enriched near developmental transcription factors and Wnt-signaling genes (e.g., irx1a, irx5a, her9, and lmo1). These elements overlap zebrafish developmental enhancers more than expected by chance but are not tied to genes emphasized by expression or coding-selection studies of endothermic lineages, marking a regulatory layer distinct from that metabolic layer. This convergence is part of a broader mosaic: endothermic lineages also share transition-biased substitution and convergent duplication signatures, including excess tandem duplications and lineage-specific gene-family expansion, whereas chromosome organization and protein-coding sequence change little. Endothermic convergence therefore leaves its clearest signal in regulatory remodeling, alongside shifts in substitution bias and gene-family evolution.

evolutionary biology↗

bioRxiv2026

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all [~]70,000 extant vertebrate species1. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for [~]95% of vertebrate orders, along with additional lineages within those orders, totaling 816 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods2-4, alongside the growth of associated consortium initiatives and international collaborations5-9. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers a reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine. Talking pointsO_LIThe flagship paper of VGP Phase I C_LIO_LIThe highest quality collection of genomes within the eukaryotic domain of life C_LIO_LIEvolution of genome sequencing technology quality throughout VGP Phase I C_LIO_LIA driver project that has been a model for multiple large-scale, high-quality reference genome projects C_LIO_LIReleases all currently unpublished genomes in Phase I from scientific study embargoes C_LIO_LIMultiple biological discoveries across the vertebrate tree of life C_LI

genomics↗

bioRxiv2026

Macroevolutionary consequences of twin neck innovations in deep-sea dragonfishes

The origin of novel phenotypes can influence access to new ecological resources, which may have positive, neutral, or negative effects on subsequent phenotypic diversification. In this study, we tested the macroevolutionary consequences of a pair of putative functional innovations occurring in deep-sea fishes of the order Stomiiformes. Integrating phylogenetic comparative methods, micro-CT scans, and external body measurements, we recover a mosaic of diversification trends associated with these innovations. We found some evidence for elevated evolutionary rates in tooth morphology associated with the predatory dragonfishes, which possess a gap between their vertebral column and skull that exposes the notochord and enables neck-like flexibility. However, a second novelty building upon the first, a functional neck joint enabling extreme cranial kinesis, was linked to faster rates of skull evolution. Our results suggest that innovations that help shift ecological roles and overcome functional constraints related to those roles, like gape-limitation in prey depauperate habitats, may play an important role in promoting phenotypic diversification. This work builds on a growing body of evidence highlighting how the deep sea promotes phenotypic diversity, generating the extreme forms that are celebrated by scientists and the public alike.

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↗

bioRxiv2026

Global adaptation to climate change in the twilight zone revealed by shared signals of selection in mesopelagic lanternfishes

Rapid accumulation of greenhouse gases threatens humanity and global diversity. The oceans absorb 30% of anthropogenic carbon emissions annually, but adaptation to climate change by the biotic components of this sink are poorly understood. Lanternfishes (Myctophiformes) are the most abundant vertebrates on the planet by biomass and the dominant mesopelagic vertebrate consumers, thus crucial components of the global carbon cycle. However, it is unknown whether lanternfishes are adapting to global warming and ocean acidification (OA). We hypothesized that warming and OA would act as major shared selective forces across diverse oceanic environments and that disparate taxa would respond in parallel through shared genetic pathways. We used whole-genome sequencing to test this hypothesis by identifying shared signals of selection across lanternfishes from multiple sites in the Atlantic and Pacific spanning three genera (Benthosema glaciale, Triphoturus mexicanus, and Diaphus theta). Across all species we found evidence of expansion from a population bottleneck possibly corresponding to the last glacial maximum and effective population sizes of only 5 million, suggesting substantial reproductive skew and spatially restricted populations. We successfully identified 34 candidate genes experiencing strong shared selection pressure across all taxa in both oceans. 81% of these candidate genes were consistent with adaptations to warming and OA, including a heat-shock protein (HSP70) and genes related to skeletal development, calcium homeostasis, and biomineralization. 14 out of 34 candidate genes are also known from experimental climate change studies to be involved in the response to hypoxia, altered pH, and thermal stress. We found significant gene ontology enrichment within these candidates for otolith morphogenesis, a major component of OA adaptation in fishes. This study provides a new approach for studying climate change adaptation at a global scale and our results imply widespread shared adaptive responses of marine species to climate change.

evolutionary biology↗

bioRxiv2026

Whole-genome phylogenomics and synteny resolve a single origin of body-plan asymmetry in flatfishes

Flatfishes display the most dramatic asymmetric body plan in vertebrates, yet whether this rare innovation evolved once (flatfish monophyly, FM) or multiple times (flatfish polyphyly, FP) has remained contentious. A recent genome-wide study supported FP by placing Psettodes, the earliest-diverging flatfish lineage, among symmetric relatives within Carangaria, the clade that also includes billfishes, jacks, mahi-mahi, and barracudas. Subsequent work traced this to base-composition artifacts and inadequate substitution modeling. Here we revisit the question using whole-genome phylogenomic and synteny data from 17 carangarian species spanning flatfishes and carangarian relatives. We contribute three new chromosome-level assemblies, including the first for Psettodes. Nucleotide-based coalescent analyses (e.g., ROADIES, CASTER) yield strong support for FM, with Psettodes sister to all other flatfishes. Microsynteny analyses built from conserved gene-order blocks corroborate this result: topology tests, cluster-profile counts, and rearrangement-based trees favor FM over two competing FP topologies. Macrosynteny, based on chromosome-scale rearrangements, yields a more mixed signal, with support for FM depending on the metric and taxon-sampling scheme. We interpret this scale-dependent pattern in the context of the explosive post-Cretaceous radiation of Carangaria. The short intervals between speciation events that characterize rapid radiations appear to have left sufficient signal in fine-grained microsyntenic rearrangements, while chromosome-scale rearrangements were too rare to consistently resolve these closely spaced splits. When integrated with evidence from conserved developmental mechanisms active during metamorphosis, the stage at which flatfish asymmetry first emerges, and from the exceptionally complete fossil record, our multi-scale genomic evidence supports a single evolutionary origin of flatfish asymmetry.

evolutionary biology↗

bioRxiv2026

Phylogenomics, Biogeography, and a New Family-level Classification of Silversides, Rainbowfishes, and Allies (Teleostei: Atheriniformes)

The order Atheriniformes (silversides, rainbowfishes, and blue-eyes) is a globally distributed group of fishes with frequent evolutionary transitions between marine and freshwater ecosystems. However, understanding the tempo and mode of these transitions has been hampered by poor phylogenetic resolution and limited taxonomic sampling, particularly within the suborder Atherinoidei. We generated a phylogenomic dataset of 1,100 exon loci for 150 species to resolve interfamilial relationships and reconstruct the groups biogeographic history. We were also able to incorporate a large number of existing GenBank sequences, producing a phylogeny with 265 species sampled for at least some genetic data (67% of known species diversity). While the New World suborder Atherinopsidae is well-resolved, we found that the family Atherinidae is polyphyletic across all analyses. We propose a revised classification that restricts Atherinidae to the genus Atherina and recognizes Atherinomoridae and Craterocephalidae as separate families. Our biogeographic inferences using explicit geographic areas suggests more frequent marine-to-freshwater transitions than previously inferred with simplified binary (marine vs. freshwater) coding, and uncover habitat transitions where marine ancestors may have gone extinct. These results highlight how explicit geographic modeling can uncover marine ancestry erased by extinction, providing a robust phylogenetic framework for future evolutionary studies of Atheriniformes.

evolutionary biology↗

bioRxiv2026

Competition among freshwater clades explains cave colonization in blind cavefishes

evolutionary biology↗

bioRxiv2024

Ancient climate changes and relaxed selection shape cave colonisation in North American cavefishes

Extreme environments serve as natural laboratories for studying evolutionary processes, with caves offering replicated instances of independent colonisations. The timing, mode, and genetic underpinnings underlying cave-obligate organismal evolution remains enigmatic. We integrate phylogenomics, fossils, paleoclimatic modeling, and newly sequenced genomes to elucidate the evolutionary history and adaptive processes of cave colonisation in the study group, the North American Amblyopsidae fishes. Amblyopsid fishes present a unique system for investigating cave evolution, encompassing surface, facultative cave-dwelling, and cave-obligate (troglomorphic) species. Using 1,105 exon markers and total-evidence dating, we reconstructed a robust phylogeny that supports the nested position of eyed, facultative cave-dwelling species within blind cavefishes. We identified three independent cave colonisations, dated to the Early Miocene (18.5 Mya), Late Miocene (10.0 Mya), and Pliocene (3.0 Mya). Evolutionary model testing supported a climate-relict hypothesis, suggesting that global cooling trends since the Early-Middle Eocene may have influenced cave colonisation. Comparative genomic analyses of 487 candidate genes revealed both relaxed and intensified selection on troglomorphy-related loci. We found more loci under relaxed selection, supporting neutral mutation as a significant mechanism in cave-obligate evolution. Our findings provide empirical support for climate-driven cave colonisation and offer insights into the complex interplay of selective pressures in extreme environments.

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↗

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

Dissecting Factors Underlying Phylogenetic Uncertainty Using Machine Learning Models

Phylogenetic inference can be influenced by both underlying biological processes and methodological factors. While biological processes can be modeled, these models frequently make the assumption that methodological factors do not significantly influence the outcome of phylogenomic analyses. Depending on their severity, methodological factors can introduce inconsistency and uncertainty into the inference process. Although search protocols have been proposed to mitigate these issues, many solutions tend to treat factors independently or assume a linear relationship among them. In this study, we capitalize on the increasing size of phylogenetic datasets, using them to train machine learning models. This approach transcends the linearity assumption, accommodating complex non-linear relationships among features. We examined two phylogenomic datasets for teleost fishes: a newly generated dataset for protacanthopterygians (salmonids, galaxiids, marine smelts, and allies), and a reanalysis of a dataset for carangarians (flatfishes and allies). Upon testing five supervised machine learning models, we found that all outperformed the linear model (p < 0.05), with the deep neural network showing the best fit for both empirical datasets tested. Feature importance analyses indicated that influential factors were specific to individual datasets. The insights obtained have the potential to significantly enhance decision-making in phylogenetic analyses, assisting, for example, in the choice of suitable DNA sequence models and data transformation methods. This study can serve as a baseline for future endeavors aiming to capture non-linear interactions of features in phylogenomic datasets using machine learning and complement existing tools for phylogenetic analyses.

evolutionary biology↗

bioRxiv2023

Conservation of affinity rather than sequence underlies a dynamic evolution of the motif-mediated p53/MDM2 interaction in teleosts

The transcription factor and cell cycle regulator p53 is marked for degradation by the ubiquitin ligase MDM2. The interaction between these two proteins is mediated by a conserved binding motif in the disordered p53 transactivation domain (p53TAD) and the folded SWIB domain in MDM2. The conserved motif in p53TAD from zebrafish displays a 20-fold weaker interaction with MDM2, compared to the interaction in human and chicken. To investigate this apparent difference, we tracked the molecular evolution of the p53TAD/MDM2 interaction among ray- finned fishes (Actinopterygii), the largest vertebrate clade. Intriguingly, phylogenetic analyses, ancestral sequence reconstructions, and binding experiments showed that different loss-of- affinity changes in the canonical binding motif within p53TAD have occurred repeatedly and convergently in different fish lineages, resulting in relatively low extant affinities (KD = 0.5-5 M). However, for eleven different fish p53TAD/MDM2 interactions, non-conserved regions flanking the canonical motif increased the affinity 4 to 73-fold to be on par with the human interaction. Our findings suggest that compensating changes at conserved and non-conserved positions within the motif, as well as in flanking regions of low conservation, underlie a stabilizing selection of "functional affinity" in the p53TAD/MDM2 interaction. Such interplay complicates bioinformatic prediction of binding and call for experimental validation. Motif- mediated protein-protein interactions involving short binding motifs and folded interaction domains are very common across multicellular life. It is likely that evolution of affinity in motif- mediated interactions often involves an interplay between specific interactions made by conserved motif residues and non-specific interactions by non-conserved disordered regions.

molecular biology↗

bioRxiv2023

Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species--all traits associated with lower dispersal ability--were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated. LAY SUMMARY- What factors are common among bird species with cryptic diversity in Panama? What role do geography, ecology, phylogeographic history, and other factors play in generating bird diversity? - 19% of widely-sampled bird species form two or more distinct DNA barcode clades, suggesting widespread unrecognized diversity. - Traits associated with reduced dispersal ability, such as use of forest understory, high territoriality, low hand-wing index, and insectivory, were more common in taxa with cryptic diversity. Filogeografia comparada revela amplia diversidad criptica causada por la ecologia en las aves de Panama RESUMENEspecies extendidas frecuentemente tiene diversidad genetica no reconocida, y investigando los factores asociados con esta variacion criptica puede ayudarnos a entender las fuerzas que impulsan la diversificacion. Aqui, identificamos especies cripticas potenciales basadas en un conjunto de datos de codigos de barras de ADN mitocondrial de 2,333 individuos de aves de Panama en 429 especies, representando 391 (59%) de las 659 especies de aves terrestres residentes del pais, ademas de algunas aves acuaticas muestreada de manera oportunista. Adicionalmente, complementamos estos datos con secuencias mitocondriales disponibles publicamente de otros loci, tal como ND2 o citocroma b, obtenidos de los genomas mitocondriales completos de 20 taxones. Utilizando los numeros de identificacion de codigo de barras (en ingles: BINs), un sistema taxonomico numerico que proporcina una estimacion imparcial de la diversidad potencial a nivel de especie, encontramos especies cripticas putativas en 19% de las especies de aves terrestres, lo que destaca la diversidad oculta en la avifauna bien descrita de Panama. Aunque algunos de estos eventos de divergencia conciden con caracteristicas geograficas que probablemente aislaron las poblaciones, la mayoria (74%) de la divergencia en las tierras bajas se encuentra entre las poblaciones orientales y occidentales. El tiempo de esta divergencia no coincidio entre los taxones, sugiriendo que eventos historicos tales como la formacion del Istmo de Panama y los ciclos climaticos del pleistoceno, no fueron los principales impulsores de la especiacion. En cambio, observamos asociaciones fuertes entre las caracteristicas ecologicas y la divergencia mitocondriale: las especies del bosque, sotobosque, con una dieta insectivora, y con territorialidad fuerte mostraton multiple BINs probables. Adicionalmente, el indice mano-ala, que esta asociado a la capacidad de dispersion, fue significativamente menor en las especies con BINs multiples, sugiriendo que la capacidad de dispersion tiene un rol importamente en la generacion de la diversidad de las aves neotropicales. Estos resultos demonstran la necesidad de que estudios evolutivos de las comunidades de aves tropicales consideren los factores ecologicos en conjunto con las explicaciones geograficos. Palabras clave: biodiversidad tropical, biogeografia, codigos de barras, dispersion, especies cripticas

evolutionary biology↗

bioRxiv2020

Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how convergent diets obfuscate traditional morphological taxonomy.

The Amazon and neighboring South American river basins harbor the worlds most diverse assemblages of freshwater fishes. One of the most prominent South American fish families are the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial. For example, the sister taxon to serrasalmids is contentious, the relationships of major clades within the family are obfuscated by different methodologies, and half of the extant serrasalmid genera are suggested to be non-monophyletic. We used exon capture to explore the evolutionary relationships among 64 (of 99) species across all 16 serrasalmid genera and their nearest outgroups, including multiple individuals per species in order to account for cryptic lineages. To reconstruct the timeline of serrasalmid diversification, we time-calibrated this phylogeny using two different fossil-calibration schemes to account for uncertainty in taxonomy with respect to fossil teeth. Finally, we analyzed diet evolution across the family and comment on associated changes in dentition, highlighting the ecomorphological diversity within serrasalmids. We document widespread non-monophyly within Myleinae, as well as between Serrasalmus and Pristobrycon, and propose that reliance on traits like teeth to distinguish among genera is confounded by ecological convergence, especially among herbivorous and omnivorous taxa. We clarify the relationships among all serrasalmid genera, propose new subfamily affiliations, and support hemiodontids as the sister taxon to Serrasalmidae.

evolutionary biology↗