Biology subjects

Mongiardino Koch, N.

Publications and source records attributed to Mongiardino Koch, N..

9 recordsLinked to original sources

bioRxiv2025

But the clock, tick-tock: the preeminence of relaxed clock models in total-evidence dated phylogenetics

Phylogenetic clock models translate inferred amounts of evolutionary change (calculated from either genotypes or phenotypes) into estimates of elapsed time, providing a mechanism for time scaling phylogenetic trees. Relaxed clock models, which accommodate variation in evolutionary rates across branches, are one of the main components of Bayesian dating, yet their consequences for total-evidence phylogenetics have not been thoroughly explored. Here, we combine morphological, molecular (both transcriptomic and Sanger-sequenced), and stratigraphic datasets for all major lineages of echinoids (sea urchins, heart urchins, sand dollars). We then perform total-evidence dated inference under the fossilized birth-death prior, varying two analytical conditions: the choice between autocorrelated and uncorrelated relaxed clocks, which enforce (or not) evolutionary rate inheritance; and the ability to recover ancestor-descendant relationships. Our results show that the latter has no impact on either topology or node ages and highlight a previously unnoticed interaction between the tree and clock models, with analyses implementing an autocorrelated clock precluding the recovery of direct ancestry. On the other hand, tree topology, fossil placement, divergence times, and downstream macroevolutionary inferences (e.g., ancestral state reconstructions) in sea urchins are all strongly affected by the type of relaxed clock implemented. In regions of the tree where molecular rate variation is pervasive and morphological signal relatively uninformative, fossil tips seem to play little to no role in informing divergence times, and instead passively move in and out of clades depending on the ages imposed upon them by molecular data. Our results highlight the extent to which the phylogenetic and macroevolutionary conclusions of total-evidence dated analyses are contingent on the choice of relaxed clock model, highlighting the need for either careful methodological validation or a thorough assessment of sensitivity. Our efforts continue to illuminate the echinoid tree of life, supporting the erection of the order-level clade Apatopygoida to include three living species last sharing a common ancestor with other extant lineages in the Jurassic. Furthermore, they also illustrate how the phylogenetic placement of extinct clades hinges upon the modelling of molecular data, evidencing the extent to which the fossil record remains subservient to phylogenomics.

evolutionary biology↗

bioRxiv2024

Chronospaces: an R package for the statistical exploration of divergence times reveals extreme dependence on molecular clocks and gene choice

O_LIMuch of our understanding of the history of life hinges upon time calibration, the process of assigning absolute times to cladogenetic events. Bayesian approaches to time scaling phylogenetic trees have dramatically grown in complexity, and depend today upon numerous methodological choices. Arriving at objective justifications for all of these is difficult and time consuming. Thus, divergence times are routinely inferred under only one or a handful of parametric conditions, often times chosen arbitrarily. Progress towards building robust biological timescales necessitate the development of better methods to visualize and quantify the sensitivity of results to these decisions. C_LIO_LIHere, we present an R package that assists in this endeavor through the use of chronospaces, i.e., graphical representations summarizing variation in the node ages contained in time-calibrated trees. We further test this approach by estimating divergence times for three empirical datasets--spanning widely differing evolutionary timeframes--using the software PhyloBayes. C_LIO_LIOur results reveal large differences in the impact of many common methodological decisions, with the choice of clock (uncorrelated vs. autocorrelated) and loci having strong effects on inferred ages. Other decisions have comparatively minor consequences, including the use of the computationally intensive site-heterogeneous model CAT-GTR, whose effect might only be discernible for exceedingly old divergences (e.g., the deepest eukaryote nodes). C_LIO_LIThe package chronospace implements a range of graphical and analytical tools that assist in the exploration of sensitivity and the prioritization of computational resources in the inference of divergence times. C_LI

evolutionary biology↗

bioRxiv2022

Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea

Sea cucumbers (Holothuroidea) are a diverse clade of echinoderms found from intertidal waters to the bottom of the deepest trenches. Their reduced skeletons and limited number of phylogenetically-informative traits have long obfuscated morphological classifications. Sanger-sequenced molecular datasets have also failed to constrain the position of major lineages. Noteworthy, topological uncertainty has hindered a resolution for Neoholothuriida, a highly diverse clade of Permo-Triassic age. We perform the first phylogenomic analysis of Holothuroidea, combining existing datasets with twelve novel transcriptomes. Using a highly-curated dataset of 1,100 orthologues, our efforts recapitulate previous results, struggling to resolve interrelationships among neoholothuriid clades. Three approaches to phylogenetic reconstruction (concatenation under both site-homogeneous and site-heterogeneous models, and coalescent-aware inference) result in alternative resolutions, all of which are recovered with strong support, and across a range of datasets filtered for phylogenetic usefulness. We explore this intriguing result using gene-wise log-likelihood scores, and attempt to correlate these with a large set of gene properties. While presenting novel ways of exploring and visualizing support for alternative trees, we are unable to discover significant predictors of topological preference, and our efforts fail to favor one topology. Neoholothuriid genomes seem to retain an amalgam of signals derived from multiple phylogenetic histories.

evolutionary biology↗

bioRxiv2021

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering much of their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context and discrepancies between molecular divergence times and fossil evidence. We employ seventeen novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace--a multidimensional representation of node ages--and use it to explore the effects of using alternative gene samples, models of molecular evolution, and clock priors. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models shows little effects. The choice of loci shows an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships among sand dollars and their close relatives, showing that the genus Apatopygus represents a relict lineage with a deep Jurassic origin. Surprisingly, the origin of sand dollars is confidently dated to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.

evolutionary biology↗

bioRxiv2021

Phylogenomic subsampling and the search for phylogenetically reliable loci

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale datasets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods, or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different datasets. Here, I calculate multiple gene properties for a range of phylogenomic datasets spanning animal, fungal and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared to alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties, and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.

evolutionary biology↗

bioRxiv2020

Fossils improve phylogenetic analyses of morphological characters

Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help elucidate macroevolutionary patterns and processes, such as ancestral states and diversification dynamics. However, the effect fossils have on phylogenetic inference from morphological data remains controversial. Previous studies have highlighted their strong impact on topologies inferred from empirical data, but have not demonstrated that they improve accuracy. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here we employ a simulation approach to explore how fossil sampling and missing data affect tree reconstruction across a range of inference methods. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses which simultaneously infer tree topology and divergence times outperform all other methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their unique morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.

evolutionary biology↗

bioRxiv2020

A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

Several unique properties of echinoids (sea urchins) make them useful for exploring macroevolutionary dynamics, including their remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. However, this potential cannot be exploited without a robust resolution of the echinoid tree of life. We revisit the phylogeny of crown group Echinoidea using both the largest phylogenomic dataset compiled for the clade, as well as a large-scale morphological matrix with a dense fossil sampling. We also gather a new compendium of both tip and node age constraints, allowing us to combine phylogenomic, morphological and stratigraphic data using a total-evidence dating approach. For this, we develop a novel method for subsampling phylogenomic datasets that selects loci with high phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our approach restructure much of the higher-level phylogeny of echinoids, and demonstrates that combining different data sources increases topological accuracy. We are able to resolve multiple alleged conflicts between molecular and morphological datasets, such as the position of Echinothurioida and Echinoneoida, as well as unravelling the relationships between sand dollars and their closest relatives. We then use this topology to trace the evolutionary history of echinoid body size through more than 270 million years, revealing a complex pattern of convergent evolution to stable peaks in macroevolutionary adaptive landscape. Our efforts show how combining phylogenomic and paleontological evidence offers new ways of exploring evolutionary forces operating across deep timescales.

evolutionary biology↗

bioRxiv2019

Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses

Fossils are the only remaining evidence of the majority of species that have ever existed, providing a direct window into events in evolutionary history that shaped the diversification of life on Earth. Phylogenies underpin our ability to make sense of evolution but are routinely inferred only from data available from living organisms. Although extinct taxa have been shown to add crucial information for inferring macroevolutionary patterns and processes including ancestral states, paleobiogeography and diversification dynamics, the role that fossils play in inferring the tree of life itself is controversial. Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Here we show paleontological data has a remarkable effect in phylogenetic inference. Fossils often have higher levels of topological influence than extant taxa, while inducing unique topological rearrangements. Previous studies have proposed a suite of explanations for the topological behavior of fossils, such as their retention of unique morphologies or their ability to break long branches. We develop predictive models that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any analysis. Our results bolster the consensus of recent empirical studies by showing the unique role of paleontological data in phylogenetic inference, and provide the first quantitative assessment of its determinants, with broad consequences for the design of taxon sampling in both morphological and total-evidence analyses.

evolutionary biology↗

bioRxiv2018

A phylogenomic resolution of the sea urchin tree of life

BackgroundEchinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1,000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved.\n\nResultsWe performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We demonstrate the strength and distribution of phylogenetic signal throughout the genome for novel resolutions of these lineages and rule out systematic biases as possible explanations.\n\nConclusionsOur investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.

evolutionary biology↗