Biology subjects

Giribet, G.

Publications and source records attributed to Giribet, G..

9 recordsLinked to original sources

bioRxiv2025

Unpouching Peracarida relationships with ultraconserved elements

Peracarida is a large group containing twelve orders of brooding crustaceans, including the large orders Amphipoda, Isopoda, Tanaidacea and Cumacea, and a series of smaller orders, some restricted to isolated habitats. The relationships of Peracarida have been disputed and no attempt has been made to use extensive taxon sampling with a modern genetic approach. Here we present a novel probe set of ultraconserved elements (UCEs) developed for peracarids to investigate higher-level relationships using newly collected Antarctic material and collection-based specimens. Concatenated and coalescent-based analyses across different levels of occupancy matrices recovered strong support for the monophyly of Peracarida and for the clade Mancoida (Isopoda + Tanaidacea + Cumacea). Thermosbaenacea was consistently resolved as the sister group to all remaining peracarids. Within Amphipoda, our results contrast with previous phylogenies by placing Corophiida and Hyperiidea as early-branching lineages. In Isopoda, Oniscidea was recovered as monophyletic and concordant with morphological hypotheses. These findings provide one of the first phylogenomic frameworks for Peracarida and demonstrate the promise of UCEs for resolving long-standing questions in malacostracan evolution.

zoology↗

bioRxiv2025

Systematic revision of the speciose sea slug genus Doto (Heterobranchia: Nudibranchia) - from the Mediterranean to South America

The genus Doto Oken, 1815 is, taxonomically, one of the most complex genera of nudibranchs due to the cryptic nature of its species, their small body size, and the homogeneity among their internal and external features. Here, an extensive molecular analysis of Mediterranean, Northeastern Atlantic, and South American specimens sheds light on the species-level taxonomy of the group. Our multilocus analyses include 171 specimens, 59 newly sequenced, corresponding to 20 species. Ten species are included in a molecular phylogeny for the first time, two being new species. Here, we provided detailed morphological and ecological descriptions of three Atlantic species, 11 Mediterranean, and one from the Pacific, complemented by live photographs evidencing their chromatic variation. The phylogenetic and species delimitation analyses suggest that coloration and external morphology often seem unreliable to differentiate among species. Molecular evidence corroborates and expands the geographical distribution of Doto species, some of which have never been included in molecular studies. The Mediterranean species currently recognized as D. coronata (Gmelin, 1791) and D. dunnei Lemche, 1976 correspond to D. millbayana Lemche, 1976. Consequently, we suggest the junior synonymy with D. dunnei syn. nov. Nevertheless, we found evidence for a restricted distribution of D. coronata in the western Mediterranean, coexisting in sympatry with D. cavernicola sp. nov. An additional new species from the Chilean Patagonia is also described as D. vrenifossorum sp. nov. Considering the present phylogenetic scenario, there is a highlighted need for further new morphological and genetic evidence, expanding the number of taxa and species to further unravel the taxonomy of Doto. This article is registered in ZooBank under https://zoobank.org/References/99a6148d-a93c-4d2d-947e-26a85329a57f

evolutionary biology↗

bioRxiv2023

From the shallows to the depths: A new probe set to target ultraconserved elements for Malacostraca

Since its introduction about a decade ago, target enrichment sequencing of ultraconserved elements (UCEs) has proven to be an invaluable tool for studies across evolutionary scales, and thus employed from population genetics, to historical biogeography and deep phylogenetics. UCE probe sets are available for an increasing range of major taxonomic groups, including cnidarians, vertebrates, terrestrial arthropods, and mollusks. Here, we present the first probe set targeting UCEs in crustaceans, specifically designed for decapods and other malacostracan lineages. Probes were designed using published genomes of nine decapod and one peracarid species, as well as raw Nanopore long reads of one additional brachyuran species. The final probe set consists of about 20,000 probes, targeting 1,348 unique UCE loci. Preliminary analyses of UCE data obtained from an intertidal mangrove crab, and from deep-sea squat lobsters indicate high UCE recovery rates (about 1,000 loci per sample) in evolutionarily shallow datasets. To test the probe set at deeper phylogenetic levels, we compiled a dataset across Malacostraca (including representatives of Decapoda, Peracarida, Euphausiacea, Stomatopoda, and Phyllocarida), and were able to recover hundreds of UCEs for the non-decapod species, expanding the targeted use of this UCE probeset to all Malacostraca. Additionally, we recovered similar numbers of UCEs from historical museum specimens up to > 150 years old, that were included in all datasets, confirming that UCEs are a fruitful technique for leveraging museum specimens for genomic studies. Overall, our results highlight the versatility of this UCE probe set and its high potential for crustacean evolutionary studies.

evolutionary biology↗

bioRxiv2021

Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. While conflicting hypotheses prevail in morphological and molecular datasets alike, the monophyly of Arachnida is nearly universally accepted. Though a small number of phylotranscriptomic analyses have recovered arachnid monophyly, these did not sample all living chelicerate orders. We generated a dataset of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternatives algorithmic approaches to species tree inference. Investigation of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the effect of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.

evolutionary biology↗

bioRxiv2019

A phylogenomic framework for Vetigastropoda (Mollusca)

Abalones, turban snails, top snails, keyhole limpets and slit shells are just some of the diverse marine Vetigastropoda. With major lineages having ancient divergences in the Paleozoic Era, basal nodes in the phylogeny have been largely unresolved. Here we present the first genomic-scale dataset focused on vetigastropods, including a comprehensive sampling of taxa with all superfamilies and about half of the extant families (41 new transcriptomes, 49 total ingroup terminals). Our recovered topology is congruent among inference methods for the majority of nodes, and differs from previous studies, in which long branch attraction artifacts seem to be pervasive. The first three divergences sequentially separate Pleurotomarioidea, Seguenzioidea and Haliotoidea from remaining vetigastropods. Fissurelloidea is sister group to Scissurelloidea, Lepetodriloidea and Lepetelloidea, which all together are the sister group to Trochoidea. A methodological discordance exists in the position of Haliotidae and Fissurellidae, possibly due to a compounded effect of small sample bias derived from gene-wide partitioning. Dense sampling of trochoids and fissurellids also provides a backbone for family and subfamily-level relationships, with Tegulidae not monophyletic.

evolutionary biology↗

bioRxiv2018

Deep gastropod relationships resolved

Gastropod mollusks are arguably the most diverse and abundant animals in the oceans, and are successful colonizers of terrestrial and freshwater environments. Here we resolve deep relationships between the five major gastropod lineages - Caenogastropoda, Heterobranchia, Neritimorpha, Patellogastropoda and Vetigastropoda - with highly congruent and supported phylogenomic analyses. We expand taxon sampling for underrepresented lineages with new transcriptomes, and conduct analyses accounting for the most pervasive sources of systematic errors in large datasets, namely compositional heterogeneity, site heterogeneity, heterotachy, variation in evolutionary rates among genes, matrix completeness and gene tree conflict. We find that vetigastropods and patellogastropods are sister taxa, and that neritimorphs are the sister group to caenogastropods and heterobranchs. With this topology, we reject the traditional Archaeogastropoda, which united neritimorphs, vetigastropods and patellogastropods, and is still used in the organization of collections of many natural history museums. Several traits related to development and life history support our molecular results. Importantly, the time of differentiation of the embryonic 4d cell (mesentoblast, responsible for mesoderm formation), differs between the two major clades, highlighting the degree of conservation and significance of development in the evolution of gastropods, as it is also known for spiralian animals more broadly.

evolutionary biology↗

bioRxiv2018

Delegating Sex: differential gene expression in stolonizing syllids uncover the hormonal control of reproduction in Annelida

Stolonization in syllid annelids is a unique mode of reproduction among animals. During the breeding season, a structure resembling the adult but containing only gametes, called stolon, is formed at the posterior end of the animal. When the stolons mature, they detach from the adult and the gametes are released into the water column. The process is synchronized within each species, and it has been reported to be under environmental and endogenous control, probably via endocrine regulation. To further understand the reproduction in syllids and to elucidate the molecular toolkit underlying stolonization, we generated Illumina RNA-seq data from different tissues of reproductive and non-reproductive individuals of Syllis magdalena, and characterized gene expression during the stolonization process. Several genes involved in gametogenesis (ovochymase, vitellogenin, testis-specific serine/threonine-kinase), immune response (complement receptor 2), neuronal development (tyrosine-protein kinase Src42A), cell proliferation (alpha-1D adrenergic receptor), and steroid metabolism (hydroxysteroid dehydrogenase 2) were found differentially expressed in the different tissues and conditions analyzed. In addition, our findings suggest that several neurohormones, such as methyl farnesoate, dopamine and serotonin, might trigger the stolon formation, the correct maturation of gametes and the detachment of stolons when gametogenesis is complete. The process seems to be under circadian control, as indicated by the expression patterns of r-opsins. Overall, our results shed light into the genes that orchestrate the onset of gamete formation, and improve our understanding of how some hormones, previously reported to be involved in reproduction and metamorphosis processes in other invertebrates, seem to also regulate reproduction via stolonization.

molecular biology↗

bioRxiv2017

Placozoans are eumetazoans related to Cnidaria

The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria (=Planulozoa), also seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that the support for Planulozoa can be assigned to this source of systematic error. In interpreting this placozoan-cnidarian clade, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.

zoology↗

bioRxiv2017

Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies

The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an example of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). In contrast, several molecular datasets have contradicted the Diplopoda-Pauropoda grouping (named Dignatha). Here we present the first transcriptomic data including a pauropod and both families of symphylans, allowing myriapod interrelationships to be inferred from phylogenomic data from representatives of all main lineages. Phylogenomic analyses consistently recovered Dignatha with strong support. Taxon removal experiments identified outgroup choice as a critical factor affecting myriapod interrelationships. Diversification of millipedes in the Ordovician and centipedes in the Silurian closely approximates fossil evidence whereas the deeper nodes of the myriapod tree date to various depths in the Cambrian-Early Ordovician, roughly coinciding with recent estimates of terrestrialisation in other arthropod lineages, including hexapods and arachnids. We provide a summary state-of-the-art Myriapoda Tree of Life at the ordinal level, the resolution of which has been improved by phylogenomics.

evolutionary biology↗