Target‐capture probes for phylogenomics of the Caenogastropoda

Abstract

Genomic data are rapidly improving our understanding of deep evolutionary relationships among metazoans and have the potential to help address many questions about the diversification of invertebrates. Mollusks are the second most diverse phylum of animals, but this diversity is vastly under-represented among available genomics resources, with approximately 33 genomes published (Schell et al., 2017;Yang et al., 2020) for the estimated 85,000 recognized extant species (MolluscaBase). Genomic data

A novel target‐enriched multilocus assay for sponges (Porifera): Red Sea Haplosclerida (Demospongiae) as a test case

“…Here, we demonstrate the applicability of target‐capture enrichment using ultraconserved element (UCE) loci as an effective and robust approach for resolving phylogenetic relationships on both deep and shallow evolutionary timescales from species across one of the most diverse demosponge orders, the Haplosclerida. Thus far, target‐capturing of UCEs has been successfully applied to other marine invertebrates, such as echinoderms (Hugall et al., 2015), anthozoans (Cowman et al., 2020; Quattrini et al., 2018), arthropods (Ballesteros et al., 2021), annelids (Petersen et al., 2022) and recently molluscs (Goulding et al., 2023; Moles & Giribet, 2020), where they successfully resolved phylogenetic relationships at both high (class) and low (species) taxonomic levels, and provided insights into evolutionary dynamics between species.…”

“…These informative sites can be used to infer the phylogenetic histories of systematically challenging groups across shallow and deep timescales (Faircloth et al., 2012; Faircloth et al., 2013; McCormack et al., 2012; Quattrini et al., 2018). UCEs have successfully resolved molecular phylogenetic relationships in taxonomically complex marine invertebrate taxa, such as molluscs (Goulding et al., 2023; Moles & Giribet, 2020), anthozoans (Cowman et al., 2020; Quattrini et al., 2018) and echinoderms (Hugall et al., 2015). The phylogenetic relationships of various groups within the phylum Porifera, particularly those belonging to the order Haplosclerida (Class Demospongiae), are still poorly understood due to the discrepancy between the morphological and molecular hypotheses proposed for this group (McCormack et al., 2002; Redmond et al., 2011, 2013).…”

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

“…While UCE probe sets have been developed for many major taxa (Faircloth et al, 2012(Faircloth et al, , e.g. 2013Goulding et al, 2023;Moles & Giribet, 2021;Quattrini et al, 2018;Smith et al, 2014;Starrett et al, 2017), no probe set was available for the most diverse marine invertebrate class: Malacostraca. Our research addresses this gap by introducing a specialized UCE probeset for investigating the intricate diversity within Malacostraca, with a specific emphasis on the diverse order Decapoda.…”

Phylogeny and Systematics of Fossil and Recent Vermicularia (Caenogastropoda: Turritellidae)

“…This is not a common morphology for turritelline protoconchs, which generally have nuclei depressed to varying degrees (Marwick, 1957;examples by Friend et al, 2023). The only protoconch that is emergent shown in Marwick's (1957) treatment of turritellid genera was Kimberia Cotton & N. H. Woods, 1935(Marwick, 1957, which is now considered to be a member of Vanikoroidea (e.g., Goulding et al, 2023). The specimen also does not appear to follow the B1A2 apical formula, because the spiral sculpture does begin medially, however, no A cord appears on the early whorls (or any whorls depicted), although a possible D cord does appear to be present.…”