Biology subjects

Bracken-Grissom, H.

Publications and source records attributed to Bracken-Grissom, H..

4 recordsLinked to original sources

bioRxiv2025

Phylogenomics supports monophyly of marsupial crustaceans: a journey to direct development

Peracarida (marsupial crustaceans) represent one of the most diverse and ecologically important crustacean groups, yet their evolutionary relationships have long been debated. Here, we present the most comprehensive phylogenomic analysis of Peracarida to date, incorporating the relict taxa Thermosbaenacea, Mictacea, Ingolfiellida, and Spelaeogriphacea for the first time in a phylogenomic framework. Our results robustly confirm peracarid monophyly and recover a well-supported clade uniting Mancoida (Isopoda, Tanaidaca, Cumacea), Mictacea, and Spelaeogriphacea. We propose the new taxon Panmancoida to encompass this expanded lineage defined by shared developmental and morphological traits. The inferred phylogeny further suggests that peracarid evolution involved a transition from an intermediate "pseudodirect" developmental mode to the direct development seen in most lineages. We further show that the shift to extensive brood care within the marsupium, accompanied by the loss of a free-swimming larval stage, may have accelerated rates of molecular evolution across lineages. Together, these findings provide a robust evolutionary framework for this major malacostracan lineage and highlight how key reproductive innovations reshaped the genomic and life-history trajectories of the marsupial crustaceans.

evolutionary biology↗

bioRxiv2024

Water volume, biological and PCR replicates influence the characterization of deep-sea pelagic fish communities.

The pelagic deep sea is challenging to investigate due to logistical constraints regarding access and collection of samples, however environmental DNA (eDNA) can potentially revolutionize our understanding of this ecosystem. Although recent advancements are being made regarding eDNA technology and autonomous underwater vehicles, no investigation has been performed to assess the impact of different experimental designs using gear found on many research vessels (i.e., CTD mounted with Niskin bottles). Here, we investigated the effects of sampled water volume, biological and PCR replicates in characterizing deep-sea pelagic biodiversity at the level of species and exact sequence variants (ESVs, representing intraspecific variation). Samples were collected at 450m depth at night in the northern Gulf of Mexico using Niskin bottles, and we targeted the fish community using the MiFish primer (12S rRNA). Our results show that 1L is insufficient to characterize deep-sea pelagic fish communities. The 5L and 10L treatments detected similar community structure (i.e., the combination of number of species and relative occurrence) and numbers of species per biological replicate, but the 10L treatment detected a higher total number of species, more ESVs, and a different community structure when considering ESVs. We found that five biological replicates can detect up to 80% of the species detected in this study in the water collected in both 5L and 10L treatments. PCR replicates also had an important role in species and ESV detection, which implies increasing PCR replicates if water volume is limited. We suggest that future studies collect at least 5L, 5 or more field replicates, and 5-10 PCR replicates to adequately investigate deep-sea pelagic biodiversity using eDNA, considering resource limitations. Our study provides guidance for future eDNA studies and a potential route to expand eDNA studies at a global scale.

ecology↗

bioRxiv2023

Fossil calibrations for molecular analyses and divergence time estimation for true crabs (Decapoda: Brachyura)

True crabs, or Brachyura, comprise over 7,600 known species and are among the most ecologically dominant, economically significant, and popularly recognized group of extant crustaceans. There are over 3,000 fossil brachyuran species known from mid and upper Jurassic, Cretaceous, and Cenozoic deposits across the globe, many of them preserved in exquisite detail, but the origins and early evolution of true crabs remain unresolved. This uncertainty hinders the identification of the stratigraphically earliest occurrence of major brachyuran groups in the fossil record, obscuring our understanding of their phylogenetic relationships and thus the ability to estimate divergence times to answer large scale macroevolutionary questions. Here, we present 36 vetted fossil node calibration points for molecular phylogenetic analysis of crabs (one Anomura and 35 Brachyura) and reassess the earliest occurrences of several key clades based on recent fossil discoveries or re-examination of previous studies. For each calibrated node, we provide the minimum and tip maximum ages for the stratigraphically oldest fossil that can be reliably assigned to the group. Disentangling the anatomical disparity of fossil forms and their phylogenetic relationships is crucial to recognize the earliest branching members among brachyuran groups. This represents a critical first step understanding the evolution of carcinization and decarcinization in true crabs, the appearance of key adaptations, and the transition from sea to land and freshwater. The identification of reliable fossils for deep time calibrations, both as tips and nodes, is pivotal to ensure not only precise but more accurate divergence time estimations when reconstructing the crab tree of life. PLAIN LANGUAGE SUMMARYWe present 36 vetted fossil calibration points for molecular phylogenetic analysis of crabs (one Anomura and 35 Brachyura) and reassess the earliest occurrences of several key groups based on recent fossil discoveries or re-examination of previous studies, together with discussions for each taxon. We also provide some general observations and recommendations on fossil age selection and stratigraphic considerations. The identification of reliable fossils for deep time calibrations, both as tips and nodes, is pivotal to ensure not only precise but more accurate divergence time estimations when reconstructing phylogenetic trees.

paleontology↗

bioRxiv2020

More from less: Genome skimming for nuclear markers for animal phylogenomics, a case study using decapod crustaceans

Low coverage genome sequencing is rapid and cost-effective for recovering complete mitochondrial genomes for animal phylogenomics. The recovery of high copy number nuclear genes, including histone H3, 18S and 28S ribosomal RNAs, is also possible using this approach. In this study, we explore the potential of the genome skimming (GS) to recover additional nuclear genes from shallow sequencing projects. Using an in silico baited approach, we recover three additional core histone genes (H2A, H2B and H4) from our existing collection of low coverage decapod crustacean dataset (99 species, 69 genera, 38 families, 10 infraorders). Phylogenetic analyses based on various combinations of mitochondrial and nuclear genes for the entire decapod dataset and 40 species of crayfish (Infraorder Astacidea) found that the evolutionary rates for different classes of genes varied widely. The highlight being a very high level of congruence found between trees from the six nuclear genes and those derived from the mitogenome sequences for freshwater crayfish. These findings indicate that nuclear genes recovered from the same genome skimming datasets designed to obtain mitogenomes can be used to support more robust and comprehensive phylogenetic analyses. Further, a search for additional intron-less nuclear genes identified several high copy number genes across the decapod dataset and recovery of NaK, PEPCK and GAPDH gene fragments is possible at slightly elevated coverage, suggesting the potential and utility of GS in recovering even more nuclear genetic information for phylogenetic studies from these inexpensive and increasingly abundant datasets.

evolutionary biology↗