Biology subjects

Wolfe, J. M.

Publications and source records attributed to Wolfe, J. M..

9 recordsLinked to original sources

bioRxiv2026

Complex interplay of biomechanics and ecology influenced crab claw morphology evolution

True crabs (Brachyura) are among the most iconic marine arthropods, representing noteworthy examples of morphological and ecological disparity. A striking feature of brachyurans are their anterior pincer-like appendages: chelipeds. These structures showcase a large diversity of morphologies that reflect ecology and overall multifunctionality. Yet, a comprehensive assessment of appendage functional morphology within phylogenetic and ecological trait contexts has never been attempted. By combining 3D geometric morphometrics, finite element analyses, multilocus molecular phylogeny, and ecological trait data for 80 crab species, including three fossil forms, we unveil a complex evolutionary history for crab chelipeds. Despite extreme shape diversity amongst chelipeds, stress distributions are very similar across taxa and hint a many-to-one pattern. High concentrations of chelipeds within constrained morphospace regions associated with peak pinch forces illustrates that brachyuran morphologies optimised for shell crushing may have arisen in the Cretaceous. Deviations from this morphospace highlight the diversification of non-shell-crushing life modes and the influence of sexual selection on appendages. Neither cheliped shape nor pinch force show phylogenetic signal. Together these results indicate that the evolution of cheliped shape is closely associated with, and inferred to have been strongly influenced by, crab ecology, biomechanical needs and sexual selection. SIGNIFICANCE STATEMENTChelipeds, the pincer-like claws of crabs, are among the most morphologically diverse appendages within Arthropoda, yet the evolutionary forces driving this diversity remain poorly understood. By integrating 3D geometric morphometrics, biomechanical modelling, molecular phylogeny, and ecological data across 80 crab species including fossil forms, we demonstrate that cheliped morphology is driven by ecology, biomechanical demands, and sexual selection rather than phylogenetic relatedness. The multifunctionality of these structures produces strong evidence for many-to-one mapping of form to function. Morphologies optimised for durophagy appear to have originated in the Cretaceous, with subsequent diversification into manipulative and sexually selected forms from a morphologically flexible foundation. These findings demonstrate that cheliped diversity reflects a complex interplay between ecological specialisation, biomechanical optimisation, and sexual selection across Brachyura.

ecology↗

bioRxiv2024

Electrophysiological correlates of visual memory search

In everyday life, we frequently engage in hybrid search, where we look for multiple items stored in memory (e.g., a mental shopping list) in our visual environment. Across three experiments, we used event-related potentials to better understand the contributions of visual working memory (VWM) and long-term memory (LTM) during the memory search component of hybrid search. Experiments 1 and 2 demonstrated that the FN400 - an index of LTM recognition - and the CDA - an index of VWM - increased with memory set size (target load), suggesting that both VWM and LTM are involved in memory search, even when memory load exceeds capacity limitations of VWM. In Experiment 3, we used these electrophysiological indices to test how categorical similarity of targets and distractors affects memory search. The CDA and FN400 were modulated by memory set size only if items resembled targets. This suggests that dissimilar distractor items can be rejected before eliciting a memory search. Together, our findings demonstrate the interplay of VWM and LTM processes during memory search for multiple targets.

neuroscience↗

bioRxiv2022

Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.

evolutionary biology↗

bioRxiv2022

Major revisions in pancrustacean phylogeny with recommendations for resolving challenging nodes

The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species. It has been the subject of several recent phylogenomic analyses, but despite analyzing hundreds of genes, relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans, using a precise tree-based approach to infer orthology. Our results show that small changes in taxon sampling have a large impact on phylogenetic estimation. By analyzing only shared orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due to the effects of taxon sampling on the phylogenetic reconstruction method, not on ortholog identification. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the ML trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. We recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this clade, which we name Stomatocaridea, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocaridea. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight the key taxa to sample in future studies.

evolutionary biology↗

bioRxiv2021

New opabiniid diversifies the weirdest wonders of the euarthropod lower stem group

Once considered weird wonders of the Cambrian, the emblematic Burgess Shale animals Anomalocaris and Opabinia are now recognized as lower stem-group euarthropods. Anomalocaris and its relatives (radiodonts) had a worldwide distribution and survived until at least the Devonian, whereas - despite intense study - Opabinia remains the only formally described opabiniid to date. Here we reinterpret a fossil from the Wheeler Formation of Utah as a new opabiniid, KUMIP 314087. By visualizing the sample of phylogenetic topologies in treespace, our results fortify support for the position of KUMIP 314087 beyond the nodal support traditionally applied. Our phylogenetic evidence expands opabiniids to multiple Cambrian Stages spanning approximately five million years. Our results underscore the power of treespace visualization for resolving imperfectly preserved fossils and expanding the known diversity and spatiotemporal ranges within the euarthropod lower stem group. Additional noteThis work contains a new biological name. New names in preprints are not considered available by the ICZN. To avoid ambiguity, the new biological name is not included in this preprint, and the specimen number (KUMIP 314087) is used as a placeholder. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/434726v1_ufig1.gif" ALT="Figure 1"> View larger version (98K): org.highwire.dtl.DTLVardef@e770aaorg.highwire.dtl.DTLVardef@95bbd3org.highwire.dtl.DTLVardef@5e460eorg.highwire.dtl.DTLVardef@1494152_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOCover image.C_FLOATNO Artistic reconstruction of the new opabiniid from the Wheeler Formation, Utah, USA (Cambrian: Drumian). Artwork by F. Anthony. C_FIG

paleontology↗

bioRxiv2020

Interpretable Deep Learning for De Novo Design of Cell-Penetrating Abiotic Polymers

There are more amino acid permutations within a 40-residue sequence than atoms on Earth. This vast chemical search space hinders the use of human learning to design functional polymers. Here we couple supervised and unsupervised deep learning with high-throughput experimentation to drive the design of high-activity, novel sequences reaching 10 kDa that deliver antisense oligonucleotides to the nucleus of cells. The models, in which natural and unnatural residues are represented as topological fingerprints, decipher and visualize sequence-activity predictions. The new variants boost antisense activity by 50-fold, are effective in animals, are nontoxic, and can also deliver proteins into the cytosol. Machine learning can discover functional polymers that enhance cellular uptake of biotherapeutics, with significant implications toward developing therapies for currently untreatable diseases. One sentence summaryDeep learning generates de novo large functional abiotic polymers that deliver antisense oligonucleotides to the nucleus.

bioinformatics↗

bioRxiv2019

Evolution of crab eye structures and the utility of ommatidia morphology in resolving phylogeny

ABSTRACTImage-forming compound eyes are such a valuable adaptation that similar visual systems have evolved independently across crustaceans. But if different compound eye types have evolved independently multiple times, how useful are eye structures and ommatidia morphology for resolving phylogenetic relationships? Crabs are ideal study organisms to explore these questions because they have a good fossil record extending back into the Jurassic, they possess a great variety of optical designs, and details of eye form can be compared between extant and fossil groups. True crabs, or Brachyura, have been traditionally divided into two groups based on the position of the sexual openings in males and females: the so-called ‘Podotremata’ (females bearing their sexual openings on the legs), and the Eubrachyura, or ‘higher’ true crabs (females bearing their sexual openings on the thorax). Although Eubrachyura appears to be monophyletic, the monophyly of podotreme crabs remains controversial and therefore requires exploration of new character systems. The earliest podotremous lineages share the plesiomorphic condition of ‘mirror’ reflecting superposition eyes with most shrimp, lobsters, and anomurans (false crabs and allies). The optical mechanisms of fossil and extant podotreme groups more closely related to Eubrachyura, however, are still poorly investigated. To better judge the phylogenetic utility of compound eye form, we investigated the distribution of eye types in fossil and extant podotreme crabs. Our findings suggest the plesiomorphic ‘mirror’ eyes—seen in most decapod crustaceans including the earliest true crabs—has been lost in several ‘higher’ podotremes and in eubrachyurans. We conclude that the secondary retention of larval apposition eyes has existed in eubrachyurans and some podotremes since at least the Early Cretaceous, and that the distribution of eye types among true crabs supports a paraphyletic podotreme grade, as suggested by recent molecular and morphological phylogenetic studies. We also review photoreceptor structure and visual pigment evolution, currently known in crabs exclusively from eubrachyuran representatives. These topics are critical for future expansion of research on podotremes to deeply investigate the homology of eye types across crabs.View Full Text

paleontology↗

bioRxiv2018

A phylogenomic framework, evolutionary timeline, and genomic resources for comparative studies of decapod crustaceans

Comprising over 15,000 living species, decapods (crabs, shrimp, and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (>86,000 bp) conserved across all lineages of Decapoda, eight times more molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, lobster, and crab groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Paleozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behavior, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.

evolutionary biology↗

bioRxiv2017

Tunneling through time: Horizontal gene transfer constrains the timing of methanogen evolution

Microbial methanogenesis may have been a major component of Earths carbon cycle during the Archaean Eon, generating a methane greenhouse that increased global temperatures enough for a liquid hydrosphere, despite the suns lower luminosity at the time. Evaluation of potential solutions to the \"faint young sun\" hypothesis by determining the age of microbial methanogenesis was limited by ambiguous geochemical evidence, and the absence of a diagnostic fossil record. To overcome these challenges, we utilize a temporal constraint: a horizontal gene transfer (HGT) event from within archaeal methanogens to the ancestor of Cyanobacteria, one of the few microbial clades with recognized crown group fossils. Results of molecular clock analyses calibrated by this HGT-propagated constraint show methanogens diverging within Euryarchaeota no later than 3.51 Ga, with methanogenesis itself likely evolving earlier. This timing provides independent support for scenarios wherein microbial methane production was important in maintaining temperatures on the early Earth.

evolutionary biology↗