Biology subjects

Harvey, M. S.

Publications and source records attributed to Harvey, M. S..

6 recordsLinked to original sources

bioRxiv2024

What are the best practices for curating eDNA custom barcode reference libraries? A case study using Australian subterranean fauna.

Identification of species for environmental assessment and monitoring is essential for understanding anthropogenic impacts on biodiversity, but for subterranean fauna this task is frequently difficult and time consuming. The implementation of environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improving the rate, accuracy and efficiency of species detection in ecosystems both above and below the ground. Importantly, for a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata--i.e., a barcode reference library (BRL)--is required. Yet, minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, that permits metadata and has a unified nomenclature) and accurate (i.e. verified) custom BRL can be achieved. Here, we present a detailed roadmap for curation of a BRL for subterranean fauna. To do this, we (1) curated a custom sequence database of subterranean fauna at an environmentally sensitive location, Bungaroo Creek in the Pilbara region of Western Australia, for four gene loci useful for eDNA metabarcoding (COI, 18S rRNA, 12S rRNA and 16S rRNA); (2) addressed major gaps in taxonomy and disparate nomenclature of subterranean fauna by estimating 17-29 putative new species with standard delimitation methods, including 34 Barcode Index Numbers (BINs) in BOLD, and (3) summarised a best practice workflow for curation of a custom BRL that has broad applicability and can be applied to any taxa. Scientific Significance StatementIn threatened ecosystems, environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improvement in the rate, efficiency and accuracy of species detection. For a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata is required. Minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, permits metadata and provides a unified nomenclature) custom barcode reference library (BRL) can be achieved for subterranean fauna. Here, we present a road map for sound and reliable curation of a BRL using subterranean fauna from Australia as a case study.

evolutionary biology↗

bioRxiv2024

Phylogenomics, Classification, and Lifestyle Evolution in Raft- and Nursery web- Spiders (Araneae: Dolomedidae and Pisauridae)

Pisauridae Simon, 1890 or "nursery web spiders" are a global and heterogenous assemblage of spider genera with diverse lifestyles, containing web builders and webless species, as well as terrestrial and semi-aquatic species, notably "fishing spiders", genus Dolomedes Latreille, 1804. Incomplete, unresolved, or conflicting phylogenies have so far hampered testing for Dolomedes and pisaurid monophyly and evolution. Here, we broadly address these questions within a phylogenomic and comparative framework. Our goals are i) reconstruction of a robust phylogeny to test the monophyly of Dolomedes and Pisauridae and to amend Dolomedes classification; ii) estimation of evolutionary shifts and trends in lifestyles and capture webs; and iii) evaluation of hypotheses of morphological trait association with a semi-aquatic lifestyle. To this end we generate subgenomic data (ultraconserved elements or UCE) for 53 Dolomedes species and 28 pisaurid genera. We analyze these data using maximum likelihood, Bayesian, and multi-species coalescence approaches, as well as using two different phylogenetic time calibration methods, RelTime and MCMCtree. Consistent across analytical approaches, our phylogenies reject the monophyly of both Pisauridae and Dolomedes. "Pisaurid" genera fall into three clades: 1) Focal Clade I groups the majority, including Pisaura Simon, 1886, hence representing true pisaurids; 2) Focal Clade II = Blandinia Tonini et al., 2016 is sister to Trechaleidae Simon, 1890 and Lycosidae Sundevall, 1833; 3) Focal Clade III with fishing and raft spiders groups Dolomedes, Megadolomedes Davies and Raven, 1980, and Ornodolomedes Raven and Hebron, 2018 and is sister to Focal Clade II, Trechaleidae, and Lycosidae. Our taxonomy, based on complementary taxa and morphological evidence, resurrects Dolomedidae Simon, 1876 to include Dolomedes and the Oceanic genera Bradystichus Simon, 1884, Megadolomedes, Caledomedes Raven and Hebron, 2018, Mangromedes Raven and Hebron, 2018, Ornodolomedes, and Tasmomedes Raven and Hebron, 2018. Both RelTime and MCMCtree analyses yield comparable divergence estimations: Pisauridae origin is estimated between 29 and 40 Ma; Blandinia between 21 and 34 Ma; Dolomedidae between 10 and 17 Ma; and Dolomedes between 9 and 16 Ma. In order to avoid misleading significant correlations and/or over-resolved ancestral states, we performed taxon sampling bias correction in all evolutionary analyses. Evolutionary analyses reconstruct semi-aquatic lifestyle as ancestral to a large clade containing pisaurids, lycosids, trechaleids, Blandinia, and dolomedids, with several reversals to terrestrial lifestyle. Capture webs evolved at least three times, with reversals. Counter to expectation, the evolution of lifestyles and capture webs are independent. Although leg and tarsus lengths do not indicate lifestyles, semi-aquatic taxa are significantly larger than terrestrial ones. We explain this pattern with a biomechanical threshold over which surface tension can be broken while spiders forage under water. Our time-calibrated analyses indicate that the evolution of terrestrial and web-building lifestyles from semi-aquatic ancestors in Pisauridae coincided with cooling and drying climates in the mid-Miocene. We therefore hypothesize that climatic changes have acted as strong selection pressures toward lifestyle diversification.

evolutionary biology↗

bioRxiv2024

A novel expression domain of extradenticle underlies the evolutionary developmental origin of the chelicerate patella

Neofunctionalization of duplicated gene copies is thought to be an important process underlying the origin of evolutionary novelty and provides an elegant mechanism for the origin of new phenotypic traits. One putative case where a new gene copy has been linked to a novel morphological trait is the origin of the arachnid patella, a taxonomically restricted leg segment. In spiders, the origin of this segment has been linked to the origin of the paralog dachshund-2, suggesting that a new gene facilitated the expression of a new trait. However, various arachnid groups that possess patellae do not have a copy of dachshund-2, disfavoring the direct link between gene origin and trait origin. We investigated the developmental genetic basis for patellar patterning in the harvestman Phalangium opilio, which lacks dachshund-2. Here, we show that the harvestman patella is established by a novel expression domain of the transcription factor extradenticle. Leveraging this definition of patellar identity, we surveyed targeted groups across chelicerate phylogeny to assess when this trait evolved. We show that a patellar homolog is present in Pycnogonida (sea spiders) and various arachnid orders, suggesting a single origin of the patella in the ancestor of Chelicerata. A potential loss of the patella is observed in Ixodida. Our results suggest that the modification of an ancient gene, rather than the neofunctionalization of a new gene copy, underlies the origin of the patella. Broadly, this work underscores the value of comparative data and broad taxonomic sampling when testing hypotheses in evolutionary developmental biology.

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↗

bioRxiv2020

Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata, as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.

evolutionary biology↗

bioRxiv2020

Phylogenomics of scorpions reveal a co-diversification of scorpion mammalian predators and mammal-specific sodium channel toxins

Scorpions constitute a charismatic lineage of arthropods and comprise more than 2,500 described species. Found throughout various tropical and temperate habitats, these predatory arachnids have a long evolutionary history, with a fossil record that began in the Silurian. While all scorpions are venomous, the asymmetrically diverse family Buthidae harbors nearly half the diversity of extant scorpions, and all but one of the 58 species that are medically significant to humans. Many aspects of scorpion evolutionary history are unclear, such as the relationships of the most toxic genera and their constituent venom peptides. Furthermore, the diversification age of toxins that act specifically on mammalian ion channels have never been inferred. To redress these gaps, we assembled a large-scale phylogenomic dataset of 100 scorpion venom transcriptomes and/or genomes, emphasizing the sampling of highly toxic buthid genera. To infer divergence times of venom gene families, we applied a phylogenomic node dating approach for the species tree in tandem with phylostratigraphic bracketing to estimate minimum ages of mammal-specific toxins. Our analyses establish a robustly supported phylogeny of scorpions, particularly with regard to relationships between medically significant taxa. Analysis of venom gene families shows that mammal-specific sodium channel toxins have independently evolved in five lineages within Buthidae. The temporal windows of mammal-specific toxin origins are contiguous with the basal diversification of major scorpion mammal predators such as carnivores, shrews, bats and rodents. These results suggest an evolutionary arms race model comprised of co-diversification of mammalian predators and NaTx homologs in buthid venom.

evolutionary biology↗