Biology subjects

Goodman, S. J.

Publications and source records attributed to Goodman, S. J..

10 recordsLinked to original sources

bioRxiv2025

A genomic perspective on the origins, evolution and adaptation of Galapagos iguanas

Island taxa provide opportunities to explore the genomic basis of species diversification and trait evolution arising from adaptation to new environmental conditions and ecological niches. Here we generate the first genomic sequences for the four endemic Galapagos iguana species to reconstruct their evolutionary history and to identify genes which may contribute to their unique adaptations. We show that the marine (Amblyrhynchus) and land (Conolophus) lineages evolved in situ on now submerged islands, following a single colonisation event 9 - 12.4 million years ago. Genomic selection scans identified genes linked to traits potentially facilitating adaptation to the Galapagos environment, including specialised pigmentation phenotypes (e.g. ASIP, BCO2 and KITLG), DNA damage and UV irradiation inflammation responses (e.g. MAPK14 and BRAF), which may contribute to increased resilience to elevated UV exposure at equatorial latitudes. A shift from eumelanin (dark) to pheomelanin (yellow-orange) dominated colouration in Conolophus species may be attributable to fixed substitutions in the MC1R gene that influence protein structure and interactions, with the depigmented skin phenotype of the pink iguana additionally linked to positive selection in regulators of MITF activity, melanosome transport and dermal vasculature unique to that lineage. Further genes with signatures of positive selection in marine iguanas have putative functions including hypoxia response, that may be associated with their transition to underwater foraging (e.g. HBA, HMOX2, HIF), as well as their unique ability to repeatedly shrink and grow in body size through tissue and bone remodelling (e.g. AREG, BMP2, CPNE7). Genome-wide patterns of genetic diversity indicate recent inbreeding coincident with the timing of human settlement. Our study provides insights into the origins and diversification of the iguanas and the molecular basis of adaptation to life in the Galapagos, facilitating future conservation genomic management of threatened iguanid populations.

evolutionary biology↗

bioRxiv2024

Rapid Caspian sea level decline requires dynamic spatio-temporal conservation planning to keep biodiversity protection measures relevant

The Caspian Sea is the worlds largest landlocked waterbody, providing habitat for hundreds of endemic and migratory species, along with ecosystem services that sustain millions of people. Global warming is projected to drive declines in water levels of up to 21 m by 2100. Using geospatial analyses, we assessed the impact of sea level decline on habitats, protected areas, and human infrastructure. We show that a water level decline of just 5-10 m will critically disrupt key ecosystems, reduce existing marine protected area coverage by up to 94%, and render billions of dollars of civil and industrial infrastructure obsolete. Urgent action is needed to replace traditional static conservation planning with a pre-emptive, dynamic approach that allows protected areas to track shifting ecosystems. This will be essential to help the Caspian Seas endemic biodiversity adapt to these changes, and avoid conflicts with mitigation efforts directed at protecting human activity. Russian abstract[A][bcy][c][t][p][a][kcy][t] [Kcy][a][c][pcy][icy][jcy][c][kcy][o][e] [m][o][p][e]- [kcy][p][u][pcy][ncy][e][jcy][shcy][icy][jcy] [v] [m][icy][p][e] [v][ncy][u][t][p][e][ncy][ncy][icy][jcy] [v][o][dcy][o][e][m], [o][bcy][e][c][pcy][e][chcy][icy][v][a][yucy][shchcy][icy][jcy] [c][p][e][dcy][u] [o][bcy][icy][t][a][ncy][icy][yacy] [dcy][lcy][yacy] [c][o][t][e][ncy] [ecy][ncy][dcy][e][m][icy][chcy][ncy][ycy][khcy] [icy] [m][icy][gcy][p][icy][p][u][yucy][shchcy][icy][khcy] [v][icy][dcy][o][v], [a] [t][a][kcy][zhcy][e] [ecy][kcy][o][c][icy][c][t][e][m][ncy][ycy][e] [u][c][lcy][u][gcy][icy], [o][bcy][e][c][pcy][e][chcy][icy][v][a][yucy][shchcy][icy][e] [zhcy][icy][z][ncy][e][dcy][e][yacy][t][e][lcy][softcy][ncy][o][c][t][softcy] [m][icy][lcy][lcy][icy][o][ncy][o][v] [lcy][yucy][dcy][e][jcy]. [C][o][gcy][lcy][a][c][ncy][o] [pcy][p][o][gcy][ncy][o][z][a][m], [gcy][lcy][o][bcy][a][lcy][softcy][ncy][o][e] [pcy][o][t][e][pcy][lcy][e][ncy][icy][e] [pcy][p][icy][v][e][dcy][e][t] [kcy] [c][ncy][icy][zhcy][e][ncy][icy][yucy] [u][p][o][v][ncy][yacy] [v][o][dcy][ycy] [dcy][o] 21 [m] [kcy] 2100 [gcy][o][dcy][u]. [C] [pcy][o][m][o][shchcy][softcy][yucy] [gcy][e][o][pcy][p][o][c][t][p][a][ncy][c][t][v][e][ncy][ncy][o][gcy][o] [a][ncy][a][lcy][icy][z][a] [pcy][p][o][v][e][dcy][e][ncy][a] [o][tscy][e][ncy][kcy][a] [v][lcy][icy][yacy][ncy][icy][yacy] [c][ncy][icy][zhcy][e][ncy][icy][yacy] [u][p][o][v][ncy][yacy] [m][o][p][yacy] [ncy][a] [m][e][c][t][a] [o][bcy][icy][t][a][ncy][icy][yacy], [o][khcy][p][a][ncy][yacy][e][m][ycy][e] [t][e][p][p][icy][t][o][p][icy][icy] [icy] [o][bcy]{cyrillic small hard sign}[e][kcy][t][ycy] [icy][ncy][fe][p][a][c][t][p][u][kcy][t][u][p][ycy]. [M][ycy] [pcy][o][kcy][a][z][ycy][v][a][e][m], [chcy][t][o] [c][ncy][icy][zhcy][e][ncy][icy][e] [u][p][o][v][ncy][yacy] [v][o][dcy][ycy] [v][c][e][gcy][o] [ncy][a] 5-10 [m] [pcy][p][icy][v][e][dcy][e][t] [kcy] [kcy][p][icy][t][icy][chcy][e][c][kcy][icy][m] [ncy][a][p][u][shcy][e][ncy][icy][yacy][m] [v] [kcy][lcy][yucy][chcy][e][v][ycy][khcy] [ecy][kcy][o][c][icy][c][t][e][m][a][khcy], [c][o][kcy][p][a][t][icy][t] [o][khcy][v][a][t] [c][u][shchcy][e][c][t][v][u][yucy][shchcy][icy][khcy] [m][o][p][c][kcy][icy][khcy] [o][khcy][p][a][ncy][yacy][e][m][ycy][khcy] [p][a][jcy][o][ncy][o][v] [dcy][o] 94% [icy] [pcy][p][icy][v][e][dcy][e][t] [kcy] [v][ycy][v][o][dcy][u] [icy][z] [ecy][kcy][c][pcy][lcy][u][a][t][a][tscy][icy][icy] [gcy][p][a][zhcy][dcy][a][ncy][c][kcy][o][jcy] [icy] [pcy][p][o][m][ycy][shcy][lcy][e][ncy][ncy][o][jcy] [icy][ncy][fe][p][a][c][t][p][u][kcy][t][u][p][ycy] [c][t][o][icy][m][o][c][t][softcy][yucy] [v] [m][icy][lcy][lcy][icy][a][p][dcy][ycy] [dcy][o][lcy][lcy][a][p][o][v]. [H][e][o][bcy][khcy][o][dcy][icy][m][ycy] [bcy][e][z][o][t][lcy][a][gcy][a][t][e][lcy][softcy][ncy][ycy][e] [m][e][p][ycy] [pcy][o] [z][a][m][e][ncy][e] [t][p][a][dcy][icy][tscy][icy][o][ncy][ncy][o][gcy][o] [c][t][a][t][icy][chcy][ncy][o][gcy][o] [pcy][lcy][a][ncy][icy][p][o][v][a][ncy][icy][yacy] [pcy][p][icy][p][o][dcy][o][o][khcy][p][a][ncy][ncy][o][jcy] [dcy][e][yacy][t][e][lcy][softcy][ncy][o][c][t][icy] [u][pcy][p][e][zhcy][dcy][a][yucy][shchcy][icy][m], [dcy][icy][ncy][a][m][icy][chcy][ncy][ycy][m] [pcy][o][dcy][khcy][o][dcy][o][m], [kcy][o][t][o][p][ycy][jcy] [pcy][o][z][v][o][lcy][icy][t] [kcy][o][p][p][e][kcy][t][icy][p][o][v][a][t][softcy] [gcy][p][a][ncy][icy][tscy][ycy] [o][khcy][p][a][ncy][yacy][e][m][ycy][khcy] [p][a][jcy][o][ncy][o][v] [v][c][lcy][e][dcy] [z][a] [c][m][e][shchcy][e][ncy][icy][e][m] [ecy][kcy][o][c][icy][c][t][e][m]. [Ecy][t][o] [ncy][e][o][bcy][khcy][o][dcy][icy][m][o] [dcy][lcy][yacy] [a][dcy][a][pcy][t][a][tscy][icy][icy] [ecy][ncy][dcy][e][m][icy][chcy][ncy][o][gcy][o] [bcy][icy][o][p][a][z][ncy][o][o][bcy][p][a][z][icy][yacy] [Kcy][a][c][pcy][icy][jcy][c][kcy][o][gcy][o] [m][o][p][yacy] [kcy] [icy][z][m][e][ncy][e][ncy][icy][yacy][m], [a] [t][a][kcy][zhcy][e] [dcy][lcy][yacy] [t][o][gcy][o], [chcy][t][o][bcy][ycy] [u][c][icy][lcy][icy][yacy] [pcy][o] [e][gcy][o] [c][o][khcy][p][a][ncy][e][ncy][icy][yucy] [ncy][e] [v][c][t][u][pcy][a][lcy][icy] [v] [kcy][o][ncy][fe][lcy][icy][kcy][t] [c] [m][e][p][a][m][icy] [pcy][o] [z][a][shchcy][icy][t][e] [dcy][e][yacy][t][e][lcy][softcy][ncy][o][c][t][icy] [chcy][e][lcy][o][v][e][kcy][a].

ecology↗

bioRxiv2024

VIRAL METAGENOMIC SURVEY OF CASPIAN SEALS

Viral diseases of pinnipeds cause substantial mortality and morbidity and can influence population demography. Viral metagenomic studies can therefore play an important role in pinniped health assessments and disease surveillance relevant to both individual species and in a One Health context. This study used a metagenomic approach with high throughput sequencing to make the first assessment of viral diversity in Caspian seals (Pusa caspica), the only marine mammal species endemic to the Caspian Sea. Sequencing libraries from 35 seals sampled 2009-2020 were analysed, finding sequences from the viral families Picornaviridae, Adenoviridae, Circoviridae, Herpesviridae, Papillomaviridae, Caliciviridae, Orthomyxoviridae, Anelloviridae, Smacoviridae, Cruciviridae and Parvoviridae. The similarity of viral contigs from Caspian seal to sequences to those recovered from other pinnipeds ranged from 63.74% (San Miguel sea lion calicivirus) to 78.79% (Seal anellovirus 4). Some may represent novel viral species, but overall, the viral repertoire of Caspian seals is similar to available viromes from other pinnipeds. Among the sequences recovered were partial contigs for influenza B, representing only the second such molecular identification in marine mammals. This work provides a foundation for further studies of viral communities in Caspian seals, the diversity of viromes in pinnipeds more generally, and contributes data relevant for disease risk assessments in marine mammals.

microbiology↗

bioRxiv2024

The potential applications of high-resolution 3D scanners in the taxonomic classification of insects

The phenotypic classification of small biological specimens, such as insects, can be dependent on phenotypic features that are difficult to observe and communicate to others. Here, we evaluate how high-resolution 3D photogrammetric scanner technology can potentially allow such features to be resolved and visualised as a 3D models, which can then be shared as a taxonomical resource for species identification, as virtual type specimens, and for educational and public engagement purposes. We test the viability and limitations of this approach using specimens digitised with a Artec Micro scanner. Ten samples from unique species were mounted and scanned. The model outputs were evaluated against an identification key, which compiled diagnostic features for the specimens from the wider literature, to describe the specimens to the lowest taxonomic level possible. The results showed that six of the ten specimens could be identified to species level using the scans. Threshold values for body length and width were 10.7 mm and 4.4 mm respectively. Below these body dimensions important diagnostic features of specimens could not be resolved reliably. This result suggests that with current technology, 3D photogrammetric modelling is a viable method for taxonomic identification of a wide range of insect groups with larger body sizes. This approach opens up novel applications for species identification and data sharing among taxonomists, international field research, conservation efforts, and entomological outreach. However, the limitations of this approach to taxonomic identification must be considered depending upon the size of the specimen and its diagnostic features. Future developments in the technology and processing methods used may alleviate the constraints on body size exhibited in this study, widening the applications for smaller bodied specimens.

scientific communication and education↗

bioRxiv2024

Inferring species interactions from co-occurrence networks with environmental DNA metabarcoding data in a coastal marine food-web

Improved understanding of biotic interactions is necessary to accurately predict the vulnerability of ecosystems to climate change. Recently, co-occurrence networks built from environmental DNA (eDNA) metabarcoding data have been advocated as a means to explore interspecific interactions in ecological communities exposed to different human and environmental pressures. Co-occurrence networks have been widely used to characterise microbial communities, but it is unclear if they are effective for characterising eukaryotic ecosystems, or whether biotic interactions drive inferred co-occurrences. Here, we assess spatiotemporal variability in the structure and complexity of a North Sea coastal ecosystem inferred from co-occurrence networks and food webs using 60 eDNA samples covering vertebrates and other eukaryotes. We compare topological characteristics and identify potential keystone species, i.e., highly connected species, across spatial and temporal subsets, to evaluate variance in community composition and structure. We find consistent trends in topological characteristics across co-occurrence networks and food webs, despite trophic interactions forming a minority of significant co-occurrences. Known keystone species in food webs were not highly connected in co-occurrence networks. The lack of significant trophic interactions detected in co-occurrence networks may result from ecological complexities such as generalist predators having flexible interactions or behavioural partitioning, as well as methodological limitations such as the inability to distinguish age class with eDNA, or co-occurrences being driven by other interaction types or shared environmental requirements. Deriving biotic interactions with co-occurrence networks constructed from eDNA requires further validation in well-understood ecosystems, and improved reporting of methodological limitations, such as species detection uncertainties, which could influence inferred ecosystem complexity.

ecology↗

bioRxiv2023

Environmental DNA reveals fine scale spatial and temporal variation of prey species for marine mammals in a Scottish marine protected area

Marine mammal foraging grounds are popular focal points for marine protected area (MPA) implementation, but may be temporally dynamic, requiring continuous monitoring to infer prey availability and abundance. Marine mammal distributions are assumed to be driven by their prey in foraging areas, but limited understanding of prey distributions often prevents us from exploring how shifting prey availability impacts both seasonal and long-term marine mammal distributions. Environmental DNA (eDNA) metabarcoding could enhance understanding of marine mammal habitat use in relation to their prey through simultaneous monitoring of both. However, eDNA applications focused on marine mammals or predator-prey dynamics have been limited to date. In this study, we assess spatiotemporal changes in the availability and abundance of minke whale (Balaenoptera acutorostrata) prey species in a newly established MPA, employing eDNA metabarcoding. We recovered 105 molecular operational taxonomic units (OTUs) from marine vertebrates using two primer sets targeting 12S and 16S genes, along with 112 OTUs from a broader eukaryotic primer set targeting 18S rRNA. Overall, key forage fish prey species, sandeels and clupeids, were the most abundant teleost fishes detected, although their availability varied temporally and with distance from shore. We also found clear spatial partitioning between coastal bottlenose dolphins and the more pelagic minke whales and harbour porpoises, paralleling availability of their main prey species. Other species of conservation interest were also detected including the critically endangered European eel (Anguilla anguilla), blue fin tuna (Thunnus thynnus), and the invasive pink salmon (Oncorhynchus gorbuscha). This study demonstrates the application of eDNA to detect spatiotemporal trends in the occurrence and abundance of cetacean predators and their prey, furthering our understanding of fine-scale habitat use within MPAs. Future, long-term monitoring of predator-prey dynamics with eDNA could improve our ability to predict climate-induced shifts in foraging grounds and enhance rapid responses with appropriate management actions.

ecology↗

bioRxiv2023

Marine predator spatial conservation priorities are taxon-specific

Marine predators are globally threatened by anthropogenic stressors, but are key for ecosystem functioning. Their worsening conservation statuses indicate that current management is failing, requiring us to urgently reimagine their conservation needs to ensure their survival. Their life histories, threats, and resource needs are diverse. Consequently, spatial conservation areas targeting all species will overlook such heterogeneity, contributing to the problem. Here, we demonstrate that marine mammals, elasmobranchs and teleost fishes return drastically different spatial conservation priority areas, based on Marxan scenarios for 42 marine predator species in the Mediterranean Sea. None of the marine predators are sufficiently covered by the current marine protected area (MPA) system, with marine mammals being the least protected despite having the greatest designated MPA extent, highlighting disconnects between conservation goals and current management outcomes. To save marine predators, taxon specific ecological requirements and resulting spatial heterogeneity need to be accounted for in marine spatial planning.

ecology↗

bioRxiv2022

Phylogenetic analyses reveal bat communities in Northwestern Mexico harbour a high diversity of novel cryptic ectoparasite species

BackgroundParasites are integral parts of ecosystem function and important drivers of evolutionary processes. Characterising ectoparasite diversity is fundamental to studies of host-parasite interactions, evolution, and conservation, and also for understanding emerging disease threats for some vector borne pathogens. With more than 1,400 species, bats represent the second most speciose mammalian clade, but their ectoparasite fauna are poorly known for most species. MethodsWe sequenced mitochondrial Cytochrome Oxidase C subunit I and nuclear 18S ribosomal gene fragments, and used Bayesian phylogenetic analyses to characterise ectoparasite taxon identity and diversity for 17 species of parasitized bats sampled along the Baja California peninsula and in Northwestern Mexico. ResultsThe sequence data revealed multiple novel lineages of bat bugs (Cimicidae), flies (Nycteribiidae and Streblidae) and ticks (Argasidae). Within families, the new linages showed more than 10% sequence divergence, which is consistent with separation at least at the species level. Both families of bat flies showed host specificity, particularly on Myotis species. We also identified new records for the Baja peninsula of one tick (Carios kelleyi), and of five Streblid bat flies. One Nycteribiid bat fly haplotype from Pallid bat (Antrozous pallidus) hosts was found throughout the peninsula, suggesting potential long distance co-dispersal with hosts. Different bat bug and tick communities were found in the north and south of the peninsula. ConclusionsThis study is the first systematic survey of bat ectoparasites in the Baja California peninsula, discovering highly genetically differentiated novel lineages compared to other parts of North America. For some ectoparasite species, haplotype distributions may reflect patterns of bat migration. This work is a first step in characterising ectoparasite diversity over the Baja California peninsula, and understanding how ecological and evolutionary interactions shape bat ectoparasite communities among host species in different parts of their ranges.

ecology↗

bioRxiv2021

Ferries and environmental DNA: underway sampling from commercial vessels provides new opportunities for systematic genetic surveys of marine biodiversity

Marine environmental DNA (eDNA) is an important tool for biodiversity research and monitoring but challenges remain in scaling surveys over large spatial areas, and increasing the frequency of sampling in remote locations at reasonable cost. Here we demonstrate the feasibility of sampling from commercial vessels (Mediterranean ferries) while underway, as a strategy to facilitate replicable, systematic marine eDNA surveys in locations that would normally be challenging and expensive for researchers to access. Sixteen eDNA samples were collected from 4 fixed sampling stations, and in response to 4 cetacean sightings, across three cruises undertaken along the 300 km ferry route between Livorno (Tuscany) and Golfo Aranci (Sardinia) in the Ligurian/Tyrrhenian Seas, June-July 2018. Using 12SrDNA and 16SrDNA metabarcoding markers, we recovered diverse marine vertebrate Molecular Operational Taxonomic Units (MOTUs) from teleost fish, elasmobranchs, and cetaceans. We detected sample heterogeneity consistent with previously known variation in species occurrences, including putative species spawning peaks associated with specific sea surface temperature ranges, and increased night time abundance of bathypelagic species known to undertake diel migrations through the water column. We suggest commercial vessel based marine eDNA sampling using the global shipping network has potential to facilitate broad-scale biodiversity monitoring in the worlds oceans.

molecular biology↗

bioRxiv2019

Novel Universal Primers For Metabarcoding eDNA Surveys Of Marine Mammals And Other Marine Vertebrates

Metabarcoding studies using environmental DNA (eDNA) and high throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals have received less attention. Similarly, there have been few attempts to identify potentially universal barcode loci which may be informative across multiple marine vertebrate Orders. Here we describe the design and validation of four new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. In silico validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators.

ecology↗