Michelle R Gaither

Durham University | DU · School of Biological and Biomedical Sciences

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome‐scale genetic diversity data for wild p...

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservat...

Fish have one of the highest occurrences of individual specialization in trophic strategies among Eukaryotes. Yet, few studies characterize this variation during trophic niche analysis, limiting our understanding of aquatic food web dynamics. Stable isotope analysis (SIA) with advanced Bayesian statistics is one way to incorporate this individual t...

Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly...

In this special issue, we assemble novel research and reviews that contribute to the growing literature on the utility of metabarcoding for the study of marine systems. Included are important contributions that highlight methodological advancements and that employ metabarcoding techniques across a diversity of taxa to answer questions ranging from...

Background Understanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in con...

Genomic data are being produced and archived at a prodigious rate, and current studies could become historical baselines for future global genetic diversity analyses and monitoring programs. However, when we evaluated the potential utility of genomic data from wild and domesticated eukaryote species in the world’s largest genomic data repository, w...

Findings from eDNA metabarcoding are strongly influenced by experimental approach, yet the effect of pre‐PCR sample processing on taxon detection and estimates of biodiversity across different water types is still poorly resolved. To fill this data gap, we investigated the impact of sampling effort, extraction method, and filter pore size on DNA yi...

The common or weedy seadragon, Phyllopteryx taeniolatus, is an iconic and endemic fish found across temperate reefs of southern Australia. Despite its charismatic nature, few studies have been published, and the extent of population sub-structuring remains poorly resolved. Here we used 7462 single nucleotide polymorphisms (SNPs) to identify the ext...

Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic O...

Non-sex-linked color polymorphism is common in animals and can be maintained in populations via balancing selection or, when under diversifying selection, can pro-mote divergence. Despite their potential importance in ecological interactions and the evolution of biodiversity, their function and the mechanisms by which these polymorphisms are mainta...

Environmental DNA (eDNA) is increasingly being used to document species distributions and habitat use in marine systems, with much of the recent effort focused on leveraging advances in next-generation DNA sequencing to assess and track biodiversity across taxonomic groups. Environmental DNA offers a number of important advantages over traditional...

Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance...

Population genetic analysis is an important tool for estimating the degree of evolutionary connectivity in marine organisms. Here, we investigate the population structure of the three-spot damselfish Dascyllus trimaculatus in the Red Sea, Arabian Sea and Western Indian Ocean, using 1174 single nucleotide polymorphisms (SNPs). Neutral loci revealed...

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. It contributes to the informatics stack – Biocode Commons – of the Genomic Observatories Network (https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-3...

Intraspecific diversity promotes evolutionary change, and when partitioned among geographic regions or habitats can form the basis for speciation. Marine species live in an environment that can provide as much scope for diversification in the vertical as in the horizontal dimension. Understanding the relevant mechanisms will contribute significantl...

The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120–253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To r...

A Bayesian time-calibrated phylogeny of Stenopus hispidus A Bayesian time-calibrated phylogeny based on the cytochrome c oxidase subunit I (COI) of Stenopus hispidus with sister species (S. pyrsonotus, S. zanzibaricus, S. scutellatus) and sister genera (Synalpheus sp. and Alpheus bellulus) as outgroups (Shi et al., 2012) (525 bp) was generated usin...

A Bayesian Skyline Plot (A) The Western Atlantic shows a relatively stable population whereas the (B) Overall Dataset with the Pacific population included shows evidence of a recent population expansion.

Unique sequences of Stenopus hispidus FASTA file of unique sequences for Stenopus hispidus.

This study investigated taxonomic validity of the pale ghost shark Hydrolagus pallidus Hardy & Stehmann, 1990, which was described as a species distinct from the smalleyed rabbitfish H. affinis (de Brito Capello 1868). While few morphological characters distinguish the two taxa, a striking difference in sex ratio and fixed differences (1·1–1·6% div...

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary...

The Arabian Sea is a heterogeneous region with high coral cover and warm stable conditions at the western end (Djibouti), in contrast to sparse coral cover, cooler temperatures, and upwelling at the eastern end (southern Oman). We tested for barriers to dispersal across this region (including the Gulf of Aden and Gulf of Oman), using mitochondrial...

Closely related marine species with large sympatric ranges provide opportunities to study the mechanisms of speciation, particularly when there is evidence of gene flow between the lineages. Here we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondri...

The pygmy angelfishes (genus Centropyge) provide numerous examples of discordance between color morphology, taxonomy and evolutionary genetic lineages. This discordance is especially evident in the Centropyge flavissima complex, which includes three primary color morphs, three previously recognized species (C. flavissima, C. eibli and C. vrolikii)...

Assortative mating based on ecologically divergent traits is a major driver of speciation among three-spined sticklebacks, however, little is known about reproductive isolation and variations in courtship behaviour among nine-spined sticklebacks. Here we demonstrate assortative mating and divergent courtship behaviours between two cryptic species o...

Briggs (1960) published the first checklist of circumtropical fishes with 107 species. This work served for a half century as the most comprehensive checklist of globally distributed fishes, but the intervening years witnessed many discoveries, and molecular data have changed the way we evaluate species. Here, we update the list guided by taxonomic...

Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic id...

Here we consider the role of depth as a driver of evolution in a genus of deep-sea fishes. We provide a phylogeny for the genus Coryphaenoides (Gadiformes: Macrouridae) that represents the breadth of habitat use and distributions for these species. In our consensus phylogeny species found at abyssal depths (> 4000 m) form a well-supported lineage,...

To resolve phylogeographical partitions in the pronghorn spiny lobster, Panulirus penicillatus, which has a nine-month pelagic larval phase and the broadest distribution among spiny lobsters. With samples from the Red Sea to the East Pacific, we test genetic partitions across two-thirds of the planet, in a species with one of the longest pelagic ph...

Conservation of ecological communities requires deepening our understanding of genetic diversity patterns and drivers at community-wide scales. Here, we use seascape genetic analysis of a diversity metric, allelic richness (AR), for 47 reef species sampled across 13 Hawaiian Islands to empirically demonstrate that large reefs high in coral cover ha...

Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographic features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two-band anemonefish...

The Red Sea is characterised by a unique fauna and historical periods of desiccation, hypersalinity and intermittent isolation. The origin and contemporary composition of reef-associated taxa in this region can illuminate biogeographical principles about vicariance and the establishment (or local extirpation) of existing species. Here we aim to: (1...

Aim The geological and palaeo-climatic forces that produced the unique biodiversity in the Red Sea are a subject of vigorous debate. Here, we review evidence for and against the hypotheses that: (1) Red Sea fauna was extirpated during glacial cycles of the Pleistocene and (2) coral reef fauna found refuge within or just outside the Red Sea during l...

A phylogeographic study of the circumtropical glasseye Heteropriacanthus cruentatus was conducted. Molecular analyses indicate two mitochondrial cytochrome c oxidase subunit I (coI) lineages that are 10·4% divergent: one in the western Atlantic (Caribbean) and another that was detected across the Indo-Pacific. A fixed single nucleotide polymorphism...

The drivers of speciation remain among the most controversial topics in evolutionary biology. Initially, Darwin emphasized natural selection as a primary mechanism of speciation, but the architects of the modern synthesis largely abandoned that view in favor of divergence by geographic isolation. The balance between selection and isolation is still...

During expeditions to Curaçao in August and October of 2013, a large number of fish infected with dermal parasites was observed. Infected individuals presented black spots and white blemishes on their skin and fins that were easily observed by divers, and which have been associated with infections by trematodes, turbellarians, and protozoans (Crypt...

Settlement-stage larvae of the widespread apogonid Gymnapogon urospilotus are described and illustrated from specimens captured with crest nets at Moorea, Society Islands. Identification was confirmed by COI mitochondrial DNA analysis. Otoliths of the larvae had no settlement mark, indicating they had not previously settled, and 33–40 presumed dail...

This study investigated the birth of a brownbanded bamboo shark Chiloscyllium punctatum at the Steinhart Aquarium. Genetic analyses suggest this is the longest documented case of sperm storage for any species of shark (45 months).

Hybridization in the ocean was once considered rare, a process prohibited by the rapid evolution of intrinsic reproductive barriers in a high-dispersal medium. However, recent genetic surveys have prompted a reappraisal of marine hybridization as an important demographic and evolutionary process. The Hawaiian Archipelago offers an unusual case hist...

What shapes variation in genetic structure within a community of co-distributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the a...

The Indo-Malay-Philippine (IMP) biodiversity hotspot, bounded by the Philip-pines, the Malay Peninsula and New Guinea, is the epicentre of marine biodi-versity. Hypotheses to explain the source of the incredible number of species found there include the centre of overlap hypothesis, which proposes that in this region the distinct faunas of the Paci...

Aim The Red Sea is a biodiversity hotspot characterized by a unique marine fauna and high endemism. This sea began forming c. 24 million years ago with the separation of the African and Arabian plates, and has been characterized by periods of desiccation, hypersalinity and intermittent connection to the Indian Ocean. We aim to evaluate the impact o...

Forecasting invasion success remains a fundamental challenge in invasion biology. The effort to identify universal characteristics that predict which species become invasive has faltered in part because of the diversity of taxa and systems considered. Here, we use an alternative approach focused on the spread stage of invasions. FST, a measure of a...

The advent of Sanger sequencing represented a scientific breakthrough that greatly advanced biogeographic studies. However, this technology has several limitations that have hampered more ad‐ vanced studies in the field. The development of novel techniques which more fully exploit the potential of Massively Parallel Sequencing (MPS) to deliver sequ...