John P Wares

• Ph.D. in Zoology
• Professor (Associate) at University of Georgia

Nearly neutral theory predicts that evolutionary processes will differ in small populations compared to large populations, a key point of concern for endangered species. The nearly-neutral threshold, the span of neutral variation, and the adaptive potential from new mutations all differ depending on $N_e$. To determine how genomes respond in small...

Fireflies use bioluminescent signals to communicate with their mates. Luciferase has been thought to be the sole contributor to light color; however, populations of the Photinus pyralis firefly display variation in the color of their emitted signals yet have identical luciferase sequences. Here, we examined whether pigments could be present in the...

Mass mortality events provide valuable insight into biological extremes and also ecological interactions more generally. The sea star wasting epidemic that began in 2013 catalyzed study of the microbiome, genetics, population dynamics, and community ecology of several high-profile species inhabiting the northeastern Pacific but exposed a dearth of...

Observations that biodiversity—particularly in coastal marine species—is redistributing itself as the environment changes have been key indicators of the climate change era. Historical surveys help us identify such patterns in taxa that might not be typically monitored for distribution or abundance. As recently as 1992, the southern ribbed mussel G...

We present the complete genome sequences of Geukensia demissa and Geukensia granosissima . Illumina sequencing was performed on genetic material from museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are available via Genbank.

Hybrid zones are important windows into the evolutionary dynamics of populations, revealing how processes like introgression and adaptation structure population genomic variation. Importantly, they are useful for understanding speciation and how species respond to their environments. Here, we investigate two closely related sea star species, Asteri...

Observations that biodiversity - particularly in coastal marine species - is redistributing itself as the environment changes has been a key indicator of the climate change era. Historical surveys help us identify such patterns in taxa that might not be typically monitored for distribution or abundance. As recently as 1992, the southern ribbed muss...

As global temperatures warm, species must adapt to a changing climate or transition to a different location suitable for their survival. Understanding the extent to which species are able to do so, particularly keystone species, is imperative to ensuring the survival of key ecosystems. The ribbed mussel Geukensia demissa is an integral part of salt...

An explanation for variation in impacts of sea star wasting disease across asteroid species remains elusive. Although various traits have been suggested to play a potential role in sea star wasting susceptibility, currently we lack a thorough comparison that explores how life-history and natural history traits shape responses to mass mortality acro...

Mass mortality events are increasing globally in frequency and magnitude, largely as a result of human-induced change. The effects of these mass mortality events, in both the long and short term, are of imminent concern because of their ecosystem impacts. Genomic data can be used to reveal some of the population-level changes associated with mass m...

We report the first verified DNA barcode data for the tropical chthamalid barnacle Rehderella belyaevi (Zevina & Kurshakova, 1973) and place it in phylogenetic and biogeographic context among other lineages of Pacific barnacles. Hitherto found on a few remote but widely separated islands across the South Pacific, R. belyaevi is the sole described s...

Sea star wasting—marked in a variety of sea star species as varying degrees of skin lesions followed by disintegration— recently caused one of the largest marine die-offs ever recorded on the west coast of North America, killing billions of sea stars. Despite the important ramifications this mortality had for coastal benthic ecosystems, such as inc...

Aim As within‐species genomic data have been shown useful in interpreting broader biogeographic trends, we analysed the mode of population genomic isolation involved in a well‐studied intertidal genomic cline to better understand the mechanisms maintaining it. These results were interpreted in the context of spatial variation in habitat use and ava...

William Anderson Newman passed away on December 26th 2020 at his home in La Jolla, California, aged 93. Bill spent much of his academic life at Scripps Institution of Oceanography, and also had a long and enduring association with the California Academy of Sciences. A marine biologist with deep interests in palaeontology and geology, Bill made spec...

Knowledge concerning the different ages of species and their distribution enhance our understanding of processes that create and maintain species diversity at both local and regional levels. The largest family of freshwater mussels (Unionidae), reach their highest species diversity in drainages of the southeastern United States. By sequencing multi...

Sea star wasting (SSW) disease describes a condition affecting asteroids that resulted in significant Northeastern Pacific population decline following a mass mortality event in 2013. The etiology of SSW is unresolved. We hypothesized that SSW is a sequela of microbial organic matter remineralization near respiratory surfaces, one consequence of wh...

Freshwater unionid bivalves currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways, and overfishing. These species are notable for their unusual life history strategy, parasite‐host coevolution, and biparental mitochondria inheritance. Amo...

Crustacea display diverse life histories and occur in all marine habitats. This makes them particularly useful when thinking about how we can predict geographical distribution from life history and ecology. As would be expected from such diversity, crustaceans exhibit various population connectivity patterns, from panmictic, well-connected populati...

This volume examines Evolution and Biogeography of Crustacea, one of the dominant groups of animals, especially in aquatic environments. The first part of this volume is dedicated to the explanation of the origins and successful establishment of the Crustacea in the oceans. In the second part the biogeography of the Crustacea is explored in order t...

The distance travelled by marine larvae varies by seven orders of magnitude. Dispersal shapes marine biodiversity, and must be understood if marine systems are to be well managed. Because warmer temperatures quicken larval development, larval durations might be systematically shorter in the tropics relative to those at high latitudes. Nevertheless,...

Sea star wasting (SSW) disease describes a condition affecting asteroids that resulted in significant Northeastern Pacific population decline following a mass mortality event in 2013. The etiology of sea star wasting is unresolved. We hypothesize that asteroid wasting is a sequela of microbial organic matter remineralization near respiratory surfac...

As organisms are faced with intense rapidly changing selective pressures, new genetic material is required to facilitate adaptation. Among sources of genetic novelty, gene duplications and transposable elements (TEs) offer new genes or new regulatory patterns that can facilitate evolutionary change. With advances in genome sequencing it is possible...

Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as ‘asteroid idiopathic wasting syndrome’ (AIWS) due to its elusive etiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progressi...

In the past 40 years, the ability to distinguish phenotypically similar species by using molecular methods has rapidly changed the study of taxonomy, biogeography, and community diversity. A cosmopolitan family of acorn barnacles, Chthamalidae Darwin, 1854, can be found on almost every non-boreal coast, with very similar habitat requirements, larva...

Better understanding of the mechanisms by which novel species arrive in marine communities is not only important for documenting such arrivals but can also lead to a better awareness of the abiotic and biotic limits on species distributions. Here we integrate spatial survey data, metapopulation hindcast modeling, and new genetic data from allozymes...

An overdominant mutation in an intron of the elongation factor 1- α (EF1A) gene in the sea star Pisaster ochraceus has shown itself to mediate tolerance to “sea star wasting disease”, a pandemic that has significantly reduced sea star populations on the Pacific coast of North America. Here we use RNA sequencing of healthy individuals to identify di...

Supplemental Table S1 Library name, EF1A genotype, RNA quality (RIN), SRA Accession, library size, righting response (seconds; standard deviation in parentheses), and percentage of reads mapped to the Trinity assembly. Libraries for Po1 and Po2 (both temperature treatments) contributed to the reduced-input assembly. All sequence data are archived a...

An overdominant mutation in the elongation factor 1-alpha (EF1A) gene in the sea star Pisaster ochraceus has shown itself to mediate tolerance to "sea star wasting disease", a pandemic that has significantly reduced sea star populations on the Pacific coast of North America. Here we use RNA sequencing of healthy individuals to identify differences...

An overdominant mutation in the elongation factor 1-alpha (EF1A) gene in the sea star Pisaster ochraceus has shown itself to mediate tolerance to "sea star wasting disease", a pandemic that has significantly reduced sea star populations on the Pacific coast of North America. Here we use RNA sequencing of healthy individuals to identify differences...

We evaluate the population genetic structure of the intertidal barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from over 3,000 km of the linear range of this species, there is only slight regional structure indicated,...

Male genitalia are extraordinarily diverse, and this diversity makes them valuable taxonomic and phylogenetic markers. Genitalia of true crabs (Brachyura) consist of two pairs of modified appendages, or gonopods. The first pair is tubular, and holds the second pair during copulation. Whether the second pair is shorter or longer than the first pair...

We evaluate the population genetic structure of the intertidal barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from over 3000km of the linear range of this species, there is only slight regional structure indicated, w...

We evaluate the population genetic structure of the intertidal barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from over 3000km of the linear range of this species, there is only slight regional structure indicated, w...

We evaluate the population genetic structure of the intertidal barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from over 3000km of the linear range of this species, there is only slight regional structure indicated, w...

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has an unusual sex...

R script detailing Palfinder output screening.

Microsatellite genotypes for each individual with individual ID and collection date.

Summary of microsatellite loci detected by Palfinder in genomic reads.

R script detailing marker characterization.

R script: Calculate genome coverage from geneious blast output.

Dispersal and adaptation are the two primary mechanisms that set the range distributions for a population or species. As such, understanding how these mechanisms interact in marine organisms in particular – with capacity for long-range dispersal and a poor understanding of what selective environments species are responding to – can provide useful i...

In recent years, a massive mortality event has killed millions of sea stars, of many different species, along the Pacific coast of North America. This disease event, known as ‘sea star wasting disease’ (SSWD), is linked to viral infection. In one affected sea star ( Pisaster ochraceus ), previous work had identified that the elongation factor 1- α...

Genotype and metadata for analyzed specimens of Pisaster All individual genotype data are provided in this spreadsheet, with the “Master Data” tab including all genotype and metadata used in analyses. Additional information specific to site collections are located on other tabs in the spreadsheet.

Binomial regression output and AIC model selection information This file provides output from model calls on raw data, sorted by model, followed by AIC model selection information.

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has a unusual sexu...

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has a unusual sexu...

Using high-throughput sequencing approaches to quantify biodiversity has a number of hurdles, in particular that the number of reads for a given taxon may not be proportional to the number of individuals of that taxon in a sample. Here, we consider whether summary statistics generated in the course of population genetic analyses (such as estimates...

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has a unusual sexu...

Androdioecy was first described by Darwin in his seminal work on barnacle diversity; he identified males and hermaphrodites in the same reproductive population. Today we realize that many androdioecious plants and animals share astonishing similarities, particularly with regard to their evolutionary history and mating system. Notably, these species...

Using high-throughput sequencing approaches to quantify biodiversity has a number of hurdles, in particular that the number of reads for a given taxon may not be proportional to the number of individuals of that taxon in a sample. Here, we consider whether summary statistics generated in the course of population genetic analyses (such as estimates...

We analyzed the population structure of the edible barnacle Austromegabalanus psittacus (Molina, 1782) along most of the coast of Chile. The analysis of population structure was based on nucleotide sequences of the mitochondrial cytochrome oxidase I (COI) gene region. We also tested for differences between the regions to the north and south of 30-3...

In recent years, a massive plague has killed millions of sea stars, of many different species, along the Pacific coast of North America. This disease, known as 'sea star wasting disease' (SSWD), is thought to be caused by viral infection. In the affected sea star Pisaster ochraceus , previous work had identified that the elongation factor 1-α (EF1A...

In recent years, a massive plague has killed millions of sea stars, of many different species, along the Pacific coast of North America. This disease, known as 'sea star wasting disease' (SSWD), is thought to be caused by viral infection. In the affected sea star Pisaster ochraceus , previous work had identified that the elongation factor 1-α (EF1A...

Coral surface mucus layer (SML) microbiota are critical components of the coral holobiont and play important roles in nutrient cycling and defense against pathogens. We sequenced 16S rRNA amplicons to examine the structure of the SML microbiome within and between colonies of the threatened Caribbean reef-building coral Acropora palmata in the Flori...

Results of permutational ANOVA based on Bray-Curtis dissimilarities of phylogenetic distance. (PDF)

Rarefaction results. (PDF)

In recent years, a massive plague has killed millions of seastars, of many different species, along the Pacific coast of North America. This disease, known as 'seastar wasting disease' (SSWD), is thought to be caused by viral infection. In the affected seastar Pisaster ochraceus, previous work had identified that the elongation factor 1-α locus har...

The barnacle Chthamalus fragilis is found along the US Atlantic seaboard historically from the Chesapeake Bay southward, and in the Gulf of Mexico. It appeared in New England circa 1900 coincident with warming temperatures, and is now a conspicuous member of rocky intertidal communities extending through the northern shore of Cape Cod, Massachusett...

Androdioecy is a sexual system characterized by the coexistence of hermaphrodites and males. It has evolved several times independently in ancestrally hermaphroditic barnacles. Life history and sex allocation theory suggest that dwarf males can occur in hermaphroditic populations with very small mating groups, low growth rates and high mortality ra...

Here I evaluate the population genetic structure of the barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from close to 3000km of the linear range of this barnacle, there is little evidence for population structure. Hud...

Here I evaluate the population genetic structure of the barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from close to 2500km of the linear range of this barnacle, there is little evidence for population structure. Hud...

Classic biogeographic studies emphasized differences in species composition between regions to define biogeographic provinces and delimit biogeographic boundaries. Here we analyze the permeability of biogeographic boundaries to different species to gain mechanistic insight into the processes that maintain species boundaries in the coastal ocean. We...

There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promi...

The major histocompatibility complex (MHC) is an important component of vertebrate immune defense involved with self/nonself recognition and disease susceptibility. The high variability of genes of the MHC is thought to arise from both parasite-mediated and sexual selection. An outstanding question involves the degree to which balancing selection c...

There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promi...

There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promi...

There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promi...

Reproductive compatibility proteins have been shown to evolve rapidly under positive selection leading to reproductive isolation, despite the potential homogenizing effects of gene flow. This process has been implicated in both primary divergence among conspecific populations and reinforcement during secondary contact; however, these two selective...

The evolutionary pressures that drive long larval planktonic durations in some coastal marine organisms, while allowing direct development in others, have been vigorously debated. We introduce into the argument the asymmetric dispersal of larvae by coastal currents and find that the strength of the currents helps determine which dispersal strategie...

A mitochondrial cline along the Chilean coast in the barnacle Notochthamalus scabrosus suggests a species history of transient allopatry and secondary contact. However, previous studies of nuclear sequence divergence suggested population genetic homogeneity across northern and central Chile. Here we collect SNP data from pooled population samples s...

Abstract Eight whole mitochondrial genomes from the barnacle Notochthamalus scabrosus, with one from the northern lineage and seven from the divergent southern lineage, are presented. The annotated and aligned data were analyzed for signals of non-neutral evolution. Overall, these data are consistent with purifying selection operating on the protei...

Shoal basses are a cryptic clade composed of Micropterus spp. restricted to the Apalachicola River system and three Atlantic slope river drainages in the southeastern US. This reciprocally monophyletic clade includes the Shoal Bass, Micropterus cataractae Williams and Burgess (endemic to the Apalachicola River system) and an undescribed form from e...

Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characte...

The fluorescent protein (FP) gene family is a highly diverse group of proteins whose expression govern color diversity in corals. Here, we examine the genetic diversity of FPs and the extent to which it can be used to assess phylogenetic relationships within the coral genus Agaricia. Tissue samples were collected throughout the Florida Keys from a...

As marine environments change, the greatest ecological shifts-including resource usage and species interactions-are likely to take place in or near regions of biogeographic and phylogeographic transition. However, our understanding of where these transitional regions exist depends on the defining criteria. Here we evaluate phylogeographic transitio...

Approximate Bayesian computation (ABC) is useful for parameterizing complex models in population genetics. In this study, ABC was applied to simultaneously estimate parameter values for a model of metapopulation coalescence and test two alternatives to a strict metapopulation model in the well-studied network of Daphnia magna populations in Finland...

Overfishing of herbivorous fishes is one of the primary causes of Caribbean coral reef decline. In Belize, herbivorous fishes comprised 28% of the catch from 2005 to 2008. In 2009, the Belize Fisheries Department implemented a national ban on herbivorous fish harvesting to mitigate high-macroalgal cover on much of the Belize Barrier Reef. However,...

A large section of the tropical Eastern Pacific coastline is nearly devoid of reef or consolidated habitat, and is known as the Central American Gap as it is associated with a biogeographic transition in fish and invertebrate species. We analyze phylogeographic data for intertidal barnacles (Chthamalus) to identify relevant temporal patterns that d...

Extinction is ubiquitous in natural systems and the ultimate fate of all biological populations. However, the factors that contribute to population extinction are still poorly understood, particularly genetic diversity and composition. A laboratory experiment was conducted to examine the influences of environmental variation and genotype diversity...

North American freshwater mussels are critically imperiled organisms that generally require fish hosts in order to complete their life cycle. Although numerous studies have focused on the parasitic relationship between mussels and fishes, few have examined the benefits that mussels provide to other organisms. During sampling of Altamaha River, Geor...

Genetic datasets can be used to date evolutionary events, even on recent time scales if sufficient data are available. We used statistics calculated from multilocus microsatellite datasets to estimate population ages in data generated through coalescent simulations and in samples from populations of known age in a metapopulation of Daphnia magna in...

In many species, alternative developmental pathways lead to the production of two distinct phenotypes, promoting the evolution of morphological novelty and diversification. Offspring type in marine invertebrates influences transport time by ocean currents, which dictate dispersal potential and gene flow, and thus has sweeping evolutionary effects o...

Using mitochondrial DNA sequence data and genotypic data from four microsatellite loci, we evaluate the population genetic structure for three common species of the freshwater mussel genus Elliptio in the Altamaha River basin in Georgia, USA. These data are intended to evaluate whether distinct management strategies should be applied to upper and l...

A significant genetic cline has previously been identified along the Chilean coast in the barnacle Notochthamalus scabrosus. Samples from the previous study, spanning 800 km, were not able to show whether the southern lineage ultimately goes to fixation at higher latitudes. In addition to expanding the geographic sampling of this species, locations...

Despite the typical assumption in studies of mitochondrial diversity that such data are useful for approximating population size and demography, studies of sequence diversity in mitochondrial DNA across the Metazoa have shown a surprising excess of rare alleles, a pattern associated either with strong selection or population growth. Previous work h...

Next-generation sequencing technology is now frequently being used to develop genomic tools for non-model organisms, which are generally important for advancing studies of evolutionary ecology. One such species, the marine annelid Streblospio benedicti, is an ideal system to study the evolutionary consequences of larval life history mode because th...

Categories and statistics for 84 SNPs. SNPs that did not meet the criterion for BLAST e- values are left blank. For substitution type, Syn is a putatively synonymous substitution and NS is a putatively nonsynonymous substitution. – designates when an allele is fixed. SNPs that have a He (heterozygosity) over 0.35 generally dropped out all genotypin...

The native trout of New Mexico and Arizona have been managed for conservation for almost 80 years and are currently listed under the US Endangered Species Act. Management of these populations has improved the outlook for these species. However, because of a history of non-native salmonids being stocked in the region, genetic analysis of the remaini...

Reanalysis of aligned sequence data from the mitochondrial cytochrome oxidase I gene region across Crustacea has generated a number of new insights into how we can interpret genetic variation in these species. Some insights, such as the relationship between genetic diversity and the latitudinal biodiversity gradient, have been predicted in earlier...