Poor data stewardship will hinder global genetic diversity surveillance.

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, we found that most archived genomic datasets (86%) lacked the spatiotemporal metadata necessary for genetic biodiversity surveillance. Labor-intensive scouring of a subset of published papers yielded geospatial coordinates and collection years for only 33% (39% if place names were considered) of these genomic datasets. Streamlined data input processes, updated metadata deposition policies, and enhanced scientific community awareness are urgently needed to preserve these irreplaceable records of today's genetic biodiversity and to plug the growing metadata gap.

Importance of timely metadata curation to the global surveillance of genetic diversity.

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 populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.

Importancia de la curación oportuna de metadatos para la vigilancia mundial de la diversidad genética Resumen La diversidad genética intraespecífica representa un nivel fundamental, pero a la vez subvalorado de la biodiversidad. La diversidad genética puede indicar la resiliencia de una especie ante el clima cambiante, por lo que su medición es relevante para muchos objetivos de la política de conservación mundial y nacional. Muchos estudios producen una gran cantidad de datos sobre la diversidad a nivel genético de las poblaciones silvestres, aunque la mayoría (87%) no incluye los metadatos espaciales y temporales asociados para que sean reutilizados en los programas de monitoreo o para reconocer la soberanía de las naciones o los pueblos indígenas. Realizamos un "datatón" distribuido para cuantificar la disponibilidad de estos metadatos faltantes y para probar la hipótesis que supone que esta disponibilidad se deteriora con el tiempo. También trabajamos para reparar los metadatos faltantes al extraerlos de los artículos asociados publicados, los repositorios en línea y la comunicación directa con los autores. Iniciamos con 838 candidatos de conjuntos de datos genómicos (representación reducida y genoma completo) tomados de la colaboración internacional para la base de datos de secuencias de nucleótidos y determinamos que 561 incluían en su mayoría muestras tomadas de poblaciones silvestres. Restauramos con éxito los metadatos espaciotemporales en el 78% de estos 561 conjuntos de datos (n = 440 conjuntos de datos con información sobre 45,105 individuos de 762 especies en 17 filos). El análisis de los artículos y los repositorios virtuales fue mucho más productivo que contactar a los 351 autores, quienes tuvieron un 45% de respuesta a nuestros correos. En general, el 23% de nuestras consultas descubrieron metadatos útiles. La probabilidad de recuperar metadatos espaciotemporales declinó de manera significativa conforme incrementó la antigüedad del conjunto de datos. Hubo una disminución anual del 13.5% en los metadatos asociados con los artículos publicados y los repositorios virtuales y hasta una disminución anual del 22% en los metadatos que sólo estaban disponibles mediante la comunicación con los autores. Este rápido deterioro en la disponibilidad de los metadatos, duplicado en estudios de otros tipos de datos biológicos, debería motivar la pronta actualización de las políticas del intercambio de datos y las prácticas de los investigadores para asegurar que en las ciencias de la conservación no se pierda para siempre el contexto valioso proporcionado por los metadatos.

The physiology of rapid ecological specialization: A look at the Midas cichlids.

Understanding the process of speciation is a primary goal of evolutionary biology, yet the question of whether speciation can reach completion in the presence of gene flow remains controversial. For more than 50 years, the cichlids of Africa, and more recently those in South and Central America, have served as model systems for the study of speciation in nature. Cichlids are distinguished by their enormous species richness, their diversity of behavioural and trophic adaptations, and their rapid rate of divergence. In both Africa and South and Central America, the repeated interaction of geology, new founder events and adaptive evolution has created a series of natural experiments with speciation occurring both within and between waterbodies of differing ages. In the "From the Cover" paper in this issue of the Journal of Molecular Ecology, Raffini, Schneider, Franchini, Kautt and Meyer move beyond the question of which mechanisms drive speciation, and instead show that divergent morphologies and physiologies translate into adaptive traits. They investigate differences in physiology and gene expression profiles in a benthic/limnetic species pair of Midas cichlidsin a 24,000-year-old Nicaraguan crater lake. While recently diverged, these two species demonstrate significant ecological, but limited genetic differentiation. The authors find that the distinct morphotypes translate into relevant differences in swimming performance and metabolic rates that correspond to differential gene expression profiles. Hence, the authors take an integrative approach examining the impacts of morphological differences on performance and niche partitioning: an approach that can advance our understanding of the drivers of morphological and physiological divergence during speciation.

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.

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 analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.

Comparative phylogeography of the ocean planet.

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 identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.

Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon).

Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site-associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister-species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174-0.263 Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.

Depth as a driver of evolution in the deep sea: Insights from grenadiers (Gadiformes: Macrouridae) of the genus Coryphaenoides.

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 (>4000m) form a well-supported lineage, which interestingly also includes two non-abyssal species, C. striaturus and C. murrayi, diverging from the basal node of that lineage. Biogeographic analyses suggest the genus may have originated in the Southern and Pacific Oceans where contemporary species diversity is highest. The abyssal lineage seems to have arisen secondarily and likely originated in the Southern/Pacific Oceans but diversification of this lineage occurred in the Northern Atlantic Ocean. All abyssal species are found in the North Atlantic with the exception of C. yaquinae in the North Pacific and C. filicauda in the Southern Ocean. Abyssal species tend to have broad depth ranges and wide distributions, indicating that the stability of the deep oceans and the ability to live across wide depths may promote population connectivity and facilitate large ranges. We also confirm that morphologically defined subgenera do not agree with our phylogeny and that the Giant grenadier (formerly Albatrossia pectoralis) belongs to Coryphaenoides, indicating that a taxonomic revision of the genus is needed. We discuss the implications of our findings for understanding the radiation and diversification of this genus, and the likely role of adaptation to the abyss.

Angelfishes, Paper Tigers, and the Devilish Taxonomy of the Centropyge flavissima Complex.

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, Centropyge eibli, and Centropyge vrolikii) and three distinct mitochondrial (mtDNA) lineages that do not align with species designations. Our previous research showed that the putative C. flavissima arose independently in the Indian and Pacific Oceans, and the three mtDNA lineages align with geography rather than species assignments. Here, we add 157 specimens to the previous dataset of 291 specimens, spread across a greater geographic range, to pinpoint the distribution of mtDNA lineages and color morphs. We found that the mtDNA lineages show remarkably strong geographic boundaries corresponding to the Indian Ocean, Central-West Pacific, and Central-South Pacific. We also test the validity of the "Black Tiger Centropyge" in the C. flavissima species complex, a taxonomic oddity that is restricted to shoals and atolls off the coast of northwestern Australia, and the newly named Centropyge cocosensis assigned to the C. flavissima lineage in the Indian Ocean. We conclude that the Black Tiger Centropyge is not a valid species but rather an intermediate between sympatric color morphs that correspond to the putative species C. eibli and C. vrolikii Our greater sampling efforts also do not support the genetic distinctiveness of C. cocosensis given shared mtDNA haplotypes with the sympatric C. eibli and C. vrolikii, but instead we find conflicting lines of evidence concerning the taxonomy of this group. We urge caution and taxonomic restraint until the true nature of this species complex can be revealed.

Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes.

Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographical 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 Amphiprion bicinctus across its entire geographical range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the southern coast of Oman. Both the Red Sea and the Arabian Sea are complex and environmentally heterogeneous marine systems that provide an ideal scenario to address these questions. Our findings confirm the presence of two genetic clusters previously reported for A. bicinctus in the Red Sea. Genetic structure analyses suggest a complex seascape configuration, with evidence of both isolation by distance (IBD) and isolation by environment (IBE). In addition to IBD and IBE, genetic structure among sites was best explained when two barriers to gene flow were also accounted for. One of these coincides with a strong oligotrophic-eutrophic gradient at around 16-20˚N in the Red Sea. The other agrees with a historical bathymetric barrier at the straight of Bab al Mandab. Finally, these data support the presence of interspecific hybrids at an intermediate suture zone at Socotra and indicate complex patterns of genomic admixture in the Gulf of Aden with evidence of introgression between species. Our findings highlight the power of recent genomic approaches to resolve subtle patterns of gene flow in marine seascapes.

Genomic signatures of geographic isolation and natural selection in coral reef fishes.

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 favour of divergence by geographic isolation. The balance between selection and isolation is still at the forefront of the evolutionary debate, especially for the world's tropical oceans where biodiversity is high, but isolating barriers are few. Here, we identify the drivers of speciation in Pacific reef fishes of the genus Acanthurus by comparative genome scans of two peripheral populations that split from a large Central-West Pacific lineage at roughly the same time. Mitochondrial sequences indicate that populations in the Hawaiian Archipelago and the Marquesas Islands became isolated approximately 0.5 Ma. The Hawaiian lineage is morphologically indistinguishable from the widespread Pacific form, but the Marquesan form is recognized as a distinct species that occupies an unusual tropical ecosystem characterized by upwelling, turbidity, temperature fluctuations, algal blooms and little coral cover. An analysis of 3737 SNPs reveals a strong signal of selection at the Marquesas, with 59 loci under disruptive selection including an opsin Rh2 locus. While both the Hawaiian and Marquesan populations indicate signals of drift, the former shows a weak signal of selection that is comparable with populations in the Central-West Pacific. This contrast between closely related lineages reveals one population diverging due primarily to geographic isolation and genetic drift, and the other achieving taxonomic species status under the influence of selection.

Large-scale introduction of the Indo-Pacific damselfish Abudefduf vaigiensis into Hawai'i promotes genetic swamping of the endemic congener A. abdominalis.

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 history in this arena, due to the recent arrival of the widely distributed Indo-Pacific sergeant (Abudefduf vaigiensis), which is hybridizing with the endemic congener, A. abdominalis. Surveys of mtDNA and three nuclear loci across Hawai'i (N = 396, Abudefduf abdominalis and N = 314, A. vaigiensis) reveal that hybridization is significantly higher in the human-perturbed southeast archipelago (19.8%), tapering off to 5.9% in the pristine northwest archipelago. While densities of the two species varied throughout Hawai'i, hybridization was highest in regions with similar species densities, contradicting the generalization that the rarity of one species promotes interspecific mating. Our finding of later generation hybrids throughout the archipelago invokes the possibility of genetic swamping of the endemic species. Exaptation, an adaptation with unintended consequences, may explain these findings: the endemic species has transient yellow coloration during reproduction, whereas the introduced species has yellow coloration continuously as adults, in effect a permanent signal of reproductive receptivity. Haplotype diversity is higher in Hawaiian A. vaigiensis than in our samples from the native range, indicating large-scale colonization almost certainly facilitated by the historically recent surge of marine debris. In this chain of events, marine debris promotes colonization, exaptation promotes hybridization, and introgression invokes the possible collapse of an endemic species.

Evolution of pygmy angelfishes: recent divergences, introgression, and the usefulness of color in taxonomy.

The pygmy angelfishes (genus Centropyge, family Pomacanthidae) are brightly colored species that occupy reef habitats in every tropical ocean. Some species are rarely observed because they occur below conventional scuba depths. Their striking coloration can command thousands of U.S. dollars in the aquarium trade, and closely related species are often distinguished only by coloration. These factors have impeded phylogenetic resolution, and every phylogeographic survey to date has reported discordance between coloration, taxonomy, and genetic partitions. Here we report a phylogenetic survey of 29 of the 34 recognized species (N=94 plus 23 outgroups), based on two mtDNA and three nuclear loci, totaling 2272 bp. The resulting ML and Baysian trees are highly concordant and indicate that the genus Centropyge is paraphyletic, consistent with a previous analysis of the family Pomacanthidae. Two recognized genera (Apolemichthys and Genicanthus) nest within Centropyge, and two subgenera (Xiphypops and Paracentropyge) comprise monophyletic lineages that should be elevated to genus level. Based on an age estimate of 38 Ma for the family Pomacanthidae, Centropyge diverged from the closest extant genus Pygoplites about 33 Ma, three deep lineages within Centropyge diverged about 18-28 Ma, and four species complexes diverged 3-12 Ma. However, in 11 of 13 cases, putative species in these complexes are indistinguishable based on morphology and genetics, being defined solely by coloration. These cases indicate either emerging species or excessive taxonomic splitting based on brightly colored variants.

Population structure in the native range predicts the spread of introduced marine species.

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 alternative fixation of alleles, is a common proxy for realized dispersal among natural populations, summarizing the combined influences of life history, behaviour, habitat requirements, population size, history and ecology. We test the hypothesis that population structure in the native range (FST) is negatively correlated with the geographical extent of spread of marine species in an introduced range. An analysis of the available data (29 species, nine phyla) revealed a significant negative correlation (R(2) = 0.245-0.464) between FST and the extent of spread of non-native species. Mode FST among pairwise comparisons between populations in the native range demonstrated the highest predictive power (R(2) = 0.464, p < 0.001). There was significant improvement when marker type was considered, with mtDNA datasets providing the strongest relationship (n = 21, R(2) = 0.333-0.516). This study shows that FST can be used to make qualitative predictions concerning the geographical extent to which a non-native marine species will spread once established in a new area.

Reclassification of the Indo-Pacific Hawkfish Cirrhitus pinnulatus (Forster).

The hawkfish Cirrhitus pinnulatus Forster (in Bloch & Schneider 1801) was regarded as one wide-ranging Indo-Pacific species, from the Red Sea and east coast of Africa to the Hawaiian Islands and the islands of French Polynesia. Schultz (1950) resurrected the name C. alternatus Gill for the population in the Hawaiian Islands and Johnston Atoll, and described the Red Sea population as a new species, C. spilotoceps, based on morphological data. Randall (1963) confirmed the differences that Schultz used to separate Cirrhitus pinnulatus into three species, but preferred to regard them as subspecies. We examined more specimens, colour photographs, and used genetic comparisons to determine the validity of the three species recognized by Schultz (1950). Combining mitochondrial cytochrome oxidase I and cytochrome b sequence data from specimens of C. pinnulatus pinnulatus from the Indo-Pacific, C. spilotoceps from the Red Sea, and C. pinnulatus maculosus from Hawai'i, we detected levels of sequence divergence (5-12%) that support the species-level designation of C. spilotoceps. We detected no genetic differentiation but maintain the subspecies designation of the Hawaiian form based on morphological and colour differences. We found a third genetic lineage in the Indian Ocean and Western Pacific that is 5% divergent from C. spilotoceps. We refrain from designating this group as a separate subspecies until further morphological and genetic study can be completed.

Coming out of the starting blocks: extended lag time rearranges genetic diversity in introduced marine fishes of Hawai'i.

Biological invasions with known histories are rare, especially in the sea, and empirical studies of the genetic consequences are even rarer. Fifty-five years ago, the state of Hawai'i began a remarkable, if unintentional, 'experiment' with the introduction of three reef fishes, Lutjanus fulvus, Cephalopholis argus and Lutjanus kasmira. All have since expanded from the initial introduction of 2204 to 3163 individuals; however, historical records show that initially L. fulvus remained scarce, C. argus had modest population expansion and L. kasmira experienced rapid population growth. The consequences of differential population growth rates are apparent in F-statistics: Hawaiian L. fulvus demonstrate strong and significant haplotype frequency shifts from the founder location (F(ST) = 0.449), C. argus shows low but significant differentiation (F(ST) = 0.066) and L. kasmira is nearly identical to the founder location (F(ST) = 0.008). All three species had higher mtDNA diversity in the introduced range, which can be explained by multiple sources for L. fulvus and L. kasmira, but not for C. argus. We conclude that lag time before population expansion, in conjunction with genetic drift, has defined the genetic architecture of these three species in the introduced range.

Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary.

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 compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon's diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.

DNA Metabarcoding Across Disciplines: Sequencing Our Way to Greater Understanding Across Scales of Biological Organization.

DNA metabarcoding describes the use of targeted DNA (i.e., amplicon) sequencing to identify community constituents from a complex sample containing genetic material from multiple organisms, such as water, soil, gut contents, microbiomes, or biofilms. This molecular approach for characterizing mixed DNA samples relies on the development of "universal primers" that allow for effective amplification of target sequences across a broad range of taxa. Armed with optimized lab protocols and rigorous bioinformatics tools, DNA metabarcoding can produce a wealth of information about the hidden biodiversity of various sample types by probing for organisms' molecular footprints. DNA metabarcoding has received considerable popular press over the last few years because of gut microbiome studies in humans and beyond. However, there are many other applications that are continually integrating molecular biology with other fields of study to address questions that have previously been unanswerable, for both prokaryotic and eukaryotic targets. For example, we can now sample mostly digested gut contents from virtually any organism to learn about ontogeny and foraging ecology. Water samples collected from different locations can be filtered to extract eDNA (i.e., environmental DNA), revealing the biodiversity of fish and other taxa targeted by carefully selected primer sets. This universal primer metabarcoding approach has even been extended to looking at diverse gene families within single species, which is particularly useful for complex immune system genetics. The purpose of this SICB symposium was to bring together researchers using DNA metabarcoding approaches to (a) showcase the diversity of applications of this technique for addressing questions spanning ecology, evolution, and physiology, and (b) to spark connections among investigators from different fields that are utilizing similar approaches to facilitate optimization and standardization of metabarcoding methods and analyses. The resulting manuscripts from this symposium represent a great diversity of metabarcoding applications and taxonomic groups of interest.

Improving stable isotope assessments of inter- and intra-species variation in coral reef fish trophic strategies.

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 trophic variation when quantifying niche size. However, studies using SIA to investigate trophodynamics have mostly focused on species- or guild-level (i.e., assumed similar trophic strategy) analyses in settings where source isotopes are well-resolved. These parameters are uncommon in an ecological context. Here, we use Stable Isotope Bayesian Ellipses in R (SIBER) to investigate cross-guild trophodynamics of 11 reef fish species within an oceanic atoll. We compared two- (δ 15N and δ 13C) versus three-dimensional (δ 15N, δ 13C, and δ 34S) reconstructions of isotopic niche space for interpreting guild-, species-, and individual-level trophic strategies. Reef fish isotope compositions varied significantly among, but also within, guilds. Individuals of the same species did not cluster together based on their isotope values, suggesting within-species specializations. Furthermore, while two-dimensional isotopic niches helped differentiate reef fish resource use, niche overlap among species was exceptionally high. The addition of δ 34S and the generation of three-dimensional isotopic niches were needed to further characterize their isotopic niches and better evaluate potential trophic strategies. These data suggest that δ 34S may reveal fluctuations in resource availability, which are not detectable using only δ 15N and δ 13C. We recommend that researchers include δ 34S in future aquatic food web studies.

Phylogeography of the reef fish Cephalopholis argus (Epinephelidae) indicates Pleistocene isolation across the Indo-Pacific Barrier with contemporary overlap in The Coral Triangle.

BACKGROUND: The Coral Triangle (CT), bounded by the Philippines, the Malay Peninsula, and New Guinea, is the epicenter of marine biodiversity. Hypotheses that explain the source of this rich biodiversity include 1) the center of origin, 2) the center of accumulation, and 3) the region of overlap. Here we contribute to the debate with a phylogeographic survey of a widely distributed reef fish, the Peacock Grouper (Cephalopholis argus; Epinephelidae) at 21 locations (N = 550) using DNA sequence data from mtDNA cytochrome b and two nuclear introns (gonadotropin-releasing hormone and S7 ribosomal protein). RESULTS: Population structure was significant (ΦST = 0.297, P < 0.001; FST = 0.078, P < 0.001; FST = 0.099, P < 0.001 for the three loci, respectively) among five regions: French Polynesia, the central-west Pacific (Line Islands to northeastern Australia), Indo-Pacific boundary (Bali and Rowley Shoals), eastern Indian Ocean (Cocos/Keeling and Christmas Island), and western Indian Ocean (Diego Garcia, Oman, and Seychelles). A strong signal of isolation by distance was detected in both mtDNA (r = 0.749, P = 0.001) and the combined nuclear loci (r = 0.715, P < 0.001). We detected evidence of population expansion with migration toward the CT. Two clusters of haplotypes were detected in the mtDNA data (d = 0.008), corresponding to the Pacific and Indian Oceans, with a low level of introgression observed outside a mixing zone at the Pacific-Indian boundary. CONCLUSIONS: We conclude that the Indo-Pacific Barrier, operating during low sea level associated with glaciation, defines the primary phylogeographic pattern in this species. These data support a scenario of isolation on the scale of 105 year glacial cycles, followed by population expansion toward the CT, and overlap of divergent lineages at the Pacific-Indian boundary. This pattern of isolation, divergence, and subsequent overlap likely contributes to species richness at the adjacent CT and is consistent with the region of overlap hypothesis.