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Context Species classification disputes can be resolved using integrative taxonomy, which involves the use of both phenotypic and genetic information to determine species boundaries. Aims Our aim was to clarify species boundaries of two commercially important cryptic species of halfbeak (Hemiramphidae), whose distributions overlap in south-eastern Australia, and assist fisheries management. Methods We applied an integrative taxonomic approach to clarify species boundaries and assist fisheries management. Key results Mitochondrial DNA and morphological data exhibited significant differences between the two species. The low level of mitochondrial DNA divergence, coupled with the lack of difference in the nuclear DNA, suggests that these species diverged relatively recently (c. 500 000 years ago) when compared with other species within the Hyporhamphus genus (>2.4 million years ago). Genetic differences between the species were accompanied by differences in modal gill raker counts, mean upper-jaw and preorbital length, and otolith shape. Conclusions On the basis of these genetic and morphological differences, as well as the lack of morphological intergradation between species along the overlapping boundaries of their geographical distributions, we propose that Hyporhamphus australis and Hyporhamphus melanochir remain valid species. Implications This study has illustrated the need for an integrative taxonomic approach when assessing species boundaries and has provided a methodological framework for studying other cryptic fish species in a management context.

A new species of deep-water epinephelid fish is described from the west coast of Australia based on 14 specimens, 99-595 mm standard length. Hyporthodus griseofasciatus sp. nov. is endemic to Western Australia from Barrow Island to Two Peoples Bay in depths of 76-470 m. It has a series of eight grey bands alternating with eight brown bands along the body and the soft dorsal, soft anal and caudal fin margins are pale cream to white. It is distinguished from its nearest congener, H. ergastularius, by the presence of a star-like pattern of radiating lines on the head versus an overall brownish colour in the latter as well as significant differences in the quantitative analyses of 25 morphological characters. The two species have allopatric distributions on either side of the Australian continent. H. griseofasciatus is distinguished from H. octofasciatus by several grey bands being distinctly narrower than other grey bands (vs. all grey bands subequal in the latter) and the presence of broad white margins on the dorsal, caudal and anal fins (vs. narrow or absent in the latter). Some scale counts appear to also differ. Analyses of mitochondrial cytochrome oxidase subunit 1 sequences revealed reciprocally monophyletic clades with fixed differences and genetic distances typical of recently diverged species of fishes.

Environmental DNA (eDNA) is increasingly being used to assess community composition in marine ecosystems. Applying eDNA approaches across broad spatial scales now provide the potential to inform biogeographic analyses. However, to date, few studies have employed this technique to assess broad biogeographic patterns across multiple taxonomic groups. Here, we compare eDNA‐derived communities of bony fishes and invertebrates, including corals and sponges, from 15 locations spanning the entire length of the Omani coast. This survey includes a variety of habitats, including coral and rocky reefs, and covers three distinct marine ecoregions. Our data support a known biogeographic break in fish communities between the north and the south of Oman; however, the eDNA data highlight that this faunal break is mostly reflected in schooling baitfish species (e.g., sardines and anchovies), whereas reef‐associated fish communities appear more homogeneous along this coastline. Furthermore, our data provide indications that these biogeographic breaks also affect invertebrate communities, which includes corals, sponges, and broader eukaryotic groups. The observed community shifts were correlated with local environmental and anthropogenic differences characteristic of this coastline, particularly for the eDNA‐derived bony fish communities. Overall, this study provides compelling support that eDNA sequencing and associated analyses may serve as powerful tools to detect community differences across biogeographic breaks and ecoregions, particularly in places where there is significant variation in oceanographic conditions or anthropogenic impacts.

Monitoring plans using environmental DNA have the potential to offer a standardized and cost‐efficient method to survey biodiversity in aquatic ecosystems. Among these ecosystems, coastal wetlands are key elements that serve as transition zones between marine and freshwater ecosystems and are today the target of many conservation and restoration efforts. In this sense, eDNA monitoring could provide a rapid and efficient tool for studying and generating baseline biodiversity information to guide coastal wetland management programs. Here, we test an eDNA metabarcoding assay as a tool to characterize vertebrate biodiversity in one of the largest coastal wetlands of Chile, the Rio Cruces Wetland, a Ramsar designated site since 1981. We sampled surface water from 49 sites along the entire wetland. Our eDNA approach detected 91genera of vertebrates including amphibians, fishes, mammals, and birds, as well as identified several cryptic, exotic, and endangered species. Our results also indicated that the spatial distribution of eDNA from different species is spatially structured despite the complex hydrodynamics inherent in this wetland due to the influence of daily tidal regimes. For amphibians and fishes, the number of taxa detected with eDNA was higher in the periphery of the wetland, and increased with proximity to the ocean, a pattern consistent with small‐scale spatial sensitivity for some species and eDNA accumulation downstream for others. Birds and mammals showed somewhat more idiosyncratic distributions. Taken together, our results add to the growing body of evidence showing eDNA can serve as a rapid cost‐effective tool to characterize vertebrate communities in protected coastal wetlands, where visual surveys are difficult and animal collections are often prohibited. The use of multiple primer sets is also recommended as it facilitates the detection of ephemeral terrestrial organisms and resident aquatic organisms that make use of these wetlands.

Determining how growth rates and body size vary spatially and among reef fish species is important to understanding functional traits and demographic trade-offs. Variability in reef fish growth trajectories may be influenced by intrinsic (e.g., biological, phylogenetic) and extrinsic factors (e.g., environmental), as well as their interaction via ecological processes. To assess interspecific variation in these traits, we estimated age and growth for a guild of butterflyfishes sampled from reefs spanning ~ 10˚ degrees of latitude in the Red Sea to the adjacent Gulf of Aden. This study region was chosen because it spans environmental gradients known to influence fish life history traits and allowed for comparisons between regional versus more widespread butterflyfish species. Across the 10 study species, we found significant interspecific differences in growth. This finding contrasted with almost no intraspecific differences between populations across the study region. Moreover, we found that maximum body size was significantly correlated with the phylogenetic placement of the butterflyfish species. These patterns suggest that intrinsic factors and a high degree of ecological specialization may elicit spatially conservative demographic profiles, even when faced with considerable environmental variation across a region.

Environmental DNA (eDNA) has revolutionized our ability to identify the presence and distributions of terrestrial and aquatic organisms. Recent evidence suggests the concentration of eDNA could also provide a rapid, cost‐effective indicator of abundance and/or biomass for fisheries stock assessments. Globally, fisheries resources are under immense pressure, and their sustainable harvest requires accurate information on the sizes of fished stocks. However, in many cases the required information remains elusive because of a reliance on imprecise or costly fishery‐dependent and independent data. Here, we review the literature describing relationships between eDNA concentrations and fish abundance and/or biomass, as well as key influencing factors, as a precursor to determining the broader utility of eDNA for monitoring fish populations. We reviewed 63 studies published between 2012 and 2020 and found 90% identified positive relationships between eDNA concentrations and the abundance and/or biomass of focal species. Key influencing biotic factors included the taxon examined as well as their body size, distribution, reproduction, and migration. Key abiotic factors mostly comprised hydrological processes affecting the dispersal and persistence of eDNA, especially water flow and temperature, although eDNA collection methods were also influential. The cumulative influence of these different factors likely explains the substantial variability observed in eDNA concentrations, both within and among studies. Nevertheless, there is considerable evidence to support using eDNA as an ancillary tool for assessing fish population abundance and/or biomass across discrete spatio‐temporal scales, following preliminary investigations to determine species‐ and context‐specific factors influencing the eDNA abundance/biomass relationship. Advantages of eDNA monitoring relative to other approaches include reduced costs, increased efficiencies, and nonlethal sampling.

The fairy wrasses (genus Cirrhilabrus) are among the most successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10$\%$ of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve evolutionary relationships among these groups using molecular and morphological data have largely been unsuccessful. Here, we use a phylogenomic approach with a data set comprising 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. Our analyses of phylogenetic signal suggest that most gene-tree incongruence is caused by estimation error, leading to poor resolution in a summary-coalescent analysis of the data. In contrast, analyses of concatenated sequences are able to resolve the major relationships of Cirrhilabrus. We determine the placements of species that were previously regarded as incertae sedis and find evidence for the nesting of Conniella, an unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating analysis indicates that the major divergences within the genus occurred around the Miocene–Pliocene boundary, followed by extensive cladogenesis of species complexes in the Pliocene–Pleistocene. Biogeographic reconstruction suggests that the fairy wrasses emerged within the Coral Triangle, with episodic fluctuations of sea levels during glacial cycles coinciding with shallow divergence events but providing few opportunities for more widespread dispersal. Our study demonstrates both the resolving power and limitations of UCEs across shallow timescales where there is substantial estimation error in individual gene trees.[Biogeography; concatenation; gene genealogy interrogation; gene trees; molecular dating; summary coalescent; UCEs.]

We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as "insularity"). Using populations from within the same studies, we were able to control for between-study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen-particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non-insular populations of the same study system-suggesting an important role for the "scope" of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population-level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.

Non‐sex‐linked color polymorphism is common in animals and can be maintained in populations via balancing selection or, when under diversifying selection, can promote divergence. Despite their potential importance in ecological interactions and the evolution of biodiversity, their function and the mechanisms by which these polymorphisms are maintained are still poorly understood. Here, we combine field observations with life history and molecular data to compare four sympatric color morphs of the coral reef fish Paracirrhites forsteri (family Cirrhitidae) in the central Red Sea. Our findings verify that the color morphs are not sex‐limited, inhabit the same reefs, and do not show clear signs of avoidance or aggression among them. A barcoding approach based on 1,276 bp of mitochondrial DNA could not differentiate the color morphs. However, when 36,769 SNPs were considered, we found low but significant population structure. Focusing on 1,121 F ST outliers, we recovered distinct population clusters that corresponded to shifts in allele frequencies with each color morph harboring unique alleles. Genetic divergence at these outlier loci is accompanied by differences in growth and marginal variation in microhabitat preference. Together, life history and molecular analysis suggest subtle divergence between the color morphs in this population, the causes for which remain elusive., Despite their potential importance in ecological interactions and the evolution of biodiversity, non‐sex‐linked color polymorphism is poorly understood. Here, we investigated four sympatric color morphs of the coral reef fish Paracirrhites forsteri (family Cirrhitidae) in the central Red Sea and show that the color morphs inhabit the same reefs. While we could not differentiate between them using mtDNA, when we considered 36,769 SNPs, we found low but significant population structure that corresponded to color morphology with accompanying differences in growth and marginal variation in microhabitat preference.

Environmental DNA (eDNA) metabarcoding methods have demonstrated their potential as noninvasive techniques for the monitoring and conservation of marine fishes, including rare and endangered taxa. However, the majority of these investigations have focused on large‐bodied taxa such as sharks and sturgeons. In contrast, eDNA studies on small‐bodied cryptic taxa are much less common. As a case in point, seahorses (members of the Syngnathidae family) have never been detected by eDNA, despite the fact that globally there are 14 species classified as “Threatened” by the IUCN. Here, we critically evaluate the ability of two existing broad‐spectrum fish metabarcoding assays (MiFish and 16S Fish) and explore the efficacy of two newly designed fish metabarcoding assays (16S_FishSyn_Short and 16S_FishSyn_Long) to detect Syngnathidae amidst a wide spectrum of fish species. Furthermore, a custom Western Australian 16S rRNA fish database was created to increase the likelihood of correct taxonomic assignments. With the newly designed assays, we detected four Syngnathidae species in a targeted eDNA survey of the Perth metropolitan area (Western Australia). These detections include the seahorse species Hippocampus subelongatus and Hippocampus breviceps, which represents the first time seahorse species have been detected using eDNA. The existing MiFish and 16S Fish assays did not detect any Syngnathidae. This evaluation of all four fish metabarcoding assays reinforces the view that every PCR assay has “blind spots”. In the context of complex environmental samples, no assay is universal and false negatives will occur due to a combination of PCR efficacy, primer binding, assay sensitivity, degeneracies in the primers, template competition, and amplicon length. Taken together, these data indicate that eDNA methodologies, with ongoing optimizations, will become an integral part of monitoring small‐bodied cryptic taxa such as seahorses, gobies, and blennies and can assist in mapping species’ distributions and prioritizing conservation areas.

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. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and primary productivity that vary both by latitude and by season. The adjacent Arabian Sea is characterized by a sharper environmental gradient, ranging from extensive coral cover and warm temperatures in the southwest, to sparse coral cover, cooler temperatures, and seasonal upwelling in the northeast. Reef fish, however, are not confined to these seas, with some Red Sea fishes extending varying distances into the northern Arabian Sea, while their pelagic larvae are presumably capable of much greater dispersal. These species must therefore cope with a diversity of conditions that invoke the possibility of steep clines in natural selection. Here, we test for genetic structure in two widespread reef fish species (a butterflyfish and surgeonfish) and eight range‐restricted butterflyfishes across the Red Sea and Arabian Sea using genome‐wide single nucleotide polymorphisms. We performed multiple matrix regression with randomization analyses on genetic distances for all species, as well as reconstructed scenarios for population subdivision in the species with signatures of isolation. We found that (a) widespread species displayed more genetic subdivision than regional endemics and (b) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events. We propose that the endemic species may be adapted to a diversity of local conditions, but the widespread species are instead subject to ecological filtering where different combinations of genotypes persist under divergent ecological regimes., We test for genetic structure in two widespread species (a butterflyfish and surgeonfish) and eight range‐restricted butterflyfishes across the Red Sea and Arabian Sea using genome‐wide single nucleotide polymorphisms, multiple matrix regression with randomization analyses, and demographic reconstruction. We found that (a) widespread species displayed more genetic subdivision than regional endemics and (b) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events.

Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for cost-effective whole-ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high-resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)-a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.

M.D. is grateful for support from the Templeton Foundation (grant #60501, “Putting the Extended Evolutionary Synthesis to the Test”) and from a Leverhulme Trust Fellowship. The problem Earth‐based observations of the biosphere are spatially biased in ways that can limit our ability to detect macroecological patterns and changes in biodiversity. To resolve this problem, we need to supplement the ad hoc data currently collected with planned biodiversity monitoring, in order to approximate global stratified random sampling of the planet. We call this all‐encompassing observational system ‘the macroscope’. The solution With a focus on the marine realm, we identify seven main biosphere observation tools that compose the macroscope: satellites, drones, camera traps, passive acoustic samplers, biologgers, environmental DNA and human observations. By deploying a nested array of these tools that fills current gaps in monitoring, we can achieve a macroscope fit for purpose and turn these existing powerful tools into more than the sum of their parts. An appeal Building a macroscope requires commitment from many fields, together with coordinated actions to attract the level of funding required for such a venture. We call on macroecologists to become advocates for the macroscope and to engage with existing global observation networks. Postprint

Aim To determine the impact of ecological and environmental histories on the evolution of coral reef damselfishes at two adjacent marine biogeographic suture zones. Location Indo-West Pacific, notably including two suture zones: Socotra and Christmas and Cocos/Keeling Islands. Taxon Chromis dimidiata, Chromis margaritifer, and Chromis fieldi. Methods We utilized a combination of nuclear and mitochondrial genetic markers in addition to visual abundance survey data of these fishes. Results Despite genetic patterns consistent with incomplete lineage sorting and relatively low genetic differentiation among the three studied Chromis species, there is evidence of hybridization between C. margaritifer and C. fieldi at Christmas Island based on molecular and visual identification. Introgression appears to be spreading westwards to other C. fieldi populations based on COI haplotype comparison. Moreover, the genetic distance between C. margaritifer and C. fieldi suggests that Pleistocene sea-level fluctuations may have contributed to allopatric divergence and secondary contact between these two closely related species. Main conclusions Our study highlights that evolutionary processes in coral reef fishes operate differently between suture zones, possibly due to different ecological and environmental predispositions regulating secondary contact of sister species. While secondary contact likely led to hybridization and introgression at Christmas and Cocos/Keeling Islands, none of those processes seem present at Socotra for the chocolate-dipped damselfish. This difference is likely due to an environmental barrier caused by hydrodynamic regimes in the Gulf of Aden.

We address a critical knowledge gap for the Eightbar Grouper, Hyporthodus octofasciatus, one of the largest groupers targeted in mostly tropical, deep-water fisheries, using genetic analyses of mitochondrial DNA (mtDNA; N = 248) and age and growth information (N = 727) from specimens collected from the eastern Indian Ocean to the western central Pacific Ocean. We additionally used a genotype-by-sequencing approach on a subset of these samples (N = 94) to determine the extent of egg and larval dispersal between tropical and temperate regions along the west coast of Australia (WA). Discontinuity in mtDNA and nuclear genomes, and marked variation in growth trajectories and longevity revealed a distinct, non-interbreeding cryptic lineage in WA. The WA lineage appears to be geographically isolated from the oceanic Indo-West Pacific (IP) lineage and precinctive to a single continuous coastline from tropical to temperate waters (covering > 2200 km and ∼20° of latitude). The Hyporthodus phylogeny reveals a possible allopatric speciation scenario with sister lineages endemic to the east (i.e. H. ergastularius) and west (i.e. WA lineage of H. octofasciatus) coasts of Australia, each diverging from a broader IP distributed ancestor (i.e. IP lineage of H. octofasciatus) in the early Pleistocene Epoch. Sustainable management of these species therefore needs to consider their evolutionary distinction, in addition to aspects of their life-history strategies and limited geographic distribution that infers high vulnerability to fishing at relatively low levels of exploitation.

Data from a large-scale restriction site-associated DNA sequencing (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction site-associated DNA (ddRAD) sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to see whether it improves the quality of RAD-Seq. Our analyses indicate (i) a modest gap between the number of nonannotated versus annotated SNPs across all species, (ii) an advantage of using genomic resources for closely related but not distantly related butterflyfish species based on the ability to assign putative gene function to SNPs and (iii) an enrichment of genes among sister butterflyfish taxa related to calcium transmembrane transport and binding. The latter result highlights the potential for this approach to reveal insights into adaptive mechanisms in populations inhabiting challenging coral reef environments such as the Red Sea, Arabian Sea and Arabian Gulf with further study.

Aim: To test hypothesized biogeographic partitions of the tropical Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location: The Indo-Pacific Ocean. Time period: Pliocene through the Holocene. Major taxa studied: Fifty-six marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo-Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦST distributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance versus environmental or geographic barriers to pairwise ΦST with a distance-based redundancy analysis (dbRDA). Results: We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦST that was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦST that were significantly larger than random expectation. Only 21 of 52 species analysed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographic or environmental barriers other than distance. Main conclusions: Although there is support for three previously described barriers, phylogeographic discordance in the Indo-Pacific Ocean indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo-Pacific species, even hard vicariance for tens of thousands of years can yield ΦSTvalues that range from 0 to nearly 0.5.

Ocean circulation, geological history, geographic distance, and seascape heterogeneity play an important role in phylogeography of coral‐dependent fishes. Here, we investigate potential genetic population structure within the yellowbar angelfish (Pomacanthus maculosus) across the Northwestern Indian Ocean (NIO). We then discuss our results with respect to the above abiotic features in order to understand the contemporary distribution of genetic diversity of the species. To do so, restriction site‐associated DNA sequencing (RAD‐seq) was utilized to carry out population genetic analyses on P. maculosus sampled throughout the species’ distributional range. First, genetic data were correlated to geographic and environmental distances, and tested for isolation‐by‐distance and isolation‐by‐environment, respectively, by applying the Mantel test. Secondly, we used distance‐based and model‐based methods for clustering genetic data. Our results suggest the presence of two putative barriers to dispersal; one off the southern coast of the Arabian Peninsula and the other off northern Somalia, which together create three genetic subdivisions of P. maculosus within the NIO. Around the Arabian Peninsula, one genetic cluster was associated with the Red Sea and the adjacent Gulf of Aden in the west, and another cluster was associated with the Arabian Gulf and the Sea of Oman in the east. Individuals sampled in Kenya represented a third genetic cluster. The geographic locations of genetic discontinuities observed between genetic subdivisions coincide with the presence of substantial upwelling systems, as well as habitat discontinuity. Our findings shed light on the origin and maintenance of genetic patterns in a common coral reef fish inhabiting the NIO, and reinforce the hypothesis that the evolution of marine fish species in this region has likely been shaped by multiple vicariance events., Metapopulation genetics of coral reef fish. Phylogeography Northwestern Indian Ocean.

[Aim] Compare the distribution and composition of temperate Labridae (wrasse) assemblages on shallow water coastal reefs in South-Western Australia between 2006 and 2015, after a decade characterized by both gradual ocean warming and severe heatwave events., [Location] South-Western Australia from Port Gregory to the Recherché Archipelago., [Methods] Surveys of Labridae fishes were conducted in 2006 and repeated in 2015 across 112 reefs spanning 2,000 km of coastline, using diver-operated stereo-video systems (stereo-DOVs). We used a hierarchical design with seven regions, four locations in each region, four reef sites in each location and twelve transects in each site., [Results] In 2015, we found an increase in abundance of tropical and subtropical labrid species that were rarely observed in 2006. Three temperate species declined in abundance, which tended to be large and slow growing fish. Twenty-two labrid species increased in abundance. There was also a discernible poleward shift in 20 of the 25 most abundant and representative labrid species from 2006 to 2015. The labrid community composition was explained predominantly by sea surface temperature (SST), physical reef structure and kelp (Ecklonia radiata) cover., [Main conclusions] Our study reveals that labrid assemblages associated with the shallow water temperate reefs of South-Western Australia have undergone rapid changes across almost 2,000 km of coastline, with warm-temperate waters showing the strongest change. However, cool-temperate waters on the south coast also showed significant changes in the composition of the labrid assemblages. Our findings provide important insights into the effects of warming and habitat loss on warm-temperate assemblages and the potential trajectory of change for cool-temperate assemblages under a warmer future.

Butterflyfish are among the most iconic of the coral reef fishes and represent a model system to study general questions of biogeography, evolution and population genetics. We assembled and annotated the genome sequence of the blacktail butterflyfish (Chaetodon austriacus), an Arabian region endemic species that is reliant on coral reefs for food and shelter. Using available bony fish (superclass Osteichthyes) genomes as a reference, a total of 28 926 high-quality protein-coding genes were predicted from 13 967 assembled scaffolds. The quality and completeness of the draft genome of C. austriacus suggest that it has the potential to serve as a resource for studies on the co-evolution of reef fish adaptations to the unique Red Sea environment, as well as a comparison of gene sequences between closely related congeneric species of butterflyfish distributed more broadly across the tropical Indo-Pacific.

Closely related species can provide valuable insights into evolutionary processes through comparison of their ecology, geographic distribution and the history recorded in their genomes. In the Indo-Pacific, many reef fishes are divided into sister species that come into secondary contact at biogeographic borders, most prominently where Indian Ocean and Pacific Ocean faunas meet. It is unclear whether hybridization in this contact zone represents incomplete speciation, secondary contact, an evolutionary dead-end (for hybrids) or some combination of the above. To address these issues, we conducted comprehensive surveys of two widely-distributed surgeonfish species, Acanthurus leucosternon (N=141) and A. nigricans (N=412), with mtDNA cytochrome b sequences and ten microsatellite loci. These surgeonfishes are found primarily in the Indian and Pacific Oceans, respectively, but overlap at the Christmas and Cocos-Keeling Islands hybrid zone in the eastern Indian Ocean. We also sampled the two other Pacific members of this species complex, A. achilles (N=54) and A. japonicus (N=49), which are known to hybridize with A. nigricans where their ranges overlap. Our results indicate separation between the four species that range from the recent Pleistocene to late Pliocene (235,000-2.25million years ago). The Pacific A. achilles is the most divergent (and possibly ancestral) species with mtDNA dcorr≈0.04, whereas the other two Pacific species (A. japonicus and A. nigricans) are distinguishable only at a population or subspecies level (ΦST=0.6533, P

The regal angelfish (Pygoplites diacanthus; family Pomacanthidae) occurs on reefs from the Red Sea to the central Pacific, with an Indian Ocean/Rea Sea color morph distinct from a Pacific Ocean morph. To assess population differentiation and evaluate the possibility of cryptic evolutionary partitions in this monotypic genus, we surveyed mtDNA cytochrome b and two nuclear introns (S7 and RAG2) in 547 individuals from 15 locations. Phylogeographic analyses revealed four mtDNA lineages (d=0.006-0.015) corresponding to the Pacific Ocean, the Red Sea, and two admixed lineages in the Indian Ocean, a pattern consistent with known biogeographic barriers. Christmas Island in the eastern Indian Ocean had both Indian and Pacific lineages. Both S7 and RAG2 showed strong population-level differentiation between the Red Sea, Indian Ocean, and Pacific Ocean (ΦST=0.066-0.512). The only consistent population sub-structure within these three regions was at the Society Islands (French Polynesia), where surrounding oceanographic conditions may reinforce isolation. Coalescence analyses indicate the Pacific (1.7Ma) as the oldest extant lineage followed by the Red Sea lineage (1.4Ma). Results from a median-joining network suggest radiations of two lineages from the Red Sea that currently occupy the Indian Ocean (0.7-0.9Ma). Persistence of a Red Sea lineage through Pleistocene glacial cycles suggests a long-term refuge in this region. The affiliation of Pacific and Red Sea populations, apparent in cytochrome b and S7 (but equivocal in RAG2) raises the hypothesis that the Indian Ocean was recolonized from the Red Sea, possibly more than once. Assessing the genetic architecture of this widespread monotypic genus reveals cryptic evolutionary diversity that merits subspecific recognition. We recommend P.d. diacanthus and P.d. flavescens for the Pacific and Indian Ocean/Red Sea forms.

A combination of mark-recapture and genetic sampling was used to extend the minimum longevity of an elasmobranch species and the life span estimate of the lemon shark Negaprion brevirostris was increased conservatively from 20·2 to 37 years. This increase in longevity means higher vulnerability and a longer recovery time from exploitation.

Aim The aim of this study was to resolve the evolutionary history, biogeographical barriers and population histories for sister species of wrasses, the African Coris (Coris cuvieri) in the Indian Ocean and Red Sea, and the Yellowtail Coris (Coris gaimard) in the Pacific Ocean. Glacial sea level fluctuations during the Pleistocene have shaped the evolutionary trajectories of Indo-Pacific marine fauna, primarily by creating barriers between the Red Sea, Indian Ocean and Pacific Ocean. Here, we evaluate the influence of these episodic glacial barriers on sister species C. cuvieri and C. gaimard. Location Red Sea, Indian Ocean, Pacific Ocean. Methods Sequences from mitochondrial DNA cytochrome oxidase c subunit I (COI), and nuclear introns gonadotropin-releasing hormone (GnRH) and ribosomal S7 protein were analysed in 426 individuals from across the range of both species. Median-joining networks, analysis of molecular variance and Bayesian estimates of the time since most recent common ancestor were used to resolve recent population history and connectivity. Results Cytochrome oxidase c subunit I haplotypes showed a divergence of 0.97% between species, and nuclear alleles were shared between species. No population structure was detected between the Indian Ocean and Red Sea. The strongest signal of population structure was in C. gaimard between the Hawaiian biogeographical province and other Pacific locations (COI ϕST = 0.040–0.173, P

Aim: This study compares the phylogeography, population structure and evolution of four butterflyfish species in the Chaetodon subgenus Corallochaetodon, with two widespread species (Indian Ocean - C. trifasciatus and Pacific Ocean - C. lunulatus), and two species that are largely restricted to the Red Sea (C. austriacus) and north-western (NW) Indian Ocean (C. melapterus). Through extensive geographical coverage of these taxa, we seek to resolve patterns of genetic diversity within and between closely related butterflyfish species in order to illuminate biogeographical and evolutionary processes. Location: Red Sea, Indian Ocean and Pacific Ocean. Methods: A total of 632 individuals from 24 locations throughout the geographical ranges of all four members of the subgenus Corallochaetodon were sequenced using a 605 bp fragment (cytochrome b) of mtDNA. In addition, 10 microsatellite loci were used to assess population structure in the two widespread species. Results: Phylogenetic reconstruction indicates that the Pacific Ocean C. lunulatus diverged from the Indian Ocean C. trifasciatus approximately 3 Ma, while C. melapterus and C. austriacus comprise a cluster of shared haplotypes derived from C. trifasciatus within the last 0.75 Myr. The Pacific C. lunulatus had significant population structure at peripheral locations on the eastern edge of its range (French Polynesia, Johnston Atoll, Hawai'i), and a strong break between two ecoregions of the Hawaiian Archipelago. The Indian Ocean C. trifasciatus showed significant structure only at the Chagos Archipelago in the central Indian Ocean, and the two range-restricted species showed no population structure but evidence of recent population expansion. Main conclusions: Patterns of endemism and genetic diversity in Corallochaetodon butterflyfishes have been shaped by (1) Plio-Pleistocene sea level changes that facilitated evolutionary divergences at biogeographical barriers between Indian and Pacific Oceans, and the Indian Ocean and Red Sea, and (2) semi-permeable oceanographic and ecological barriers working on a shorter time-scale. The evolution of range-restricted species (Red Sea and NW Indian Ocean) and isolated populations (Hawai'i) at peripheral biogeographical provinces indicates that these areas are evolutionary incubators for reef fishes.

Effective biomonitoring is critical for driving management outcomes that ensure long-term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data are needed on how to best implement eDNA field sampling approaches to maximize their utility for each specific application. The effect of the substrate chosen for eDNA sampling on the diversity of marine taxa detected by DNA metabarcoding has not yet been systematically analysed, despite aquatic systems being those most commonly targeted for eDNA studies. We investigated the effect of four commonly used eDNA substrates to explore taxonomic diversity: (a) surface water, (b) marine sediment, (c) settlement plates and (d) planktonic tows. With a focus on coastal ports, 332 eDNA samples from Australia (Indian and Southern oceans) and Kazakhstan (Caspian Sea) were collected and analysed by multi-assay DNA metabarcoding. Across study locations, between 30% and 52% of eukaryotic families detected were unique to a particular substrate and

Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty‐two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs’ spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (∼35 km2). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems., Article impact statement: Use of video and environmental genomics in conservation will greatly improve capacity to effectively monitor fish biodiversity.

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.

Aim Broadly distributed reef fishes tend to have high gene flow mediated by a pelagic larval phase. Here, we survey a reef-associated fish distributed across half the tropical oceans, from the Red Sea to the central Pacific. Our goal is to determine whether genetic structure of the broadly distributed Yellowstripe Goatfish (Mulloidichthys flavolineatus) is defined by biogeographical barriers, or facilitated via larval dispersal. Location Red Sea, Indian Ocean, Pacific Ocean Methods Specimens were obtained at 19 locations from the Red Sea to Hawai'i. Genetic data include mtDNA cytochrome b (n = 217) and 12 microsatellite loci (n = 185). Analysis of molecular variance (AMOVA), structure, a parsimony network and coalescence analyses were used to resolve recent population history and connectivity. Results Population structure was significant (mtDNA ϕST = 0.68, P

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 low sea level stands when conditions were inhospitable. Location: Red Sea and Western Indian Ocean. Methods: We review the literature on palaeontological, geological, biological and genetic evidence that allow us to explore competing hypotheses on the origins and maintenance of shallow-water reef fauna in the Red Sea. Results: Palaeontological (microfossil) evidence indicates that some areas of the central Red Sea were devoid of most plankton during low sea level stands due to hypersaline conditions caused by almost complete isolation from the Indian Ocean. However, two areas may have retained conditions adequate for survival: the Gulf of Aqaba and the southern Red Sea. In addition to isolation within the Red Sea, which separated the northern and southern faunas, a strong barrier may also operate in the region: the cold, nutrient-rich water upwelling at the boundary of the Gulf of Aden and the Arabian Sea. Biological data are either inconclusive or support these putative barriers and refugia, but no data set, that we know of rejects them. Genetic evidence suggests that many endemic lineages diverged from their Indian Ocean counterparts long before the most recent glaciations and/or are restricted to narrow areas, especially in the northern Red Sea. Main conclusions: High endemism observed in the Red Sea and Gulf of Aden appears to have multiple origins. A cold, nutrient-rich water barrier separates the Gulf of Aden from the rest of the Arabian Sea, whereas a narrow strait separates the Red Sea from the Gulf of Aden, each providing potential isolating barriers. Additional barriers may arise from environmental gradients, circulation patterns and the constriction at the mouth of the Gulf of Aqaba. Endemics that evolved within the Red Sea basin had to survive glacial cycles in relatively low salinity refugia. It therefore appears that the unique conditions in the Red Sea, in addition to those characteristics of the Arabian Peninsula region as a whole, drive the divergence of populations via a combination of isolation and selection.

Aim We assess genetic differentiation among biogeographical provinces and colour morphs of the threadfin butterflyfish, Chaetodon auriga. This species is among the most broadly distributed butterflyfishes in the world, occurring on reefs from the Red Sea and western Indian Ocean to French Polynesia and Hawai'i. The Red Sea form lacks a conspicuous ‘eye-spot’ on the dorsal fin, which may indicate an evolutionary distinction. Location Red Sea, Indian Ocean and Pacific Ocean. Methods Specimens were obtained at 17 locations (n = 358) spanning the entire range of this species. The genetic data included 669 base pairs of mitochondrial DNA (mtDNA) cytochrome b and allele frequencies at six microsatellite loci. Analysis of molecular variance, structure plots, haplotype networks and estimates of population expansion time were used to assess phylogeographical patterns. Results Population structure was low overall, but significant and concordant between molecular markers (mtDNA: ΦST = 0.027, P

Understanding the drivers of dispersal among populations is a central topic in marine ecology and fundamental for spatially explicit management of marine resources. The extensive coast of Northwestern Australia provides an emerging frontier for implementing new genomic tools to comparatively identify patterns of dispersal across diverse and extreme environmental conditions. Here, we focused on the stripey snapper (Lutjanus carponotatus), which is important to recreational, charter-based and customary fishers throughout the Indo-West Pacific. We collected 1,016 L. carponotatus samples at 51 locations in the coastal waters of Northwestern Australia ranging from the Northern Territory to Shark Bay and adopted a genotype-by-sequencing approach to test whether realized connectivity (via larval dispersal) was related to extreme gradients in coastal hydrodynamics. Hydrodynamic simulations using CONNIE and a more detailed treatment in the Kimberley Bioregion provided null models for comparison. Based on 4,402 polymorphic single nucleotide polymorphism loci shared across all individuals, we demonstrated significant genetic subdivision between the Shark Bay Bioregion in the south and all locations within the remaining, more northern bioregions. More importantly, we identified a zone of admixture spanning a distance of 180 km at the border of the Kimberley and Canning bioregions, including the Buccaneer Archipelago and adjacent waters, which collectively experiences the largest tropical tidal range and some of the fastest tidal currents in the world. Further testing of the generality of this admixture zone in other shallow water species across broader geographic ranges will be critical for our understanding of the population dynamics and genetic structure of marine taxa in our tropical oceans.

Molecular genetic surveys of marine fishes have revealed that some widely distributed species are actually a composite of multiple evolutionary lineages. This is apparent in the round herrings (genus Etrumeus), wherein a globally distributed taxon (Etrumeus sadina Mitchill 1814) has proven to contain at least seven valid taxa, with more likely awaiting discovery. Here, we survey evolutionary lineages of the nominal E. sadina (formerly E. teres, a junior synonym) across the southern temperate zone of Australia, a marine region divided into three biogeographic provinces based primarily on the distribution of intertidal faunas. Results from morphological and mitochondrial DNA data reveal two evolutionary lineages corresponding to eastern and southwestern provinces (d = 0.007 for cytochrome c oxidase subunit I and d = 0.017 for cytochrome b), possibly initiated by the Bassian Isthmus between Australia and Tasmania during low sea-level stands. The Australian round herring is also genetically distinct from the nearest congeneric forms in the Indian and Pacific Oceans, with a corresponding modal difference in gill-raker counts in most cases. Based on these data, we resurrect the title Etrumeus jacksoniensis for the Australian round herring. While the Bassian Isthmus may have initiated the partition of evolutionary lineages within Australia, additional oceanographic and ecological factors must reinforce this separation in order to maintain diagnostic genetic differences along a continuous temperate coastline.

Sharks are a globally threatened group of marine fishes that often breed in their natal region of origin. There has even been speculation that female sharks return to their exact birthplace to breed (‘natal philopatry’), which would have important conservation implications. Genetic profiling of lemon sharks (Negaprion brevirostris) from 20 consecutive cohorts (1993–2012) at Bimini, Bahamas, showed that certain females faithfully gave birth at this site for nearly two decades. At least six females born in the 1993– 1997 cohorts returned to give birth 14–17 years later, providing the first direct evidence of natal philopatry in the chondrichthyans. Long-term fidelity to specific nursery sites coupled with natal philopatry highlights the merits of emerging spatial and local conservation efforts for these threatened predators.

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 of these events on the genetic architecture of the Red Sea reef fish fauna. Location: Red Sea and Western Indian Ocean. Methods: We surveyed seven reef fish species from the Red Sea and adjacent Indian Ocean using mitochondrial DNA cytochrome c oxidase subunit I and cytochrome b sequences. To assess genetic variation and evolutionary connectivity within and between these regions, we estimated haplotype diversity (h) and nucleotide diversity (π), reconstructed phylogenetic relationships among haplotypes, and estimated gene flow and time of population separation using Bayesian coalescent-based methodology. Results: Our analyses revealed a range of scenarios from shallow population structure to diagnostic differences that indicate evolutionary partitions and possible cryptic species. Conventional molecular clocks and coalescence analyses indicated time-frames for divergence between these bodies of water ranging from 830,000 years to contemporary exchange or recent range expansion. Colonization routes were bidirectional, with some species moving from the Indian Ocean to the Red Sea compared with expansion out of the Red Sea for other species. Main conclusions: We conclude that: (1) at least some Red Sea reef fauna survived multiple salinity crises; (2) endemism is higher in the Red Sea than previously reported; and (3) the Red Sea is an evolutionary incubator, occasionally contributing species to the adjacent Indian Ocean. The latter two conclusions – elevated endemism and species export – indicate a need for enhanced conservation priorities for the Red Sea.

Aim: 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) outline the distribution of shallow water fauna between the Red Sea and adjacent regions, (2) explore mechanisms for maintaining these distributions and (3) propose hypotheses to test these mechanisms. Location: Red Sea, Gulf of Aden, Arabian Sea, Arabian Gulf and Indian Ocean. Methods: Updated checklists for scleractinian corals, fishes and non-coral invertebrates were used to determine species richness in the Red Sea and the rest of the Arabian Peninsula and assess levels of endemism. Fine-scale diversity and abundance of reef fishes within the Red Sea were explored using ecological survey data. Results: Within the Red Sea, we recorded 346 zooxanthellate and azooxanthellate scleractinian coral species of which 19 are endemic (5.5%). Currently 635 species of polychaetes, 211 echinoderms and 79 ascidians have been documented, with endemism rates of 12.6%, 8.1% and 16.5% respectively. A preliminary compilation of 231 species of crustaceans and 137 species of molluscs include 10.0% and 6.6% endemism respectively. We documented 1071 shallow fish species, with 12.9% endemic in the entire Red Sea and 14.1% endemic in the Red Sea and Gulf of Aden. Based on ecological survey data of endemic fishes, there were no major changes in species richness or abundance across 1100km of Saudi Arabian coastline. Main conclusions: The Red Sea biota appears resilient to major environmental fluctuations and is characterized by high rates of endemism with variable degrees of incursion into the Gulf of Aden. The nearby Omani and Arabian Gulfs also have variable environments and high levels of endemism, but these are not consistently distinct across taxa. The presence of physical barriers does not appear to explain species distributions, which are more likely determined by ecological plasticity and genetic diversity.

Aim: We use genetic and age-based analyses to assess the evidence for a biogeographical barrier to larval dispersal in the yellowfin hind, Cephalopholis hemistiktos, a commercially important species found across the Arabian Peninsula. Location: Red Sea, Gulf of Aden, Gulf of Oman and Arabian Gulf. Methods: Mitochondrial DNA cytochrome-c oxidase subunit-I and nuclear DNA (S7) sequences were obtained for C. hemistiktos sampled throughout its distributional range. Phylogeographical and population-level analyses were used to assess patterns of genetic structure and to identify barriers to dispersal. Concurrently, age-based demographic analyses using otoliths determined differences in growth and longevity between regions. Results: Our analyses revealed significant genetic structure congruent with growth parameter differences observed across sampling sites, suggesting cryptic speciation between populations in the Red Sea and Gulf of Aden versus the Gulf of Oman and Arabian Gulf. Coalescence analyses indicated these two regions have been isolated for > 800,000 years. Main conclusions: Our results indicate historical disruption to gene flow and a contemporary dispersal barrier in the Arabian Sea, which C. hemistiktos larvae are unable to effectively traverse. This provides yet another example of a (cryptic) species with high dispersive potential whose range is delimited by a lack of suitable habitat between locations or an inability to successfully recruit at the range edge.

For marine predators there is a paucity of studies on social behaviour, and even fewer studies have quantified interactions between individuals. In the present study, we looked at the social structure and leadership of free-ranging juvenile lemon shark Negaprion brevirostris in a known aggregation site, Bimini, the Bahamas. Observations of these sharks were made from towers placed in a mangrove inlet, where clear, shallow, protected waters made it possible to record group compo- sitions of externally colour-code tagged wild juvenile lemon sharks. Thirty-eight different individual sharks were observed to use the area over a 2 yr period. Results show repeated social interactions suggestive of active partner preference. In addition, we found that group structure was mostly explained by body length, and possibly by preference for relatives but not by sex. Finally, we observed that some sharks led more groups than others and that those lead individuals were usually larger than those following them. This study quantifies the social structure of a free-ranging shark population and provides novel insights into the social behaviour of juvenile sharks.

The level of genetic variation in natural populations influences evolutionary potential, and may therefore influence responses to selection in the face of future environmental changes. By combining long-term monitoring of marked individuals with genetic pedigree reconstruction, we assessed whether habitat loss influenced genetic variation in a lemon shark (Negaprion brevirostris) population at an isolated nursery lagoon (Bimini, Bahamas). We also tracked changes in the strength and direction of natural selection. Contrary to initial expectations, we found that after the habitat loss neutral genetic variation increased, as did additive genetic variance for juvenile morphological traits (body length and mass). We hypothesize that these effects might result from philopatric behavior in females coupled with a possible influx of male genotypes from other nursery sites. We also found changes in the strength of selection on morphological traits, which weakened considerably after the disturbance; habitat loss therefore changed the phenotypes favored by natural selection. Because such human-induced shifts in the adaptive landscape may be common, we suggest that conservation biologists should not simply focus on neutral genetic variation per se, but also on assessing and preserving evolutionary parameters, such as additive genetic variation and selection.

Eight polymorphic microsatellite loci were developed for sister species, Ornate butterflyfish (Chaetodon ornatissimus) and Scrawled butterflyfish (Chaetodon meyeri). All loci were scored from samples collected at geographically distinct locations (C. ornatissimus, N = 37, Republic of Palau; C. meyeri, N = 30, Republic of Kiribati). There were 14.00 or 13.50 mean alleles per locus (A) for C. ornatissimus and C. meyeri, respectively, with observed heterozygosity (H O) ranging from 0.61 to 0.97 and 0.60 to 1.00. Most loci conformed to Hardy–Weinberg expectations, were in linkage equilibrium, and lacked confounding null alleles. We expect these markers to be useful for resolving population structure and patterns of hybridization.

Ten polymorphic microsatellite loci were developed for sister surgeonfish species: the white cheek surgeonfish (Acanthurus nigricans) which occurs primarily in the Pacific Ocean, and the powder blue tang (Acanthurus leucosternon) in the Indian Ocean. All loci were scored for widely separated collections (A. nigricans, N = 30, French Polynesia; A. leucosternon, N = 27, Republic of Seychelles; hybrids, N = 17, Cocos/Keeling Island, eastern Indian Ocean). For A. nigricans, A. leucosternon, and hybrids, respectively, the mean number of alleles per locus is A = 17.80, A = 16.60, and A = 14.60, while observed heterozygosity ranges from HO = 0.78–1.00, HO = 0.74–0.96, and HO = 0.69–1.00. With the exception of locus Ahy54, all loci conformed to Hardy–Weinberg expectations, most loci were in linkage equilibrium, and there was little evidence for confounding null alleles. These markers will be used to resolve range-wide population structure and patterns of hybridization.

Although many sharks begin their life confined in nursery habitats, it is unknown how rapidly they disperse away from their natal area once they leave the nursery. We examine this issue in immature lemon sharks (Negaprion brevirostris) from the time they leave the nursery (approximately age 3) at a subtropical island (Bimini, Bahamas), through to the onset of sexual maturity (approximately age 12). From 1995 to 2007 we tagged and genotyped a large fraction of the nursery-bound sharks at this location (0-3 years of age, N = 1776 individuals). From 2003 to 2007 we sampled immature sharks aged from 3 to 11 years (N = 150) living around the island and used physical/genetic tag recaptures coupled with kinship analysis to determine whether or not each of these 'large immature sharks' was locally born. We show that many island-born lemon sharks remain close to their natal area for long periods (years) after leaving the nursery; more than half of the sampled sharks up to 135 cm total length ( approximately 6 years old) were locally born. The fraction of locally born sharks gradually declined with increasing shark size, indicating that dispersal is relatively slow and does not primarily occur after sharks reach a threshold size. Local conservation measures (e.g. localized fishery closures, marine protected areas) can therefore help protect island-born lemon sharks even after they leave the nursery habitat.

Estimating quantitative genetic parameters ideally takes place in natural populations, but relatively few studies have overcome the inherent logistical difficulties. For this reason, no estimates currently exist for the genetic basis of life-history traits in natural populations of large marine vertebrates. And yet such estimates are likely to be important given the exposure of this taxon to changing selection pressures, and the relevance of life-history traits to population productivity. We report such estimates from a long-term (1995-2007) study of lemon sharks (Negaprion brevirostris) conducted at Bimini, Bahamas. We obtained these estimates by genetically reconstructing a population pedigree (117 dams, 487 sires, and 1351 offspring) and then using an "animal model" approach to estimate quantitative genetic parameters. We find significant additive genetic (co)variance, and hence moderate heritability, for juvenile length and mass. We also find substantial maternal effects for these traits at age-0, but not age-1, confirming that genotype-phenotype interactions between mother and offspring are strongest at birth; although these effects could not be parsed into their genetic and nongenetic components. Our results suggest that human-imposed selection pressures (e.g., size-selective harvesting) might impose noteworthy evolutionary change even in large marine vertebrates. We therefore use our findings to explain how maternal effects may sometimes promote maladaptive juvenile traits, and how lemon sharks at different nursery sites may show "constrained local adaptation." We also show how single-generation pedigrees, and even simple marker-based regression methods, can provide accurate estimates of quantitative genetic parameters in at least some natural systems.

We here employ 11 microsatellite markers and recently developed litter reconstruction methods to infer mating system parameters (i.e. polyandry and breeding-site fidelity) at a lemon shark nursery site in Marquesas Key, Florida. Four hundred and eight juvenile or subadult sharks were genotyped over eight complete breeding seasons. Using this information, we were able to infer family structure, as well as fully or partially reconstruct genotypes of 46 mothers and 163 fathers. Multiple litter reconstruction methods were used, and novel simulations helped define apparent bias and precision of at least some mating system parameters. For Marquesas Key, we find that adult female lemon sharks display high levels of polyandry (81% of all litters sampled) and stronger fidelity to the nursery site than do males. Indeed, few male sharks sired offspring from more than one litter during the course of the study. These findings were quite similar to previous results from another lemon shark nursery site (Bimini, Bahamas), suggesting conserved mating system parameters despite significant variation in early life-history traits (i.e. body size and growth) among sites. The finding of at least some site fidelity in females also supports the need for careful conservation of each nursery.

Multiple mating has clear fitness benefits for males, but uncertain benefits and costs for females. We tested for indirect genetic benefits of polyandry in a natural population, by using data from a long-term genetic and demographic study of lemon sharks (Negaprion brevirostris) at Bimini, Bahamas. To do so, we followed the fates of individuals from six cohorts (450 age-0 and 254 age-1 fish) in relation to their individual level of genetic variation, and whether they were from polyandrous or monoandrous litters. We find that offspring from polyandrous litters did not have a greater genetic diversity or greater survival than did the offspring of monoandrous litters. We also find no evidence of positive associations between individual offspring genetic diversity metrics and our surrogate measure of fitness (i.e. survival). In fact, age-1 individuals with fewer heterozygous microsatellite loci and more genetically similar parents were more likely to survive to age-2. Thus, polyandry in female lemon sharks does not appear to be adaptive from the perspective of indirect genetic benefits to offspring. It may instead be the result of convenience polyandry, whereby females mate multiply to avoid harassment by males. Our inability to find indirect genetic benefits of polyandry despite detailed pedigree and survival information suggests the need for similar assessments in other natural populations.

Genetic variation is considered critical for allowing natural populations to adapt to their changing environment, and yet the effects of human disturbance on genetic variation in the wild are poorly understood. Different types of human disturbances may genetically impact natural populations in a predictable manner and so the aim of this study was to provide an overview of these changes using a quantitative literature review approach. I examined both allozyme and microsatellite estimates of genetic variation from peer-reviewed journals, using the mean number of alleles per locus and expected heterozygosity as standardized metrics. Populations within each study were categorized according to the type of human disturbance experienced (“hunting/harvest”, “habitat fragmentation”, or “pollution”), and taxon-specific, as well as time- and context-dependent disturbance effects were considered. I found that human disturbances are associated with weak, but consistent changes in neutral genetic variation within natural populations. The direction of change was dependent on the type of human disturbance experienced, with some forms of anthropogenic challenges consistently decreasing genetic variation from background patterns (e.g., habitat fragmentation), whereas others had no effect (e.g., hunting/harvest) or even slightly increased genetic variation (e.g., pollution). These same measures appeared sensitive to both the time of origin and duration of the disturbance as well. This suggests that the presence or absence, strength, type, as well as the spatial and temporal scale of human disturbance experienced may warrant careful consideration when conservation management plans are formulated for natural populations, with particular attention paid to the effects of habitat fragmentation.