ORCID Profile
0000-0002-5485-4197
Current Organisation
University of Queensland
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Marine and Estuarine Ecology (incl. Marine Ichthyology) | Environmental Science and Management | Invasive Species Ecology | Genetics | Population, Ecological and Evolutionary Genetics | Ecological Impacts of Climate Change | Conservation and Biodiversity | Natural Resource Management | Conservation And Biodiversity | Environmental Management And Rehabilitation | Conservation
ANZSRC Socio-Economic Objective (SEO)
Marine Flora, Fauna and Biodiversity | Control of Pests, Diseases and Exotic Species in Marine Environments | Ecosystem Assessment and Management of Coastal and Estuarine Environments | Climate Change Mitigation Strategies | Aquaculture Molluscs (excl. Oysters) | Tourism not elsewhere classified | Marine protected areas | Ecosystem Assessment and Management of Marine Environments |
Related Links
Publications
Influence of offshore oil and gas structures on seascape ecological connectivity
Publisher: Wiley
Date: 16-03-2022
DOI: 10.1111/GCB.16134
Abstract: Offshore platforms, subsea pipelines, wells and related fixed structures supporting the oil and gas (O& G) industry are prevalent in oceans across the globe, with many approaching the end of their operational life and requiring decommissioning. Although structures can possess high ecological ersity and productivity, information on how they interact with broader ecological processes remains unclear. Here, we review the current state of knowledge on the role of O& G infrastructure in maintaining, altering or enhancing ecological connectivity with natural marine habitats. There is a paucity of studies on the subject with only 33 papers specifically targeting connectivity and O& G structures, although other studies provide important related information. Evidence for O& G structures facilitating vertical and horizontal seascape connectivity exists for larvae and mobile adult invertebrates, fish and megafauna including threatened and commercially important species. The degree to which these structures represent a beneficial or detrimental net impact remains unclear, is complex and ultimately needs more research to determine the extent to which natural connectivity networks are conserved, enhanced or disrupted. We discuss the potential impacts of different decommissioning approaches on seascape connectivity and identify, through expert elicitation, critical knowledge gaps that, if addressed, may further inform decision making for the life cycle of O& G infrastructure, with relevance for other industries (e.g. renewables). The most highly ranked critical knowledge gap was a need to understand how O& G structures modify and influence the movement patterns of mobile species and dispersal stages of sessile marine species. Understanding how different decommissioning options affect species survival and movement was also highly ranked, as was understanding the extent to which O& G structures contribute to extending species distributions by providing rest stops, foraging habitat, and stepping stones. These questions could be addressed with further dedicated studies of animal movement in relation to structures using telemetry, molecular techniques and movement models. Our review and these priority questions provide a roadmap for advancing research needed to support evidence‐based decision making for decommissioning O& G infrastructure.
Can sea snakes slither through seascape structure? Comparative phylogeography and population genetics of Hydrophis group sea snakes in Australia and Southeast Asia
Publisher: California Digital Library (CDL)
Date: 07-09-2022
DOI: 10.21425/F5FBG56342
Deep connections: Divergence histories with gene flow in mesophotic Agaricia corals.
Publisher: Wiley
Date: 27-02-2022
DOI: 10.1111/MEC.16391
Abstract: Largely understudied, mesophotic coral ecosystems lie below shallow reefs (at >30 m depth) and comprise ecologically distinct communities. Brooding reproductive modes appear to predominate among mesophotic-specialist corals and may limit genetic connectivity among populations. Using reduced representation genomic sequencing, we assessed spatial population genetic structure at 50 m depth in an ecologically important mesophotic-specialist species Agaricia grahamae, among locations in the Southern Caribbean. We also tested for hybridisation with the closely related (but depth-generalist) species Agaricia lamarcki, within their sympatric depth zone (50 m). In contrast to our expectations, no spatial genetic structure was detected between the reefs of Curaçao and Bonaire (~40 km apart) within A. grahamae. However, cryptic taxa were discovered within both taxonomic species, with those in A. lamarcki (incompletely) partitioned by depth and those in A. grahamae occurring sympatrically (at the same depth). Hybrid analyses and demographic modelling identified contemporary and historical gene flow among cryptic taxa, both within and between A. grahamae and A. lamarcki. These results (1) indicate that spatial connectivity and subsequent replenishment may be possible between islands of moderate geographic distances for A. grahamae, an ecologically important mesophotic species, (2) that cryptic taxa occur in the mesophotic zone and environmental selection along shallow to mesophotic depth gradients may drive ergence in depth-generalists such as A. lamarcki, and (3) highlight that gene flow links taxa within this relativity erse Caribbean genus.
Incorporating larval dispersal into MPA design for both conservation and fisheries
Publisher: Wiley
Date: 15-03-2017
DOI: 10.1002/EAP.1495
Abstract: Larval dispersal by ocean currents is a critical component of systematic marine protected area (MPA) design. However, there is a lack of quantitative methods to incorporate larval dispersal in support of increasingly erse management objectives, including local population persistence under multiple types of threats (primarily focused on larval retention within and dispersal between protected locations) and benefits to unprotected populations and fisheries (primarily focused on larval export from protected locations to fishing grounds). Here, we present a flexible MPA design approach that can reconcile multiple such potentially conflicting management objectives by balancing various associated treatments of larval dispersal information. We demonstrate our approach based on alternative dispersal patterns, combinations of threats to populations, management objectives, and two different optimization strategies (site vs. network-based). Our outcomes highlight a consistently high effectiveness in selecting priority locations that are self-replenishing, inter-connected, and/or important larval sources. We find that the opportunity to balance these three dispersal attributes flexibly can help not only to prevent meta-population collapse, but also to ensure effective fisheries recovery, with average increases in the number of recruits at fishing grounds at least two times higher than achieved by standard habitat-based or ad-hoc MPA designs. Future applications of our MPA design approach should therefore be encouraged, specifically where management tools other than MPAs are not feasible.
Global connections with some genomic differentiation occur between Indo‐Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish
Publisher: Wiley
Date: 24-05-2021
DOI: 10.1111/JBI.14135
Abstract: Globally distributed pelagic fishes are typified by very low to negligible genetic differentiation at oceanic scales arising from high gene flow and (or) large population sizes. However, genomic approaches employing thousands of loci to characterise genetic variation can illuminate subtle patterns of genetic structure and facilitate demographic inference, such that effects arising from gene flow and population size can be partially decoupled. We used a population genomics approach to identify putative stocks in a circumtropical pelagic fish, wahoo, and to assess global connectivity in this species. Indo‐Pacific and Atlantic Oceans. Wahoo, Acanthocybium solandri (Cuvier, 1832). Globally distributed wahoo s les from 11 locations (representing a total of 296 in iduals) were sequenced using a pool‐seq ezRAD approach to obtain 1289–9825 genome‐wide SNP loci per population pair for analyses of genetic structure at a minor allele frequency (MAF) .05. Demographic inference using a diffusion approximation method ( ∂a∂i ) was performed using 11,495–12,812 SNPs per population pair at a MAF .02. Genetic structure, measured as F ST , was overall low, suggesting very little heterogeneity amongst s le pairs (pairwise F ST ≤ 0.021). However, there was a clear signal of regional genetic structuring between ocean basins. A principal coordinate analysis separated s les from the Indo‐Pacific with those from the Atlantic and an analysis of molecular variance suggested that ~77% of variation in genetic structure was amongst regions. Our demographic analyses found greater support for models including migration over simple models of isolation. Our study provides the most thorough genetic investigation of wahoo to date. We provide evidence for global connectivity of wahoo populations over their evolutionary history, but we also provide the first indication of subtle regional structure between the Indo‐Pacific and Atlantic Oceans, which occurs against a background of high gene flow. The identification of regional stocks will inform new management strategies and guide future investigations in wahoo, an increasingly important species in global fisheries.
Green, yellow or black? Genetic differentiation and adaptation signatures in a highly migratory marine turtle
Publisher: The Royal Society
Date: 07-07-2021
Abstract: Marine species may exhibit genetic structure accompanied by phenotypic differentiation related to adaptation despite their high mobility. Two shape-based morphotypes have been identified for the green turtle ( Chelonia mydas ) in the Pacific Ocean: the south-central/western or yellow turtle and north-central/eastern or black turtle. The genetic differentiation between these morphotypes and the adaptation of the black turtle to environmentally contrasting conditions of the eastern Pacific region has remained a mystery for decades. Here we addressed both questions using a reduced-representation genome approach (Dartseq 9473 neutral SNPs) and identifying candidate outlier loci (67 outlier SNPs) of biological relevance between shape-based morphotypes from eight Pacific foraging grounds ( n = 158). Our results support genetic ergence between morphotypes, probably arising from strong natal homing behaviour. Genes and enriched biological functions linked to thermoregulation, hypoxia, melanism, morphogenesis, osmoregulation, diet and reproduction were found to be outliers for differentiation, providing evidence for adaptation of C. mydas to the eastern Pacific region and suggesting independent evolutionary trajectories of the shape-based morphotypes. Our findings support the evolutionary distinctness of the enigmatic black turtle and contribute to the adaptive research and conservation genomics of a long-lived and highly mobile vertebrate.
Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia
Publisher: Wiley
Date: 18-09-2020
DOI: 10.1111/EVA.12857
Abstract: Introduced species can impose profound impacts on the evolution of receiving communities with which they interact. If native and introduced taxa remain reproductively semi‐isolated, human‐mediated secondary contact may promote genetic exchange across newly created hybrid zones, potentially impacting native genetic ersity and invasive species spread. Here, we investigate the contributions of recent ergence histories and ongoing (post‐introduction) gene flow between the invasive marine mussel, Mytilus galloprovincialis, and a morphologically indistinguishable and taxonomically contentious native Australian taxon, Mytilus planulatus . Using transcriptome‐wide markers, we demonstrate that two contemporary M. galloprovincialis introductions into south‐eastern Australia originate from genetically ergent lineages from its native range in the Mediterranean Sea and Atlantic Europe, where both introductions have led to repeated instances of admixture between introduced and endemic populations. Through increased genome‐wide resolution of species relationships, combined with demographic modelling, we validate that mussels s led in Tasmania are representative of the endemic Australian taxon ( M. planulatus ), but share strong genetic affinities to M. galloprovincialis . Demographic inferences indicate late‐Pleistocene ergence times and historical gene flow between the Tasmanian endemic lineage and northern M. galloprovincialis , suggesting that native and introduced taxa have experienced a period of historical isolation of at least 100,000 years. Our results demonstrate that many genomic loci and sufficient s ling of closely related lineages in both sympatric (e.g. Australian populations) and allopatric (e.g. northern hemisphere Mytilus taxa) ranges are necessary to accurately (a) interpret patterns of intraspecific differentiation and to (b) distinguish contemporary invasive introgression from signatures left by recent ergence histories in high dispersal marine species. More broadly, our study fills a significant gap in systematic knowledge of native Australian bio ersity and sheds light on the intrinsic challenges for invasive species research when native and introduced species boundaries are not well defined.
Historical divergences associated with intermittent land bridges overshadow isolation by larval dispersal in co‐distributed species of Tridacna giant clams
Publisher: Wiley
Date: 10-02-2018
DOI: 10.1111/JBI.13163
Geographic variation and positive selection on M7 lysin, an acrosomal sperm protein in mussels (Mytilus spp.)
Publisher: Oxford University Press (OUP)
Date: 19-07-2006
Abstract: Successful fertilization in free-spawning marine organisms depends on the interactions between genes expressed on the surfaces of eggs and sperm. Positive selection frequently characterizes the molecular evolution of such genes, raising the possibility that some common deterministic process drives the evolution of gamete recognition genes and may even be important for understanding the evolution of prezygotic isolation and speciation in the marine realm. One hypothesis is that gamete recognition genes are subject to selection for prezygotic isolation, namely, reinforcement. In a previous study, positive selection on the gene coding for the acrosomal sperm protein M7 lysin was demonstrated among allopatric populations of mussels in the Mytilus edulis species group (M. edulis, Mytilus galloprovincialis, and Mytilus trossulus). Here, we expand s ling to include M7 lysin haplotypes from populations where mussel species are sympatric and hybridize to determine whether there is a pattern of reproductive character displacement (RCD), which would be consistent with reinforcement driving selection on this gene. We do not detect a strong pattern of RCD neither are there unique haplotypes in sympatry nor is there consistently greater population structure in comparisons involving sympatric populations. One distinct group of haplotypes, however, is strongly affected by natural selection, and this group of haplotypes is found within M. galloprovincialis populations throughout the Northern Hemisphere concurrent with haplotypes common to M. galloprovincialis and M. edulis. We suggest that balancing selection, perhaps resulting from sexual conflicts between sperm and eggs, maintains old allelic ersity within M. galloprovincialis.
Refined Global Analysis of Bemisia tabaci (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidae) Mitochondrial Cytochrome Oxidase 1 to Identify Species Level Genetic Boundaries
Publisher: Oxford University Press (OUP)
Date: 03-2010
DOI: 10.1603/AN09061
Abstract: Identifying species boundaries within morphologically indistinguishable cryptic species complexes is often contentious. For the whitefly Bemisia tabaci (Gennadius) (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidae), the lack of a clear understanding about the genetic limits of the numerous genetic groups and biotypes so far identified has resulted in a lack of consistency in the application of the terms, the approaches used to apply them and in our understanding of what genetic structure within B. tabaci means. Our response has been to use mitochondrial gene cytochrome oxidase one to consider how to clearly and consistently define genetic separation. Using Bayesian phylogenetic analysis and analysis of sequence pairwise ergence we found a considerably higher number of genetic groups than had been previously determined with two breaks in the distribution, one at 11% and another at 3.5%. At & % ergence, 11 distinct groups were resolved, whereas at & .5% ergence 24 groups were identified. Consensus sequences for each of these groups were determined and were shown to be useful in the correct assignment of sequences of unknown origin. The 3.5% ergence bound is consistent with species level separations in other insect taxa and suggests that B. tabaci is a cryptic species composed of at least 24 distinct species. We further show that the placement of Bemesia atriplex (Froggatt) within the B. tabaci in group adds further weight to the argument for species level separation within B. tabaci. This new analysis, which constructs consensus sequences and uses these as a standard against which unknown sequences can be compared, provides for the first time a consistent means of identifying the genetic bounds of each species with a high degree of certainty.
Marine Reserve Targets to Sustain and Rebuild Unregulated Fisheries
Publisher: Public Library of Science (PLoS)
Date: 05-01-2017
Seascape features, rather than dispersal traits, predict spatial genetic patterns in co-distributed reef fishes
Publisher: Wiley
Date: 14-10-2016
DOI: 10.1111/JBI.12647
Selecting species for restoration in foundational assemblages
Publisher: Cold Spring Harbor Laboratory
Date: 04-11-2021
DOI: 10.1101/2021.11.03.467181
Abstract: Humans have long sought to restore species, but little attention has been directed at how to best select a subset of foundation species for maintaining rich assemblages that support ecosystems, like coral reefs and rainforests that are increasingly threatened by environmental change. We propose a two-part hedging approach that selects optimized sets of species for restoration. The first part acknowledges that bio ersity supports ecosystem functions and services, and so it takes precaution against loss by ensuring an even spread of phenotypic traits. The second part maximizes species and ecosystem persistence by weighting species based on characteristics that are known to improve ecological persistence—e.g., abundance, species range and tolerance to environmental change. Using existing phenotypic trait and ecological characteristic data for reef building corals, we identified sets of ecologically persistent species by examining marginal returns in occupancy of phenotypic trait space. We compared optimal sets of species with those from the world’s southern-most coral reef which naturally harbors low coral ersity to show these occupy much of the trait space. Comparison with an existing coral restoration program indicated that current corals used for restoration only cover part of the desired trait space and may be improved by including species with different traits. Synthesis and applications . While there are many possible criteria for selecting species for restoration, the approach proposed here addresses the need to insure against unpredictable losses of ecosystem services by focusing on a wide range of phenotypic traits and ecological characteristics. Furthermore, the flexibility of the approach enables the functional goals of restoration to vary depending on environmental context, stakeholder values, and the spatial and temporal scales at which meaningful impacts can be achieved.
Regional patterns of mtDNA diversity in Styela plicata, an invasive ascidian, from Australian and New Zealand marinas
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/MF12289
Abstract: The ascidian Styela plicata is abundant in harbours and marinas worldwide and has likely reached this distribution via human-mediated dispersal. Previous worldwide surveys based on mitochondrial cytochrome oxidase one (COI) sequences have described two ergent clades, showing overlapping distributions and geographically widespread haplotypes. These patterns are consistent with recent mixing among genetically differentiated groups arising from multiple introductions from historically distinct sources. In contrast, a study of Australian S. plicata using nuclear markers found that population differentiation along the eastern coast related to geographic distance and no evidence for admixture between previously isolated genetic groups. We re-examined the genetic patterns of Australian S. plicata populations using mtDNA (CO1) to place their genetic patterns within a global context, and we examined New Zealand populations for the first time. We found that the haplotypic compositions of Australian and New Zealand populations are largely representative of other worldwide populations. The New Zealand populations, however, exhibited reduced ersity, being potentially indicative of a severely bottlenecked colonisation event. In contrast to results from nuclear markers, population differentiation of mtDNA among Australian S. plicata was unrelated to geographic distance. The discrepancy between markers is likely to be a consequence of non-equilibrium population genetic processes that typify non-indigenous species.
Reserve Sizes Needed to Protect Coral Reef Fishes
Publisher: Wiley
Date: 17-10-2018
DOI: 10.1111/CONL.12415
North Atlantic marine communities through time
Publisher: Wiley
Date: 10-2010
Models based on individual level movement predict spatial patterns of genetic relatedness for two Australian forest birds
Publisher: Springer Science and Business Media LLC
Date: 19-10-2011
Anthropogenic hybridization at sea: three evolutionary questions relevant to invasive species management
Publisher: The Royal Society
Date: 13-07-2020
Abstract: Species introductions promote secondary contacts between taxa with long histories of allopatric ergence. Anthropogenic contact zones thus offer valuable contrasts to speciation studies in natural systems where past spatial isolations may have been brief or intermittent. Investigations of anthropogenic hybridization are rare for marine animals, which have high fecundity and high dispersal ability, characteristics that contrast to most terrestrial animals. Genomic studies indicate that gene flow can still occur after millions of years of ergence, as illustrated by invasive mussels and tunicates. In this context, we highlight three issues: (i) the effects of high propagule pressure and demographic asymmetries on introgression directionality, (ii) the role of hybridization in preventing introduced species spread, and (iii) the importance of postzygotic barriers in maintaining reproductive isolation. Anthropogenic contact zones offer evolutionary biologists unprecedented large scale hybridization experiments. In addition to breaking the highly effective reproductive isolating barrier of spatial segregation, they allow researchers to explore unusual demographic contexts with strong asymmetries. The outcomes are erse, from introgression sw ing to strong barriers to gene flow, and lead to local containment or widespread invasion. These outcomes should not be neglected in management policies of marine invasive species. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
Intertidal gobies acclimate rate of luminance change for background matching with shifts in seasonal temperature
Publisher: Wiley
Date: 13-04-2020
Comparative genomics reveals divergent thermal selection in warm- and cold-tolerant marine mussels.
Publisher: Wiley
Date: 03-01-2020
DOI: 10.1111/MEC.15339
Abstract: Investigating the history of natural selection among closely related species can elucidate how genomes erge in response to disparate environmental pressures. Molecular evolutionary approaches can be integrated with knowledge of gene functions to examine how evolutionary ergence may affect ecologically relevant traits such as temperature tolerance and species distribution limits. Here, we integrate transcriptome-wide analyses of molecular evolution with knowledge from physiological studies to develop hypotheses regarding the functional classes of genes under positive selection in one of the world's most widespread invasive species, the warm-tolerant marine mussel Mytilus galloprovincialis. Based on existing physiological information, we test the hypothesis that genomic functions previously linked to ergent temperature adaptation at the whole-organism level show accelerated molecular ergence between warm-adapted M. galloprovincialis and cold-adapted congeners. Combined results from codon model tests and analyses of polymorphism and ergence reveal that ergent selection has affected genomic functions previously associated with species-specific expression responses to heat stress, namely oxidative stress defence and cytoskeletal stabilization. Examining specific loci implicated in thermal tolerance among Mytilus species (based on interspecific biochemical or expression patterns), we find close functional similarities between known thermotolerance candidate genes under positive selection and positively selected loci under predicted genomic functions (those associated with ergent expression responses). Taken together, our findings suggest a contribution of temperature-dependent selection in the molecular ergence between warm- and cold-adapted Mytilus species that is largely consistent with results from physiological studies. More broadly, this study provides an ex le of how independent experimental evidence from ecophysiological investigations can inform evolutionary hypotheses about molecular adaptation in closely related nonmodel species.
Patterns of mtDNA diversity in North Atlantic populations of the mussel Mytilus edulis
Publisher: Springer Science and Business Media LLC
Date: 13-08-2008
Asymmetric dispersal is a critical element of concordance between biophysical dispersal models and spatial genetic structure in Great Barrier Reef corals
Publisher: Wiley
Date: 17-07-2019
DOI: 10.1111/DDI.12969
Effects of geography and life history traits on genetic differentiation in benthic marine fishes
Publisher: Wiley
Date: 08-2011
Characterisation and cross-amplification of 19 novel microsatellite loci for the sandbar shark, Carcharhinus plumbeus
Publisher: Springer Science and Business Media LLC
Date: 19-10-2015
Evaluating edge-of-range genetic patterns for tropical echinoderms, Acanthaster planci and Tripneustes gratilla, of the Kermadec Islands, southwest Pacific
Publisher: Bulletin of Marine Science
Date: 2014
Largest of all electric-fish snouts: Hypermorphic facial growth in male Apteronotus hasemani and the identity of Apteronotus anas (Gymnotiformes: Apteronotidae)
Publisher: American Society of Ichthyologists and Herpetologists (ASIH)
Date: 02-2002
High germline mutation rates but not extreme population size outbreaks influence genetic diversity in crown-of-thorns sea stars
Publisher: Cold Spring Harbor Laboratory
Date: 30-06-2023
DOI: 10.1101/2023.06.28.546961
Abstract: Lewontin’s paradox, the observation that levels of genetic ersity (π) among animals do not scale linearly with variation in census population sizes ( N c ), is an evolutionary conundrum, where the most extreme mismatches between π and N c are found for highly abundant marine invertebrates. Yet, whether new mutations influence π relative to extrinsic processes remains unknown for most taxa. Here, we provide the first direct germline mutation rate ( μ ) estimate for a marine invertebrate, using high-coverage (60x) whole-genome sequencing of wild-caught Acanthaster cf. solaris crown-of-thorns sea stars (Echinodermata). We also provide empirical estimates of adult N c in Australia’s Great Barrier Reef to jointly examine the determinants of π. Based on direct observations of 63 de novo mutations across 14 parent-offspring trios, the A. cf. solaris mean μ was 9.13 x 10 -09 mutations per-site per-generation (95% CI: 6.51 x 10 -09 to 1.18 x 10 -08 ). This value exceeds estimates for other invertebrates, showing greater concordance with reported vertebrate germline mutation rates. Lower-than-expected N e (∼70,000-180,000) and low N e / N c values (0.0047-0.048) indicated significant genetic drift and weak influences of contemporary population outbreaks on long-term π. Our findings of elevated μ and low N e in A. cf. solaris may help explain high mutational loads and extreme polymorphism levels observed in some marine invertebrate taxa and are consistent with μ evolving in response to N e (drift-barrier hypothesis). This study advances our understanding of the processes controlling levels of natural genetic variation and provides new data valuable for further testing hypotheses about mutation rate evolution across animal phyla.
Vicariance and dispersal across an intermittent barrier: population genetic structure of marine animals across the Torres Strait land bridge
Publisher: Springer Science and Business Media LLC
Date: 28-05-2011
Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats
Publisher: Springer Science and Business Media LLC
Date: 2011
Poor data stewardship will hinder global genetic diversity surveillance
Publisher: Proceedings of the National Academy of Sciences
Date: 17-08-2021
Abstract: Genomic data are being produced and archived at a prodigious rate, and current studies could become historical baselines for future global genetic ersity 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 (87%) lacked the spatiotemporal metadata necessary for genetic bio ersity surveillance. Labor-intensive scouring of a subset of published papers yielded geospatial coordinates and collection years for only 39% (51% 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 bio ersity and to plug the growing metadata gap.
Genetic and phenotypic diversity in the wedgefish Rhynchobatus australiae, a threatened ray of high value in the shark fin trade
Publisher: Inter-Research Science Center
Date: 21-04-2016
DOI: 10.3354/MEPS11617
Incorporating Genetic Measures of Connectivity and Adaptation in Marine Spatial Planning for Corals
Publisher: Springer International Publishing
Date: 2022
Metadata preservation and stewardship for genomic data is possible, but must happen now
Publisher: Cold Spring Harbor Laboratory
Date: 15-09-2022
DOI: 10.1101/2022.09.12.507034
Abstract: Genetic ersity within species represents a fundamental yet underappreciated level of bio ersity. Because genetic ersity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic ersity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a “distributed datathon” to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 561 contained s les from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 78% of these 561 datasets (N = 440 BioProjects comprising 45,105 in iduals or BioS les from 762 species in 17 phyla). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the s les were taken was the most easily found information about s ling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, 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 forever.
Reproductive Output and Duration of the Pelagic Larval Stage Determine Seascape-Wide Connectivity of Marine Populations
Publisher: Oxford University Press (OUP)
Date: 19-07-2012
DOI: 10.1093/ICB/ICS101
Abstract: Connectivity among marine populations is critical for persistence of metapopulations, coping with climate change, and determining the geographic distribution of species. The influence of pelagic larval duration (PLD) on connectivity has been studied extensively, but relatively little is known about the influence of other biological parameters, such as the survival and behavior of larvae, and the fecundity of adults, on population connectivity. Furthermore, the interaction between the seascape (habitat structure and currents) and these biological parameters is unclear. We explore these interactions using a biophysical model of larval dispersal across the Indo-Pacific. We describe an approach that quantifies geographic patterns of connectivity from demographically relevant to evolutionarily significant levels across a range of species. We predict that at least 95% of larval settlement occurs within 155 km of the source population and within 13 days irrespective of the species' life history, yet long-distant connections remain likely. Self-recruitment is primarily driven by the local oceanography, larval mortality, and the larval precompetency period, whereas broad-scale connectivity is strongly influenced by reproductive output (abundance and fecundity of adults) and the length of PLD. The networks we have created are geographically explicit models of marine connectivity that define dispersal corridors, barriers, and the emergent structure of marine populations. These models provide hypotheses for empirical testing.
Genetic connectivity patterns of Pocillopora verrucosa in southern African Marine Protected Areas
Publisher: Inter-Research Science Center
Date: 07-02-2008
DOI: 10.3354/MEPS07245
Moving beyond heritability in the search for coral adaptive potential
Publisher: Wiley
Date: 29-04-2023
DOI: 10.1111/GCB.16719
Abstract: Global environmental change is happening at unprecedented rates. Coral reefs are among the ecosystems most threatened by global change. For wild populations to persist, they must adapt. Knowledge shortfalls about corals' complex ecological and evolutionary dynamics, however, stymie predictions about potential adaptation to future conditions. Here, we review adaptation through the lens of quantitative genetics. We argue that coral adaptation studies can benefit greatly from “wild” quantitative genetic methods, where traits are studied in wild populations undergoing natural selection, genomic relationship matrices can replace breeding experiments, and analyses can be extended to examine genetic constraints among traits. In addition, in iduals with advantageous genotypes for anticipated future conditions can be identified. Finally, genomic genotyping supports simultaneous consideration of how genetic ersity is arrayed across geographic and environmental distances, providing greater context for predictions of phenotypic evolution at a metapopulation scale.
Characterisation and cross-amplification of 21 novel microsatellite loci for the dusky shark, Carcharhinus obscurus
Publisher: Springer Science and Business Media LLC
Date: 22-10-2015
Site fidelity, size, and morphology may differ by tidal position for an intertidal fish, Bathygobius cocosensis (Perciformes-Gobiidae), in Eastern Australia.
Publisher: PeerJ
Date: 28-07-2016
DOI: 10.7717/PEERJ.2263
Abstract: The intertidal zone is a transitional environment that undergoes daily environmental fluctuations as tides rise and fall. Relatively few fish species are adapted to endure the physiological pressures of this environment. This study focused on Bathygobius cocosensis (Gobiidae), a common intertidal fish in New South Wales, Australia. We investigated whether shore height impacted site fidelity, survival probability, fish size, and morphological traits with respect to tidal height. Mark-recapture methods were used over a five month period to determine if in iduals in high shore pools had greater site fidelity fish in high tide pools were more than twice as likely to be recaptured in their original pool than fish from low tide pools. High pool in iduals were, on average, smaller with larger eyes and longer snouts relative to their size as compared to low pool in iduals. We discuss several mechanisms that could cause the observed pattern in morphological variation. Ultimately, this study suggests that within species behaviour and morphology differ by tidal position for an intertidal fish.
Positive selection on an acrosomal sperm protein, M7 lysin, in three species of the mussel genus Mytilus
Publisher: Oxford University Press (OUP)
Date: 02-2003
Abstract: Marine invertebrate sperm proteins are particularly interesting because they are characterized by positive selection and are likely to be involved in prezyogotic isolation and, thus, speciation. Here, we present the first survey of interspecific and intraspecific variation of a bivalve sperm protein among a group of species that regularly hybridize in nature. M7 lysin is found in sperm acrosomes of mussels and dissolves the egg vitelline coat, permitting fertilization. We sequenced multiple alleles of the mature protein-coding region of M7 lysin from allopatric populations of mussels in the Mytilus edulis species group (M. edulis, M. galloprovincialis, and M. trossulus). A significant McDonald-Kreitman test showed an excess of fixed amino acid replacing substitutions between species, consistent with positive selection. In addition, Kolmogorov-Smirnov tests showed significant heterogeneity in polymorphism to ergence ratios for both synonymous variation and combined synonymous and nonsynonymous variation within M. galloprovincialis. These results indicate that there has been adaptive evolution at M7 lysin and, furthermore, show that positive selection on sperm proteins can occur even when postzygotic reproductive isolation is incomplete.
Population genetics of Anopheles koliensis through Papua New Guinea: New cryptic species and landscape topography effects on genetic connectivity
Publisher: Wiley
Date: 04-11-2019
DOI: 10.1002/ECE3.5792
Not the time or the place: the missing spatio-temporal link in publicly available genetic data
Publisher: Wiley
Date: 23-06-2015
DOI: 10.1111/MEC.13254
Abstract: Genetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be 'repurposed' to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy, we assessed the genetic, spatial and temporal data archived for 419 data sets from 289 articles in Molecular Ecology from 2009 to 2013. We then determined whether archived data could be used to reproduce analyses as presented in the manuscript. We found that the journal's mandatory archiving policy has had a substantial positive impact, increasing genetic data archiving from 49 (pre-2011) to 98% (2011-present). However, 31% of publicly archived genetic data sets could not be recreated based on information supplied in either the manuscript or public archives, with incomplete data or inconsistent codes linking genetic data and metadata as the primary reasons. While the majority of articles did provide some geographic information, 40% did not provide this information as geographic coordinates. Furthermore, a large proportion of articles did not contain any information regarding date of s ling (40%). Although the inclusion of spatio-temporal data does require an increase in effort, we argue that the enduring value of publicly accessible genetic data to the molecular ecology field is greatly compromised when such metadata are not archived alongside genetic data.
genomalicious: serving up a smorgasbord of R functions for population genomic analyses
Publisher: Cold Spring Harbor Laboratory
Date: 12-06-2019
DOI: 10.1101/667337
Abstract: Turning SNP data into biologically meaningful results requires considerable computational acrobatics, including importing, exporting, and manipulating data among different analytical packages and programming environments, and finding ways to visualise results for data exploration and presentation. We introduce genomalicious , an R package designed to provide a selection of functions for population genomicists to simply, intuitively, and flexibly, guide SNP data through their analytical pipelines, within and outside R. Moreover, researchers using pooled allele frequencies, or in idually sequenced genotypes, are sure to find functions that accommodate their tastes in genomalicious. The source code for this package is freely available on GitHub.
Evolving coral reef conservation with genetic information
Publisher: Bulletin of Marine Science
Date: 2014
The scope of published population genetic data for Indo-Pacific marine fauna and future research opportunities in the region
Publisher: Bulletin of Marine Science
Date: 2014
Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research
Publisher: Wiley
Date: 27-10-2020
Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies
Publisher: Oxford University Press (OUP)
Date: 06-07-2016
DOI: 10.1093/CZ/ZOW067
Latitudinal variability in spatial genetic structure in the invasive ascidian, Styela plicata
Publisher: Springer Science and Business Media LLC
Date: 09-05-2010
Comparative phylogeography in the genomic age: Opportunities and challenges
Publisher: Wiley
Date: 05-10-2022
DOI: 10.1111/JBI.14481
Abstract: We consider the opportunities and challenges comparative phylogeography (CP) faces in the genomic age to determine: (1) how we can maximise the potential of big CP analyses to advance biogeographic and macroevolutionary theory and (2) what we can, and will struggle, to achieve using CP approaches in this era of genomics. World‐wide. All. We review the literature to discuss the future of CP ‐ particularly examining CP insights enabled by genomics that may not be possible for single species and/or few molecular markers. We focus on how geography and species' natural histories interact to yield congruent and incongruent patterns of neutral and adaptive processes in the context of both historical and recent rapid evolution. We also consider how CP genomic data are being stored, accessed, and shared. With the widespread availability of genomic data, the shift from a single‐ to a multi‐locus perspective is resulting in detailed historical inferences and an improved statistical rigour in phylogeography. However, the time and effort required for collecting co‐distributed species and accruing species‐specific ecological knowledge continue to be limiting factors. Bioinformatic skills and user‐friendly analytical tools, alongside the computational infrastructure required for big data, can also be limiting. Over the last ~35 years, there has been much progress in understanding how intraspecific genetic variation is geographically distributed. The next major steps in CP will be to incorporate evolutionary processes and community perspectives to account for patterns and responses among co‐distributed species and across temporal scales, including those related to anthropogenic change. However, the full potential of CP will only be realised if we employ robust study designs within a sound comparative framework. We advocate that phylogeographers adopt such consistent approaches to enhance future comparisons to present‐day findings.
Rapid larval growth is costly for post-metamorphic thermal performance in a Great Barrier Reef fish
Publisher: Springer Science and Business Media LLC
Date: 24-05-2019
Clones in space-how sampling can bias genetic diversity estimates in corals: editorial comment on the feature article by Gorospe et al.
Publisher: Springer Science and Business Media LLC
Date: 10-03-2015
Moving beyond heritability in the search for coral adaptive potential
Publisher: California Digital Library (CDL)
Date: 16-01-2023
DOI: 10.32942/X2T596
Abstract: Global environmental change is happening at unprecedented rates. Coral reefs are among the ecosystems most threatened by global change and for wild populations to persist, they must adapt. However, little is known about corals’ complex ecological and evolutionary dynamics making prediction about potential adaptation to future conditions precarious. Here, we review the process of adaptation through the lens of quantitative genetics and make suggestions about how incorporating genomic tools can help to both understand and predict adaptive potential in corals. In many cases, small changes in experimental design may provide large increases in the power, precision, and accuracy of information produced for predicting corals’ adaptation to environmental changes. We also outline where quantitative genetic principles may be incorporated into current research programs that aim to bolster coral tolerance to future warming conditions.
Do tiny fish rule the reefs?
Publisher: American Association for the Advancement of Science (AAAS)
Date: 21-06-2019
Abstract: Covert fish larvae may serve as crucial cuisine in coral reef ecosystems
A Novel Widespread Cryptic Species and Phylogeographic Patterns within Several Giant Clam Species (Cardiidae: Tridacna) from the Indo-Pacific Ocean
Publisher: Public Library of Science (PLoS)
Date: 20-11-2013
Reproducibility in ecology and evolution: Minimum standards for data and code
Publisher: Wiley
Date: 05-2023
DOI: 10.1002/ECE3.9961
Abstract: We call for journals to commit to requiring open data be archived in a format that will be simple and clear for readers to understand and use. If applied consistently, these requirements will allow contributors to be acknowledged for their work through citation of open data, and facilitate scientific progress.
Environmental and geographic variables are effective surrogates for genetic variation in conservation planning
Publisher: Proceedings of the National Academy of Sciences
Date: 31-10-2017
Abstract: To protect bio ersity for the long term, nature reserves and other protected areas need to represent a broad range of different genetic types. However, genetic data are expensive and time-consuming to obtain. Here we show that freely available environmental and geographic variables can be used as effective surrogates for genetic data in conservation planning. This means that conservation planners can, with some confidence, design protected area systems to represent intraspecific genetic ersity without investing in expensive programs to obtain and analyze genetic data.
Seascape Genetics: Populations, Individuals, and Genes Marooned and Adrift
Publisher: Wiley
Date: 03-2013
DOI: 10.1111/GEC3.12032
Cleaning up the biogeography of Labroides dimidiatus using phylogenetics and morphometrics
Publisher: Springer Science and Business Media LLC
Date: 27-10-2013
Taking the Plunge: An Introduction to Undertaking Seascape Genetic Studies and using Biophysical Models
Publisher: Wiley
Date: 03-2013
DOI: 10.1111/GEC3.12031
Congruent patterns of connectivity can inform management for broadcast spawning corals on the Great Barrier Reef.
Publisher: Wiley
Date: 15-05-2016
DOI: 10.1111/MEC.13649
Abstract: Connectivity underpins the persistence and recovery of marine ecosystems. The Great Barrier Reef (GBR) is the world's largest coral reef ecosystem and managed by an extensive network of no-take zones however, information about connectivity was not available to optimize the network's configuration. We use multivariate analyses, Bayesian clustering algorithms and assignment tests of the largest population genetic data set for any organism on the GBR to date (Acropora tenuis, >2500 colonies >50 reefs, genotyped for ten microsatellite loci) to demonstrate highly congruent patterns of connectivity between this common broadcast spawning reef-building coral and its congener Acropora millepora (~950 colonies 20 reefs, genotyped for 12 microsatellite loci). For both species, there is a genetic ide at around 19°S latitude, most probably reflecting allopatric differentiation during the Pleistocene. GBR reefs north of 19°S are essentially panmictic whereas southern reefs are genetically distinct with higher levels of genetic ersity and population structure, most notably genetic sub ision between inshore and offshore reefs south of 19°S. These broadly congruent patterns of higher genetic ersities found on southern GBR reefs most likely represent the accumulation of alleles via the southward flowing East Australia Current. In addition, signatures of genetic admixture between the Coral Sea and outer-shelf reefs in the northern, central and southern GBR provide evidence of recent gene flow. Our connectivity results are consistent with predictions from recently published larval dispersal models for broadcast spawning corals on the GBR, thereby providing robust connectivity information about the dominant reef-building genus Acropora for coral reef managers.
The complete mitochondrial genome of Bathygobius cocosensis (Perciformes, Gobiidae)
Publisher: Informa UK Limited
Date: 02-01-2018
Planning for Field Based Biological Sample Collection: Using the Genomic Observatories Metadatabase Project Interface
Publisher: Pensoft Publishers
Date: 05-07-2018
DOI: 10.3897/BISS.2.25651
Abstract: The Genomic Observatories Metadatabase (GeOMe, www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with bios les and genetic data. It contributes to the informatics stack – Biocode Commons – of the Genomic Observatories Network (rticles/10.1186/2047-217X-3-2). The GeOMe project interface enables administrators to plan and execute field based s le collection efforts. GeOMe projects specify a core set of s le metadata fields based on community standard vocabularies and also includes plugins for associating s les with photos, subs les, NextGen sequence metadata, and permits. Users can upload their own expedition-specific metadata, which contributes to the overall project dataset while providing the user a convenient method for updating and refining their contributed data. GeOMe provides connection points to the Global Bio ersity Information Facility and archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA), linking specimens and seqeuences via unique persistent identifiers.
Cryptic vicariance in gulf of california fishes parallels vicariant patterns found in Baja California mammals and reptiles
Publisher: The Society for the Study of Evolution
Date: 2005
DOI: 10.1554/05-257.1
Human effects on ecological connectivity in aquatic ecosystems: Integrating scientific approaches to support management and mitigation
Publisher: Elsevier BV
Date: 11-2015
DOI: 10.1016/J.SCITOTENV.2015.04.034
Abstract: Understanding the drivers and implications of anthropogenic disturbance of ecological connectivity is a key concern for the conservation of bio ersity and ecosystem processes. Here, we review human activities that affect the movements and dispersal of aquatic organisms, including damming of rivers, river regulation, habitat loss and alteration, human-assisted dispersal of organisms and climate change. Using a series of case studies, we show that the insight needed to understand the nature and implications of connectivity, and to underpin conservation and management, is best achieved via data synthesis from multiple analytical approaches. We identify four key knowledge requirements for progressing our understanding of the effects of anthropogenic impacts on ecological connectivity: autecology population structure movement characteristics and environmental tolerance henotypic plasticity. Structuring empirical research around these four broad data requirements, and using this information to parameterise appropriate models and develop management approaches, will allow for mitigation of the effects of anthropogenic disturbance on ecological connectivity in aquatic ecosystems.
Sharing and reporting benefits from biodiversity research
Publisher: Wiley
Date: 06-11-2020
DOI: 10.1111/MEC.15702
Genetic Divergence across Habitats in the Widespread Coral Seriatopora hystrix and Its Associated Symbiodinium
Publisher: Public Library of Science (PLoS)
Date: 27-05-2010
Dispersal Capacity Predicts Both Population Genetic Structure and Species Richness in Reef Fishes
Publisher: University of Chicago Press
Date: 07-2014
DOI: 10.1086/676505
Abstract: Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of ersity across a erse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological ersification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.
Importance of timely metadata curation to the global surveillance of genetic diversity
Publisher: Wiley
Date: 10-03-2023
DOI: 10.1111/COBI.14061
Abstract: Genetic ersity within species represents a fundamental yet underappreciated level of bio ersity. Because genetic ersity 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 ersity 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 s les from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets ( n = 440 data sets with data on 45,105 in iduals 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.
Gene flow in the green mirid, Creontiades dilutus (Hemiptera: Miridae), across arid and agricultural environments with different host plant species
Publisher: Wiley
Date: 25-02-2013
DOI: 10.1002/ECE3.510
Latitude-wide genetic patterns reveal historical effects and contrasting patterns of turnover and nestedness at the range peripheries of a tropical marine fish
Publisher: Wiley
Date: 19-03-2015
DOI: 10.1111/ECOG.01398
Genetic and phenotypic variation exhibit both predictable and stochastic patterns across an intertidal fish metapopulation
Publisher: Wiley
Date: 04-05-2021
DOI: 10.1111/MEC.15829
Abstract: Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We s led juvenile and adult life stages, at three sites, over three years. Genome‐wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak‐but‐significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially ergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments.
An intertidal fish shows thermal acclimation despite living in a rapidly fluctuating environment
Publisher: Springer Science and Business Media LLC
Date: 14-03-2019
DOI: 10.1007/S00360-019-01212-0
Abstract: The co-evolution of acclimation capacity and thermal performance breadth has been a contentious issue for decades, and little is known regarding the extent to which acclimation alters the shape of acute thermal performance curves. Current acclimation theory suggests that when daily variation is large and unpredictable ectotherms should not acclimate but should evolve wide performance breadths, allowing maintenance of performance across a wide thermal range. The subtropical intertidal zone, however, experiences a large amount of daily thermal variation, but daily means and ranges shift in predictable ways with season, where daily and seasonal variation is roughly equal. We predicted that animals in this habitat would maintain their capacity to acclimate and that performance breadth would not be altered by acclimation to maintain function with rapidly fluctuating daily temperatures. We tested our prediction using a subtropical goby, Bathygobius cocosensis, which lives in tide pools that vary widely, over days and seasons. We exposed B. cocosensis to winter (12-17 °C) and summer (30-35 °C) thermal conditions for six weeks and then measured the thermal dependence of burst swimming speed, routine and maximum metabolic rate, and ventilation rate between 12 and 36 °C. B. cocosensis exhibited an acclimation response for burst swimming speed, maximum metabolic rate and metabolic scope, but acclimation did not alter the shape of acute thermal performance curves. These results indicate that thermal acclimation can occur when short-term thermal variability is large and equal to seasonal variation, and wide performance breadths can be maintained with acclimation in heterogeneous environments.
Urban development explains reduced genetic diversity in a narrow range endemic freshwater fish
Publisher: Springer Science and Business Media LLC
Date: 08-01-2015
Larval spatial distributions and other early life-history characteristics predict genetic differentiation in eastern Pacific blennioid fishes
Publisher: The Royal Society
Date: 22-09-2001
Women in biogeography
Publisher: Wiley
Date: 26-07-2021
DOI: 10.1111/JBI.14223
Abstract: Despite increasing awareness of issues affecting inclusivity, equity and ersity, change has been slow in science and academia, and gender disparities remain significant. Biogeography has not escaped this pattern. Here, we present a virtual issue compiling some of the most cited papers led by women that have been published in the Journal of Biogeography since 2009 in an effort to equalize visibility of women's influential work. We summarize leading gender disparities and their potential underlying causes, and present our motivation and methodology in compiling this issue. We further provide a blog, website and social media links to highlight the research of the authors whose work is showcased here. Highlighting influential contributions by women biogeographers is a small step towards equalizing visibility across genders. We hope that this virtual issue will also contribute in some way to creating a greater sense of belonging for women biogeographers.
Revisiting the “Centre Hypotheses” of the Indo‐West Pacific: Idiosyncratic genetic diversity of nine reef species offers weak support for the Coral Triangle as a centre of genetic biodiversity
Publisher: Wiley
Date: 07-06-2018
DOI: 10.1111/JBI.13376
Selecting coral species for reef restoration
Publisher: Wiley
Date: 02-07-2023
Abstract: Humans have long sought to restore species but little attention has been directed at how to best select a subset of foundation species for maintaining rich assemblages that support ecosystems, like coral reefs and rainforests, which are increasingly threatened by environmental change. We propose a two‐part hedging approach that selects optimized sets of species for restoration. The first part acknowledges that bio ersity supports ecosystem functions and services, and so it ensures precaution against loss by allocating an even spread of phenotypic traits. The second part maximizes species and ecosystem persistence by weighting species based on characteristics that are known to improve ecological persistence—for ex le abundance, species range and tolerance to environmental change. Using existing phenotypic‐trait and ecological data for reef building corals, we identified sets of ecologically persistent species by examining marginal returns in occupancy of phenotypic trait space. We compared optimal sets of species with those from the world's southern‐most coral reef, which naturally harbours low coral ersity, to show these occupy much of the trait space. Comparison with an existing coral restoration program indicated that current corals used for restoration only cover part of the desired trait space and programs may be improved by including species with different traits. Synthesis and applications . While there are many possible criteria for selecting species for restoration, the approach proposed here addresses the need to insure against unpredictable losses of ecosystem services by focusing on a wide range of phenotypic traits and ecological characteristics. Furthermore, the flexibility of the approach enables the functional goals of restoration to vary depending on environmental context, stakeholder values, and the spatial and temporal scales at which meaningful impacts can be achieved.
Population structure, mitochondrial polyphyly and the repeated loss of human biting ability in anopheline mosquitoes from the southwest Pacific
Publisher: Wiley
Date: 02-07-2012
Return of the ghosts of dispersal past: historical spread and contemporary gene flow in the blue sea star <I>Linckia laevigata</I>
Publisher: Bulletin of Marine Science
Date: 2014
Gene flow throughout the evolutionary history of a polymorphic and generalist clownfish
Publisher: Cold Spring Harbor Laboratory
Date: 22-10-2023
The Genomic Observatories Metadatabase
Publisher: Pensoft Publishers
Date: 22-08-2017
The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples
Publisher: Public Library of Science (PLoS)
Date: 03-08-2017
Pre‐introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels
Publisher: Wiley
Date: 14-12-2021
DOI: 10.1111/JEB.13746
Abstract: Non‐native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis , in the absence (South Africa and California) and presence of hybridization with a native congener ( Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post‐introduction differentiation from native‐range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic‐derived introductions displaying high differentiation (max F ST 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein‐coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages ( M. planulatus and Atlantic M. galloprovincialis ). Additionally, contigs putatively introgressed with ergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome‐wide trends and also erged in parallel in both Atlantic‐derived introductions. These results suggest that ergent demographic histories experienced by introduced lineages, including pre‐introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
Research priorities for the sustainability of coral-rich western Pacific seascapes
Publisher: Springer Science and Business Media LLC
Date: 21-04-2023
DOI: 10.1007/S10113-023-02051-0
Abstract: Nearly a billion people depend on tropical seascapes. The need to ensure sustainable use of these vital areas is recognised, as one of 17 policy commitments made by world leaders, in Sustainable Development Goal (SDG) 14 (‘Life below Water’) of the United Nations. SDG 14 seeks to secure marine sustainability by 2030. In a time of increasing social-ecological unpredictability and risk, scientists and policymakers working towards SDG 14 in the Asia–Pacific region need to know: (1) How are seascapes changing? (2) What can global society do about these changes? and (3) How can science and society together achieve sustainable seascape futures? Through a horizon scan, we identified nine emerging research priorities that clarify potential research contributions to marine sustainability in locations with high coral reef abundance. They include research on seascape geological and biological evolution and adaptation elucidating drivers and mechanisms of change understanding how seascape functions and services are produced, and how people depend on them costs, benefits, and trade-offs to people in changing seascapes improving seascape technologies and practices learning to govern and manage seascapes for all sustainable use, justice, and human well-being bridging communities and epistemologies for innovative, equitable, and scale-crossing solutions and informing resilient seascape futures through modelling and synthesis. Researchers can contribute to the sustainability of tropical seascapes by co-developing transdisciplinary understandings of people and ecosystems, emphasising the importance of equity and justice, and improving knowledge of key cross-scale and cross-level processes, feedbacks, and thresholds.
Asymmetric dispersal is a critical element of concordance between biophysical dispersal models and spatial genetic structure in Great Barrier Reef corals
Publisher: Cold Spring Harbor Laboratory
Date: 25-10-2018
DOI: 10.1101/453001
Abstract: Widespread coral bleaching, crown-of-thorns seastar outbreaks, and tropical storms all threaten foundational coral species of the Great Barrier Reef, with impacts differing over time and space. Yet, dispersal via larval propagules could aid reef recovery by supplying new settlers and enabling the spread of adaptive variation among regions. Documenting and predicting spatial connections arising from planktonic larval dispersal in marine species, however, remains a formidable challenge. The Great Barrier Reef, Australia Contemporary biophysical larval dispersal models were used to predict longdistance multigenerational connections for two common and foundational coral species ( Acropora tenuis and Acropora millepora ). Spatially extensive genetic surveys allowed us to infer signatures of asymmetric dispersal for these species and evaluate concordance against expectations from biophysical models using coalescent genetic simulations, directions of inferred gene flow, and spatial eigenvector modelling. At long distances, biophysical models predicted a preponderance of north to south connections and genetic results matched these expectations: coalescent genetic simulations rejected an alternative scenario of historical isolation the strongest signals of inferred gene flow were from north to south and asymmetric eigenvectors derived from north to south connections in the biophysical models were significantly better predictors of spatial genetic patterns than eigenvectors derived from symmetric null spatial models. Results are consistent with biophysical dispersal models yielding approximate summaries of past multigenerational gene flow conditioned upon directionality of connections. For A. tenuis and A. millepora , northern and central reefs have been important sources to downstream southern reefs over the recent evolutionary past and should continue to provide southward gene flow. Endemic genetic ersity of southern reefs suggests substantial local recruitment and lack of long distance gene flow from south to north.
Species composition and hybridisation of mussel species (Bivalvia: Mytilidae) in Australia
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/MF15307
Abstract: Mussels belonging to the Mytilus edulis species complex have been the focus of numerous studies exploring the systematics and origin of this commercially and ecologically important genus. Species have wide geographical ranges and hybridise where their distributions overlap, making identification difficult. Several molecular markers have been used to distinguish between the species within the M. edulis species complex however, no single marker system has been found to be completely diagnostic, and a combination of markers are used. Here, we used a combination of three nuclear genes and a mitochondrial gene region to assess the species composition of Mytilus mussels collected across its geographical range in Australia. Our results show that the majority (98.5%) of in iduals s led from Australian populations are Mytilus galloprovincialis, with 56.2% of them displaying a southern hemisphere haplotype, 10.3% displaying a putatively northern hemisphere haplotype, and 32% having M. galloprovincialis genotypes consistent with either northern or southern hemisphere M. galloprovincialis lineages. The taxonomic origin of the remaining 1.5% of s les (n=3) could not be conclusively determined. Our results suggest that there have been significant introductions of non-native M. galloprovincialis lineages into both southern and northern hemisphere populations.
Magnificent dimensions, varied forms, and brilliant colors: the molecular ecology and evolution of the Indian and Pacific oceans
Publisher: Bulletin of Marine Science
Date: 2014
neogen: A tool to predict genetic effective population size (N e ) for species with generational overlap and to assist empirical N e study design
Publisher: Wiley
Date: 16-10-2019
Abstract: Molecular genetic estimates of population effective size (N
Patterns of mtDNA diversity in North Atlantic populations of the mussel Mytilus edulis (vol 155, pg 399, 2008)
Publisher: Springer Science and Business Media LLC
Date: 11-2009
Larval traits show temporally consistent constraints, but are decoupled from postsettlement juvenile growth, in an intertidal fish
Publisher: Wiley
Date: 21-06-2018
Abstract: Complex life cycles may evolve to dissociate distinct developmental phases in an organism's lifetime. However, genetic or environmental factors may restrict trait independence across life stages, constraining ontogenetic trajectories. Quantifying covariance across life stages and their temporal variability is fundamental in understanding life-history phenotypes and potential distributions and consequences for selection. We studied developmental constraints in an intertidal fish (Bathygobius cocosensis: Gobiidae) with a discrete pelagic larval phase and benthic juvenile phase. We tested whether traits occurring earlier in life affected those expressed later, and whether larval traits were decoupled from postsettlement juvenile traits. S ling distinct cohorts from three annual breeding seasons afforded tests of temporally variability in trait covariance. From otoliths (fish ear stones), we measured hatch size, larval duration, pelagic growth (larval traits) and early postsettlement growth (juvenile trait) in 124 juvenile B. cocoensis. We used path analyses to model trait relationships with respect to their chronological expression, comparing models among seasons. We also modelled the effect of season and hatch date on each in idual trait to quantify their inherent variability. Our path analyses demonstrated a decoupling of larval traits on juvenile growth. Within the larval phase, longer larval durations resulted in greater pelagic growth, and larger size-at-settlement. There was also evidence that larger hatch size might reduce larval durations, but this effect was only marginally significant. Although pelagic and postsettlement growth were decoupled, pelagic growth had postsettlement consequences: in iduals with high pelagic growth were among the largest fish at settlement, and remained among the largest early postsettlement. We observed no evidence that trait relationships varied among breeding seasons, but larval duration differed among breeding seasons, and was shorter for larvae hatching later within each season. Overall, we demonstrate mixed support for the expectation that traits in different life stages are independent. While postsettlement growth was decoupled from larval traits, pelagic development had consequences for the size of newly settled juveniles. Temporal consistency in trait covariances implies that genetic and/or environmental factors influencing them were stable over our three-year study. Our work highlights the importance of in idual developmental experiences and temporal variability in understanding population distributions of life-history traits.
Extensive genetic population structure in the Indo-West Pacific spot-tail shark, Carcharhinus sorrah
Publisher: Bulletin of Marine Science
Date: 2014
A phylogenetic analysis of egg size, clutch size, spawning mode, adult body size, and latitude in reef fishes
Publisher: Springer Science and Business Media LLC
Date: 10-12-2016
Systematics and phylogenetic species delimitation within Polinices s.l. (Caenogastropoda: Naticidae) based on molecular data and shell morphology
Publisher: Springer Science and Business Media LLC
Date: 19-10-2012
Comparative phylogeography of two co-distributed but ecologically distinct rainbowfishes of far-northern Australia
Publisher: Wiley
Date: 10-11-2018
DOI: 10.1111/JBI.13117
ECOLOGICAL GENETICS IN THE NORTH ATLANTIC: ENVIRONMENTAL GRADIENTS AND ADAPTATION AT SPECIFIC LOCI
Publisher: Wiley
Date: 11-2008
DOI: 10.1890/07-1162.1
Abstract: The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.
Rapid genetic turnover in populations of the insect pestBemisia tabaciMiddle East: Asia Minor 1 in an agricultural landscape
Publisher: Cambridge University Press (CUP)
Date: 15-03-2012
DOI: 10.1017/S0007485312000077
Abstract: Organisms differ greatly in dispersal ability, and landscapes differ in amenability to an organism's movement. Thus, landscape structure and heterogeneity can affect genetic composition of populations. While many agricultural pests are known for their ability to disperse rapidly, it is unclear how fast and over what spatial scale insect pests might respond to the temporally dynamic agricultural landscapes they inhabit. We used population genetic analyses of a severe crop pest, a member of the Bemisia tabaci (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidea) cryptic species complex known as Middle East-Asia Minor 1 (commonly known as biotype B), to estimate spatial and temporal genetic ersity over four months of the 2006–2007 summer growing season. We examined 559 in iduals from eight sites, which were scored for eight microsatellite loci. Temporal genetic structure greatly exceeded spatial structure. There was significant temporal change in local genetic composition from the beginning to the end of the season accompanied by heterozygote deficits and inbreeding. This temporal structure suggests entire cohorts of pests can occupy a large and variable agricultural landscape but are rapidly replaced. These rapid genetic fluctuations reinforce the concept that agricultural landscapes are dynamic mosaics in time and space and may contribute to better decisions for pest and insecticide resistance management.
Skeletal deformities and meristic trait variations are common in the intertidal fish Bathygobiuscocosensis (Perciformes‐Gobiidae)
Publisher: Wiley
Date: 05-01-2021
DOI: 10.1111/JFD.13327
The emergent geography of biophysical dispersal barriers across the Indo-West Pacific
Publisher: Wiley
Date: 04-02-2015
DOI: 10.1111/DDI.12307
The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns
Publisher: Wiley
Date: 22-04-2019
DOI: 10.1111/GEB.12905
Differential patterns of male and female MTDNA exchange across the Atlantic ocean in the blue mussel, Mytilus edulis
Publisher: Wiley
Date: 11-2004
DOI: 10.1111/J.0014-3820.2004.TB00873.X
Abstract: Comparisons among loci with differing modes of inheritance can reveal unexpected aspects of population history. We employ a multilocus approach to ask whether two types of independently assorting mitochondrial DNAs (maternally and paternally inherited: F- and M-mtDNA) and a nuclear locus (ITS) yield concordant estimates of gene flow and population ergence. The blue mussel, Mytilus edulis, is distributed on both North American and European coastlines and these populations are separated by the waters of the Atlantic Ocean. Gene flow across the Atlantic Ocean differs among loci, with F-mtDNA and ITS showing an imprint of some genetic interchange and M-mtDNA showing no evidence for gene flow. Gene flow of F-mtDNA and ITS causes trans-Atlantic population ergence times to be greatly underestimated for these loci, although a single trans-Atlantic population ergence time (1.2 MYA) can be accommodated by considering all three loci in combination in a coalescent framework. The apparent lack of gene flow for M-mtDNA is not readily explained by different dispersal capacities of male and female mussels. A genetic barrier to M-mtDNA exchange between North American and European mussel populations is likely to explain the observed pattern, perhaps associated with the double uniparental system of mitochondrial DNA inheritance.
Population genetic diversity in the Australian 'seascape': A bioregion approach
Publisher: Public Library of Science (PLoS)
Date: 16-09-2015
Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef
Publisher: Wiley
Date: 07-07-2022
DOI: 10.1111/EVA.13435
Abstract: Genomic studies are uncovering extensive cryptic ersity within reef‐building corals, suggesting that evolutionarily and ecologically relevant ersity is highly underestimated in the very organisms that structure coral reefs. Furthermore, endosymbiotic algae within coral host species can confer adaptive responses to environmental stress and may represent additional axes of coral genetic variation that are not constrained by taxonomic ergence of the cnidarian host. Here, we examine genetic variation in a common and widespread, reef‐building coral, Acropora tenuis , and its associated endosymbiotic algae along the entire expanse of the Great Barrier Reef (GBR). We use SNPs derived from genome‐wide sequencing to characterize the cnidarian coral host and organelles from zooxanthellate endosymbionts (genus Cladocopium ). We discover three distinct and sympatric genetic clusters of coral hosts, whose distributions appear associated with latitude and inshore–offshore reef position. Demographic modelling suggests that the ergence history of the three distinct host taxa ranges from 0.5 to 1.5 million years ago, preceding the GBR's formation, and has been characterized by low‐to‐moderate ongoing inter‐taxon gene flow, consistent with occasional hybridization and introgression typifying coral evolution. Despite this differentiation in the cnidarian host, A. tenuis taxa share a common symbiont pool, dominated by the genus Cladocopium (Clade C). Cladocopium plastid ersity is not strongly associated with host identity but varies with reef location relative to shore: inshore colonies contain lower symbiont ersity on average but have greater differences between colonies as compared with symbiont communities from offshore colonies. Spatial genetic patterns of symbiont communities could reflect local selective pressures maintaining coral holobiont differentiation across an inshore–offshore environmental gradient. The strong influence of environment (but not host identity) on symbiont community composition supports the notion that symbiont community composition responds to habitat and may assist in the adaptation of corals to future environmental change.
Population subdivision in marine environments: The contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus
Publisher: Wiley
Date: 06-2001
DOI: 10.1046/J.1365-294X.2001.01294.X
Abstract: The relative importance of factors that may promote genetic differentiation in marine organisms is largely unknown. Here, contributions to population structure from a biogeographic boundary, geographical distance and the distribution of suitable habitat were investigated in Axoclinus nigricaudus, a small subtidal rock-reef fish, throughout its range in the Gulf of California. A 408-bp fragment of the mitochondrial control region was sequenced from 105 in iduals. Variation was significantly partitioned between 28 of 36 possible combinations of population pairs. Phylogenetic analyses, hierarchical analyses of variance and a modified Mantel test substantiated a major break between two putative biogeographic regions. This genetic discontinuity coincides with an abrupt change in ecological characteristics, including temperature and salinity, but does not coincide with known oceanographic circulation patterns or any known historic barriers. There was an overall relationship of increasing genetic distance with increasing geographical distance between population pairs, in a manner consistent with isolation-by-distance. A significant habitat-by-geographical-distance interaction term indicated that, for a given geographical distance, populations separated by discontinuous habitat (sand) are more distinct genetically than are populations separated by continuous habitat (rock). In addition, populations separated by deep open waters were more genetically distinct than populations separated by continuous habitat (rock). These results indicate that levels of genetic differentiation among populations of A. nigricaudus cannot be explained by a single factor, but are due to the combined influences of biogeography, geographical distance and availability of suitable habitat.
Seascape Genomics: Contextualizing Adaptive and Neutral Genomic Variation in the Ocean Environment
Publisher: Springer International Publishing
Date: 2019
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