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0000-0001-5977-5327
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James Cook University
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Queensland Museum Network
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Molecular Evolution | Speciation and Extinction | Biogeography and Phylogeography | Evolutionary Biology
Expanding Knowledge in the Biological Sciences | Marine Flora, Fauna and Biodiversity |
Publisher: Springer Science and Business Media LLC
Date: 29-05-2020
DOI: 10.1038/S41467-020-16498-W
Abstract: Reef fishes are an exceptionally speciose vertebrate assemblage, yet the main drivers of their ersification remain unclear. It has been suggested that Miocene reef rearrangements promoted opportunities for lineage ersification, however, the specific mechanisms are not well understood. Here, we assemble near-complete reef fish phylogenies to assess the importance of ecological and geographical factors in explaining lineage origination patterns. We reveal that reef fish ersification is strongly associated with species’ trophic identity and body size. Large-bodied herbivorous fishes outpace all other trophic groups in recent ersification rates, a pattern that is consistent through time. Additionally, we show that omnivory acts as an intermediate evolutionary step between higher and lower trophic levels, while planktivory represents a common transition destination. Overall, these results suggest that Miocene changes in reef configurations were likely driven by, and subsequently promoted, trophic innovations. This highlights trophic evolution as a key element in enhancing reef fish ersification.
Publisher: Wiley
Date: 22-11-2019
DOI: 10.1111/ELE.13180
Abstract: Signal ergence is an important process underpinning the ersification of lineages. Research has shown that signal ergence is greatest in species pairs that possess high geographic range overlap. However, the influence of range-size differences within pairs is less understood. We investigated how these factors have shaped signal ergence within brightly coloured coral reef butterflyfishes (genus: Chaetodon). Using a novel digital imaging methodology, we quantified both colouration and pattern using 250 000 s le points on each fish image. Surprisingly, evolutionary age did not affect colour pattern dissimilarity between species pairs, with average differences arising in just 300 000 years. However, the effect of range overlap and range symmetry was significant. Species-pair colour patterns become more different with increasing overlap, but only when ranges are similar in size. When ranges differ markedly in area, species-pair colour patterns become more similar with increasing overlap. This suggests that species with small ranges may maintain non-colour-based species boundaries.
Publisher: Elsevier BV
Date: 03-2014
DOI: 10.1016/J.CUB.2014.01.049
Abstract: Beyond the loss of species richness, human activities may also deplete the breadth of evolutionary history (phylogenetic ersity) and the ersity of roles (functional ersity) carried out by species within communities, two overlooked components of bio ersity. Both are, however, essential to sustain ecosystem functioning and the associated provision of ecosystem services, particularly under fluctuating environmental conditions. We quantified the effect of human activities on the taxonomic, phylogenetic, and functional ersity of fish communities in coral reefs, while teasing apart the influence of biogeography and habitat along a gradient of human pressure across the Pacific Ocean. We detected nonlinear relationships with significant breaking points in the impact of human population density on phylogenetic and functional ersity of parrotfishes, at 25 and 15 inhabitants/km(2), respectively, while parrotfish species richness decreased linearly along the same population gradient. Over the whole range, species richness decreased by 11.7%, while phylogenetic and functional ersity dropped by 35.8% and 46.6%, respectively. Our results call for caution when using species richness as a benchmark for measuring the status of ecosystems since it appears to be less responsive to variation in human population densities than its phylogenetic and functional counterparts, potentially imperiling the functioning of coral reef ecosystems.
Publisher: Oxford University Press (OUP)
Date: 27-07-2023
DOI: 10.1093/ZOOLINNEAN/ZLAD062
Abstract: Molecular phylogenetics has fundamentally altered our understanding of the taxonomy, systematics and biogeography of corals. Recently developed phylogenomic techniques have started to resolve species-level relationships in the erse and ecologically important genus Acropora, providing a path to resolve the taxonomy of this notoriously problematic group. We used a targeted capture dataset (2032 loci) to investigate systematic relationships within an Acropora clade containing the putatively widespread species Acropora tenuis and its relatives. Using maximum likelihood phylogenies and genetic clustering of single nucleotide polymorphisms from specimens, including topotypes, collected across the Indo-Pacific, we show ≥ 11 distinct lineages in the clade, only four of which correspond to currently accepted species. Based on molecular, morphological and geographical evidence, we describe two new species Acropora rongoi n. sp. and Acropora tenuissima n. sp. and remove five additional nominal species from synonymy. Systematic relationships revealed by our molecular phylogeny are incongruent with traditional morphological taxonomy and demonstrate that characters traditionally used to delineate species boundaries and infer evolutionary history are homoplasies. Furthermore, we show that species within this clade have much smaller geographical ranges and, consequently, population sizes than currently thought, a finding with profound implications for conservation and management of reef corals.
Publisher: University of Chicago Press
Date: 04-2015
DOI: 10.1086/680052
Abstract: A new view is emerging of the interplay between mutation at the genomic level, substitution at the population level, and ersification at the lineage level. Many studies have suggested that rate of molecular evolution is linked to rate of ersification, but few have evaluated competing hypotheses. By analyzing sequences from 130 families of angiosperms, we show that variation in the synonymous substitution rate is correlated among genes from the mitochondrial, chloroplast, and nuclear genomes and linked to differences in traits among families (average height and genome size). Within each genome, synonymous rates are correlated to nonsynonymous substitution rates, suggesting that increasing the mutation rate results in a faster rate of genome evolution. Substitution rates are correlated with species richness in protein-coding sequences from the chloroplast and nuclear genomes. These data suggest that species traits contribute to lineage-specific differences in the mutation rate that drive both synonymous and nonsynonymous rates of change across all three genomes, which in turn contribute to greater rates of ergence between populations, generating higher rates of ersification. These observations link mutation in in iduals to population-level processes and to patterns of lineage ergence.
Publisher: Wiley
Date: 27-11-2019
DOI: 10.1111/ELE.13184
Abstract: Mutualisms are important ecological interactions that underpin much of the world's bio ersity. Predation risk has been shown to regulate mutualism dynamics in species-specific case studies however, we lack studies which investigate whether predation can also explain broader patterns of mutualism evolution. We report that fish-anemone mutualisms have evolved on at least 55 occasions across 16 fish families over the past 60 million years and that adult body size is associated with the ontogenetic stage of anemone mutualisms: larger-bodied species partner with anemones as juveniles, while smaller-bodied species partner with anemones throughout their lives. Field and laboratory studies show that predators target smaller prey, that smaller fishes associate more with anemones, and that these relationships confer protection to small fishes. Our results indicate that predation is likely driving the recurrent convergent evolution of fish-anemone mutualisms and suggest that similar ecological processes may have selected convergence in interspecies interactions in other animal clades.
Publisher: Wiley
Date: 10-10-2011
DOI: 10.1111/J.1420-9101.2011.02391.X
Abstract: Diversification rates within four conspicuous coral reef fish families (Labridae, Chaetodontidae, Pomacentridae and Apogonidae) were estimated using Bayesian inference. Lineage through time plots revealed a possible late Eocene/early Oligocene cryptic extinction event coinciding with the collapse of the ancestral Tethyan/Arabian hotspot. Rates of ersification analysis revealed elevated cladogenesis in all families in the Oligocene/Miocene. Throughout the Miocene, lineages with a high percentage of coral reef-associated taxa display significantly higher net ersification rates than expected. The development of a complex mosaic of reef habitats in the Indo-Australian Archipelago (IAA) during the Oligocene/Miocene appears to have been a significant driver of cladogenesis. Patterns of ersification suggest that coral reefs acted as a refuge from high extinction, as reef taxa are able to sustain ersification at high extinction rates. The IAA appears to support both cladogenesis and survival in associated lineages, laying the foundation for the recent IAA marine bio ersity hotspot.
Publisher: Elsevier BV
Date: 12-2020
Publisher: Cold Spring Harbor Laboratory
Date: 26-02-2020
DOI: 10.1101/2020.02.25.965517
Abstract: The phylogenetic utility of targeted enrichment methods has been demonstrated in taxa that often have a history of single gene marker development. These genomic capture methods are now being applied to resolve evolutionary relationships from deep to shallow timescales in clades that were previously deficient in molecular marker development and lacking robust morphological characters that reflect evolutionary relationships. Effectively capturing 1000s of loci, however, in a erse group across a broad time scale requires a bait set that incorporates multiple baits per locus. We redesigned a custom bait set for the cnidarian class Anthozoa to target 1,436 UCE loci and 1,572 exon regions within the subclass Hexacorallia. We test this redesigned bait set on 99 specimens of hard corals (Scleractinia) spanning both the “complex” (Acroporidae, Agariciidae) and “robust” (Fungiidae) clades. With focused s ling in the staghorn coral genus Acropora we explore the ability of capture data to inform the taxonomy of a clade deficient in molecular resolution. A mean of 1850 (± 298) loci were captured per taxon (955 UCEs, 894 exons). A 75% complete concatenated alignment included 1792 loci (991 UCE, 801 exons) and ∼1.87 million base pairs. Parsimony informative sites varied from 48% for alignments including all three families, to 1.5% among s les within a single Acropora species. Maximum likelihood and Bayesian analyses recover highly resolved topologies and robust molecular relationships not previously found with traditional markers within the Acroporidae. Species level relationships within the Acropora genus do not support traditional morphological groups or morphological phylogenies. Both UCE and exon datasets delineated six well-supported clades within Acropora. The enhanced bait set for Hexacorallia will allow researchers to survey the evolutionary history of important groups of reef building corals where previous molecular marker development has been unsuccessful.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 30-05-2014
Abstract: Climate fluctuations have occurred repeatedly in Earth's history, and so there is much to be learned from examining the responses of past systems. Pellessier et al. reconstructed paleoenvironments over the past 3 million years from sediment cores collected across coral reef systems to explore the impacts of past conditions on reef fish ersity. Coral reefs survived in the Indo-Australian regions during times of otherwise extensive habitat loss. These robust reefs can explain much of the ersity found in present-day reef fish species. Science , this issue p. 1016
Publisher: Springer Science and Business Media LLC
Date: 31-08-2020
Publisher: Cambridge University Press
Date: 31-03-2015
Publisher: Elsevier BV
Date: 06-2021
Publisher: Japanese Coral Reef Society
Date: 2023
Publisher: Wiley
Date: 16-11-2015
DOI: 10.1111/ECOG.01638
Publisher: Elsevier BV
Date: 11-2021
DOI: 10.1016/J.YMPEV.2021.107265
Abstract: While the escalating impacts of climate change and other anthropogenic pressures on coral reefs are well documented at the coral community level, studies of species-specific trends are less common, owing mostly to the difficulties and uncertainties in delineating coral species. It has also become clear that traditional coral taxonomy based largely on skeletal macromorphology has underestimated the ersity of many coral families. Here, we use targeted enrichment methods to sequence 2476 ultraconserved elements (UCEs) and exonic loci to investigate the relationship between populations of Fungia fungites from Okinawa, Japan, where this species reproduces by brooding (i.e., internal fertilization), and Papua New Guinea and Australia, where it reproduces by broadcast-spawning (i.e., external fertilization). Moreover, we analyzed the relationships between populations of additional fungiid species (Herpolitha limax and Ctenactis spp.) that reproduce only by broadcast-spawning. Our phylogenetic and species delimitation analyses reveal strong biogeographic structuring in both F. fungites and Herpolitha limax, consistent with cryptic speciation in Okinawa in both species and additionally for H. limax in the Red Sea. By combining UCE/exon data and mitochondrial sequences captured in off-target reads, we reinforce earlier findings that Ctenactis, a genus consisting of three nominal morphospecies, is not a natural group. Our results highlight the need for taxonomic and systematic re-evaluations of some species and genera within the family Fungiidae. This work demonstrates that sequence data generated by the application of targeted capture methods can provide objective criteria by which we can test phylogenetic hypotheses based on morphological and/or life history traits.
Publisher: Springer Science and Business Media LLC
Date: 19-01-2019
Publisher: Wiley
Date: 12-11-2012
DOI: 10.1111/JBI.12003
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: Society of Exploration Geophysicists
Date: 12-2018
Abstract: Routinely applied methods in seismic reservoir characterization such as forward modeling, wavelet extraction, litude-variation-with-offset (AVO) analysis, AVO inversion, and interpretation of seismic data usually assume that the earth can be modeled by a stack of isotropic layers. This assumption may cause significant problems where there are nonnegligible differences in the anisotropic parameters between the various lithologies that cause vertical profiles of V P /V S and the anisotropy parameters to be dissimilar. In this case, a significant mismatch between the seismic data and the isotropic synthetic seismogram AVO response will occur, making far-angle stack interpretation difficult. In some cases, the mismatch might be misinterpreted as a data quality issue. In an offshore Western Australia field, three lithofacies (volcanic rock, sandstone, and shale) need to be correctly identified for detailed reservoir characterization. Here, the AVO response of the actual seismic data is significantly affected by velocity anisotropy. Originally, it was thought that the far-angle stack could be used to detect volcanic rock in the field however, after accounting for the velocity anisotropy effect, it was found that the far-angle stack enables us to identify sandstone. A proper understanding of the anisotropy effect allows the interpreter to use seismic data more effectively, which leads to a more robust estimation of the distribution of lithofacies in the target area.
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.YMPEV.2019.106596
Abstract: Marine angelfishes (F: Pomacanthidae) are amongst the most conspicuous reef fish families inhabiting reefs on tropical and subtropical latitudes. While being disproportionately represented in the marine ornamental fish trade, only a handful of taxonomically restricted studies explored their biogeographic history and the evolution body size and trophic guilds. Here, we reconstruct the phylogenetic history for 70 pomacanthid species (85% of nominal species), based on previously published data for three nuclear and four mitochondrial markers. We use the resulting phylogenetic framework to explore the ancestral biogeography and ecological ersification of the family. Divergence times and ancestral range estimation highlight the origins of the family most likely lie in the Central Pacific region. Vicariance among ocean basins reflects the impact of the Terminal Tethyan Event and the closure of the Isthmus of Panama in the historical biogeography of Pomacanthus and Holacanthus genera. The reconstruction also uncovers ancestral colonization pathways via the Pacific Ocean into the western Atlantic waters for Holacanthus. We confirm the Indian Ocean invasion scenario previously proposed for the "acanthops" complex (genus: Centropyge). Finally, interspecific variation in body size among clades appeared to be correlated to some degree with trophic guilds, whereby 15% of variance in body size was explained by trophic modes. This suggests that the higher ecological ersification observed in the Centropyge clade might be promoted by smaller body sizes acting as an ecological novelty allowing the expansion of the genus within available niches.
Publisher: Wiley
Date: 02-05-2018
DOI: 10.1111/BRV.12336
Abstract: Functional traits have been fundamental to the evolution and ersification of entire fish lineages on coral reefs. Yet their relationship with the processes promoting speciation, extinction and the filtering of local species pools remains unclear. We review the current literature exploring the evolution of diet, body size, water column use and geographic range size in reef-associated fishes. Using published and new data, we mapped functional traits on to published phylogenetic trees to uncover evolutionary patterns that have led to the current functional ersity of fishes on coral reefs. When examining reconstructed patterns for diet and feeding mode, we found ex les of independent transitions to planktivory across different reef fish families. Such transitions and associated morphological alterations may represent cases in which ecological opportunity for the exploitation of different resources drives speciation and adaptation. In terms of body size, reconstructions showed that both large and small sizes appear multiple times within clades of mid-sized fishes and that extreme body sizes have arisen mostly in the last 10 million years (Myr). The reconstruction of range size revealed many cases of disparate range sizes among sister species. Such range size disparity highlights potential vicariant processes through isolation in peripheral locations. When accounting for peripheral speciation processes in sister pairs, we found a significant relationship between labrid range size and lineage age. The ersity and evolution of traits within lineages is influenced by trait-environment interactions as well as by species and trait-trait interactions, where the presence of a given trait may trigger the development of related traits or behaviours. Our effort to assess the evolution of functional ersity across reef fish clades adds to the burgeoning research focusing on the evolutionary and ecological roles of functional traits. We argue that the combination of a phylogenetic and a functional approach will improve the understanding of the mechanisms of species assembly in extraordinarily rich coral reef communities.
Publisher: Springer Science and Business Media LLC
Date: 06-05-2016
DOI: 10.1038/NCOMMS11461
Abstract: The Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine bio ersity distribution patterns are still unknown. Here, we show that a spatial ersification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of ersity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna ersification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven ersification and dispersal yields realistic predictions of current bio ersity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef bio ersity dynamics.
Publisher: Wiley
Date: 21-06-2021
DOI: 10.1111/FAF.12580
Abstract: Latitude and body size are generally considered key drivers of swimming performance for larval marine fishes, but evidence suggests that evolutionary relationships and habitat may also be important. We used a comparative phylogenetic framework, data synthesis and case study approach to investigate how swimming performance differs among larvae of fish species across latitude. First, we investigated how swimming performance changed with body length, and we found that temperate reef fishes have the greatest increases in swimming performance with length. Secondly, we compared differences in three swimming performance metrics (critical swimming speed, in situ swimming, and endurance) among post‐flexion larvae, whilst considering phylogenetic relationships and morphology, and we found that reef fishes have higher swimming capacity than non‐reef (pelagic and non‐reef demersal) fishes, which is likely due to larger, more robust body sizes. Thirdly, we compared swimming performance of late‐stage larvae of tropical fishes with oceanographic data to better understand the ecological relevance of their high‐capacity swimming. We found that reef fishes have high swimming performance and grow larger than non‐reef fish larvae, which we suggest is due to the pressures to find a specific, patchily distributed habitat upon which to settle. Given the current bias towards studies on percomorph fishes at low latitudes, we highlight that there is a need for more research on temperate reef fish larvae and other percomorph lineages from high latitudes. Overall, our findings provide valuable context to understand how swimming and morphological traits that are important for dispersal and recruitment processes are selected for among teleost fish larvae.
Publisher: The Royal Society
Date: 07-10-2013
Abstract: The marine tropics contain five major biogeographic regions (East Pacific, Atlantic, Indian Ocean, Indo-Australian Archipelago (IAA) and Central Pacific). These regions are separated by both hard and soft barriers. Reconstructing ancestral vicariance, we evaluate the extent of temporal concordance in vicariance events across three major barriers (Terminal Tethyan Event (TTE), Isthmus of Panama (IOP), East Pacific Barrier, EPB) and two incomplete barriers (either side of the IAA) for the Labridae, Pomacentridae and Chaetodontidae. We found a marked lack of temporal congruence within and among the three fish families in vicariance events associated with the EPB, TTE and IOP. Vicariance across hard barriers separating the Atlantic and Indo-Pacific (TTE, IOP) is temporally diffuse, with many vicariance events preceding barrier formation. In marked contrast, soft barriers either side of the IAA hotspot support tightly concordant vicariance events (2.5 Myr on Indian Ocean side 6 Myr on Central Pacific side). Temporal concordance in vicariance points to large-scale temporally restricted gene flow during the Late Miocene and Pliocene. Despite different and often complex histories, both hard and soft barriers have comparably strong effects on the evolution of coral reef taxa.
Publisher: Springer Science and Business Media LLC
Date: 14-07-2022
Publisher: Cold Spring Harbor Laboratory
Date: 06-11-2017
DOI: 10.1101/214544
Abstract: For many animals, affiliative relationships such as pair bonds form the foundation of society, and are highly adaptive. Animal systems amenable for comparatively studying pair bonding are important for identifying underlying biological mechanisms, but mostly exist in mammals. Better establishing fish systems will enable comparison of pair bonding mechanisms across taxonomically distant lineages that may reveal general underlying principles. We examined the utility of wild butterflyfishes (f: Chaetodontidae g: Chaetodon ) for comparatively studying pair bonding. Stochastic character mapping inferred that within the family, pairing is ancestral, with at least seven independent transitions to group formation and seven transition to solitary behavior from the late Miocene to recent. In six sympatric and wide-spread species representing a clade with one ancestrally reconstructed transition from paired to solitary grouping, we then verified social systems at Lizard Island, Australia. In situ observations confirmed that Chaetodon baronessa, C. lunulatus , and C. vagabundus are predominantly pair bonding, whereas C. rainfordi, C. plebeius , and C. trifascialis are predominantly solitary. Even in the predominantly pair bonding species, C. lunulatus , a proportion of adults (15 %) are solitary. Importantly, inter- and intra-specific differences in social systems do not co-vary with other previously established attributes (geographic occurrence, parental care, diet, or territoriality). Hence, the proposed butterflyfish populations are promising for comparative analyses of pair bonding and its mechanistic underpinnings. Avenues for further developing the system are proposed, including determining whether the utility of these species applies across their geographic disruptions.
Publisher: Elsevier BV
Date: 09-2009
DOI: 10.1016/J.YMPEV.2009.05.015
Abstract: We estimated ages of ergence between major labrid tribes and the timing of the evolution of trophic novelty. Sequence data for 101 labrid taxa and 14 outgroups consisting of two mitochondrial gene regions (12s, 16s), and two nuclear protein-coding genes (RAG2, TMO4c4), a combined 2567 bp of sequence, were examined using novel maximum likelihood, maximum parsimony and mixed model Bayesian inference methods. These analyses yielded well supported trees consistent with published phylogenies. Bayesian inference using five fossil calibration points estimated the minimum ages of lineages. With origins in the late Cretaceous to early tertiary, the family ersified quickly with both major lineages (hypsigenyine and julidine) present at approximately 62.7 Ma, shortly after the K/T boundary. All lineages leading to major tribes were in place by the beginning of the Miocene (23 Ma) with most ersification in extant lineages occurring within the Miocene. Optimisation of trophic information onto the chronogram revealed multiple origins of novel feeding modes with two distinct periods of innovation. The Palaeocene/Eocene saw the origins of feeding modes that are well represented in other families: gastropod feeders, piscivores and browsing herbivores. A wave of innovation in the Oligocene/Miocene resulted in specialized feeding modes, rarely seen in other groups: coral feeding, foraminifera feeding and fish cleaning. There is little evidence of a general relationship between trophic specialization and species ersity. The current trophic ersity of the Labridae is a result of the accumulation of feeding modes dating back to the K/T boundary at 65 Ma, with all major feeding modes on present day reefs already in place 7.5 million years ago.
Publisher: Springer Science and Business Media LLC
Date: 12-01-2016
DOI: 10.1038/NCOMMS10359
Abstract: Although coral reefs support the largest concentrations of marine bio ersity worldwide, the extent to which the global system of marine-protected areas (MPAs) represents in idual species and the breadth of evolutionary history across the Tree of Life has never been quantified. Here we show that only 5.7% of scleractinian coral species and 21.7% of labrid fish species reach the minimum protection target of 10% of their geographic ranges within MPAs. We also estimate that the current global MPA system secures only 1.7% of the Tree of Life for corals, and 17.6% for fishes. Regionally, the Atlantic and Eastern Pacific show the greatest deficit of protection for corals while for fishes this deficit is located primarily in the Western Indian Ocean and in the Central Pacific. Our results call for a global coordinated expansion of current conservation efforts to fully secure the Tree of Life on coral reefs.
Publisher: Wiley
Date: 23-02-2017
DOI: 10.1111/BRV.12323
Abstract: The largest marine bio ersity hotspot straddles the Indian and Pacific Oceans, driven by taxa associated with tropical coral reefs. Centred on the Indo-Australian Archipelago (IAA), this bio ersity hotspot forms the 'bullseye' of a steep gradient in species richness from this centre to the periphery of the vast Indo-Pacific region. Complex patterns of endemism, wide-ranging species and assemblage differences have obscured our understanding of the genesis of this bio ersity pattern and its maintenance across two-thirds of the world's oceans. But time-calibrated molecular phylogenies coupled with ancestral biogeographic estimates have provided a valuable framework in which to examine the origins of coral reef fish bio ersity across the tropics. Herein, we examine phylogenetic and biogeographic data for coral reef fishes to highlight temporal patterns of marine endemism and tropical provinciality. The ages and distribution of endemic lineages have often been used to identify areas of species creation and demise in the marine tropics and discriminate among multiple hypotheses regarding the origins of bio ersity in the IAA. Despite a general under-s ling of endemic fishes in phylogenetic studies, the majority of locations today contain a mixture of potential paleo- and neo-endemic fishes, pointing to multiple historical processes involved in the origin and maintenance of the IAA bio ersity hotspot. Increased precision and s ling of geographic ranges for reef fishes has permitted the ision of discrete realms, regions and provinces across the tropics. Yet, such metrics are only beginning to integrate phylogenetic relatedness and ancestral biogeography. Here, we integrate phylogenetic ersity with ancestral biogeographic estimation of lineages to show how assemblage structure and tropical provinciality has changed through time.
Publisher: Springer Science and Business Media LLC
Date: 07-2018
DOI: 10.1038/S41586-018-0273-1
Abstract: Far more species of organisms are found in the tropics than in temperate and polar regions, but the evolutionary and ecological causes of this pattern remain controversial
Publisher: Proceedings of the National Academy of Sciences
Date: 15-02-2021
Abstract: For decades, marine biogeographers have been intrigued by the origins of the Indo-Australian Archipelago (IAA) bio ersity hotspot. Yet one important ecological factor remained unexplored: the trophic status of species across the ersity gradient. Here we show how trophic identity crucially underpins coral reef fish ersity patterns via a disproportional concentration of plankton-feeding species in the IAA. This planktivore hotspot, however, vanishes abruptly away from the IAA. Over the recent geological past, planktivorous reef fishes successfully partitioned constant resources promoted by unique oceanographic conditions in the IAA while likely undergoing disproportional extinctions in peripheral regions. This intriguing case of ecological success intertwined with differential extinctions offers key insights into the origins of bio ersity gradients.
Publisher: Wiley
Date: 11-07-2020
DOI: 10.1002/ECE3.6509
Publisher: Cold Spring Harbor Laboratory
Date: 13-07-2021
DOI: 10.1101/2021.07.12.452083
Abstract: Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and comprise more than a quarter of all living vertebrate species 1–3 . It is believed that this dominance resulted from explosive lineage and phenotypic ersification coincident with the Cretaceous-Paleogene (K-Pg) mass-extinction event 4 . It remains unclear, however, if living acanthomorph ersity is the result of a punctuated burst or gradual accumulation of ersity following the K-Pg. We assess these hypotheses with a time-calibrated phylogeny inferred using ultraconserved elements from a s ling of species that represent over 91% of all acanthomorph families, as well as an extensive body shape dataset of extant species. Our results indicate that several million years after the end-Cretaceous, acanthomorphs underwent a prolonged and significant expansion of morphological disparity primarily driven by changes in body elongation, and that acanthomorph lineages containing the bulk of the living species ersity originated throughout the Cenozoic. These acanthomorph lineages radiated into distinct regions of morphospace and retained their iconic phenotypes, including a large group of laterally compressed reef fishes, fast-swimming open-ocean predators, bottom-dwelling flatfishes, seahorses, and pufferfishes. The evolutionary success of spiny-rayed fishes is the culmination of a post K-Pg adaptive radiation in which rates of lineage ersification were decoupled from periods of high phenotypic disparity.
Publisher: Public Library of Science (PLoS)
Date: 17-08-2012
Publisher: Oxford University Press (OUP)
Date: 28-01-2021
Abstract: Anthozoan cnidarians (corals and sea anemones) include some of the world’s most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, analyses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds of ultraconserved elements and exon loci, we explore the evolutionary origins of the major clades of Anthozoa and some of their salient morphological features. The phylogeny supports reciprocally monophyletic Hexacorallia and Octocorallia, with Ceriantharia as the earliest erging hexacorals two reciprocally monophyletic clades of Octocorallia and monophyly of all hexacoral orders with the exception of the enigmatic sea anemone Relicanthus daphneae. Divergence dating analyses place Anthozoa in the Cryogenian to Tonian periods (648–894 Ma), older than has been suggested by previous studies. Ancestral state reconstructions indicate that the ancestral anthozoan was a solitary polyp that had bilateral symmetry and lacked a skeleton. Colonial growth forms and the ability to precipitate calcium carbonate evolved in the Ediacaran (578 Ma) and Cambrian (503 Ma) respectively these hallmarks of reef-building species have subsequently arisen multiple times independently in different orders. Anthozoans formed associations with photosymbionts by the Devonian (383 Ma), and photosymbioses have been gained and lost repeatedly in all orders. Together, these results have profound implications for the interpretation of the Precambrian environment and the early evolution of metazoans.[Bilateral symmetry coloniality coral early metazoans exon capture Hexacorallia Octocorallia photosymbiosis sea anemone ultraconserved elements.]
Publisher: Wiley
Date: 23-10-2018
DOI: 10.1002/ECE3.4566
Publisher: Magnolia Press
Date: 23-11-2022
DOI: 10.11646/ZOOTAXA.5213.1.1
Abstract: We describe five new species of black corals from the Great Barrier Reef and Coral Sea, collected at depths ranging from 14 to 789 m: two in the family Antipathidae (Antipathes falkorae sp. nov. and Antipathes morrisi sp. nov.), two in the family Aphanipathidae (Aphanipathes flailum sp. nov. and Rhipidipathes helae sp. nov.), and one in the family Cladopathidae (Hexapathes bikofskii sp. nov.). We also present a phylogeny of 80 black corals reconstructed from a target capture dataset of ultraconserved elements and exons, to show the systematic relationships among new and nominal species. This phylogeny also represents a backbone for future species descriptions and research into the evolutionary history of the Antipatharia.
Publisher: Oxford University Press (OUP)
Date: 23-02-2022
Abstract: 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 ersification 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 ergences 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 ergence 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 in idual gene trees.[Biogeography concatenation gene genealogy interrogation gene trees molecular dating summary coalescent UCEs.]
Publisher: American Society of Ichthyologists and Herpetologists (ASIH)
Date: 30-12-2013
Publisher: Frontiers Media SA
Date: 13-11-2014
Publisher: Magnolia Press
Date: 03-08-2020
DOI: 10.11646/ZOOTAXA.4821.3.7
Abstract: Blastopathes medusa gen. nov., sp. nov., is described from Kimbe Bay, Papua New Guinea, based on morphological and molecular data. Blastopathes, assigned to the Antipathidae, is a large, mythology-inspiring black coral characterized by clusters of elongate stem-like branches that extend out at their base and then curve upward. Colonies are not pinnulate and contain single branches, which could represent new branch cluster formations. Morphological and molecular (mitochondrial DNA and targeted capture of nuclear loci) evidence supporting the establishment of a new genus is discussed. This is the first study to utilize the target capture of ultraconserved elements (UCEs) and exonic loci to elucidate phylogenetic relationships among black corals and to identify and place a new genus and species.
Publisher: Wiley
Date: 04-06-2019
DOI: 10.1111/JBI.13631
Publisher: Cold Spring Harbor Laboratory
Date: 27-09-2022
DOI: 10.1101/2022.09.26.509594
Abstract: The patterns of speciation in marine fishes are largely unknown, in part due to the deficiency of species-level phylogenies and information on species’ distributions, and partly due to conflicting relationships between species’ dispersal, range size, and patterns of co- occurrence. Most research on global patterns of marine fish speciation has focused on coral reef or pelagic species. Carangoidei is a clade of marine fishes including the trevallies, remoras, and dolphinfishes that utilize both coral reef and pelagic environments, spanning the ecologies of coral reef obligate and open-ocean species. We used sequence capture of 1314 ultraconserved elements (UCEs) from 154 taxa to generate a phylogeny of Carangoidei and its parent clade, Carangiformes. Age-range correlation analyses of the geographic distributions and ergence times of sister species pairs reveal widespread sympatry, with 73% of sister species pairs exhibiting a sympatric geographic distribution, regardless of node age, and most species pairs co-existing across large portions of their ranges. We also observe greater disparity in body size and water column depth utilization between sympatric than allopatric sister species. These and other ecological or behavioral attributes likely facilitate sympatry among the most closely related carangoid species, which exhibit sympatry at a larger taxonomic scale than has previously been described in marine fishes.
Publisher: Oxford University Press (OUP)
Date: 05-06-2015
Abstract: The mitochondrial theory of ageing proposes that the cumulative effect of biochemical damage in mitochondria causes mitochondrial mutations and plays a key role in ageing. Numerous studies have applied comparative approaches to test one of the predictions of the theory: That the rate of mitochondrial mutations is negatively correlated with longevity. Comparative studies face three challenges in detecting correlates of mutation rate: Covariation of mutation rates between species due to ancestry, covariation between life-history traits, and difficulty obtaining accurate estimates of mutation rate. We address these challenges using a novel Poisson regression method to examine the link between mutation rate and lifespan in rockfish (Sebastes). This method has better performance than traditional sister-species comparisons when sister species are too recently erged to give reliable estimates of mutation rate. Rockfish are an ideal model system: They have long life spans with indeterminate growth and little evidence of senescence, which minimizes the confounding tradeoffs between lifespan and fecundity. We show that lifespan in rockfish is negatively correlated to rate of mitochondrial mutation, but not the rate of nuclear mutation. The life history of rockfish allows us to conclude that this relationship is unlikely to be driven by the tradeoffs between longevity and fecundity, or by the frequency of DNA replications in the germline. Instead, the relationship is compatible with the hypothesis that mutation rates are reduced by selection in long-lived taxa to reduce the chance of mitochondrial damage over its lifespan, consistent with the mitochondrial theory of ageing.
Publisher: The Royal Society
Date: 27-02-2019
Abstract: Herbivory by fishes has been identified as a key ecological process shaping coral reefs through time. Although taxonomically limited, herbivorous reef fishes display a wide range of traits, which results in varied ecosystem functions on reefs around the world. Yet, we understand little about how these trait combinations and functions in ecosystems changed through time and across biogeographic realms. Here, we used fossils and phylogenies in a functional ecological framework to reveal temporal changes in nominally herbivorous fish assemblages among oceanic basins in both trait space and lineage richness among functions. We show that the trait space occupied by extant herbivorous fishes in the Indo-Pacific resulted from an expansion of traits from the ancestral Tethyan assemblages. By contrast, trait space in the Atlantic is the result of lineage turnover, with relatively recent colonization by lineages that arose in the east Tethys/Indo-Pacific. From an ecosystem function perspective, the Atlantic supports a depauperate fauna, with few extant herbivorous reef fish lineages performing each function. Indo-Pacific fishes support both more functions and more lineages within each function, with a marked Miocene to Pleistocene expansion. These disparities highlight the importance of history in explaining global variation in fish functional composition on coral reefs.
Publisher: Public Library of Science (PLoS)
Date: 11-04-2018
Publisher: Wiley
Date: 30-08-2016
DOI: 10.1111/GEB.12506
Publisher: Public Library of Science (PLoS)
Date: 18-10-2012
Publisher: Wiley
Date: 02-2010
DOI: 10.1111/J.1420-9101.2009.01904.X
Abstract: Of the 5000 fish species on coral reefs, corals dominate the diet of just 41 species. Most (61%) belong to a single family, the butterflyfishes (Chaetodontidae). We examine the evolutionary origins of chaetodontid corallivory using a new molecular phylogeny incorporating all 11 genera. A 1759-bp sequence of nuclear (S7I1 and ETS2) and mitochondrial (cytochrome b) data yielded a fully resolved tree with strong support for all major nodes. A chronogram, constructed using Bayesian inference with multiple parametric priors, and recent ecological data reveal that corallivory has arisen at least five times over a period of 12 Ma, from 15.7 to 3 Ma. A move onto coral reefs in the Miocene foreshadowed rapid cladogenesis within Chaetodon and the origins of corallivory, coinciding with a global reorganization of coral reefs and the expansion of fast-growing corals. This historical association underpins the sensitivity of specific butterflyfish clades to global coral decline.
Publisher: Wiley
Date: 22-04-2019
DOI: 10.1111/GEB.12905
Publisher: Wiley
Date: 07-03-2021
DOI: 10.1111/EVO.14197
Start Date: 2020
End Date: 2023
Funder: Directorate for Biological Sciences
View Funded ActivityStart Date: 2017
End Date: 2020
Funder: Australian Research Council
View Funded ActivityStart Date: 06-2017
End Date: 06-2020
Amount: $372,000.00
Funder: Australian Research Council
View Funded Activity