Peter F. Cowman

Peter F. Cowman
James Cook University | JCU · ARC Centre of Excellence for Coral Reef Studies

PhD

About

92
Publications
52,462
Reads
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4,479
Citations
Introduction
Evolutionary Biologist interested in using bioinformatics and genomic methods to explore patterns of diversification and rates of molecular evolution.
Additional affiliations
April 2016 - May 2020
James Cook University
Position
  • Fellow
May 2014 - present
Yale University
Position
  • PostDoc Position
November 2012 - December 2013
Australian National University
Position
  • PostDoc Position

Publications

Publications (92)
Article
Full-text available
Biodiversity patterns across the marine tropics have intrigued evolutionary biologists and ecologists alike. Tropical coral reefs host 1/3 of all marine species of fish on 0.1% of the ocean’s surface. Yet our understanding of how mechanistic processes have underpinned the generation of this diversity is limited. However, it has become clear that th...
Article
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The largest marine biodiversity hotspot straddles the Indian and Pacific Oceans, driven by taxa associated with tropical coral reefs. Centred on the Indo-Australian Archipelago (IAA), this biodiversity hotspot forms the 'bullseye' of a steep gradient in species richness from this centre to the periphery of the vast Indo-Pacific region. Complex patt...
Article
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Identifying how past environmental conditions shaped the evolution of corals and their skeletal traits provides a framework for predicting their persistence and that of their non-calcifying relatives under impending global warming and ocean acidification. Here we show that ocean geochemistry, particularly aragonite–calcite seas, drives patterns of...
Article
Targeted enrichment of genomic DNA can profoundly increase the phylogenetic resolution of clades and inform taxonomy. Here, we redesign a custom bait set previously developed for the cnidarian class Anthozoa to more efficiently target and capture ultraconserved elements (UCEs) and exonic loci within the subclass Hexacorallia. We test this enhanced...
Article
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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 pinn...
Article
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The targeted capture of ultraconserved elements (UCEs) has substantially increased the amount of genetic data available for phylogenomic reconstructions. These capture datasets frequently contain mitochondrial DNA as a by‐product, often in the form of complete mitogenomes. These can be efficiently harvested to expand existing datasets without addit...
Article
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Efforts to conserve biodiversity have been hampered by long-standing biases, including a disproportionate focus on particular taxa and ecosystems with minimal attention to underlying genetic diversity. We assessed whether these biases have persisted over the past four decades by analyzing trends in 17,502 research articles published in four top con...
Article
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Understanding the numerous roles that colouration serves in the natural world has remained a central focus in many evolutionary and ecological studies. However, to accurately characterise and then compare colours or patterns among individuals or species has been historically challenging. In recent years, there have been a myriad of new resources de...
Article
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A universal paradigm describing patterns of speciation across the tree of life has been debated for decades. In marine organisms, inferring patterns of speciation using contemporary and historical patterns of biogeography is challenging due to the deficiency of species-level phylogenies and information on species' distributions, as well as conflict...
Article
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Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain...
Article
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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 diverse and ecologically important genus Acropora, providing a path to resolve the taxonomy of this notoriously problematic...
Article
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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...
Preprint
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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...
Article
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Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and account for more than a quarter of all living vertebrate species. Previous time-calibrated phylogenies and patterns from the fossil record explain this dominance by correlating the origin of major acanthomorph lineages with the Cretaceous–Palaeogene mass extinction. Here we infe...
Article
Distinguishing coral species is not only crucial for physiological, ecological and evolutionary studies, but also to enable effective management of threatened reef ecosystems. However, traditional hypotheses that delineate coral species based on morphological traits from the coral skeleton are frequently at odds with tree-based molecular approaches...
Preprint
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Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and comprise more than a quarter of all living vertebrate species1-3. It is believed that this dominance resulted from explosive lineage and phenotypic diversification coincident with the Cretaceous-Paleogene (K-Pg) mass-extinction event4. It remains unclear, however, if living acan...
Article
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...
Article
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 fi...
Article
Significance For decades, marine biogeographers have been intrigued by the origins of the Indo-Australian Archipelago (IAA) biodiversity hotspot. Yet one important ecological factor remained unexplored: the trophic status of species across the diversity gradient. Here we show how trophic identity crucially underpins coral reef fish diversity patter...
Article
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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 relationship...
Article
Evolution via natural selection has continually shaped the colouration of numerous organisms. One colouration of particular importance is the eyespot: a phylogenetically widespread, conspicuous marking that has been shown to effectively reduce predation, often through its resemblance to the eye. Although widely studied, most research has been exper...
Article
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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...
Article
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...
Article
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Numerous organisms display conspicuous eyespots. These eye‐like patterns have been shown to effectively reduce predation by either deflecting strikes away from nonvital organs or by intimidating potential predators. While investigated extensively in terrestrial systems, determining what factors shape eyespot form in colorful coral reef fishes remai...
Article
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Reef fishes are an exceptionally speciose vertebrate assemblage, yet the main drivers of their diversification remain unclear. It has been suggested that Miocene reef rearrangements promoted opportunities for lineage diversification, however, the specific mechanisms are not well understood. Here, we assemble near-complete reef fish phylogenies to a...
Preprint
The phylogenetic utility of targeted enrichment methods has been demonstrated in 34 taxa that often have a history of single gene marker development. These genomic capture 35 methods are now being applied to resolve evolutionary relationships from deep to shallow 36 timescales in clades that were previously deficient in molecular marker development...
Preprint
Full-text available
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 lack...
Article
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 trop...
Article
Aim: To describe the global biogeography of key herbivorous coral reef fish groups since their presumed origins, using data from both fossil and extant species. Location: Global Cenozoic reefs. Taxon: Acanthuridae (surgeonfishes), Siganidae (rabbitfishes) and Scarini (parrotfishes). Methods: We applied the fossilized birth-death model to build ch...
Article
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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...
Article
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The pelagic larval stage is a critical component of the life cycle of most coral reef fishes, but the adaptive significance of this stage remains controversial. One hypothesis is that migrating through the pelagic environment reduces the risk a larval fish has of being parasitised. Most organisms interact with parasites, often with significant, det...
Article
The published fossil record of the Labridae is critically evaluated. In total, fossils from 14 genera are provisionally placed within the family (the Scaridae is recognized as a tribe Scarini within the Labridae). Numerous specimens, previously recorded as Labridae, are now placed within other families, most notably the Phyllodontidae (Elopiformes)...
Article
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Aim To test hypothesized biogeographic partitions of the tropical Indo‐Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location The Indo‐Pacific Ocean. Time period Pliocene through the Holocene. Major taxa studied Fifty‐six marine species. Methods We tested eight...
Article
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Mutualisms are important ecological interactions that underpin much of the world's biodiversity. 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...
Article
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Signal divergence is an important process underpinning the diversification of lineages. Research has shown that signal divergence 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 divergence w...
Article
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For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of...
Chapter
Climate-induced coral bleaching poses a significant threat to coral reef ecosystems, causing extensive coral loss and degradation of reef habitats. Moreover, many reef fishes exhibit declines in abundance following severe episodes of coral bleaching, attributable to loss of live coral and/or declines in the structural complexity of reef habitats. T...
Article
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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 controversial1,2. Tropical marine fish communities are much more diverse than cold-water fish communities found at higher latitudes3,4, and several explanations for this latitudinal diversity...
Article
Full-text available
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 me...
Data
Species-typical group sizes and mating systems in butterflyfishes. (DOCX)
Preprint
Full-text available
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 m...
Article
Full-text available
Functional traits have been fundamental to the evolution and diversification 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 ge...
Research
Full-text available
Proceedings of the 13th International Coral Reef Symposium, Honolulu: 24-26
Article
Aim: To examine the dynamics among the processes of speciation, extinction and dispersal in marine environments using phylogenies to reveal the evolutionary mechanisms that promote latitudinal differences in biodiversity. Using phylogenetic comparative methods we assess whether tropical reef fish lineages show higher diversification rates and wheth...
Article
Full-text available
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 biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification m...
Article
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Although coral reefs support the largest concentrations of marine biodiversity worldwide, the extent to which the global system of marine-protected areas (MPAs) represents individual 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%...
Article
Identifying the main determinants of tropical marine biodiversity is essential for devising appropriate conservation measures mitigating the ongoing degradation of coral reef habitats. Based on a gridded distribution database and phylogenetic information, we compared the phylogenetic structure of assemblages for three tropical reef fish families (L...
Article
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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 longevit...
Chapter
Full-text available
The local diversity and global richness of coral reef fishes, along with the diversity manifested in their morphology, behaviour and ecology, provides fascinating and diverse opportunities for study. Reflecting the very latest research in a broad and ever-growing field, this comprehensive guide is a must-read for anyone interested in the ecology of...
Article
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A new view is emerging of the interplay between mutation at the genomic level, substitution at the population level, and diversification at the lineage level. Many studies have suggested that rate of molecular evolution is linked to rate of diversification, but few have evaluated competing hypotheses. By analyzing sequences from 130 families of ang...
Article
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The most prominent pattern in global marine biogeography is the biodiversity peak in the Indo-Australian Archipelago. Yet the processes that underpin this pattern are still actively debated. By reconstructing global marine paleoenvironments over the past 3 million years on the basis of sediment cores, we assessed the extent to which Quaternary clim...
Article
Full-text available
The most prominent pattern in global marine biogeography is the biodiversity peak in the Indo-Australian Archipelago. Yet the processes that underpin this pattern are still actively debated. By reconstructing global marine paleoenvironments over the past 3 million years on the basis of sediment cores, we assessed the extent to which Quaternary clim...
Article
Full-text available
Beyond the loss of species richness [1-3], human activities may also deplete the breadth of evolutionary history (phylogenetic diversity) and the diversity of roles (functional diversity) carried out by species within communities, two overlooked components of biodiversity. Both are, however, essential to sustain ecosystem functioning and the associ...
Article
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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 (T...
Article
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Background Theoretical models and experimental evidence suggest that rates of molecular evolution could be raised in parasitic organisms compared to non-parasitic taxa. Parasitic plants provide an ideal test for these predictions, as there are at least a dozen independent origins of the parasitic lifestyle in angiosperms. Studies of a number of par...
Article
Aim To use recently published phylogenies of three major reef fish families to explore global patterns of species origin and dispersal over the past 65 million years. The key questions are: when and where did reef fishes arise, and how has this shaped current biodiversity patterns? Location Biogeographic reconstructions were performed on globally...