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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 chronograms including a comprehensive sampling of extant species and all the fossil occurrences described for each group. With the resulting chronograms, we built biogeographical models considering the geological changes in reef habitat availability since the ancient Tethys Sea. Finally, we used biogeographical stochastic mappings to trace the routes of colonization of the Atlantic Ocean by lineages in our focal taxa. Results: We found that the Palaeocene-Eocene was a period of significant lineage origination for surgeonfishes and rabbitfishes in the central Tethys Sea with the appearance of ancient genera. Most of these genera were probably extinct by the Eocene-Oligocene boundary as they do not correspond with modern taxa. Parrotfishes, however, originated in the early Oligocene, an epoch that corresponds with the geographical transition of the marine biodiversity hotspot. In all groups, extant genera had similar origin times and all expanded in the Miocene, mainly in the Indo-Pacific. In the Atlantic, only one parrotfish lineage with Tethyan ancestry appears to have survived. It subsequently gave rise to extant endemic genera (Sparisoma and Cryptotomus). The other extant lineages in the Atlantic all have Indo-Pacific origins and colonized more recently using different dispersal pathways. Main conclusions: The Indo-Pacific herbivorous fish fauna is the result of ongoing lineage expansion that started in the central Tethys. The Atlantic is a composite fauna with just one endemic lineage and at least four colonization events from the Indo-Pacific.

Aim: To understand how geography has influenced the generation and maintenance of biodiversity. We examined the relative importance of biogeographical barriers in the divergence of extant coral reef fish species. Location: Pan-tropical coral reefs. Methods: Sister-species were identified from a recent phylogeny encompassing four fish families (Chaetodontidae, Epinephelidae, Labridae and Pomacanthidae) and classified as allopatric or overlapping based on data compiled from IUCN maps. Nearest linear distances were mapped as indicators of vicariance and compared with previously identified biogeographical barriers. Congruent vicariance versus regional richness determined the relative influence of barriers. Patterns of overlap among non-allopatric sister-species were mapped and assessed. Results: Congruent vicariance was detected across six previously described biogeographical barriers: the Amazon and Orinoco rivers, Isthmus of Panama, Hawaiian Archipelago, Indo-Pacific, and a previously understudied barrier separating the Western Indian Ocean from the Central Indo-Pacific (CIP) termed the Mid-Indian Ocean Barrier (MIOB). The MIOB showed the strongest vicariant signal. None of the barriers had significantly more or less relative influence. The majority of sister-species were non-allopatric. Overlap was concentrated in an area concordant with the biodiversity hotspot in the CIP, where sister-pairs had significantly low overlap. Main conclusions: Biogeographical barriers may have influenced vicariance of extant species during the past 5Myr. Older barriers influenced divergence between clades. Turbidity currents produced by outflow from the Ganges and Indus river systems likely explain the strength of the MIOB. Despite the array of described barriers within the CIP, the Sunda Margin Barrier (SMB) was the only vicariant signal detected in the region. Low relative influence of the SMB and significantly low overlap among non-allopatric sister-pairs in the CIP highlights its importance as an area of evolutionary dynamism, where the separation of Indian and Pacific Ocean faunas and their subsequent range expansion has led to increased species overlap and higher regional biodiversity.

Aim Many coral reef regions have a history of isolation and extinction. Our aim was to test whether the disparate evolutionary and biogeographical histories of the world's coral reef regions have significantly impacted temporal patterns of speciation within regions. In essence, do assemblages in peripheral locations contain the youngest coral reef fish species? Location Pan-tropical coral reef systems. Methods Molecular data (mitochondrial 16S rRNA, 12S rRNA, CO1, cytochrome b; nuclear TMO-4C4, S7 intron 1) were assembled for genera with near-complete taxon sampling (minimum 70% nominal species) from four major coral reef fish families (Chaetodontidae, Labridae, Pomacanthidae and Serranidae). This was combined with fossil data to simultaneously infer the phylogeny and estimate species' divergence times. Species' distributions were quantified using IUCN maps and the ages of species with different biogeographical extents were compared. Model fitting was used to compare the distribution of species' ages across the whole phylogeny with age distributions of species restricted to the Red Sea and Hawaiian Islands. Results Temporal patterns of coral reef fish divergence were similar among major marine realms and regions. However, notable differences were recorded between the Red Sea and Hawaiian Islands. Red Sea endemics have diverged consistently throughout the last 16 Myr, whereas endemic species colonized the Hawaiian Islands in two distinct waves (0–3 Ma and 8–12 Ma). Differences in the proportions of allopatric and sympatric sister-species between Red Sea and Hawaiian endemics were also detected. Main conclusions Despite differing geological histories, marine realms and regions have all experienced comparable and relatively recent divergences of extant coral reef fish species. Differences in age distributions and spatial relationships of endemic species in the Red Sea and Hawaiian Islands suggest that markedly different processes have shaped patterns of diversification in these peripherally isolated locations.

Aim: To establish a spatial and temporal framework within which we can begin to investigate the role of geography in the evolution of Pomacanthus species. This study examines the phylogenetic relationships among Pomacanthus species, tests whether the degree of sympatry among sister taxa correlates with their age, and explores potential modes of diversification. Location: Pan-tropical coral reef systems. Methods: Three gene regions (12S rRNA, 16S rRNA and nuclear S7) from all 13 Pomacanthus species were used in conjunction with fossil calibration to reconstruct a chronogram. IUCN maps were used to evaluate geographical range overlap. Various age–range correlation (ARC) analyses were used to test for a correlation between range overlap and node age. Range-size symmetry and node age were also examined. Results: Biogeographical splits within the phylogeny corroborated key biogeographical events well, suggesting a potential role for allopatric speciation in the evolutionary history of the genus. ARC analyses suggested that speciation leading to sympatry is widespread in Pomacanthus, with 80% of sister species showing complete or substantial (> 85%) range overlap. No significant relationship between degree of sympatry and node age was recovered, which demonstrates that, for this group, exceptional sympatry is not necessarily a result of relatively old lineages. Range-size symmetry analysis was consistent with models of peripatric speciation within a finite area. Main conclusions: We present evidence consistent with allopatric speciation, while our ARC results are consistent with simulations of sympatric speciation, with the possibility of peripheral budding having led to the richness of sympatric species in the West Indian Ocean. We discuss how these processes can affect the interpretation of temporal and spatial analyses, and provide a basis for future investigations into the processes driving speciation.

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 distributed reef fish lineages. Patterns of lineage origination and dispersal were explored in five major biogeographic regions: the East Pacific, the Atlantic, the Indian Ocean, the Indo-Australian Archipelago hotspot, and the Central Pacific. Methods A dispersal, extinction and cladogenesis (DEC) model implemented in Lagrange was used to infer the most likely biogeographic scenarios at nodes on chronograms of three diverse reef fish families (Labridae, Pomacentridae, Chaetodontidae). For the terminal branches ANOVA was used to compare patterns of origination on a regional and global scale. Patterns of origination and dispersal were examined within discrete time periods for the five biogeographic regions. Results Temporal examination of hypothetical ancestral lineages reveal a pattern of increasing isolation of the East Pacific and Atlantic regions from the Eocene, and the changing role of the Indo-Australian Archipelago from a location of accumulating ranges in the Palaeo/Eocene, a centre of origination in the Miocene, to extensive expansion of lineages into adjacent regions from the Pliocene to Recent. Main conclusions While the East Pacific and Atlantic have a history of isolation, the Indo-Australian Archipelago has a history of connectivity. It has sequentially and then simultaneously acted as a centre of accumulation (Palaeocene/Eocene onwards), survival (Eocene/Oligocene onwards), origin (Miocene onwards), and export (Pliocene/Recent) for reef fishes. The model suggests that it was the proliferation and expansion of lineages in the Indo-Australian Archipelago (the Coral Triangle) during the Miocene that underpinned the current biodiversity in the Indian and Pacific Oceans.

Aim: We examined comparative data for cryptobenthic reef fishes to determine how variation in regional species richness relates to local species richness, abundance, and taxonomic and trophic composition, and to test whether systems with higher species richness exhibit finer habitat partitioning. Locations: Lizard Island, Great Barrier Reef (GBR), Australia; Bahia de Loreto, Gulf of California (GoC), Mexico. Methods: Cryptobenthic reef fish assemblages from four habitats (coral heads, rubble, and horizontal and vertical surfaces of boulders) were collected using clove oil. Differences in density, species richness and biomass were examined between regions and among habitats. Habitat associations were identified for each habitat/location based on multivariate ordination, and the statistical significance of patterns was tested using analysis of similarity (ANOSIM). In addition, the trophic group composition of the assemblages for both regions was examined. Results: A total of 91 species in 20 families were recorded (GBR, 66 species; GoC, 25 species). Total and habitat species richness were higher on the GBR, whereas biomass was higher in the GoC. No difference in fish density between regions was found. Habitat division among assemblages was greater in the depauperate GoC. Only coral head associations proved to be distinctive on the GBR, whereas three sample groups were found in the GoC (coral heads, horizontal boulders and vertical boulders/rubble). Trophic composition in the two regions was markedly different, with omnivores dominating the GBR fauna and planktivores the GoC. Main conclusions: A positive regional–local relationship in fish diversity was found between regions, but fish abundance in both regions remained similar. Contrary to expectations, habitat partitioning, at a community level, was greater in the depauperate GoC. Differences in trophic composition and patterns of habitat use appear to reflect the disparate history of the regions, whereas patterns of abundance may reflect the influence of fundamental relationships between size and abundance in communities. This study highlights the potential of reef faunas to conform to universal numerical trends while maintaining an ability to respond ecologically to local/evolutionary influences. The GoC fauna appears to be exceptionally vulnerable to natural and anthropogenic disturbance owing to the high numerical dominance of habitat-specific species and to the limited potential for functional redundancy within the system.

Coral reefs exhibit highly congruent patterns of biodiversity, with a prominent hotspot in the Indo-Australian Archipelago (IAA). Unlike many terrestrial systems, the IAA hotspot exhibits extensive latitudinal and longitudinal biodiversity gradients. Conflicting hypotheses have highlighted the importance of the area as a centre of origin, overlap or accumulation, with the location of endemics being used as the primary criterion for testing these hypotheses, by identifying the presumed geographical origins of species. We evaluate the utility of marine endemics for resolving these hypotheses, and examine recent molecular phylogenetic evidence for coral reef species that has revealed the antiquity of the endemics and the other species that make up this hotspot. These analyses emphasize the importance of the IAA in the survival rather than the origins of species.

In a recent paper (Bellwood & Meyer, Journal of Biogeography, 2009, 36, 569–576), we critically evaluated the utility of marine endemics for marking the geographical origins of species. In reply, Briggs (2009) identified two issues that needed clarification: (1) whether endemics are assumed to mark the geographical origins of species or areas of exceptionally high rates of origination, and (2) whether our evaluation of the role of endemics disproves the centre of origin hypothesis. Of these two issues, the first can be clearly resolved by recourse to the original literature that explicitly states that it has been assumed that endemics do indeed mark the probable sites of origin of species. The second is equally clear: our evidence does not and can not disprove the centre of origin theory. We suggest, however, that the current data, and endemics in particular, provide limited support for centre of origin theories and that they are more consistent with some centre of accumulation theories. The Indo-Australian Archipelago (IAA; Coral Triangle) therefore appears to be an area where species persist, a centre of survival, regardless of the site of origin of species.