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Coral reefs as drivers of cladogenesis
... As the nine reef fish families are prominent on coral reef around the globe they have been examined with phylogenetic (Betancur-R et al., 2013); % R is the percent sampling of species in the published phylogeny of Rabosky et al. (2013); % N is the percent sampling of species in the published phylogeny of Near et al. (2013); % GASPAR is the percent of family richness that are present in the checklists of the GASPAR database . Superscript denotes source of family level phylogeny: 1- Cowman and Bellwood (2011);2-Choat et al. (2012); 3- Hundt et al. (2014); 4- Dornburg et al. (in press);5-Frédérich et al. (2013); 6- Sorenson et al. (2013); 7- Reed et al. (2002). *No phylogeny from a family level study was accessible for the Mullidae. ...
... Those families that have more completely sampled phylogenies have achieved it through the combination of multiple sequence datasets and the use of supermatrix phylogenetic methods. The combination of datasets for the butterflyfish family Chaetodontidae (Fessler and Westneat, 2007;Bellwood et al., 2010) has resulted in a phylogeny that is over 70% complete ( Table 1; Cowman and Bellwood, 2011). Similarly, the family Acanthuridae is nearly complete (76%) through the combination of previously published and new sequence data . ...
... Similarly, the family Acanthuridae is nearly complete (76%) through the combination of previously published and new sequence data . Other families have been the focus of several phylogenetic studies, incrementally increasing taxon sampling as more data or specimens become available, e.g., the wrasses, family Labridae (now inclusive of odacids and parrotfishes; Westneat and Alfaro, 2005;Alfaro et al., 2009;Cowman et al., 2009;Kazancioglu et al., 2009;Cowman and Bellwood, 2011); and the damselfishes, family Pomacentridae (Cooper et al., 2009;Cowman and Bellwood, 2011;Frédérich et al., 2013). Within the Labridae and Pomacentridae, shallower lineages have also been examined with increased sampling to explore a variety of evolutionary and ecological questions Choat et al., 2012;Hodge et al., 2012;Litsios et al., 2012). ...
... These climatic and oceanographic changes resulted in a sea-level drop, upwelling and extinction of warmer climate fauna (Zachos et al. 2001;Livermore et al. 2007;Ma et al. 2016). This extinction formed vacant niches and the emerging Indo-Australian Archipelago probably gave rise to new reef habitats and high species-richness in the cooler oceans (Cowman and Bellwood 2011;Ma et al. 2016). This divergence time corresponds to the one shown by Near et al. (2012) for the same his- torical event in Haemulids. ...
... Within the Plectorhinchus IWP Clade, two factors, the Indo-Australian Archipelago (IAA) uplift and major global cooling, were associated with the diversification of sweetlips subclades. These factors were inferred from other reef fish in the Miocene period (Zachos et al. 2001;Bellwood and Wainwright 2002;Shevenell et al. 2004;Cowman and Bellwood 2011;Ma et al. 2016). An estimate of divergence times of each Plectorhinchus subclade suggests further diversification occurred during the Miocene that slow indicated by the long branches, followed by slower diversification in Pliocene to Pleistocene epochs (Fig. 5). ...
The subfamily Plectorhinchinae (sweetlips) is composed of poorly-known species with high commercially and ecologically values that exhibit phenotypic plasticity and various morphologies. Few studies have assessed the validity of sweetlips, intergeneric relationships and evolutionary survey in this subfamily, which have not yet been resolved. This study investigated the DNA sequences of (1) the mitochondrial COI gene to delimit species, and (2) two mitochondrial (COI and Cyt b), and one nuclear (RAG1) markers to infer phylogenetic relationships and evolutionary and biogeographic history. The molecular results could differentiate Diagramma punctatum from the other species, but failed to distinguish D. labiosum as a distinct species with considerably lower genetic distances for the COI (0.53%) and Cyt b (0.51%) markers. However, additional taxonomic investigations are required to shed light on this issue. All previously described nominal species of sweetlips in the northwest Indian Ocean were found to be well supported. The monophyly of Plectorhinchus is not supported and Diagramma pictum and D. punctatum should be assigned to the genus Plectorhinchus. The biogeographic history of Plectorhinchinae likely originated in the Indo-Pacific ca. 34 Ma (30–39 Ma; late Eocene/ middle Oligocene) and subsequently colonised the Western Indian Ocean and the Central Indo-Pacific. Maximum diversification within the subfamily occurred from the middle Miocene to Pliocene, coinciding with dispersal and vicariance events. Diversification was probably driven by both biological and geographical factors.
... Most importantly, lineages descended from these relatively old colonizations of the CIP persisted in the region up to the present-day (figure 2). Historical extinction events likely con- tributed to the lower richness of other warm marine regions [3,[43][44][45]. For example, a biodiversity hotspot also existed in the Western Indian Ocean from 23 to 16 Ma, during the for- mation of the present-day CIP hotspot [35]. ...
... Several studies have reported higher diversification rates in reef-inhabiting lineages relative to nonreef lineages [44,48] (but see [20]). The CIP supports greater area of reef habitat than other tropical oceans [2], including during times of extensive Pleistocene glaciation [3]. ...
For most marine organisms, species richness peaks in the Central Indo-Pacific region and declines longitudinally, a striking pattern that remains poorly understood. Here, we used phylogenetic approaches to address the causes of richness patterns among global marine regions, comparing the relative importance of colonization time, number of colonization events, and diversification rates (speciation minus extinction). We estimated regional richness using distributional data for almost all percomorph fishes (17 435 species total, including approximately 72% of all marine fishes and approximately 33% of all freshwater fishes). The high diversity of the Central Indo-Pacific was explained by its colonization by many lineages 5.3-34 million years ago. These relatively old colonizations allowed more time for richness to build up through in situ diversification compared to other warm-marine regions. Surprisingly, diversification rates were decoupled from marine richness patterns, with clades in low-richness cold-marine habitats having the highest rates. Unlike marine richness, freshwater diversity was largely derived from a few ancient colonizations, coupled with high diversification rates. Our results are congruent with the geological history of the marine tropics, and thus may apply to many other organisms. Beyond marine biogeography, we add to the growing number of cases where colonization and time-for-speciation explain large-scale richness patterns instead of diversification rates.
... Interactions between reef fishes and corals are important to reef ecosystems both ecologically and evolutionarily (Jones et al., 2004;Graham et al., 2006;Cowman and Bellwood, 2011), therefore it is important to understand the history of their associations (Bellwood and Wainwright, 2002;Rocha and Bowen, 2008;Kiessling et al., 2010). Reef fishes and reef building corals are both known for their extraordinary diversity; however, the evolutionary links between these two groups of coral reef organisms is not fully understood. ...
... Studies on the evolutionary history of reef fishes have suggested that the interaction between fishes and coral reefs became common soon after the Cretaceous-Tertiary (K/Pg) boundary (Cowman and Bellwood, 2011). However, little is known about the evolutionary history of the interaction between gobies and corals. ...
The rich diversity of coral reef organisms is supported, at least in part, by the diversity of coral reef habitat. Some of the most habitat specialised fishes on coral reefs are obligate coral-dwelling gobies of genus Gobiodon that inhabit a range of coral species, mostly of the genus Acropora. However, the role of this specialised pattern of habitat use in the evolution of coral-dwelling gobies is not well understood. Diversification of coral-dwelling gobies may be driven by the diversification of their host corals (cospeciation), or alternatively, diversification of these fishes may have occurred independently of the diversification of host corals. The cospeciation hypothesis assumes similar timing in evolution of the gobies and their host corals. We used four genes for each group and the available fossil records to reconstruct and date phylogenies for 20 species of Gobiodon from the Indo-Pacific and the Red Sea, and for 28 species of the coral genus Acropora. Our results indicate that Gobiodon diversified mostly in the last ∼5My, whereas Acropora corals have consistently diversified since the Eocene, making the hypothesis of cospeciation untenable. The fully resolved molecular phylogeny of the genus Gobiodon is in part at odds with previous analyses incorporating morphological data and indicates that some morphological traits form paraphyletic clades within Gobiodon. Our phylogeny supports a hypothesis in which Gobiodon diversified in the Indo-Pacific Ocean and then radiated recently, with multiple new variants found in the Red Sea.
... Fossil-based estimates of the ecological distribution of Mesozoic ray-finned fishes remain to be completed. However, the large post-Mesozoic diversification of reef-associated demersal fish lineages ( Alfaro et al., 2007;Cowman and Bellwood, 2011) and the absence during the Mesozoic of typical demersal clades such as the flatfishes (Pleuronectiformes) (Friedman, 2008), or of extinct clades with similar ecology, indicate that the demersal component of rayfinned fishes was even lower during the Mesozoic than during the Cenozoic. These results are consistent with the expectation that habitat area and geographic barriers more strongly influence species richness of clades dominated by benthic taxa, which are more prone to vicariance due to limited dispersal capabilities (Hart and Pearson, 2011). ...
Both biotic and abiotic factors likely played a role in influencing the diversification patterns of clades. Although the role of environmental forcing on the long-term evolution of biodiversity has been explored for invertebrate clades, little is known about how vertebrate groups responded to environmental changes. Among vertebrates, fishes (ray-finned fishes and elasmobranchs) have a long, rich, and complex evolutionary history comprising numerous diversification and extinction events. Yet, knowledge on the causes for the diversity fluctuations of these most speciose aquatic vertebrate clades in modern marine and continental ecosystems were restricted to qualitative interpretations. Here we use multiple regression methods to quantitatively examine the role of six abiotic parameters over the long-term variations of elasmobranch and actinopterygian genus-level diversity. We find that marine actinopterygian diversity is mainly controlled by temperature while continental fragmentation is the primary driver of the diversity fluctuations of elasmobranchs. Sea-level variations correlate positively with the diversity variations of both marine groups, whereas none of the tested proxies explains the diversity variation of freshwater ray-finned fishes. Our results indicate that such contrasting responses are mainly due to ecological and life-history trait differences between these groups.
... Myctophidae) have species-specific bioluminescence hypothesized to facilitate speciation [87], and might therefore represent exceptions to a general rule. These patterns, and the contrasts they might make with the better-documented macroevolutionary histories of fishes in other environmental settings like reefs [22,23,88], are little studied but could help provide a more inclusive comparative perspective on the evolution of diversity in fishes. ...
The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide a time-calibrated phylogeny for this widely distributed clade. Some inferred relationships have clear precedents (e.g. the monophyly of ‘core’ Stromateoidei, and a clade comprising ‘Gempylidae’ and Trichiuridae), but others are unexpected despite strong support (e.g. Chiasmodontidae + Tetragonurus). Relaxed molecular clock analysis using node-based fossil calibrations estimates a latest Cretaceous origin for Pelagiaria, with crown-group families restricted to the Cenozoic. Estimated mean speciation rates decline from the origin of the group in the latest Cretaceous, although credible intervals for root and tip rates are broad and overlap in most cases, and there is higher-than-expected partitioning of body shape diversity (measured as fineness ratio) between clades concentrated during the Palaeocene–Eocene. By contrast, more direct measures of ecology show either no substantial deviation from a null model of diversification (diet) or patterns consistent with evolutionary constraint or high rates of recent change (depth habitat). Collectively, these results indicate a mosaic model of diversification. Pelagiarians show high morphological disparity and modest species richness compared to better-studied fish radiations in contrasting environments. However, this pattern is also apparent in other clades in open-ocean or deep-sea habitats, and suggests that comparative study of such groups might provide a more inclusive model of the evolution of diversity in fishes.
... The diversification of ecosystem functions among herbivor- ous fishes coincides with a period of major realignment of the marine hotspots that took place in the east Tethys/ Indo-Pacific during the Miocene. This period not only marks the rise of most modern reef fish genera with increased subsequent lineage diversification [20,65], but coincides with the shift of the centre of tropical marine diversity to the IAA [15]. In parallel with the taxonomic diversification, this was also an important time for reef fish functional and trophic innovation [55,66,67], which was clearly reflected in our eco- system functions results. ...
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.
... Finally, Kuhlia nutabunda was closely related to a species lar- gely distributed in the Pacific while Myripristis tiki likely emerged from a founder-event and was found to be related to an East Tropi- cal Pacific species. which was a period of high diversification of coral reef fishes in the Indo-Australian Archipelago (Alfaro, Santini, & Brock, 2007;Cowman & Bellwood, 2011;Hodge, Read, van Herwerden, & Bellwood, 2012;Hodge et al., 2014;Klanten, van Herwerden, Choat, & Blair, 2004). ...
Aim
To understand the origin of the most isolated endemic fish fauna of the Indo‐Pacific, Easter Island (Rapa Nui), and to infer divergence times and colonization routes of the endemic coral reef fish fauna from their closest relatives.
Location
Easter Island, Pacific Ocean.
Methods
Samples of ten species were used: six small‐range species endemic to Rapa Nui and Motu Motiro Hiva (Salas y Gómez) (i.e. small‐range endemic species) and four large‐range species endemic to the southern subtropical Pacific (i.e. large‐range endemic species). We present phylogenetic reconstruction results based on mitochondrial (1 to 5) and nuclear (1 to 6) loci to place these endemic species in their respective family phylogenies (8). Using these newly calibrated phylogenetic trees, information of species distributions and geological data, we inferred the divergence times from the closest relatives of these ten endemic fishes, compared biogeographical history estimation models to reconstruct their ancestral geographic ranges, colonization routes and underlying mechanisms of speciation.
Results
The divergence times (i.e. divergence times from the closest relatives) of all of the small‐range endemics studied were more recent than the age of Rapa Nui and Motu Motiro Hiva; thus, these species can be considered as neoendemics. Biogeographical history estimation models indicated that speciation following a founder‐event is the most likely scenario. In contrast, the divergence estimates of the large‐range endemic species were highly variable. This being said, the divergence times of all species were more recent than the age of the oldest islands within their distributions.
Main conclusions
Taken together, these results demonstrate that Rapa Nui acts as a cradle of coral reef biodiversity, being responsible for the emergence of small‐range endemic fish species, but also a route of dispersion for several large‐range endemics and as a stepping stone in the diversification of the Myripristis and Pseudolabrus genera. While no common divergence time was recovered for all of the ten endemic species studied here, the common mechanism of speciation following a founder event was recovered for most of the small‐range endemic species.
Maximum likelihood and Bayesian phylogenies for the brachyuran crab superfamily Xanthoidea were estimated based on three mitochondrial and four nuclear genes to infer phylogenetic relationships and inform taxonomy. Habitat data was then used in conjunction with several diversification rates analyses (BAMM, BiSSE, HiSSE, and FiSSE) to test evolutionary hypotheses regarding the diversification of xanthoid crabs. The phylogenies presented are the most comprehensive to date in terms of global diversity as they include all four constituent families (Xanthidae, Panopeidae, Pseudorhombilidae, and Linnaeoxanthidae) spanning all oceans in which xanthoid crabs occur. Six Xanthoidea families are recognised. Panopeidae and Xanthidae sensu stricto are the two largest family-level clades, which are reciprocally monophyletic. Pseudorhombilidae is nested within, and is here treated as a subfamily of Panopeidae. Former subfamilies or tribes of Xanthidae sensu lato are basally positioned clades in Xanthoidea and are here assigned family-level ranks: Garthiellidae, Linnaeoxanthidae, Antrocarcinidae, and Nanocassiopidae. The genera Linnaeoxantho and Melybia were recovered in separate clades, with Linnaeoxantho being sister to the family Antrocarcinidae, while Melybia was recovered within the family Panopeidae. The existing subfamily classification of Xanthidae and Panopeidae is drastically restructured, with 20 xanthid and four panopeid subfamilies provisionally recognised. Diversification-time analyses inferred the origin of Xanthoidea and Garthiellidae in the Eocene, while the other families originated during the Oligocene. The majority of genus- and species-level diversification took place during the Miocene. Ancestral state reconstruction based on depth of occurrence (shallow vs. deep water) shows some ambiguity for the most recent common ancestor of Xanthoidea and Nanocassiopidae. The most recent common ancestors of Antrocarcinidae and Panopeidae were likely deep-water species, while those of Garthiellidae and Xanthidae were probably shallow-water species. Several shifts in net diversification rates were detected but they were not associated with depth-related habitat transitions, therefore indicating that the diversification of xanthoid crabs was not driven by the emergence of reefal habitats in shallow seas.
Predatory reef fishes regularly visit mutualistic cleaner fish (Labroides dimidiatus) to get their ectoparasites removed but show no interest in eating them. The concept of compensated trait loss posits that characters can be lost if a mutualistic relationship reduces the need for a given trait. Thus, selective pressures on escape performance might have relaxed in L. dimidiatus due to its privileged relationship with predators. However, the cost of failing to escape a predatory strike is extreme even if predation events on cleaners are exceptionally rare. Additionally, cleaners must escape from non-predatory clients that regularly punish them for eating mucus instead of parasites. Therefore, strong escape capabilities might instead be maintained in cleaner fish because they must be able to flee when in close proximity to predators or dissatisfied clients. We compared the fast-start escape performance of L. dimidiatus with that of five closely related wrasse species and found that the mutualistic relationship that cleaners entertain with predators has not led to reduced escape performance. Instead, conflicts in cleaning interactions appear to have maintained selective pressures on this trait, suggesting that compensated trait loss might only evolve in cases of high interdependence between mutualistic partners that are not tempted to cheat. © 2017 The Author(s) Published by the Royal Society. All rights reserved.
Living reef fishes are one of the most diverse vertebrate assemblages on Earth. Despite its prominence and ecological importance, the origins and assembly of the reef fish fauna is poorly described. A patchy fossil record suggests that the major colonization of reef habitats must have occurred in the Late Cretaceous and early Palaeogene, with the earliest known modern fossil coral reef fish assemblage dated to 50 Ma. Using a phylogenetic approach, we analysed the early evolutionary dynamics of modern reef fishes. We find that reef lineages successively colonized reef habitats throughout the Late Cretaceous and early Palaeogene. Two waves of invasion were accompanied by increasing morphological convergence: one in the Late Cretaceous from 90 to 72 Ma and the other immediately following the end-Cretaceous mass extinction. The surge in reef invasions after the Cretaceous-Palaeogene boundary continued for 10 Myr, after which the pace of transitions to reef habitats slowed. Combined, these patterns match a classic niche-filling scenario: early transitions to reefs were made rapidly by morphologically distinct lineages and were followed by a decrease in the rate of invasions and eventual saturation of morphospace. Major alterations in reef composition, distribution and abundance, along with shifts in climate and oceanic currents, occurred during the Late Cretaceous and early Palaeogene interval. A causal mechanism between these changes and concurrent episodes of reef invasion remains obscure, but what is clear is that the broad framework of the modern reef fish fauna was in place within 10 Myr of the end-Cretaceous extinction.
The species of the two Recent genera of scatophagids, Scatophagus Cuvier and Selenotoca Myers, are shown to share two derived features not found in the Eocene and Oligocene species, whereas the Eocene (Monte Bolca, ltaly; Lutetian) and Oligocene (Chiavon, ltaly; Rupelian) fossil species share one derived feature not found in the Recent species. Additionally, autapomorphies are recognized for three of the genera. Numerous other features, external and osteological, distinguish these two clades, but these cannot be polarized. The morphological differences between the two fossil species are greater than those between the two Recent genera. The fossil species, always previously placed in Scatophagus, are assigned to the new genera Eoscatophagus and Oligoscatophagus. The fossil species are redescribed and reconstructions of their skeletons are presented in comparison to those of the more common of the species of the two Recent genera.
Key words: Scatophagidae, Scatophagus, Selenotoca, Eoscatophagus, Oligoscatophagus, Eocene, Oligocene, fossil fishes.
A new species of Apogon (A. bryx) from deep water is described from the Philippines. It is the sixth species with six first dorsal spines, a completely serrated preopercular edge, black stomach and intestine, pored lateral line scales from the posttemporal bone to the caudal fin and eight anal fin-rays. The new species is compared with other six-spined (first dorsal) species with these characters and a key is provided. One rare, deep-dwelling Apogon from the Philippines and two underscribed species from the Indian Ocean and West Pacific Ocean are briefly discussed in relation to the new species. Two species have identifiable synonyms: Apogon gularis (Apogon smithvanizi) and Apogon thermalis (Apogon sangiensis). Apogon unicolor is removed from the subgenus Pristicon.
A new genus Eocoris and new species E. bloti are described.
Eocoris bloti presents some specialized characters and can be considered a member of Labridae (Pisces).
With 5 figures and 4 plates) Manuscript received August 31 st 1990 Summary The status of 7 fossil species and 6 unidentified fossil fragments, currently placed in the family Scaridae are reviewed. Of these, two fragments are considered to be scarid material, both belonging to the genus Bolbometopon SMITH, 1956. The remainder include fragments of Diodontidae, Labridae and Oplegnathidae. Most are of uncertain affinity. A new species, Calotomus preisli n. sp., from the Upper Badenian (Middle Miocene) of the Bay of Eisenstadt, Austria, is described. This new species is the first unequivocal fossil representative of the Scaridae from Europe and provides new evidence for tropical conditions in the Central Paratethys during the Upper Badenian. Zusammenfassung Es erfolgt die Überprüfung der systematischen Zugehörigkeit von 7 fossilen Arten und weiteren 6 fossilen Fragmenten, die bisher der Familie Scaridae (Papageifische) zugeordnet wurden. Nur zwei der Fragmente sind aber eindeutige Belege für Scaridae; es handelt sich um Belege für die Gattung Bolbometopon SMITH, 1956. Einige der übrigen Fossilreste stammen von Diodontidae, Labridae und Oplegnathidae, aber die meisten lassen nicht einmal eine Zuordnung zu einer Familie zu. Ein Neufund aus der gebankten Fazies des Leithakalkes (Oberes Badenien, Mittel-Miozän) der Eisenstädter Bucht (St. Margarethen, Burgenland, Österreich) wird als neue Art beschrieben: Calotomus preisli n. sp. Diese neue Art ist der erste und einzige unzweifelhafte Beleg für fossile Scaridae in Europa und ein weiterer Beleg für tropische Verhältnisse in der Zentralen Paratethys zur Zeit des Oberen Badeniens.
The modern Indo-West Pacific centre of marine diversity, embracing SE Asia, has the highest zooxanthellate coral di-versity in the world, and is characterised by abundant coral reefs. In contrast, field and literature studies show that in Paleogene carbonates of SE Asia, corals are rare, and exten-sive coral reefs have not been reported. Corals and reefs of this age may have been better developed in the mid-Pacific, especially in the late Eocene, but the most diverse regions at this time were in Europe, and to a lesser degree, the Carib-bean. The apparent scarcity of Paleogene corals in SE Asia is surprising in view of the long-standing theory that the Indo-West Pacific is a Centre of Origin. The question therefore arises whether this Paleogene gap is a sampling problem, and if not what are its causes and implications? A review of SE Asian Tertiary carbonates in their tectonic context shows that many shallow-water Eocene-Oligocene carbonates were dominated by larger benthic foraminifera and coralline algae. A new Eocene coral fauna (12 spp.) from Sulawesi accords with earlier views that there was little en-demicity in SE Asia during the Paleogene. The general pau-city of corals in carbonate platform deposits confirms that the Paleogene gap is real, and not an artefact. Since SE Asia, particularly the western part, has remained in, or close to, tropical latitudes throughout the Tertiary, climatic reasons cannot account for this. Although local ecological factors would have been important, the tectonics point to a degree of geographical isolation from other coral rich regions as a key factor. These patterns changed dramatically, however, in the earliest Neogene, as Australian fragments collided with SE Asia. Collision led to decreased isolation of the region and generation of numerous shallow-water areas, with diverse and abundant zooxanthellate corals occurring in the Miocene of SE Asia, similarly to the present day. The geographical complexity of SE Asia appears to have favoured localized isolation and origination of new taxa, though the fauna also consists of older relicts and taxa which migrated into the region from elsewhere. All these processes contributed to making the Indo-West Pacific the richest region for corals from the Neogene onwards. We compare these patterns with the three main models of high diversity in the Indo-West Pacific Centre (Centres of Origin, Accumulation and Survival). During the Paleogene the region was not a centre of any kind. From the Neogene onwards, no single model is applicable, but a combination of all three models is preferred. Comparison with Mesozoic coral data and the history of the region suggests that the patterns discussed here also apply to the Late Triassic and Late Jurassic. As with the Neogene, these were times when blocks rifted from Gondwana moved across the tropics to dock against Asia. We therefore emphasize the role of plate tectonics in controlling regional high diversity patterns of zooxanthellate corals. Since corals and coral reefs provide habitats for a myriad of marine organisms, the biogeographic history of Cenozoic reef corals has implications for the evolu-tion of tropical reef ecosystems.
A labrid fish, Bellwoodilabrus landinii n. gen., n. sp., is described based on a single specimen collected from the Eocene locality of Monte Bolca, northern Italy. Bellwoodilabrus landinii n. gen., n. sp. is characterized by a prominent frontal relief, broad ethmoid-frontal depression, strongly developed supraoccipital crest, bar-like nasal, jaw teeth arranged in a single row, posterior preopercular margin apparently entire, rounded and molariform lower pharyngeal teeth, six branchiostegal rays, 24 (9+15) vertebrae, moderately reduced neural spine of the first vertebra, parhypurapophysis absent, XI + 9 dorsal fin elements, III + 9 anal fin elements and 12 pectoral-fin rays. The comparative analysis of morphological and meristic features reveals that Bellwoodilabrus landinii n. gen., n. sp. possesses a combination of plesiomorphic and derived features, which is unique within the Labridae. Bellwoodilabrus landinii n. gen., n. sp. Represents the third valid species of the family Labridae described up to now from Monte Bolca. The morphofunctional analysis of the cranial and appendicular skeleton suggests that Bellwoodilabrus landinii n. gen., n. sp. was a benthic invertebrate feeder that inhabited the deep and calm settings along the northern coasts of the central Tethys. The evolutionary significance of the Eocene labrids from Monte Bolca is also discussed. © Publications Scientifiques du Muséum national d'Histoire naturelle, Paris.
One of the central goals in paleoecology is to understand the nature and consequences of biotic interactions. In marine systems, it has been argued that one of the major steps in the escalation of biotic interactions was marked by the origins of grazing fishes in the Cenozoic. Here I investigate the origins of herbivory and grazing in marine fishes using analyses of functional morphospace. Closing and opening lever ratios and relative length of the lower jaw are used to construct a plot of functional morphospace, a quantitative description of the potential feeding modes of fishes. Four fish faunas were examined, spanning the Mesozoic and Cenozoic (Triassic, Jurassic, Eocene and Recent). All three fossil faunas are from conservation Lagerstätten in the central Tethys, in the vicinity of coral reefs or coral-bearing hardgrounds. Changes in functional morphospace occupation reveal a marked shift in the Cenozoic, with the appearance of fishes with relatively small forceful jaws. In Recent faunas, this functional morphospace is occupied almost exclusively by grazing herbivores. This taxon-independent morphological signal of herbivory was lacking in the Mesozoic faunas, was first recorded in the Eocene, and persisted throughout the Cenozoic. This suggests that the Cenozoic did indeed witness the appearance and proliferation of herbivory and grazing by marine fishes. The arrival of these piscine herbivores had the potential to fundamentally alter the dynamics of benthic marine communities.
The fossil oral jaw teeth traditionally known as Trigonodon oweni and the pharyngeal tooth plates known since SCHULTZ 1978 as Asima jugleri, but before described as Radamas jugleri, Taurinichthys Sacheri and Stylodus Lebescontei, are all parts of the same fossil fish, and bear a close similarity to the Recent Chisel- tooth Wrasse Pseudodax moluccanus. The fossil fish and P. moluccanus share a number of unique derived characters. The fossil representative is therefore placed in the Trigonodontinae (syn.: Pseudodacinae), Labridae. According to the ICZN rules the fossil fish has to be designated as Trigonodon jugleri (MÜNSTER, 1846). The oldest fossils of this species are from the Early Miocene of Italy and Austria. Most specimens were obtained from the Badenian, Middle Miocene, of the Vienna Basin within the Central Paratethys.
Although they typically do not provide reliable information on divergence times, supertrees are nevertheless attractive candidates for the study of diversification rates: by combining a collection of less inclusive source trees, they promise to increase both the number and density of taxa included in the composite phylogeny. The relatively large size and possibly more dense taxonomic sampling of supertrees have the potential to increase the statistical power and decrease the bias, respectively, of methods for studying diversification rates that are robust to uncertainty regarding the timing of diversification events. These considerations motivate the development of atemporal methods that can take advantage of recent and anticipated advances in supertree estimation. Herein, we describe a set of whole-tree, topology- based methods intended to address two questions pertaining to the study of diversification rates. First, has a given (super)tree experienced significant variation in diversification rates among its branches? Second, if so, where have significant shifts in diversification rate occurred? We present results of simulation studies that characterize the statistical behavior of these methods, illustrating their increased power and decreased bias. We also applied the methods to a published supertree of primates, demonstrating their ability to contend with relatively large, incompletely resolved (super)trees. All the methods described in this chapter have been implemented in the freely available program, SYMMETREE.
Changes in taxonomic and morphologic diversity within the paleoguild of predatory mammals were explored within a mammalian chronofauna spanning a twelve million year interval, from the latest Eocene to the end of the Oligocene of North America (36–24 ma). The timespan encompassed a modest extinction event among terrestrial mammals (circa 34 ma) followed by a period of relative stability. Morphological diversity was assessed with estimates of body mass, relative tooth size, and tooth shape. Principal component, nearest‐neighbor, and minimum‐spanning‐tree analyses were used to compare morphological diversity and species packing within predator paleoguilds in the mid‐Chadronian (37–34 ma), Orellan (34–32), Whitneyan (32–29.5), and early Arikareean (29.5–24) land mammal ages. Species richness of predators throughout the interval was relatively constant, fluctuating between 15 and 18 total taxa. Moreover, despite significant differences in taxonomic composition and a modest extinction event among terrestrial mammals, morphological diversity within the paleoguild was very similar in the Chadronian and Orellan. In the Whitneyan and especially the early Arikareean, the diversity of feeding adaptations among species declined slightly, largely due to the loss of several highly specialized meat‐eaters (creodonts, nimravids) and the addition of small omnivores (canids).
Global climate change is having devastating effects on habitat structure in coralreef ecosystems owing to extreme environmental sensitivities and consequent bleaching of reef-building scleractinian corals. Coral bleaching frequently causes immediate loss of live coral and may lead to longer-term declines in topographic complexity. This review identifies coral cover and topographic complexity as critical and distinct components of coral-reef habitats that shape communities of coral-reef fishes. Coral loss has the greatest and most immediate effect on fishes that depend on live corals for food or shelter, and many such fishes may face considerable risk of extinction with increasing frequency and severity of bleaching. Coral loss may also 'have longer-term consequences for fishes that require live corals at settlement, which are compounded by devastating effects of declining topographic complexity. Topographic complexity moderates major biotic factors, such as predation and competition, contributing to the high diversity of fishes on coral reefs. Many coral-reef fishes that do not depend on live coral are nonetheless dependent on the topographic complexity provided by healthy coral growth. Ecological and economic consequences of declining topographic complexity are likely to be substantial compared with selective effects of coral loss but both coral cover and topographic complexity must be recognised as a critical component of habitat structure and managed accordingly. Urgent action on the fundamental causes of climate change and appropriate management of critical elements of habitat structure (coral cover and topographic complexity) are key to ensuring long-term persistence of coral-reef fishes. © R. N. Gibson, R. J. A. Atkinson, and J. D. M. Gordon, Editors Taylor & Francis.
After a 12-million-year (My) process, the Central American Isthmus was completed 2.8 My ago. Its emergence affected current flow, salinity, temper-ature, and primary productivity of the Pacific and the Atlantic and launched marine organisms of the two oceans into independent evolutionary trajec-tories. Those that did not go extinct have diverged. As no vicariant event is better dated than the isthmus, molecular divergence between species pairs on its two coasts is of interest. A total of 38 regions of DNA have been sequenced in 9 clades of echinoids, 38 of crustaceans, 42 of fishes, and 26 of molluscs with amphi-isthmian subclades. Of these, 34 are likely to have been separated at the final stages of Isthmus completion, 73 split earlier and 8 maintained post-closure genetic contact. Reproductive isolation has developed between several isolates, but is complete in only the sea urchin Diadema. Adaptive divergence can be seen in life history parameters. Lower primary productivity in the Caribbean has led to the evolution of higher levels of maternal provisioning in marine invertebrates.
The Labridae (including wrasses, the Odacidae and the Scaridae) is a species-rich group of perciform fishes whose members are prominent inhabitants of warm-temperate and tropical reefs worldwide. We analyse functionally relevant morphometrics for the feeding apparatus of 130 labrid species found on the Great Barrier Reef and use these data to explore the morphological and mechanical basis of trophic diversity found in this assemblage. Morphological measurements were made that characterize the functional and mechanical properties of the oral jaws that are used in prey capture and handling, the hyoid apparatus that is used in expanding the buccal cavity during suction feeding, and the pharyngeal jaw apparatus that is used in breaking through the defences of shelled prey, winnowing edible matter from sand and other debris, and pulverizing the algae, detritus and rock mixture eaten by scarids (parrotfishes). A Principal Components Analysis on the correlation matrix of a reduced set of ten variables revealed complete separation of scarids from wrasses on the basis of the former having a small mouth with limited jaw protrusion, high mechanical advantage in jaw closing, and a small sternohyoideus muscle and high kinematic transmission in the hyoid four-bar linkage. Some scarids also exhibit a novel four-bar linkage conformation in the oral jaw apparatus. Within wrasses a striking lack of strong associations was found among the mechanical elements of the feeding apparatus. These weak associations resulted in a highly diverse system in which functional properties occur in many different combinations and reflect variation in feeding ecology. Among putatively monophyletic groups of labrids, the cheilines showed the highest functional diversity and scarids were moderately diverse, in spite of their reputation for being trophically monomorphic and specialized. We hypothesize that the functional and ecological diversity of labrids is due in part to a history of decoupled evolution of major components of the feeding system (i.e. oral jaws, hyoid and pharyngeal jaw apparatus) as well as among the muscular and skeletal elements of each component. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82, 1–25.
Covering <0·1% of the ocean’s surface, coral reefs harbour about one-third of all marine fishes or c. 5000 species. Allopatry (geographic isolation) is believed to be the primary mode of speciation, yet few biogeographic barriers exist between reefs, and most reef fishes have a pelagic larval stage capable of extensive dispersal. Under these circumstances, why are there so many species of reef fishes? Since most biogeographic barriers in the oceans are either spatially or temporally permeable on a relatively short time frame, the requirement of isolation during allopatric speciation is hard to satisfy. Evidence from empirical and theoretical studies, the biological characteristics of coral reefs, and a reanalysis of biogeographic barriers indicate that sympatric speciation is possible but not common at small spatial scales and that parapatric speciation is a common (and probably the prevalent) mode of diversification in coral-reef fishes. Regardless of the speciation mode, previous hypotheses of accelerated diversification in the Pleistocene due to sea level fluctuations are not supported by phylogenetic analyses. Recent developments in the area of comparative genomics can fuel a new revolution in the way marine speciation is studied.
The first fossils of the tholichthys larval stage of a chaetodontid from the lower Oligocene (Rupelian, Fish Shales; about 30.1 MYA) of Frauenweiler (Baden-Württemberg, S Germany) are described, along with two less well-preserved probable tholichthys from the lower Oligocene Menilite-Formation (IPM3, 30-29 MYA and IPM4A, 29-28 MYA) of Przemyśl (Outer Carpathians, SE Poland). The fossils are compared with tholichthys larvae of the extant genus of Chaetodontidae to which they are most similar, namely Chaetodon. The German specimens are identified as tholichthys larvae by the plate-like expansions of the supracleithrum and posttemporal that extend posteriorly well behind the head and by an expanded preopercle with a large posterior spine; these bones, and the frontals and supraoccipital, are distinctively rugose. The Polish specimen from IPM3 has similar features so it is safe to assume that it also is a chaetodontid tholichthys, whereas the specimen from IPM4A is so poorly preserved that it can only very tentatively be referred to the Chaetodontidae. The occurrence of tholichthys larvae prompts reconsideration of the paleoenvironmental situation at their respective fossil sites.
The fish assemblage from the Eocene deposits of Monte Bolca, Northern Italy, are compared with those of Recent coral reefs. A family-level taxonomic definition of a Recent coral reef fish assemblage is formulated to permit direct comparisons. On this basis, the Monte Bolca fishes represent the earliest clearly defined coral reef fish assemblage. Quantitative analyses of the relative abundance of fish families revealed significant differences between the two assemblages. The Bolca assemblage has Mesozoic links (Pycnodontiformes) and non-perciform taxa are relatively abundant, particularly the Beryciformes (Holocentridae). However, Bolca represents the earliest record of a perciform-dominated benthic fish assemblage (68.4% of all non-clupeid taxa). Within the Perciformes, the abundance of the major reef fish lineages (higher squamipinnes and Labroidei) differs markedly between the two assemblages. The numerical dominance of labroid fishes on coral reefs appears to have been a relatively recent occurrence.
Wrasses in the genus Thalassoma comprise 27 recognized species that occur predominantly on coral reefs and subtropical rocky reefs worldwide. The phylogenetic relationships for 26 species were examined based on two mitochondrial genes (cytochromeb and 16S rRNA) and one nuclear intron (the first intron of the ribosomal protein S7). Two closely related species, the bird-wrasses (Gomphosus varius Lacepde, 1801 and G. caerulaeus Lacepde, 1801), were also included in the analysis. These species grouped within the genus Thalassoma. Thalassoma newtoni (Osrio, 1891) from Sao Tome, which is generally synonymized with the Atlantic/Mediterranean Thalassoma pavo (Linnaeus, 1758) appears to be a valid species. Using a molecular clock, the genus was estimated to have originally diverged 8–13million years ago, with Thalassoma ballieui (Vaillant and Sauvage, 1875) from Hawaii and Thalassoma septemfasciata Scott, 1959 from Western Australia as the ancestral species. Approximately 5–10million years ago, a sudden burst of speciation resulted in seven clades, which were resolved with the sequence data. The terminal Tethyan event and the closing of the Isthmus of Panama were probably the major historical factors shaping the evolution of species in the genus Thalassoma. These data on the spatio-temporal pattern of speciation in the Indo-Pacific indicate that peripheral species have been generated at various times throughout the history of the genus, and that none of the widespread species are relatively young. Thus, there is no clear support for centrifugal (youngest at the periphery) versus centripetal (oldest at the periphery) modes of generation of species, two theories which have been used to account for geographic gradients in species diversity.
Key morphological traits reveal changes in functional morphospace occupation of reef fish assemblages over time. We used measurements of key functional attributes (i.e., lower jaw length and orbit diameter) of 208 fossil fish species from five geological periods to create bivariate plots of functional morphological traits through time. These plots were used to examine possible function and ecological characteristics of fossil reef fish assemblages throughout the Mesozoic and Cenozoic. A previously unknown trend of increasing orbit diameter over time became apparent. The Teleostei are the principal drivers of this change. The Eocene appears to mark a dramatic increase in two previously rare feeding modes in fishes: nocturnal feeding and high-precision benthic feeding. Interestingly, members of the Pycnodontiformes had relatively large eyes since the Triassic and appear to be the ecological precursors of their later teleost counterparts and may have been among the earliest nocturnal feeding fishes. Our results highlight potential changes in the roles of fishes on coral reefs through time.
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.
Cradle of Diversity
Is the biological diversity of reefs a result of attracting species that originated elsewhere, or are they particularly important as cradles of evolution? Kiessling et al. (p. 196 ; see the cover) examine a large database of fossil benthic marine organisms dating back to the Cambrian to test these questions. It seems that reefs, even in comparison to other shallow marine environments, were indeed important during the origination of new species, including ones that migrate elsewhere.
Major modifications to the pharyngeal jaw apparatus are widely regarded as a recurring evolutionary key innovation that has enabled adaptive radiation in many species-rich clades of percomorph fishes. However one of the central predictions of this hypothesis, that the acquisition of a modified pharyngeal jaw apparatus will be positively correlated with explosive lineage diversification, has never been tested. We applied comparative methods to a new time-calibrated phylogeny of labrid fishes to test whether diversification rates shifted at two scales where major pharyngeal jaw innovations have evolved: across all of Labridae and within the subclade of parrotfishes.
Diversification patterns within early labrids did not reflect rapid initial radiation. Much of modern labrid diversity stems from two recent rapid diversification events; one within julidine fishes and the other with the origin of the most species-rich clade of reef-associated parrotfishes. A secondary pharyngeal jaw innovation was correlated with rapid diversification within the parrotfishes. However diversification rate shifts within parrotfishes are more strongly correlated with the evolution of extreme dichromatism than with pharyngeal jaw modifications.
The temporal lag between pharyngeal jaw modifications and changes in diversification rates casts doubt on the key innovation hypothesis as a simple explanation for much of the richness seen in labrids and scarines. Although the possession of a secondarily modified PJA was correlated with increased diversification rates, this pattern is better explained by the evolution of extreme dichromatism (and other social and behavioral characters relating to sexual selection) within Scarus and Chlorurus. The PJA-innovation hypothesis also fails to explain the most dominant aspect of labrid lineage diversification, the radiation of the julidines. We suggest that pharyngeal jaws might have played a more important role in enabling morphological evolution of the feeding apparatus in labrids and scarines rather than in accelerating lineage diversification.
Characters distinguishing 10 subgenera recognized in the genus Apogon of the cardinalfish family Apogonidae by the authors are given in a key. Diagnostic accounts of the two subgenera Pristiapogon and Zoramia are provided. A key to the six species of the subgenus Pristiapogon includes A. abrogramma, new species, A. kallopterus Bleeker, A. exostigma (Jordan and Starks), A. fraenatus Valenciennes, A. menesemus Jenkins, and A. taeniopterus Bennett. The key to the four species of the subgenus Zoramia includes A. leptacanthus Bleeker, A. perlitus, new species, A. gilberti (Jordan and Seale), and A. fragilis Smith. Data for important meristic and certain morphological characters are tabulated. All species are illustrated by photographs or drawings. The accounts of the species include primary synonymy, diagnosis, description, geographic distribution, life history data pertaining to oral incubation, discussion
of relationships, and material studied. Apogon abrogramma is characterized by having seven first dorsal spines; the preopercular ridge and infraorbital edges serrated; a narrow, dark mid-body stripe from snout to base of caudal fin; no basicaudal spot; and well-developed
gillrakers numbering 10-13. Apogon perlitus is characterized by having a
black alimentary canal; six first dorsal spines; nine soft anal fin rays; a very small basicaudal spot; a dark gular mark; the side of caudal peduncle with a cluster of diffuse melanophores; 4 to 8 short, dark, vertical lines on body just above base of anal fin; and the second dorsal fin is not produced as a filament. Geographic distributions are plotted on maps for the 10 species comprising the two subgenera. Several species are widespread, extending from the Red Sea or the East African coast to eastern Oceania, whereas other species have more restricted distributions in parts of the Indo-West Pacific region. Apogon kallopterus has the most extensive distribution, extending from the Red Sea
eastward to the Tuamotu Archipelago, Pitcairn Island, and the Hawaiian
islands. Apogon menesemus is restricted to the Hawaiian and Johnston islands, whereas A. perlitus and A. gilberti share similar and limited distributions in the central portion of the study region, in the Philippine Islands, southern Palau Islands and the New Guinea area. Other distributional patterns were observed, such as the occurrence of A. abrogramma in the Indian Ocean eastward to the Philippine Islands.
One of the main explanations for the stunning diversity of teleost fishes (approximately 29,000 species, nearly half of all vertebrates) is that a fish-specific whole-genome duplication event (FSGD) in the ancestor to teleosts triggered their subsequent radiation. However, one critical assumption of this hypothesis, that diversification rates in teleosts increased soon after the acquisition of a duplicated genome, has never been tested.
Here we show that one of three major diversification rate shifts within ray-finned fishes occurred at the base of the teleost radiation, as predicted by the FSGD hypothesis. We also find evidence for two rate increases that are much younger than the inferred age of the FSGD: one in the common ancestor of most ostariophysan fishes, and a second one in the common ancestor of percomorphs. The biodiversity contained within these two clades accounts for more than 88% of living fish species.
Teleosts diversified explosively in their early history and this burst of diversification may have been caused by genome duplication. However, the FSGD itself may be responsible for a little over 10% of living teleost biodiversity. ~88% of species diversity is derived from two relatively recent radiations of freshwater and marine fishes where genome duplication is not suspected. Genome duplications are a common event on the tree of life and have been implicated in the diversification of major clades like flowering plants, vertebrates, and gnathostomes. However our results suggest that the causes of diversification in large clades are likely to be complex and not easily ascribed to a single event, even a dramatic one such as a whole genome duplication.
The uneven distribution of species richness is a fundamental and unexplained pattern of vertebrate biodiversity. Although species richness in groups like mammals, birds, or teleost fishes is often attributed to accelerated cladogenesis, we lack a quantitative conceptual framework for identifying and comparing the exceptional changes of tempo in vertebrate evolutionary history. We develop MEDUSA, a stepwise approach based upon the Akaike information criterion for detecting multiple shifts in birth and death rates on an incompletely resolved phylogeny. We apply MEDUSA incompletely to a diversity tree summarizing both evolutionary relationships and species richness of 44 major clades of jawed vertebrates. We identify 9 major changes in the tempo of gnathostome diversification; the most significant of these lies at the base of a clade that includes most of the coral-reef associated fishes as well as cichlids and perches. Rate increases also underlie several well recognized tetrapod radiations, including most modern birds, lizards and snakes, ostariophysan fishes, and most eutherian mammals. In addition, we find that large sections of the vertebrate tree exhibit nearly equal rates of origination and extinction, providing some of the first evidence from molecular data for the importance of faunal turnover in shaping biodiversity. Together, these results reveal living vertebrate biodiversity to be the product of volatile turnover punctuated by 6 accelerations responsible for >85% of all species as well as 3 slowdowns that have produced "living fossils." In addition, by revealing the timing of the exceptional pulses of vertebrate diversification as well as the clades that experience them, our diversity tree provides a framework for evaluating particular causal hypotheses of vertebrate radiations.
Scaridae (parrotfishes) is a prominent clade of 96 species that shape coral reef communities worldwide through their actions as grazing herbivores. Phylogenetically nested within Labridae, the profound ecological impact and high species richness of parrotfishes suggest that their diversification and ecological success may be linked. Here, we ask whether parrotfish evolution is characterized by a significant burst of lineage diversification and whether parrotfish diversity is shaped more strongly by sexual selection or modifications of the feeding mechanism. We first examined scarid diversification within the greater context of labrid diversity. We used a supermatrix approach for 252 species to propose the most extensive phylogenetic hypothesis of Labridae to date, and time-calibrated the phylogeny with fossil and biogeographical data. Using divergence date estimates, we find that several parrotfish clades exhibit the highest diversification rates among all labrid lineages. Furthermore, we pinpoint a rate shift at the shared ancestor of Scarus and Chlorurus, a scarid subclade characterized by territorial behaviour and strong sexual dichromatism, suggesting that sexual selection was a major factor in parrotfish diversification. Modifications of the pharyngeal and oral jaws that happened earlier in parrotfish evolution may have contributed to this diversity by establishing parrotfishes as uniquely capable reef herbivores.
Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.
[Extract] Coral reefs have been around since the Ordovician
(Wood, 1999), and throughout their 450-million year history they have shared the oceans with fishes. Modern scleractinian-dominated coral reefs and their associated fish faunas represent only the latest manifestation of a reefal ecosystem. It is almost self-evident that history is important to coral reefs, as the reefs build on the skeletons of past generations. But what of the associated fauna? Today, fishes form an integral part of
reef communities, modifying benthic community structure and forming a major conduit for the movement of energy and material. Like the reefs, reef fish faunas have been shaped by history, but this historical influence may not be as apparent. Although it is becoming increasingly clear that history plays an important role in structuring local communities (Rickleffs and Schluter, 1993a), its influence on the ecology and biogeography
of fishes on coral reefs remains largely unknown.
Most studies of reef systems have addressed the question of how biogeographic and ecological patterns are maintained; relatively few consider how these patterns arose or their consequences. However, it is the combination of these two factors, origins and maintenance, that offers the clearest understanding of the nature of biogeographic patterns in reef organisms. Studies of the history of coral reefs have been largely restricted to documenting the history of the reef builders, which have left an outstanding fossil record (Wood,
1999). The history of associated faunas, and fish in particular, is less clear. However, this is changing, primarily as a result of phylogenetic analyses of reef fishes and from a reappraisal of the fossil record.
Three new species of the genus Archamia are described from specimens collected on the Omani coast of the Arabian Sea and in the Red Sea. A. pallida, from Oman, has 14 pectoral rays, 13–14 soft anal rays, 15–17 developed gill rakers, and 9 gill rakers on the first ceratobranchial bone; A. irida, from the Gulf of Suez, has 14 pectoral rays, 15–17 soft anal rays, 20–21 developed gill rakers, and usually 11 gill rakers on the first ceratobranchial bone. Both species have a small black spot at the middle of the caudal-fin base, and no distinctive markings on the body. A. bilineata, from the Gulf of Aqaba, has 13 pectoral rays, 12–13 soft anal rays, 18–21 developed gill rakers, usually 11 gill rakers on the first ceratobranchial bone, two dark narrow stripes on the body, and a large dark spot on the caudal peduncle. A key to the western Indian Ocean (including the Red Sea and the Persian Gulf) species of Archamia is provided.
Understanding the nature and causes of global gradients in species richness is a perennial ecological problem, and recent work has highlighted the need to assess these gradients relative to an appropriate statistical expectation. This paper examines latitudinal and longitudinal gradients in species richnesses of corals and reef fishes in the Indo-Pacific domain and compares them with gradients predicted by a mid-domain model in which geographic domains are located at random between the latitudinal and longitudinal bound- aries of this region. We test for significant differences between observed and predicted species-richness patterns, and we identify regions that are enriched or depauperate in spe- cies, relative to expectation. In addition, we move beyond previous mid-domain analyses by directly comparing observed spatial distributions of geographic ranges with those pre- dicted by a mid-domain model. This comparison indicates precisely how species-richness anomalies are produced by nonrandomness in the distribution of species ranges. For both corals and fishes, large and statistically significant differences exist between observed latitudinal and longitudinal species-richness gradients and those predicted by mid-domain models. Longitudinally, species richness is markedly higher than predicted along the African coast and, to a lesser extent, within the Indo-Australian Archipelago (IAA), and it is mark- edly lower than expected in the eastern Pacific. Latitudinally, species richness becomes increasingly higher than predicted as one moves from the equator to the tropical margins; then it becomes sharply lower than predicted beyond the tropics. Unexpectedly, differences between observed and predicted spatial distributions of range endpoints and midpoints reveal a pattern of nonrandomness that is highly congruent with the hypothesis that gyres in the Indian and Pacific Oceans, with the IAA forming a porous boundary between them, have a major influence on Indo-Pacific species-richness patterns. Our analyses indicate that the perspective offered by a focus on explaining nonrandomness in the location of geo- graphic ranges (rather than explaining why species numbers vary in space) is likely to dramatically alter our assessments of alternative explanations for global species-richness
A three-phase kinetic model with time-specific perturbations is used to describe large-scale patterns in the diversification of Phanerozoic marine families. The basic model assumes that the Cambrian, Paleozoic, and Modern evolutionary faunas each diversified logistically as a consequence of early exponential growth and of later slowing of growth as the ecosystems became filled; it also assumes interaction among the evolutionary faunas such that expansion of the combined diversities of all three faunas above any single fauna's equilibrium caused that fauna's diversity to begin to decline. This basic model adequately describes the diversification of the evolutionary faunas through the Paleozoic Era as well as the asymmetrical rise and fall of background extinction rates through the entire Phanerozoic. Declines in diversity and changes in faunal dominance associated with mass extinctions can be accommodated in the model with short-term accelerations in extinction rates or declines in equilibria. Such accelerations, or perturbations, cause diversity to decline exponentially and then to rebound sigmoidally following release. The amount of decline is dependent on the magnitude and duration of the perturbation, the timing of the perturbation with respect to the diversification of the system, and the system's initial per-taxon rates of diversification and turnover. When applied to the three-phase model, such perturbations describe the changes in diversity and faunal dominance during and after major mass extinctions, the long-term rise in total diversity following the Late Permian and Norian mass extinctions, and the peculiar diversification and then decline of the remnants of the Palaeozoic fauna during the Mesozoic and Cenozoic Eras. The good fit of this model to data on Phanerozoic familial diversity suggests that many of the large-scale patterns of diversification seen in the marine fossil record of animal families are simple consequences of nonlinear interrelationships among a small number of parameters that are intrinsic to the evolutionary faunas and are largely (but not completely) invariant through time. -Author
The fossil record of the Pomacentridae has been based on species from six genera. The status of these taxa is reviewed. Only two are tentatively accepted as belonging to the Pomacentridae: Chromis savomini from the Miocene of Algeria and Izuus nakamurai from the Miocene of Japan. In addition, a new genus and species Palaeopomacentrus orphae is described from the lower Middle Eocene of Monte Bolca, Northern Italy. This is the first substantiated record of a pomacentrid from the Eocene, and represents the oldest record of the family.
Abstract The extraordinary contemporary species richness and ecological predominance of flowering plants (angiosperms) are even more remarkable when considering the relatively recent onset of their evolutionary diversification. We examine the evolutionary diversification of angiosperms and the observed differential distribution of species in angiosperm clades by estimating the rate of diversification for angiosperms as a whole and for a large set of angiosperm clades. We also identify angiosperm clades with a standing diversity that is either much higher or lower than expected, given the estimated background diversification rate. Recognition of angiosperm clades, the phylogenetic relationships among them, and their taxonomic composition are based on an empirical compilation of primary phylogenetic studies. By making an integrative and critical use of the paleobotanical record, we obtain reasonably secure approximations for the age of a large set of angiosperm clades. Diversification was modeled as a stochastic, time-homogeneous birth-and-death process that depends on the diversification rate (r) and the relative extinction rate (∈). A statistical analysis of the birth and death process was then used to obtain 95% confidence intervals for the expected number of species through time in a clade that diversifies at a rate equal to that of angiosperms as a whole. Confidence intervals were obtained for stem group and for crown group ages in the absence of extinction (∈= 0.0) and under a high relative extinction rate (∈= 0.9). The standing diversity of angiosperm clades was then compared to expected species diversity according to the background rate of diversification, and, depending on their placement with respect to the calculated confidence intervals, exceedingly species-rich or exceedingly species-poor clades were identified. The rate of diversification for angiosperms as a whole ranges from 0.077 (∈= 0.9) to 0.089 (∈= 0.0) net speciation events per million years. Ten clades fall above the confidence intervals of expected species diversity, and 13 clades were found to be unexpectedly species poor. The phylogenetic distribution of clades with an exceedingly high number of species suggests that traits that confer high rates of diversification evolved independently in different instances and do not characterize the angiosperms as a whole.
Abstract It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question—Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data—the branch lengths in the tree—and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth-death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools.
The long-term diversification of life probably cannot be modelled as a simple equilibrial process: the time scales are too long, the potential for exploring new ecospace is too large and it is unlikely that ecological controls can act at global scales. The sum of many clade expansions and reductions, each of which happens according to its own dynamic, probably approximates more a damped exponential curve when translated into a global-scale species diversification curve. Unfortunately, it is not possible to plot such a meaningful global-scale species diversification curve through time, but curves at higher taxonomic levels have been produced. These curves are subject to the vagaries of the fossil record, but it is unlikely that the sources of error entirely overwhelm the biological signal. Clades radiate when the external and internal conditions are right: a new territory or ecospace becomes available, and the lineage has acquired a number of characters that open up a new diet or mode of life. Modern high levels of diversity in certain speciose clades may depend on such ancient opportunities taken. Dramatic climatic changes through the Quaternary must have driven extinctions and originations, but many species responded simply by moving to more favourable locations. Ecological communities appear to be no more than merely chance associations of species, but there may be real interactions among species. Ironically, high species diversity may lead to more speciation, not, as had been assumed, less: more species create more opportunities and selective pressures for other species to respond to, rather than capping diversity at a fixed equilibrium level. Studies from the scale of modern ecosystems to global long-term patterns in the fossil record support a model for the exponential diversification of life, and one explanation for a pattern of exponential diversification is that as diversity increases, new forms become ever more refinements of existing forms. In a sense the world becomes increasingly divided into finer niche space. Organisms have a propensity to speciate freely, species richness within ecosystems appears to generate opportunities for more speciation, clades show all kinds of patterns from sluggish speciation rates and constant diversity through time to apparently explosive speciation, and there is no evidence that rapidly speciating clades have reached a limit, nor that they are driving other clades to extinction. A corollary of this view is that current biodiversity must be higher than it has ever been. Limits to infinite growth are clearly local, regional, and global turnover and extinction events, when climate change and physical catastrophes knock out species and whole clades, and push the rising exponential curve down a notch or two.
Species-range information forms the empirical data base for much of biogeography, but even with a huge amount of data on species occurrences, many of the ecological and evolutionary processes generating biogeographic patterns remain obscure. Molecular genetic data from closely related, widely distributed species can help address biogeographic mechanisms by (1) providing independent evidence for genetic boundaries between cryptic species, (2) estimating species divergence times, (3) providing phylogenetic reconstructions of species divergence patterns, and (4) allowing us to examine the geography of allelic variants within species and ask if intra-specific alleles show the same biogeographic patterns as do species. Data from mitochondrial DNA variation in Pacific sea urchins and butterfly fishes show that congeneric species diverged within the Pleistocene. Thus, the processes that generate species diversity patterns probably have been acting throughout the recent past, and are ongoing aspects of Pacific marine biology. Phylogenetic analysis of mtDNA variants suggests that sea urchin species arise throughout the Pacific, with some originating by peripheral speciation and some evolving in the high diversity center of the Indo-West Pacific. Clines of mtDNA variation within species are similar to diversity clines in the entire fauna. Similar biogeographic patterns for species and for alleles within species may provide unique clues about the processes that generate biological diversity both within and between species.
It is currently widely accepted that the hermatypic coral fauna in the Eastern Pacific Ocean underwent massive extinction during the mid-Tertiary, with subsequent transoceanic colonizatiion by planulae from the Indo-West Pacific region during periods of favorable conditions. We suggest that the available evidence does not strongly support this biogeographic hypothesis; moreover, we contend that it is untestable in its present form. In its place we propose an alternative hypothesis based upon modification of a previously widespread, pan-Tethyan coral biota which has since been modified by tectonic events, speciations, and extinctions.
We estimated ages of divergence 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 diversified 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 diversification 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 diversity. The current trophic diversity 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.
A detailed morphological analysis of the Miocene butterflyfish Chaetodon ficheuri Arambourg, 1927 is provided. The description is based on six specimens collected from the Upper Miocene (Messinian) diatomites of the Chelif Basin, in the vicinity of Oran, north-western Algeria. Based on the new information presented here, this species represents the only member of a new subgenus Arambourgchaetodon. This new subgenus is diagnosed by a unique combination of characters and belongs to the large clade formed by the Indo-Pacific subgenera of the genus Chaetodon. A morphofunctional analysis of the feeding structures suggests that C. ficheuri was an omnivore that probably browsed on a wide variety of benthic prey. Stratigraphical and palaeoenvironmental studies of the type localities of C. ficheuri indicate that this fish inhabited a wide variety of environments, from coral systems to deep coastal basins. The placement of C. ficheuri in the large Indo-Pacific clade of Chaetodon subgenera suggests that this fish represents a descendant (relict) of the Tethyan biota that survived in the Mediterranean up to the Messinian. The occurrences of butterflyfishes in the fossil record are listed and commented upon. © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society, 2006, 146, 251–267.
As phylogenetic data sets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing data directly and in principle provide effective syntheses of phylogenetic information that may reveal new relationships. However, several serious difficulties exist in the construction of large supermatrices that must be overcome before these approaches will enjoy broad utility. We present analyses that examine the performance of sparse supermatrices constructed from large sequence databases for the reconstruction of species-level phylogenies. We develop a largely automated informatics pipeline that allows for the construction of sparse supermatrices from GenBank data. In doing so, we develop strategies for alleviating some of the outstanding impediments to accurate phylogenetic inference using these approaches. These include taxonomic standardization, automated alignment, and the identification of rogue taxa. We use turtles as an exemplar clade and present a well-supported species-level phylogeny for two-thirds of all turtle species based on a approximately 50 kb supermatrix consisting of 93% missing data. Finally, we discuss some of the remaining pitfalls and concerns associated with supermatrix analyses, provide comparisons to supertree approaches, and suggest areas for future research.
The association between diversification and evolutionary innovations has been well documented and tested in studies of taxonomic richness but the impact that such innovations have on the diversity of form and function is less well understood. Using phylogenetically rigorous techniques, we investigated the association between morphological diversity and two design breakthroughs within the jaws of parrotfish. Similar intramandibular joints and other modifications of the pharyngeal jaws have evolved repeatedly in teleost fish and are frequently hypothesized to promote diversity. We quantified morphological diversity within six functionally important oral jaw traits using the Brownian motion rate of evolution to correct for phylogenetic and time-related biases and compared these rates across clades that did and did not possess the intramandibular joint and the parrotfish pharyngeal jaw. No change in morphological diversity was associated with the pharyngeal jaw modification alone but rates of oral jaw diversification were up to 8× faster in parrotfish species that possessed both innovations. Interestingly, this morphological diversity may not have led to differential resource uses as available data suggest that members of this clade show remarkable homogeneity of diet.
Molecular phylogenies contain information about the tempo and mode of species diversification through time. Because extinction leaves a characteristic signature in the shape of molecular phylogenetic trees, many studies have used data from extant taxa only to infer extinction rates. This is a promising approach for the large number of taxa for which extinction rates cannot be estimated from the fossil record. Here, I explore the consequences of violating a common assumption made by studies of extinction from phylogenetic data. I show that when diversification rates vary among lineages, simple estimators based on the birth-death process are unable to recover true extinction rates. This is problematic for phylogenetic trees with complete taxon sampling as well as for the simpler case of clades with known age and species richness. Given the ubiquity of variation in diversification rates among lineages and clades, these results suggest that extinction rates should not be estimated in the absence of fossil data.
Recent application of time-varying birth-death models to molecular phylogenies suggests that a decreasing diversification rate can only be observed if there was a decreasing speciation rate coupled with extremely low or no extinction. However, from a paleontological perspective, zero extinction rates during evolutionary radiations seem unlikely. Here, with a more comprehensive set of computer simulations, we show that substantial extinction can occur without erasing the signal of decreasing diversification rate in a molecular phylogeny. We also find, in agreement with the previous work, that a decrease in diversification rate cannot be observed in a molecular phylogeny with an increasing extinction rate alone. Further, we find that the ability to observe decreasing diversification rates in molecular phylogenies is controlled (in part) by the ratio of the initial speciation rate (Lambda) to the extinction rate (Mu) at equilibrium (the LiMe ratio), and not by their absolute values. Here we show in principle, how estimates of initial speciation rates may be calculated using both the fossil record and the shape of lineage through time plots derived from molecular phylogenies. This is important because the fossil record provides more reliable estimates of equilibrium extinction rates than initial speciation rates.
How biodiversity is generated and maintained underlies many major questions in evolutionary biology, particularly relating to the tempo and pattern of diversification through time. Molecular phylogenies and new analytical methods provide additional tools to help interpret evolutionary processes. Evolutionary rates in lineages sometimes appear punctuated, and such "explosive" radiations are commonly interpreted as adaptive, leading to causative key innovations being sought. Here we argue that an alternative process might explain apparently rapid radiations ("broom-and-handle" or "stemmy" patterns seen in many phylogenies) with no need to invoke dramatic increase in the rate of diversification. We use simulations to show that mass extinction events can produce the same phylogenetic pattern as that currently being interpreted as due to an adaptive radiation. By comparing simulated and empirical phylogenies of Australian and southern African legumes, we find evidence for coincident mass extinctions in multiple lineages that could have resulted from global climate change at the end of the Eocene.
The cardinalfishes (Apogonidae) are a diverse clade of small, mostly reef-dwelling fishes, for which a variety of morphological data have not yielded a consistent phylogeny. We use DNA sequence to hypothesize phylogenetic relationships within Apogonidae and among apogonids and other acanthomorph families, to examine patterns of evolution including the distribution of a visceral bioluminescence system. In conformance with previous studies, Apogonidae is placed in a clade with Pempheridae, Kurtidae, Leiognathidae, and Gobioidei. The apogonid genus Pseudamia is recovered outside the remainder of the family, not as sister to the superficially similar genus Gymnapogon. Species sampled from the Caribbean and Western Atlantic (Phaeoptyx, Astrapogon, and some Apogon species) form a clade, as do the larger-bodied Glossamia and Cheilodipterus. Incidence of visceral bioluminescence is found scattered throughout the phylogeny, independently for each group in which it is present. Examination of the fine structure of the visceral bioluminescence system through histology shows that light organs exhibit a range of morphologies, with some composed of complex masses of tubules (Siphamia, Pempheris, Parapriacanthus) and others lacking tubules but containing chambers formed by folds of the visceral epithelium (Acropoma, Archamia, Jaydia, and Rhabdamia). Light organs in Siphamia, Acropoma, Pempheris and Parapriacanthus are distinct from but connected to the gut; those in Archamia, Jaydia, and Rhabdamia are simply portions of the intestinal tract, and are little differentiated from the surrounding tissues. The presence or absence of symbiotic luminescent bacteria does not correlate with light organ structure; the tubular light organs of Siphamia and chambered tubes of Acropoma house bacteria, those in Pempheridae and the other Apogonidae do not.