Francesco Santini

Diversity versus disparity and the radiation of modern cetaceans

Modern whales are frequently described as an adaptive radiation spurred by either the evolution of various key innovations (such as baleen or echolocation) or ecological opportunity following the demise of archaic whales. Recent analyses of diversification rate shifts on molecular phylogenies raise doubts about this interpretation since they find no evidence of increased speciation rates during the early evolution of modern taxa. However, one of the central predictions of ecological adaptive radiation is rapid phenotypic diversification, and the tempo of phenotypic evolution has yet to be quantified in cetaceans. Using a time-calibrated molecular phylogeny of extant cetaceans and a morphological dataset on size, we find evidence that cetacean lineages partitioned size niches early in the evolutionary history of neocetes and that changes in cetacean size are consistent with shifts in dietary strategy. We conclude that the signature of adaptive radiations may be retained within morphological traits even after equilibrium diversity has been reached and high extinction or fluctuations in net diversification have erased any signature of an early burst of diversification in the structure of the phylogeny.

DO REEFS DRIVE DIVERSIFICATION IN MARINE TELEOSTS? EVIDENCE FROM THE PUFFERFISH AND THEIR ALLIES (ORDER TETRAODONTIFORMES)

Abstract A major challenge in evolutionary biology lies in explaining patterns of high species numbers found in biodiversity hot spots. Tropical coral reefs underlie most marine hot spots and reef-associated fish faunas represent some of the most diverse assemblages of vertebrates on the planet. Although the standing diversity of modern reef fish clades is usually attributed to their ecological association with corals, untangling temporal patterns of codiversification has traditionally proved difficult. In addition, owing to uncertainty in higher-level relationships among acanthomorph fish, there have been few opportunities to test the assumption that reef-association itself leads to higher rates of diversification compared to other habitats. Here we use relaxed-clock methods in conjunction with statistical measures of species accumulation and phylogenetic comparative methods to clarify the temporal pattern of diversification in reef and nonreef-associated lineages of tetraodontiforms, a morphologically diverse order of teleost fish. We incorporate 11 fossil calibrations distributed across the tetraodontiform tree to infer divergence times and compare results from models of autocorrelated and uncorrelated evolutionary rates. All major tetraodontiform reef crown groups have significantly higher rates of diversification than the order as a whole. None of the nonreef-associated families show this pattern with the exception of the aracanid boxfish. Independent contrasts analysis also reveals a significantly positive relationship between diversification rate and proportion of reef-associated species within each family when aracanids are excluded. Reef association appears to have increased diversification rate within tetraodontiforms. We suggest that both intrinsic factors of reef habitat and extrinsic factors relating to the provincialization and regionalization of the marine biota during the Miocene (about 23–5 MY) played a role in shaping these patterns of diversity

Phylogeny of the ocean sunfishes (Molidae, Tetraodontiformes), a highly derived group of teleost fishes

Abstract A phylogenetic hypothesis based on the cladistic analysis of 48 morphological characters for the pelagic tetraodontiform ocean sunfishes of the family Molidae is proposed. Strong support is evidenced for the traditional idea that Mola and Masturus are very closely related to each other, and this clade is shown to be the sister group of Ranzania. The monophyly of the Molidae also is strongly supported, not just by characters associated with the dramatic modifications of the caudal region, but also by many additional osteological features from other parts of the body.

First molecular scombrid timetree (Percomorpha: Scombridae) shows recent radiation of tunas following invasion of pelagic habitat

Abstract Scombrid fishes represent one of the major radiations of marine vertebrates in the pelagic realm, and have historically been a commercially important group. Their rich fossil record dates to the Late Paleocene, and it has recently been suggested that the current scombrid diversity is due to a post-Cretaceous radiation that saw the survivors of the KPg extinction replace a number of non-acanthomorph fish lineages that did not survive the Mesozoic Era. In this paper we present the result of the first quantitative macroevolutionary study of scombrid evolution. We assembled a supermatrix consisting of seven nuclear and mitochondrial loci, including 47 of the 52 extant scombrid species. We then used seven fossils to time-calibrate this new molecular phylogeny, the first ever assembled for scombrids that included more than 50% of the diversity of this family, and investigated macroevolutionary patterns within this clade. Our results support a Late Cretaceous origin of the scombrids, and show that many lineages originated in the Eocene and Oligocene. Our findings, however, fail to support the hypothesis of a rapid scombrid radiation in the post-KPg ecosystems. We show how the most significant radiation within scombrids has taken place since the Late Miocene in tunas, possibly triggered by a transition from pelagic-neritic to pelagic-oceanic habitats, and matched by a dramatic increase in body size.

First multi-locus timetree of seabreams and porgies (Percomorpha: Sparidae)

Abstract Sparid fishes represent one of the major radiations of predominantly temperate-water benthic fishes. Previous molecular phylogenetic studies suggested that many traditional taxonomic groups, often based on dentition characters, do not correspond to monophyletic groups, suggesting repeated convergence in trophic ecology. In spite of the rich sparid fossil record, no comprehensive, multi-locus timetree based on sparid fossils currently exists for this group. We used a supermatrix approach to assemble a dataset of five loci and 91 sparid species, and time-calibrated this new phylogeny using eight sparid fossils. Our study corroborates the non-monophyly of the traditional sparids without the inclusion of the family Centracanthidae, as well as that of many sparid genera. Based on phylogenetic comparative analyses we find robust support for a scenario of multiple radiations and suggest that these were driven by the invasion of multiple geographic regions by different lineages, as well as by the transition to different trophic ecologies.

Phylogeny and biogeography of the extant species of triplespine fishes (Triacanthidae, Tetraodontiformes)

A new phylogenetic hypothesis for the living species of triplespine fishes of the Indo‐Western Pacific family Triacanthidae (Tetraodontiformes, Teleostei) is proposed. A data set of 55 morphological characters (34 osteological and 21 morphometric) was constructed. A cladistic analysis of the osteological data set yielded a single most‐parsimonious tree. This cladogram does not support the monophyly of one of the four genera, Tripodichthys, but Bremer values for this analysis are low. The osteological data set was then combined with a data set of 21 morphometric characters that had previously been used to diagnose the four genera. The analysis of the combined data set produced the same phylogenetic hypothesis, but with greater nodal support. The biogeographical distribution of the living species is then interpreted with the use of this new phylogenetic information.

Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics

BackgroundVertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebrates, including lampreys, teleosts, amphibians, reptiles, birds, and mammals. The SWS1 genes exhibit many of the characteristics of genes typically targeted for phylogenetic analyses. This study investigates both the utility of SWS1 as a marker for inferring vertebrate phylogenetic relationships, and the characteristics of the gene that contribute to its phylogenetic utility.ResultsPhylogenetic analyses of vertebrate SWS1 genes produced topologies that were remarkably congruent with generally accepted hypotheses of vertebrate evolution at both higher and lower taxonomic levels. The few exceptions were generally associated with areas of poor taxonomic sampling, or relationships that have been difficult to resolve using other molecular markers. The SWS1 data set was characterized by a substantial amount of among-site rate variation, and a relatively unskewed substitution rate matrix, even when the data were partitioned into different codon sites and individual taxonomic groups. Although there were nucleotide biases in some groups at third positions, these biases were not convergent across different taxonomic groups.ConclusionOur results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups. This may result from constraints imposed by the functional role of SWS1 pigments in visual transduction.

First timetree of Sphyraenidae (Percomorpha) reveals a Middle Eocene crown age and an Oligo-Miocene radiation of barracudas

Abstract The 27 extant species of the family Sphyraenidae represent one of the major groups of piscivorous teleost fishes in tropical and subtropical marine waters. In spite of their ecological importance, currently, no phylogenetic hypothesis is available for this group, and we do not know the tempo of evolution of this clade. In this study, we used a supermatrix approach to assemble a dataset of three mitochondrial loci for 20 sphyraenid species, and time-calibrated this new phylogeny. Our study supports the existence of three main groups of barracudas, which we labelled the “S. barracuda” group, the “S. obtusata” group and the “S. sphyraena” group. The timetree indicates a Late Paleocene age (~57 Ma) for the origin of the groups, and a Middle Eocene (~45 Ma) timing for the beginning of the radiation of extant lineages. Most extant species appear to belong to phylogenetic lineages dating to the Miocene (~5 to 23 Ma). Our study reveals multiple shifts between coral reef-associated and non-reef (usually more pelagic) habitats, as well as two independent origins of large body size within this group.

Non-reef environments impact the diversification of extant jacks, remoras and allies (Carangoidei, Percomorpha)

Various factors may impact the processes of diversification of a clade. In the marine realm, it has been shown that coral reef environments have promoted diversification in various fish groups. With the exception of requiem sharks, all the groups showing a higher level of diversity in reefs than in non-reef habitats have diets based predominantly on plankton, algae or benthic invertebrates. Here we explore the pattern of diversification of carangoid fishes, a clade that includes numerous piscivorous species (e.g. trevallies, jacks and dolphinfishes), using time-calibrated phylogenies as well as ecological and morphological data from both extant and fossil species. The study of carangoid morphospace suggests that reef environments played a role in their early radiation during the Eocene. However, contrary to the hypothesis of a reef-association-promoting effect, we show that habitat shifts to non-reef environments have increased the rates of morphological diversification (i.e. size and body shape) in extant carangoids. Piscivory did not have a major impact on the tempo of diversification of this group. Through the ecological radiation of carangoid fishes, we demonstrate that non-reef environments may sustain and promote processes of diversification of different marine fish groups, at least those including a large proportion of piscivorous species.

Molecular Evolutionary Analysis of Vertebrate Transducins: A Role for Amino Acid Variation in Photoreceptor Deactivation

Abstract Transducin is a heterotrimeric G protein that plays a critical role in phototransduction in the rod and cone photoreceptor cells of the vertebrate retina. Rods, highly sensitive cells that recover from photoactivation slowly, underlie dim-light vision, whereas cones are less sensitive, recover more quickly, and underlie bright-light vision. Transducin deactivation is a critical step in photoreceptor recovery and may underlie the functional distinction between rods and cones. Rods and cones possess distinct transducin α subunits, yet they share a common deactivation mechanism, the GTPase activating protein (GAP) complex. Here, we used codon models to examine patterns of sequence evolution in rod (GNAT1) and cone (GNAT2) α subunits. Our results indicate that purifying selection is the dominant force shaping GNAT1 and GNAT2 evolution, but that GNAT2 has additionally been subject to positive selection operating at multiple phylogenetic scales; phylogeny-wide analysis identified several sites in the GNAT2 helical domain as having substantially elevated dN/dS estimates, and branch-site analysis identified several nearby sites as targets of strong positive selection during early vertebrate history. Examination of aligned GNAT and GAP complex crystal structures revealed steric clashes between several positively selected sites and the deactivating GAP complex. This suggests that GNAT2 sequence variation could play an important role in adaptive evolution of the vertebrate visual system via effects on photoreceptor deactivation kinetics and provides an alternative perspective to previous work that focused instead on the effect of GAP complex concentration. Our findings thus further the understanding of the molecular biology, physiology, and evolution of vertebrate visual systems.