Papers by Francesco Santini
Various factors may impact the processes of diversification of a clade. In the marine realm, it h... more 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 caran-goid 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.
Bodianus wrasses comprise one of the most diverse genera of labrids. Also known as hogfishes due ... more Bodianus wrasses comprise one of the most diverse genera of labrids. Also known as hogfishes due to the presence of a large pig-like snout, Bodianus species are found in warm waters across the Pacific, Atlantic and Indian Oceans. To this date no densely sampled molecular phylogeny is available for this group, and a single morphological study did not include two genera (Clepticus and Semicossyphus) that have been shown to belong within hogfishes by molecular studies. Our study produced the first multi-locus molecular phylogeny of Bodianus species, and corroborated the non-monophyly of this group without the inclusion of the Creole wrasse (Clepticus) and the sheepheads (Semicossyphus). We further showed that hogfishes and allies started to radiate during the Early Miocene, 20 Ma, and that while this group originated in the Indo-western and Southwestern Pacific, it experienced multiple episodes during which it successfully invaded different geographic regions and/or ocean basins.
Molecular Phylogenetics and Evolution
Carangoid fishes (trevallies, pompanos, jacks, dolphinfishes, cobias and remoras) include about 1... more Carangoid fishes (trevallies, pompanos, jacks, dolphinfishes, cobias and remoras) include about 159 species of marine fishes found in tropical and temperate waters worldwide (Froese and Pauly, 2014). Many carangoids are powerful swimmers and active piscivores in and around coral-reef ecosystems. Some carangoid lineages, such as dolphinfishes, have evolved a pelagic lifestyle, while remoras spend their adult life attached to cetaceans, sharks, manta rays and large teleosts, feeding off skin parasites or leftovers from their host's meals. In spite of their taxonomic diversity, ecological dominance, economic importance to humans, and a rich fossil record dating to the Paleogene, relatively little is currently known about the tempo of evolution of this group. Here we present the results of the first time calibration study of carangoid fishes. Using a fossil-calibrated molecular timetree that includes 133 species of carangoids (85% of extant species), we show that this group originated in the Late Cretaceous and that several major lineages were already present before the K-Pg extinction. All major clades were in existence by the end of the Eocene, even though significant diversification has continued to occur throughout the history of this group.
Frontiers in Marine Science
The Acanthomorpha is the largest group of teleost fishes with about one third of extant vertebrat... more The Acanthomorpha is the largest group of teleost fishes with about one third of extant vertebrate species. In the course of its evolution this lineage experienced several episodes of radiation, leading to a large number of descendant lineages differing profoundly in morphology, ecology, distribution and behavior. Although Acanthomorpha was recognized decades ago, we are only now beginning to decipher its large-scale, time-calibrated phylogeny, a prerequisite to test various evolutionary hypotheses explaining the tremendous diversity of this group. In this study, we provide new insights into the early evolution of the acanthomorphs and the euteleost allies based on the phylogenetic analysis of a newly developed dataset combining nine nuclear and mitochondrial gene markers. Our inferred tree is time-calibrated using 15 fossils, some of which have not been used before. While our phylogeny strongly supports a monophyletic Neoteleostei, Ctenosquamata (i.e., Acanthomorpha plus Myctophiformes), and Acanthopterygii, we find weak support (bootstrap value < 48%) for the traditionally defined Acanthomorpha, as well as evidence of non-monophyly for the traditional Paracanthopterygii, Beryciformes, and Percomorpha. We corroborate the new Paracanthopterygii sensu including Polymixiiformes, Zeiformes, Gadiformes, Percopsiformes, and likely the enigmatic Stylephorus chordatus. Our timetree largely agrees with other recent studies based on nuclear loci in inferring an Early Cretaceous origin for the acanthomorphs followed by a Late Cretaceous/Early Paleogene radiation of major lineages. This is in contrast to mitogenomic studies mostly inferring Jurassic or even Triassic ages for the origin of the acanthomorphs. We compare our results to those of previous studies, and attempt to address some of the issues that may have led to incongruence between the fossil record and the molecular clock studies, as well as between the different molecular timetrees.
J . EVOL. BI OL . 27 ( 2 0 14 ) 1536–1548
Sharks occupy marine habitats ranging from shallow, inshore environments to pelagic, and deepwate... more Sharks occupy marine habitats ranging from shallow, inshore environments to pelagic, and deepwaters, and thus provide a model system for testing how gross habitat differences have shaped vertebrate macroevolution. Palaeontological studies have shown that onshore lineages diversify more quickly than offshore taxa. Among onshore habitats, coral reef-association has been shown to increase speciation rates in several groups of fishes and invertebrates. In this study, we investigated whether speciation rates are habitat dependent by generating the first comprehensive molecular timescale for shark divergence. Using phylogenetic comparative methods, we rejected the hypothesis that shelf (i.e. onshore) lineages have higher speciation rates compared to those occupying deepwater and oceanic (i.e. offshore) habitats. Our results, however, support the hypothesis of increased speciation rates in
coral reef-associated lineages within the Carcharhinidae. Our new timetree suggests that the two major shark lineages leading to the extant shark diversity began diversifying mostly after the end-Permian mass extinction: the
squalimorphs into deepwater and the galeomorphs into shelf habitats. We suggest that the breakdown of the onshore–offshore speciation rate pattern in sharks is mediated by success in deepwater environments through ecological partitioning, and in some cases, the evolution of morphological novelty.
Sparid fishes represent one of the major radiations of predominantly temperate-water benthic fish... more 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.
Journal of Molecular Evolution
Transducin is a heterotrimeric G protein that plays a critical role in phototransduction in the r... more 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 a 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) a 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.
Italian Journal of Zoology
Billfishes (Order Istiophoriformes) represent a major radiation of pelagic predators in most trop... more Billfishes (Order Istiophoriformes) represent a major radiation of pelagic predators in most tropical and temperate ecosystems. This group includes species that are commercially harvested, and several species that are considered the most prized of game fishes. Like other pelagic teleost groups, relatively little is known about the mode and tempo of billfish evolution compared to groups that predominantly inhabit coastal and benthic ecosystems. We generated a time-calibrated molecular hypothesis of the timing of billfish evolution using 10 loci and utilizing the rich fossil record dating back to the Early Eocene. Our timetree infers a Late Cretaceous origin for the istiophoriforms, with istiophorid diversification beginning in the Middle to Late Miocene (~17 Ma), but with most splits having occurred since the Pliocene (~5 Ma). This timing of diversification coincides with the radiation of tunas, and may have been driven by the establishment of modern upwelling regimes across the world's oceans.
Molecular Phylogenetics and Evolution
and sharing with colleagues.
PLoS ONE
Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Alth... more Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular
phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is
no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous
potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here,
we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned
fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our
workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by
traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a wellsupported
phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and
Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages.
Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous
potential for resolving phylogenetic relationships within ray-finned fishes.
Nature Communications
Several evolutionary theories predict that rates of morphological change should be positively ass... more Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000 þ living species of ray-finned fishes that comprise the majority of vertebrate biological diversity. This coupling is a general feature of fish evolution and transcends vast differences in ecology and body-plan organization. Our results may reflect a widespread speciational mode of character change in living fishes. Alternatively, these findings are consistent with the hypothesis that phenotypic 'evolvability'-the capacity of organisms to evolve-shapes the dynamics of speciation through time at the largest phylogenetic scales.
Molecular phylogenetics and evolution, 2013
We present a new hypothesis of tetraodontiform relationships based on 22 genes.We conduct Bayesia... more We present a new hypothesis of tetraodontiform relationships based on 22 genes.We conduct Bayesian and maximum likelihood analyses.This study supports the monophyly of all extant families.The study also reveals novel relationships among some of the families.Several morphological features need to be re-evaluated.Tetraodontiform fishes represent one of the most peculiar radiations of teleost fishes. In spite of this, we do not currently have a consensus on the phylogenetic relationships among the major tetraodontiform lineages, with different morphological and molecular datasets all supporting contrasting relationships. In this paper we present the results of the analysis of tetraodontiform interrelationships based on two mitochondrial and 20 nuclear loci for 40 species of tetraodontiforms (representing all of the 10 currently recognized families), as well as three outgroups. Bayesian and maximum likelihood analyses of the concatenated dataset (18.682 nucleotides) strongly support novel relationships among the major tetraodontiform lineages. Our results recover two large clades already found in mitogenomic analyses (although the position of triacanthids differ), while they strongly conflict with hypotheses of tetraodontiform relationships inferred by previous studies based on morphology, as well as studies of higher-level teleost relationships based on nuclear loci, which included multiple tetraodontiform lineages. A parsimony gene-tree, species-tree analysis recovers relationships that are mostly congruent with the analyses of the concatenated dataset, with the significant exception of the position of the pufferfish + porcupine fish clade. Our findings suggest that while the phylogenetic placement of some tetraodontiform lineages (triacanthids, molids) remains problematic even after sequencing 22 loci, an overall molecular consensus is beginning to emerge regarding the existence of several major clades. This new hypothesis will require a re-evaluation of the phylogenetic usefulness of several morphological features, such as the fusion of several jaw bones into a parrot-like beak, or the reduction and loss of some of the fins, which may have occurred independently more times than previously thought.
Molecular phylogenetics and evolution, 2013
We generated a phylogenetic hypothesis of balistoid fishes using 5 nuclear and mitochondrial gene... more We generated a phylogenetic hypothesis of balistoid fishes using 5 nuclear and mitochondrial genes.We time-calibrated the molecular phylogeny using several fossil calibrations.This study supports the monophyly of both extant families, as well as that of most balistid genera.Several monacanthid genera are shown to be non-monophyletic.The greater diversity of filefishes can be attributed to their more ancient crown age compared to triggerfishes.Balistoid fishes (triggerfishes, filefishes, leatherjackets) represent one of the most successful radiations of tetraodontiform fishes across the world’s oceans. Balistids (triggerfishes) are largely circumtropical in coral reef environments while most monacanthids (filefishes, leatherjackets) are distributed across reef and non-reef habitats in the Indo-western Pacific. Although members of these clades share a distinctive mode of locomotion that relies upon coordinated oscillation or undulation of enlarged dorsal and anal fins, species richness as well as morphologial and ecological diversity are generally considered to be higher in monacanthids than in triggerfishes. Explicit evolutionary comparisons of diversity patterns between these sister clades have been hampered by the paucity of systematic studies of filefishes relative to triggerfishes. Furthermore, a well-sampled molecular timescale for balistoids is lacking, hindering our understanding of the evolutionary history of these fishes. Here, we produce the largest balistoid molecular dataset to date, based on two mitochondrial and three nuclear loci, for a total of 86 species, and we time-calibrate it using three tetraodontiform fossils. We show that several of the traditional monacanthid genera are not monophyletic and that the balistid Xenobalistes tumidipectoris is nested within the genus Xanthichthys, and suggest that the generic name Xenobalistes be dissolved. Our timetree reveals a Late Miocene origin of balistids, in accordance with previous studies, but a Late Eocene age for the crown monacanthids, which experienced significant diversification during the Late Oligocene and Early Miocene. Comparative analyses reveal no significant family-level differences in rates of speciation or body size evolution, suggesting that the greater diversity of filefishes can be attributed to their more ancient crown age compared to triggerfishes.
Journal Of Evolutionary Biology
Habitat shifts are implicated as the cause of many vertebrate radiations, yet
relatively few emp... more Habitat shifts are implicated as the cause of many vertebrate radiations, yet
relatively few empirical studies quantify patterns of diversification following
colonization of new habitats in fishes. The pufferfishes (family Tetraodontidae)
occur in several habitats, including coral reefs and freshwater, which
are thought to provide ecological opportunity for adaptive radiation, and
thus provide a unique system for testing the hypothesis that shifts to new
habitats alter diversification rates. To test this hypothesis, we sequenced
eight genes for 96 species of pufferfishes and closely related porcupine
fishes, and added 19 species from sequences available in GenBank. We
time-calibrated the molecular phylogeny using three fossils, and performed
several comparative analyses to test whether colonization of novel habitats
led to shifts in the rate of speciation and body size evolution, central predictions
of clades experiencing ecological adaptive radiation. Colonization of
freshwater is associated with lower rates of cladogenesis in pufferfishes,
although these lineages also exhibit accelerated rates of body size evolution.
Increased rates of cladogenesis are associated with transitions to coral reefs,
but reef lineages surprisingly exhibit significantly lower rates of body size
evolution. These results suggest that ecological opportunity afforded by
novel habitats may be limited for pufferfishes due to competition with other
species, constraints relating to pufferfish life history and trophic ecology,
and other factors.
Ray-finned fishes constitute the dominant radiation of vertebrates with over 30,000 species. 9 Al... more Ray-finned fishes constitute the dominant radiation of vertebrates with over 30,000 species. 9 Although molecular phylogenetics has begun to disentangle major evolutionary relationships 10 within this vast section of the Tree of Life, there is no widely available approach for effi-11 ciently collecting phylogenomic data within fishes, leaving much of the enormous potential 12 of massively parallel sequencing technologies for resolving major radiations in ray-finned 13 fishes unrealized. Here, we provide a genomic perspective on longstanding questions regard-14 ing the diversification of major groups of ray-finned fishes through targeted enrichment of 15 ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow 16 efficiently and economically generates data sets that are orders of magnitude larger than 17 those produced by traditional approaches and is well-suited to working with museum speci-18 mens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and 19 deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus 20 (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging 21 teleost lineages. Divergence time estimation based upon 14 fossil calibrations reveals that 22 crown teleosts appeared 270 Ma at the end of the Permian and that elopomorphs, osteoglos-23 somorphs, ostarioclupeomorphs, and euteleosts diverged from one another by 205 Ma during 24 the Triassic. Our approach additionally reveals that sequence capture of UCE regions and 25 their flanking sequence offers enormous potential for resolving phylogenetic relationships 26 within ray-finned fishes. 27 2
Molecular phylogenetics and evolution, 2013
We present the most comprehensive time-calibrated, species-level hypothesis of the timing of Acan... more We present the most comprehensive time-calibrated, species-level hypothesis of the timing of Acanthuridae (surgeonfishes and allies) evolution based on 76% of the extant diversity and nine genes. We recover two major acanthurid clades, Nasinae and Acanthurinae, and infer a much more recent Nasinae crown age (17 Ma) compared to a previous dating study for Naso. The Acanthurinae represe nt an older group that originated $42 Ma, with most diversification occurri ng since the Early Miocene (beginning $21 Ma). Our results strongly support a paraphyletic Acanthurus and Ctenochaetus, with multiple analyses recoveri ng a clade grouping Ctenochaetus, A. nubilus and A. pyroferus . Contrary to previous studies, we also provide strong evidence that thick-walled, gizzard-like stomachs evolved only once within Acanthurus and that this morphology has a common origin in Acanthurus and Ctenochaetus. Based on our molecular analyses, in conjunction with the large body of morphological evidence, we recommen d dissolving the genus Ctenochaetus into the genus Acanthurus.
The American naturalist, 2013
Coral reef fishes represent one of the most spectacularly diverse assemblages of vertebrates on t... more Coral reef fishes represent one of the most spectacularly diverse assemblages of vertebrates on the planet, but our understanding of their mode of diversification remains limited. Here we test whether the diversity of the damselfishes (Pomacentridae), one of the most species-rich families of reef-associated fishes, was produced by a single or multiple adaptive radiation(s) during their evolutionary history. Tests of the tempo of lineage diversification using a timecalibrated phylogeny including 208 species revealed that crown pomacentrid diversification has not slowed through time as expected under a scenario of a single adaptive radiation resulting from an early burst of diversification. Evolutionary modeling of trophic traits similarly rejected the hypothesis of early among-lineage partitioning of ecologically important phenotypic diversity. Instead, damselfishes are shown to have experienced iterative convergent radiations wherein subclades radiate across similar trophic strategies (i.e., pelagic feeders, benthic feeders, intermediate) and morphologies. Regionalization of coral reefs, competition, and functional constraints may have fueled iterative ecological radiation and convergent evolution of damselfishes. Through the Pomacentridae, we illustrate that radiations may be strongly structured by the nature of the constraints on diversification.
Molecular phylogenetics and evolution, 2013
Boxfishes (superfamily Ostracioidea, order Tetraodontiformes) are comprised of 37 species within ... more Boxfishes (superfamily Ostracioidea, order Tetraodontiformes) are comprised of 37 species within the families Aracanidae (13 sp.) and Ostracidae (24 sp.). These species are characterized by several dramatic reductive trends in their axial and appendicular skeleton, and by the presence of a carapace formed by enlarged and thickened scale plates. While strong support exists for the monophyly of both families, interspecific relationships remain unclear as no species-level molecular phylogeny currently exists for either of these two clades, and the only hypotheses of relationships are based on morphological studies that were mostly restricted to generic-level relationships. Here we present the results of a new phylogenetic study of a dataset composed of 9 loci for 26 species of boxfishes using both likelihood and Bayesian methods. Our topology strongly supports the monophyly of both groups, and additionally provides strongly supported resolution for the vast majority of species-level interrelationships. Based on this new phylogeny, we suggest changing the taxonomic status of the species Lactoria fornasini to Tetrasomus fornasini, and Rhynchostracion nasus to Ostracion nasus. Using a Bayesian approach to divergence time estimation we inferred a Paleocene origin of the Ostracioidea, with an estimated origin of the reefassociated ostraciids spanning the Eocene and Oligocene, and a Miocene/Pliocene origin of the aracanids.
Evolutionary Biology, 2012
Evolution; international journal of organic evolution, 2011
of novel locomotion strategies on marine fish diversification remains largely unexplored. Using t... more of novel locomotion strategies on marine fish diversification remains largely unexplored. Using triggerfish as a case study, we determine whether the evolution of the distinctive synchronization of enlarged dorsal and anal fins that triggerfish use to swim may have catalyzed the ecological diversification of the group. By adopting a comparative phylogenetic approach to quantify median fin and body shape integration and to assess the tempo of functional and morphological evolution in locomotor traits, we find that: (1) functional and morphological components of the locomotive system exhibit a strong signal of correlated evolution;
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Papers by Francesco Santini
coral reef-associated lineages within the Carcharhinidae. Our new timetree suggests that the two major shark lineages leading to the extant shark diversity began diversifying mostly after the end-Permian mass extinction: the
squalimorphs into deepwater and the galeomorphs into shelf habitats. We suggest that the breakdown of the onshore–offshore speciation rate pattern in sharks is mediated by success in deepwater environments through ecological partitioning, and in some cases, the evolution of morphological novelty.
phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is
no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous
potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here,
we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned
fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our
workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by
traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a wellsupported
phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and
Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages.
Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous
potential for resolving phylogenetic relationships within ray-finned fishes.
relatively few empirical studies quantify patterns of diversification following
colonization of new habitats in fishes. The pufferfishes (family Tetraodontidae)
occur in several habitats, including coral reefs and freshwater, which
are thought to provide ecological opportunity for adaptive radiation, and
thus provide a unique system for testing the hypothesis that shifts to new
habitats alter diversification rates. To test this hypothesis, we sequenced
eight genes for 96 species of pufferfishes and closely related porcupine
fishes, and added 19 species from sequences available in GenBank. We
time-calibrated the molecular phylogeny using three fossils, and performed
several comparative analyses to test whether colonization of novel habitats
led to shifts in the rate of speciation and body size evolution, central predictions
of clades experiencing ecological adaptive radiation. Colonization of
freshwater is associated with lower rates of cladogenesis in pufferfishes,
although these lineages also exhibit accelerated rates of body size evolution.
Increased rates of cladogenesis are associated with transitions to coral reefs,
but reef lineages surprisingly exhibit significantly lower rates of body size
evolution. These results suggest that ecological opportunity afforded by
novel habitats may be limited for pufferfishes due to competition with other
species, constraints relating to pufferfish life history and trophic ecology,
and other factors.
coral reef-associated lineages within the Carcharhinidae. Our new timetree suggests that the two major shark lineages leading to the extant shark diversity began diversifying mostly after the end-Permian mass extinction: the
squalimorphs into deepwater and the galeomorphs into shelf habitats. We suggest that the breakdown of the onshore–offshore speciation rate pattern in sharks is mediated by success in deepwater environments through ecological partitioning, and in some cases, the evolution of morphological novelty.
phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is
no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous
potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here,
we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned
fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our
workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by
traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a wellsupported
phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and
Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages.
Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous
potential for resolving phylogenetic relationships within ray-finned fishes.
relatively few empirical studies quantify patterns of diversification following
colonization of new habitats in fishes. The pufferfishes (family Tetraodontidae)
occur in several habitats, including coral reefs and freshwater, which
are thought to provide ecological opportunity for adaptive radiation, and
thus provide a unique system for testing the hypothesis that shifts to new
habitats alter diversification rates. To test this hypothesis, we sequenced
eight genes for 96 species of pufferfishes and closely related porcupine
fishes, and added 19 species from sequences available in GenBank. We
time-calibrated the molecular phylogeny using three fossils, and performed
several comparative analyses to test whether colonization of novel habitats
led to shifts in the rate of speciation and body size evolution, central predictions
of clades experiencing ecological adaptive radiation. Colonization of
freshwater is associated with lower rates of cladogenesis in pufferfishes,
although these lineages also exhibit accelerated rates of body size evolution.
Increased rates of cladogenesis are associated with transitions to coral reefs,
but reef lineages surprisingly exhibit significantly lower rates of body size
evolution. These results suggest that ecological opportunity afforded by
novel habitats may be limited for pufferfishes due to competition with other
species, constraints relating to pufferfish life history and trophic ecology,
and other factors.