Giorgio Carnevale

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

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.

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

BackgroundOne of the main explanations for the stunning diversity of teleost fishes (~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.ResultsHere 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.ConclusionTeleosts 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.

New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha)

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 Miya et al. (2005) 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.

A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy

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 represent an older group that originated ~42 Ma, with most diversification occurring since the Early Miocene (beginning ~21 Ma). Our results strongly support a paraphyletic Acanthurus and Ctenochaetus, with multiple analyses recovering 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 recommend dissolving the genus Ctenochaetus into the genus Acanthurus.

VOLHYNIAN (EARLY SARMATIAN SENSU LATO) FISHES FROM TSUREVSKY, NORTH CAUCASUS, RUSSIA

Abstract A new fish fauna is described from the late Middle Miocene (Volhynian; early Sarmatian sensu lato) of Tsurevsky, North Caucasus, Russia. Ten taxa belonging to nine families are described, of which two may be new (Micromesistius sp., Bothus sp.), but not formally described awaiting better-preserved material. The predominant faunal element is Sardinella sardinites, including more than 42% of all investigated specimens. The paleoecological analysis reveals a semienclosed marine environment not far from the coast, characterized by shallow depths and a soft bottom. The sedimentological features of the deposits and the preservation of the specimens suggest that periodic oxygen minima affected the bottom waters, causing repeated hypoxic events, probably related to the decay of organic matter previously accumulated in the basin. Paleoenvironmental considerations of fish faunas from several Paratethyan localities suggest that marine waters characterized by a little shift in chemical composition (high alkalinity) filled up the entire basin during the Sarmatian.

The first fossil ribbonfish (Teleostei, Lampridiformes, Trachipteridae)

Abstract – The first fossil ribbonfish, Trachipterus mauritanicus sp. nov., based on a single specimen,is described from Sidi-Brahim, an Upper Miocene (Messinian) locality situated in the central sectorof the Chelif Basin, northwestern Algeria. Trachipterus mauritanicus sp. nov. is characterized by aflattened neurocranium and an advanced insertion of the dorsal fin. Based on skeletal morphology, T. mauritanicus sp. nov. appears to be related to T. arawatae and T. trachypterus . Trachipterusmauritanicus sp. nov. represents the eighth taxon described up to now from Sidi-Brahim. TheoccurrenceofthefirstfossilmemberofthefamilyTrachipteridaefromtheUpperMiocenesedimentsofnorthwesternAlgeriaemphasizesthecrucialimportanceoftheMessinianichthyofaunasfromAlgeriato our knowledge of the fossil record of the Teleostei.Keywords: Teleostei, Lampridiformes, Trachipterus mauritanicus sp. nov., Miocene, Algeria. 1. Introduction TheLampridiformesareagroupofexclusivelymarinefishes with a poor fossil record dating from to LateCretaceous. They consist 12 living genera included inseven families. All living lampridiforms are coastal orpelagic in temperate and tropical seas. This group ischaracterized by an extreme morphological disparity,and it includes some of the most bizarre vertebratespecies. One of the most peculiar representative ofthe order is the oarfish,

A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes).

Anguilliformes are an ecologically diverse group of predominantly marine fishes whose members are easily recognized by their extremely elongate bodies, and universal lack of pelvic fins. Recent studies based on mitochondrial loci, including full mitogenomes, have called into question the monophyly of both the Anguilliformes, which appear to be paraphyletic without the inclusion of the Saccopharyngiformes (gulper eels and allies), as well as other more commonly known eel families (e.g., Congridae, Serrivomeridae). However, no study to date has investigated anguilliform interrelationships using nuclear loci. Here we present a new phylogenetic hypothesis for the Anguilliformes based on five markers (the nuclear loci Early Growth Hormone 3, Myosin Heavy Polypeptide 6 and Recombinase Activating Gene 1, as well as the mitochondrial genes Cytochrome b and Cytochrome Oxidase I). Our sampling spans 148 species and includes 19 of the 20 extant families of anguilliforms and saccopharyngiforms. Maximum likelihood analysis reveals that saccopharyngiform eels are deeply nested within the anguilliforms, and supports the non-monophyly of Congridae and Nettastomatidae, as well as that of Derichthyidae and Chlopsidae. Our analyses suggest that Protanguilla may be the sister group of the Synaphobranchidae, though the recent hypothesis that this species is the sister group to all other anguilliforms cannot be rejected. The molecular phylogeny, time-calibrated using a Bayesian relaxed clock approach and seven fossil calibration points, reveals a Late Cretaceous origin of this expanded anguilliform clade (stem age ~116 Ma, crown age ~99 Ma). Most major (family level) lineages originated between the end of the Cretaceous and Early Eocene, suggesting that anguilliform radiation may have been facilitated by the recovery of marine ecosystems following the KP extinction.

Bellwoodilabrus landinii n. gen., n. sp., a new genus and species of labrid fish (Teleostei, Perciformes) from the Eocene of Monte Bolca

ABSTRACT 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 ethimoid-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.

An Eocene anchovy from Monte Bolca, Italy: The earliest known record for the family Engraulidae

Engraulids, also known as anchovies, are a distinctive group of clupeoid fishes characterized by a series of derived morphological features of the snout and infraorbital bones, suspensorium and branchial arches. Although anchovies are very abundant today, they are scarcely represented in the fossil record. A new genus and species of anchovy, † Eoengraulis fasoloi gen. et sp. nov., is described from the Eocene (late Ypresian, c . 50 Ma) locality of Monte Bolca, Italy. It is based on a single well-preserved articulated skeleton that exhibits a unique combination of characters that supports its recognition as a new genus of the family Engraulidae, including: nine branchiostegal rays; 40 preural vertebrae and 17 pairs of pleural ribs; pleural ribs – preural vertebrae ratio 0.42; seven supraneurals; dorsal-fin origin at about mid-length of the body; about 16 dorsal-fin rays; anal-fin origin slightly behind the base of the last dorsal-fin ray; 19 anal-fin rays; seven pelvic-fin rays; and small needle-like pre-pelvic scutes. The morphological structure of the single available specimen suggests that † Eoengraulis fasoloi is the sister taxon of all other engrauline taxa. † Eoengraulis fasoloi is the oldest member of the family Engraulidae known to date. This taxon suggests that the earliest phases of diversification of engrauline anchovies probably occurred in the coastal palaeobiotopes of the western Tethys during Eocene time.

The Eocene sardine †Bolcaichthys catopygopterus (Woodward, 1901) from Monte Bolca, Italy: osteology, taxonomy, and paleobiology

ABSTRACT Clupeid fishes are abundant in the Eocene fossiliferous limestone of Monte Bolca, representing by far the most common group from this celebrated locality. However, despite of their abundance, the clupeid fishes from Monte Bolca have seldom been investigated. An analysis of about 300 well-preserved clupeid specimens from Monte Bolca housed in several institutions clearly indicates that more than 95% of the available material belongs to different developmental stages of a single taxon, traditionally referred to as †Clupea catopygoptera Woodward. †Bolcaichthys, a new genus of clupeid fish, erected to contain †Clupea catopygoptera Woodward from the Eocene of Monte Bolca, Italy, is described and compared with extant and fossil genera of the family Clupeidae. This new genus shows a unique combination of characters (head length approximately one third to one quarter standard length; skull roof with 10–14 frontoparietal striae; mouth terminal; two supramaxillae; edentulous jaws and palate; complete series of about 20–22 abdominal keeled scutes with ascending arms; no dorsal scutes; five or six branchiostegal rays; eight supraneurals; 40–42 vertebrae and 20–22 pleural ribs; three epurals) supporting its recognition as a new genus of the family Clupeidae. Paleobiological considerations suggest that the presence of a very large number of schooling clupeids belonging to the genus †Bolcaichthys at all stages of development (larval, juvenile, and adult) support the hypothesis that the sediments were deposited close to the coast in a context subject to the ecological influence of the open sea.