A correction corrected: consensus over the meaning of Crocodylia and why it matters

Lost to the Sea: Predicted Climate Change Threats to Saltwater Crocodile Nesting Habitat

Climate change is predicted to have devastating impacts on apex predators such as eliminating their required habitats. Crocodilians are no exception as most species require freshwater for nesting, and such freshwater habitats are particularly vulnerable to saltwater inundation (SWI) caused by the sea level rise (SLR) from global warming. Here, we examined the impacts of climate change on saltwater crocodiles Crocodylus porosus in terms of the potential loss of nesting habitat in the Northern Territory, Australia; an area that contains the world’s most extensive nesting habitat for the species. Our spatial model, derived from 730 nest locations and selected environmental features, estimated a total of 32,306.91 km2 of current suitable habitat across the study region. The most important variable was distance to perennial lakes (71.0% contribution, 87.5% permutation importance), which is negatively correlated with nesting habitat suitability. We found that projected changes in temperature and rainfall by 2100 could impact the area of suitable nesting habitat negatively or positively (0.33% decrease under low future emission climate scenario, and 32.30% increase under high emission scenario). Nevertheless, this can be canceled by the strong negative impact of SLR and concomitant SWI on nesting areas. A portion (16.40%) of the modeled suitable habitat for a subsection of our study area, the Kakadu Region, were already subject to > 0.25 m SWI in 2013. The suitable area for nesting in this region is predicted to be further reduced to 1775.70 km2 with 1.1 m SLR predicted for 2100, representing 49.81% loss between 2013 and 2100. Although the estimates of habitat loss do not account for the potential creation of new habitat, nor for the uncertainty in the degree of future SLR, our results suggest that SLR driven by continuing global warming can be the major threat to mound-nest-building crocodilians including C. porosus, rather than direct impacts from changes in temperature and rainfall. The degree of impact on saltwater crocodiles will be determined by the interplay between the loss of nesting habitat, which would appear inevitable under current global warming, and the ability to expand into new areas created by the expansion of the tropics.

Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids ('thoracosaurs') are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a 'basal' alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous-early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition

Since their origin in the Late Triassic, crocodylomorphs have had a long history of evolutionary change. Numerous studies examined their phylogeny, but none have attempted to unify their morphological characters into a single, combined dataset. Following a comprehensive review of published character sets, we present a new dataset for the crocodylomorph clade Neosuchia consisting of 569 morphological characters for 112 taxa. For the first time in crocodylian phylogenetic studies, quantitative variation was treated as continuous data (82 characters). To provide the best estimate of neosuchian relationships, and to investigate the origins of longirostry, these data were analysed using a variety of approaches. Our results show that equally weighted parsimony and Bayesian methods cluster unrelated longirostrine forms together, producing a topology that conflicts strongly with their stratigraphic distributions. By contrast, applying extended implied weighting improves stratigraphic congruence and removes longirostrine clustering. The resulting topologies resolve the major neosuchian clades, confirming several recent hypotheses regarding the phylogenetic placements of particular species (e.g. Baryphracta deponiae as a member of Diplocynodontinae) and groups (e.g. Tethysuchia as non-eusuchian neosuchians). The longirostrine condition arose at least three times independently by modification of the maxilla and premaxilla, accompanied by skull roof changes unique to each longirostrine clade.

The evolution of the meatal chamber in crocodyliforms

The unique outer ear of crocodylians consists of a large meatal chamber (MC) concealed by a pair of muscular earlids that shape a large part of the animal's head. This chamber is limited medially by the enlarged tympanic membrane. Yet, the anatomy of this distinctive and complex region is underexplored and its evolutionary history untraced. The osteology and soft tissues of the MC in extant crocodylians was analysed to describe it and establish osteological correlates within this region. A broad survey of the osteological correlates was conducted in major clades of fossil crocodyliforms to estimate evolutionary trends of the MC. The reorganization of the MC at the origin of crocodyliforms includes characters also present in more basal taxa such as 'sphenosuchians' as well as unique traits of crocodyliforms. Three major patterns are recognized in the MC of basal mesoeucrocodylians. The distinct 'thalattosuchian pattern' indicates that extensive modifications occurred in this clade of aquatic fossil crocodyliforms, even when multiple alternative phylogenetic positions are taken into account. Some traits already established in putative closely related clades are absent or modified in this group. The 'basal notosuchian/sebecian pattern' is widespread among basal metasuchians, and establishes for the first time characters maintained later in neosuchians and extant forms. The 'advanced notosuchian pattern' includes modifications of the MC possibly related to a terrestrial lifestyle and potentially a structure analogous to the mammalian pinna. The main variation in the MC of neosuchians is associated with the homoplastic secondary opening of the cranioquadrate passage. The inferred phylogenetic trends in the crocodyliform MC suggest the great anatomical disparity in this region followed a complex evolutionary pattern, and tympanic hearing played an important role in the origin and diversification of Crocodyliformes.

The first definitive Middle Jurassic atoposaurid (Crocodylomorpha, Neosuchia), and a discussion on the genus Theriosuchus

Atoposaurids were a clade of semiaquatic crocodyliforms known from the Late Jurassic to the latest Cretaceous. Tentative remains from Europe, Morocco, and Madagascar may extend their range into the Middle Jurassic. Here we report the first unambiguous Middle Jurassic (late Bajocian–Bathonian) atoposaurid: an anterior dentary from the Isle of Skye, Scotland, UK. A comprehensive review of atoposaurid specimens demonstrates that this dentary can be referred to Theriosuchus based on several derived characters, and differs from the five previously recognized species within this genus. Despite several diagnostic features, we conservatively refer it to Theriosuchus sp., pending the discovery of more complete material. As the oldest known definitively diagnostic atoposaurid, this discovery indicates that the oldest members of this group were small‐bodied, had heterodont dentition, and were most likely widespread components of European faunas. Our review of mandibular and dental features in atoposaurids not only allows us to present a revised diagnosis of Theriosuchus, but also reveals a great amount of variability within this genus, and indicates that there are currently five valid species that can be differentiated by unique combinations of dental characteristics. This variability can be included in future broad‐scale cladistics analyses of atoposaurids and closely related crocodyliforms, which promise to help untangle the complicated taxonomy and evolutionary history of Atoposauridae.  © 2015 The Authors. Zoological Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of The Linnean Society of London

Diversification events and the effects of mass extinctions on Crocodyliformes evolutionary history

The rich fossil record of Crocodyliformes shows a much greater diversity in the past than today in terms of morphological disparity and occupation of niches. We conducted topology-based analyses seeking diversification shifts along the evolutionary history of the group. Our results support previous studies, indicating an initial radiation of the group following the Triassic/Jurassic mass extinction, here assumed to be related to the diversification of terrestrial protosuchians, marine thalattosuchians and semi-aquatic lineages within Neosuchia. During the Cretaceous, notosuchians embodied a second diversification event in terrestrial habitats and eusuchian lineages started diversifying before the end of the Mesozoic. Our results also support previous arguments for a minor impact of the Cretaceous/Palaeogene mass extinction on the evolutionary history of the group. This argument is not only based on the information from the fossil record, which shows basal groups surviving the mass extinction and the decline of other Mesozoic lineages before the event, but also by the diversification event encompassing only the alligatoroids in the earliest period after the extinction. Our results also indicate that, instead of a continuous process through time, Crocodyliformes diversification was patchy, with events restricted to specific subgroups in particular environments and time intervals.

Revision of the Late Jurassic crocodyliform Alligatorellus, and evidence for allopatric speciation driving high diversity in western European atoposaurids

Atoposaurid crocodyliforms represent an important faunal component of Late Jurassic to Early Cretaceous Laurasian semi-aquatic to terrestrial ecosystems, with numerous spatiotemporally contemporaneous atoposaurids known from western Europe. In particular, the Late Jurassic of France and Germany records evidence for high diversity and possible sympatric atoposaurid species belonging to Alligatorellus, Alligatorium and Atoposaurus. However, atoposaurid taxonomy has received little attention, and many species are in need of revision. As such, this potentially high European diversity within a narrow spatiotemporal range might be a taxonomic artefact. Here we provide a taxonomic and anatomical revision of the Late Jurassic atoposaurid Alligatorellus. Initially described as A. beaumonti from the Kimmeridgian of Cerin, eastern France, additional material from the Tithonian of Solnhofen, south-eastern Germany, was subsequently referred to this species, with the two occurrences differentiated as A. beaumonti beaumonti and A. beaumonti bavaricus, respectively. We provide a revised diagnosis for the genus Alligatorellus, and note a number of anatomical differences between the French and German specimens, including osteoderm morphology and the configuration and pattern of sculpting of cranial elements. Consequently, we restrict the name Alligatorellus beaumonti to include only the French remains, and raise the rank of the German material to a distinct species: Alligatorellus bavaricus. A new diagnosis is provided for both species, and we suggest that a recently referred specimen from a coeval German locality cannot be conclusively referred to Alligatorellus. Although it has previously been suggested that Alligatorellus, Alligatorium and Atoposaurus might represent a single growth series of one species, we find no conclusive evidence to support this proposal, and provide a number of morphological differences to distinguish these three taxa that appear to be independent of ontogeny. Consequently, we interpret high atoposaurid diversity in the Late Jurassic island archipelago of western Europe as a genuine biological signal, with closely related species of Alligatorellus, Alligatorium and Atoposaurus in both French and German basins providing evidence for allopatric speciation, potentially driven by fluctuating highstand sea levels.

Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation

Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted crocodile (Mecistops cataphractus) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation probability was assessed by using 11 mitochondrial and nuclear genes, and cranial morphology for over 100 specimens, representing the full geographical extent of the species distribution. Molecular Bayesian and phylogenetic species delimitation showed unanimous support for two Mecistops species isolated to the Upper Guinean and Congo (including Lower Guinean) biomes that were supported by 13 cranial characters capable of unambiguously diagnosing each species. Fossil-calibrated phylogenetic reconstruction estimated that the species split ± 6.5-7.5 Ma, which is congruent with intraspecies divergence within the sympatric crocodile genus Osteolaemus and the formation of the Cameroon Volcanic Line. Our results underscore the necessity of comprehensive phylogeographic analyses within currently recognized taxa to detect cryptic species within the Crocodylia. We recommend that the community of crocodilian researchers reconsider the conceptualization of crocodilian species especially in the light of the conservation ramifications for this economically and ecologically important group.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

Survival of Theriosuchus (Mesoeucrocodylia: Atoposauridae) in a Late Cretaceous archipelago: a new species from the Maastrichtian of Romania

Small terrestrial non-eusuchian mesoeucrocodylians are common components of Cretaceous assemblages of Gondwanan provinces with notosuchians and araripesuchids as flagship taxa in South America, Africa and Madagascar, well into the Late Cretaceous. On the other hand, these are exceedingly rare in Laurasian landmasses during the Late Cretaceous. Small terrestrial mesoeucrocodylians from Europe were often referred to the genus Theriosuchus, a taxon with stratigraphic range extending from the Late Jurassic to the late Early Cretaceous. Theriosuchus is abundantly reported from various European localities, although Asiatic and possibly North American members are also known. It has often been closely associated with the first modern crocodilians, members of the Eusuchia, because of the presence of procoelous vertebrae, a widespread key character diagnosing the Eusuchia. Nevertheless, the relationships of Theriosuchus have not been explored in detail although one species, Theriosuchus pusillus, has been extensively described and referred in numerous works. Here, we describe a new basal mesoeucrocodylian, Theriosuchus sympiestodon sp. nov. from the Maastrichtian of the Haţeg Basin, Romania, suggesting a large temporal gap (about 58 myr) in the fossil record of the genus. Inclusion of the new taxon, along with Theriosuchus guimarotae, in a phylogenetic analysis confirms its referral to the genus Theriosuchus, within a monophyletic atoposaurid clade. Although phylogenetic resolution within this clade is still poor, the new taxon appears, on morphological grounds, to be most closely related to T. pusillus. The relationships of Atoposauridae within Mesoeucrocodylia and especially to Neosuchia are discussed in light of the results of the present contribution as well as from recent work. Our results raise the possibility that Atoposauridae might not be regarded as a derived neosuchian clade anymore, although further investigation of the neosuchian interrelationships is needed. Reports of isolated teeth referable to a closely related taxon from the Upper Cretaceous of Romania and France, together with the presence of Doratodon and Ischyrochampsa, indicate a previously unsuspected diverse assemblage of non-eusuchian mesoeucrocodylians in the Late Cretaceous European archipelago.

Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution

BACKGROUND

Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water.

METHODOLOGY/PRINCIPAL FINDINGS

We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, Creodonta, Lipotyphla, and the raoellid artiodactylan Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to Indohyus, with Mesonychia outside of Artiodactyla. The relationships of Mesonychia and Indohyus are highly unstable, however--in trees only two steps longer than minimum length, Mesonychia falls inside Artiodactyla and displaces Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result.

CONCLUSIONS/SIGNIFICANCE

Integration of new fossil material of Indohyus impacts placement of another extinct clade Mesonychia, pushing it much farther down the tree. The phylogenetic position of Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales+hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup.