Tip-dating Analysis Research Articles

Phylogenetic and taxonomic revisions of Jurassic sea stars support a delayed evolutionary origin of the Asteriidae.

The superorder Forcipulatacea is a major clade of sea stars with approximately 400 extant species across three orders (Forcipulatida, Brisingida, Zorocallida). Over the past century, the systematics of Forcipulatacea have undergone multiple revisions by various authors, with some considering numerous families such as Asteriidae, Zoroasteridae, Pedicellasteridae, Stichasteridae, Heliasteridae, Labidiasteridae, and Neomorphasteridae, while others recognized only two families (i.e., Asteriidae and Zoroasteridae). Recent molecular analyses have shown the artificial nature of some of these groupings. Notably, four well-supported clades (Zorocallida, Brisingida, Stichasteridae, and Asteriidae) emerged from a synthesis of morphological and molecular evidence. The majority of extinct forcipulatacean species have been placed in modern families. However, many of these fossil species are in need of revision, especially those species placed within the Asteriidae, the largest of all forcipulatacean families. In light of recent advancements in forcipulatacean systematics, we comprehensively reassess six well-preserved Jurassic forcipulatacean taxa, including the earliest crown-group members from the Hettangian (∼201.4 Ma), and also describe two new Jurassic genera, Forbesasterias gen. nov. and Marbleaster gen. nov. We assembled the largest and most comprehensive phylogenetic matrix for this group, sampling 42 fossil and extant forcipulatacean species for 120 morphological characters. To infer phylogenetic relationships and construct an evolutionary timeline for the diversification of major clades, we conducted a Bayesian tip-dating analysis incorporating the fossilized birth-death process. A total of 13 fossil species were sampled in our analysis, including six taxonomically revaluated herein, two recently reappraised species from the Jurassic, and five additional species from the Cretaceous and Miocene. Contrary to prior assumptions, our results indicate that none of the Jurassic taxa investigated belong to Asteriidae or any other modern families, and instead represent stem-forcipulatids. Furthermore, our phylogenetic results suggest that Asteriidae likely originated during the late Cretaceous. Our findings highlight a greater early diversity within the Forcipulatacea than previously presumed, challenging existing perceptions of the evolutionary history of this significant clade of marine invertebrates.

Oldest record of a crown anomaluroid rodent from sub-Saharan Africa: a new genus and species from the early Oligocene Topernawi formation of northern Kenya

ABSTRACT Anomaluroid rodents (i.e. Anomaluridae + Zenkerellidae) have a long evolutionary history in Africa dating back to at least the middle Eocene, but Palaeogene fossil members of the anomaluroid crown group have never been found south of the Sahara. Here, we describe the oldest crown anomaluroid from sub-Saharan Africa, Eliwourus topernawiensis (new genus and species) from the early Oligocene Topernawi Formation of northern Kenya. Bayesian phylogenetic tip-dating analysis of a combined molecular-morphological dataset places ~29.5 Ma Eliwourus as an advanced stem anomalurid, and suggests that crown Anomaluridae originated ~28.2 Ma. The gliding behaviour seen in all crown anomalurids had, therefore, likely evolved before the close of the early Oligocene. Bayesian geocoordinates analysis places the origin of crown Anomaluroidea (~47.2 Ma) in northern Africa, and identifies a stem anomalurid dispersal into equatorial eastern Africa in the latest Eocene or earliest Oligocene. We present the first quantitative analysis of the pace of anomaluroid dental evolution and confirm a remarkably slow or bradytelic rate of phenotypic change, despite significant transformations in postcranial morphology related to the evolution of gliding behaviour during the same interval. The Topernawi area was evidently sufficiently forested during the early Oligocene to support both arboreal rodents and primates.

Tip dating and Bayes factors provide insight into the divergences of crown bird clades across the end-Cretaceous mass extinction.

The origin of crown birds (Neornithes) remains contentious owing to conflicting divergence time hypotheses obtained from alternative sources of data. The fossil record suggests limited diversification of Neornithes in the Late Mesozoic and a substantial radiation in the aftermath of the Cretaceous-Palaeogene (K-Pg) mass extinction, approximately 66 Ma. Molecular clock studies, however, have yielded estimates for neornithine origins ranging from the Early Cretaceous (130 Ma) to less than 10 Myr before the K-Pg. We use Bayes factors to compare the fit of node ages from different molecular clock studies to an independent morphological dataset. Our results allow us to reject scenarios of crown bird origins deep in the Early Cretaceous, as well as an origin of crown birds within the last 10 Myr of the Cretaceous. The scenario best supported by our analyses is one where Neornithes originated between the Early and Late Cretaceous (ca 100 Ma), while numerous divergences within major neoavian clades either span or postdate the K-Pg. This study affirms the importance of the K-Pg on the diversification of modern birds, and the potential of combined-evidence tip-dating analyses to illuminate recalcitrant 'rocks versus clocks' debates.

Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches

There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8–27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.

A new early diverging thalattosuchian (Crocodylomorpha) from the Early Jurassic (Pliensbachian) of Dorset, U.K. and implications for the origin and evolution of the group

ABSTRACT Among archosaurs, thalattosuchian crocodylomorphs experienced the most extensive adaptations to the marine realm. Despite significant attention, the phylogenetic position of the group remains uncertain. Thalattosuchians are either the sister-group to Crocodyliformes, basal mesoeucrocodylians, or nest among longirostrine neosuchians. The earliest definite thalattosuchians are Toarcian, and already possess many synapomorphies of the group. All phylogenetic hypotheses imply a ghost lineage extending at least to the Sinemurian, and a lack of older or more plesiomorphic forms may contribute to the uncertain phylogenetic placement of the group. Here we describe a new species, Turnersuchus hingleyae, gen. et sp. nov., from the early Pliensbachian Belemnite Marl Member of the Charmouth Mudstone Formation (Dorset, U.K.). The specimen includes partially articulated cranial, mandibular, axial, and appendicular elements. It can be attributed to Thalattosuchia based on the following features: distinct fossa on the posterolateral corner of the squamosal; broad ventrolateral process of the otoccipital covering the dorsal surface of the quadrate; large supratemporal fenestrae lacking a flattened skull table; broadly exposed prootic; orbital process of quadrate lacking bony attachment with the braincase. This specimen represents the earliest thalattosuchian currently known from diagnostic material. Phylogenetic analyses of two published datasets recover Turnersuchus as the earliest diverging thalattosuchian, and sister to Teleosauroidea + Metriorhynchoidea. Bayesian tip-dating analyses suggest a Rhaetian or Sinemurian divergence of Thalattosuchia from other crocodylomorphs, depending on topology, with confidence intervals spanning from the Norian to the Pliensbachian. The new specimen extends the fossil record of Thalattosuchia, but the time-scaling analyses demonstrate that a significant ghost lineage remains.

Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models

AbstractPhylogenetic relationships among sloths (Folivora) have been extensively studied in the past few decades using maximum parsimony approaches. Recently, Bayesian phylogenetic methods also began to be employed for this task, with advances in methods for data partitioning and tip-dating analyses leading to exciting new possibilities in morphological phylogenetics. In this context, we assembled the largest morphological data set ever applied to sloths and reassessed their phylogeny and divergence times, evaluating alternative models of partitioning and dating in a Bayesian framework. The updated phylogeny of sloths is largely in agreement with previous morphological studies, with Bradypus recovered as sister to Eufolivora, the presence of two major sloth clades (Mylodontoidea and Megatherioidea) and Choloepus among Megalonychidae. However, the present study yields some important advances in understanding the relationships of genera with historically unresolved or controversial allocations. The major sloth clades diversified from the Late Eocene to the Early Miocene. Homoplasy-based partition models outperformed anatomical partitioning and unpartitioned analyses, with considerable impacts on topology and posterior probabilities. Estimates obtained using homoplasy-partitioned models with Bayesian analyses were in strong agreement with those of maximum parsimony. We emphasize the importance of model comparison with Bayes factors and the assessment of synapomorphies in Bayesian morphological phylogenetics.

The rapid evolution of lungfish durophagy

Innovations relating to the consumption of hard prey are implicated in ecological shifts in marine ecosystems as early as the mid-Paleozoic. Lungfishes represent the first and longest-ranging lineage of durophagous vertebrates, but how and when the various feeding specializations of this group arose remain unclear. Two exceptionally preserved fossils of the Early Devonian lobe-finned fish Youngolepis reveal the origin of the specialized lungfish feeding mechanism. Youngolepis has a radically restructured palate, reorienting jaw muscles for optimal force transition, coupled with radiating entopterygoid tooth rows like those of lungfish toothplates. This triturating surface occurs in conjunction with marginal dentition and blunt coronoid fangs, suggesting a role in crushing rather than piercing prey. Bayesian tip-dating analyses incorporating these morphological data indicate that the complete suite of lungfish feeding specializations may have arisen in as little as 7 million years, representing one of the most striking episodes of innovation during the initial evolutionary radiations of bony fishes.

A new Pleistocene Ctenomys and divergence dating of the hyperdiverse South American rodent family Ctenomyidae

The South American Ctenomys is the most speciose genus among both hystricomorphs and subterranean rodents of the world. Here, we present the most exhaustive phylogenies and timetree of living and extinct Ctenomys attempted thus far. We describe Ctenomys rusconii sp. nov., a small-sized species from the upper Early Pleistocene of central Argentina. We analyse its cranial and mandibular shape as well as its phylogenetic position in the context of other extinct Ctenomys and a wide sample of living species. A parsimony analysis shows that Ctenomys rusconii sp. nov. integrates the stem group of Ctenomys together with late Pliocene to Middle Pleistocene species, while the crown group comprises only Middle Pleistocene to recent representatives. Within the crown Ctenomys, nine well-supported major clades were recovered, eight of which are consistent with previously recognized extant species groups. A Bayesian tip-dating analysis provided divergence age estimates of 3.8 Ma and 1.3 Ma for the origin of the genus and the crown clade, respectively. Remarkably, the extinct species recovered as members of the crown clade, i.e. C. dasseni, C. kraglievichi, C. subassentiens and C. viarapaensis, were clustered into the earliest diverging clade corresponding to the frater species group. Age estimates for the divergence of the crown and its major clades are markedly younger than what has been generally considered so far, which implies a new view on the timing of taxonomic, ecological and geographical diversification of the genus. Even considering that this interpretation is affected by biases inherent to the fossil record, the phylogenetic delimitation of the crown clade as restricted to species recorded since the Middle Pleistocene seems to configure a pattern underlain by a fast and late cladogenesis. http://zoobank.org/urn:lsid:zoobank.org:pub:14D8C3B2-CD37-4F30-84A2-14FDC20F1193

Radiation and Divergence Times of Batoidea

ABSTRACT We present a time-scaled analysis based on morphological characters to estimate the divergence ages for the major batoid clades. Two approaches were used: tip-dating, which allows the extinct taxa to be included as terminals, assessing the phylogenetic relations and their divergence time simultaneously; and basic and minimum branch length (‘a posteriori’ methods) that date a pre-existing unscaled topology, given a set of stratigraphic data for the taxa involved. We used stratigraphic indexes to compare the divergence ages recovered by both methods. The tip-dating approach obtained a more resolved topology and slightly better stratigraphic index scores than the other methods. Overall the tip-dating analysis recovered slightly earlier divergence ages than the rest of the time dating analyses and the known fossil record of the groups. However, these divergence ages were not as old as those estimated by molecular analysis. Our results suggest the diversity increase through the Late Jurassic–Early Cretaceous might not be gradual, and that Early Cretaceous diversity could be significantly higher. As several divergence events are placed in the Early Cretaceous, there is a suggestion that an active period of cladogenesis leads to the Late Cretaceous high diversity. The last divergence events recovered by the present analysis occurred in the Paleogene and led to the extant groups of batoids.

A Total Evidence Phylogenetic Analysis of Pinniped Phylogeny and the Possibility of Parallel Evolution Within a Monophyletic Framework

In the present study, a series of phylogenetic analyses of morphological, molecular, and combined morphological-molecular datasets were conducted to investigate the relationships of 23 extant and 44 fossil caniforme genera, in order to test the phylogenetic position of putative stem pinniped Puijila within a comprehensive evolutionary framework. With Canis as an outgroup, a Bayesian Inference analysis employing tip-dating of a combined molecular-morphological (i.e., Total Evidence) dataset recovered a topology in which musteloids are the sister group to a monophyletic pinniped clade, to the exclusion of ursids, and recovered Puijila and Potamotherium along the stem of Pinnipedia. A similar topology was recovered in a parsimony analysis of the same dataset. These results suggest the pinniped stem may be expanded to include additional fossil arctoid taxa, including Puijila, Potamotherium, and Kolponomos. The tip-dating analysis suggested a divergence time between pinnipeds and musteloids of ~45.16 million years ago (Ma), though a basal split between otarioids and phocids is not estimated to occur until ~26.52 Ma. These results provide further support for prolonged freshwater and nearshore phases in the evolution of pinnipeds, prior to the evolution of the extreme level of aquatic adaptation displayed by extant taxa. Ancestral character state reconstruction was used to investigate character evolution, to determine the frequency of reversals and parallelisms characterizing the three extant clades within Pinnipedia. Although the phylogenetic analyses did not directly provide any evidence of parallel evolution within the pinniped extant families, it is apparent from the inspection of previously-proposed pinniped synapomorphies, within the context of a molecular-based phylogenetic framework, that many traits shared between extant pinnipeds have arisen independently in the three clades. Notably, those traits relating to homodonty and limb-bone specialization for aquatic locomotion appear to have multiple origins within the crown group, as suggested by the retention of the plesiomorphic conditions in early-diverging fossil members of the three extant families. Thus, while the present analysis identifies a new suite of morphological synapomorphies for Pinnipedia, the frequency of reversals and other homoplasies within the clade limit their diagnostic value.

Revision of Oligocene ‘Paraphiomys’ and an origin for crown Thryonomyoidea (Rodentia: Hystricognathi: Phiomorpha) near the Oligocene–Miocene boundary in Africa

Abstract‘Paraphiomys’ simonsi is a phiomorph rodent from the early Oligocene of Egypt (~29–30 Mya) that has historically been aligned with much younger (< ~20 Mya) Miocene species of the genera Paraphiomys and Neosciuromys. Here, we use Bayesian tip-dating analysis of a 109-character morphological matrix containing 57 living and extinct ctenohystricans to test these proposed placements for ‘Paraphiomys’ simonsi. Our analyses provide support for the exclusion of ‘Paraphiomys’ simonsi from both Paraphiomys and Neosciuromys and justify the establishment of a new genus (Monamys gen. nov.) for this stem thryonomyoid. These analyses also indicate that the divergence of the extant dassie rat Petromus from the extant cane rat Thryonomys (i.e. origin of crown Thryonomyoidea) occurred ~23.7 Mya, close to the Oligocene–Miocene boundary and in close agreement with recent molecular estimates for this split. Miocene Neosciuromys, Paraulacodus, Protohummus and the type species of Paraphiomys are identified as stem thryonomyids, whereas the Namibian species Apodecter stromeri, Tufamys woodi, ‘Paraphiomys’ australis and ‘Paraphiomys’ roessneri are identified for the first time as stem petromurids, raising the possibility of a long period of endemic petromurid evolution in south-west Africa. Comparison of molecular divergence estimates with our optimal tip-dated topology suggests that stem bathyergoids are most likely to have arisen from late Eocene and early Oligocene ‘phiomyids’.

Paleogene mammalian fauna exchanges and the paleogeographic pattern in Asia

Mammals are the most important elements in Cenozoic terrestrial ecosystem. The composition and the character of a mammalian fauna are controlled by evolution time and evolutionary rate. Here we took 50 Asian Paleogene mammalian faunas as representatives and applied Bayesian Tip-dating method to infer the relationships and divergence times among these faunas. Based on the results of Bayesian Tip-dating analyses, we discussed the correlation between the paleogeographic changes and the mammalian fauna turn-overs. Compared with the traditional fauna correlation and sorting, Bayesian Tip-dating analyses revealed more detailed similarities reflected via the divergence times among the 50 faunas. We discovered that the early Eocene mammalian fauna, which firstly appeared in India subcontinent, is similar to the faunas of the same age in other parts of Asia. It is likely that a passage for the mammalian dispersal was formed before early Eocene. Bayesian inferring suggests that the first appearance of the dispersal passage is during 64.8–61.3 Ma. This time window is close to the time estimation for the initial time of India-Asia collision. During 57.1–47.2 Ma, India subcontinent probably had a habitat different from the main part of Asia, as it was reflected from the composition of the mammalian faunas. It is probably correlated with the uplifted Gangdese Mountain and shallow seas and lowlands on both sides of the collision region. The very remote divergence time (64.8 Ma) estimated by Bayesian inferring reflects the mammalian fauna turnover during the Eocene-Oligocene transition, obviously affected by the global cooling. Till the end of Oligocene, the Arabic Peninsula and Asian mainland remained separated and the mammalian faunas did not show clear connection.

Emergence of hystricognathous rodents: Palaeogene fossil record, phylogeny, dental evolution and historical biogeography

AbstractAlthough phylogenetic trees imply Asia as the ancestral homeland of the Hystricognathi clade (Rodentia: Ctenohystrica), curiously the oldest known fossil occurrences of hystricognathous rodents are not from Asia, but from Africa and South America, where they appear suddenly in the fossil record of both landmasses by the Late Middle Eocene. Here we performed cladistic and Bayesian (standard and tip-dating analyses) assessments of the dental evidence documenting early ctenohystricans, including several Asian ‘ctenodactyloids’, virtually all Palaeogene Asian and African hystricognaths known thus far and two representatives of the earliest known South American hystricognaths. Our results provide a phylogenetic context of early hystricognaths (with implications on systematics) and suggest that some Eocene Asian ‘ctenodactyloids’ could be considered as stem hystricognaths and pre-hystricognaths, although they were not recognized as such originally. However, this view does not fill the gap of the Eocene Asian hystricognath record, as the proposed results imply many ghost lineages extending back to the Middle Eocene for several Asian and African taxa. They also imply a complex early historical biogeography of the group, involving multiple dispersal events from Asia to Africa (and possibly from Africa back to Asia) and then to South America sometime during the Middle Eocene. Based on these phylogenetic considerations, we discuss the emergence of hystricognathous rodents from a morpho-anatomical perspective by analysing the differentiation of their masticatory apparatus and chewing movements, notably through the evolution of their dental patterns.

Morphological phylogeny of Megachilini and the evolution of leaf-cutter behavior in bees (Hymenoptera: Megachilidae)

A unique feature among bees is the ability of some species of Megachile Latreille s.l. to cut and process fresh leaves for nest construction. The presence of a razor between the female mandibular teeth (interdental laminae) to facilitate leaf-cutting (LC) is a morphological novelty that might have triggered a subsequent diversification in this group. However, we have a limited understanding of the phylogeny of this group despite the large number of described species and the origins and patterns of variations of this mandibular structure are unknown. Herein, using a cladistic analysis of adult external morphological characters, we explored the relationships of all genera of Megachilini and the more than 50 subgenera of Megachile s.l. We coded 272 characters for 8 outgroups and 114 ingroup species. Depending on the weighting scheme (equal or implied weighting), our parsimony analyses suggested the monophyly of Megachile s.l. and that either Noteriades Cockerell or the clade Coelioxys Latreille + Radoszkowskiana Popov is the extant sister group of all other Megachilini. In addition, we conducted Bayesian total-evidence tip-dating analyses to examine other possible hypotheses of relationships and patterns of variation of the interdental lamina. Our analyses suggest that interdental laminae developed asynchronicaly from two different structures in the mandible, and differ in their phenotypic plasticity. Character correlation tests using phylogenetic pairwise comparisons indicated that the presence of interdental lamina is not associated with head size, mandible size and shape, and pubescence on the adductor interspace. We discuss the implications of our findings for the classification of Megachilini and the development of novel evolutionary, ecological, and functional hypotheses on this behavior. New taxa established are Pseudoheriadini Gonzalez & Engel, new tribe, Ochreriadini Gonzalez & Engel, new tribe, Cremnomegachile Gonzalez & Engel, new genus, Rozenapis Gonzalez & Engel, new genus, and Saucrochile Gonzalez & Engel, new genus, along with the following new combinations: Cremnomegachile dolichosoma (Benoist), new combination, Rozenapis ignita (Smith), new combination, and Saucrochile heriadiformis (Smith), new combination.

New remains of Condorchelys antiqua (Testudinata) from the Early-Middle Jurassic of Patagonia: anatomy, phylogeny, and paedomorphosis in the early evolution of turtles

ABSTRACT—New cranial and postcranial remains of the Early–Middle Jurassic turtle, Condorchelys antiqua, are described here in detail, providing new insights into the early evolution of turtles. Unconstrained and constrained cladistic analyses in addition to newly developed total-evidence Bayesian analysis were performed to explore large-scale turtle relationships and evolutionary trends. All the analyses show a similar resolution at the base of the tree, recovering several species of small-sized, fresh water turtles of the Early–Middle Jurassic at the base of the tree following the most basal, large-sized, terrestrial turtles from the Late Triassic. The calibration of the cladistic analyses and the tip-dating analysis provided similar results in the main nodes Testudines, Pan-Cryptodira, Cryptodira, Pan-Pleurodira, and Pleurodira, corroborating that the Jurassic is a key period for turtle evolution. The significant reduction in size in Early–Middle Jurassic stem turtles and the combination of certain characters (e.g., presence of fontanelles, loss of bones, loss of scutes) shown by those taxa suggests heterochronic changes, paedomorphosis in particular, at the base of the turtle tree. These morphological novelties could have trigged, or facilitated, the occupation of the aquatic niche as seen in Jurassic stem turtles.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Sterli, J., M. S. de la Fuente, and G. W. Rougier. 2019. New remains of Condorchelys antiqua (Testudinata) from the Early–Middle Jurassic of Patagonia: anatomy, phylogeny, and paedomorphosis in the early evolution of turtles. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2018.1480112.

Out of the Antilles: Fossil phylogenies support reverse colonization of bats to South America

AbstractAimPrevious phylogenies of extant short‐faced bats (Chiroptera: Stenodermatina) supported either two colonization events from the mainland to the Antilles, or reverse colonization, but lacked both fossil data and statistical modelling of biogeography. Recent multi‐locus phylogenies of noctilionoid bats and likelihood modelling of ancestral ranges support a continental origin for the clade. We include all known extinct and extant stenodermatina species and apply statistical modelling to test competing biogeographical hypotheses.LocationThe Neotropics, including the Antilles.MethodsWe combined mitochondrial and nuclear sequences with 302 new morphological characters to infer phylogenies. Bayesian tip‐dating analyses applied codon models to protein‐coding genes, with relaxed molecular clocks fitting a compound Poisson process. The combined maximum clade credibility tree was used in comparisons of alternative biogeographical models.ResultsThe new phylogenies support the fossil Cubanycteris silvai as sister to all extant species of short‐faced bats. Among Artibeus (the sister group to short‐faced bats), the Antillean fossil A. anthonyi has distinctive characters and is nested within the subgenus Artibeus. The common ancestor of all short‐faced bats is inferred to be Antillean, as a mainland origin is unlikely. Founder‐event speciation is the most probable process explaining the distribution of these highly divergent fossil lineages.Main conclusionsDated, character‐based phylogenies of fossil species are indispensable for biogeographical inference: without fossils, biogeographical analyses find a mainland origin for short‐faced bats. The rate of founder speciation in this clade is twice as high as the estimate from noctilionoids in general, highlighting the role of founder events in the diversification of island taxa. Although rare, reverse colonization contributes key species to continental communities. Short‐faced bats, including Cubanycteris, share biomechanical adaptations for a strong bite conferring access to harder figs. We hypothesize these adaptations and characters related to roosting ecology enabled ancestral lineages to successfully establish and diversify on the mainland.

Inferring 'weak spots' in phylogenetic trees: application to mosasauroid nomenclature.

Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the ‘weak spots’ in the phylogeny of mosasauroids, we revise the nomenclature of the ‘traditionally’ recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.

New adapiform primate fossils from the late Eocene of Egypt

Caenopithecine adapiform primates are currently represented by two genera from the late Eocene of Egypt (Afradapis and Aframonius) and one from the middle Eocene of Switzerland (Caenopithecus). All are somewhat anthropoid-like in several aspects of their dental and gnathic morphology, and are inferred to have been highly folivorous. Here we describe a new caenopithecine genus and species, Masradapis tahai, from the ~37 million-year-old Locality BQ-2 in Egypt, that is represented by mandibular and maxillary fragments and isolated teeth. Masradapis is approximately the same size as Aframonius but differs in having a more dramatic distal increase in molar size, more complex upper molar shearing crests, and an exceptionally deep mandibular corpus. We also describe additional mandibles and part of the orbit and rostrum of Aframonius which suggest that it was probably diurnal. Phylogenetic analyses place Masradapis either as the sister taxon of Aframonius (parsimony), or as the sister taxon of Afradapis and Caenopithecus (Bayesian methods). Bayesian tip-dating analysis, when combined with Bayesian biogeographic analysis, suggests that a common ancestor of known caenopithecines dispersed to Afro-Arabia from Europe between 49.4 and 47.4 Ma, and that a trans-Tethyan back-dispersal explains Caenopithecus’ later presence in Europe.For Masradapis: https://www.zoobank.org/urn:lsid:zoobank.org:act:41BC8459-7CCE-487F-BC59-1C34257D5C4EFor Masradapis tahai: https://www.zoobank.org/urn:lsid:zoobank.org:act:C0A620AD-6FCA-4649-A980-FCA237AFE39D

Hyainailourine and teratodontine cranial material from the late Eocene of Egypt and the application of parsimony and Bayesian methods to the phylogeny and biogeography of Hyaenodonta (Placentalia, Mammalia).

Hyaenodonta is a diverse, extinct group of carnivorous mammals that included weasel- to rhinoceros-sized species. The oldest-known hyaenodont fossils are from the middle Paleocene of North Africa and the antiquity of the group in Afro-Arabia led to the hypothesis that it originated there and dispersed to Asia, Europe, and North America. Here we describe two new hyaenodont species based on the oldest hyaenodont cranial specimens known from Afro-Arabia. The material was collected from the latest Eocene Locality 41 (L-41, ∼34 Ma) in the Fayum Depression, Egypt. Akhnatenavus nefertiticyon sp. nov. has specialized, hypercarnivorous molars and an elongate cranial vault. In A. nefertiticyon the tallest, piercing cusp on M1–M2 is the paracone. Brychotherium ephalmos gen. et sp. nov. has more generalized molars that retain the metacone and complex talonids. In B. ephalmos the tallest, piercing cusp on M1–M2 is the metacone. We incorporate this new material into a series of phylogenetic analyses using a character-taxon matrix that includes novel dental, cranial, and postcranial characters, and samples extensively from the global record of the group. The phylogenetic analysis includes the first application of Bayesian methods to hyaenodont relationships. B. ephalmos is consistently placed within Teratodontinae, an Afro-Arabian clade with several generalist and hypercarnivorous forms, and Akhnatenavus is consistently recovered in Hyainailourinae as part of an Afro-Arabian radiation. The phylogenetic results suggest that hypercarnivory evolved independently three times within Hyaenodonta: in Teratodontinae, in Hyainailourinae, and in Hyaenodontinae. Teratodontines are consistently placed in a close relationship with Hyainailouridae (Hyainailourinae + Apterodontinae) to the exclusion of “proviverrines,” hyaenodontines, and several North American clades, and we propose that the superfamily Hyainailouroidea be used to describe this relationship. Using the topologies recovered from each phylogenetic method, we reconstructed the biogeographic history of Hyaenodonta using parsimony optimization (PO), likelihood optimization (LO), and Bayesian Binary Markov chain Monte Carlo (MCMC) to examine support for the Afro-Arabian origin of Hyaenodonta. Across all analyses, we found that Hyaenodonta most likely originated in Europe, rather than Afro-Arabia. The clade is estimated by tip-dating analysis to have undergone a rapid radiation in the Late Cretaceous and Paleocene; a radiation currently not documented by fossil evidence. During the Paleocene, lineages are reconstructed as dispersing to Asia, Afro-Arabia, and North America. The place of origin of Hyainailouroidea is likely Afro-Arabia according to the Bayesian topologies but it is ambiguous using parsimony. All topologies support the constituent clades–Hyainailourinae, Apterodontinae, and Teratodontinae–as Afro-Arabian and tip-dating estimates that each clade is established in Afro-Arabia by the middle Eocene.

A mixed relaxed clock model

Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may have both long-term trends and short-term fluctuations, suggesting that more sophisticated clock models unfolding over multiple time scales should ultimately be developed. Here, a mixed relaxed clock model is introduced, which can be mechanistically interpreted as a rate variation process undergoing short-term fluctuations on the top of Brownian long-term trends. Statistically, this mixed clock represents an alternative solution to the problem of choosing between autocorrelated and uncorrelated relaxed clocks, by proposing instead to combine their respective merits. Fitting this model on a dataset of 105 placental mammals, using both node-dating and tip-dating approaches, suggests that the two pure clocks, Brownian and white noise, are rejected in favour of a mixed model with approximately equal contributions for its uncorrelated and autocorrelated components. The tip-dating analysis is particularly sensitive to the choice of the relaxed clock model. In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation. By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders. Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.