Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions

Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.

The Fossil Record of Ray-Finned Fishes (Actinopterygii) in Greece

The nowadays hyper-diverse clade of Actinopterygii (ray-finned bony fishes) is characterized by a long evolutionary history and an extremely rich global fossil record. This work builds upon 170 years of research on the fossil record of this clade in Greece. The taxonomy and spatiotemporal distribution of the ray-finned fish record of Greece are critically revisited and placed in an updated systematic and stratigraphic framework, while some new fossil data and interpretations are also provided. Greece hosts diverse ray-finned fish assemblages, which range in age from Lower Jurassic to Quaternary. Most known assemblages are of Miocene–Pliocene age and of marine affinities. A minimum of 32 families, followed by at least 34 genera and 22 species, have been recognized in Greece. From originally two named genera and seven species, only two fossil species, established on Greek material, are accepted as valid. Additional taxonomic diversity is anticipated, pending detailed investigations. From a taxonomic perspective, previous knowledge lies on preliminary or authoritative assessments of fossils, with many decades-old treatments needing revision. Little is known about Mesozoic–early Cenozoic occurrences or freshwater assemblages. Given the proven potential of the Greek fossil record, this chapter stresses the need for additional exploration and the establishment of permanent, curated collections of fossil fishes in Greek institutions. Directions for future research are discussed.

First study of the bat fossil record of the mid-Atlantic volcanic islands

ABSTRACT Bats are one of the most abundant and important mammals in ecosystems. However, their fossil record is scarce and fragile, making them difficult to find. Accordingly, there is no record of this group in the volcanic islands of the mid-Atlantic Ocean apart from the Canary Islands. This paper studies the first bat fossil record of the Canary Islands (Spain). The material studied is found within two Quaternary lava tubes, Cueva de los Verdes on Lanzarote and Cueva Roja on the island of El Hierro. The dental and humeral morphology and biometry are analysed and compared with current specimens. Among our results we highlight the first fossil data of two species endemic to the islands of the mid-Atlantic Ocean, Plecotus teneriffae and Pipistrellus maderensis, the former from the Canary Islands and the latter from the Azores, Madeira and the Canary Islands. We also confirm the presence of Pipistrellus kuhlii in the fossil record of the island of Lanzarote. No differences are observed between the dental morphology of the current and the fossil populations of P. maderensis and Pl. teneriffae. In the case of P. kuhlii, the populations of the Canary Islands and the Iberian Peninsula show differences in the paraconule with respect to the populations from central Europe. Palaeoecological studies of these taxa suggest that these islands presented a similar habitat when the sites were formed to the present-day habitat.

Appearance and disappearance rates of Phanerozoic marine animal paleocommunities

Ecological observations and paleontological data show that communities of organisms recur in space and time. Various observations suggest that communities largely disappear in extinction events and appear during radiations. This hypothesis, however, has not been tested on a large scale due to a lack of methods for analyzing fossil data, identifying communities, and quantifying their turnover. We demonstrate an approach for quantifying turnover of communities over the Phanerozoic Eon. Using network analysis of fossil occurrence data, we provide the first estimates of appearance and disappearance rates for marine animal paleocommunities in the 100 stages of the Phanerozoic record. Our analysis of 124,605 fossil collections (representing 25,749 living and extinct marine animal genera) shows that paleocommunity disappearance and appearance rates are generally highest in mass extinctions and recovery intervals, respectively, with rates three times greater than background levels. Although taxonomic change is, in general, a fair predictor of ecologic reorganization, the variance is high, and ecologic and taxonomic changes were episodically decoupled at times in the past. Extinction rate, therefore, is an imperfect proxy for ecologic change. The paleocommunity turnover rates suggest that efforts to assess the ecological consequences of the present-day biodiversity crisis should focus on the selectivity of extinctions and changes in the prevalence of biological interactions.

Biogeographic and demographic history of the Mediterranean snakes Malpolon monspessulanus and Hemorrhois hippocrepis across the Strait of Gibraltar

Background The contribution of North Africa to the assembly of biodiversity within the Western Palaearctic is still poorly documented. Since the Miocene, multiple biotic exchanges occurred across the Strait of Gibraltar, underlying the high biogeographic affinity between the western European and African sides of the Mediterranean basin. We investigated the biogeographic and demographic dynamics of two large Mediterranean-adapted snakes across the Strait and assess their relevance to the origin and diversity patterns of current European and North African populations. Results We inferred phylogeographic patterns and demographic history of M. monspessulanus and H. hippocrepis, based on range-wide multilocus data, combined with fossil data and species distribution modelling, under present and past bioclimatic envelopes. For both species we identified endemic lineages in the High Atlas Mountains (Morocco) and in eastern Iberia, suggesting their persistence in Europe during the Pleistocene. One lineage is shared between North Africa and southern Iberia and likely spread from the former to the latter during the sea-level low stand of the last glacial stage. During this period M. monspessulanus shows a sudden demographic expansion, associated with increased habitat suitability in North Africa. Lower habitat suitability is predicted for both species during interglacial stages, with suitable areas restricted to coastal and mountain ranges of Iberia and Morocco. Compiled fossil data for M. monspessulanus show a continuous fossil record in Iberia at least since the Pliocene and throughout the Pleistocene. Conclusions The previously proposed hypothesis of Pleistocene glacial extinction of both species in Europe is not supported based on genetic data, bioclimatic envelopes models, and the available fossil record. A model of range retraction to mountain refugia during arid periods and of glacial expansion (demographic and spatial) associated to an increase of Mediterranean habitats during glacial epochs emerges as a general pattern for mesic vertebrates in North Africa. Moreover, the phylogeographic pattern of H. hippocrepis conforms to a well-established biogeographic partition between western and eastern Maghreb.

True hopper fossils (Fulgoromorpha and Cicadomorpha) in the Jurassic to Cretaceous of eastern Asia and their evolutionary implications

True hoppers, consisting of Fulgoromorpha and Cicadomorpha, are plant feeders with very high species-level diversity. A large amount of true hopper fossils have been reported from eastern Asia, especially from the Middle to Late Jurassic Yanliao Biota, the Early Cretaceous Jehol Biota and mid-Cretaceous Kachin amber in the last two decades. Herein, true hoppers from the Jurassic and Cretaceous of eastern Asia are reviewed, and combining palaeontological data from other regions of the world and recent advances of molecular studies, the evolutionary history of true hoppers in the mid-late Mesozoic is discussed. Permocicada beipiaoensis Wang, 1987 and Archijassus plurinervis Zhang, 1985 are here excluded from Prosboloidea and Archijassidae respectively. To the end of 2020, a total of 203 species with definite systematic position have been documented in the Jurassic and Cretaceous of eastern Asia (China, Myanmar, Siberia, Mongolia, Japan and Korea), and were attributed to 116 genera in 22 families and 7 superfamilies. Available fossil data suggest that true hopper components strongly changed in the Cretaceous: primitive groups reduced and went extinct successively, and the origin and/or early diversification of most lineages (family or subfamily level) occurred, likely owing to the displacement of host-plants in the angiosperm floristic revolution.

Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity

There is a prevailing view that the inclusion of fossil data could remedy identifiability issues related to models of diversification, by drastically reducing the number of congruent models. The fossilized birth-death (FBD) model is an appealing way of directly incorporating fossil information when estimating diversification rates. Here we explore the benefits of including fossils by implementing and then testing two-types of FBD models in more complex likelihood-based models that assume multiple rate classes across the tree. We also assess the impact of severely undersampling, and even not including fossils that represent samples of lineages that also had sampled descendants (i.e., k-type fossils), as well as converting a fossil set to represent stratigraphic ranges. Under various simulation scenarios, including a scenario that exists far outside the set of models we evaluated, including fossils rarely outperforms analyses that exclude them altogether. At best, the inclusion of fossils improves precision but does not influence bias. We also found that severely undercounting the number of k-type fossils produces highly inflated rates of turnover and extinction fraction. Similarly, we found that converting the fossil set to stratigraphic ranges results in turnover rates and extinction fraction estimates that are generally underestimated. While fossils remain essential for understanding diversification through time, in the specific case of understanding diversification given an existing, largely modern tree, they are not especially beneficial.

Kinematics of wings from Caudipteryx to modern birds

This study seeks to better quantify the parameters that drove the evolution of flight from non-volant winged dinosaurs to modern birds. In order to explore this issue, we used fossil data to model the feathered forelimbs of Caudipteryx, the most basal non-volant maniraptoran dinosaur with elongated pennaceous feathers that could be described as forming proto-wings. In order to quantify the limiting flight factors, we created three hypothetical wing profiles for Caudipteryx with incrementally larger wingspans. We compared them with what revealed through fossils in wing morphology. These four models were analyzed under varying air speed, wing beat amplitude, and wing beat frequency to determine lift, thrust potential, and metabolic requirements. We tested these models using theoretical equations in order to mathematically describe the evolutionary changes observed during the evolution of modern birds from a winged terrestrial theropod like Caudipteryx. Caudipteryx could not fly, but this research indicates that with a large enough wing span, Caudipteryx-like animal could have flown. The results of these analyses mathematically confirm that during the evolution of energetically efficient powered flight in derived maniraptorans, body weight had to decrease and wing area/wing profile needed to increase together with the flapping angle and surface area for the attachment of the flight muscles. This study quantifies the morphological changes that we observe in the pennaraptoran fossil record in the overall decrease in body size in paravians, the increased wing surface area in Archaeopteryx relative to Caudipteryx, and changes observed in the morphology of the thoracic girdle, namely, the orientation of the glenoid and the enlargement of the sternum.

Integrated phylogenomics and fossil data illuminate the evolution of beetles

With over 380,000 described species and possibly several million more yet unnamed, beetles represent the most biodiverse animal order. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here we use a dataset of 68 single-copy nuclear protein coding genes sampling 129 out of the 194 recognized extant families as well as the first comprehensive set of fully-justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov., and Staphyliniformia sensu nov., alongside changes below the superfamily level. The heterogeneous former superfamily Cucujoidea is divided into three monophyletic groups: Erotyloidea stat. nov., Nitiduloidea stat. nov., and Cucujoidea sensu nov. Our divergence time analysis recovered an evolutionary timescale congruent with the fossil record: a late Carboniferous origin of Coleoptera, a late Paleozoic origin of all modern beetle suborders, and a Triassic–Jurassic origin of most extant families. While fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution, many polyphagan superfamilies exhibited increases in richness with Cretaceous flowering plants.

New fossil discoveries illustrate the diversity of past terrestrial ecosystems in New Caledonia

New Caledonia was, until recently, considered an old continental island harbouring a rich biota with outstanding Gondwanan relicts. However, deep marine sedimentation and tectonic evidence suggest complete submergence of the island during the latest Cretaceous to the Paleocene. Molecular phylogenies provide evidence for some deeply-diverging clades that may predate the Eocene and abundant post-Oligocene colonisation events. Extinction and colonization biases, as well as survival of some groups in refuges on neighbouring paleo-islands, may have obscured biogeographic trends over long time scales. Fossil data are therefore crucial for understanding the history of the New Caledonian biota, but occurrences are sparse and have received only limited attention. Here we describe five exceptional fossil assemblages that provide important new insights into New Caledonia’s terrestrial paleobiota from three key time intervals: prior to the submersion of the island, following re-emergence, and prior to Pleistocene climatic shifts. These will be of major importance for elucidating changes in New Caledonia’s floristic composition over time.