Calibrated chronograms,fossils, outgroup relationships,and root priors: re‐examining the historical biogeography of Geraniales

We re‐examined the recent study by Palazzesi et al., (2012) published in the Biological Journal of the Linnean Society (107: 67–85), that presented the historical diversification of Geraniales using BEAST analysis of the plastid spacer trnL–F and of the non‐coding nuclear ribosomal internal transcribed spacers (ITS). Their study presented a set of new fossils within the order, generated a chronogram for Geraniales and other rosid orders using fossil‐based priors on five nodes, demonstrated an Eocene radiation of Geraniales (and other rosid orders), and argued for more recent (Pliocene–Pleistocene) and climate‐linked diversification of genera in the five recognized families relative to previous studies. As a result of very young ages for the crown of Geraniales and other rosid orders, unusual relationships of Geraniales to other rosids, and apparent nucleotide substitution saturation of the two gene regions, we conducted a broad series of BEAST analyses that incorporated additional rosid fossil priors, used more accepted rosid ordinal topologies, or altered the placement of one fossil Geraniales prior. Our results indicate that their ages are 20–50% too young owing to a combination of (1) strong nucleotide saturation of the DNA regions starting at 65 Mya, (2) lack of a root (rosid stem) or other rosid ordinal stem fossil‐based priors, (3) the inability of the two DNA regions (with alignment issues) to obtain a monophyletic Geraniales as well as reasonable relationships of Geraniales to other rosid orders, and (4) apparent issues with the nodal placement of a Pelargonium fossil. The Geraniales crown is much older (Campanian of the Cretaceous; 86 Mya), the posterior age distribution on all but two fossil nodes are well older than the priors, the placement of a Pelargonium‐like fossil is more likely at the crown rather than the stem, but their models of diversification within several clades linked to climatic and orogeny appear supported. We discuss a number of the inherent issues of relaxed‐clock dating and outline some ‘best practice’ approaches for such studies. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 29–49.     

Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences

The temperate South American lizard genus Liolaemus is the one of the most widely distributed and species‐rich genera of lizards on earth. The genus is divided into two subgenera, Liolaemus sensu stricto (the ‘Chilean group’) and Eulaemus (the ‘Argentino group’), a division that is supported by recent molecular and morphological data. Owing to a lack of reliable fossil data, previous studies have been forced to use either global molecular clocks, a standardized mutation rate adopted from previous studies, or the use of geological events as calibration points. However, simulations indicate that these types of assumptions may result in less accurate estimates of divergence times when clock‐like models or mutation rates are violated. We used a multilocus data set combined with a newly described fossil to provide the first calibrated phylogeny for the crown groups of the clade Eulaemus, and derive new fossil‐calibrated substitution rates (with error) of both nuclear and mtDNA gene regions for Eulaemus specifically. Divergence date estimates for each of the crown groups and appropriate rate estimates will provide the foundation for understanding rates of speciation, historical biogeography, and phylogeographical history for various clades in one of the most diverse lizard genera in the poorly studied Patagonian region. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 825–835.     

A non‐aquatic otter (Mammalia,Carnivora, Mustelidae) from the Late Miocene (Vallesian,MN 10) of La Roma 2 (Alfambra,Teruel, Spain): systematics and functional anatomy

A new genus and species of otter‐like mustelid, Teruelictis riparius, is created on the basis of a partial skeleton from the Late Miocene (Vallesian age, MN 10) locality of La Roma 2 (Teruel, Spain), including several postcranial elements, the skull, and the mandible. The combination of a typically lutrine dentition, similar to that of other fossil otters such as Paralutra jaegeri, with a very slender postcranial skeleton, including a long back and gracile long bones and metacarpals, thus lacking any aquatic adaptations, was previously unknown in the fossil record. This mosaic of features strongly suggests the possibility that the aquatic lifestyle of otters could have appeared after the initial development of the distinctive dental morphology of this specialized group of mustelids. © 2013 The Linnean Society of London     

A presumed spelaeogriphacean crustacean from an upper Barremian wetland (Las Hoyas; Lower Cretaceous; Central Spain)

Abstract: A third fossil attributable to the crustacean peracarid order Spelaeogriphacea is described from an Upper Barremian (125 Ma) lacustrine environment in Central Spain. Neither the new taxon, Spinogriphus ibericus gen. et sp. nov., nor the two already described fossil forms can be identified with certainty as crown‐group spelaeogriphaceans. We consider that Schram’s 1974 family Acadiocarididae represents stem‐lineage spelaeogriphaceans and should accommodate these fossil taxa that display very generalised peracaridan features and lack any conspicuous autapomorphies, except for a short carapace, undifferentiated pereiopods, foliaceous pleopods and a tail fan‐like (uropods + telson) caudal structure where the unsegmented uropodal endopod lacks annulation. The zoogeography of the Acadiocarididae is Laurasian in contrast to the modern, crown‐group spelaeogriphaceans (Spelaeogriphidae), which are limited to Gondwanan territories.     

Eoandromeda and the origin of Ctenophora

The Ediacaran fossil Eoandromeda octobrachiata had a high conical body with eight arms in helicospiral arrangement along the flanks. The arms carried transverse bands proposed to be homologous to ctenophore ctenes (comb plates). Eoandromeda is interpreted as an early stem‐group ctenophore, characterized by the synapomorphies ctenes, comb rows, and octoradial symmetry but lacking crown‐group synapomorphies such as tentacles, statoliths, polar fields, and biradial symmetry. It probably had a pelagic mode of life. The early appearance in the fossil record of octoradial ctenophores is most consistent with the Planulozoa hypothesis (Ctenophora is the sister group of Cnidaria + Bilateria) of metazoan phylogeny.     

Saccoglossus testa from the Mazon Creek fauna (Pennsylvanian of Illinois) and the evolution of acorn worms (Enteropneusta: Hemichordata)

The limited fossil record of enteropneust hemichordates (acorn worms) and the few external features that distinguish the four families have provided a challenge to our understanding of the evolution of the group and their various feeding adaptations. The middle Pennsylvanian Saccoglossus testa sp. nov. from the Mazon Creek, Westfalian D Carbonate Formation, Francis Creek Shale of northern Illinois provides evidence for the exploitation of surface sediments. Saccoglossus testa has a long proboscis characteristic of the extant genus Saccoglossus, a specialist in surface deposit feeding. The collar is as long as it is wide. The anterior trunk lacks a distinctively wide branchial region. These three features distinguish it from its sympatric enteropneust species Mazoglossus ramsdelli Bardack that has a proboscis characteristic of an infaunal deposit feeder. It is the seventh known species of fossil enteropneust, including a resting trace of a Lower Triassic fossil that has collar lips that characterize the extant deep‐sea family Torquaratoridae, and which represents a second parallel evolution of surface deposit feeding. An analysis of the seven fossils shows that the earliest Enteropneusta had a relatively simple harrimaniid‐like body plan, and that the spengelid, the torquaratorid and lastly the most complex ptychoderid body plan appeared in that chronological order.     

Australia's oldest Anseriform fossil: a quadrate from the Early Eocene Tingamarra Fauna

Abstract: A partial quadrate (essentially the otic part) from the nonmarine, earliest Eocene (54.6 Ma) Tingamarra Local Fauna in Queensland, Australia, has been identified as the oldest Australian anseriform fossil. The Tingamarra quadrate shows a combination of plesiomorphic anseriform characters with a unique synapomorphic character complex of the Anhimidae (screamers), which today are endemic to South America. In concert with the basal position of the Anhimidae among the crown‐group anseriforms, this set of characters suggests a stem group of the Anhimidae, raising a possibility of the Transantarctic migration of stem anhimids to South America. The quadrate morphology supports palaeognathous rather than recently claimed anhimid relationships of the Dromornithidae and identifies Sylviornis as an anseriform rather than a galliform.     

Carboniferous Onychophora from Montceau‐les‐Mines,France, and onychophoran terrestrialization

The geological age of the onychophoran crown‐group, and when the group came onto land, have been sources of debate. Although stem‐group Onychophora have been identified from as early as the Cambrian, the sparse record of terrestrial taxa from before the Cretaceous is subject to contradictory interpretations. A Late Carboniferous species from the Mazon Creek biota of the USA, Helenodora inopinata, originally interpreted as a crown‐group onychophoran, has recently been allied to early Cambrian stem‐group taxa. Here we describe a fossil species from the Late Carboniferous Montceau‐les‐Mines Lagerstätte, France, informally referred to as an onychophoran for more than 30 years. The onychophoran affinities of Antennipatus montceauensis gen. nov., sp. nov. are indicated by the form of the trunk plicae and the shape and spacing of their papillae, details of antennal annuli, and the presence of putative slime papillae. The poor preservation of several key systematic characters for extant Onychophora, however, prohibits the precise placement of the Carboniferous fossil in the stem or crown of the two extant families, or the onychophoran stem‐group as a whole. Nevertheless, A. montceauensis is the most compelling candidate to date for a terrestrial Paleozoic onychophoran.     

The skull of the Upper Cretaceous snake Dinilysia patagonica Smith‐Woodward, 1901, and its phylogenetic position revisited

The cranial anatomy of Dinilysia patagonica, a terrestrial snake from the Upper Cretaceous of Argentina, is redescribed and illustrated, based on high‐resolution X‐ray computed tomography and better preparations made on previously known specimens, including the holotype. Previously unreported characters reinforce the intriguing mosaic nature of the skull of Dinilysia, with a suite of plesiomorphic and apomorphic characters with respect to extant snakes. Newly recognized plesiomorphies are the absence of the medial vertical flange of the nasal, lateral position of the prefrontal, lizard‐like contact between vomer and palatine, floor of the recessus scalae tympani formed by the basioccipital, posterolateral corners of the basisphenoid strongly ventrolaterally projected, and absence of a medial parietal pillar separating the telencephalon and mesencephalon, amongst others. We also reinterpreted the structures forming the otic region of Dinilysia, confirming the presence of a crista circumfenestralis, which represents an important derived ophidian synapomorphy. Both plesiomorphic and apomorphic traits of Dinilysia are treated in detail and illustrated accordingly. Results of a phylogenetic analysis support a basal position of Dinilysia, as the sister‐taxon to all extant snakes. The fossil taxa Yurlunggur, Haasiophis, Eupodophis, Pachyrhachis, and Wonambi appear as derived snakes nested within the extant clade Alethinophidia, as stem‐taxa to the crown‐clade Macrostomata. The hypothesis of a sister‐group relationship between Dinilysia and Najash rionegrina, as suggested by some authors, is rejected by the results of our analysis. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 194–238.     

Harvesting Betulaceae sequences from GenBank to generate a new chronogram for the family

Betulaceae, with 120–150 species in six genera, are a family of Fagales that occurs mainly in the Northern Hemisphere. Previous studies of the evolution of Alnus, Betula, Carpinus, Corylus, Ostrya and Ostryopsis have relied on a relatively small number of sequence data and molecular clocks with fixed‐point calibrations. We exploited GenBank to construct Betulaceae matrices of up to 900 sequence accessions and 9300 nucleotides of nuclear and plastid DNA; we also computed species consensus sequences to build 46‐ and 29‐species matrices that strike a balance between species sampling and nucleotide sampling. Trees were rooted on Ticodendraceae and Casuarinaceae, and divergence times were inferred under relaxed and strict molecular clocks, using alternative fossil constraints. The data support the traditional two subfamilies, Betuloideae (Alnus, Betula) and Coryloideae, and show that Ostryopsis is sister to Ostrya/Carpinus. The fossil record and molecular clocks calibrated with alternating fossils indicate that the stem lineage of Betulaceae dates back to the Upper Cretaceous, the two subfamilies to the Palaeocene and the most recent common ancestors of each of the living genera to the mid‐ to late Miocene. A substitution rate shift in Coryloideae between 25 and 15 Mya preceded the mid‐Miocene climatic optimum and may be linked to temperate niches that became available following the mid‐Miocene. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 465–477.     

A chiton without a foot

Abstract: The palaeoloricate ‘polyplacophorans’ are an extinct paraphyletic group of basal chiton‐like organisms known primarily from their fossilized valves. Their phylogenetic placement remains contentious, but they are likely to include both stem‐group Polyplacophora and stem‐group Aplacophora. Candidates for the latter position include ‘Helminthochiton’thraivensis from the Ordovician of Scotland, which we redescribe here through a combined optical and micro‐CT (XMT) restudy of the type material. The 11 specimens in the type series are all articulated, presenting partial or complete valve series as well as mouldic preservation of the girdle armature; they demonstrate a vermiform body plan. The valves are typically palaeoloricate in aspect, but differ in detail from all existing palaeoloricate genera; we hence erect Phthipodochiton gen. nov. to contain the species. The most notable feature of the fossils is the spicular girdle; this is impersistently preserved, but demonstrably wraps entirely around the ventral surface of the animal, implying that a ‘true’ (i.e. polyplacophoran like) foot was absent, although we do not exclude the possibility of a narrow solenogastre‐like median pedal groove having been present. Phthipodochiton thraivensis presents an apparent mosaic of aplacophoran and polyplacophoran features and as such will inform our understanding of the relationship between these groups of extant molluscs. An inference may also be drawn that at least some other palaeoloricates possessed an ‘armoured aplacophoran’ body plan, in contrast to the ‘limpet‐like’ body plan of extant Polyplacophora.     

Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves,Coracii)

We report a nearly complete skeleton of a new species of stem roller (Aves, Coracii) from the early Eocene Green River Formation of North America. The new species is most closely related to two species‐depauperate lineages, Coraciidae (rollers) and Brachypteraciidae (ground rollers), that form a monophyletic crown clade (Coracioidea) with an exclusively Old World extant distribution. Phylogenetic analysis utilizing a matrix of 133 morphological characters and sequence data from three genes (RAG‐1, c‐myc, and ND2) identifies the new species as a stem member of the Coracii more closely related to the crown clade than the only previously identified New World taxon, Primobucco mcgrewi. The phylogenetic placement of the new species and Primobucco mcgrewiindicates a widespread northern hemisphere distribution in the Eocene with subsequent restriction to Africa, Madagascar, Australia, and temperate to tropical parts of Europe and Asia. It provides evidence of further ecological diversity in early stem Coracii and convergence on crown morphologies. The new species contributes to mounting evidence that extant distributions for major avian subclades may be of comparatively recent origin. Further late Palaeogene sampling is needed to elucidate potential drivers for shifting avian distributions and disappearance of Coracii from North America. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157 , 586–611.     

Testing the phylogenetic position of Cambrian pancrustacean larval fossils by coding ontogenetic stages

The study of ontogeny as an integral part of understanding the pattern of evolution dates back over 200 years, but only recently have ontogenetic data been explicitly incorporated into phylogenetic analyses. Pancrustaceans undergo radical ontogenetic changes. The spectacular upper Cambrian “Orsten” fauna preserves phosphatized fossil larvae, including putative crown‐group pancrustaceans with amazingly complete developmental sequences. The putative presence and nature of adult stages remains a source of debate, causing spurious placements in a traditional morphological analysis. We introduce a new coding method where each semaphoront (discrete larval or adult stage) is considered an operational taxonomic unit. This avoids a priori assumptions of heterochrony. Characters and their states are defined to identify changes in morphology throughout ontogeny. Phylogenetic analyses of semaphoronts produced possible relationships of each Orsten fossil to the crown‐group clade expected from morphology shared with extant larvae. Bredocaris is a member of the stem lineage of Thecostraca or (Thecostraca + Copepoda), and Yicaris and Rehbachiella are probably members of the stem lineage of Cephalocarida. These placements rely directly on comparisons between extant and fossil larval character states. The position of Phosphatocopina remains unresolved. This method may have broader applications to other phylogenetic problems which may rely on ontogenetically variable homology statements.     

Evidence of early evolution of Australidelphia (Metatheria,Mammalia) in South America: phylogenetic relationships of the metatherians from the Late Palaeocene of Itaboraí (Brazil) based on teeth and petrosal bones

New metatherian petrosal bones from the mid to Late Palaeocene of Itaboraí, belonging to three morphotypes (VI, VII, and VII), are formally described and compared to fossil and extant taxa known by their auditory region. An attempt at assigning petrosal types to tooth‐based taxa from Itaboraí was made by combining parsimony and morphometric methods. The first large scale phylogenetic analysis of the Itaboraían metatherians, involving basicranial and dental characters in a larger number of taxa, is provided here and is at the basis of a systematic revision of the metatherians from Itaboraí. The combination of morphometric and cladistic analyses helps in understanding the affinities between the petrosals and the tooth‐based taxa. The metatherians from Itaboraí were taxonomically diverse, belonging to each of the most important radiations in marsupial evolutionary history (Didelphimorphia, Paucituberculata, Eometatheria). The inclusion of Palaeocene taxa in the crown group Marsupialia and above all in the Eometatheria radiation points to an early emergence of these clades in South America and corroborates the main molecular hypotheses. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 159 , 746–784.     

A crown‐group demosponge from the early Cambrian Sirius Passet Biota,North Greenland

Calibration of the divergence times of sponge lineages and understanding of their phylogenetic history are hampered by the difficulty in recognizing crown versus stem groups in the fossil record. A new specimen from the lower Cambrian (Series 2, Stage 3; approximately 515 Ma) Sirius Passet Biota of North Greenland has yielded a diagnostic spicule assemblage of the extant demosponge lineages Haploscleromorpha and/or Heteroscleromorpha. The specimen has disarticulated approximately in situ, but represents an individual sponge that possessed monaxon spicules combined with a range of slightly smaller sigma, toxa and unique spiral morphologies. The combination of spicule forms, together with their relatively large size, suggests that the sponge represents the stem lineage of Haploscleromorpha + Heteroscleromorpha. This is the first crown‐group demosponge described from the early Cambrian and provides the most reliable calibration point currently available for phylogenetic studies.     

Cranial osteology of Exostinus serratus (Squamata: Anguimorpha), fossil sister taxon to the enigmatic clade Xenosaurus

Within the squamate clade Anguimorpha, Xenosaurus is an enigmatic taxon combining several apparently primitive features with a highly specialized set of autapomorphies. This combination makes the fossil record along the Xenosaurus stem particularly important for resolving the relationships of Xenosaurus with other anguimorphs, and between species of Xenosaurus.Exostinus serratus Cope, 1873 from the Oligocene of the western United States is currently hypothesized to be the immediate sister taxon to Xenosaurus. The cranial osteology of this pivotal taxon is described here for the first time from all known material, using high‐resolution X‐ray computerized tomography (CT) scanning to visualize individual elements. Exostinus serratus displays a mosaic of ancestral anguimorph features that are transformed in Xenosaurus, as well as unique synapomorphies shared with Xenosaurus. The region of the external nares is less transformed than in Xenosaurus, as are the general proportions of the bones surrounding the cartilaginous nasal capsule. However, the forms of the teeth and of the osteodermal sculpture, as well as several details of maxillary and mandibular morphology, are distinctly Xenosaurus‐like. Several autapomorphies are also present, including an abbreviated tooth row and an unusually wide palatal shelf of the maxilla. An understanding of the ways in which the non‐ossified tissues of the head influenced the development of the bones is crucial to interpreting their morphology. Furthermore, subtle anatomical features often provide important comparative information, and are emphasized herein. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 159 , 921–953.     

Early Eocene fossil illuminates the ancestral (diurnal) ecomorphology of owls and documents a mosaic evolution of the strigiform body plan

We describe a partial skeleton of a fossil owl (Strigiformes) from the early Eocene London Clay of Walton-on-the-Naze (Essex, UK). The holotype of Ypresiglaux michaeldanielsi, gen. et sp. nov. is one of the most complete specimens of a Palaeogene owl and elucidates the poorly known ecomorphology of stem group Strigiformes. Whereas most of the postcranial bones show the characteristic strigiform morphology, the new species exhibits plesiomorphic features of the skull and cervical vertebrae that differ distinctly from extant owls. A well-developed supraorbital process of the lacrimal bone suggests that the eyes were not as greatly enlarged and forward-facing as in extant owls. A plesiomorphic quadrate morphology indicates differences in the otic region, and a proportionally longer axis suggests that the fossil species was not able to rotate its head to the degree found in crown group Strigiformes. Therefore, the fossil documents a mosaic evolution of the strigiform body plan, with owls developing raptorial adaptations before specializations of the visual and acoustic systems evolved. Because the latter relate to a crespuscular or nocturnal activity pattern, we hypothesize that Ypresiglaux was diurnal. Nocturnality in owls may have evolved in response to the emergence of evolutionary opportunities, which enabled owls to exploit new ecological niches, or owls may have been driven into nocturnal habits by ecological competition.     

Gobekko cretacicus (Reptilia: Squamata) and its bearing on the interpretation of gekkotan affinities

Gobekko cretacicus, a Cretaceous lizard from the Gobi Desert of Mongolia, is a key fossil for understanding gecko phylogeny. We revisit this fossil using high‐resolution X‐ray computed tomography. The application of this imaging method reveals new information about sutures, bone shape, and structural details of the palate and basicranium. These data were used to assess the phylogenetic affinities of Gobekko in the context of an existing squamate data set. The effects of character ordering, search strategy, and the addition of another putative gekkonomorph (Hoburogekko suchanovi) on inferred gekkonomorph relationships were explored. Available specimens of G. cretacicus are skeletally mature but have unfused nasals, frontals, and parietals, and (possibly) a persistent basicranial fenestra. Some putative gekkonomorphs are not consistently supported as closer to crown clade gekkotans than to autarchoglossans. In a strict consensus both Gobekko and Hoburogekko form a polytomy with extant geckos. Some of the adult character states of Gobekko are observable in embryos of extant species. The evolution of tubular frontals and dentaries in gekkotans may be structurally related to the loss of the postorbital and supratemporal bars in this lineage. The complete lack of a parietal foramen, and presumably a light‐sensitive parietal eye, in this clade is of interest and could indicate an early origin of nocturnality in geckos. © 2013 The Linnean Society of London     

Explaining gregarious behaviour in Banffia constricta from the Middle Cambrian Burgess Shale,British Columbia

Banffia constricta is an enigmatic Burgess Shale animal originally described by Charles Walcott in 1911 as an annelid, and more recently as a stem‐group deuterostome. Interpreted, on the basis of anatomy, to have been bottom‐feeders, there are few other data from which to draw interpretations of Banffia's life habit. A slab of Burgess Shale with a dense aggregation of B. constricta may indicate a gregarious habit for the animal, as taphonomic and stratigraphical data indicate an in situ origin for the assemblage. Clustering of individuals, high density of the individuals and non‐random within‐cluster orientation support the hypothesis that detritus‐feeding B. constricta congregated to feed on a local, rich food source. Presumed opportunistic feeding aggregations have been documented in at least one other Burgess Shale taxon and have been described for other fossil benthic marine invertebrates. Extant benthic marine invertebrates such as holothurians and echinoids exhibit mass feeding behaviour and may serve as modern analogs for the behaviour represented by the B. constricta assemblage.     

Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae: Thorius)

The small size and apparent external morphological similarity of the minute salamanders of the genus Thorius have long hindered evolutionary studies of the group. We estimate gene and species trees within the genus using mitochondrial and nuclear DNA from nearly all named and many candidate species and find three main clades. We use this phylogenetic hypothesis to examine patterns of morphological evolution and species coexistence across central and southern Mexico and to test alternative hypotheses of lineage divergence with and without ecomorphological divergence. Sympatric species differ in body size more than expected after accounting for phylogenetic relationship, and morphological traits show no significant phylogenetic signal. Sympatric species tend to differ in a combination of body size, presence or absence of maxillary teeth, and relative limb or tail length, even when they are close relatives. Sister species of Thorius tend to occupy climatically similar environments, which suggests that divergence across climatic gradients does not drive species formation in the genus. Rather than being an example of cryptic species formation, Thorius more closely resembles an adaptive radiation, with ecomorphological divergence that is bounded by organism‐level constraints. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 622–643.