Anthropoid versus strepsirhine status of the African Eocene primates Algeripithecus and Azibius: craniodental evidence

Recent fossil discoveries have demonstrated that Africa and Asia were epicentres for the origin and/or early diversification of the major living primate lineages, including both anthropoids (monkeys, apes and humans) and crown strepsirhine primates (lemurs, lorises and galagos). Competing hypotheses favouring either an African or Asian origin for anthropoids rank among the most hotly contested issues in paleoprimatology. The Afrocentric model for anthropoid origins rests heavily on the >45 Myr old fossil Algeripithecus minutus from Algeria, which is widely acknowledged to be one of the oldest known anthropoids. However, the phylogenetic position of Algeripithecus with respect to other primates has been tenuous because of the highly fragmentary fossils that have documented this primate until now. Recently recovered and more nearly complete fossils of Algeripithecus and contemporaneous relatives reveal that they are not anthropoids. New data support the idea that Algeripithecus and its sister genus Azibius are the earliest offshoots of an Afro–Arabian strepsirhine clade that embraces extant toothcombed primates and their fossil relatives. Azibius exhibits anatomical evidence for nocturnality. Algeripithecus has a long, thin and forwardly inclined lower canine alveolus, a feature that is entirely compatible with the long and procumbent lower canine included in the toothcomb of crown strepsirhines. These results strengthen an ancient African origin for crown strepsirhines and, in turn, strongly challenge the role of Africa as the ancestral homeland for anthropoids.     

Evidence for a grooming claw in a North American adapiform primate: implications for anthropoid origins

Among fossil primates, the Eocene adapiforms have been suggested as the closest relatives of living anthropoids (monkeys, apes, and humans). Central to this argument is the form of the second pedal digit. Extant strepsirrhines and tarsiers possess a grooming claw on this digit, while most anthropoids have a nail. While controversial, the possible presence of a nail in certain European adapiforms has been considered evidence for anthropoid affinities. Skeletons preserved well enough to test this idea have been lacking for North American adapiforms. Here, we document and quantitatively analyze, for the first time, a dentally associated skeleton of Notharctus tenebrosus from the early Eocene of Wyoming that preserves the complete bones of digit II in semi-articulation. Utilizing twelve shape variables, we compare the distal phalanges of Notharctus tenebrosus to those of extant primates that bear nails (n = 21), tegulae (n = 4), and grooming claws (n = 10), and those of non-primates that bear claws (n = 7). Quantitative analyses demonstrate that Notharctus tenebrosus possessed a grooming claw with a surprisingly well-developed apical tuft on its second pedal digit. The presence of a wide apical tuft on the pedal digit II of Notharctus tenebrosus may reflect intermediate morphology between a typical grooming claw and a nail, which is consistent with the recent hypothesis that loss of a grooming claw occurred in a clade containing adapiforms (e.g. Darwinius masillae) and anthropoids. However, a cladistic analysis including newly documented morphologies and thorough representation of characters acknowledged to have states constituting strepsirrhine, haplorhine, and anthropoid synapomorphies groups Notharctus tenebrosus and Darwinius masillae with extant strepsirrhines rather than haplorhines suggesting that the form of pedal digit II reflects substantial homoplasy during the course of early primate evolution.     

Cladistic relationships of extant and fossil hominoids

There is general agreement that the hominoid primates form a monophyletic group, that the extant great apes and humans form a second clade within that group with the gibbons as the sister group, and that the African apes and humans form a third clade. Although it has recently been proposed that humans and orang utans are sister taxa and also that the great apes form a clade to the exclusion of humans, our analysis, particularly of the molecular evidence, supports the existence of an African ape and human clade. The major problem in hominoid phylogeny at present is the relationships of the species within this clade: morphological data generally support the existence of an African ape clade which is the sister group to humans; some molecular data also support this conclusion, but most molecular evidence indicates the existence of a chimpanzee/human clade. We have cladistically re-analysed the DNA and protein sequence data for which apomorphic character states can be assessed. It is clear that there is a high degree of homoplasy whichever branching pattern is produced, with some characters supporting the existence of a chimpanzee/human clade and others supporting an African ape clade. When the cladistic analyses of morphological and molecular data are combined we believe that the most parsimonious interpretation of the data is that the African apes form a clade which is the sister taxon of the human (i.e., Australopithecus, Homo and Paranthropus) clade.This paper is not intended as a survey of all hominoid fossils but as a study of branching points in hominoid evolution and fossils are included which are relevant to this branching pattern. The analysis of fossil taxa in this study leads us to conclude that Proconsul is the sister taxon to the later Hominoidea. A number of middle Miocene forms such as Dryopithecus, Kenyapithecus, Heliopithecus and Afropithecus are shown to share derived characters with great apes and humans and provide evidence for the divergence of that clade from the gibbon lineage prior to 18 Ma. The position that Sivapithecus represents the sister group of the orang utan clade is supported here and shows that the orang utan lineage had diverged from the African ape and human lineage prior to 11·5 Ma. There is unfortunately no definitive fossil cvidence on branching sequences within the African ape and human clade, although a new specimen from Samburu, Kenya may be related to the gorilla.     

The oldest Gondwanan fossil of Leiinae (Diptera,Mycetophilidae): Phylogenetic and evolutionary implications

A fossil Mycetophilidae from the Aptian Crato Formation—Cretomanota gondwanica gen. nov., sp. nov.—is described, which is the first mycetophilid from the Crato Formation and corresponds to the oldest known fossil leiine and only the second Gondwanan fossil mycetophilid described so far. Cretomanota gondwanica and both species of Alavamanota Blagoderov and Arillo were added as terminals to the data matrix of a general phylogenetic analysis of the Mycetophilidae, and both fit into the Leiinae. Alavamanota is monophyletic, sister to the clade composed by Cretomanota and the extant genus Manota Williston. The biology of the extant members of this fungivorous family corroborates the reconstruction of the Crato palaeoenvironment as including woodlands with humid habitats and microhabitats. The presence of a Cretaceous member of the tribe Manotini at low latitudes in South America reinforces the hypothesis that the clade with all manotines except Leiella Edwards corresponds to a Lower Cretaceous offshoot from a group in southern Gondwana expanding its distribution to more northern areas into the Gondwana and into Laurasia.     

A phylogeny of fossil and living neocoleoid cephalopods

Coleoid cephalopod phylogeny is well studied via both molecular and morphological data, yet although some agreement has been reached (e.g. that extant Decapodiformes and Octopoda are monophyletic) many details remain poorly resolved. Fossil coleoids, for which much data exists, have hitherto not been incorporated into analyses. Their inclusion is highly desirable for the support of neontological phylogenies, to better reconstruct character‐state histories, and to investigate the placement of the fossil groups themselves. In this study we present and analyse a morphological data matrix including both extinct and extant taxa. Homology assumptions in our data are discussed. Our results are presented both with and without the constraint of a monophyletic Decapodiformes imposed. When analysed with this constraint our results are strikingly congruent with those from molecular phylogeny, for instance placing Idiosepius in a basal position within Decapodiformes, and recovering Oegopsida and Bathyteuthoidea (although as grades). Our results support an Octopodiformes clade (“vampire squid” Vampyroteuthis as sister to Octopoda) and an octopodiform interpretation for most fossil coleoids. They suggest the fossil sister taxon to the octopods to be Plesioteuthididae. Most fossil higher taxa are supported, although many genera, especially within suborder Teudopseina, appear para‐ or polyphyletic.     

Endocranial preservation of a Carboniferous actinopterygian from Lancashire,UK, and the interrelationships of primitive actinopterygians

The gross brain structure of an Upper Carboniferous (ca. 310 Myr ago) ray-finned fish (Actinopterygii) is described from exceptionally well-preserved fossil material from the Burnley region of Lancashire, UK. Previously identified as ''Rhadinichthys'' planti, the species is reassigned to the genus Mesopoma. Morphological characters derived from these data are combined with reviews of cranial skeletal anatomy, enamel composition, oculomoter muscle insertion and paired fin morphology to test and reanalyse hypotheses of primitive actinopterygian interrelationships. Results indicate that ancestral chondrostean (sturgeon and paddlefish) and neopterygian (teleost, amiid and gar) lineages diverged earlier than current theories suggest. Palaeonisciformes, a taxonomic group widely used to include most Palaeozoic actinopterygians, include a significant number of primitive neopterygians, several of which may form a distinct monophyletic clade. Within this revised phylogenetic context, changes in gross brain morphology from primitive conditions, as revealed by fossil data, highlight likely specializations in extant non-teleostean actinopterygians.     

Evolution of the primate cytochrome c oxidase subunit II gene

We examined the nucleotide and amino acid sequence variation of the cytochrome c oxidase subunit II (COII) gene from 25 primates (4 hominoids, 8 Old World monkeys, 2 New World monkeys, 2 tarsiers, 7 lemuriforms, 2 lorisiforms). Marginal support was found for three phylogenetic conclusions: (1) sister-group relationship between tarsiers and a monkey/ape clade, (2) placement of the aye-aye (Daubentonia) sister to all other strepsirhine primates, and (3) rejection of a sister-group relationship of dwarf lemurs (i.e., Cheirogaleus) with lorisiform primates. Stronger support was found for a sister-group relationship between the ring-tail lemur (Lemur catta) and the gentle lemurs (Hapalemur). In congruence with previous studies on COII, we found that the monkeys and apes have undergone a nearly two-fold increase in the rate of amino acid replacement relative to other primates. Although functionally important amino acids are generally conserved among all primates, the acceleration in amino acid replacements in higher primates is associated with increased variation in the amino terminal end of the protein. Additionally, the replacement of two carboxyl-bearing residues (glutamate and aspartate) at positions 114 and 115 may provide a partial explanation for the poor enzyme kinetics in cross-reactions between the cytochromes c and cytochrome c oxidases of higher primates and other mammals. Correspondence to: R.L. Honeycutt     

Genomic data reject the hypothesis of a prosimian primate clade

The phylogenetic position of tarsiers within the primates has been a controversial subject for over a century. Despite numerous morphological and molecular studies, there has been weak support for grouping tarsiers with either strepsirrhine primates in a prosimian clade or with anthropoids in a haplorrhine clade. Here, we take advantage of the recently released whole genome assembly of the Philippine tarsier, Tarsius syrichta, in order to infer the phylogenetic relationship of Tarsius within the order Primates. We also present estimates of divergence times within the primates. Using a 1.26 million base pair multiple sequence alignment derived from 1078 orthologous genes, we provide overwhelming statistical support for the presence of a haplorrhine clade. We also present divergence date estimates using local relaxed molecular clock methods. The estimated time of the most recent common ancestor of extant Primates ranged from 64.9 Ma to 72.6 Ma, and haplorrhines were estimated to have a most recent common ancestor between 58.9 Ma and 68.6 Ma. Examination of rates of nucleotide substitution in the three major extant primate clades show that anthropoids have a slower substitution rate than either strepsirrhines or tarsiers. Our results provide the framework on which primate morphological, reproductive, and genomic features can be reconstructed in the broader context of mammalian phylogeny.     

The phylogenetic relationships of the early catarrhine primates: a review of the current evidence

This paper presents a review of the evolutionary relationships of the early catarrhine primates. The first stage of the analysis involves the reconstruction of the inferred ancestral morphotypes of the major groups of extant anthropoids. The introduction of the fossil taxa into the phylogenetic scheme represents the second and final stage of the analysis. The results of this cladistic analysis suggests that: (1) the parapithecids are a specialized group of basal anthropoids, (2) Oligopithecus savagei may represent the earliest recognizable catarrhine, (3) Propliopithecus (= Aegvptopithecus) and Pliopithecus apparently represent the successive sister taxa to the modern catarrhines, (4) Dendropithecus and Proconsul are best regarded as basal catarrhines of modern aspect, and (5) Victoriapithecus is a primitive cercopithecoid monkey which represents the siter taxon of the extant Old World monkeys.     

Phylogeny of the Augochlora clade with the description of four new species (Hymenoptera,Apoidea)

The Augochlora clade includes four genera: Augochlora Smith, Augochlorella Sandhouse, Ceratalictus Moure, and Pereirapis Moure. This is one of the richest and most widespread groups of Augochlorini bees. There are about 150 species, which occur from Argentina to Canada. The species of Augochlora clade are considered solitary to facultatively social, except Ceratalictus for which nothing is known. Wood nesting behavior arose once in the clade, in Augochlora sensu strictu. The objective of this study is to describe four new species and to present a revised phylogenetic analysis of the Augochlora clade for the placement of these species. The morphological matrix comprised 77 characters and 42 terminals, and resulted in two most parsimonious trees. The monophyly of the Augochlora clade is corroborated. Ceratalictus and Pereirapis are considered as sister groups and Ceratalictus inflexus sp. nov. came as sister to other species of Ceratalictus. Augochlora and Augochlorella are monophyletic and sister groups. Both extant subgenera of Augochlora were corroborated as monophyletic. Augochlorella comis is considered as sister group to the rest of Augochlorella species. All Augochlorella new species described belong to the Augochlorella ephyra group. Augochlorella kelliae sp. nov. is phylogenetically related to Augochlorella una. Augochlorella procliva sp. nov. and Augochlorella mavricera sp. nov. constitute a clade with Augochlorella acarinata. Including the new species, Augochlorella has 19 species and Ceratalictus 11 species. A revised key for species of Augochlorella and Ceratalictus is also presented in the Supplementary Information.     

PHYLOGENETIC RELATIONSHIPS IN SEED PLANTS

Abstract— The phylogenetic relationships of nineteen extant and fossil seed plants are considered. Analysis of 31 characters produced ten topologically similar and equally parsimonious cladograms. A strict consensus tree derived from these cladograms places Lyginopteris as the sister taxon to the other seed plants included. Within this clade all the taxa considered, except medullosans and cycads, form a single monophyletic group defined by the presence of flattened seeds and saccate pollen ("platy-sperms"). Relationships between medullosans, cycads, and "platysperms" were not resolved, but within the "platysperm" clade conifers and cordaites ( Cordaixylon, Mesoxylon ) + Ginkgo form a monophyletic group ("coniferophytes"). The "higher platysperms" (glossopterids, Caytonia , corystosperms, Bennettitales, Pentoxylon , Gnetales, and angiosperms) are also monophyletic, but their relationship to "coniferophytes," peltasperms, and Callistophyton is unresolved. Pentoxylon is placed as sister taxon to the Bennettitales, and together they form the sister group to a clade in which Gnetales and angiosperm are sister taxa. The Bennettitales + Pentoxylon + Gnetales + angiosperms ("anthophytes") form a monophyletic sister group to the corystosperms. This analysis is compared with current classifications of seed plants. It does not support a close relationship between Bennettitales and cycads, it provides no evidence for seed plant polyphyly, and it strongly suggests that the current concept of seed ferns has little value in a phylogenetic context.     

The systematics of right whales (Mysticeti: Balaenidae)

Balaenidae (right whales) are large, critically endangered baleen whales represented by four living species. The evolutionary relationships of balaenids are poorly known, with the number of genera, relationships to fossil taxa, and position within Mysticeti in contention. This study employs a comprehensive set of morphological characters to address aspects of balaenid phylogeny. A sister‐group relationship between neobalaenids and balaenids is strongly supported, although this conflicts with molecular evidence, which may be an artifact of long‐branch attraction (LBA). Monophyly of Balaenidae is supported, and three major clades are recognized: (1) extinct genus Balaenula, (2) extant and extinct species of the genus Eubalaena, and (3) extant and extinct species of the genus Balaena plus the extinct taxon, Balaenella. The relationships of these clades to one another, as well as to the early Miocene stem balaenid, Morenocetus parvus, remain unresolved. Pliocene taxa, Balaenula astensis and Balaenula balaenopsis, form a clade that is the sister group to the Japanese Pliocene Balaenula sp. Eubalaena glacialis and Pliocene Eubalaena belgica, are in an unresolved polytomy with a clade including E. japonica and E. australis. Extant and fossil species of Balaena form a monophyletic group that is sister group to the Dutch Pliocene Balaenella, although phylogenetic relationships within Balaena remain unresolved.     

Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes

Portions of two mitochondrial genes (12S and 16S ribosomal RNA) were sequenced to determine the phylogenetic relationships among the major clades of snakes. Thirty-six species, representing nearly all extant families, were examined and compared with sequences of a tuatara and three families of lizards. Snakes were found to constitute a monophyletic group (confidence probability [CP] = 96%), with the scolecophidians (blind snakes) as the most basal lineages (CP = 99%). This finding supports the hypothesis that snakes underwent a subterranean period early in their evolution. Caenophidians (advanced snakes), excluding Acrochordus, were found to be monophyletic (CP = 99%). Among the caenophidians, viperids were monophyletic (CP = 98%) and formed the sister group to the elapids plus colubrids (CP = 94%). Within the viperids, two monophyletic groups were identified: true vipers (CP = 98%) and pit vipers plus Azemiops (CP = 99%). The elapids plus Atractaspis formed a monophyletic clade (CP = 99%). Within the paraphyletic Colubridae, the largely Holarctic Colubrinae was found to be a monophyletic assemblage (CP = 98%), and the Xenodontinae was found to be polyphyletic (CP = 91%). Monophyly of the henophidians (primitive snakes) was neither supported nor rejected because of the weak resolution of relationships among those taxa, except for the clustering of Calabaria with a uropeltid, Rhinophis (CP = 94%).      

Tarsier brain component composition and its implications for systematics

The taxonomic position ofTarsius has been a topic of some debate. Recent molecular and anatomical studies have shoen that tarsiers share a number of derived traits with Anthropoids. These include aspects of their reporductive biology and aspects of their olfactory and visual systems. It has, therefore, been suggested that, despite a number of convergences with strepsirhine primates, tarsiers should be classified with the Anthropoid primates. We use comparative analyses of relative primate brain part volumes to determine whetherTarsius should be classified as a Haplorhine. We show that, for each of seven brain components whose relative size discriminates unequivocally between Strepsirhines and Haplorhines, the tarsiers fall in the Haplorhine distribution. These results confirm their classification with the Haplorhines.     

A new primate from the Eocene Pondaung Formation of Myanmar and the monophyly of Burmese amphipithecids

The family Amphipithecidae is one of the two fossil primate taxa from Asia that appear to be early members of the anthropoid clade. Ganlea megacanina, gen. et sp. nov., is a new amphipithecid from the late middle Eocene Pondaung Formation of central Myanmar. The holotype of Ganlea is distinctive in having a relatively enormous lower canine showing heavy apical wear, indicating an important functional role of the lower canine in food preparation and ingestion. A phylogenetic analysis of amphipithecid relationships suggests that Ganlea is the sister taxon of Myanmarpithecus, a relatively small-bodied taxon that has often, but not always, been included in Amphipithecidae. Pondaungia is the sister taxon of the Ganlea + Myanmarpithecus clade. All three Pondaung amphipithecid genera are monophyletic with respect to Siamopithecus, which is the most basal amphipithecid currently known. The inclusion of Myanmarpithecus in Amphipithecidae diminishes the likelihood that amphipithecids are specially related to adapiform primates. Extremely heavy apical wear has been documented on the lower canines of all three genera of Burmese amphipithecids. This distinctive wear pattern suggests that Burmese amphipithecids were an endemic radiation of hard object feeders that may have been ecological analogues of living New World pitheciin monkeys.     

Ontogeny and phyletic size change in living and fossil lemurs

Lemurs are notable for encompassing the range of body‐size variation for all primates past and present—close to four orders of magnitude. Benefiting from the phylogenetic proximity of subfossil lemurs to smaller‐bodied living forms, we employ allometric data from the skull to probe the ontogenetic bases of size differentiation and morphological diversity across these clades. Building upon prior pairwise comparisons between sister taxa, we performed the first clade‐wide analyses of craniomandibular growth allometries in 359 specimens from 10 lemuroids and 176 specimens from 8 indrioids. Ontogenetic trajectories for extant forms were used as a criterion of subtraction to evaluate morphological variation, and putative adaptations among sister taxa. In other words, do species‐level differences in skull form result from the differential extension of common patterns of relative growth? In lemuroids, a pervasive pattern of ontogenetic scaling is observed for facial dimensions in all genera, with three genera also sharing relative growth trajectories for jaw proportions (Lemur, Eulemur, Varecia). Differences in masticatory growth and form characterizing Hapalemur and fossil Pachylemur likely reflect dietary factors. Pervasive ontogenetic scaling characterizes the facial skull in extant Indri, Avahi, and Propithecus, as well as their larger, extinct sister taxa Mesopropithecus and Babakotia. Significant interspecific differences are observed in the allometry of indrioid masticatory proportions, with variation in the mechanical advantage of the jaw adductors and stress‐resisting elements correlated with diet. As the growth series and adult data are largely coincidental in each clade, interspecific variation in facial form may result from selection for body‐size differentiation among sister taxa. Those cases where trajectories are discordant identify potential dietary adaptations linked to variation in masticatory forces during chewing and biting. Although such dissociations highlight selection to uncouple shared ancestral growth patterns, they occur largely via transpositions and retention of primitive size‐shape covariation patterns or relative growth coefficients. Am. J. Primatol. 72:161–172, 2010. © 2009 Wiley‐Liss, Inc.     

Complementary approaches of cytogenetics and molecular biology to the taxonomy and study of speciation processes in lemurs

The lemurs, prosimian primates of Madagascar, constitute a zoological group containing numerous species and subspecies. Their taxonomy remains controversial. Depending on the authors and the techniques they have used, the number of species varies between 39 and 52. In addition, although a monophyletic origin of the settlement of Madagascar is the most commonly held opinion, recent studies based on molecular biology do not exclude two independent colonization events, one involving Daubentonia and a second giving rise to the other lemurs. 1 .     

Une nouvelle espèce de Podocnemis (Pleurodira, Podocnemididae) provenant du Néogène de la formation Solimões, Acre, Brésil

A Neogene turtle from Brasil is described. It represents the first find of a new species close to the extant Podocnemis sextuberculata. Both species constitute a new clade in the genus. The synapomorphies they share and the differences between them are given. P. negrii nov. sp. is the second fossil species of the genus, after P. bassleri from the Neogene of Peru, which constitutes another clade with the extant P. expansa. The relationships between these two clades and the other species of the genus are not determinate.     

More DNA support for a Cetacea/Hippopotamidae clade: the blood-clotting protein gene gamma-fibrinogen

Recent phylogenetic analyses of DNA sequences suggest that cetaceans (whales) and hippopotamid artiodactyls (hippos) are extant sister taxa. Consequently, the shared aquatic specializations of these taxa may be synapomorphies. This molecular view is contradicted by paleontological data that overwhelmingly support a monophyletic Artiodactyla (even-toed ungulates) and a close relationship between Cetacea and extinct mesonychian ungulates. According to the fossil evidence, molecular, behavioral, and anatomical resemblances between hippos and whales are interpreted as convergences or primitive retentions. In this report, competing interpretations of whale origins are tested through phylogenetic analyses of the blood-clotting protein gene gamma- fibrinogen from cetaceans, artiodactyls, perissodactyls (odd-toed ungulates), and carnivores (cats, dogs, and kin). In combination with published DNA sequences, the gamma-fibrinogen data unambiguously support a hippo/whale clade and are inconsistent with the paleontological perspective. If the phylogeny favored by fossil evidence is accepted, the convergence at the DNA level between Cetacea and Hippopotamidae is remarkable in its distribution across three genetic loci: gamma-fibrinogen, the linked milk casein genes, and mitochondrial cytochrome b.      

Exploring the phylogeny of the marattialean ferns

The eusporangiate marattialean ferns represent an ancient radiation with a rich fossil record but limited modern diversity in the tropics. The long evolutionary history without close extant relatives has confounded studies of the phylogenetic origin, rooting and timing of marattialean ferns. Here we present new complete plastid genomes of six marattialean species and compiled a plastid genome dataset representing all of the currently accepted marattialean genera. We further supplemented this dataset by compiling a large dataset of mitochondrial genes and a phenotypic data matrix covering both extant and extinct representatives of the lineage. Our phylogenomic and total-evidence analyses corroborated the postulated position of marattialean ferns as the sister to leptosporangiate ferns, and the position of Danaea as the sister to the remaining extant marattialean genera. However, our results provide new evidence that Christensenia is sister to Marattia and that M. cicutifolia actually belongs to Eupodium. The apparently highly reduced rate of molecular evolution in marattialean ferns provides a challenge for dating the key phylogenetic events with molecular clock approaches. We instead applied a parsimony-based total-evidence dating approach, which suggested a Triassic age for the extant crown group. The modern distribution can best be explained as mainly resulting from vicariance following the breakup of Pangaea and Gondwana. We resolved the fossil genera Marattiopsis, Danaeopsis and Qasimia as members of the monophyletic family Marattiaceae, and the Carboniferous genera Sydneia and Radstockia as the monophyletic sister of all other marattialean ferns.