Mitochondrial data are not suitable for resolving placental mammal phylogeny

Mitochondrial data have traditionally been used in reconstructing a variety of species phylogenies. The low rates of recombination and thorough characterization of mitochondrial data across vertebrate species make it a particularly attractive phylogenetic marker. The relatively low number of fully sequenced mammal genomes and the lack of extensive sampling within Superorders have posed a serious problem for reaching agreement on the placement mammal species. The use of mitochondrial data sequences from large numbers of mammals could serve to circumvent the taxon-sampling deficit. Here we assess the suitability of mitochondrial data as a phylogenetic marker in mammal phylogenetics. MtDNA datasets of mammal origin have been filtered as follows: (i) we have sampled sparsely across the phylogenetic tree, (ii) we have constrained our sampling to genes with high taxon coverage, (iii) we have categorised rates across sites in a phylogeny independent manner and have removed fast evolving sites, and (iv), we have sampled from very shallow divergence times to reduce phylogenetic conflict. However, topologies obtained using these filters are not consistent with previous studies and are discordant across different genes. Individual mitochondrial genes, and indeed all mitochondrial genes analysed as a supermatrix, resulted in poor resolution of the species phylogeny. Overall, our study highlights the limitations of mitochondrial data, not only for resolving deep divergences and but also for shallow divergences in the mammal phylogeny.     

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

The fossil record suggests a rapid radiation of placental mammals following the Cretaceous-Paleogene (K-Pg) mass extinction 65 million years ago (Ma); nevertheless, molecular time estimates, while highly variable, are generally much older. Early molecular studies suffer from inadequate dating methods, reliance on the molecular clock, and simplistic and over-confident interpretations of the fossil record. More recent studies have used Bayesian dating methods that circumvent those issues, but the use of limited data has led to large estimation uncertainties, precluding a decisive conclusion on the timing of mammalian diversifications. Here we use a powerful Bayesian method to analyse 36 nuclear genomes and 274 mitochondrial genomes (20.6 million base pairs), combined with robust but flexible fossil calibrations. Our posterior time estimates suggest that marsupials diverged from eutherians 168-178 Ma, and crown Marsupialia diverged 64-84 Ma. Placentalia diverged 88-90 Ma, and present-day placental orders (except Primates and Xenarthra) originated in a ～20 Myr window (45-65 Ma) after the K-Pg extinction. Therefore we reject a pre K-Pg model of placental ordinal diversification. We suggest other infamous instances of mismatch between molecular and palaeontological divergence time estimates will be resolved with this same approach.     

Molecules consolidate the placental mammal tree

Deciphering relationships among the orders of placental mammals remains an important problem in evolutionary biology and has implications for understanding patterns of morphological character evolution, reconstructing the ancestral placental genome, and evaluating the role of plate tectonics and dispersal in the biogeographic history of this group. Until recently, both molecular and morphological studies provided only a limited and questionable resolution of placental relationships. Studies based on larger and more diverse molecular datasets, and using an array of methodological approaches, are now converging on a stable tree topology with four major groups of placental mammals. The emerging tree has revealed numerous instances of convergent evolution and suggests a role for plate tectonics in the early evolutionary history of placental mammals. The reconstruction of mammalian phylogeny illustrates both the pitfalls and the powers of molecular systematics.     

Permian terebratulids of Eurasia: Morphology,systematics, and phylogeny

The Permian terebratulids of Eurasia are revised. The taxonomic composition of the Permian terebratulids of the Russian Platform, Northern Caucasus, Transcaucasia, northern and southeastern Pamirs, and northern China (Inner Mongolia) is elucidated. Fifty-one species (13 described here as new), 21 genera (3 described here as new), 7 families, and 6 superfamilies are described. During the progress of the study, the author (Smirnova, 2004a, 2004b, 2006a, 2006b) and Smirnova and Grunt (2002, 2003a, 2003b) described for the first time 19 species, nine genera, two families, and one superfamily. Morphofunctional analysis reveals a great diversity of internal structures, of the time of their appearance in the ontogeny, and of their taxonomic significance. Ontogenetic study reveals phylogenetic relationships between the Permian and Meso-Cenozoic terebratulids, the presence of the superfamilies Terebratuloidea and Loboidothyroidea in the Permian, and a new type of brachidium ontogeny characterizing the superfamily Compositelasmatoidea. This book is intended for paleontologists and biologists interested in problems of taxonomy and phylogeny, and includes 5 plates, 80 figures, and 75 bibliographic references.     

The new framework for understanding placental mammal evolution

An unprecedented level of confidence has recently crystallized around a new hypothesis of how living placental mammals share a pattern of common descent. The major groups are afrotheres (e.g., aardvarks, elephants), xenarthrans (e.g., anteaters, sloths), laurasiatheres (e.g., horses, shrews), and euarchontoglires (e.g., humans, rodents). Compared with previous hypotheses this tree is remarkably stable; however, some uncertainty persists about the location of the placental root, and (for example) the position of bats within laurasiatheres, of sea cows and aardvarks within afrotheres, and of dermopterans within euarchontoglires. A variety of names for sub‐clades within the new placental mammal tree have been proposed, not all of which follow conventions regarding priority and stability. More importantly, the new phylogenetic framework enables the formulation of new hypotheses and testing thereof, for example regarding the possible developmental dichotomy that seems to distinguish members of the newly identified southern and northern radiations of living placental mammals.     

Molecular dating and biogeography of the early placental mammal radiation

The timing and phylogenetic hierarchy of early placental mammal divergences was determined based on combined DNA sequence analysis of 18 gene segments (9779 bp) from 64 species. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support for the divergence of four principal clades of eutherian mammals was achieved. Minimum divergence dates of the earliest nodes in the placental mammal phylogeny were estimated with a quartet-based maximum-likelihood method that accommodates rate variation among lineages using conservative fossil calibrations from nine different nodes in the eutherian tree. These minimum estimates resolve the earliest placental mammal divergence nodes at periods between 64 and 104 million years ago, in essentially every case predating the Cretaceous-Tertiary (K-T) boundary. The pattern and timing of these divergences allow a geographic interpretation of the primary branching events in eutherian history, likely originating in the southern supercontinent Gondwanaland coincident with its breakup into Africa and South America 95-105 million years ago. We propose an integrated genomic, paleontological, and biogeographic hypothesis to account for these earliest splits on the placental mammal family tree and address current discrepancies between fossil and molecular evidence.     

Morphology,molecules and the phylogeny of Characidae (Teleostei,Characiformes)

This is the most comprehensive phylogenetic analysis of the Characidae to date and the first large-scale hypothesis of the family, combining myriad morphological data with molecular information. A total of 520 morphological characters were analysed herein, of which 98 are newly defined. Among the analysed taxa, 259 species were coded by examining specimens, three fossil species were coded from the literature, one species was coded almost completely from published figures, 122 were partially coded from the literature, and 88 were analysed exclusively from molecular data. The total number of species in the analysed dataset is 473. Analyses were made by parsimony under equal and extended implied weighting with a broad range of parameters. The final hypothesis was selected using a stability criterion that chooses among the most parsimonious trees of all searches. It was found by weighting molecular characters with the average homoplasy of entire partitions (markers). The resulting hypothesis is congruent with previous molecular-based phylogenies of the family. The Characidae are monophyletic, with four main clades: the Spintherobolinae new subfamily; an expanded Stethaprioninae including the Grundulini, Gymnocharacini, Rhoadsiini and Stethaprionini; the Stevardiinae; and a clade composed of the Aphyocharacinae, Characinae, Cheirodontinae, Exodontinae and Tetragonopterinae. Also, a stem Characidae was found, as formed by the Eocene–Oligocene genera †Bryconetes and †Paleotetra as successive sister groups of extant members of the family. A subfamilial classification is proposed, but deep changes in the systematics that are beyond the scope of this study are still needed to classify the Characidae into monophyletic genera.     

Morphology ofCoptis japonica and its meaning in phylogeny

In the genusCoptis, some interesting features are found which are considered important phylogenetically. The median bundles of petiole and petiolule, and the midrib of lamina are double. They seem to represent a transitional situation between a dichotomy and a single median bundle found in usual angiospermous venation. The double bundle is either derived from 2 independent leaf trace bundles or formed by dichotomy of a leaf trace bundle, and it does not seem so important whether the number of trace bundles is even or odd. The nodal structure is trilacunar or pentalacunar with 3, 4, 6 or 8 trace bundles. The upper part of the carpel does not produce ovules and is open from the initiation of the carpel. It is suggested that the carpel becomes open secondarily concomitant with the reduction of ovules. This shows that the closure of the carpel is not perfectly established.     

Echinoderm phylogeny: Morphology and molecules approach accord

Phylogenetic relationships of echinoderms at various taxonomic levels have come under intense focus recently from both a morphological and a molecular standpoint. Initial conflict between molecular and morphological results is gradually being resolved to produce a consensus that places echinoderm Phylogeny on a new robust footing.     

Morphology of gametes of mollusks, echinoderms, and brachiopods in systematics and phylogeny

The morphology of eggs and sperm of echinoderms, mollusks, and brachiopods was studied and compared. The gametes of inarticulate brachiopods (two classes Lingulata and Craniata and two subphyla Linguliformea and Craniaformea) are shown to have significant morphological differences from those of articulate brachiopods (extant class Rhynchonellata, subphylum Rhynchonelliformea). Inarticulate brachiopods have similar sperm morphology to that of primitive brachiopods, bivalves and some polychaetes that have external fertilization. Sperm morphology of articulate brachiopods is similar to that of echinoderms, which are considered to be typical deuterostomate invertebrates. This similarity supports an early deviation of lophophore-bearing animals from Bilateria, before this lineage branched into Protostomia and Deuterostomia. Similar gamete morphology in Lingulata and Craniata supports the view that inarticulate brachiopods should be retained as a supraclass taxon for comparison with other Lophotrochozoa, in particular with phoronids, bryozoans, and mollusks. Based on the new data on the gamete morphology in inarticulate brachiopods, we propose the name Lingulophyles with the type genus Lingula, and for articulate brachiopods Coptothyrophyles with the type genus Coptothyris.     

Torpor and hibernation in a basal placental mammal, the Lesser Hedgehog Tenrec Echinops telfairi

The patterns of heterothermy were measured in Lesser Hedgehog Tenrecs, Echinops telfairi, under semi-natural conditions in an outdoor enclosure during the austral mid-winter in southwestern Madagascar. The animals were implanted with miniaturized body temperature (Tb) loggers (iButtons) that measured body temperature every 42 min for 2 months (May and June). The tenrecs entered daily torpor on all 60 consecutive days of measurement, that is, on 100% of animal days, with body temperature closely tracking ambient temperature (Ta) during the ambient heating phase. The mean minimum daily Tb of the tenrecs was 18.44 +/- 0.50 degrees C (n = 174, N = 3), and never exceeded 25 degrees C whereas, apart from a few hibernation bouts in one animal, the mean maximum daily Tb was 30.73 +/- 0.15 degrees C (n = 167, N = 3). Thus during winter, tenrecs display the lowest normothermic Tb of all placental mammals. E. telfairi showed afternoon and early evening arousals, but entered torpor before midnight and remained in torpor for 12-18 h each day. One animal hibernated on two occasions for periods of 2-4 days. We consider E. telfairi to be a protoendotherm, and discuss the relevance and potential of these data for testing models on the evolution of endothermy.     

Morphology, taxonomy, and phylogeny of megacerines (Megacerini, Cervidae, Artiodactyla)

Giant deer or megacerines (tribe Megacerini, family Cervidae, order Artiodactyla) dwelt in Eurasia from the Late Miocene to Holocene and in Africa in the Late Pleistocene. Based on comparative morphological data and morphofunctional analysis, morphogenetic and ecogenetic trends in this group are improved. Classification, taxonomy, phylogeny, and geographical and stratigraphical ranges of megacerines are revised.     

Morphology versus molecules in moss phylogeny: new insights (or controversies) from placental and vascular anatomy in Oedipodium griffithianum

New data on the placenta and water-conducting cells of Oedipodium griffithianum challenge current ideas on moss phylogeny. The placental region in O.?griffithianum consists of cells with highly convolute wall labyrinths on both the sporophytic and gametophytic side. This type of placenta distinguishes an assemblage of mosses including Tetraphis, Buxbaumia and all arthrodontous mosses but is not found in basal lineages including polytrichopsid mosses. Other features that distinguish Oedipodium from polytrichopsid mosses are the foot entirely ensheathed by the parenchymatous tissue of the gametophyte vaginula, the lack of a necrotic foot tip, the lack of intercellular spaces in the foot parenchyma and the presence of typical bryopsid hydroids with uniformly thin cell walls in the leafy shoot. These results do not support molecular phylogenies resolving Oedipodium as the sister group to polytrichopsid mosses or to all peristomate mosses, but are compatible with a sister relationship to a clade encompassing Tetraphis, Buxbaumia and arthrodontous mosses.