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.     

Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes

Many phylogenetic analyses that include numerous terminals but few genes show high resolution and branch support for relatively recently diverged clades, but lack of resolution and/or support for "basal" clades of the tree. The various benefits of increased taxon and character sampling have been widely discussed in the literature, albeit primarily based on simulations rather than empirical data. In this study, we used a well-sampled gene-tree analysis (based on 100 mitochondrial genomes of higher teleost fishes) to test empirically the efficiency of different methods of data sampling and phylogenetic inference to "correctly" resolve the basal clades of a tree (based on congruence with the reference tree constructed using all 100 taxa and 7990 characters). By itself, increased character sampling was an inefficient method by which to decrease the likelihood of "incorrect" resolution (i.e., incongruence with the reference tree) for parsimony analyses. Although increased taxon sampling was a powerful approach to alleviate "incorrect" resolution for parsimony analyses, it had the general effect of increasing the number of, and support for, "incorrectly" resolved clades in the Bayesian analyses. For both the parsimony and Bayesian analyses, increased taxon sampling, by itself, was insufficient to help resolve the basal clades, making this sampling strategy ineffective for that purpose. For this empirical study, the most efficient of the six approaches considered to resolve the basal clades when adding nucleotides to a dataset that consists of a single gene sampled for a small, but representative, number of taxa, is to increase character sampling and analyze the characters using the Bayesian method.     

Resolving the root of the avian mitogenomic tree by breaking up long branches

Incomplete taxon sampling has been a major problem in resolving the early divergences in birds. Five new mitochondrial genomes are reported here (brush-turkey, lyrebird, suboscine flycatcher, turkey vulture, and a gull) and three break up long branches that tended to attract the distant reptilian outgroup. These long branches were to galliforms, and to oscine and suboscine passeriformes. Breaking these long branches leaves the root, as inferred by maximum likelihood and Bayesian phylogenetic analyses, between paleognaths and neognaths. This means that morphological, nuclear, and mitochondrial data are now in agreement on the position of the root of the avian tree and we can, move on to other questions. An overview is then given of the deepest divisions in the mitogenomic tree inferred from complete mitochondrial genomes. The strict monophyly of both the galloanseres and the passerines is strongly supported, leaving the deep six-way split within Neoaves as the next major question for which resolution is still lacking. Incomplete taxon sampling was also a problem for Neoaves, and although some resolution is now available there are still problems because current phylogenetic methods still fail to account for real features of DNA sequence evolution.     

The misleading effects of composite taxa in supermatrices

With the amount of available sequence data rapidly increasing, supermatrices are at the forefront of systematic studies. As an alternative to supertrees, supermatrices utilize a total evidence approach where different genes and other lines of data are merged into a single data matrix, which is then analyzed in an attempt to obtain the phylogeny that best explains the data. However, questions may arise when combining data sets in which one or more taxa do not have sequences available for each individual gene. Two possible solutions to this situation are to either leave all taxa separate and code unavailable sequences as missing, or to combine taxa at a level for which monophyly is assumed a priori. By reanalyzing the previous work of, we show that combining taxa may yield misleading results, i.e., hypotheses of relationships that are not supported by the underlying data.     

Habitat assessment for a rare, arboreal forest mammal, the tree hyrax Dendrohyrax arboreus

Recent findings have suggested that there has been a change in the structural nature of forests in the Eastern Cape, South Africa, which explains decreases in forest fauna. One of these (rare) forest species is the tree hyrax Dendrohyrax arboreus, a nocturnal, arboreal folivore, which makes use of cavity‐bearing trees as dens. However, a conflict exists between the use of forest resources and in protecting habitats for the tree hyrax. In order to design appropriate management strategies, conservation authorities and forest managers require information regarding the specific habitat requirements of fauna in their forest, particularly those that are already threatened by resource use. The aims of this study were thus: (i) to characterise the den trees of D. arboreus, (ii) to determine whether D. arboreus selects for certain den tree characteristics (i.e. relative to the abundance of that characteristic); and (iii) to develop a habitat assessment model for D. arboreus. The tree hydrax was found to select for den trees with particular characteristics: seven tree species were selected as den trees, which were usually the tallest trees in the canopy (4–8 m). Den trees were usually only partly decayed, with multiple cavity entrances and trunk angles of between 45° and 68°. Cavity entrance and orientation did not appear to play a role in den tree selection by D. arboreus. A function which discriminated between den trees and non‐den trees was calculated, and can be used to determine the suitability of a tree as a den for a tree hyrax (and thus to prevent it from being removed during commercial logging operations), or to assess the suitability of an area for habitation by tree hyraxes. This model can therefore help to alleviate the conflict between forest conservation managers and resource users in the Eastern Cape.     

Elevational distribution of restricted range forest tree taxa in eastern Tanzania

The forests of eastern Tanzania are a globally important biodiversity hotspot. In this study 361 eastern Tanzanian restricted range forest tree taxa were assessed. Of these taxa, 223 occurred in the Eastern Arc, 150 in Coastal forests, 17 in Northern forests and 21 in the Lake Nyasa forests. The majority of the taxa had restricted elevational ranges with 76.3% occurring in no more than two 200 m elevational bands out of a total potential elevation range of 3000 m. The majority of the taxa occupied a small area in the eastern Tanzanian forests, with 201 taxa being only found at a few sites. In determining priority areas for conservation, selection of taxon definitions can have important effects. For example, tree size varies with elevation, so if only large trees are used then site selection will be biased towards particular areas.     

Insect and small mammal herbivores limit tree establishment in northern Mongolian steppe

The extent to which human activities expanded the range of central and north-eastern Asian steppes into the forest is controversial. Natural versus anthropogenic causes of the inhibition of tree growth were investigated in a case study in the western Khentey Mountains in montane meadow steppe on sun-exposed southern slopes, representing treeless outposts within the northern Mongolian mountain taiga. Sowing and planting experiments with Mongolia’s most common tree species, Larix sibirica, did not result in the successful establishment of any tree during one growing season, despite the exclusion of grazing by large herbivores from the sample plots by fencing. Less than 1% of the seeds germinated 4 weeks after sowing in spring. All seedlings died within a further 3 weeks due to drought and heat. Two-year-old seedlings suffered from drought as well as from feeding by of gypsy moth larvae (Lymantria dispar), grasshoppers and rodents. While the gypsy moth was effective at damaging L. sibirica only during few weeks at the beginning of the growing season, feeding by grasshoppers and rodents persisted through the entire growing season. At the end of the growing season two thirds of the seedlings died due to insect and small mammal herbivory and one third due to drought-related damage. Herbivores attacked larch seedlings more rapidly on the open meadow steppe than at the forest edge. Drought and high temperature at the soil–air interface are crucial for inhibiting tree encroachment on the studied steppe slopes. Competition by non-arboreal plants is of subordinate significance for the establishment of L. sibirica. Trees can only establish at especially favorable microsites under humid weather conditions. Such trees, however, are exposed to a high risk of mortality from insect or small mammal herbivory.     

Phylogenetic tree of tRNAs using a simple algorithm

A simple method for phylogenetic tree construction is described. In this method each node is calculated considering the distance between the elements and the difference between these elements and an average element, allowing the selection of the most probable node.Two examples of tRNA phylogenies (E. coli set and Phe family) are analyzed, giving both reliable trees. Data from these dendrograms give support to the idea of an early cloverleaf arising.     

New inferences from tree shape: numbers of missing taxa and population growth rates

The relative positions of branching events in a phylogeny contain information about evolutionary and population dynamic processes. We provide new summary statistics of branching event times and describe how these statistics can be used to infer rates of species diversification from interspecies trees or rates of population growth from intraspecies trees. We also introduce a phylogenetic method for estimating the level of taxon sampling in a clade. Different evolutionary models and different sampling regimes can produce similar patterns of branching events, so it is important to consider explicitly the model assumptions involved when making evolutionary inferences. Results of an analysis of the phylogeny of the mosquito-borne flaviviruses suggest that there could be several thousand currently unidentified viruses in this clade.     

Epigenetic processes in a tetraploid mammal

Polyploidy has played a most important role in speciation and evolution of plants and animals. It is thought that low frequency of polyploidy in mammals is due to a dosage imbalance that would interfere with proper development in mammalian polyploids. The first tetraploid mammal, Tympanoctomys barrerae (Octodontidae), appears to be an exception to this rule. In this study we investigated X chromosome inactivation (XCI) and genomic imprinting in T. barrerae, two epigenetic processes usually involved in dosage control in mammalian genomes. The imprinting status of the Peg1 gene was determined by Peg1 allelic expression studies. The inactive X chromosome was identified on interphase nuclei by immunofluorescence using specific antisera raised against Met3H3K27 and macroH2A1. Quantitative PCR was used to compare the Peg1/Dmd ratio in T. barrerae and in its most closely related diploid species, Octomys mimax. Our data demonstrate that parental-specific silencing of at least one gene and normal X chromosomal dosage mechanism are conserved in the tetraploid genome. We hypothesize a concerted action of genetic and epigenetic mechanisms during the process of functional diploidization of this tetraploid genome.     

Perfect phylogeny haplotyper: haplotype inferral using a tree model

SUMMARY: We have developed an efficient program, the Perfect Phylogeny Haplotyper (PPH) that takes in unphased population genotype data, and determines if that data can be explained by haplotype pairs that could have evolved on a perfect phylogeny.     

Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective

Background  

The teleost order Lophiiformes, commonly known as the anglerfishes, contains a diverse array of marine fishes, ranging from benthic shallow-water dwellers to highly modified deep-sea midwater species. They comprise 321 living species placed in 68 genera, 18 families and 5 suborders, but approximately half of the species diversity is occupied by deep-sea ceratioids distributed among 11 families. The evolutionary origins of such remarkable habitat and species diversity, however, remain elusive because of the lack of fresh material for a majority of the deep-sea ceratioids and incompleteness of the fossil record across all of the Lophiiformes. To obtain a comprehensive picture of the phylogeny and evolutionary history of the anglerfishes, we assembled whole mitochondrial genome (mitogenome) sequences from 39 lophiiforms (33 newly determined during this study) representing all five suborders and 17 of the 18 families. Sequences of 77 higher teleosts including the 39 lophiiform sequences were unambiguously aligned and subjected to phylogenetic analysis and divergence time estimation.     

Identification of proteins from non-model organisms using mass spectrometry: application to a hibernating mammal

A major challenge in the life sciences is the extraction of detailed molecular information from plants and animals that are not among the handful of exhaustively studied "model organisms." As a consequence, certain species with novel phenotypes are often ignored due to the lack of searchable databases, tractable genetics, stock centers, and more recently, a sequenced genome. Characterization of phenotype at the molecular level commonly relies on the identification of differentially expressed proteins by combining database searching with tandem mass spectrometry (MS) of peptides derived from protein fragmentation. However, the identification of short peptides from nonmodel organisms can be hampered by the lack of sufficient amino acid sequence homology with proteins in existing databases; therefore, a database search strategy that encompasses both identity and homology can provide stronger evidence than a single search alone. The use of multiple algorithms for database searches may also increase the probability of correct protein identification since it is unlikely that each program would produce false negative or positive hits for the same peptides. In this study, four software packages, Mascot, Pro ID, Sequest, and Pro BLAST, were compared in their ability to identify proteins from the thirteen-lined ground squirrel (Spermophilus tridecemlineatus), a hibernating mammal that lacks a completely sequenced genome. Our results show similarities as well as the degree of variability among different software packages when the identical protein database is searched. In the process of this study, we identified the up-regulation of succinyl CoA-transferase (SCOT) in the heart of hibernators. SCOT is the rate-limiting enzyme in the catabolism of ketone bodies, an important alternative fuel source during hibernation.     

Multiple invasions into freshwater by pufferfishes (teleostei: tetraodontidae): a mitogenomic perspective

Pufferfishes of the Family Tetraodontidae are the most speciose group in the Order Tetraodontiformes and mainly inhabit coastal waters along continents. Although no members of other tetraodontiform families have fully discarded their marine lives, approximately 30 tetraodontid species spend their entire lives in freshwaters in disjunct tropical regions of South America, Central Africa, and Southeast Asia. To investigate the interrelationships of tetraodontid pufferfishes and thereby elucidate the evolutionary origins of their freshwater habitats, we performed phylogenetic analysis based on whole mitochondrial genome sequences from 50 tetraodontid species and closely related species (including 31 newly determined sequences). The resulting phylogenies reveal that the family is composed of four major lineages and that freshwater species from the different continents are independently nested in two of the four lineages. A monophyletic origin of the use of freshwater habitats was statistically rejected, and ancestral habitat reconstruction on the resulting tree demonstrates that tetraodontids independently entered freshwater habitats in different continents at least three times. Relaxed molecular-clock Bayesian divergence time estimation suggests that the timing of these invasions differs between continents, occurring at 0-10 million years ago (MA) in South America, 17-38 MA in Central Africa, and 48-78 MA in Southeast Asia. These timings are congruent with geological events that could facilitate adaptation to freshwater habitats in each continent.