Highly congruent molecular support for a diverse superordinal clade of endemic African mammals

A solution to higher level mammalian phylogeny is going to depend on the congruent establishment of superordinal groupings followed by a linking together of these clades. We present congruent and convincing evidence from four disparate nuclear protein coding genes and from a tandem alignment of the 12S-16S mitochondrial region, for a superordinal clade of endemic African mammals that includes elephant shrews, aardvarks, golden mole, elephants, sirenians, and hyraxes. Because of strong support for golden mole as part of this clade, the Insectivora are rendered paraphyletic or polyphyletic, with constrained monophyly of the insectivores judged significantly worse in the vast majority of tests. Branching arrangement within this clade remains highly uncertain; however, a tandem alignment of the protein coding genes suggests elephant shrew is the earliest African lineage. None of the individual data sets or combinations of data sets support the widely held view of a mirorder Tethytheria (Sirenia/Proboscidea), although only a tandem alignment of protein coding and mitochondrial loci significantly rejects this association. The majority of the data sets and analyses provide strong support for Caviomorpha as part of a monophyletic Rodentia.

Duplicate genes and the root of angiosperms, with an example using phytochrome sequences

The root of the angiosperm tree has not yet been established. Major morphological and molecular differences between angiosperms and other seed plants have introduced ambiguities and possibly spurious results. Because it is unlikely that extant species more closely related to angiosperms will be discovered, and because relevant fossils will almost certainly not yield molecular data, the use of duplicate genes for rooting purposes may provide the best hope of a solution. Simultaneous analysis of the genes resulting from a gene duplication event along the branch subtending angiosperms would yield an unrooted network, wherein two congruent gene trees should be connected by a single branch. In these circumstances the best rooted species tree is the one that corresponds to the two gene trees when the network is rooted along the connecting branch. In general, this approach can be viewed as choosing among rooted species trees by minimizing hypothesized events such as gene duplication, gene loss, lineage sorting, and lateral transfer. Of those gene families that are potentially relevant to the angiosperm problem, phytochrome genes warrant special attention. Phylogenetic analysis of a sample of complete phytochrome (PHY) sequences implies that an initial duplication event preceded (or occurred early within) the radiation of seed plants and that each of the two resulting copies duplicated again. In one of these cases, leading to the PHYA and PHYC lineages, duplication appears to have occurred before the diversification of angiosperms. Duplicate gene trees are congruent in these broad analyses, but the sample of sequences is too limited to provide much insight into the rooting question. Preliminary analyses of partial PHYA and PHYC sequences from several presumably basal angiosperm lineages are promising, but more data are needed to critically evaluate the power of these genes to resolve the angiosperm radiation.

Biogeography of Sulawesian shrews: testing for their origin with a parametric bootstrap on molecular data

In order to identify the zoogeographic origin of shrews (genus Crocidura) living on the oceanic island of Sulawesi, 15 taxa from Southeast Asia and 1 from Europe were examined for sequence variation in a segment (617 bp) of the mitochondrial cytochrome b gene. The null hypothesis of a monophyletic origin of all Sulawesian shrews was investigated by a phylogenetic reconstruction using maximum parsimony. According to a parametric bootstrap which simulated sequence evolution for these taxa, the null hypothesis could be rejected as highly unlikely (P < 0.01). Therefore, the molecular phylogeny strongly suggests that overwater colonization of Sulawesi by shrews succeeded on at least two occasions. The first, relatively ancient wave of colonizers radiated and gave rise to a surprizingly diverse assemblage of at least five species which now coexist in perfect sympatry on Sulawesi. The second wave, of more recent origin, gave rise to Crocidura nigripes, a species which retained close genetic affinities with other Malay shrews.

Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data

Until a few decades ago, phylogenetic relationships among placental orders were ambiguous and usually depicted to radiate as an unresolved "bush." Resolution of this bush by various workers has been progressing slowly, but with promising results corroborated by nondental, dental, and molecular characters. In this study we continue to seek resolution. A total of 258 nondental and 2 dental characters was analyzed by PAUP and MacClade on 39 vertebrate taxa (3 reptiles, 1 nonmammalian therapsid, and 35 mammals; 20 of the mammals are extant and 15 are extinct) to study higher taxonomic relationships with emphasis on Placentalia (Eutheria). About two-thirds of the characters are osteological, the rest concern soft tissues, including myological but excluding molecular characters (most are our data, the rest are from the literature). Cladistic analysis included all 39 taxa (fossil taxa help to evaluate polarities of characters) and all characters were given equal weight. Extant Mammalia are divided into Prototheria and Theria, the latter into Marsupialia and Placentalia. Placentalia comprises Xenarthra and Epitheria. Within Epitheria, Lipotyphla and Preptotheria (emended) are sister-taxa. Preptotherian taxa group into: ungulate-related taxa and various nonungulates. The former include Carnivora, Pholidota, Tubulidentata, Artiodactyla, Cetacea, Perissodactyla, Hyracoidea, Proboscidea, and Sirenia. A possible association to embrace Lagomorpha, Rodentia, Macroscelidea, Scandentia, Primates, Chiroptera, and Dermoptera is suggested. Significant differences between our findings and those of recent investigators include the dissociation of Pholidota from Xenarthra and the plesiomorphous position of Lipotyphla within Epitheria. Congruence between morphological and molecular results is closer than previously reported.

The turning- and linear-maneuvering performance of birds: the cost of efficiency for coursing insectivores

To examine the performance compromises necessitated by adaptations for high efficiency in flight, such as highaspect ratio wings, the flight morphology and acceleration performance of a guild of coursing aerial insectivores (swifts andswallows) were compared with those of a guild of avian generalists. Though phylogenetic non-independence made inference ofadaptation difficult, biologically significant differences in aspect ratio and acceleration performance probably exist between thetwo groups of birds. A model of aerial insectivory is presented to illustrate the performance demands of this foraging methodand the impacts of the compromises between high efficiency in sustained flight and turning- and linear-maneuveringperformance.

Phylogenetic reconstruction of the yeast genus Kluyveromyces: restriction map analysis of the 5.8S rRNA gene and the two ribosomal internal transcribed spacers

We have constructed restriction site maps of the 5.8S rRNA gene and two ITS regions in 60 strains of Kluyveromyces genus. We test the value of this region as a phylogenetic indicator, and its possible use as a fast and easy method to identify species of this genus. Despite some minor incongruences, our results are in good agreement with previous phylogenetic reconstructions based on the 18S rRNA gene sequencing (Cai et al., 1996; James et al., 1997). A highly significant monophyletic group was formed by K. lactis, K. marxianus, K. aestuarii, K. dobzhanskii and K. wickerhamii, which should be considered the true Kluyveromyces genus. The other species of the genus were grouped with lower bootstrap levels. Finally, the restriction map showed by three K. lactis strains, previously identified as K. marxianus var. drosophilarum, could be interpreted as indicatory of the possible existence of different species.

Geographical variation in agonistic behaviour in a ring species of salamander, Ensatina eschscholtzii

Ensatina eschscholtzii is a plethodontid salamander with several geographical races distributed in a ring-like series throughout the coastal mountains and inland Sierra Nevada mountains of California. Populations of these salamanders show genetic and morphological divergence, and in this study, we examined divergence in overt aggressive, passive aggressive/exploratory, avoidance and sensory behaviours in four populations. Two of the populations represent a zone of secondary contact between coastal and inland lineages of Ensatina. We recorded behaviour of resident salamanders paired with same-sex intruders during the non-courtship season. The residents' behaviour was affected independently by the population of the resident and the population of the intruder but not by the interaction between the resident population and the intruder population. Levels of agonistic and sensory behaviour showed a high degree of constraint among the populations. These behaviours also showed divergence among coastal and inland populations, and the geographical variation in behaviour is consistent with the phylogenetic history of Ensatina. Convergent evolution of behaviour appears to have occurred at the zone of secondary contact between the coastal and inland lineages. Variation in agonistic and sensory behaviour among the populations observed and between the sexes suggests that there may be geographical and sexual variation in territoriality or competition. Copyright 1998 The Association for the Study of Animal Behaviour. Copyright 1999 The Association for the Study of Animal Behaviour.

A priori estimation of phylogenetic information conserved in aligned sequences

A new phenomenological approach to explorative data analysis, the estimation of spectra of supporting positions, allows the search for conserved tracks left by phylogeny in DNA sequences. Spectra of supporting positions can be generated without reference to a tree topology or a model of sequence evolution and are therefore an ideal tool for a priori estimation of information content of data sets. Analysis of published 18S rDNA alignments shows that signal to noise relationship varies greatly in a way not detected by conventional tree-construction methods.

Weighting and congruence: a case study based on three mitochondrial genes in pitvipers

Weighting strategies in a total evidence approach are often conducted in order to remove homoplasy, with the implicit hope to increase congruence between data partitions. Incongruence was measured using the test of Farris et al. (J. S. Farris, M. Källersjö, A. G. Kluge, and C. Bult, 1995, Cladistics 10, 315-319) within and between three mitochondrial genes from pitvipers (Crotalinae) in partitioning each codon position for the coding genes. Incongruence between codon positions of a gene can be worse than incongruence between genes at analogous positions. Third positions of codons behave very differently in terms of incongruence from one gene to another while showing similar patterns in saturation tests. Instead of removing characters in order to discard homoplasy, which is hopeless and does not increase general congruence, we advocate for the removal of those substitutions that are incongruent with the rest. The genus Calloselasma and its sister group the genus Hypnale are the most basal Crotalinae. Asiatic pitvipers are paraphyletic, while American pitvipers are monophyletic.

Homology of Hox genes and the zootype concept in early metazoan evolution

The correct identification of homologous Hox genes within and between diplo- and triploblastic animals is of crucial importance for recent hypotheses on the anagenetic evolution of animal bauplans. While the homology discussion in general has reached new heights, we apply traditional homology criteria to assign homology to Hox genes from diploblastic animals. Comparison of the Trox-2 gene from the presumably most basal metazoan animal, the placozoan Trichoplax adhaerens, to other Hox genes suggests the presence of unambiguous homologs in Hydrozoa and Scyphozoa and the absence of any specific homolog in triploblasts. Furthermore, the comparisons provide support for the idea that Hox genes-at least in diploblastic animals-are composed of functional subunits (modules), which to some degree have undergone independent evolution. The findings are not readily compatible with the existence of the "zootype" in diploblastic animals.

Molecular and morphological phylogenies of mammals: congruence with stratigraphic data

Tests of a sample of 206 cladograms of mammals show that morphological data seem to predict phylogenies that match the known fossil record better than molecular trees. Three metrics that assess the rank order of branching points, the stratigraphic consistency of those nodes, and the ratio of ghost range to known range show a considerable diversity of values. Some published trees show excellent matching with fossil-record data; others show almost no correspondence whatsoever. Morphological trees are nearly twice as good as molecular trees in terms of matching of the rank orders of nodes and oldest fossils, while morphological trees are 10% better than molecular in terms of stratigraphic consistency of the nodes. The ratios of ghost range to known range are lower for molecular trees. Among the molecular trees, those based on gene data are considerably better than those based on protein sequences, at least in terms of the rank order of nodes and the stratigraphic consistency of nodes. Protein trees, however, were best of all in terms of minimizing the proportion of ghost range. These findings probably indicate real phenomena, but the match of molecular trees to the expectations of stratigraphy may improve as the study of molecular phylogeny matures.

Assessing the relative contribution of molecular and morphological characters in simultaneous analysis trees

We examined the contribution of morphological and molecular character information for 15 systematics studies in which these two kinds of data were used in combined or simultaneous analyses. Assessment of the disagreement between these data sources, as measured by the incongruence length difference, reveals substantial conflict for the studies surveyed. In addition, the partitioned Bremer support was used to measure the degree of support provided by each data partition when analyzed together. Despite the significant incongruence found for nearly half the studies, the PBS indices suggest both types of data contribute positively to the combined analyses and that, when standardized by the number of phylogenetically informative characters, morphology data generally provide equal or greater support than do the molecular data. This result, combined with the fact that morphological characters generally exhibit higher consistency, indicates that this source of character information continues to be useful in systematics studies despite the increasing volume of available molecular data.

What does palaeontology contribute to systematics in a molecular world?

Palaeontology provides the only direct record for morphological and genetic change through time and uniquely contributes to systematics in two ways: by providing access to denser taxon sampling than is otherwise possible and by dating divergence times. Claims that ancient DNA has survived millions of years in certain fossils suggested the possibility that palaeontology could contribute directly to molecular systematic studies. Unfortunately, none of the supposed geologically ancient DNA records stands up to detailed scrutiny and fossils therefore contribute primarily through the morphological information they preserve. Denser taxon sampling can improve the accuracy of phylogenetic estimates primarily through allowing better discrimination of homoplasy from homology. This in turn leads to more accurate hypotheses of character transformation. Denser taxon sampling also offers the opportunity for more accurate rooting, since more characters can be polarized by reference to a stem-group taxon than to an extant sister-group taxon. Missing data can be a problem for fossils, but is not crippling. Finally the temporal order of clade appearances in the fossil record can provide ancillary evidence for selecting a working phylogeny from among a number of equally most parsimonious cladograms.

The position of arthropods in the animal kingdom: a search for a reliable outgroup for internal arthropod phylogeny

Morphological evidence for the phylogeny of the animal kingdom has been discussed by numerous authors. DNA sequencing and phylogenetic methods for analyzing these data are alternative approaches to animal phylogeny, but the phenomenon of long branch attraction and poor taxonomic sampling have caused misinterpretations of metazoan relationships. Here we report a cladistic approach to metazoan evolution including 133 18S rDNA sequences of 31 animal phyla. Despite the difficulties associated with analyzing large data sets, our data suggest that the Bilateria and Protostomia are monophyletic. The internal phylogeny of the protostomes is divided into two main clades. One clade includes the classical protostome worms (annelids, sipunculans, echiurans, pogonophorans, and vestimentiferans), mollusks, nemerteans, "lophophorates," platyhelminths, rotiferans, and acanthocephalans, although the internal resolution of the clade is very low. The second clade includes arthropods and other molting animals: tardigrades, onychophorans, nematodes, nematomorphans, kinorhynchs, and priapulans. The arthropods and related phyla lack a ciliated larvae, lack a multiciliate (locomotory) epithelium, and share many features, notably, a reduced coelomic cavity and the presence of a cuticle which molts. The use of these outgroups within the molting clade to root arthropod phylogenies is recommended instead of using annelids or other spiralians. The data are quite conclusive in those phyla with a good taxonomic sampling (i.e., platyhelminths and arthropods).

Phylogeny of West African Caryedon (coleoptera: bruchidae): congruence between molecular and morphological data

Seed beetles belonging to the Old World genus Caryedon feed in the seeds of various Caesalpinioideae, Mimosoideae, and Combretaceae. In an attempt to resolve broad phylogenetic relationships within the genus, we obtained 332 base pair sequences of mitochondrial 12S ribosomal DNA and morphological data for the 16 West African Caryedon species. Morphological characters were analyzed under maximum parsimony and sequences were compared under maximum parsimony, maximum likelihood, and neighbor joining. Using a partition homogeneity test, we determined that morphological and molecular data sets were combinable. Combined data were analyzed under maximum parsimony. Morphological and molecular trees were congruent at the species group level and total evidence analyses yielded the same topologies as molecular data with each of the three outgroups used. Four main terminal clades are recognized, each corresponding with a group of species generally feeding on the same host plant family, subfamily, genus, or species. The monophyly of legume feeding Caryedon is supported by both data sets, and Combretaceae feeders split in two monophyletic assemblages.

Molecules and morphology: conflicts and congruence within the fern genus Trichomanes (Hymenophyllaceae)

The interaction between three independent data sets (anatomy/morphology, cytology, molecules) has been evaluated within the controversial genus Trichomanes (Hymenophyllaceae). Anatomy/morphology, cytology, and rbcL sequences, despite their high and significant level of incongruence, were thus empirically combined with differential weighting in a cladistic analysis within Trichomanes in order to give an appreciation of the contribution of each data set in the resulting topologies and to study more precisely the nature of potential conflicts. Results show that any standard statistics values (such as bootstrap) do not appear to be objectively useful for the choice of the "best" topology or the "good" clades provided by the combination. This weighting approach reveals three cases: (i) some clades (such as subgenus Didymoglossum) are always retrieved and correspond to the absence of conflicts between the different data, (ii) some new clades (such as subgenus Achomanes) are either provided or reenforced as a "synergetic" result of the combination of the data and (iii) that remaining conflicting clades reflect the persistence of incongruence between data whatever the weighting.

Estimating ancestral states of a communicative display: a comparative study of Cyclura rock iguanas

In this study we describe the signature headbob displays of seven of the eight extant species of Cyclura iguanas using data collected from the field and from captive animals. We used phylogenetic comparative methods to estimate the ancestral states of several measures of the headbob displays, including number of headbobs and the duration of headbobs and inter-bob pauses. Divergence in the headbob display among species has been substantial, with some major changes occurring within only a few (about six) generations. Otherwise, results are consistent with those obtained previously for other lizards which suggest that there is an evolutionary limit on the total duration of headbob displays. Differences in the results obtained using different phylogenetic methods suggest that although estimates of ancestral states are reasonably robust to violations of evolutionary assumptions, we cannot determine the standard errors of those ancestral phenotypes accurately without more detailed information about the types of forces (e.g. selection, drift) underlying evolutionary change in these traits. In particular, within-species variation had a substantial impact on the standard errors of estimated ancestral states, and should be included in such estimations whenever possible. Finally, our results emphasize the importance of conserving behavioural as well as genetic diversity in trying to preserve endangered species for possible reintroduction into the wild. Copyright 1998 The Association for the Study of Animal Behaviour. Copyright 1998 The Association for the Study of Animal Behaviour.

Finding optimal ingroup topologies and convexities when the choice of outgroups is not obvious

Considerable confusion remains among theoreticians and practicioners of phylogenetic science on the use of outgroup taxa. Here, we show that, despite claims to the contrary, details of the optimal ingroup topology can be changed by switching outgroup taxa. This has serious implications for phylogenetic accuracy. We delineate between the process of outgroup selection and the various possible processes involved in using an outgroup taxon after one has been selected. Criteria are needed for the determination that particular outgroup taxa do not reduce the accuracy of evolutionary tree topologies and inferred character state transformations. We compare previous results from a sensitivity bootstrap analysis of the mitochondrial cytochrome b phylogenetic relationships among whales to the results of a Bremer support sensitivity analysis and of a recently developed application of RASA theory to the question of putative outgroup taxon plesiomorphy content.

Characterization of the myoglobin and its coding gene of the mollusc Biomphalaria glabrata

A cDNA clone isolated from a Biomphalaria glabrata (Mollusca, Gastropoda) neural cDNA library was identified as encoding a myoglobin-like protein of 148 amino acids with a single domain and a calculated mass of 16,049.29. Alignment with globin sequences with known tertiary structure confirms its overall globin nature. The expressed myoglobin was identified in the radular muscle and isolated. Oxygen equilibrium measurements on the protein reveal a high oxygen affinity. Val-B10 and Gln-E7, important residues for the determination of the oxygen affinity, are strikingly different from the standard molluscan pattern (Conti, E., Moser, C., Rizzi, M., Mattevi, A., Lionetti, C., Coda, A., Ascenzi, P., Brunori, M., Bolognesi, M. (1993) J. Mol. Biol. 233, 498-508). The single gene encoding the globin chain is interrupted by three introns at positions A3.2, B12.2, and G7.0. Comparison with other nonvertebrate globin genes reveals on the one hand conservation (B12.2 and G7.0) and on the other hand variability of the insertion positions (A3.2). The Biomphalaria myoglobin sequence was used together with all other molluscan globin sequences available to assess the origin and phylogeny of the phylum. Our results confirm the doubts raised about monophyletic origin of the Mollusca, which was first observed using SSU rRNA as a molecular marker.

Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution

Estimation of evolutionary distances has always been a major issue in the study of molecular evolution because evolutionary distances are required for estimating the rate of evolution in a gene, the divergence dates between genes or organisms, and the relationships among genes or organisms. Other closely related issues are the estimation of the pattern of nucleotide substitution, the estimation of the degree of rate variation among sites in a DNA sequence, and statistical testing of the molecular clock hypothesis. Mathematical treatments of these problems are considerably simplified by the assumption of a stationary process in which the nucleotide compositions of the sequences under study have remained approximately constant over time, and there now exist fairly extensive studies of stationary models of nucleotide substitution, although some problems remain to be solved. Nonstationary models are much more complex, but significant progress has been recently made by the development of the paralinear and LogDet distances. This paper reviews recent studies on the above issues and reports results on correcting the estimation bias of evolutionary distances, the estimation of the pattern of nucleotide substitution, and the estimation of rate variation among the sites in a sequence.

Evolution of DNA or amino acid sequences with dependent sites

A framework is outlined to study the evolution of DNA or amino acid sequences, if sequence sites do not evolve independently. The units of evolution are nonoverlapping subsequences of length l. Each subsequence evolves independently of the others, but within a subsequence the sequences show a Markov order one dependency. We describe an algorithm to mimic the evolution of such sequences. The influence of dependencies between sites on distance estimates and the reliability of tree reconstruction methods is investigated. We show that an inappropriate model of sequence evolution in the tree reconstruction process will lead to a nonempty Felsenstein zone. Finally, we describe a method to infer l from sequence data. Examples from the evolution of DNA sequences as well as from amino acids are given.

Duplication-based measures of difference between gene and species trees

In the framework of a duplication-based method for comparing gene and species trees, the concepts of "duplication" and "loss" are reformulated in set-theoretic terms. A number of related tree dissimilarity measures is suggested, and relations between them are analyzed. For any node in the species tree, the number of gene duplications for which it is a "non-child" loss coincides with the number of times when the node's parent is an intermediate between the mapping images of a gene node and its parent. This implies that the total number of losses is equal to the number of intermediate nodes plus the number of one-side duplications and, thus, provides an alternative proof for a conjecture made by Mirkin, Muchnik, and Smith (1995). Another formula proven involves crossings (incompatible gene-species node pairs): the number of losses equals the number of crossings plus the number of duplications.

New phylogenetic perspectives on the Cervidae (Artiodactyla) are provided by the mitochondrial cytochrome b gene

The entire mitochondrial cytochrome b (cyt b) gene was compared for 11 species of the artiodactyl family Cervidae, representing all living subfamilies, i.e., the antlered Cervinae (Cervus elaphus, C. nippon, Dama dama), Muntiacinae (Muntiacus reevesi), and Odocoileinae (Odocoileus hemionus, Mazama sp., Capreolus capreolus, C. pygargus, Rangifer tarandus, Alces alces); and the antlerless Hydropotinae (Hydropotes inermis). Phylogenetic analyses using Tragulidae, Antilocapridae, Giraffidae and Bovidae as outgroups provide evidence for three multifurcating principal clades within the monophyletic family Cervidae. First, Cervinae and Muntiacus are joined in a moderately-to-strongly supported clade of Eurasian species. Second, Old World Odocoileinae (Capreolus and Hydropotes) associate with the Holarctic Alces. Third, New World Odocoileinae (Mazama and Odocoileus) cluster with the Holarctic Rangifer. The combination of mitochondrial cyt b and nuclear k-casein sequences increases the robustness of these three clades. The Odocoileini + Rangiferini clade is unambiguously supported by a unique derived cranial feature, the expansion of the vomer which divides the choana. Contrasting with current taxonomy, Hydropotes is not the sister group of all the antlered deers, but it is nested within the Odocoileinae. Therefore, Hydropotes lost the antlers secondarily. Thus, the mitochondrial cyt b phylogeny splits Cervidae according to plesiometacarpal (Cervinae + Muntiacinae) versus telemetacarpal (Odocoileinae + Hydropotinae) conditions, and suggests paraphyly of antlered deer.

Fluctuating asymmetry in an ornamental trait in the cave weta, Pleioplectron simplex Hutton (Orthoptera: Rhaphidophoridae): no role for parasites

Using digitised pictures of the pronotum, we investigated the influence of nematomorph and mermithid parasites on the expression (intensity and fluctuating asymmetry) of cuticular ornamentation in the cave weta, Pleioplectron simplex. Because P. simplex is nocturnal, this ornamentation is probably not subject to strong directional or stabilising selection. Based on measurements of brightness, we found no significant difference in the amount of pigmented area between unparasitised and parasitised males or females. Parasitised individuals were not significantly more asymmetrical than unparasitised ones. This result was not due to measurement error. Among parasitised wetas, brightness and the fluctuating asymmetry were not related to the length of the parasite, even when the size of the host was taken into account. These results are discussed in relation to current ideas concerning the influence of parasites on fluctuating asymmetry of traits in the host.

Structured-tree topology and adaptive evolution of the simian immunodeficiency virus SIVsm envelope during serial passage in rhesus macaques according to likelihood mapping and quartet puzzling

Species-specific strains of simian immunodeficiency virus (SIV) are nonpathogenic in African primates. The SIV strain most closely related to human immunodeficiency virus type 2 (HIV-2) is SIVsm, the strain specific to the sooty mangabey (Cercocebus atys). Infection of Asian primates with SIV causes AIDS and allows the study of the adaptive evolution of a lentivirus to replicate efficiently in a new host, providing a useful animal model of HIV infection and AIDS in humans. Serial passage of SIVsm from sooty mangabeys in rhesus macaques drastically shortened the time of disease progression from 1.5 years to 1 month as the retrovirus adapted to these Asian hosts. In the present study we analyzed the quasispecies nature of the SIVsm envelope gene (env) during serial population passage in rhesus macaques. We asked ourselves if phylogenetic evidence could be provided for the structured topology of the SIVsm env tree and subsequently for the adaptive evolution of SIVsm env. Likelihood mapping showed that phylogenetic reconstruction of the passage was possible because a high percentage of the sequence data had a "tree-like" form. Subsequently, quartet puzzling was used and produced a phylogeny with a structure parallel to the known infection history. The adaptation of SIVsm to Asian rhesus macaques appears to be an ordered process in which the env evolves in a tree-like manner, particularly in its constant regions.

Parasite extinction and colonisation and the evolution of parasite communities: a simulation study

We determined what evolutionary processes influence the likelihood of detecting an effect of host ecological characteristics on the richness of parasite communities in comparative analyses among related host species. We used a mathematical model to generate phylogenies of hosts in which parasite communities varied over evolutionary time as parasite species were either gained or lost during host speciation events. Gain or loss of parasites were stochastic and could either be strongly, moderately, weakly, or not, affected by host ecological characteristics. The model was evaluated over this range of effects of host ecology, and for various mean probabilities of parasite gain and loss and various rates of change in host ecological characteristics at speciation events. Our results suggest that phylogenetic effects (the passing of parasite species from mother to daughter host species) are likely to obscure ecological effects (the effect of host body size, diet, habitat, lifespan, etc.) except when the effects of host ecology are strong, and the probabilities of gain or loss of parasites are high, or host ecological characteristics change markedly at speciation events. This outcome was not influenced by the shape of the phylogenetic tree used in the simulations. Sensitivity analysis of our model also shows this result to be robust to a wide range of assumptions and parameter values. Thus, because the composition of parasite communities tends to reflect their ancestry, the effect of host ecology will often be very difficult to detect.

Jungles: a new solution to the host/parasite phylogeny reconciliation problem

The problem of finding least-cost reconstructions of past host/parasite associations, given the phylogenetic histories of a set of host taxa and of their associated parasites, is known to be complex. I provide in this article a new method of implicitly listing all the potentially optimal solutions to the problem, by considering each hypothesised past association individually, in a structure I have termed a Jungle. These structures are demonstrated to enable fast acquisition of globally optimal solutions under general weighting schemes, including minimisation of total number of postulated events and maximization of postulated cospeciation events. A simple example is given, and the pocket gopher/chewing louse system investigated by Hafner and Nadler [Hafner and Nadler, Nature 332 (1988) 258] is re-examined.

The impact of traveling to endemic areas on the spread of hepatitis E virus infection: epidemiological and molecular analyses

Traveling to endemic areas carries a risk of hepatitis E virus (HEV) infection, but no molecular analysis to document sources of infection is available. Eighteen (38%) of 47 patients with acute non-A, non-B, non-C hepatitis were positive for antibody to HEV (anti-HEV), and 9 (50%) of these were also positive for serum HEV RNA by polymerase chain reaction following reverse transcription. Only 1 (5%) of the 21 patients with acute hepatitis A was positive for HEV RNA. Travel to endemic areas (mostly to China; odds ratio, 22.2; 95% confidence interval, 4.7-105.8) and deeper jaundice (odds ratio, 5.2; 95% confidence interval, 1.01-27.2) were the only factors associated with HEV infection in multivariate analysis. The two HEV isolates from two patients who had traveled to China and the HEV isolate from a patient whose travel history was obscure formed a monophyletic group with the isolates from Guangzhou. The HEV isolates from our patients show a homology of 72% to 78% in nucleotide sequence with the Burma, Beijing, India, Pakistan, and Xiangjiang strains; a homology of 81% to 91% with the Guangzhou strains; and a homology of 76% with the Mexico strain. The close relationship between the Taiwan isolates and the Guangzhou strains was further supported by the short Kimura's two-parameter distances among them. In summary, HEV infection does occur in this area. Epidemiological and molecular analyses strongly indicate that most cases of HEV infection originated from travel to HEV-endemic areas.

Phylogenetic placement of rickettsiae from the ticks Amblyomma americanum and Ixodes scapularis

A rickettsial isolate (isolate MOAa) belonging to the spotted fever group (SFG) was obtained from the lone star tick Amblyomma americanum. We used PCR to characterize the genes for the rickettsial outer membrane proteins rOmpA and rOmpB. We sequenced the PCR products (domains I of both the rompA gene and the rompB gene) of MOAa and WB-8-2, another rickettsial isolate from A. americanum. To place MOAa and WB-8-2 and two other nonpathogenic isolates (Rickettsia rickettsii Hip2 and Rickettsia montana M5/6) with respect to their putative sister species, we included them in a phylogenetic analysis of 9 Rickettsia species and 10 Rickettsia strains. Our phylogenetic results implied three evolutionary lineages of SFG rickettsiae and that WB-8-2 and MOAa were most closely related to R. montana. New World isolates were not the most closely related to each other (they did not form a clade). Rather, our results supported four independent origins (introductions) of rickettsiae into North America from different Old World regions. The results of our phylogenetic analysis did not support the hypothesis of a stable coevolution of rickettsiae and their tick hosts. Finally, we examined the rompA gene of a nonpathogenic rickettsial symbiont isolated from the tick Ixodes scapularis. In a phylogenetic analysis, the symbiont was placed as the sister to R. montana and its isolates. The relationship of this symbiont to R. montana raised questions as to the potential origin of pathogenic SFG rickettsiae from nonpathogenic tick symbionts, or vice versa.

Host and environmental correlates of body size in ticks (Acari: Argasidae and Ixodidae)

To evaluate the influence of host mass and environmental temperature on the evolution of body size in ticks, a comparative analysis was performed using data from 193 species. Using the 20 possible phylogenetically independent contrasts among tick species, no relationship was found between body size of female ticks and either host mass or temperature. The statistical power of these analyses was low. Within the two most speciose genera of soft ticks, however, separate cross-species analyses revealed a positive and highly significant relationship between female tick size and host mass. Also, within the two most speciose genera of hard ticks, cross-species analyses showed a positive and highly significant relationship between scutum size of female ticks and host mass. The latter correlation is based on measurements of tick body size that are independent of the level of blood engorgement. No effect of temperature was observed in the within-genera analyses. These within-genera trends may be artefacts of unknown phylogenetic relationships. Another explanation, however, is that host body mass may have influenced the evolution of tick body size.

Invasion genetics of the Mediterranean fruit fly: variation in multiple nuclear introns

Biological invasions generally start from low initial population sizes, leading to reduced genetic variation in nuclear and especially mitochondrial DNA. Consequently, genetic approaches for the study of invasion history and population structure are difficult. An extreme example is the Mediterranean fruit fly, Ceratitis capitata (Medfly), for which successive invasions during this century have resulted in a loss of 60% of ancestral genetic variation in isozymes and 75% of variation in mitochondrial DNA. Using Medflies as an example, we present a new approach to invasion genetics that measures DNA sequence variation within introns from multiple nuclear loci. These loci are so variable that even relatively recently founded Medfly populations within California and Hawaii retain ample genetic diversity. Invading populations have only lost 35% of the ancestral genetic variation. Intron variation will allow high-resolution genetic characterization of invading populations in both natural and managed systems, although non-equilibrium methods of analysis may be necessary if the genetic diversity represents sorting ancestral polymorphism.

Base-compositional biases and the bat problem. III. The questions of microchiropteran monophyly

Using single-copy DNA hybridization, we carried out a whole genome study of 16 bats (from ten families) and five outgroups (two primates and one each dermopteran, scandentian, and marsupial). Three of the bat species represented as many families of Rhinolophoidea, and these always associated with the two representatives of Pteropodidae. All other microchiropterans, however, formed a monophyletic unit displaying interrelationships largely in accord with current opinion. Thus noctilionoids comprised one clade, while vespertilionids, emballonurids, and molossids comprised three others, successively more closely related in that sequence. The unexpected position of rhinolophoids may be due either to the high AT bias they share with pteropodids, or it may be phylogenetically authentic. Reanalysis of the data with varying combinations of the five outgroups does not indicate a rooting problem, and the inclusion of many bat lineages divided at varying levels similarly discounts long branch attraction as an explanation for the pteropodid-rhinolophoid association. If rhinolophoids are indeed specially related to pteropodids, many synapomorphies of Microchiroptera are called into question, not least the unitary evolution of echolocation (although this feature may simply have been lost in pteropodids). Further, a rhinolophoid-pteropodid relationship--if true--has serious implications for the classification of bats. Finally, among the outgroups, an apparent sister-group relation of Dermoptera and Primates suggests that flying lemurs do not represent the ancestors of some or all bats; yet, insofar as gliding of the type implemented in dermopterans is an appropriate model for the evolution of powered mammalian flying, the position of Cynocephalus in our tree indirectly strengthens the argument that true flight could have evolved more than once among bats.

The heart of metamorphosing Mexican axolotl but not that of the cardiac mutant is associated with the upregulation of Hox A5

The Mexican axolotl (Ambystoma mexicanum) is a facultative neotene which rarely undergoes metamorphosis in the wild. We now report for the first time a dramatic increase in the expression of HoxA5 in axolotl hearts as determined by RT-PCR and in situ hybridization analyses during spontaneous metamorphosis. The Mexican axolotl has a naturally occurring mutation called gene c which allows hearts in homozygous (c/c) embryos to form but never to beat. RT-PCR analysis has not shown any significant differences of HoxA5 expression in normal and mutant hearts. The predicted open reading frame of our already published partial cDNA clone of HoxA5 was confirmed by expressing it as a fusion protein with Glutathione transferase (GST fusion protein). Phylogenetic analysis with the deduced amino acid sequence of the isolated cDNA of the axolotl homolog of the murine HoxA5 shows that the axolotl sequence clusters more closely with the human and mouse HoxA5 homologs than with axolotl sequence. Western blot analysis revealed that anti-mouse HoxA5 antibody recognizes the axolotl HoxA5 protein.

Evolutionary relationships among Japanese pond frogs inferred from mitochondrial DNA sequences of cytochrome b and 12S ribosomal RNA genes

The evolutionary relationships among Japanese pond frogs (Rana nigromaculata, R.porosa porosa, and R. p. brevipoda) were investigated by analyzing nucleotide sequences of mitochondrial cytochrome b (cyt b) and 12S rRNA genes. The nucleotide sequences of 444-bp segment of the cyt b gene and 410-bp segment of 12S rRNA gene were determined by the PCR-direct sequencing method using 18 frogs from 13 populations of Japanese pond frogs, and phylogenetic trees were constructed by the neighbor-joining and maximum likelihood methods using R. catesbeiana as an outgroup. The sequenced 444-bp segment of cyt b gene provided 69 variables sites, and the sequenced 410-bp segment of 12S rRNA gene provided 21 variables sites. The numbers of nucleotide substitutions per site of the cyt b gene within ingroup were 0.0022-0.0205 at the populational level, 0.0368-0.0462 at the racial or subspecific level, and 0.1038-0.1244 at the specific level, whereas those of the 12S rRNA gene were 0-0.0074 at the populational or subspecific level, and 0.0378-0.0456 at the specific level. Most nucleotide substitutions within ingroup occurred at the third codon position of the cyt b gene and were silent mutations. High frequencies of transitions relative to transversions were shown at cyt b and 12S rRNA genes within ingroup. The phylogenetic trees constructed from the nucleotide sequences of the cyt b gene showed that after outgroup R. catesbeiana separated from ingroup frogs, ingroup Japanese pond frogs diverged into R.nigromaculata and R.porosa, then the latter diverged into R.p. porosa, R.p. brevipoda (the typical Okayama race), and the Nagoya race of R.p.porosa. The phylogenetic trees constructed from the nucleotide sequences of the 12S rRNA gene also showed distinct divergence between two species, but not any divergence within species.

Speciation and phylogeography of Hawaiian terrestrial arthropods

The Hawaiian archipelago is arguably the world's finest natural laboratory for the study of evolution and patterns of speciation. Arthropods comprise over 75% of the endemic biota of the Hawaiian Islands and a large proportion belongs to species radiations. We classify patterns of speciation within Hawaiian arthropod lineages into three categories: (i) single representatives of a lineage throughout the islands; (ii) species radiations with either (a) single endemic species on different volcanoes or islands, or (b) multiple species on each volcano or island; and (iii) single widespread species within a radiation of species that exhibits local endemism. A common pattern of phylogeography is that of repeated colonization of new island groups, such that lineages progress down the island chain, with the most ancestral groups (populations or species) on the oldest islands. While great dispersal ability and its subsequent loss are features of many of these taxa, there are a number of mechanisms that underlie diversification. These mechanisms may be genetic, including repeated founder events, hybridization, and sexual selection, or ecological, including shifts in habitat and/or host affiliation. The majority of studies reviewed suggest that natural selection is a primary force of change during the initial diversification of taxa.

Who's related to whom? Recent results from molecular systematic studies

Similarities among model systems can lead to generalizations about plants, but understanding the differences requires systematic data. Molecular phylogenetic analyses produce results similar to traditional classifications in the grasses (Poaceae), and relationships among the cereal crops are quite clear. Chloroplast-based phylogenies for the Solanaceae show that tomato is best considered as a species of Solanum, closely related to potatoes. Traditional classifications in the Brassicaceae are misleading with regard to true phylogenetic relationships and data are only now beginning to clarify the situation. Molecular data are also being used to revise our view of relationships among flowering plant families. Phylogenetic data are critical for interpreting hypotheses of the evolution of development.

Character congruence of multiple data partitions and the origin of the Hawaiian Drosophilidae

We address two systematic questions, the origin and monophyly of the Hawaiian Drosophilidae and the question of how to analyze multiple data partitions containing disparate kinds of information, in this study. New evidence, from analysis of characters from morphology, mitochondrial DNA, and nuclear DNA suggests that the Hawaiian Drosophilidae are a monophyletic assemblage. Although we are not able to suggest a single species group which may represent the continental sister taxon to the Hawaiian Drosophilidae, the candidates suggested by our analysis, the melanicarobusta lineage and the virilis-repleta lineage, have been suggested by other investigators as probable sister taxa. Through analyses of our data partitions separately and in a variety of combinations, we conclude that the best phylogenetic hypothesis to be generated from multiple data partitions will be obtained if the data from these partitions are combined and analyzed simultaneously. We advocate performing tests for congruence between and among data partitions not to justify keeping them apart, but for understanding the interactions among the signals included in the analysis and how they affect the topology of, and support for, the total evidence tree.

Comparative mtDNA phylogeography of neotropical freshwater fishes: testing shared history to infer the evolutionary landscape of lower Central America

Historical biogeography seeks to explain contemporary distributions of taxa in the context of intrinsic biological and extrinsic geological and climatic factors. To decipher the relative importance of biological characteristics vs. environmental conditions, it is necessary to ask whether groups of taxa with similar distributions share the same history of diversification. Because all of the taxa will have shared the same climatic and geological history, evidence of shared history across multiple species provides an estimate of the role of extrinsic factors in shaping contemporary biogeographic patterns. Similarly, differences in the records of evolutionary history across species will probably be signatures of biological differences. In this study, we focus on inferring the evolutionary history for geographical populations and closely related species representing three genera of primary freshwater fishes that are widely distributed in lower Central America (LCA) and northwestern Colombia. Analysis of mitochondrial gene trees provides the opportunity for robust tests of shared history across taxa. Moreover, because mtDNA permits inference of the temporal scale of diversification we can test hypotheses regarding the chronological development of the Isthmian corridor linking North and South America. We have focused attention on two issues. First, we show that many of the distinct populations of LCA fishes diverged in a relatively brief period of time thus limiting the phylogenetic signal available for tests of shared history. Second, our results provide reduced evidence of shared history when all drainages are included in the analysis because of inferred dispersion events that obscure the evolutionary history among drainage basins. When we restrict the analysis to areas that harbour endemic mitochondrial lineages, there is evidence of shared history across taxa. We hypothesize that there were two to three distinct waves of invasion into LCA from putative source populations in northwestern Colombia. The first probably happened in the late Miocene, prior to the final emergence of the Isthmus in the mid-Pliocene; the second was probably coincident with the rise of the Isthmus in the mid-Pliocene, and the third event occurred more recently, perhaps in the Pleistocene. In each case the geographical scale of the dispersion of lineages was progressively more limited, a pattern we attribute to the continuing development of the landscape due to orogeny and the consequent increase in the insularization of drainage basins. Thus, the fisheye view of LCA suggests a complex biogeographic history of overlaid cycles of colonization, diversification, sorting and extinction of lineages.