Body size and feeding specificity: macrolepidoptera in Britain

Within a geographic assemblage, large-bodied species of macrolepidopteran moths tend, on average, to be less host-specific than small-bodied. Five possible explanations for this pattern are identified, based respectively on (i) phylogenetic relationships between species, (ii) latitudinal gradients in body size and feeding specificity, (iii) the relationship between range size and body size, (iv) larger body size as a buffer from environmental variation, and (v) the relationship between endophagous host associations and small body size. These mechanisms are tested using data for British macrolepidoptera and also evaluated using evidence from the literature at large. Although some of their assumptions are found to be justified, there is no significant support for any single mechanism. This lack of evidence for previously proposed mechanisms is discussed in the light of a recently proposed alternative explanation which combines theories of host quality and host defence mechanisms.Copyright 1998 The Linnean Society of London

Sex determination in plants

The majority of flowering plants produce flowers that are "perfect." These flowers are both staminate (with stamens) and pistillate (with one or more carpels). In a small number of species, there is spatial separation of the sexual organs either as monoecy, where the male and female organs are carried on separate flowers on the same plant, or dioecy, where male and female flowers are carried on separate male (staminate) or female (pistillate) individuals. Sex determination systems in plants, leading to unisexuality as monoecy or dioecy, have evolved independently many times. In dioecious plant species, the point of divergence from the hermaphrodite pattern shows wide variation between species, implying that the genetic bases are very different. This review considers monoecious and dioecious flowering plants and focuses on the underlying genetic and molecular mechanisms. We propose that dioecy arises either from monoecy as an environmentally unstable system controlled by plant growth substances or from hermaphroditism where the underlying mechanisms are highly stable and control does not involve plant growth substances.

Adaptive evolution via a major gene effect: paedomorphosis in the Mexican axolotl

Although adaptive evolution is thought to depend primarily on mutations of small effect, major gene effects may underlie many of the important differences observed among species in nature. The Mexican axolotl (Ambystoma mexicanum) has a derived mode of development that is characterized by metamorphic failure (paedomorphosis), an adaptation for an entirely aquatic life cycle. By using an interspecific crossing design and genetic linkage analysis, a major quantitative trait locus for expression of metamorphosis was identified in a local map of amplified fragment length polymorphisms. These data are consistent with a major gene hypothesis for the evolution of paedomorphosis in A. mexicanum.

The interphotoreceptor retinoid binding protein gene in therian mammals: implications for higher level relationships and evidence for loss of function in the marsupial mole

The subclass Theria of Mammalia includes marsupials (infraclass Metatheria) and placentals (infraclass Eutheria). Within each group, interordinal relationships remain unclear. One limitation of many studies is incomplete ordinal representation. Here, we analyze DNA sequences for part of exon 1 of the interphotoreceptor retinoid binding protein gene, including 10 that are newly reported, for representatives of all therian orders. Among placentals, the most robust clades are Cetartiodactyla, Paenungulata, and an expanded African clade that includes paenungulates, tubulidentates, and macroscelideans. Anagalida, Archonta, Altungulata, Hyracoidea + Perissodactyla, Ungulata, and the "flying primate" hypothesis are rejected by statistical tests. Among marsupials, the most robust clade includes all orders except Didelphimorphia. The phylogenetic placement of the monito del monte and the marsupial mole remains unclear. However, the marsupial mole sequence contains three frameshift indels and numerous stop codons in all three reading frames. Given that the interphotoreceptor retinoid binding protein gene is a single-copy gene that functions in the visual cycle and that the marsupial mole is blind with degenerate eyes, this finding suggests that phenotypic degeneration of the eyes is accompanied by parallel changes at the molecular level as a result of relaxed selective constraints.

Cross-species comparisons

Cognitive and neural adaptations in animals have been analysed using the comparative method. Comparisons between closely related species that differ in a cognitive or neural character, and comparison between distantly related species that share a cognitive or neural character, can be used to identify adaptations. Recent research has identified adaptive modifications of memory and the hippocampus that have evolved convergently in two clades of food-storing birds, the chickadees and tits (Paridae), and the jays and nutcrackers (Corvidae). Similar modifications of the hippocampus occur in other groups of animals, such as the cowbird brood parasites, in which there has been selection for spatial memory. Three general patterns that emerge from the comparative study of animal cognition provide a framework for research on human psychological adaptations: the existence of both specialized and general cognitive capacities; a clear relation between specialized capacities and specific selective pressures; and evolutionary change in the relative size of brain areas with cognitive functions.

Inferring species trees from gene trees: a phylogenetic analysis of the Elapidae (Serpentes) based on the amino acid sequences of venom proteins

Toward the goal of recovering the phylogenetic relationships among elapid snakes, we separately found the shortest trees from the amino acid sequences for the venom proteins phospholipase A2 and the short neurotoxin, collectively representing 32 species in 16 genera. We then applied a method we term gene tree parsimony for inferring species trees from gene trees that works by finding the species tree which minimizes the number of deep coalescences or gene duplications plus unsampled sequences necessary to fit each gene tree to the species tree. This procedure, which is both logical and generally applicable, avoids many of the problems of previous approaches for inferring species trees from gene trees. The results support a division of the elapids examined into sister groups of the Australian and marine (laticaudines and hydrophiines) species, and the African and Asian species. Within the former clade, the sea snakes are shown to be diphyletic, with the laticaudines and hydrophiines having separate origins. This finding is corroborated by previous studies, which provide support for the usefulness of gene tree parsimony.

Phylogeny of the avian family Ciconiidae (storks) based on cytochrome b sequences and DNA-DNA hybridization distances

This study is a phylogenetic analysis of the avian family Ciconiidae, the storks, based on two molecular data sets: 1065 base pairs of sequence from the mitochondrial cytochrome b gene and a complete matrix of single-copy nuclear DNA-DNA hybridization distances. Sixteen of the nineteen stork species were included in the cytochrome b data matrix, and fifteen in the DNA-DNA hybridization matrix. Both matrices included outgroups from the families Cathartidae (New World vultures) and Threskiornithidae (ibises, spoonbills). Optimal trees based on the two data sets were congruent in those nodes with strong bootstrap support. In the best-fit tree based on DNA-DNA hybridization distances, nodes defining relationships among very recently diverged species had low bootstrap support, while nodes defining more distant relationships had strong bootstrap support. In the optimal trees based on the sequence data, nodes defining relationships among recently diverged species had strong bootstrap support, while nodes defining basal relationships in the family had weak support and were incongruent among analyses. A combinable-component consensus of the best-fit DNA-DNA hybridization tree and a consensus tree based on different analyses of the cytochrome b sequences provide the best estimate of relationships among stork species based on the two data sets.

Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh

The Archaea present in salt marsh sediment samples from a tidal creek and from an adjacent area of vegetative marshland, both of which showed active methanogenesis and sulfate reduction, were sampled by using 16S rRNA gene libraries created with Archaea-specific primers. None of the sequences were the same as reference sequences from cultured taxa, although some were closely related to sequences from methanogens previously isolated from marine sediments. A wide range of Euryarchaeota sequences were recovered, but no sequences from Methanococcus, Methanobacterium, or the Crenarchaeota were recovered. Clusters of closely related sequences were common and generally contained sequences from both sites, suggesting that some related organisms were present in both samples. Recovery of sequences closely related to those of methanogens such as Methanococcoides and Methanolobus, which can use substrates other than hydrogen, provides support for published hypotheses that such methanogens are probably important in sulfate-rich sediments and identifies some likely candidates. Sequences closely related to those of methanogens such as Methanoculleus and Methanogenium, which are capable of using hydrogen, were also discovered, in agreement with previous inhibitor and process measurements suggesting that these taxa are present at low levels of activity. More surprisingly, we recovered a variety of sequences closely related to those from different halophilic Archaea and a cluster of divergent sequences specifically related to the marine group II archaeal sequences recently shown by PCR and probing to have a cosmopolitan distribution in marine samples.

Allometric patterning in the limb skeleton of bats: Implications for the mechanics and energetics of powered flight

Allometric analysis was employed to compare linear dimensions of forelimb and hindlimb bones (humeri, radii, third and fifth metacarpals, third and fifth manual phalanges, femora, and tibiae) of 227 species of bats and 105 species of nonvolant mammals of varying degrees of phylogenetic affinity to bats. After accounting for body size, all forelimb bones are longer in bats than in nonvolant species, with the exception of humeri and radii of a few highly arboreal primates. Hindlimb bones are generally, but not uniformly, shorter in bats than in other mammals. For the humerus, radius, and metacarpals, midshaft diameters are greater in bats than in their comparably sized relatives. Proximal phalangeal midshaft diameters are statistically indistinguishable from those of other mammals, and distal phalanges show significantly reduced outer diameters. The pattern of relative reduction in wing bone diameters along the wing's proximodistal axis parallels the reduction in bone mineralization along the same axis, and a similar pattern of change in cortical thickness from the smallest wall thicknesses among mammals in the humerus and radius to the greatest wall thicknesses among mammals in the phalanges. The combination of altered cross-sectional geometry and mineralization appears significantly to reduce the mass moment of inertia of the bat wing relative to a theoretical condition in which elongated bones preserve primitive mammalian mineralization levels and patterns of scaling of long bone diameters. This intercorrelated suite of skeletal specializations may significantly reduce the inertial power of flight, contributing significant energetic savings to the total energy budgets of the only flying mammals. J. Morphol. 234: 277-294, 1997. © 1997 Wiley-Liss, Inc.

Escaping from the Felsenstein zone by detecting long branches in phylogenetic data

Long branches in a true phylogeny tend to disrupt hierarchical character covariation (phylogenetic signal) in the distribution of traits among organisms. The distortion of hierarchical structure in character-state matrices can lead to errors in the estimation of phylogenetic relationships and inconsistency of methods of phylogenetic inference. Examination of trees distorted by long-branch attraction will not reveal the identities of problematic taxa, in part because the distortion can mask long branches by reducing inferred branch lengths and through errors in branching order. Here we present a simple method for the detection of taxa whose placement in evolutionary trees is made difficult by the effects of long-branch attraction. The method is an extension of a tree-independent conceptual framework of phylogenetic data exploration (RASA). Taxa that are likely to attract are revealed because long branches leave distinct footprints in the distribution of character states among taxa, and these traces can be directly observed in the error structure of the RASA regression. Problematic taxa are identified using a new diagnostic plot called the taxon variance plot, in which the apparent cladistic and phenetic variances contributed by individual taxa are compared. The procedure for identifying long edges employs algorithms solved in polynomial time and can be applied to morphological, molecular, and mixed characters. The efficacy of the method is demonstrated using simulated evolution and empirical evidence of long branches in a set of recently published sequences. We show that the accuracy of evolutionary trees can be improved by detecting and combating the potentially misleading influences of long-branch taxa.

The potential of Betv1 homologues, a nuclear multigene family, as phylogenetic markers in flowering plants

Betv1 homologues are a ubiquitous group of genes in flowering plants encoding a class of highly conserved defense-related proteins and containing open reading frames from 465 to 480 bp. Betv1-like genes consist of two exons interrupted by an intron of 76-359 bp, with the intron position highly conserved. The pairwise p distance ranged from 0 to 0.583 among flowering plants. Within plant families, the ranges of the p distance were 0-0.403, 0-0.253, and 0.011-0.369, for Apiaceae, Betulaceae, and Fabaceae, respectively. The most striking feature of the betv1 gene phylogeny was that the multiple sequences from each plant family formed a monophyletic group and sequences from each species were generally more similar to each other than those from other species. The almost exclusive paralogous relationships of genes from the same species suggested that the genes of the multigene family underwent strong concerted evolution. Phylogenies of Betulaceae and Fabaceae inferred from betv1 gene trees were generally congruent with those based on morphology and other molecules. Betv1 homologues constitute potential phylogenetic markers at the intrafamilial level or among closely related families in flowering plants.

Molecular phylogenetics and the evolution of antarctic notothenioid fishes

The monophyly of the antarctic fish suborder Notothenioidei and the monophyly of its earliest family the Bovichtidae have been investigated with 12S and 16S mitochondrial DNA sequences. New data from Cottoperca, Pseudaphritis, Harpagifer and several outgroups, in addition to available sequences, show that the bovichtids are paraphyletic. Pseudaphritis is the sister group of all the non-bovichtid notothenioids. The same results are found from two independent genetic markers, the nuclear 28S rDNA and the 12S and 16S mitochondrial rDNA. This reliably refutes a previous hypothesis that placed Pseudaphritis as the sister group of all the remaining notothenioids (including Cottoperca and Bovichtus). Bootstrap analyses show that the Notothenioidei are monophyletic (although members of the suborder Trachinoidei have not been surveyed). Subsequent data from hemoglobin composition confirm the present relationships. After discussions between members of the European Science Foundation (ESF) network during its last two meetings, we point out here some fundamental aspects of comparative biology to improve understanding between the physiologist community and phylogeneticists. The most important points are differences in how the concept of homology is used and differences in the consideration of adaptation. When adaptation is evoked or questioned, endless speculations and untestable scenarios are often developed. We strongly advocate the use of phylogenetic trees for testing hypotheses of adaptation (through multiple character mapping). Such a "research program" in comparative biology has the power to improve knowledge because it can potentially lead to new experiments for testing adaptive hypotheses.

Determining divergence times with a protein clock: update and reevaluation

A recent study of the divergence times of the major groups of organisms as gauged by amino acid sequence comparison has been expanded and the data have been reanalyzed with a distance measure that corrects for both constraints on amino acid interchange and variation in substitution rate at different sites. Beyond that, the availability of complete genome sequences for several eubacteria and an archaebacterium has had a great impact on the interpretation of certain aspects of the data. Thus, the majority of the archaebacterial sequences are not consistent with currently accepted views of the Tree of Life which cluster the archaebacteria with eukaryotes. Instead, they are either outliers or mixed in with eubacterial orthologs. The simplest resolution of the problem is to postulate that many of these sequences were carried into eukaryotes by early eubacterial endosymbionts about 2 billion years ago, only very shortly after or even coincident with the divergence of eukaryotes and archaebacteria. The strong resemblances of these same enzymes among the major eubacterial groups suggest that the cyanobacteria and Gram-positive and Gram-negative eubacteria also diverged at about this same time, whereas the much greater differences between archaebacterial and eubacterial sequences indicate these two groups may have diverged between 3 and 4 billion years ago.

Immunocytochemical localization of somatostatin and autoradiographic distribution of somatostatin binding sites in the brain of the African lungfish, Protopterus annectens

The anatomical distribution of somatostatin-immunoreactive structures and the autoradiographic localization of somatostatin binding sites were investigated in the brain of the African lungfish, Protopterus annectens. In general, there was a good correlation between the distribution of somatostatin-immunoreactive elements and the location of somatostatin binding sites in several areas of the brain, particularly in the anterior olfactory nucleus, the rostral part of the dorsal pallium, the medial subpallium, the anterior preoptic area, the tectum, and the tegmentum of the mesencephalon. However, mismatching was found in the mid-caudal dorsal pallium, the reticular formation, and the cerebellum, which contained moderate to high concentrations of binding sites and very low densities of immunoreactive fibers. In contrast, the caudal hypothalamus and the neural lobe of the pituitary exhibited low concentrations of binding sites and a high to moderate density of somatostatin-immunoreactive fibers. The present results provide the first localization of somatostatin in the brain of a dipnoan and the first anatomical distribution of somatostatin binding sites in the brain of a fish. The location of somatostatin-immunoreactive elements in the brain of P. annectens is consistent with that reported in anuran amphibians, suggesting that the general organization of the somatostatin peptidergic systems occurred in a common ancestor of dipnoans and tetrapods. The anatomical distribution of somatostatin-immunoreactive elements and somatostatin binding sites suggests that somatostatin acts as a hypophysiotropic neurohormone as well as a neurotransmitter and/or neuromodulator in the lungfish brain.

Can skull morphology be used to predict ecological relationships between bat species? A test using two cryptic species of pipistrelle

Can ecological relationships between bat species be predicted largely on the basis of morphology? This question was addressed by investigating skull morphology of two cryptic species of the pipistrelle bat. Since 45 Pipistrellus pipistrellus apparently eats larger prey than 55 P. pipistrellus, we predicted that it would have a larger overall skull size, a larger dentary apparatus, and a larger gape. To test these predictions, variables were measured from skulls of the two cryptic species, and comparisons made between them. In accordance with our predictions, overall skull size was larger in 45 P. pipistrellus than in 55 P. pipistrellus, and 45 P. pipistrellus had a longer lower jaw and the distance between the jaws at maximum gape was larger. In addition, 45 P. pipistrellus had longer upper canines, which may allow it to pierce harder prey items than 55 P. pipistrellus. Only some aspects of dietary differences between the two cryptic species could be explained by differences in skull morphology, and we suggest that empirical data, at least on diet and habitat use, are also required to explain mechanisms of resource partitioning among species in bat communities.

Evolution of the genus Leishmania revealed by comparison of DNA and RNA polymerase gene sequences

Previous hypotheses of Leishmania evolution are undermined by limitations in the phylogenetic reconstruction method employed or due to the omission of key parasites. In this experiment, sequences of the gene encoding the DNA polymerase alpha catalytic polypeptide (POLA) were analysed phylogenetically in combination with those encoding the RNA polymerase II largest subunit gene (RPOIILS) to infer a comprehensive phylogeny of Leishmania. Nineteen species of parasites were studied, comprising representatives of each Leishmania species-complex (Leishmania Leishmania tropica, Leishmania Leishmania donovani, Leishmania Leishmania mexicana, Leishmania Leishmania hertigi and Leishmania Viannia braziliensis), as well as parasites of questionable taxonomy (Leishmania herreri, Sauroleishmania adleri, Sauroleishmania deanei, Sauroleishmania gymnodactyli and Sauroleishmania tarentolae). The analyses presented here provide strong support for the hypothesis that the Leishmania that infect reptiles (also known as Sauroleishmania) evolved from mammalian Leishmania. One implication of this finding is that the taxonomic definition of Leishmania should be broadened to encompass characteristics of the reptilian parasites. However, this taxonomic revision is complicated in that Leishmania (L.) hertigi, Leishmania (L.) deanei and Leishmania herreri, which exhibit some biological properties of Leishmania, are more closely related to Endotrypanum on the basis of these sequence comparisons. Consequently, the taxonomic discrimination between Leishmania that infect mammals, Leishmania that infect reptiles and Endotrypanum may be more problematic than has been previously thought. Since our resulting phylogenetic hypothesis is supported by the analyses of two different genes, we speculate on the origin and evolutionary expansion of this lineage of kinetoplastid protozoa.

Origin and evolution of the slime molds (Mycetozoa)

The Mycetozoa include the cellular (dictyostelid), acellular (myxogastrid), and protostelid slime molds. However, available molecular data are in disagreement on both the monophyly and phylogenetic position of the group. Ribosomal RNA trees show the myxogastrid and dictyostelid slime molds as unrelated early branching lineages, but actin and beta-tubulin trees place them together as a single coherent (monophyletic) group, closely related to the animal-fungal clade. We have sequenced the elongation factor-1alpha genes from one member of each division of the Mycetozoa, including Dictyostelium discoideum, for which cDNA sequences were previously available. Phylogenetic analyses of these sequences strongly support a monophyletic Mycetozoa, with the myxogastrid and dictyostelid slime molds most closely related to each other. All phylogenetic methods used also place this coherent Mycetozoan assemblage as emerging among the multicellular eukaryotes, tentatively supported as more closely related to animals + fungi than are green plants. With our data there are now three proteins that consistently support a monophyletic Mycetozoa and at least four that place these taxa within the "crown" of the eukaryote tree. We suggest that ribosomal RNA data should be more closely examined with regard to these questions, and we emphasize the importance of developing multiple sequence data sets.

Resolution of the phylogenetic position of the Congo peafowl, Afropavo congensis: a biogeographic and evolutionary enigma

Afropavo congensis, the Congo peafowl, has long fascinated ornithologists because of its uncertain phylogenetic position and unusual geographic distribution. While some researchers have placed Afropavo as a sister taxon to the true peafowl, Pavo species, others have suggested relationships with the guineafowl or an Old World partridge, Francolinus. These divergent opinions are due, at least in part, to (i) the unique morphological characteristics, lack of elaborate ornamentation, and monogamous mating system in Afropavo which differentiates it from Pavo; and (ii) the restricted distribution of Afropavo in Zaire, which is far removed from the Asian distribution of all other pheasant species. We obtained complete cytochrome b and partial D-loop sequences of Afropavo and compared them to Pavo, guineafowl, Francolinus and other galliform taxa. Our results strongly support a close relationship between Afropavo and Pavo, and we were able to reject alternative phylogenetic hypotheses. Molecular clock estimates of the divergence time place the separation of Afropavo and Pavo in the late Miocene. We also discuss other relatives of Afropavo and Pavo and use this information to propose hypotheses regarding the evolution of ornamentation and sexual dimorphism within this group of pheasants.

Human syntaxin 7: a Pep12p/Vps6p homologue implicated in vesicle trafficking to lysosomes

The movement of hydrolases and other proteins to lysosomes is accomplished by vesicle trafficking. Specific vesicles are targeted from the trans-Golgi network via a prelysosomal compartment to lysosomes. The specificity of vesicle transport is thought to occur through the interaction of vesicle proteins with receptors on a particular target membrane. The syntaxins are a family of transmembrane proteins that have been implicated as vesicle receptors involved in vesicle docking and fusion. Syntaxins 1-4 are localized to the plasma membrane, and in particular, syntaxin 1a mediates synaptic vesicle docking in the nerve terminal. Syntaxins 5 and 6 have been localized to cis-Golgi and trans-Golgi network compartments, respectively. We now report the identification of syntaxin 7 from a human brain cDNA library. The syntaxin 7 gene is localized to human chromosome 6. By Northern analysis, the syntaxin RNA was found to be broadly distributed. Based on its homology to yeast and plant vacuolar syntaxins, we propose that syntaxin 7 has a role in vesicle trafficking between the Golgi complex and lysosomes. In vitro binding studies reveal that syntaxin 7 binds alphaSNAP, a key regulator of transport vesicle fusion at multiple stages of the secretory pathway.

Conserved anterior boundaries of Hox gene expression in the central nervous system of the leech Helobdella

Molecular developmental studies of fly and mouse embryos have shown that the identity of individual body segments is controlled by a suite of homeobox-containing genes called the Hox cluster. To examine the conservation of this patterning mechanism in other segmented phyla, we here describe four Hox gene homologs isolated from glossiphoniid leeches of the genus Helobdella. Based on sequence similarity and phylogenetic analysis, the leech genes Lox7, Lox6, Lox20, and Lox5 are deemed to be orthologs of the Drosophila genes lab, Dfd, Scr, and Antp, respectively. Sequence similarities between Lox5 and Antp outside the homeodomain and phylogenetic reconstructions suggest that the Antennapedia family of Hox genes (as defined by Bürglin, 1994) had already expanded to include at least two discrete Antp and Ubx/abdA precursors prior to the annelid/arthropod divergence. In situ hybridization reveals that the four Lox genes described in this study are all expressed at high levels within the segmented portion of the central nervous system (CNS), with variable levels of expression in the segmental mesoderm. Little or no expression was seen in peripheral ectoderm or endoderm, or in the unsegmented head region (prostomium). Each Lox gene has a distinct anterior expression boundary within one of the four rostral segments, and the anterior-posterior (AP) order of these expression boundaries is identical to that reported for the orthologous Hox gene products in fly and mouse. This finding supports the idea that the process of AP axis differentiation is conserved among the higher metazoan phyla with respect to the regional expression of individual Hox genes along that axis. One unusual feature of leech Hox genes is the observation that some genes are only expressed during later development -- beginning at the time of terminal cell differentiation -- whereas others begin expression at a much earlier stage, and their RNA ceases to be detectable shortly after the onset of expression of the 'late' Hox genes. The functional significance of this temporal disparity is unknown, but it is noteworthy that only the two 'early' Hox genes display high levels of mesodermal expression.

Accelerated evolution as a consequence of transitions to mutualism

Differential rates of nucleotide substitutions among taxa are a common observation in molecular phylogenetic studies, yet links between rates of DNA evolution and traits or behaviors of organisms have proved elusive. Likelihood ratio testing is used here for the first time to evaluate specific hypotheses that account for the induction of shifts in rates of DNA evolution. A molecular phylogenetic investigation of mutualist (lichen-forming fungi and fungi associated with liverworts) and nonmutualist fungi revealed four independent transitions to mutualism. We demonstrate a highly significant association between mutualism and increased rates of nucleotide substitutions in nuclear ribosomal DNA, and we demonstrate that a transition to mutualism preceded the rate acceleration of nuclear ribosomal DNA in these lineages. Our results suggest that the increased rate of evolution after the adoption of a mutualist lifestyle is generalized across the genome of these mutualist fungi.

Phylogeny of North American Cicindela tiger beetles inferred from multiple mitochondrial DNA sequences

Tiger beetles in the genus Cicindela (Coleoptera: Cicindelidae) have been used as a model system for studies in ecology and conservation biology. Work on this group will greatly benefit from the availability of a phylogenetic hypothesis. We selected a representative sample of 23 North American Cicindela and 6 outgroups to reconstruct a phylogeny based on 1896 nucleotide positions from three mitochondrial genes (Cytochrome b, Cytochrome oxidase III, and 16S rRNA). Cladistic analysis of these three data sets yielded widely different tree topologies, but character conflict between them appears to be relatively low. The combined analysis of all data resulted in three similar shortest trees of 3453 steps. One of these was also recovered after successive weighting and was considered the best estimate of relationships. The most basal taxa of North American Cicindela (s.l.) were in the cosmopolitan subgenus Cylindera. The derived taxa were in the subgenus Cicindela (s. str.), a group dominating at higher latitudes in the Nearctic and Palearctic Region. The molecular analysis was essentially in agreement with the traditional classification which has been worked out based on male genitalic structures by E. Rivalier (1954, Rev. Entomol. Française 21:249-268). In the molecular analysis, Rivalier's species groups and subgenera were mostly found to be composed of closely related taxa but several of them were not monophyletic. Implicit in the traditional classification is a sequence from basal to derived groups which we found to be essentially reversed in the molecular analysis. We also discuss the conceptual differences in the establishment of the traditional classification by Rivalier (1954) and the cladistic analysis presented in this study.

Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndhF gene sequences

Forty-eight representatives of 12 tribes attributed to the subfamily Pooideae s.l. of grasses (Monocots) have been studied by sequencing the more variable 3' end of the chloroplast ndhF gene. Six representatives from 5 different tribes of Poaceae (Oryzeae, Streptogyneae, Bambuseae, Arundineae, Phareae) and from Joinvilleaceae were used as outgroups. Phylogenetic analyses of the data render a monophyletic Pooideae clade and provide an evolutionary hypothesis for all its tribes (Poeae, Aveneae, Bromeae, Triticeae, Brachypodieae, Meliceae, Stipeae, Lygeae, Nardeae, Diarrheneae, Brachyelytreae, Phaenospermatae). The subfamily is composed of two subsets of tribes, a basal group that includes six old lineages or satellite tribes, in which Brachyelytreae is the first diverging branch followed by the Lygeae/Nardeae clade, and a group of six more recently evolved tribes (Pooideae s.s.), in which the divergence of Diarrheneae antedates that of Brachypodieae, sister group to the "core pooids." The character changes found within the sequenced nucleotide positions of the ndhF gene also have proven to be informative at lower hierarchical levels (genus and species) for some tribes.

Fluctuating asymmetry, mate choice and experimental designs

No Abstract Copyright 1997 The Association for the Study of Animal Behaviour1997The Association for the Study of Animal Behaviour

Phylogeny of the grassland leafhopper genus Flexamia (Homoptera: Cicadellidae) based on mitochondrial DNA sequences

Leafhoppers (Cicadellidae) are a highly diverse group of sap-sucking insects, many species of which specialize on grasses. Past attempts to examine the roles of host transfer or host plant coevolution in the diversification of leafhopper species using cladistic methods have been hindered by a paucity of discrete, phylogenetically informative morphological characters. To demonstrate the utility of DNA sequence data for species-level phylogenetic studies of Cicadellidae, we estimated phylogenetic relationships among species in the North American grassland leafhopper genus Flexamia DeLong using partial nucleotide sequences of mitochondrial 16S rDNA and NADH dehydrogenase 1, totaling 1496 base pairs and 810 potentially informative characters. Analyses of the partitioned and combined sequence data using maximum parsimony, neighbor-joining, and maximum likelihood criteria yielded similar estimates of relationships in which most nodes were well-supported by bootstrap and decay indices. These estimates largely agreed with a previously published, intuitive, morphology-based phylogeny for the genus. A parsimony reconstruction of host associations based on these results suggests that the origins of various Flexamia clades coincided with host transfers among grass subfamilies or genera. Nevertheless, associations with certain subfamilies, genera, or species of grasses appear to have been largely conserved in the evolutionary diversification of Flexamia.

A multigene assessment of phylogenetic relationships within the dasyurid marsupial subfamily Sminthopsinae

We report sequences of the mitochondrial cytochrome b (1146 bp) and 12S rRNA (961 bp) genes, as well as the nuclear protamine P1 (608 bp) gene, from 13 species representing all four genera of the dasyurid marsupial subfamily Sminthopsinae. Mitochondrial sequences are partitioned into five categories (three codon positions in cytochrome b, and stems and loops in 12S rRNA) with distinct substitution rates, transition biases, and base compositions. We extract estimates of these biases from the sequences and employ them to calculate two overall distances based on the DNAML model. Phylogenetic analyses using distance and parsimony methods yield trees with different topologies for mtDNA and protamine. These trees are compatible with respect to highly resolved nodes, but incompatible with respect to length differences in a parsimony framework. The tree from combined-data analysis is dominated by the larger data set (mtDNA). The balance of evidence favors a basal separation of Planigale from other sminthopsines. Within Planigale, Pl. maculata is sister to the remaining species. Although the precise intergeneric affinities of Antechinomys are unresolved, A. laniger does not appear to be part of the genus Sminthopsis as suggested by morphological data. The 12S rRNA resolves Ningaui ridei and N. yvonnae as sister species.

Molecular phylogenetic study of the Ranunculaceae: utility of the nuclear 26S ribosomal DNA in inferring intrafamilial relationships

There are only a small number of molecular markers currently proven to be useful for phylogenetic inference within the flowering plants. We demonstrate that the 5' end of the 26S ribosomal DNA (ca. 1100 bp) is of great value for investigating generic to subfamilial relationships. We analyzed DNA sequences from 31 species of the Ranunculaceae and four species of the Berberidaceae to test phylogenetic relationships within the Ranunculaceae. The inferred phylogeny strongly supports the concept that the Thalictrum chromosome group is not monophyletic, but consists of three independent lineages: (1) Hydrastis, (2) Xanthorhiza and Coptis, and (3) Thalictrum, Aquilegia, and Enemion. Based on comparison with conventional taxonomic characters, we propose a hypothesis that the third group also includes the rest of the Thalictrum chromosome taxa that have a base chromosome number of seven. For the Ranunculus chromosome group, our study suggests several relationships that have not been recognized by conventional systematics. The inferred 26S rDNA topology is compared with results from two previously published molecular data sets: DNA sequences from rbcL, atpB, and 18S rDNA genes and restriction fragment length polymorphism data from chloroplast DNA. The three topologies are highly congruent and agree with karyological characters, but not with fruit type, both of which have often been used for the higher classification of the Ra- nunculaceae.

Genetic Diversity in Hominoid Primates

Humans are only one of the species produced by the hominoid evolutionary radiation. Common and pygmy chimpanzees (our closest relatives), gorillas, orangutans, and the lesser apes also belong to this group. In humans, patterns of genetic variation are becoming increasingly better characterized by modern molecular methods. Understanding human variation in an evolutionary context, however, requires comparison of human patterns with those of other hominoids, to reveal features shared among hominoids and those unique to humans. Genetic variation among chimpanzees, gorillas, and orangutans is beginning to be characterized, so that comparisons are now possible.

From genetic data, several different kinds of information can be reconstructed, including the evolutionary relatedness of subspecies and populations, time estimates for evolutionary divergences, past population dynamics, extent of gene flow over geographical landscapes, and group social structure. Knowledge of hominoid genetic variation is also relevant to applied fields such as primate conservation and medicine.

The effectiveness of mitochondrial rRNA gene sequences for the reconstruction of the phylogeny of an insect order (Orthoptera)

We investigated the value of mitochondrial rRNA sequences for analyzing pre-Cainozoic divergence events in insects. Using small subunit and large subunit rRNA sequences from 38 orthopteroid species, we examined several aspects of sequence evolution including secondary structure, substitution rate, and base composition. Substitution matrices calculated from the two genes were very similar, though differences were detected in rates of C-T transitions between paired and unpaired positions in secondary structures. By contrast, extreme disparities between substitution frequencies at different phylogenetic levels make character-transition weighting essential in parsimony reconstruction. The analysis of base composition indicated that branch attraction of at least two important lineages was due to shared base composition biases and to long branch attraction. The importance of taxonomic sampling and sequence length for the effectiveness of phylogenetic recovery using the rRNA fragments was also assessed. Significantly, combining the two sequences seemed both justifiable and necessary for this taxonomic sample. However, for reconstructing deep branches of phylogeny, it seems that increasing either or both the number of taxa or nucleotide positions will not necessarily solve all problems. Instead, the resolution of ancient branching events using mtDNA sequences probably depends upon the development and application of better specified reconstruction methods.