Branching Lineages Research Articles

CONTRASTING PATTERNS OF SYNONYMOUS AND NONSYNONYMOUS SEQUENCE EVOLUTION IN ASEXUAL AND SEXUAL FRESHWATER SNAIL LINEAGES

In asexual lineages, both synonymous and nonsynonymous sequence polymorphism may be reduced due to severe founder effects when asexual lineages originate. However, mildly deleterious (nonsynonymous) mutations may accumulate after asexual lineages are formed, because the efficiency of purifying selection is reduced even in the nonrecombining mitochondrial genome. Here we examine patterns of synonymous and nonsynonymous mitochondrial sequence polymorphism in asexual and sexual lineages of the freshwater snail Campeloma. Using clade-specific estimates, we found that synonymous sequence polymorphism was significantly reduced by 75% in asexuals relative to sexuals, whereas nonsynonymous sequence polymorphism did not differ significantly between sexuals and asexuals. Two asexual clades had high negative values for Tajima's D statistic. Coalescent simulations confirmed that various bottleneck scenarios can account for this result. We also used branch-specific estimates of the ratio of amino acid to silent substitutions, K(a)/K(s). Our study revealed that K(a)/K(s) ratios are six times higher in terminal branches of independent asexual lineages compared to sexuals. Coalescent-based reconstruction of gene networks for all sexual and asexual clades indicated that nonsynonymous mutations occurred at a higher frequency in recently derived asexual haplotypes. These findings suggest that patterns of synonymous and nonsynonymous nucleotide polymorphism in asexual snail lineages may be shaped by both severe founder effect and relaxed purifying selection.

The sequential determination model of hematopoiesis

Analysis of hematopoietic development has for decades been central to understanding lineage diversification. Some models consider hematopoietic commitment to be random, and branching lineage maps often include an early myeloid or lymphoid bifurcation. However, the existence of joint lymphoid or myeloid intermediate progenitors argues against both. One of us earlier proposed the sequential determination (SD) model, which features a limited and stepwise set of binary choices across the full hematopoietic spectrum. This model arose from observations that hematopoietic progenitors show preferences for particular associations of lineage potentials--indicating that these linked fates are neighbours developmentally. An updated SD model complemented by several recently recognized processes--spatiotemporal fluctuations in transcription factor concentrations, asymmetric cell division, and Notch signalling--still offers a sound summary of hematopoiesis.

History and Diversity: Explorations at the Intersection of Ecology and Evolution

Phylogenetic analysis provides an important tool for assessing the influence of historical and evolutionary processes on the structure of contemporary ecological systems. Patterns of diversity, for example, represent the regional buildup of species through immigration and diversification, their loss through extinction, and the sorting of species ecologically within the region. Colonization-extinction dynamics on islands can be inferred from lineage accumulation through time. Lineage branching within clades can be used to estimate rates of speciation and extinction. However, simulations of these processes show potential ambiguities in the interpretation of data. Clade size is unrelated to age in many studies, suggesting that speciation and extinction might be in long-term equilibrium and raising questions about unobserved past diversity. Among passerine birds and other groups, the size of similar-aged clades is positively related to the size of the region within which they have diversified, and it is greater in tropical than in temperate regions. There is no consensus on the causes of these patterns. Finally, the ecological interactions between populations within regions brings the timescale of species sorting and species production close to each other and emphasizes the important interaction of ecological and evolutionary processes in shaping ecological systems.

Classification of a large and widespread genus of Neotropical trees, Guatteria (Annonaceae) and its three satellite genera Guatteriella, Guatteriopsis and Heteropetalum

Guatteria (Annonaceae) is with ca. 265 species one of the largest genera of Neotropical trees together with Inga and Ocotea. Use of Guatteria in evolutionary studies has been hampered by taxonomic problems caused by lack of morphological variability in the genus. This study focuses on molecular phylogenetic relationships within Guatteria and its satellites Guatteriopsis, Guatteriella and Heteropetalum, and implications of these relationships for classification and character evolution. Results show that Guatteriopsis, Guatteriella and Heteropetalum should be merged with Guatteria. Heteropetalum may be recognized at subgeneric level because of its aberrant morphology and Guatteriopsis and Guatteriella might be given sectional status. Most of the currently recognised sections in Guatteria are probably non‐monophyletic. A completely new infrageneric classification of Guatteria would be premature, however, due to the lack of molecular and morphological synapomorphies to define the sections. Synapomorphies defining Guatteria s.str. probably evolved after divergence of several early branching lineages.

Structural characterization of diabolic acid-based tetraester, tetraether and mixed ether/ester, membrane-spanning lipids of bacteria from the order Thermotogales

The distribution of core lipids in the membranes of nine different species of the order Thermotogales, one of the early and deep branching lineages in the Bacteria, were examined by HPLC/MS and demonstrated to consist of membrane-spanning diglycerol lipids comprised of diabolic acid-derived alkyl moieties. In the Thermotoga species the core membrane lipids are characterized by the presence of both ester and ether bonds, whereas in the phylogenetically more distinct Thermosipho and Fervidobacterium spp. only ester bonds occur. A tentative biosynthetic route for the biosynthesis of these membrane-spanning lipids is proposed. Since species of the order Thermotogales are assumed to have occurred early during the evolution of life on Earth, as suggested by its position in the phylogenetic tree of life, these data suggest that the ability to produce both ether and ester glycerol membrane lipids developed relatively early during microbial evolution.

Phylogenetic analysis of Nymphaeales using fast-evolving and noncoding chloroplast markers

The Nymphaeales (water-lilies and relatives) represent one of the earliest branching lineages of angiosperms and comprise about 70 aquatic species. Here, we present a comprehensive study of phylogenetic relationships within the Nymphaeales from a dataset containing 24 representatives of the order, including all currently recognized genera and all subgenera of the genus Nymphaea, plus 5 outgroup taxa. Nine different regions of the chloroplast genome − comprising spacers, group II introns, a group I intron, and a protein coding gene − were analysed. This resulted in a character matrix of 6597 positions and an additional 369 characters obtained from coded length mutations. Maximum parsimony and Bayesian analyses of the complete dataset yielded congruent, fully resolved and well-supported trees. Our data confirm the monophyly of the Cabombaceae but do not provide convincing support for the monophyly of Nymphaeaceae with respect to Nuphar. Moreover, the genus Nymphaea is inferred to be paraphyletic with respect to Ondinea, Victoria and Euryale. In fact, the Australian endemic Ondinea forms a highly supported clade with members of the Australian Nymphaea subgenus Anecphya. In addition, Victoria and Euryale are inferred to be closely related to a clade comprising all night-blooming water-lilies (Nymphaea subgenera Hydrocallis and Lotos). An experimental approach showed taxon sampling to be of influence on the nodes reconstructed in core Nymphaeaceae. The results underscore that more diverse genera, if not clearly known to be monophyletic, should be represented by all major lineages. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154, 141–163.

High-resolution nannofossil biochronology of middle Paleocene to early Eocene at ODP Site 1262: Implications for calcareous nannoplankton evolution

Over the last several decades debates on the ‘tempo and mode’ of evolution have centered on the question whether morphological evolution preferentially occurs gradually or punctuated, i.e., with long periods of stasis alternating with short periods of rapid morphological change and generation of new species. Another major debate is focused on the question whether long-term evolution is driven by, or at least strongly influenced by changes in the environment, or by interaction with other life forms. Microfossils offer a unique opportunity to obtain the large datasets as well as the precision in dating of subsequent samples to study both these questions. We present high-resolution analyses of selected calcareous nannofossils from the deep-sea section recovered at ODP Site 1262 (Leg 208) in the South-eastern Atlantic. The studied section encompasses nannofossil Zones NP4–NP12 (equivalent to CP3–CP10) and Chrons C27r–C24n.We document more than 70 biohorizons occurring over an about 10 Myr time interval, (∼ 62.5 Ma to ∼ 52.5 Ma), and discuss their reliability and reproducibility with respect to previous data, thus providing an improved biostratigraphic framework, which we relate to magnetostratigraphic information, and present for two possible options of a new Paleocene stratigraphic framework based on cyclostratigraphy. This new framework enabled us to tentatively reconstruct steps in the evolution of early Paleogene calcareous nannoplankton through documentation of transitional morphotypes between genera and/or species and of the phylogenetic relations between the genera Fasciculithus, Heliolithus, Discoasteroides and Discoaster, as well as between Rhomboaster and Tribrachiatus. The exceptional record provided by the continuous, composite sequence recovered at Walvis Ridge allows us to describe the mode of evolution among calcareous nannoplankton: new genera and/or new species usually originated through branching of lineages via gradual, but relatively rapid, morphological transitions, as documented by the presence of intermediate forms between the end-member ancestral and descendant forms. Significant modifications in the calcareous nannofossil assemblages are often “related” to significant changes in environmental conditions, but the appearance of structural innovations and radiations within a single genus also occurred during “stable” environmental conditions. These lines of evidence suggest that nannoplankton evolution is not always directly triggered by stressed environmental conditions but could be also driven by endogenous biotic control.

Phylogeny of the African representatives of the catfish family Clariidae (Teleostei, Siluriformes) based on a combined analysis: independent evolution towards anguilliformity

Clariid catfishes span a broad range of body forms ranging between fusiform and anguilliform morphotypes. Although such variation in body shape has been observed in other families of teleost fishes, amphibians and reptiles, it is rarely as extreme as within the Clariidae. Although the Clariidae were thought to have undergone anagenetic evolution (i.e. progressive evolution within a lineage), more recent studies indicate that anguilliformity evolved several times through a process of cladogenesis (i.e. branching of evolutionary lineages). In this study, it is shown that the phylogenetic analysis of morphological data mainly gives a reflection of the cranial evolution in the Clariidae despite the use of 18 post-cranial characters (out of a total of 53 characters). A combined phylogenetic analysis of both morphological and molecular data rather suggests the derived nature of body elongation. The corresponding morphological changes that co-occur with this elongation can be regarded as an extreme case of convergent evolution at the genus level within the Clariidae.

PARASITIC SPECIES OF THE GENUS BLASTODINIUM (BLASTODINIPHYCEAE) ARE PERIDINIOID DINOFLAGELLATES1

The taxonomic position of Blastodinium navicula Chatton and B. contortum Chatton, parasites of marine copepods, was investigated on the basis of morphological observations and molecular data. The life cycle of Blastodinium includes a parasitic stage, a trophont, and free‐swimming dinospores. The individual cells in the trophont, as well as the dinospores that they produced, were thecate. Dinospores of B. contortum and B. navicula had peridinioid plate tabulation formula, demonstrating an affiliation to the order Peridiniales Heackel (subdivision Dinokaryota Fensome et al.). This systematic position is in contrast to current classifications, in which the order Blastodiniales Chatton is thought to represent an early evolutionary branch of the dinokaryote lineage. Small‐subunit rRNA gene sequences were generated from six Blastodinium individuals isolated from three different host species. In phylogenetic analyses based on SSU rRNA genes, Blastodinium spp. branched with the typical dinoflagellates. Even though overall statistical support was low, the analyses suggested that Blastodinium spp. are late‐branching, dinokaryote dinoflagellates. Species currently included in Blastodiniales are all parasites, but they are morphologically and functionally diverse. Emerging molecular data also reveal high genetic diversity, and therefore, the taxonomy of the group requires reevaluation.

New home for tiny aquatics

A shake-up of current thinking about the evolution of the angiosperms — the flowering plants — is a consequence of the relocation of a hitherto obscure branch on the angiosperm evolutionary tree. The Hydatellaceae are small aquatic plants living modest lives away from the limelight, and conventionally assumed to be monocotyledonous flowering plants related to grasses. Now they have been subjected to the latest molecular techniques, and they turn out to be close relatives of basal angiosperms such as water lilies, increasing their importance immensely. They belong to a previously unrecognized lineage branching near the root of the angiosperms — a radical addition to the three deepest branches discovered in 1999 that rekindled interest amongst molecular biologists in the origin of angiosperms, what Darwin called an “abominable mystery”.

Cryptic species ofDidymobothrium rudolphii(Cestoda: Spathebothriidea) from the sand sole,Solea lascaris, off the Portuguese coast, with an analysis of their molecules, morphology, ultrastructure and phylogeny

Didymobothrium rudolphii (Cestoda: Spathebothriidea) was collected seasonally from the sand sole, Solea lascaris, off the northern, central and southern areas of the Portuguese coast. Morphological and molecular analyses were conducted in order to examine the possible existence of cryptic species and to facilitate the circumscription of their morphological boundaries. Data were compared between D. rudolphii specimens from each of the 3 geographical areas and 4 seasons, and principal components analysis of 18 morphological characters was used to detect differences. Two distinct genotypes were present with sequence divergences of 1.9% and 2.1% in the large subunit (lsrDNA) and second internal transcribed spacer (ITS-2) of ribosomal DNA (rDNA), respectively. The less common 'central' genotype was present only off the central area from summer to winter, whereas the 'common' genotype was present throughout the year off the northern and southern areas, but only during spring in the central area. No sequence variation was found within each genotype. The presence of 2 distinct genetic entities was supported by morphological analyses, which showed the 'central' genotype specimens to be more slender and elongate, although morphometric ranges overlapped considerably for most characters. Molecular phylogenetic analysis of 4 of the 5 known genera of the Spathebothriidea showed Spathebothrium to be the earliest branching lineage and the 2 genotypes of Didymobothrium formed a sister group to Cyathocephalus. The concordance of genetic differences with variation in host diet according to season and locality could account for sympatric speciation occurring in the central region of the Portuguese coast.

Cycloheximide: No ordinary bitter stimulus

Cycloheximide (CyX), a toxic antibiotic with a unique chemical structure generated by the actinomycete, Streptomyces griseus, has emerged as a primary focus of studies on mammalian bitter taste. Rats and mice avoid it at concentrations well below the thresholds for most bitter stimuli and T2R G-protein-coupled receptors specific for CyX with appropriate sensitivity are identified for those species. Like mouse and rat, golden hamsters, Mesocricetus auratus, also detected and rejected micromolar levels of CyX, although 1 mM CyX failed to activate the hamster chorda tympani nerve. Hamsters showed an initial tolerance for 500 μM CyX, but after that, avoidance of CyX dramatically increased, plasticity not reported for rat or mouse. As the hamster lineage branches well before division of the mouse–rat lineage in evolutionary time, differences between hamster and mouse–rat reactions to CyX are not surprising. Furthermore, unlike hamster LiCl-induced learned aversions, the induced CyX aversion neither specifically nor robustly generalized to other non-ionic bitter stimuli; and unlike adverse reactions to other chemosensory stimuli, aversions to CyX were not mollified by adding a sweetener. Thus, CyX is unlike other bitter stimuli. The gene for the high-affinity CyX receptor is a member of a cluster of five orthologous T2R genes that are likely rodent-specific; this “CyX clade” is found in the mouse, rat and probably hamster, but not in the human or rabbit genome. The rodent CyX–T2R interaction may be one of multiple lineage-specific stimulus-receptor interactions reflecting a response to a particular environmental toxin. The combination of T2R multiplicity, species divergence and gene duplication results in diverse ligands for multiple species-specific T2R receptors, which confounds definition of ‘bitter’ stimuli across species.

STATISTICAL TESTS FOR TAXONOMIC DISTINCTIVENESS FROM OBSERVATIONS OF MONOPHYLY

The observation of monophyly for a specified set of genealogical lineages is often used to place the lineages into a distinctive taxonomic entity. However, it is sometimes possible that monophyly of the lineages can occur by chance as an outcome of the random branching of lineages within a single taxon. Thus, especially for small samples, an observation of monophyly for a set of lineages--even if strongly supported statistically--does not necessarily indicate that the lineages are from a distinctive group. Here I develop a test of the null hypothesis that monophyly is a chance outcome of random branching. I also compute the sample size required so that the probability of chance occurrence of monophyly of a specified set of lineages lies below a prescribed tolerance. Under the null model of random branching, the probability that monophyly of the lineages in an index group occurs by chance is substantial if the sample is highly asymmetric, that is, if only a few of the sampled lineages are from the index group, or if only a few lineages are external to the group. If sample sizes are similar inside and outside the group of interest, however, chance occurrence of monophyly can be rejected at stringent significance levels (P < 10(-5)) even for quite small samples (approximately 20 total lineages). For a fixed total sample size, rejection of the null hypothesis of random branching in a single taxon occurs at the most stringent level if samples of nearly equal size inside and outside the index group--with a slightly greater size within the index group--are used. Similar results apply, with smaller sample sizes needed, when reciprocal monophyly of two groups, rather than monophyly of a single group, is of interest. The results suggest minimal sample sizes required for inferences to be made about taxonomic distinctiveness from observations of monophyly.

History and Diversity: Explorations at the Intersection of Ecology and Evolution

Phylogenetic analysis provides an important tool for assessing the influence of historical and evolutionary processes on the structure of contemporary ecological systems. Patterns of diversity, for example, represent the regional buildup of species through immigration and diversification, their loss through extinction, and the sorting of species ecologically within the region. Colonization‐extinction dynamics on islands can be inferred from lineage accumulation through time. Lineage branching within clades can be used to estimate rates of speciation and extinction. However, simulations of these processes show potential ambiguities in the interpretation of data. Clade size is unrelated to age in many studies, suggesting that speciation and extinction might be in long‐term equilibrium and raising questions about unobserved past diversity. Among passerine birds and other groups, the size of similar‐aged clades is positively related to the size of the region within which they have diversified, and it is greater in tropical than in temperate regions. There is no consensus on the causes of these patterns. Finally, the ecological interactions between populations within regions brings the timescale of species sorting and species production close to each other and emphasizes the important interaction of ecological and evolutionary processes in shaping ecological systems.

The age and evolution of sociality in Stegodyphus spiders: a molecular phylogenetic perspective

Social, cooperative breeding behaviour is rare in spiders and generally characterized by inbreeding, skewed sex ratios and high rates of colony turnover, processes that when combined may reduce genetic variation and lower individual fitness quickly. On these grounds, social spider species have been suggested to be unstable in evolutionary time, and hence sociality a rare phenomenon in spiders. Based on a partial molecular phylogeny of the genus Stegodyphus, we address the hypothesis that social spiders in this genus are evolutionary transient. We estimate the age of the three social species, test whether they represent an ancestral or derived state and assess diversification relative to subsocial congeners. Intraspecific sequence divergence was high in all of the social species, lending no support for the idea that they are young, transient species. The age of the social lineages, constant lineage branching and the likelihood that social species are independently derived suggest that either the social species are 'caught in sociality' or they have evolved into cryptic species.

Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations

In placental mammals and birds, molecular data generally support a view that they diverged into their ordinal groups in good response to mid-Cretaceous continental fragmentations. However, such divergence patterns have rarely been studied for reptiles for which phylogenetic relationships among their major groups have not yet been established molecularly. Here, I determined complete or nearly complete mitochondrial DNA sequences from seven lizard families and reconstructed phylogenetic relationships between major lizard families. When snakes were included, maximum likelihood analysis did not support a morphological view of the snakes–varanoids affinity, although several other competing hypotheses on the position of snakes still cannot be discriminated presumably due to extremely long branches of the snake lineages. I also conducted clock-free Bayesian analyses to show that divergence times between major lizard families were centered in Triassic–Jurassic times. Thus, lizards include much deeper divergences than the mammals and birds and they appear to have already radiated into various families prior to the mid-Cretaceous major continental fragmentation.

Apología y censura: posibles autores de las crónicas favorables a Pedro I de Castilla

The present historiography considers that from the times of Pedro I of Castile, favorable stories to this king must have existed which were destroyed after the triumph of the Trastamara dynasty, only interested in making sure a negative picure of the Cruel king was shown. In this work we have analyzed possible authors of the chronicles called true versus Ayala's false, as well as the Relacion de la vida del Rey D. Pedro attributed to Gracia Dei. The research allows us to conclude that various characteristics attributed to these characters, as well as the authorship of the chronicles they are adscripted to, are part of an advertising campaign started in the sixteenth century by one branch of the Castilla lineage that looks for the reaffirmation as legitimate descendants of Pedro I.

Molecular systematics of basal subfamilies of ants using 28S rRNA (Hymenoptera: Formicidae)

For many years, the ant subfamily Ponerinae was hypothesized to contain the basal (early branching) lineages of ants. Recently the Ponerinae were reclassified into six poneromorph subfamilies based on morphological analysis. We evaluate this new poneromorph classification using 1240 base pairs of DNA sequence data obtained from 28S rRNA gene sequences of 68 terminal taxa. The molecular tree supported the monophyly of the ant family Formicidae, with 100% parsimony bootstrap (PB) support and posterior probabilities (PP) of 1.00, with the ant subfamily Leptanillinae as a sister group to all other ants (PB = 62, PP = 93). However, our analyses strongly support the polyphyly of the Poneromorph subfamilies (sensu Bolton). The Ectatomminae and Heteroponerinae are more closely related to the Formicoid subfamilies than to the rest of the poneromophs (PB = 96, PP = 100). The Amblyoponinae (PB = 52, PP = 96), Paraponerinae (PB = 100, PP = 100), Ponerinae (PB < 50, PP = 71), and Proceratiinae (PB = 98, PP = 100) appear as distinct lineages at the base of the tree and are identified as a poneroid grade. Monophyletic origins for the poneroid subfamilies Amblyoponinae, Paraponerinae, Ponerinae and Proceratiinae are supported in our analysis. However, the genus Platythyrea forms a distinct sister group to the Ponerini within the Ponerinae. The Heteroponerinae, based on our sample of Heteroponera, are associated with the subfamily Ectatomminae (PB = 98, PP = 100). Furthermore, our data indicate the genus Probolomyrmex belongs to the Proceratiinae as suggested by recent morphological analysis (PB = 98, PP = 100).

Evidence from SSU rRNA Phylogeny that Octomitus is a Sister Lineage to Giardia

Octomitus intestinalis is a diplomonad flagellate inhabiting the digestive tract of rodents and amphibians. Octomitus is of evolutionary interest because, based on ultrastructural characteristics, it is thought to be closely related to the morphologically derived genus Giardia, and together they have been proposed to make up the Giardiinae. In molecular trees of diplomonads, Giardia is the deepest branching lineage, so identifying a sister group to Giardia that is less derived would be informative. Octomitus is a logical candidate for this position, but unfortunately there are no molecular data from it, and it is not available in culture. To determine the position of Octomitus, and specifically test whether it is more closely related to Giardia than other diplomonads, we have isolated it directly from the caecum of wild mice and characterized its small subunit ribosomal RNA (SSU rRNA) gene. Phylogenetic analysis showed Octomitus to be the sister to Giardia with strong support, together occupying one side of the deepest split in the diplomonad tree.

Identification of Three Distinct Polytomella Lineages Based on Mitochondrial DNA Features

Polytomella is composed of colorless green algae closely related to Chlamydomonas reinhardtii. Species in the genus have been used in diverse fields of biological research, most recently to study mitochondrial function and mitochondrial genome evolution in the Chlorophyceae, but the phylogenetic relationship between the various available taxa has not yet been clarified and it is not known whether they also possess fragmented mitochondrial genomes, as reported for Polytomella parva. We therefore examined cox1 sequence from seven Polytomella taxa with the goal of establishing their phylogenetic relationships and relating this information to their mitochondrial DNA (mtDNA) fragmentation pattern. We found that the Polytomella isolates examined fall into three distinct lineages, two of which possess fragmented mitochondrial genomes. The third and earliest branching lineage, represented by Polytomella capuana, appears to possess an intact mtDNA. In addition, there is evidence for variation in both size and number of mtDNA fragments between various Polytomella isolates, even within the same lineage. The considerable amount of sequence divergence between lineages seems to correlate with the geographic origin of the strains, leading us to believe that greater amounts of sequence divergence could be uncovered by a broader sampling of Polytomella.