Molecular phylogeographic evidence for multiple shifts in habitat preference in the diversification of an amphipod species

An earlier study of ours demonstrated polygenic control of habitat preference between sympatric populations of an estuarine amphipod (Stanhope et al. 1992). Knowledge of the ecological history in this estuary suggested that two new and distinct habitat types (wood debris and Fucus ) had been formed immediately adjacent to each other, in an area which was previously the habitat type common to the rest of the estuary (bank). This suggested the possibility that the ancestral population had been split into two resource specialists (disruptive selection on habitat preference). The genetic relatedness of these three populations (the proposed ancestor and the two proposed descendants) and six others occupying the same three habitat types were investigated on a regional geographic scale, using an extensive set of genomic DNA RFLPs. These data were combined with measures of habitat preference (including genetic tests) in the additional populations. A very strongly supported phylogeographic tree, unequivocally supported a shift in habitat preference in the wood-debris population of this estuary. The data did not, however, support the hypothesis of disruptive selection on the ancestor (bank) with a consequent split into two resource specialists. Instead, it clearly indicated that the occupants of the Fucus habitat type were members of a habitat specific race, and thus their presence in this estuary reflected the expansion of an old resource base. Furthermore, the combined RFLP and habitat preference data, for all nine populations, indicated that the same polygenically based shift in habitat preference that had occurred in the original estuary had occurred independently, in another estuary, 700 km removed, that had similar environmental circumstances.     

Craniofacial variation and growth in the Prader-Labhart-Willi syndrome

A study of anthropometric variation and craniofacial growth in individuals with the Prader-Labhart-Willi syndrome (PLWS) illustrates the utility of anthropometry in clinical evaluation and research. Anthropometric measurements, including head length and breadth, minimum frontal diameter, and head circumference, were obtained on 38 PLWS individuals (21 with chromosome 15 deletions) with an age range from 2 weeks to 39 years. No anthropometric differences were found between the two chromosome subgroups. A relative deceleration in the growth of certain craniofacial dimensions (head circumference and length) is suggested by the negative correlations between age and Z-scores for the measurements. Raw values for minimum frontal diameter and head breadth were near or below the 5th percentile curve, while almost all values for head length and circumference fell within normal limits. The data support suggestions that dolichocephaly be considered an early diagnostic feature of PLWS. Furthermore, the status of narrow bifrontal diameter as a major feature of PLWS is confirmed.     

PTPN22 genetic variation: evidence for multiple variants associated with rheumatoid arthritis

The minor allele of the R620W missense single-nucleotide polymorphism (SNP) (rs2476601) in the hematopoietic-specific protein tyrosine phosphatase gene, PTPN22, has been associated with multiple autoimmune diseases, including rheumatoid arthritis (RA). These genetic data, combined with biochemical evidence that this SNP affects PTPN22 function, suggest that this phosphatase is a key regulator of autoimmunity. To determine whether other genetic variants in PTPN22 contribute to the development of RA, we sequenced the coding regions of this gene in 48 white North American patients with RA and identified 15 previously unreported SNPs, including 2 coding SNPs in the catalytic domain. We then genotyped 37 SNPs in or near PTPN22 in 475 patients with RA and 475 individually matched controls (sample set 1) and selected a subset of markers for replication in an additional 661 patients with RA and 1,322 individually matched controls (sample set 2). Analyses of these results predict 10 common (frequency >1%) PTPN22 haplotypes in white North Americans. The sole haplotype found to carry the previously identified W620 risk allele was strongly associated with disease in both sample sets, whereas another haplotype, identical at all other SNPs but carrying the R620 allele, showed no association. R620W, however, does not fully explain the association between PTPN22 and RA, since significant differences between cases and controls persisted in both sample sets after the haplotype data were stratified by R620W. Additional analyses identified two SNPs on a single common haplotype that are associated with RA independent of R620W, suggesting that R620W and at least one additional variant in the PTPN22 gene region influence RA susceptibility.     

Craniofacial morphology of Homo floresiensis: description, taxonomic affinities, and evolutionary implication

This paper describes in detail the external morphology of LB1/1, the nearly complete and only known cranium of Homo floresiensis. Comparisons were made with a large sample of early groups of the genus Homo to assess primitive, derived, and unique craniofacial traits of LB1 and discuss its evolution. Principal cranial shape differences between H. floresiensis and Homo sapiens are also explored metrically. The LB1 specimen exhibits a marked reductive trend in its facial skeleton, which is comparable to the H. sapiens condition and is probably associated with reduced masticatory stresses. However, LB1 is craniometrically different from H. sapiens showing an extremely small overall cranial size, and the combination of a primitive low and anteriorly narrow vault shape, a relatively prognathic face, a rounded oval foramen that is greatly separated anteriorly from the carotid canal/jugular foramen, and a unique, tall orbital shape. Whereas the neurocranium of LB1 is as small as that of some Homo habilis specimens, it exhibits laterally expanded parietals, a weak suprameatal crest, a moderately flexed occipital, a marked facial reduction, and many other derived features that characterize post-habilis Homo. Other craniofacial characteristics of LB1 include, for example, a relatively narrow frontal squama with flattened right and left sides, a marked frontal keel, posteriorly divergent temporal lines, a posteriorly flexed anteromedial corner of the mandibular fossa, a bulbous lateral end of the supraorbital torus, and a forward protruding maxillary body with a distinct infraorbital sulcus. LB1 is most similar to early Javanese Homo erectus from Sangiran and Trinil in these and other aspects. We conclude that the craniofacial morphology of LB1 is consistent with the hypothesis that H. floresiensis evolved from early Javanese H. erectus with dramatic island dwarfism. However, further field discoveries of early hominin skeletal remains from Flores and detailed analyses of the finds are needed to understand the evolutionary history of this endemic hominin species.     

Latitudinal variation in the shape of the species body size distribution: an analysis using freshwater fishes

Many taxonomic and ecological assemblages of species exhibit a right-skewed body size-frequency distribution when characterized at a regional scale. Although this distribution has been frequently described, factors influencing geographic variation in the distribution are not well understood, nor are mechanisms responsible for distribution shape. In this study, variation in the species body size-frequency distributions of 344 regional communities of North American freshwater fishes is examined in relation to latitude, species richness, and taxonomic composition. Although the distribution of all species of North American fishes is right-skewed, a negative correlation exists between latitude and regional community size distribution skewness, with size distributions becoming left-skewed at high latitudes. This relationship is not an artifact of the confounding relationship between latitude and species richness in North American fishes. The negative correlation between latitude and regional community size distribution skewness is partially due to the geographic distribution of families of fishes and apparently enhanced by a nonrandom geographic distribution of species within families. These results are discussed in the context of previous explanations of factors responsible for the generation of species size-frequency distributions related to the fractal nature of the environment, energetics, and evolutionary patterns of body size in North American fishes.     

The value of infracranial nonmetric variation in studies of modern Homo sapiens: an Australian focus

The value of quantitative infracranial nonmetric variation is examined in the study of population relationships by using samples from populations originating from five major geographic regions: Australia (two populations), Africa, East Asia, Europe, and Polynesia. According to the nonspecificity hypothesis, there are no distinct large classes of genes affecting one group of attributes exclusively; thus infracranial nonmetric traits should compare with other osteologic data sets in addressing questions of population relationships. By using the mean measure of divergence, infracranial nonmetric traits are shown to be useful in separating populations, particularly when using female and pooled-sex samples. The two Australian female samples (New South Wales coastal Australian and South Australian Aboriginals) are shown to be closer than any other two samples. The picture of intrapopulation and interpopulation variation in infracranial nonmetric traits is extended and clarified. Distance studies with infracranial nonmetric traits are possible but more illuminating if the sexes are first separated. Infracranial nonmetric variation does extend the knowledge of human population studies in yielding biologically meaningful results relating to development and ontogeny.     

Early evidence of the genus Homo in East Asia

The timing and route of the earliest dispersal from Africa to Eastern Asia are contentious topics in the study of early human evolution because Asian hominin fossil sites with precise age constraints are very limited. Here we report new high-resolution magnetostratigraphic results that place stringent age controls on excavated hominin incisors and stone tools from the Yuanmou Basin, southwest China. The hominin-bearing layer resides in a reverse polarity magnetozone just above the upper boundary of the Olduvai subchron, yielding an estimated age of 1.7Ma. The finding represents the age of the earliest documented presence of Homo, with affinities to Homo erectus, in mainland East Asia. This age estimate is roughly the same as for H. erectus in island Southeast Asia and immediately prior to the oldest archaeological evidence in northeast Asia. Mammalian fauna and pollen obtained directly from the hominin site indicate that the Yuanmou hominins lived in a varied habitat of open vegetation with patches of bushland and forest on an alluvial fan close to a lake or swamp. The age and location are consistent with a rapid southern migration route of initial hominin populations into Eastern Asia.     

Flow cytometric evidence for multiple ploidy levels in the endosperm of some gymnosperm species

 Considered to be haploid tissue, the endosperm of coniferous trees has been extensively used by forest geneticists. Using laser flow cytometry, we show that endosperm ploidy level depends on the systematic position. The Abies, Cedrus and Pinus species tested exhibited uniform haploid endosperm compared to the diploid DNA content of the corresponding embryo. Endosperm of Cupressaceae contained multiple ploidy levels: Cupressus arizonica, Juniperus oxycedrus and Thuja orientalis endosperms exhibited a mixture of haploid–diploid nuclei, while C. atlantica and C. sempervirens endosperms contained six ploidy levels: 1C, 2C, 3C, 4C, 5C and 6C. Physiological and genetic implications of this original feature are discussed. Received: 17 August 1996 / Accepted: 18 October 1996     

Immunodetection of multiple species of retinoic acid receptor alpha: evidence for phosphorylation.

Polyclonal and monoclonal antibodies were raised against synthetic peptides (or fusion protein) corresponding to cDNA-deduced amino acid sequences unique to the human and mouse retinoic acid (RA) receptor alpha 1 (hRAR-alpha 1 and mRAR-alpha 1, respectively). Two rabbit polyclonal antibodies directed against either the F region fused to DHFR [RP alpha (F)] or the D2 region [RP alpha (D2)] were selected. Using either immunocytochemistry, Western blotting analysis, or immunoprecipitation, they were found to be specific for human and mouse RAR-alpha 1 proteins produced by COS-1 cells transiently transfected with vectors expressing the RAR-alpha 1 cDNA. Three mouse monoclonal antibodies directed against either the F region [(Ab9 alpha (F) and Ab12 alpha (F)] or the A1 region [Ab10 alpha 1(A1)] recognized transiently expressed human and mouse RAR-alpha 1 proteins, when either immunocytochemistry or immunoprecipitation was used. In addition, Ab9 alpha (F) and Ab12 alpha (F), but not Ab10 alpha 1(A1), revealed the RAR-alpha 1 proteins by Western blotting analysis. Ab9 alpha (F) was also able to "supershift" RAR-alpha 1 protein-RARE oligonucleotide probe complexes in gel retardation assays. All these antibodies recognized also the transiently expressed mRAR-alpha 2 isoform, with the exception of Ab10 alpha 1 (A1), which is specific for the A1 region of RAR-alpha 1. These antibodies have enabled us to detect the presence of mRAR-alpha as multiple species in mouse embryo and adult tissue extracts as well as in embryonal carcinoma (EC) cells. Moreover, we found that one of these species (51 kDa) was phosphorylated in EC cells. This phosphorylation was not affected by RA treatment, but appeared to be dependent on the differentiation state of the EC cells.     

Correlations of life-history and distributional-range variation with salamander diversification rates: evidence for species selection

Evolutionary biologists have long debated the relative influence of species selection on evolutionary patterns. As a test, we apply a statistical phylogenetic approach to evaluate the influence of traits related to species distribution and life-history characteristics on patterns of diversification in salamanders. We use independent contrasts to test trait-mediated diversification while accommodating phylogenetic uncertainty in relationships among all salamander families. Using a neontological data set, we find several species-level traits to be variable, heritable, and associated with differential success (i.e., higher diversification rates) at higher taxonomic categories. Specifically, the macroecological trait of small geographic-range size is strongly correlated with a higher rate of net diversification. We further consider the role that plasticity in life-history traits appears to fulfill in macroevolutionary processes of lineage divergence and durability. We find that pedotypy--wherein some, but not all, organisms of a species mature in the gilled form without metamorphosing-is also associated with higher net diversification rate than is the absence of developmental plasticity. Often dismissed as an insignificant process in evolution, we provide direct evidence for the role of species selection in lineage diversification of salamanders.     

Comparing G: multivariate analysis of genetic variation in multiple populations

The additive genetic variance–covariance matrix (G) summarizes themultivariate genetic relationships among a set of traits. The geometry of Gdescribes the distribution of multivariate genetic variance, and generates geneticconstraints that bias the direction of evolution. Determining if and how the multivariategenetic variance evolves has been limited by a number of analytical challenges incomparing G-matrices. Current methods for the comparison of G typically shareseveral drawbacks: metrics that lack a direct relationship to evolutionary theory, theinability to be applied in conjunction with complex experimental designs, difficultieswith determining statistical confidence in inferred differences and an inherentlypair-wise focus. Here, we present a cohesive and general analytical framework for thecomparative analysis of G that addresses these issues, and that incorporates andextends current methods with a strong geometrical basis. We describe the application ofrandom skewers, common subspace analysis, the 4th-order genetic covariance tensor and thedecomposition of the multivariate breeders equation, all within a Bayesian framework. Weillustrate these methods using data from an artificial selection experiment on eighttraits in Drosophila serrata, where a multi-generational pedigree was availableto estimate G in each of six populations. One method, the tensor, elegantlycaptures all of the variation in genetic variance among populations, and allows theidentification of the trait combinations that differ most in genetic variance. The tensorapproach is likely to be the most generally applicable method to the comparison ofG-matrices from any sampling or experimental design.     

Visualizing patterns of craniofacial shape variation in Homo sapiens

The geometric morphometric analysis of shape variation in complex biological structures such as the human skull poses a number of specific challenges: the registration of homologous morphologies, the treatment of bilateral symmetry, the graphical representation of form variability in three dimensions and the interpretation of the results in terms of differential growth processes. To visualize complex patterns of shape change, we propose an alternative to classical Cartesian deformation grids in the style of D'Arcy W. Thompson. Reference to the surface structures of the organism under investigation permits a comprehensive visual grasp of shape change and its tentative interpretation in terms of differential growth. The application of this method to the analysis of human craniofacial shape variation reveals distinct modes of growth and development of the neurocranial and viscerocranial regions of the skull. Our data further indicate that variations in the orientation of the viscerocranium relative to the neurocranium impinge on the shapes of the face and the cranial vault.     

Phylogenetic relationships of cultivated Prunus species from an analysis of chloroplast DNA variation

Chloroplast DNA (cpDNA) restriction-site mutations in seven cultivated Prunus species were compared to establish the phylogenetic relationships among them. Mutations were detected in 3.2-kb and 2.1-kb amplified regions of variable cpDNA, cut with 21 and 10 restriction endonucleases, respectively, to reveal polymorphisms. Parsimony and cluster analyses were performed. The species pairs P. persica-P. dulcis, P. domestica-P. salicina, and P.cerasus-P. fruticosa were completely monophyletic. All of the species were grouped with conventional subgenus classifications. The subgenus Cerasus was the most diverged. Cerasus ancestors separated from the remainder of Prunus relatively early in the development of the genus. P. persica-P. dulcis, P. domestica-P. salicina and P. armeniaca formed a second monophyletic group. Prunophora species were less diverged than Amygdalus species. The results also suggest that the rate of mutation in Cerasus spp. chloroplast genomes is significantly greater than for the other subgenera sampled.     

Repetition, conservation, and variation: the multiple cp32 plasmids of Borrelia species

Members of the spirochete genus Borrelia contain large numbers of extrachromosomal DNAs. Sequence analysis of the B. burgdorferi strain B31 genome indicated that its many plasmids contain large quantities of repeated sequences, the most obvious of which are the cp32 plasmid family. Individual spirochetes may carry nine or more different, but homologous, cp32 plasmids. Every other species of Borrelia examined thus far also contains multiple plasmids related to the B. burgdorferi cp32s. These plasmids are arguably the best characterized of all the borrelial plasmids, and epitomize the apparent redundancy evident in the many plasmids carried by these bacteria. Despite their extensive similarities, cp32 plasmids contain some open reading frames whose sequences often vary between plasmids, and which encode proteins synthesized by the bacteria during vertebrate infection. In this review, we analyze the hypervariable and conserved regions of the cp32 plasmid family, and discuss possible reasons why borreliae harbor multiple gene paralogs.     

The taxonomic implications of cranial shape variation in Homo erectus

The taxonomic status of Homo erectus sensu lato has been a source of debate since the early 1980s, when a series of publications suggested that the early African fossils may represent a separate species, H. ergaster. To gain further resolution regarding this debate, 3D geometric morphometric data were used to quantify overall shape variation in the cranial vault within H. erectus using a new metric, the sum of squared pairwise Procrustes distances (SSD). Bootstrapping methods were used to compare the H. erectus SSD to a broad range of human and nonhuman primate samples in order to ascertain whether variation in H. erectus most clearly resembles that seen in one or more species. The reference taxa included relevant phylogenetic, ecological, and temporal analogs including humans, apes, and both extant and extinct papionin monkeys. The mean cranial shapes of different temporogeographic subsets of H. erectus fossils were then tested for significance using exact randomization tests and compared to the distances between regional groups of modern humans and subspecies/species of the ape and papionin monkey taxa. To gauge the influence of sexual dimorphism on levels of variation, comparisons were also made between the mean cranial shapes of single-sex samples for the reference taxa. Results indicate that variation in H. erectus is most comparable to single species of papionin monkeys and the genus Pan, which included two species. However, H. erectus encompasses a limited range of variation given its extensive geographic and temporal range, leading to the conclusion that only one species should be recognized. In addition, there are significant differences between the African/Georgian and Asian H. erectus samples, but not between H. ergaster (Georgia+Africa, excluding OH 9 and Daka) and H. erectus sensu stricto. This finding is in line with expectations for intraspecific variation in a long-lived species with a wide, but probably discontinuous, geographic distribution.     

Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes

Most previous work on the evolution of mobile DNA was limited by incomplete sequence information. Whole genome sequences allow us to overcome this limitation. I study the nucleotide diversity of prominent members of five insertion sequence families whose transposition activity is encoded by a single transposase gene. Eighteen among 376 completely sequenced bacterial genomes and plasmids carry between 3 and 20 copies of a given insertion sequence. I show that these copies generally show very low DNA divergence. Specifically, more than 68% of the transposase genes are identical within a genome. The average number of amino acid replacement substitutions at amino acid replacement sites is Ka = 0.013, that at silent sites is Ks = 0.1. This low intragenomic diversity stands in stark contrast to a much higher divergence of the same insertion sequences among distantly related genomes. Gene conversion among protein-coding genes is unlikely to account for this lack of diversity. The relation between transposition frequencies and silent substitution rates suggests that most insertion sequences in a typical genome are evolutionarily young and have been recently acquired. They may undergo periodic extinction in bacterial lineages. By implication, they are detrimental to their host in the long run. This is also suggested by the highly skewed and patchy distribution of insertion sequences among genomes. In sum, one can think of insertion sequences as slow-acting infectious diseases of cell lineages.     

Allozymic variation in four Indian species of genusMus: A comparative analysis

The present study focusses on allozyme variation in the commensal house mouseMus musculus, the pygmy field miceM. booduga andM. terricolor, and the spiny mouseM. platythrix. Genetic heterozygosity was estimated using a set of 24 polymorphic biochemical genetic markers. The extent of variability present inM. booduga, M. terricolor andM. platythrix has been compared with that in theM. musculus complex. Levels of allozyme variation at species level indicate thatM. musculus has the maximum heterogeneity, followed byM. booduga andM. terricolor, whileM. platythrix shows comparatively homogeneous genetic make-up. Gene frequency data have been used to trace phylogenetic relationships among these four species.     

OrthoClust: an orthology-based network framework for clustering data across multiple species

Increasingly, high-dimensional genomics data are becoming available for many organisms.Here, we develop OrthoClust for simultaneously clustering data across multiple species. OrthoClust is a computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific. We demonstrate the application of OrthoClust using the RNA-Seq expression profiles of Caenorhabditis elegans and Drosophila melanogaster from the modENCODE consortium. A potential application of cross-species modules is to infer putative analogous functions of uncharacterized elements like non-coding RNAs based on guilt-by-association.

Electronic supplementary material

The online version of this article (doi:10.1186/gb-2014-15-8-r100) contains supplementary material, which is available to authorized users.     

Reactive oxygen species production in association with suberization: evidence for an NADPH-dependent oxidase

In response to wounding, potato tubers generate reactive oxygen species (ROS) in association with suberization. Immediately following wounding, an initial burst of ROS occurs, reaching a maximum within 30 to 60 min. In addition to this initial oxidative burst, at least three other massive bursts occur at 42, 63 and 100 h post-wounding. These latter bursts are associated with wound healing and are probably involved in the oxidative cross-linking of suberin poly(phenolics). The source of ROS is likely to be a plasma membrane NADPH-dependent oxidase immunorelated to the human phagocyte plasma membrane oxidase. The initial oxidative burst does not appear to be dependent on new protein synthesis, but the subsequent bursts are associated with an increase in oxidase protein components. Oxidase activity is enhanced in vitro by hydroxycinnamic acids and conjugates associated with the wound healing response in potato.