Phylogenetic position of <em>Diania</em> challenged

Liu et al.1 describe a new and remarkable fossil, Diania cactiformis. This animal apparently combined the soft trunk of lobopodians (a group including the extant velvet worms in addition to many Palaeozoic genera) with the jointed limbs that typify arthropods. They go on to promote Diania as the immediate sister group to the arthropods, and conjecture that sclerotized and jointed limbs may therefore have evolved before articulated trunk tergites in the immediate arthropod stem. The data published by Liu et al.1 do not un-ambiguously support these conclusions; rather, we believe that Diania probably belongs within an unresolved clade or paraphyletic grade of lobopodians

A quantitative framework for characterizing the evolutionary history of mammalian gene expression

The evolutionary history of a gene helps predict its function and relationship to phenotypic traits. Although sequence conservation is commonly used to decipher gene function and assess medical relevance, methods for functional inference from comparative expression data are lacking. Here, we use RNA-seq across seven tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein–Uhlenbeck process, a commonly proposed model of continuous trait evolution. We apply this model to identify expression pathways under neutral, stabilizing, and directional selection. We further demonstrate novel applications of this model to quantify the extent of stabilizing selection on a gene’s expression, parameterize the distribution of each gene’s optimal expression level, and detect deleterious expression levels in expression data from individual patients. Our work provides a statistical framework for interpreting expression data across species and in disease

Molecular phylogeny and diversification history of Prosopis (Fabaceae: Mimosoideae)

The genus Prosopis is an important member of arid and semiarid environments around the world. To study Prosopis diversification and evolution, a combined approach including molecular phylogeny, molecular dating, and character optimization analysis was applied. Phylogenetic relationships were inferred from five different molecular markers (matK-trnK, trnL-trnF, trnS-psbC, G3pdh, NIA). Taxon sampling involved a total of 30 Prosopis species that represented all Sections and Series and the complete geographical range of the genus. The results suggest that Prosopis is not a natural group. Molecular dating analysis indicates that the divergence between Section Strombocarpa and Section Algarobia plus Section Monilicarpa occurred in the Oligocene, contrasting with a much recent diversification (Late Miocene) within each of these groups. The diversification of the group formed by species of Series Chilenses, Pallidae, and Ruscifoliae is inferred to have started in the Pliocene, showing a high diversification rate. The moment of diversification within the major lineages of American species of Prosopis is coincident with the spreading of arid areas in the Americas, suggesting a climatic control for diversification of the group. Optimization of habitat parameters suggests an ancient occupation of arid environments by Prosopis species.Fil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Vilardi, Juan Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; ArgentinaFil: Tosto, Daniela Sandra. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas; ArgentinaFil: Saidman, Beatriz Ofelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentin

Phylogenetic position and revised classification of Acacia s.l. (Fabaceae: Mimosoideae) in Africa, including new combinations in Vachellia and Senegalia

Previous phylogenetic studies have indicated that Acacia Miller s.l. is polyphyletic and in need of reclassification. A proposal to conserve the name Acacia for the larger Australian contingent of the genus (formerly subgenus Phyllodineae) resulted in the retypification of the genus with the Australian A. penninervis. However, Acacia s.l. comprises at least four additional distinct clades or genera, some still requiring formal taxonomic transfer of species. These include Vachellia (formerly subgenus Acacia), Senegalia (formerly subgenus Aculeiferum), Acaciella (formerly subgenus Aculeiferum section Filicinae) and Mariosousa (formerly the A. coulteri group). In light of this fragmentation of Acacia s.l., there is a need to assess relationships of the non-Australian taxa. A molecular phylogenetic study of Acacia s.l and close relatives occurring in Africa was conducted using sequence data from matK/trnK, trnL-trnF and psbA-trnH with the aim of determining the placement of the African species in the new generic system. The results reinforce the inevitability of recognizing segregate genera for Acacia s.l. and new combinations for the African species in Senegalia and Vachellia are formalized.Web of Scienc

Molecular Variation at a Candidate Gene Implicated in the Regulation of Fire Ant Social Behavior

The fire ant Solenopsis invicta and its close relatives display an important social polymorphism involving differences in colony queen number. Colonies are headed by either a single reproductive queen (monogyne form) or multiple queens (polygyne form). This variation in social organization is associated with variation at the gene Gp-9, with monogyne colonies harboring only B-like allelic variants and polygyne colonies always containing b-like variants as well. We describe naturally occurring variation at Gp-9 in fire ants based on 185 full-length sequences, 136 of which were obtained from S. invicta collected over much of its native range. While there is little overall differentiation between most of the numerous alleles observed, a surprising amount is found in the coding regions of the gene, with such substitutions usually causing amino acid replacements. This elevated coding-region variation may result from a lack of negative selection acting to constrain amino acid replacements over much of the protein, different mutation rates or biases in coding and non-coding sequences, negative selection acting with greater strength on non-coding than coding regions, and/or positive selection acting on the protein. Formal selection analyses provide evidence that the latter force played an important role in the basal b-like lineages coincident with the emergence of polygyny. While our data set reveals considerable paraphyly and polyphyly of S. invicta sequences with respect to those of other fire ant species, the b-like alleles of the socially polymorphic species are monophyletic. An expanded analysis of colonies containing alleles of this clade confirmed the invariant link between their presence and expression of polygyny. Finally, our discovery of several unique alleles bearing various combinations of b-like and B-like codons allows us to conclude that no single b-like residue is completely predictive of polygyne behavior and, thus, potentially causally involved in its expression. Rather, all three typical b-like residues appear to be necessary

Hyptiogastrites electrinus Cockerell, 1917, from Myanmar (Burmese) amber: Redescription and its placement within the Evanioidea (Insecta: Hymenoptera)

© The Natural History MuseumThe wasp Hyptiogastrites electrinus Cockerell, 1917, from the Lower Cretaceous (Upper Albian) Myanmar (Burmese) amber is redescribed from the well-preserved holotype and its relationship with extant Aulacidae and Gasteruptiidae (Hymenoptera: Evanioidea) evaluated. Although the wing venation is identical to the majority of extant Hyptiogastrinae (Gasteruptiidae), phylogenetic analysis places H. electrinus as sister taxon to the Aulacidae s.str., (i.e. Aulacus + Pristaulacus). Thus, Hyptiogastrinae is confirmed as having a restricted Southern Hemisphere distribution (i.e. Australasia and South America). Consistent with this result, H. electrinus is included within a slightly more broadly defined Aulacidae rather than being placed in a new monotypic family. Characters that align this species with the Aulacidae include: having small circular eyes, percurrent Y-shaped notauli, pyramidal shape of the propodeum and the presence of a groove or ovipositor guide on the hind coxae.John T. Jennings, Andrew D. Austin and Nicholas B. Steven

Loss of Wolbachia infection during colonisation in the invasive Argentine ant Linepithema humile

WOLBACHIA are maternally inherited bacteria, which are very common in arthropods and nematodes. Wolbachia infection may affect host reproduction through feminisation, parthenogenesis, male-killing, cytoplasmic incompatibility and increased fecundity. Previous studies showing discrepancies between the phylogenies of Wolbachia and its arthropod hosts indicate that infection is frequently lost, but the causes of symbiont extinction have so far remained elusive. Here, we report data showing that colonisation of new habitats is a possible mechanism leading to the loss of infection. The presence and prevalence of Wolbachia were studied in three native and eight introduced populations of the Argentine ant Linepithema humile. The screening shows that the symbiont is common in the three native L. humile populations analysed. In contrast, Wolbachia was detected in only one of the introduced populations. The loss of infection associated with colonisation of new habitats may result from drift (founder effect) or altered selection pressures in the new habitat. Furthermore, a molecular phylogeny based on sequences of the Wolbachia wsp gene indicates that L. humile has been infected by a single strain. Horizontal transmission of the symbiont may be important in ants as suggested by the sequence similarity of strains in the three genera Linepithema, Acromyrmex, and Solenopsis native from South and Central America

Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B

Background: Canine osteosarcoma is clinically nearly identical to the human disease, but is common and highly heritable, making genetic dissection feasible. Results: Through genome-wide association analyses in three breeds (greyhounds, Rottweilers, and Irish wolfhounds), we identify 33 inherited risk loci explaining 55% to 85% of phenotype variance in each breed. The greyhound locus exhibiting the strongest association, located 150 kilobases upstream of the genes CDKN2A/B, is also the most rearranged locus in canine osteosarcoma tumors. The top germline candidate variant is found at a >90% frequency in Rottweilers and Irish wolfhounds, and alters an evolutionarily constrained element that we show has strong enhancer activity in human osteosarcoma cells. In all three breeds, osteosarcoma-associated loci and regions of reduced heterozygosity are enriched for genes in pathways connected to bone differentiation and growth. Several pathways, including one of genes regulated by miR124, are also enriched for somatic copy-number changes in tumors. Conclusions: Mapping a complex cancer in multiple dog breeds reveals a polygenic spectrum of germline risk factors pointing to specific pathways as drivers of disease