Lineages Within the Trichophyton rubrum Complex

The most important species of the Trichophyton rubrum group are T. rubrum, causing mainly skin and nail infections, and T. violaceum which is mostly scalp-associated. The status of a third species, T. soudanense, has been under debate. With a polyphasic approach, using molecular phylogenetic techniques, MALDI-TOF mass spectrometry and physiological and morphological analysis, we re-evaluated the T. rubrum complex. Our results support four genetic lineages within the complex each with a distinct morphology and identifiable via MALDI-TOF MS: T. rubrum, T. violaceum, T. soudanense and the T. yaoundei clade. However, ITS and Bt2 sequencing data could not confirm these taxa as four monophyletic species. Our results also suggest that strains formerly identified as T. kuryangei and T. megninii should be considered in future taxonomic studies.

     

Evolution of Primate Social Systems

We review evolutionary processes and mechanisms that gave rise to the diversity of primate social systems. We define social organization, social structure and mating system as distinct components of a social system. For each component, we summarize levels and patterns of variation among primates and discuss evolutionary determinants of this variation. We conclude that conclusive explanations for a solitary life and pair-living are still lacking. We then focus on interactions among the 3 components in order to identify main targets of selection and potential constraints for social evolution. Social organization and mating system are more closely linked to each other than either one is to social structure. Further, we conclude that it is important to seek a priori measures for the effects of presumed selective factors and that the genetic contribution to social systems is still poorly examined. Finally, we examine the role of primate socio-ecology in current evolutionary biology and conclude that primates are not prominently represented because the main questions asked in behavioral ecology are often irrelevant for primate behavior. For the future, we see a rapprochement of these areas as the role of disease and life-history theory are integrated more fully into primate socio-ecology.     

腐蚀生物膜垢中硫酸盐还原菌的系统进化分析

从油田回注水系统加压泵后的管道管壁生物膜垢里分离得到的一株嗜热、嗜酸、异养型硫酸盐还原菌,编号为CW-04.该菌株兼性厌氧、革兰氏阳性、有极生鞭毛、直或弯曲的短杆状,能产孢子,最佳生长温度47℃,在20℃～63℃下培养基中均能使测试瓶有黑色沉淀产生,从腐蚀防治的角度研究该菌株的生长曲线.主要生理生化特性包括:生长pH范围为3.7～10,最佳生长pH为6～6.5,最佳生长盐度为0.7%.能够在H2 醋酸盐、甲酸盐、乙酸盐、丙酸盐、乳酸盐、丙酮酸盐和乙醇等电子供体中生长,也能够利用葡萄糖、果糖和简单的氨基酸作为唯一碳源生长;能够在硫酸钠、硫代硫酸钠、亚硫酸钠等电子受体中生长,但是不能利用硝酸盐和硫磺.通过16S rDNA测序以及系列比对分析:该菌属于细菌界(Bacteria)、厚壁菌门(Firmicutes)、梭菌纲(Clostridia)、梭菌目(Clostridiales)、蛋白胨链球菌科(Peptococcaceae)、脱硫肠状菌属(Desulfotomaculum),与该属中的种Desulfotomaculum aeronauticumd相似性达到99%.     

腐蚀生物膜垢中硫酸盐还原菌的系统进化分析

从油田回注水系统加压泵后的管道管壁生物膜垢里分离得到的一株嗜热、嗜酸、异养型硫酸盐还原菌, 编号为CW-04。该菌株兼性厌氧、革兰氏阳性、有极生鞭毛、直或弯曲的短杆状,能产孢子, 最佳生长温度47℃, 在20℃~63℃下培养基中均能使测试瓶有黑色沉淀产生。从腐蚀防治的角度研究该菌株的生长曲线。主要生理生化特性包括: 生长pH范围为3.7~10, 最佳生长pH为6~6.5, 最佳生长盐度为0.7%。能够在H2+醋酸盐、甲酸盐、乙酸盐、丙酸盐、乳酸盐、丙酮酸盐和乙醇等电子供体中生长, 也能够利用葡萄糖、果糖和简单的氨基酸作为唯一碳源生长; 能够在硫酸钠、硫代硫酸钠、亚硫酸钠等电子受体中生长, 但是不能利用硝酸盐和硫磺。通过16S rDNA测序以及系列比对分析: 该菌属于细菌界(Bacteria)、厚壁菌门(Firmicutes)、梭菌纲(Clostridia)、梭菌目(Clostridiales)、蛋白胨链球菌科(Peptococcaceae)、脱硫肠状菌属(Desulfotomaculum), 与该属中的种Desulfotomaculum aeronauticumd 相似性达到99%。     

Vif Proteins from Diverse Primate Lentiviral Lineages Use the Same Binding Site in APOBEC3G

APOBEC3G (A3G) is a cytidine deaminase that restricts human immunodeficiency virus type 1 (HIV-1) and other lentiviruses. Most of these viruses encode a Vif protein that directly binds A3G and leads to its proteasomal degradation. Both Vif proteins of HIV-1 and African green monkey simian immunodeficiency virus (SIVagm) bind residue 128 of A3G. However, this position does not control the A3G degradation by Vif variants derived from HIV-2 and SIVmac, which both originated from SIV of sooty mangabey monkeys (SIVsmm), suggesting that the A3G binding site for Vif proteins of the SIVsmm/HIV-2 lineage differs from that of HIV-1. To map the SIVsmm Vif binding site of A3G, we performed immunoprecipitations of individual A3G domains, Vif/A3G degradation assays and a detailed mutational analysis of human A3G. We show that A3G residue 129, but not the adjacent position 128, confers susceptibility to degradation by SIVsmm Vif. An artificial A3G mutant, the P129D mutant, was resistant to degradation by diverse Vifs from HIV-1, HIV-2, SIVagm, and chimpanzee SIV (SIVcpz), suggesting a conserved lentiviral Vif binding site. Gorilla A3G naturally contains a glutamine (Q) at position 129, which makes its A3G resistant to Vifs from diverse lineages. We speculate that gorilla A3G serves as a barrier against SIVcpz strains. In summary, we show that Vif proteins from distinct lineages bind to the same A3G loop, which includes positions 128 and 129. The multiple adaptations within this loop among diverse primates underscore the importance of counteracting A3G in lentiviral evolution.     

Substrate Size and Primate Forelimb Mechanics: Implications for Understanding the Evolution of Primate Locomotion

International Journal of Primatology - Did the anatomical and locomotor specializations of primates evolve in response to requirements of locomotion and foraging on thin branches? Laboratory...     

Evolution of the Chloroplast trnL-trnF Region in the Gymnosperm Lineages Taxaceae and Cephalotaxaceae

The trnL-trnF region is located in the large single-copy region of the chloroplast genome. It consists of the trnL gene, a group I intron, and the trnL-F intergenic spacer. We analyzed the evolution of the region in three gymnosperm families, Taxaceae, Cephalotaxaceae, and Podocarpaceae, with especially dense sampling in Taxaceae and Cephalotaxaceae, for which we sequenced 43 accessions, representing all species. The trnL intron has a conserved secondary structure and contains elements that are homologous across land plants, and the spacer is highly variable in length and composition. The spatial distribution of nucleotide diversity along the trnL-F region suggests that different portions of this region have different evolutionary patterns. Tandem repeats that form stem–loop structures were detected in both the trnL intron and the trnL-F spacer, and the spacer sequences contain promoter elements for the trnF gene. The presence of promoters and stem–loop structures in the trnL-F spacer and high sequence variation in this region suggest that trnL and trnF are independently transcribed. Stem–loop regions P6, P8, and P9 of the trnL intron and the trnL-F spacer (except the promoter elements) might undergo neutral evolution with respect to their escape from functional constraints.     

Molecular Evolution of the Primate Antiviral Restriction Factor Tetherin

Background

Tetherin is a recently identified antiviral restriction factor that restricts HIV-1 particle release in the absence of the HIV-1 viral protein U (Vpu). It is reminiscent of APOBEC3G and TRIM5a that also antagonize HIV. APOBEC3G and TRIM5a have been demonstrated to evolve under pervasive positive selection throughout primate evolution, supporting the red-queen hypothesis. Therefore, one naturally presumes that Tetherin also evolves under pervasive positive selection throughout primate evolution and supports the red-queen hypothesis. Here, we performed a detailed evolutionary analysis to address this presumption.

Methodology/Principal Findings

Results of non-synonymous and synonymous substitution rates reveal that Tetherin as a whole experiences neutral evolution rather than pervasive positive selection throughout primate evolution, as well as in non-primate mammal evolution. Sliding-window analyses show that the regions of the primate Tetherin that interact with viral proteins are under positive selection or relaxed purifying selection. In particular, the sites identified under positive selection generally focus on these regions, indicating that the main selective pressure acting on the primate Tetherin comes from virus infection. The branch-site model detected positive selection acting on the ancestral branch of the New World Monkey lineage, suggesting an episodic adaptive evolution. The positive selection was also found in duplicated Tetherins in ruminants. Moreover, there is no bias in the alterations of amino acids in the evolution of the primate Tetherin, implying that the primate Tetherin may retain broad spectrum of antiviral activity by maintaining structure stability.

Conclusions/Significance

These results conclude that the molecular evolution of Tetherin may be attributed to the host–virus arms race, supporting the Red Queen hypothesis, and Tetherin may be in an intermediate stage in transition from neutral to pervasive adaptive evolution.     

Behavioral Flexibility and the Evolution of Primate Social States

Comparative approaches to the evolution of primate social behavior have typically involved two distinct lines of inquiry. One has focused on phylogenetic analyses that treat social traits as static, species-specific characteristics; the other has focused on understanding the behavioral flexibility of particular populations or species in response to local ecological or demographic variables. Here, we combine these approaches by distinguishing between constraining traits such as dispersal regimes (male, female, or bi-sexual), which are relatively invariant, and responding traits such as grouping patterns (stable, fission-fusion, sometimes fission-fusion), which can reflect rapid adjustments to current conditions. Using long-term and cross-sectional data from 29 studies of 22 species of wild primates, we confirm that dispersal regime exhibits a strong phylogenetic signal in our sample. We then show that primate species with high variation in group size and adult sex ratios exhibit variability in grouping pattern (i.e., sometimes fission-fusion) with dispersal regime constraining the grouping response. When assessing demographic variation, we found a strong positive relationship between the variability in group size over time and the number of observation years, which further illustrates the importance of long-term demographic data to interpretations of social behavior. Our approach complements other comparative efforts to understand the role of behavioral flexibility by distinguishing between constraining and responding traits, and incorporating these distinctions into analyses of social states over evolutionary and ecological time.     

The Developmental Origins of Mosaic Evolution in the Primate Limb Skeleton

The central hypothesis of this paper is that basic properties of vertebrate limb development bias the generation of phenotypic variation in certain directions, and that these biases establish focal units, or regions, of evolutionary change within the primate hand and foot. These focal units include (1) a preaxial domain (digit I, hallux or pollex, metapodial and proximal phalanx), (2) a postaxial domain (metapodials and phalanges of digits II?CV), and (3) a digit tip domain (terminal phalanges and nails/claws of rays I?CV). The existence of these focal units therefore provides a mechanistic basis for mosaic evolution within the hand and foot, and can be applied to make specific predictions about which features of the limb skeleton are most likely to be altered in primate adaptive radiations over time. Examination of the early primate fossil record provides support for this model, and suggests that the existence of variational tendencies in limb development has played a major role in guiding the origin and evolution of primate skeletal form.     

The Roles of Phytoestrogens in Primate Ecology and Evolution

Most primates depend heavily on plant foods; thus their chemical composition is key to understanding primate ecology and evolution. One class of plant compounds of strong current interest are phytoestrogens, which have the potential to alter fertility, fecundity, and survival. These plant compounds mimic the activity of vertebrate estrogens, resulting in altered physiology and behavior. Here, we review what is known about phytoestrogens from an ecological and evolutionary perspective. Much of what is known about the effects of phytoestrogens on the endocrine system comes from research on human foods, especially soybeans (Glycine max). Two opposing perspectives have resulted from this research: 1) phytoestrogens provide health benefits, such as cancer prevention, or 2) phytoestrogens act as endocrine disruptors and threaten reproductive health. Studies of wild primates have only recently begun examining the presence of estrogenic plants in the primate diet and the effects of their consumption. Evidence that a number of primate species eat plants containing phytoestrogens and research documenting behavioral and hormonal effects of estrogenic plant consumption for red colobus monkeys (Procolobus rufomitratus) augment captive and laboratory studies to suggest that these compounds promote differential survival and reproduction. Although much debate is currently taking place over the role of phytoestrogens and other endocrine disruptors in human health issues and in threatening biodiversity, we argue that an ecological and evolutionary approach is needed to reach appropriate conclusions.     

Evolution of Acyl-Substrate Recognition by a Family of Acyl-Homoserine Lactone Synthases

Members of the LuxI protein family catalyze synthesis of acyl-homoserine lactone (acyl-HSL) quorum sensing signals from S-adenosyl-L-methionine and an acyl thioester. Some LuxI family members prefer acyl-CoA, and others prefer acyl-acyl carrier protein (ACP) as the acyl-thioester substrate. We sought to understand the evolutionary history and mechanisms mediating this substrate preference. Our phylogenetic and motif analysis of the LuxI acyl-HSL synthase family indicates that the acyl-CoA-utilizing enzymes evolved from an acyl-ACP-utilizing ancestor. To further understand how acyl-ACPs and acyl-CoAs are recognized by acyl-HSL synthases we studied BmaI1, an octanoyl-ACP-dependent LuxI family member from Burkholderia mallei, and BjaI, an isovaleryl-CoA-dependent LuxI family member from Bradyrhizobium japonicum. We synthesized thioether analogs of their thioester acyl-substrates to probe recognition of the acyl-phosphopantetheine moiety common to both acyl-ACP and acyl-CoA substrates. The kinetics of catalysis and inhibition of these enzymes indicate that they recognize the acyl-phosphopantetheine moiety and they recognize non-preferred substrates with this moiety. We find that CoA substrate utilization arose through exaptation of acyl-phosphopantetheine recognition in this enzyme family.     

Considering the Influence of Nonadaptive Evolution on Primate Color Vision

Color vision in primates is variable across species, and it represents a rare trait in which the genetic mechanisms underlying phenotypic variation are fairly well-understood. Research on primate color vision has largely focused on adaptive explanations for observed variation, but it remains unclear why some species have trichromatic or polymorphic color vision while others are red-green color blind. Lemurs, in particular, are highly variable. While some species are polymorphic, many closely-related species are strictly dichromatic. We provide the first characterization of color vision in a wild population of red-bellied lemurs (Eulemur rubriventer, Ranomafana National Park, Madagascar) with a sample size (87 individuals; N_{X chromosomes} = 134) large enough to detect even rare variants (0.95 probability of detection at ≥ 3% frequency). By sequencing exon 5 of the X-linked opsin gene we identified opsin spectral sensitivity based on known diagnostic sites and found this population to be dichromatic and monomorphic for a long wavelength allele. Apparent fixation of this long allele is in contrast to previously published accounts of Eulemur species, which exhibit either polymorphic color vision or only the medium wavelength opsin. This unexpected result may represent loss of color vision variation, which could occur through selective processes and/or genetic drift (e.g., genetic bottleneck). To indirectly assess the latter scenario, we genotyped 55 adult red-bellied lemurs at seven variable microsatellite loci and used heterozygosity excess and M-ratio tests to assess if this population may have experienced a recent genetic bottleneck. Results of heterozygosity excess but not M-ratio tests suggest a bottleneck might have occurred in this red-bellied lemur population. Therefore, while selection may also play a role, the unique color vision observed in this population might have been influenced by a recent genetic bottleneck. These results emphasize the need to consider adaptive and nonadaptive mechanisms of color vision evolution in primates.     

Evolution of Conifer Diterpene Synthases: Diterpene Resin Acid Biosynthesis in Lodgepole Pine and Jack Pine Involves Monofunctional and Bifunctional Diterpene Synthases

Abscisic acid (ABA) induces stomatal closure and inhibits light-induced stomatal opening. The mechanisms in these two processes are not necessarily the same. It has been postulated that the ABA receptors involved in opening inhibition are different from those involved in closure induction. Here, we provide evidence that four recently identified ABA receptors (PYRABACTIN RESISTANCE1 [PYR1], PYRABACTIN RESISTANCE-LIKE1 [PYL1], PYL2, and PYL4) are not sufficient for opening inhibition in Arabidopsis (Arabidopsis thaliana). ABA-induced stomatal closure was impaired in the pyr1/pyl1/pyl2/pyl4 quadruple ABA receptor mutant. ABA inhibition of the opening of the mutant’s stomata remained intact. ABA did not induce either the production of reactive oxygen species and nitric oxide or the alkalization of the cytosol in the quadruple mutant, in accordance with the closure phenotype. Whole cell patch-clamp analysis of inward-rectifying K⁺ current in guard cells showed a partial inhibition by ABA, indicating that the ABA sensitivity of the mutant was not fully impaired. ABA substantially inhibited blue light-induced phosphorylation of H⁺-ATPase in guard cells in both the mutant and the wild type. On the other hand, in a knockout mutant of the SNF1-related protein kinase, srk2e, stomatal opening and closure, reactive oxygen species and nitric oxide production, cytosolic alkalization, inward-rectifying K⁺ current inactivation, and H⁺-ATPase phosphorylation were not sensitive to ABA.The phytohormone abscisic acid (ABA), which is synthesized in response to abiotic stresses, plays a key role in the drought hardiness of plants. Reducing transpirational water loss through stomatal pores is a major ABA response (Schroeder et al., 2001). ABA promotes the closure of open stomata and inhibits the opening of closed stomata. These effects are not simply the reverse of one another (Allen et al., 1999; Wang et al., 2001; Mishra et al., 2006).A class of receptors of ABA was identified (Ma et al., 2009; Park et al., 2009; Santiago et al., 2009; Nishimura et al., 2010). The sensitivity of stomata to ABA was strongly decreased in quadruple and sextuple mutants of the ABA receptor genes PYRABACTIN RESISTANCE/PYRABACTIN RESISTANCE-LIKE/REGULATORY COMPONENT OF ABSCISIC ACID RECEPTOR (PYR/PYL/RCAR; Nishimura et al., 2010; Gonzalez-Guzman et al., 2012). The PYR/PYL/RCAR receptors are involved in the early ABA signaling events, in which a sequence of interactions of the receptors with PROTEIN PHOSPHATASE 2Cs (PP2Cs) and subfamily 2 SNF1-RELATED PROTEIN KINASES (SnRK2s) leads to the activation of downstream ABA signaling targets in guard cells (Cutler et al., 2010; Kim et al., 2010; Weiner et al., 2010). Studies of Commelina communis and Vicia faba suggested that the ABA receptors involved in stomatal opening are not the same as the ABA receptors involved in stomatal closure (Allan et al., 1994; Anderson et al., 1994; Assmann, 1994; Schwartz et al., 1994). The roles of PYR/PYL/RCAR in either stomatal opening or closure remained to be elucidated.Blue light induces stomatal opening through the activation of plasma membrane H⁺-ATPase in guard cells that generates an inside-negative electrochemical gradient across the plasma membrane and drives K⁺ uptake through voltage-dependent inward-rectifying K⁺ channels (Assmann et al., 1985; Shimazaki et al., 1986; Blatt, 1987; Schroeder et al., 1987; Thiel et al., 1992). Phosphorylation of the penultimate Thr of the plasma membrane H⁺-ATPase is a prerequisite for blue light-induced activation of the H⁺-ATPase (Kinoshita and Shimazaki, 1999, 2002). ABA inhibits H⁺-ATPase activity through dephosphorylation of the penultimate Thr in the C terminus of the H⁺-ATPase in guard cells, resulting in prevention of the opening (Goh et al., 1996; Zhang et al., 2004; Hayashi et al., 2011). Inward-rectifying K⁺ currents (I_Kin) of guard cells are negatively regulated by ABA in addition to through the decline of the H⁺ pump-driven membrane potential difference (Schroeder and Hagiwara, 1989; Blatt, 1990; McAinsh et al., 1990; Schwartz et al., 1994; Grabov and Blatt, 1999; Saito et al., 2008). This down-regulation of ion transporters by ABA is essential for the inhibition of stomatal opening.A series of second messengers has been shown to mediate ABA-induced stomatal closure. Reactive oxygen species (ROS) produced by NADPH oxidases play a crucial role in ABA signaling in guard cells (Pei et al., 2000; Zhang et al., 2001; Kwak et al., 2003; Sirichandra et al., 2009; Jannat et al., 2011). Nitric oxide (NO) is an essential signaling component in ABA-induced stomatal closure (Desikan et al., 2002; Guo et al., 2003; Garcia-Mata and Lamattina, 2007; Neill et al., 2008). Alkalization of cytosolic pH in guard cells is postulated to mediate ABA-induced stomatal closure in Arabidopsis (Arabidopsis thaliana) and Pisum sativum and Paphiopedilum species (Irving et al., 1992; Gehring et al., 1997; Grabov and Blatt, 1997; Suhita et al., 2004; Gonugunta et al., 2008). These second messengers transduce environmental signals to ion channels and ion transporters that create the driving force for stomatal movements (Ward et al., 1995; MacRobbie, 1998; Garcia-Mata et al., 2003).In this study, we examined the mobilization of second messengers, the inactivation of I_Kin, and the suppression of H⁺-ATPase phosphorylation evoked by ABA in Arabidopsis mutants to clarify the downstream signaling events of ABA signaling in guard cells. The mutants included a quadruple mutant of PYR/PYL/RCARs, pyr1/pyl1/pyl2/pyl4, and a mutant of a SnRK2 kinase, srk2e.     

Recombination in Tula Hantavirus Evolution: Analysis of Genetic Lineages from Slovakia

To examine the evolution of Tula hantavirus (TUL), carried by the European common vole (Microtus arvalis and M. rossiaemeridionalis), we have analyzed genetic variants from Slovakia, the country where the virus is endemic. Phylogenetic analysis (PHYLIP) based on either partial (nucleotides [nt] 441 to 898) or complete N-protein-encoding sequences divided Slovakian TUL variants into two main lineages: (i) strains from eastern Slovakia, which clustered with Russian strains, and (ii) strains from western Slovakia situated closer to those from the Czech Republic. We found genetic diversity of 19% between the two groups and 4% within the western Slovakian TUL strains. Phylogenetic analysis of the 3′ noncoding region (3′-NCR), however, placed the eastern Slovakian strains closer to those from western Slovakia and the Czech Republic, with a greater distance to the Russian strains, suggesting a recombinant nature of the S segment in the eastern Slovakian TUL lineage. A bootscan search of the S-segment sequences of TUL strains revealed at least two recombination points in the S sequences of eastern Slovakian TUL strains (nt 400 to 415 and around 1200) which agreed well with the pattern of amino acid substitutions in the N protein and deletions/insertions in the 3′-NCR of the S segment. These data suggest that homologous recombination events occurred in the evolution of hantaviruses.