Evidence for male-driven evolution in Drosophila

In several vertebrate taxa studied to date, mutation rates arehigher in males than females (male-driven evolution). The male-to-femalemutation rate () can be estimated by contrasting DNA divergencedata at X-linked, Y-linked, and autosomal loci. Previous studiesin Drosophila, comparing X-linked and autosomal divergence,have found no evidence for male-driven evolution in this genus.Here, I compare levels of nucleotide divergence between homologousX- and Y-linked loci in Drosophila miranda. Using divergenceat both synonymous sites and at short introns, I estimate tobe approximately 2. This study thus provides the first evidencefor male-biased mutation rates outside vertebrates, supportingthe view that DNA sequence evolution is male driven in a widevariety of taxa.     

CHOLESTEROL AS AN EVOLUTIONARY RESPONSE TO LIVING WITH OXYGEN

Although often considered in a negative light, cholesterol is an essential molecule with unusually diverse functions. Cholesterol and related sterols (ergosterol in yeast, phytosterols in plants) is considered a hallmark of eukaryotes, and may even have triggered the evolution of multicellular organisms. Synthesis of cholesterol is an extremely oxygen‐intensive process and requires sufficient terrestrial oxygen to proceed. In turn, several lines of evidence support the argument that cholesterol evolved at least in part as an adaptation to the hazards of oxygen. This evolutionary perspective usefully informs medical research on cholesterol to address health‐related issues, as illustrated by examples drawn from three prominent human diseases: cataracts, heart disease, and cancer.     

谈系统发生树建立的分子标准

随着进化生物学以及生物信息学的发展 ,研究不同物种间进化关系的方法也有了新的进展。其中分子进化方法使得系统发生树的建立更加简便和精确。几种系统发生树的建树方法及相关分子标准目前比较流行。。     

African Haplogroup L mtDNA sequences show violations of clock-like evolution

A set of 96 complete mtDNA sequences that belong to the three major African haplogroups (L1, L2, and L3) was analyzed to determine if mtDNA has evolved as a molecular clock. Likelihood ratio tests (LRTs) were carried out with each of the haplogroups and with combined haplogroup sequence sets. Evolution has not been clock-like, neither for the coding region nor for the control region, in combined sets of African haplogroup L mtDNA sequences. In tests of individual haplogroups, L2 mtDNAs showed violations of a molecular clock under all conditions and in both the control and coding regions. In contrast, haplogroup L1 and L3 sequences, both for the coding and control regions, show clock-like evolution. In clock tests of individual L2 subclades, the L2a sequences showed a marked violation of clock-like evolution within the coding region. In addition, the L2a and L2c branch lengths of both the coding and control regions were shorter relative to those of the L2b and L2d sequences, a result that indicates lower levels of sequence divergence. Reduced median network analyses of the L2a sequences indicated the occurrence of marked homoplasy at multiple sites in the control region. After exclusion of the L2a and L2c sequences, African mtDNA coding region evolution has not significantly departed from a molecular clock, despite the results of neutrality tests that indicate the mitochondrial coding region has evolved under nonneutral conditions. In contrast, control region evolution is clock-like only at the haplogroup level, and it thus appears to have evolved essentially independently from the coding region. The results of the clock tests, the network analyses, and the branch length comparisons all caution against the use of simple mtDNA clocks.     

Prior evolution in stochastic versus constant temperatures affects RNA virus evolvability at a thermal extreme

It is unclear how historical adaptation versus maladaptation in a prior environment affects population evolvability in a novel habitat. Prior work showed that vesicular stomatitis virus (VSV) populations evolved at constant 37°C improved in cellular infection at both 29°C and 37°C; in contrast, those evolved under random changing temperatures between 29°C and 37°C failed to improve. Here, we tested whether prior evolution affected the rate of adaptation at the thermal‐niche edge: 40°C. After 40 virus generations in the new environment, we observed that populations historically evolved at random temperatures showed greater adaptability. Deep sequencing revealed that most of the newly evolved mutations were de novo. Also, two novel evolved mutations in the VSV glycoprotein and replicase genes tended to co‐occur in the populations previously evolved at constant 37°C, whereas this parallelism was not seen in populations with prior random temperature evolution. These results suggest that prior adaptation under constant versus random temperatures constrained the mutation landscape that could improve fitness in the novel 40°C environment, perhaps owing to differing epistatic effects of new mutations entering genetic architectures that earlier diverged. We concluded that RNA viruses maladapted to their previous environment could “leapfrog” over counterparts of higher fitness, to achieve faster adaptability in a novel environment.     

REVIEW: Optimality models in the age of experimental evolution and genomics

Optimality models have been used to predict evolution of many properties of organisms. They typically neglect genetic details, whether by necessity or design. This omission is a common source of criticism, and although this limitation of optimality is widely acknowledged, it has mostly been defended rather than evaluated for its impact. Experimental adaptation of model organisms provides a new arena for testing optimality models and for simultaneously integrating genetics. First, an experimental context with a well‐researched organism allows dissection of the evolutionary process to identify causes of model failure – whether the model is wrong about genetics or selection. Second, optimality models provide a meaningful context for the process and mechanics of evolution, and thus may be used to elicit realistic genetic bases of adaptation – an especially useful augmentation to well‐researched genetic systems. A few studies of microbes have begun to pioneer this new direction. Incompatibility between the assumed and actual genetics has been demonstrated to be the cause of model failure in some cases. More interestingly, evolution at the phenotypic level has sometimes matched prediction even though the adaptive mutations defy mechanisms established by decades of classic genetic studies. Integration of experimental evolutionary tests with genetics heralds a new wave for optimality models and their extensions that does not merely emphasize the forces driving evolution.     

分子系统学在微体古生物及相关领域中的应用

核酸（ＤＮＡ和ＲＮＡ）和蛋白等生物大分子（尤其是它们的序列资料）可作为重要的生物性状用于系统分类和演化等主题的研究。相对于形态学性状而言,分子性状不仅是前者的补充,而且具有许多前者无法比拟的优点;比如ＤＮＡ作为遗传信息的直接载体能较准确地反映生物类群之间的系统发生关系、信息量巨大、易于定量化和进行计算机分析等等。分子古生物研究包含两个方面：一、发掘化石生物分子,以提供历史生物界演化过程中的直接遗传学证据以及检验分子演化速率等方面的独特数据;二、利用现代分子生物学数据,探讨化石生物界的系统发生问题。上述两个研究方向均已成为当今演化生物学领域的热点。有孔虫等具有重要化石记录的微体生物的分子系统学研究已经开始。随着现生的和化石的生物分子资料的逐渐积累,预期在不久的将来,分子资料将成为微体古生物研究中不可缺少的重要数据之一。     

Molecular Relationships Among Octodontidae (Mammalia: Rodentia: Caviomorpha)

We examined ten species of octodontid rodents and representatives of three outgroups in a complete 13 × 13 DNA-hybridization matrix. The results were indexed as differences in median melting-point depressions (T,_ms), symmetrized, subjected to phylogenetic analysis using FITCH, bootstrapped, and exhaustively taxon-jackknifed. Within Octodontidae, four clades were recovered with 100% bootstrap and complete jackknife support: Tympanoctomys barrerae with Octomys mimax, Octodontomys gliroides alone, Octodon spp., and Aconaemys spp. with Spalacopus cyanus; the latter two clades were closer to each other than either was to Octodontomys or Octomys-Tympanoctomys, but were slightly nearer to and united with Octodontomys, with 89% bootstrap support. However, relationships among the three Aconaemys species and Spalacopus were not completely resolved by our experiments. Ctenomys coyhaiquensis, Abrocoma bennetti, and Lagostomus maximus represented successive outgroups to Octodontidae, while one-way comparisons with Cavia porcellus and Microcavia australis suggested that these caviids are almost as distant from octodontoids as is the chinchilloid Lagostomus. When the data were suitably corrected for percentage hybridization and saturation, division of the distances by the rate previously determined for most amniotes (0.48%/myr) suggested that the basal divergence among the caviomorph rodents examined occurred about 59 myrbp, and that Octodontidae originated 40 myrbp and diversified into extant lineages beginning 14 myr ago. Calibration against the date of the earliest known caviomorph (late Eocene or about 37.5 myrbp) gave a rate of 0.75%/myr, which would suggest later dates for subsequent caviomorph cladogenesis. It is notable that, based respectively on the slower or faster rates, the tetraploid Tympanoctomys barrerae must have diverged from its sister-taxon Octomys mimax 10 or 6.5 myr ago.     

DNA重排及体外分子进化

ＤＮＡ重排是目前为止最简便、最有效的体外定向进化技术,可以对单一基因、质粒、代谢途径、部分甚至整个基因组进行改造。本综述了ＤＮＡ重排的基本原理、特点、与其它体外进化技术的不同,着重介绍了其在体外分子进化上的广泛应用,并对应用前景进行了展望。     

A phylogenetic study of chthamaloids (Cirripedia; Thorcica; Chthamaloidae) based on 16S rDNA and COI sequence analysis

The sequences of gene fragments encoding cytochrome  c oxidase subunit I (COI) and 16S rDNA were obtained and used to construct phylograms of eight taxa of chthamaloid barnacles using the scalpelloid Calantica as an out-group. The phylograms support the basal position of Catomerus within the chthamaloids . Analysis of 16S rDNA shows that Octomeris and the four-plated barnacle Chamaesipho are located on the same clade, while Chthamalus , Euraphia and Tetrachthamalus are located on a second clade, indicating that reduction in the number of shell plates occurred twice in the evolution of the chthamaloids. The topology of phylograms based on COI sequences is poorly resolved: 93% of third position nucleotides in this fragment are polymorphic while the amino acid sequences are strictly conserved. We assume that in the chthamaloids, at least at the generic level, polymorphism in the COI gene is saturated beyond phylogenetic information and cannot resolve the phylogenetic relationships within this superfamily.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 39–45.     

The evolution and evolutionary consequences of marginal thermostability in proteins

When we seek to explain the characteristics of living systems in their evolutionary context, we are often interested in understanding how and why certain properties arose through evolution, and how these properties then affected the continuing evolutionary process. This endeavor has been assisted by the use of simple computational models that have properties characteristic of natural living systems but allow simulations over evolutionary timescales with full transparency. We examine a model of the evolution of a gene under selective pressure to code for a protein that exists in a prespecified folded state at a given growth temperature. We observe the emergence of proteins with modest stabilities far below those possible with the model, with a denaturation temperature tracking the simulation temperature, despite the absence of selective pressure for such marginal stability. This demonstrates that neither observations of marginally stable proteins, nor even instances where increased stability interferes with function, provide evidence that marginal stability is an adaptation. Instead the marginal stability is the result of a balance between predominantly destabilizing mutations and selection that shifts depending on effective population size. Even if marginal stability is not an adaptation, the natural tendency of proteins toward marginal stability, and the range of stabilities that occur during evolution, may have significant effect on the evolutionary process.     

Phylogeny recapitulates geography, or why New Zealand has so many species of skinks

The evolutionary history of 25 New Zealand scincid lizards in the endemic genera Oligosoma and Cyclodina was examined using 12S rRNA sequence data. Phylogenetic resolution was poor, despite there being up to 9% sequence divergence between taxa. Lack of resolution was not attributable to biases in the data, such as site saturation or differences in sites free to vary, so we infer that New Zealand skinks underwent two relatively rapid phases of divergence. The rate of substitution for the skink sequences appears to be similar to some bird and mammal groups for which times of divergence have been estimated. Using fhese calibrations diversification of Oligosoma skinks probably began at least 23 million years ago (Mya). The pattern of relationships and the timing of this diversification are interpreted as resulting from rapid allopatric speciation during the Oligocene (25–35 Mya) when New Zealand was fragmented into many low lying islands. A second major phase of speciation involving the Cyclodina seems to have occurred during the Miocene (15–24 Mya), probably as a consequence of increasing land area and habitat diversity. This pattern of skink evolution contrasts with the Oligocene 'environmental crisis' hypodiesis of Cooper & Cooper (Proc. R. Soc. Land. B. 261, 293–302), but can be attributed to differences in the ecology of different taxa. This can be tested by examination of other groups, such as land snails and geckos. The large number of lizard species in New Zealand can be considered a legacy both of past geography as well as the absence of small mammals which would have been both competitors and predators.     

分子生物学与进化的新理论

论述了由于分子生物学取得的成就,而形成的生物进化的新理论,并阐述了若干新理论指导生产实践取得的巨大应用成果。     

Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences

Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for members of Cornales, a well-supported monophyletic group comprising Cornaceae and close relatives. The shortest trees resulting from this analysis were highly concordant with those based on previous phylogenetic analysis of rbcL sequences. Analysis of a combined matK and rbcL sequence data set (a total of 2652 bp [base pairs]) provided greater resolution of relationships and higher internal support for clades compared to the individual data sets. Four major clades (most inclusive monophyletic groups) of Cornales are indicated by both sets of genes: (1) Cornus-Alangium, (2) nyssoids (Nyssa-Davidia-Camptotheca)- mastixioids (Mastixia, Diplopanax), (3) Curtisia, and (4) Hydrangeaceae-Loasaceae. The combined evidence indicates that clades 2 and 3 are sisters, with clade 4 sister to the remainder of Cornales. These relationships are also supported by other lines of evidence, including synapomorphies in fruit and pollen morphology and gynoecial vasculature. Comparisons of matK and rbcL sequences based on one of the most parsimonious rbcL-matK trees indicate that matK has a much higher A-T content (66.9% in matK vs. 55.8% in rbcL) and a lower transition:transversion ratio (1.23 in matK vs. 2.21 in rbcL). The total number of nucleotide substitutions per site for matK is 2.1 times that of rbcL in Cornales. These findings are similar to recent comparisons of matK and rbcL in other dicots. Variable sites of matK are almost evenly distributed among the three codon positions (1.0:1.0:1.3), whereas variable sites of rbcL are mostly at the third position (1.8:1.0 :7.5). Among- lineages rates of nucleotide substitutions in rbcL are basically homogeneous throughout Cornales, but are more heterogeneous in matK.     

Polyphyly of Limoniastrum (Plumbaginaceae): evidence from DNA sequences of plastid rbcL, trnL intron and trnL-F intergene spacer

Phylogenetic relationships of Limoniastrum and other genera of subfamily Staticoideae (Plumb-aginaceae) were studied using parsimony analysis of the plastid gene rbc L, the intron of trn L and the intergene spacer of trnL-trn F. Our analysis showed that Limoniastrum was polyphyletic. Limoniastrum ifniense , in both rbc L and combined data analyses, is sister to Armeria and Psylliostachys , whereas in the trn L-F (intron and spacer combined) analysis it is sister to a clade composed of Acantholimon, Dictyolimon and the remaining species of Limoniastrum . In all analyses, the five remaining species of Limoniastrum (excluding Limoniatrum ifniense ) formed a clade with two groups of species: L. monopetalum+L. guyonianum and those sometimes considered as the segregate genus Bubania ( L.feei, L. weygandiorum and L. rechingeri ). Levels of sequence divergence among these three groups of Limoniatrum were greater than for other well supported genera in the family and, in combination with morphological differences and paucity of synapomorphies, led us to conclude that separate generic status for each of the three clades is warranted.