Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes

Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older than those in the Southern Hemisphere on average. This study provides an evolutionary framework for future studies on gymnosperms.     

Mitochondrial and Nuclear Genes of Mitochondrial Components in Cancer

Although the observation of aerobic glycolysis of tumor cells by Otto v. Warburg had demonstrated abnormalities of mitochondrial energy metabolism in cancer decades ago, there was no clear evidence for a functional role of mutant mitochondrial proteins in cancer development until the early years of the 21^st century. In the year 2000, a major breakthrough was achieved by the observation, that several genes coding for subunits of the respiratory chain (ETC) complex II, succinate dehydrogenase (SDH) are tumor suppressor genes in heritable paragangliomas, fulfilling Knudson’s classical two-hit hypothesis. A functional inactivation of both alleles by germline mutations and chromosomal losses in the tumor tissue was found in the patients. Later, SDH mutations were also identified in sporadic paragangliomas and pheochromocytomas. Genes of the mitochondrial ATP-synthase and of mitochondrial iron homeostasis have been implicated in cancer development at the level of cell culture and mouse experiments. In contrast to the well established role of some nuclear SDH genes, a functional impact of the mitochondrial genome itself (mtDNA) in cancer development remains unclear. Nevertheless, the extremely high frequency of mtDNA mutations in solid tumors raises the question, whether this small circular genome might be applicable to early cancer detection. This is a meaningful approach, especially in cancers, which tend to spread tumor cells early into bodily fluids or faeces, which can be screened by non-invasive methods.     

线粒体和核基因密码子的若干统计特征及其关联

基于归1000密码子使用频次,从垂直和水平两个方向比较研究了不同进化阶层生物线粒体基因和核基因密码子使用的若干统计特征及其关联．结果表明：线粒体基因密码子多样性、相对分子质量和相对π电子共振能低于相应核基因且变异较大;不同进化阶层生物线粒体基因和核基因归1000密码子的相对π电子共振能呈极显著负相关且两者之和接近定值：真菌-真菌线粒体、植物-植物线粒体、无脊椎动物-无脊椎动物线粒体的密码子使用频次匹配较好;线粒体基因AU含量、密码子第三位碱基AU3s含量高于相应核基因;给出了密码子各位点碱基含量随进化以及在线粒体一核间的变化规律．由于线粒体环境不如核环境稳定,线粒体基因密码子的多个统计特征较核基因在不同进化阶层生物间变异较大,但二者在归1000密码子相对π电子共振能等若干特征方面仍存在明显关联．     

A Phylogeny of the Bears (Ursidae) Inferred from Complete Sequences of Three Mitochondrial Genes

Complete sequences of DNA are described for the cytochrome b, tRNA^Thrand tRNA^Progenes of mitochondria of four extant species of ursids and compared to sequences of four other species of ursids previously studied by us. Phylogenetic analyses indicate that the giant panda and the spectacled bear are the basal taxa of the ursid radiation. The ursines, a group which includes the sun bear, sloth bear, American black bear, Asiatic black bear, brown bear, and polar bear, experienced a rapid radiation during the mid Pliocene to early Pleistocene. The Asiatic black bear and American black bear are sister taxa. The brown bear and polar bear are the most recently derived of the ursines, with the polar bear originating from within a clade of brown bears during the Pleistocene. This paraphyletic association suggests that the rate of morphological evolution may be accelerated relative to that of molecular evolution when a new ecological niche is occupied. Calibration of the corrected average number of nucleotide differences per site with the fossil record indicates that transitions at third positions of codons in the ursid cytochrome b gene occur at a rate of approximately 6% per million years, which is considerably slower than comparable values reported for other species of mammal.     

A Phylogenetic View on Species Radiation in Apodemus Inferred from Variation of Nuclear and Mitochondrial Genes

Species of field mice (genus Apodemus) are the most common rodents inhabiting woodlands and forests of the Palaearctic region. We examined the cytochrome b (cyt b) gene in mitochondrial DNA (1140 bp) and the interphotoreceptor retinoid binding protein (IRBP) gene in nuclear DNA (1152 bp) in nine species of Apodemus. Based on the genetic variation, the nine species were grouped into four lineages: (1) Agrarius group (A. agrarius, A. peninsulae, A. semotus, and A. speciosus), (2) Argenteus group (A. argenteus), (3) Gurkha group (A. gurkha), and (4) Sylvaticus group (A. alpicola, A. flavicollis, and A. sylvaticus). It was shown that these four lineages diverged within a short period of evolutionary time, suggestive of a radiation event. Soon after the radiation, the Agrarius group was likely to have differentiated again into the species lineages simultaneously. In contrast, the European clade, the Sylvaticus group, radiated rather recently. The relative ratio of the extent of sequence divergence among the four main lineages to that among the members of the subfamily Murinae (including Mus and Rattus) was calculated to be 72.4% in the cyt b gene with transversional substitutions, and 58.5% in the IRBP gene with all substitutions, using the Kimura two-parameter method. The value for the three European lineages was 27.6% in the cyt b gene and 12.3% in the IRBP gene. These results may have a correlation with the notion that deciduous broadleaf forests remained in Central East Asia through the late Tertiary to the present, while those in Europe to a large extent had disappeared by the Pliocene.     

A Phylogeny and Timescale for Marsupial Evolution Based on Sequences for Five Nuclear Genes

Even though marsupials are taxonomically less diverse than placentals, they exhibit comparable morphological and ecological diversity. However, much of their fossil record is thought to be missing, particularly for the Australasian groups. The more than 330 living species of marsupials are grouped into three American (Didelphimorphia, Microbiotheria, and Paucituberculata) and four Australasian (Dasyuromorphia, Diprotodontia, Notoryctemorphia, and Peramelemorphia) orders. Interordinal relationships have been investigated using a wide range of methods that have often yielded contradictory results. Much of the controversy has focused on the placement of Dromiciops gliroides (Microbiotheria). Studies either support a sister-taxon relationship to a monophyletic Australasian clade or a nested position within the Australasian radiation. Familial relationships within the Diprotodontia have also proved difficult to resolve. Here, we examine higher-level marsupial relationships using a nuclear multigene molecular data set representing all living orders. Protein-coding portions of ApoB, BRCA1, IRBP, Rag1, and vWF were analyzed using maximum parsimony, maximum likelihood, and Bayesian methods. Two different Bayesian relaxed molecular clock methods were employed to construct a timescale for marsupial evolution and estimate the unrepresented basal branch length (UBBL). Maximum likelihood and Bayesian results suggest that the root of the marsupial tree is between Didelphimorphia and all other marsupials. All methods provide strong support for the monophyly of Australidelphia. Within Australidelphia, Dromiciops is the sister-taxon to a monophyletic Australasian clade. Within the Australasian clade, Diprotodontia is the sister taxon to a Notoryctemorphia + Dasyuromorphia + Peramelemorphia clade. Within the Diprotodontia, Vombatiformes (wombat + koala) is the sister taxon to a paraphyletic possum group (Phalangeriformes) with kangaroos nested inside. Molecular dating analyses suggest Late Cretaceous/Paleocene dates for all interordinal divergences. All intraordinal divergences were placed in the mid to late Cenozoic except for the deepest splits within the Diprotodontia. Our UBBL estimates of the marsupial fossil record indicate that the South American record is approximately as complete as the Australasian record. The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Inferring Diffusion Dynamics from FCS in Heterogeneous Nuclear Environments

Fluorescence correlation spectroscopy (FCS) is a noninvasive technique that probes the diffusion dynamics of proteins down to single-molecule sensitivity in living cells. Critical mechanistic insight is often drawn from FCS experiments by fitting the resulting time-intensity correlation function, G(t), to known diffusion models. When simple models fail, the complex diffusion dynamics of proteins within heterogeneous cellular environments can be fit to anomalous diffusion models with adjustable anomalous exponents. Here, we take a different approach. We use the maximum entropy method to show—first using synthetic data—that a model for proteins diffusing while stochastically binding/unbinding to various affinity sites in living cells gives rise to a G(t) that could otherwise be equally well fit using anomalous diffusion models. We explain the mechanistic insight derived from our method. In particular, using real FCS data, we describe how the effects of cell crowding and binding to affinity sites manifest themselves in the behavior of G(t). Our focus is on the diffusive behavior of an engineered protein in 1) the heterochromatin region of the cell’s nucleus as well as 2) in the cell’s cytoplasm and 3) in solution. The protein consists of the basic region-leucine zipper (BZip) domain of the CCAAT/enhancer-binding protein (C/EBP) fused to fluorescent proteins.     

Phylogeny and Characterization of Three nifH-Homologous Genes from Paenibacillus azotofixans

In this paper, we report the cloning and characterization of three Paenibacillus azotofixans DNA regions containing genes involved in nitrogen fixation. Sequencing analysis revealed the presence of nifB1H1D1K1 gene organization in the 4,607-bp SacI DNA fragment. This is the first report of linkage of a nifB open reading frame upstream of the structural nif genes. The second (nifB2H2) and third (nifH3) nif homologues are confined within the 6,350-bp HindIII and 2,840-bp EcoRI DNA fragments, respectively. Phylogenetic analysis demonstrated that NifH1 and NifH2 form a monophyletic group among cyanobacterial NifH proteins. NifH3, on the other hand, clusters among NifH proteins of the highly divergent methanogenic archaea.     

初探低拷贝核基因在低等分类阶元系统发育重建中的适用性——以十字花科为例

分子系统学已被广泛用于解决物种之间的亲缘关系.迄今为止,被子植物分子系统学大都采用叶绿体和线粒体基因.但叶绿体和线粒体多数采用单亲遗传方式,不能完全记录物种的进化历史.而且叶绿体和线粒体基因相对保守,可用于系统发育重建的信息有限,很难用来解决科以下类群之间的亲缘关系.相反,核基因遵守双亲遗传方式并能提供大量信息位点,但却没有得到广泛运用.本文以十字花科为例,从17种十字花科植物中得到了5个编码蛋白的单拷贝核基因序列,采用最大简约法、最大似然法和贝叶斯法重建它们之间的亲缘关系.结果表明,和目前常用的基因相比,这些基因能提供更多的信息位点,由此得到的系统发育树具有很高的支持,利用最大简约法得到的5个核基因的系统树中各分支均得到了100％的自展支持率.结果表明,我们选取的核基因可以用来进行科、属及种间的系统发育重建.因此,这5个基因可以用来解决被子植物其它科内的亲缘关系,而且也可以作为DNA条形码研究的有效分子标记.     

Performance of Single and Concatenated Sets of Mitochondrial Genes at Inferring Metazoan Relationships Relative to Full Mitogenome Data

Mitochondrial (mt) genes are some of the most popular and widely-utilized genetic loci in phylogenetic studies of metazoan taxa. However, their linked nature has raised questions on whether using the entire mitogenome for phylogenetics is overkill (at best) or pseudoreplication (at worst). Moreover, no studies have addressed the comparative phylogenetic utility of mitochondrial genes across individual lineages within the entire Metazoa. To comment on the phylogenetic utility of individual mt genes as well as concatenated subsets of genes, we analyzed mitogenomic data from 1865 metazoan taxa in 372 separate lineages spanning genera to subphyla. Specifically, phylogenies inferred from these datasets were statistically compared to ones generated from all 13 mt protein-coding (PC) genes (i.e., the “supergene” set) to determine which single genes performed “best” at, and the minimum number of genes required to, recover the “supergene” topology. Surprisingly, the popular marker COX1 performed poorest, while ND5, ND4, and ND2 were most likely to reproduce the “supergene” topology. Averaged across all lineages, the longest ∼2 mt PC genes were sufficient to recreate the “supergene” topology, although this average increased to ∼5 genes for datasets with 40 or more taxa. Furthermore, concatenation of the three “best” performing mt PC genes outperformed that of the three longest mt PC genes (i.e, ND5, COX1, and ND4). Taken together, while not all mt PC genes are equally interchangeable in phylogenetic studies of the metazoans, some subset can serve as a proxy for the 13 mt PC genes. However, the exact number and identity of these genes is specific to the lineage in question and cannot be applied indiscriminately across the Metazoa.     

A Molecular Phylogeny of Hemiptera Inferred from Mitochondrial Genome Sequences

Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses.     

从细胞色素b基因序列变异分析中国鲇形目鱼类的系统发育

采用PCR技术获得中国鲇形目鱼类11科24属27个代表种类细胞色素b基因1138bp全序列,比较分析了来自北美洲、非洲的部分鲇形目鱼类同一基因序列,并选取脂鲤目、鲤形目和鲱形目鱼类作外类群,采用Bayesian方法和最大简约法(MP)构建分子系统树。结果表明：(1)鲇形目鱼类细胞色素b基因序列中,与脂鲤目、鲤形目以及鲱形目鱼类相比存在3bp的缺失;(2)鲇形目鱼类各科代表种类形成一单系群;(3)两种建树方法均支持铫科、粒鲇科和钝头鮠科形成一单系群;而胡子鲇科、刀鲇科、海鲇科、鮰科、长臀鮠科、鲢科、鲇科、棘脂鲿科、鲿科形成一大的单系群;但鳗鲇科的系统位置两种建树方法没有取得一致结果;而其中长臀鲍科与北美的鮰科形成姐妹群,胡子鲇、鮰科、鲇科、鲿科和鮡科是较明显的单系群。     

A Preliminary Molecular Phylogeny of Planthoppers (Hemiptera: Fulgoroidea) Based on Nuclear and Mitochondrial DNA Sequences

The planthopper superfamily Fulgoroidea (Insecta: Hemiptera) is one of the most dominant groups of phytophagous insects. It comprises about 20 families, containing a total of 9000 species worldwide. Despite several recent studies, the phylogeny of Fulgoroidea is not yet satisfactorily resolved and the phylogenetic positions of several key families, especially Cixiidae, Delphacidae, Tettigometridae, Nogodinidae, Acanaloniidae and Issidae, are contentious. Here, we expand upon recent phylogenetic work using additional nuclear (18S and 28S) and novel mitochondrial (16S and cytb) markers. Maximum likelihood and Bayesian analyses yielded robust phylogenetic trees. In these topologies, a group containing Cixiidae and Delphacidae is recovered as the sister group to the remaining taxa. Tettigometridae is placed in a more nested position and is grouped with Caliscelidae. Sister relationships are found between Flatidae and Ricaniidae, and between Dictyopharidae and Fulgoridae. Nogodinidae and Issidae are confirmed to be non-monophyletic families. For major nodes of interest, divergence date estimates are generally older than those from the fossil record.     

Incongruent Nuclear and Mitochondrial Genetic Structure of New World Screwworm Fly Populations Due to Positive Selection of Mutations Associated with Dimethyl- and Diethyl-Organophosphates Resistance

Livestock production is an important economic activity in Brazil, which has been suffering significant losses due to the impact of parasites. The New World screwworm (NWS) fly, Cochliomyia hominivorax, is an ectoparasite and one of the most important myiasis-causing flies endemic to the Americas. The geographic distribution of NWS has been reduced after the implementation of the Sterile Insect Technique (SIT), being eradicated in North America and part of Central America. In South America, C. hominivorax is controlled by chemical insecticides, although indiscriminate use can cause selection of resistant individuals. Previous studies have associated the Gly137Asp and Trp251Leu mutations in the active site of carboxylesterase E3 to resistance of diethyl and dimethyl-organophosphates insecticides, respectively. Here, we have sequenced a fragment of the carboxylesterase E3 gene (ChαE7), comprising part of intron iII, exon eIII, intron iIII and part of exon eIV, and three mitochondrial gene sequences (CR, COI and COII), of NWS flies from 21 locations in South America. These markers were used for population structure analyses and the ChαE7 gene was also investigated to gain insight into the selective pressures that have shaped its evolution. Analysis of molecular variance (AMOVA) and pairwise FST analysis indicated an increased genetic structure between locations in the ChαE7 compared to the concatenated mitochondrial genes. Discriminant analysis of principal components (DAPC) and spatial analysis of molecular variance (SAMOVA) indicated different degrees of genetic structure for all markers, in agreement with the AMOVA results, but with low correlation to geographic data. The NWS fly is considered a panmitic species based on mitochondrial data, while it is structured into three groups considering the ChαE7 gene. A negative association between the two mutations related to organophosphate resistance and Fay & Wu’s H significant negative values for the exons, suggest that these mutations evolved under positive selection.     

Inferring Bacterial Genome Flux While Considering Truncated Genes

Bacterial gene content variation during the course of evolution has been widely acknowledged and its pattern has been actively modeled in recent years. Gene truncation or gene pseudogenization also plays an important role in shaping bacterial genome content. Truncated genes could also arise from small-scale lateral gene transfer events. Unfortunately, the information of truncated genes has not been considered in any existing mathematical models on gene content variation. In this study, we developed a model to incorporate truncated genes. Maximum-likelihood estimates (MLEs) of the new model reveal fast rates of gene insertions/deletions on recent branches, suggesting a fast turnover of many recently transferred genes. The estimates also suggest that many truncated genes are in the process of being eliminated from the genome. Furthermore, we demonstrate that the ignorance of truncated genes in the estimation does not lead to a systematic bias but rather has a more complicated effect. Analysis using the new model not only provides more accurate estimates on gene gains/losses (or insertions/deletions), but also reduces any concern of a systematic bias from applying simplified models to bacterial genome evolution. Although not a primary purpose, the model incorporating truncated genes could be potentially used for phylogeny reconstruction using gene family content.GENE content variation as a key feature of bacterial genome evolution has been well recognized (Garcia-Vallvé et al. 2000; Ochman and Jones 2000; Snel et al. 2002; Welch et al. 2002; Kunin and Ouzounis 2003; Fraser-Liggett 2005; Tettelin et al. 2005) and gained increasing attention in recent years. Various methods have been employed to study the variation of gene content in the form of gene insertions/deletions (or gene gains/losses); there are studies of population dynamics (Nielsen and Townsend 2004), birth-and-death evolutionary models (Berg and Kurland 2002; Novozhilov et al. 2005), phylogeny-dependent studies including parsimony methods (Mirkin et al. 2003; Daubin et al. 2003a,b; Hao and Golding 2004), and maximum-likelihood methods (Hao and Golding 2006, 2008b; Cohen et al. 2008; Cohen and Pupko 2010; Spencer and Sangaralingam 2009). The pattern of gene presence/absence also contains phylogenetic signals (Fitz-Gibbon and House 1999; Snel et al. 1999; Tekaia et al. 1999) and has been used for phylogenetic reconstruction (Dutilh et al. 2004; Gu and Zhang 2004; Huson and Steel 2004; Zhang and Gu 2004; Spencer et al. 2007a,b). All these studies make use of the binary information of gene presence or absence and neglect the existence of gene segments or truncated genes.Bacterial genomes are known to harbor pseudogenes. An intracellular species Mycobacterium leprae is an extreme case for both the proportion and the number of pseudogenes: estimated as 40% of the 3.2-Mb genome and 1116 genes (Cole et al. 2001). In free-living bacteria, pseudogenes can make up to 8% of the annotated genes in the genome (Lerat and Ochman 2004). Many pseudogenes result from the degradation of native functional genes (Cole et al. 2001; Mira et al. 2001). Pseudogenes could also result from the degradation of transferred genes and might even be acquired directly via lateral gene transfer. For instance, in plant mitochondrial genomes, which have an α-proteobacterial ancestry, most, if not all, of the laterally transferred genes are pseudogenes (Richardson and Palmer 2007). Furthermore, evidence has been documented that gene transfer could take place at the subgenic level in a wide range of organisms, e.g., among bacteria (Miller et al. 2005; Choi and Kim 2007; Chan et al. 2009), between ancient duplicates in archaea (Archibald and Roger 2002), between different organelles (Hao and Palmer 2009; Hao 2010), and between eukaryotes (Keeling and Palmer 2001). A large fraction of pseudogenes have been shown to arise from failed lateral transfer events (Liu et al. 2004) and most of them are transient in bacterial genomes (Lerat and Ochman 2005). Zhaxybayeva et al. (2007) reported that genomes with truncated homologs might erroneously lead to false inferences of “gene gain” rather than multiple instances of “gene loss.” This raises the question of how a false diagnosis of gene absence affects the estimation of insertion/deletion rates. Recently, we showed that the effect of a false diagnosis of gene absence on estimation of insertion/deletion rates is not systematic, but rather more complicated (Hao and Golding 2008a). To further address the problem, a study incorporating the information of truncated genes is highly desirable. This will not only yield more accurate estimates of the rates of gene insertions/deletions, but also provide a quantitative view of the effect of truncated genes on rate estimation, which has been understudied in bacterial genome evolution.In this study, we developed a model that considers the information of truncated genes and makes use of a parameter-rich time-reversible rate matrix. Rate variation among genes is allowed in the model by incorporating a discrete Γ-distribution. We also allow rates to vary on different parts of the phylogeny (external branches vs. internal branches). Consistent with previous studies, the rates of gene insertions/deletions are comparable to or larger than the rates of nucleotide substitution and the rates of gene insertions/deletions are further inflated in closely related groups and on external branches, suggesting high rates of gene turnover of recently transferred genes. The results from the new model also suggest that many recently truncated genes are in the process of being rapidly deleted from the genome. Some other interesting estimates in the model are also presented and discussed. One implication of the study, though not primary, is that the state of truncated genes could serve as an additional phylogenetic character for phylogenetic reconstruction using gene family content.     

A Molecular Phylogeny of the Tiger Beetles (Cicindelidae): Congruence of Mitochondrial and Nuclear rDNA Data Sets

As a basis for comparative studies in the family Cicindelidae (tiger beetles), a phylogenetic hypothesis for major groups was established based on molecular data, focusing on the taxa of the New World. Two markers, mitochondrial 16S rRNA and nuclear 18S rRNA, were sequenced for a total of 912 nucleotides and 30 taxa. All Cicindelidae were inferred to be a monophyletic group by the presence of a segment in the 5′ region of the 18S rDNA which is predicted to fold into a single stem-loop structure not present in the outgroup. The total number of variable and potentially informative positions was smaller in the 18S data set, but their higher internal consistency resulted in a strong phylogenetic signal. Inferred relationships were stable over a wide range of alignment parameters, but the inclusion of alignment-sensitive positions and presumptive gap characters added substantially to the resolution and overall support of the tree. Both data sets were in general congruence. The combined evidence suggests that relationships in Cicindelidae as currently recognized have to be reconsidered. No convincing evidence could be found for the traditional subdivision into two subfamilies, Cicindelinae and Collyrinae. The latter is embedded within the Cicindelinae and clearly not the sister to all other cicindelids. Most of the current tribes and subtribes, particularly in the Megacephalini, are paraphyletic groups, whereas monophyly of the large tribe Cicindelini is well supported by the molecular data.     

Congruent Avian Phylogenies Inferred from Mitochondrial and Nuclear DNA Sequences

Recent molecular studies addressing the phylogenetic relationships of avian orders have had conflicting results. While studies using nuclear DNA sequences tend to support traditional taxonomic views, also supported by morphological data [(paleognaths (galloanseres (all other birds)))], with songbirds forming a clade within Neoaves (all other birds), analyses with complete mtDNA genomes have resulted in topologies that place songbirds as one of the earliest-diverging avian lineages. Considering that over half of the extant bird species are songbirds, these different results have very different implications for our understanding of avian evolution. We analyzed data sets comprising nearly 4 kb of mitochondrial DNA (mtDNA) (complete 12S, ND1, ND2, and cytochrome b) plus 600 bp of the nuclear gene c-mos for 15 birds that were chosen to represent all major avian clades and to minimize potential long-branch attraction problems; we used a partition-specific maximum likelihood approach. Our results show congruence with respect to the ingroup among phylogenies obtained with mtDNA and the nuclear gene c-mos, separately or combined. The data sets support a traditional avian taxonomy, with paleognaths (ratites and tinamous) occupying a basal position and with songbirds more derived and forming a monophyletic group. We also show that, for mtDNA studies, turtles may be a better outgroup for birds than crocodilians because of their slower rate of sequence evolution.     

Anterograde and Retrograde Regulation of Nuclear Genes Encoding Mitochondrial Proteins during Growth,Development, and Stress

Mitochondrial biogenesis and function in plants require the expression of over 1000 nuclear genes encoding mitochondrial proteins （NGEMPs）. The expression of these genes is regulated by tissue-specific, developmental, internal, and external stimuli that result in a dynamic organelle involved in both metabolic and a variety of signaling processes. Although the metabolic and biosynthetic machinery of mitochondria is relatively well understood, the factors that regu- late these processes and the various signaling pathways involved are only beginning to be identified at a molecular level. The molecular components of anterograde （nuclear to mitochondrial） and retrograde （mitochondrial to nuclear） signaling pathways that regulate the expression of NGEMPs interact with chloroplast-, growth-, and stress-signaling pathways in the cell at a variety of levels, with common components involved in transmission and execution of these signals. This positions mitochondria as important hubs for signaling in the cell, not only in direct signaling of mitochondrial function per se, but also in sensing and/or integrating a variety of other internal and external signals. This integrates and optimizes growth with energy metabolism and stress responses, which is required in both photosynthetic and non-photosynthetic cells.