Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci

Plant molecular systematic studies of closely related taxa have relied heavily on sequence data from nuclear ITS and cpDNA. Positive attributes of using ITS sequence data include the rapid rate of evolution compared to most plastid loci and availability of universal primers for amplification and sequencing. On the other hand, ITS sequence data may not adequately track organismal phylogeny if concerted evolution and high rDNA array copy number do not permit identification of orthologous copies. Shaw et al. (American Journal of Botany 92: 142-166) recently identified nine plastid regions that appear to provide more potentially informative characters than many other plastid loci. In the present study, sequences of these loci and ITS were obtained for six taxonomic groups in which phylogenetic relationships have been difficult to establish using other data. The relative utility of these regions was compared by assessing the number of parsimony informative characters, character congruence, resolution of inferred trees, clade support, and accuracy. No single locus emerged as the best in all lineages for any of these measures of utility. Results further indicated that in preliminary studies, sampling strategy should include at least four exemplar taxa. The importance of sampling data from independent distributions is also discussed.     

The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a three-dimensional reconstruction of the organ. We will seek proof of concept for the organ atlas by elucidating genetic pathways involved in development and pathophysiology of the kidney. Such a kidney atlas may provide a paradigm for a new systems-biology approach in functional genome research aimed at understanding the genetic bases of organ development, physiology and disease.Key Words: EuReGene, kidney, genome, development, pathophysiology, genetics     

Arms races with mitochondrial genome soft sweeps in a gynodioecious plant,Plantago lanceolata

Biological situations involving conflict can create arms race situations with repeated fixations of different functional variants, producing selective sweeps and lowering neutral diversity in genome regions linked to the functional locus. However, they can sometimes lead to balancing selection, potentially creating long coalescent times for sites with functionally different variants, and, if recombination occurs rarely, for extended haplotypes carrying such variants. We tested between these possibilities in a gynodioecious plant, Plantago lanceolata, in which cytoplasmic male‐sterility factors conflict with nuclear restorers of male fertility. We find low mitochondrial diversity, which does not support very long‐term coexistence of highly diverged mitochondrial haplotypes. Interestingly, however, we found a derived haplotype that is associated with male fertility in a restricted geographic region, and that has fixed differences from the ancestral sequence in several genes, suggesting that it did not arise very recently. Taken together, the results suggest arms race events that involved “soft" selective sweeps involving a moderately old‐established haplotype, consistent with the frequency fluctuations predicted by theoretical models of gynodioecy.     

The adaptive potential of Populus balsamifera L. to phenology requirements in a warmer global climate

The manner in which organisms adapt to climate change informs a broader understanding of the evolution of biodiversity as well as conservation and mitigation plans. We apply common garden and association mapping approaches to quantify genetic variance and identify loci affecting bud flush and bud set, traits that define a tree's season for height growth, in the boreal forest tree Populus balsamifera L. (balsam poplar). Using data from 478 genotypes grown in each of two common gardens, one near the southern edge and another near the northern edge of P. balsamifera's range, we found that broad‐sense heritability for bud flush and bud set was generally high (H² > 0.5 in most cases), suggesting that abundant genetic variation exists for phenological response to changes in the length of the growing season. To identify the molecular genetic basis of this variation, we genotyped trees for 346 candidate single nucleotide polymorphisms (SNPs) from 27 candidate genes for the CO/FT pathway in poplar. Mixed‐model analyses of variance identified SNPs in 10 genes to be associated with variation in either bud flush or bud set. Multiple SNPs within FRIGIDA were associated with bud flush, whereas multiple SNPs in LEAFY and GIGANTEA 5 were associated with bud set. Although there was strong population structure in stem phenology, the geographic distribution of multilocus association SNP genotypes was widespread except at the most northern populations, indicating that geographic regions may harbour sufficient diversity in functional genes to facilitate adaption to future climatic conditions in many sites.     

Classic clover cline clues

Adaptive clines are striking examples of natural selection in action, yet few have been studied in depth. In this issue of Molecular Ecology, Kooyers & Olsen (2012) introduce modern analyses and thinking towards studies of a classical example of the rapid and repeated evolution of latitudinal and altitudinal clines in cyanogenesis in white clover, Trifolium repens L. Recognizing that adaptive clines represent trade-offs in the selective benefits of traits at different ends of a geographical transect, these researchers focus on whether evidence for selection can be found at regional (coarse) and local (fine) scales. After adjusting for population genetic patterns generated by demographic processes, Kooyers and Olsen provide evidence that the cyanogenesis cline is adaptive across a transect from Louisiana to Wisconsin, USA. Within local populations, divergent selection on coupling dominant and recessive alleles that underlie cyanogenesis is predicted to drive populations to gametic phase disequilibrium (LD), a pattern that has been found in several other studies reviewed by Kooyers and Olsen. The absence of LD within any sampled populations in this study leads the authors to suggest that selective patterns within these clines may be more complex than previously proposed, perhaps even following theoretical predictions of a geographic mosaic.     

棉花和香瓜的甘薯粉虱Bemisia tabaci (同翅目 ,粉虱科 )B生态型虫体大小和重量的田间调查(英文)

20 0 0和 2 0 0 1年在美国凤凰城和北达科塔州法哥城田间 ,调查棉花和香瓜上甘薯粉虱BemisiatabaciB生态型所有虫期虫体大小和重量。从若虫大小计算出若虫的体积。第一到第四龄晚期 ,若虫平均体积以指数方式增加。体积增加最快的是第三到第四龄早期。棉花上的若虫比香瓜上的宽 ,但是并不比较长。香瓜上第一到第四龄早期的若虫 ,最厚部位的腹部和背部厚度比例显著比棉花上的要高。两种寄主作物上的若虫从第一到第四龄发育期 ,腹部厚度平均增加将近 5 1倍 ,而背部厚度只增加 2 8倍。雌虫和雄虫从头顶到翅尖平均长度分别为 112 6和 95 3微米 ,重量为 39和 17微克。棉花和香瓜上的虫卵平均长 ,宽 ,重分别为 197微米 ,99微米 ,和0 8微克。未被寄生的蛹壳长 ,宽 ,重分别为 6 73微米 ,4 92微米和 1 2微克 ;被寄生的蛹壳为 6 6 5微米 ,4 5 2微米 ,和 3 6微克。棉花上未被寄生和被寄生的蛹壳比香瓜上的长 ,宽 ,和更重。     

Gas exchange patterns of Pterostichus niger (Carabidae) in dry and moist air

Gas exchange patterns of adult male Pterostichus niger Schaller after hydration (i.e. given access to food and water) are compared in dry air [5–7% relative humidity (RH)] and moist air (90–97% RH) by means of flow‐through CO₂ respirometry combined with infrared probe actography. Of thirty beetles examined, slightly more than 50% showed continuous gas exchange and are not considered further. Of the remaining beetles, the majority (approximately 71%) display a pattern of cyclic gas exchange in both dry and moist air (i.e. CO₂ gas is released in bursts, with a low level of CO₂ release during the interburst periods). A minority of the beetles (four out of 30) are found to exhibit discontinuous gas exchange in both dry and moist air; this is characterized by three clearly separated states of the spiracles: closed (C), flutter (F) and open (O) phases. The pattern of cyclic gas exchange is associated with weak abdominal pulsations. After switching from moist to dry air, a small modulation of the discontinuous gas exchange cycles (maximum mean CO₂ production rate) occurs, providing no clear support for the hygric theory of discontinuous gas exchange in this species (i.e. that it serves to restrict respiratory water loss).