Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison

Principal components analysis (PCA) and hierarchical clustering are two of the most heavily used techniques for analyzing the differences between nucleic acid sequence samples taken from a given environment. They have led to many insights regarding the structure of microbial communities. We have developed two new complementary methods that leverage how this microbial community data sits on a phylogenetic tree. Edge principal components analysis enables the detection of important differences between samples that contain closely related taxa. Each principal component axis is a collection of signed weights on the edges of the phylogenetic tree, and these weights are easily visualized by a suitable thickening and coloring of the edges. Squash clustering outputs a (rooted) clustering tree in which each internal node corresponds to an appropriate “average” of the original samples at the leaves below the node. Moreover, the length of an edge is a suitably defined distance between the averaged samples associated with the two incident nodes, rather than the less interpretable average of distances produced by UPGMA, the most widely used hierarchical clustering method in this context. We present these methods and illustrate their use with data from the human microbiome.     

Cytokine Induced Phenotypic and Epigenetic Signatures Are Key to Establishing Specific Macrophage Phenotypes

Macrophages (MΦ) play an essential role in innate immune responses and can either display a pro-inflammatory, classically activated phenotype (M1) or undergo an alternative activation program (M2) promoting immune regulation. M-CSF is used to differentiate monocytes into MΦ and IFN-γ or IL-4+IL-13 to further polarize these cells towards M1 or M2, respectively. Recently, differentiation using only GM-CSF or M-CSF has been described to induce a M1- or M2-like phenotype, respectively. In this study, we combined both approaches by differentiating human MΦ in GM-CSF or M-CSF followed by polarization with either IFN-γ or IL-4+IL-13. We describe the phenotypic differences between CD14^hi CD163^hi CD206^int FOLR2-expressing M-CSF MΦ and CD14^lo CD163^lo CD206^hi GM-CSF MΦ but show that both macrophage populations reacted similarly to further polarization with IFN-γ or IL-4+IL-13 with up- and down-regulation of common M1 and M2 marker genes. We also show that high expression of the mannose receptor (CD206), a marker of alternative activation, is a distinct feature of GM-CSF MΦ. Changes of the chromatin structure carried out by chromatin modification enzymes (CME) have been shown to regulate myeloid differentiation. We analyzed the expression patterns of CME during MΦ polarization and show that M1 up-regulate the histone methyltransferase MLL and demethylase KDM6B, while resting and M2 MΦ were characterized by DNA methyltransferases and histone deacetylases. We demonstrate that MLL regulates CXCL10 expression and that this effect could be abrogated using a MLL-Menin inhibitor. Taken together we describe the distinct phenotypic differences of GM-CSF or M-CSF MΦ and demonstrate that MΦ polarization is regulated by specific epigenetic mechanisms. In addition, we describe a novel role for MLL as marker for classical activation. Our findings provide new insights into MΦ polarization that could be helpful to distinguish MΦ activation states.     

Aedes species in treeholes and fruit husks between dry and wet seasons in southeastern Senegal

During the dry season in February, 2010 and the wet season in September, 2011 we sampled mosquito larvae and eggs from treeholes of seven native hardwood species and the husks of Saba senegalensis in 18 sites in the PK‐10 forest in southeastern Senegal. Larvae were reared to adults for species identification. In the dry season, we recovered 408 Aedes mosquitoes belonging to seven species. Aedes aegypti s.l. comprised 42.4% of the collection, followed by Ae. unilineatus (39%). In contrast to reports from East Africa, both Ae. aegypti aegypti and Ae. aegypti formosus were recovered, suggesting that both subspecies survive the dry season in natural larval habitats in West Africa. In the wet season, 455 mosquitoes were collected but 310 (68.1%) were the facultatively predaceous mosquito Eretmapodites chrysogaster. The remaining 145 mosquitoes consisted of ten Aedes species. Aedes aegypti s.l. comprised 55.1% of these, followed by Ae. apicoargenteus (15.2%) and Ae. cozi (11.7%). Similar to East Africa, most (90%) of Ae. aegypti s.l. in the wet season were subspecies formosus.     

重庆晚侏罗世两处兽脚类足迹组合与四川盆地侏罗纪地层(英文)

重庆市已报道了4处侏罗纪的恐龙足迹点,包括下侏罗统珍珠冲组的大足化石点,该地点发现了中国迄今最古老的蜥脚类行迹;另外两处化石点(南岸和金鸡)的层位曾被视为中或上侏罗统,这里首次将其确认为上侏罗统上沙溪庙组;第4处化石点(成渝), 本文全部作者目前都未曾观察,这里不做描述。南岸化石点是南岸重庆足迹(Chongqingpus nananensis)模式标本的所在地,位于重庆市中心,曾发现过大量兽脚类足迹,如今已消逝在城市化进程中。幸运的是,这批标本被保存于重庆自然博物馆,本文作者曾前后两次对其进行研究,并得出文中的结论。南岸重庆足迹为中型足迹(平均长约29 cm), 最可能被卡岩塔足迹(Kayentapus)所囊括,这批标本中有一些保存着边界不清的拇趾迹。该化石点的其他足迹被归于似异样龙足迹(cf. Anomoepus)。其他较小的、来自重庆市周边中侏罗统中部的足迹此前已被归于跷脚龙足迹(Grallator)。金鸡化石点保存了一条孤立的兽脚类行迹,因其粗壮的特征而被暂时归于似窄足龙足迹(cf. Therangospodus)。金鸡点的行迹也保存了非连续出现的拇趾迹。虽然重庆市和四川盆地及其周边更广泛地区之侏罗纪地层发现的兽脚类足迹日渐增多,但要明确其确切地质年龄及有效的足迹分类依然需要进一步工作。这是因为侏罗纪的恐龙足迹尽管丰富,但显示出连续变化的形态学特征,而保存状况的变化更使其难以在时间与空间上做出定义与鉴别。     

Crassulacean acid metabolism photosynthesis in Bromeliaceae: an evolutionary key innovation

Crassulacean acid metabolism (CAM) is a photosynthetic pathway that significantly increases water use efficiency in plants. It has been proposed that CAM photosynthesis, which evolved from the ancestral C3 pathway, has played a role in the diversification of some prominent plant groups because it may have allowed them to colonize and successfully spread into arid or semi‐arid environments. However, the hypothesis that CAM photosynthesis constitutes an evolutionary key innovation, thereby enhancing diversification rates of the clades possessing it, has not been evaluated quantitatively. We tested whether CAM photosynthesis is a key innovation in the Bromeliaceae, a large and highly diversified plant family that has successfully colonized arid environments. We identified five pairs of sister groups with and without the CAM feature, including 31 genera and over 2000 species. In all five cases, the clades with CAM photosynthesis were more diverse than their C3 counterparts. We provide quantitative evidence that the evolution of CAM photosynthesis is significantly associated with increased diversification in Bromeliaceae and thus constitutes an evolutionary key innovation. We also found preliminary evidence of an association between the CAM pathway and growth habit in bromeliads, with terrestrial species being more likely to show CAM photosynthesis than epiphytic species. To our knowledge, this is the first case of a physiological attribute shown to be a key innovation in plants. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 480–486.     

Palate Variation and Evolution in New World Leaf-Nosed and Old World Fruit Bats (Order Chiroptera)

Two bat families, the leaf-nosed (Phyllostomidae) and fruit bats (Pteropodidae), have independently evolved the ability to consume plant resources. However, despite their similar ages, species richness and the strong selective pressures placed on the evolution of skull shape by plant-based foods, phyllostomids display more craniofacial diversity than pteropodids. In this study, we used morphometrics to investigate the distribution of palate variation and the evolution of palate diversity in these groups. We focused on the palate because evolutionary alterations in palate morphology are thought to underlie much feeding specialization in bats. We hypothesize that the distribution of palate variation differs in phyllostomids and pteropodids, and that the rate of palate evolution is higher in phyllostomids than pteropodids. The results suggest that the overall level of palate integration is higher in adult populations of pteropodids than phyllostomids but that the distribution of palate variation is otherwise generally conserved among phyllostomids and pteropodids. Furthermore, the results are consistent with these differences in palate integration likely having a developmental basis. The results also suggest that palate evolution has occurred significantly more rapidly in phyllostomids than pteropodids. These findings are consistent with a scenario in which the greater integration of the pteropodid palate has limited its evolvability.