Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time

In this study, we collected water from different locations in 32 drinking water distribution networks in the Netherlands and analysed the spatial and temporal variation in microbial community composition by high‐throughput sequencing of 16S rRNA gene amplicons. We observed that microbial community compositions of raw source and processed water were very different for each distribution network sampled. In each network, major differences in community compositions were observed between raw and processed water, although community structures of processed water did not differ substantially from end‐point tap water. End‐point water samples within the same distribution network revealed very similar community structures. Network‐specific communities were shown to be surprisingly stable in time. Biofilm communities sampled from domestic water metres varied distinctly between households and showed no resemblance to planktonic communities within the same distribution networks. Our findings demonstrate that high‐throughput sequencing provides a powerful and sensitive tool to probe microbial community composition in drinking water distribution systems. Furthermore, this approach can be used to quantitatively compare the microbial communities to match end‐point water samples to specific distribution networks. Insight in the ecology of drinking water distribution systems will facilitate the development of effective control strategies that will ensure safe and high‐quality drinking water.     

Expression patterns of fork head and goosecoid homologues in the mollusc Patella vulgata supports the ancestry of the anterior mesendoderm across Bilateria

We have characterised orthologues of the genes fork head and goosecoid in the gastropod Patella vulgata. In this species, the anterior-posterior (AP) axis is determined just before gastrulation, and leads to the specification of two mesodermal components on each side of the presumptive endoderm, one anterior (ectomesoderm), and one posterior (endomesoderm). Both fork head and goosecoid are expressed from the time the AP axis is specified, up to the end of gastrulation. fork head mRNA is detected in the whole endoderm, as well as in the anterior mesoderm, whereas goosecoid is only expressed anteriorly, in the three germ layers. The two genes are thus coexpressed in the anterior mesoderm, suggesting the latter's homology with vertebrate prechordal mesoderm. In addition, since prechordal plate is known to belong to an anterior, so called "head organiser", and since its inductive role is dependent on the function of the vertebrate fork head and goosecoid orthologues, we further suggest that the anterior mesoderm may also have a role in anterior inductive patterning in Spiralia. Finally, we propose that a mode of axial development involving two organisers, one anterior and one posterior, is ancestral to the Bilateria, and that both organisers evolved from the single head organiser of a putative hydra-like ancestor.     

Modulation of microbial predator-prey dynamics by phosphorus availability: growth patterns and survival strategies of bacterial phylogenetic clades

We simultaneously studied the impact of top-down (protistan grazing) and bottom-up (phosphorus availability) factors on the numbers and biomasses of bacteria from various phylogenetic lineages, and on their growth and activity parameters in the oligo-mesotrophic Piburger See, Austria. Enhanced grazing resulted in decreased proportions of bacteria with high nucleic acid content (high-NA bacteria) and lower detection rates by FISH. There was a change in the composition of the bacterial assemblage, whereby Betaproteobacteria were heavily grazed while Alphaproteobacteria and Cytophaga-Flavobacterium-Bacteroides were less affected by predators. Changes in bacterial assemblage composition were also apparent in the treatments enriched with phosphorus, and even more pronounced in the incubations in dialysis tubes (allowing relatively free nutrient exchange). Here, Betaproteobacteria became dominant and appeared to act as successful opportunistic competitors for nutrients. In contrast, Actinobacteria did not respond to surplus phosphorus by population growth, and, moreover, maintained their small size, which resulted in a very low biomass contribution. In addition, significant relationships between high-NA bacteria and several bacterial phylogenetic clades were found, indicating an enhanced activity status. By combining several single-cell methods, new insight is gained into the competitive abilities of freshwater bacteria from a variety of phylogenetic lineages under contrasting sets of bottom-up and top-down constraints.     

Informing conservation by identifying range shift patterns across breeding habitats and migration strategies

A species distribution combines the resources and climatic tolerances that allow an individual or population to persist. As these conditions change, one mechanism to maintain favorable resources is for an organism to shift its range. Much of the research examining range shifts has focused on dynamic distribution boundaries wheras the role of species breeding habitat or migration strategies on shift tendencies has received less attention. We expand on previous research by using a large suite of avian species (i.e., 277), analyzing observed abundance-weighted average latitudes, and categorizing species by breeding environment and migration strategy. We used the North American Breeding Bird Survey dataset to address two questions: (1) Has the center of observed abundance for individual species shifted latitudinally? (2) Is there a relationship between migration strategy or breeding habitat and range shifts? Results indicate the majority of species have experienced poleward range shifts over the last 43 years, and birds breeding in all habitat showed trends of poleward shift but only those species breeding in scrub-shrub and grassland environments were different from zero. Additionally, species that are short distance migrants are experiencing significant poleward shifts while Neotropical and permanent residents had shifts that were not different from zero. Our findings do support the general trend expected from climate driven changes (i.e., > 52 % shifting poleward), however, the proportion of species exhibiting equatorial shifts (24 %) or no significant shifts (23 %) illustrates the complex interplay between land cover, climate, species interactions, and other forces that can interact to influence breeding ranges over time. Regardless of the mechanisms driving range shifts, our findings emphasize the need for connecting and expanding habitats for those species experiencing range shifts. This research describes the patterns of breeding birds through central North America and we encourage future research to focus on the mechanisms driving these patterns.     

Leaf anatomy of Bruniaceae: ecological, systematic and phylogenetic aspects

CARLQUIST, S., 1991. Leaf anatomy of Bruniaceae: ecological, systematic and phylogenetic aspects. Quantitative and qualitative data are given for 60 species of the 12 genera of Bruniaceae; most data are based on liquid-preserved material. Leaves of Bruniaceae are basically linear (broader forms are probably derived) with an apicula that contains phellogen activity. Most bruniaceous leaves have some degree of isolateral construction, with transition to normal bifacial construction in a few species, but more commonly transition to 'inverse' bifacial structure (stomata on adaxial face, palisade on abaxial face). The latter type is correlated with the tendency for leaves to be appressed to stems. Tannins and very likely other dark-staining materials are very characteristic of mesophyll cells. Six genera have a large strand of fibres on the midvein and rhomboidal crystals in bundle sheath cells. The other six genera have few or no fibres on veins and have druses in mesophyll cells (but not in bundle sheath cells). These distinctions may relate to intrafamilial taxonomy, but they also support the primitive position usually accorded to Audouinia, Thamnea and Tittmannia. A key to genera based on leaf antomy is offered. Details of epidermal cell shape, cuticular relief and trichome form and structure based on scanning electron microscopy are given. Leaf anatomy, combined with other features, favours a relationship between Bruniaceae and Grubbiaceae in particular and in broader contexts allies Bruniaceae to rosalean and possibly hamamelidalean families.     

Spatial and temporal variations among fish with similar strategies: patterns of reproductive guilds in a floodplain

Seasonal flooding regimes are closely related to the life history of neotropical fish, especially with regard to their reproduction. The classification of fish into reproductive guilds serves to identify broad patterns in reproductive types, which are important in developing management and conservation measures. We tested the hypothesis that the fish reproductive guilds in the Upper Paraná River floodplain exhibit spatial and temporal distributions. Samples were taken each quarter in 2010 from several environments (i.e., biotopes) and rivers of the plain. Fish were categorized into four reproductive guilds based on migration, external fertilization, and parental care. Moreover, the abundance and species richness within each guild were used to evaluate their patterns. Guilds were spatially structured, possibly due to species dispersion as well as the influence of the hydrological and limnological characteristics of the biotopes and rivers of the plain. The Paraná River presented lower analyzed metric values, which demonstrates the negative effects of the dam built upstream of the study area. The guilds also presented temporal structure. During the flood season, the guilds presented similar spatial structures, and the local environmental characteristics led to spatial differentiation in the structure of guilds (i.e., flooding promoted the homogenization of the reproductive guilds).     

Anoxygenic phototrophy across the phylogenetic spectrum: current understanding and future perspectives

The phylogenetic heterogeneity of anoxygenic phototrophic bacteria has been revealed by 16S rRNA sequence analysis, the results of which have led to extensive taxonomic rearrangements within previously defined taxa of phototrophs and stimulated interest in this group of organisms. Anoxygenic photosynthetic bacteria can be found within 4 of the 12 phylogenetic lineages, and in some cases are highly related to non-photosynthetic members of these groups. The largest number of phototrophs are found in the class Proteobacteria. Comparative phylogenetic analysis using 23S rDNA sequences generally supports the topology obtained from 16S rDNA sequences. The photosynthetic reaction centers are conserved in all photosynthetic bacteria, and are of two types. One is shared by the Proteobacteria and Chloroflexus aurantiacus and is similar to Photosystem II of cyanobacteria, while heliobacteria and Chlorobium and relatives possess a reaction center similar to the cyanobacterial Photosystem I. These similarities are supported by sequence analysis of core reaction center peptides, but contradict phylogenies reconstructed from rRNA sequence analysis. Genome analysis by means of physical mapping has been performed for only three species of anoxygenic phototrophs. Some conservation of operon structure and gene sequence has been found within the Proteobacteria, but does not extend to other phototrophs. Received: 29 December 1995 / Accepted: 19 July 1996     

Contrasting phylogenetic patterns of anther smuts (Pucciniomycotina: Microbotryum) reflect phylogenetic patterns of their caryophyllaceous hosts

Anther smuts in the genus Microbotryum often show very high host specificity toward their caryophyllaceous hosts, but some of the larger host groups such as Dianthus are crucially undersampled for these parasites so that the question of host specificity cannot be answered conclusively. In this study we sequenced the internal transcribed spacer (ITS) region of members of the Microbotryum dianthorum species complex as well as their Dianthus hosts. We compared phylogenetic trees of these parasites including sequences of anther smuts from other Caryophyllaceae, mainly Silene, with phylogenies of Caryophyllaceae that are known to harbor anther smuts. Additionally we tested whether observed patterns in parasites are due to shared ancestry or if geographic separation is a factor that should be taken into consideration in delimitating species. Parasites on Dianthus showed mainly an arbitrary distribution on Dianthus hosts, whereas parasites on other Caryophyllaceae formed well-supported monophyletic clades that corresponded to restricted host groups. The same pattern was observed in the Caryophyllaceae studied: morphologically described Dianthus species did not correspond well with monophyletic clades based on molecular data, whereas other Caryophyllaceae mainly did. We suggest that these different patterns primarily result from different breeding systems and speciation times between different host groups as well as difficulties in species delimitations in the genus Dianthus.     

稀有鮈鲫(Gobiocypris rarus)的骨骼特征及系统发育地位

稀有鮈鲫(Gobiocypris rarus)已作为新型实验动物而逐渐成为生物学研究各领域的热门对象,但是,其系统分类位置仍存在争议。本研究制作了稀有鮈鲫的透明骨骼标本,对其骨骼特征进行描述;选取47个形态特征,与鲤科各亚科鱼类的典型特征进行比较,建立了分支分析特征矩阵,并使用PAUP4.0软件中的最大简约法(MP)构建系统发育树。结果显示,稀有鮈鲫和鮈亚科鱼类聚在一起,属于鮈亚科。     

Signatures of reproductive isolation in patterns of single nucleotide diversity across inbred strains of mice

Reproductive isolation is often caused by the disruption of genic interactions that evolve in geographically separate populations. Identifying the genomic regions and genes involved in these interactions, known as Dobzhansky-Muller incompatibilities, can be challenging but is facilitated by the wealth of genetic markers now available in model systems. In recent years, the complete genome sequence and thousands of single nucleotide polymorphisms (SNPs) from laboratory mice, which are largely genetic hybrids between Mus musculus and M. domesticus, have become available. Here, we use these resources to locate genomic regions that may underlie reproductive isolation between these two species. Using genotypes from 332 SNPs that differ between wild-derived strains of M. musculus and M. domesticus, we identified several physically unlinked SNP pairs that show exceptional gametic disequilibrium across the lab strains. Conspecific alleles were associated in a disproportionate number of these cases, consistent with the action of natural selection against hybrid gene combinations. As predicted by the Dobzhansky-Muller model, this bias was differentially attributable to locus pairs for which one hybrid genotype was missing. We assembled a list of potential Dobzhansky-Muller incompatibilities from locus pairs that showed extreme associations (only three gametic types) among conspecific alleles. Two SNPs in this list map near known hybrid sterility loci on chromosome 17 and the X chromosome, allowing us to nominate partners for disrupted interactions involving these genomic regions for the first time. Together, these results indicate that patterns produced by speciation between M. musculus and M. domesticus are visible in the genomes of lab strains of mice, underscoring the potential of these genetic model organisms for addressing general questions in evolutionary biology.     

Alternative reproductive strategies and tactics: diversity within sexes

Not all members of a sex behave in the same way. Frequency- and statusdependent selection have given rise to many alternative reproductive phenotypes within the sexes. The evolution and proximate control of these alternatives are only beginning to be understood. Although game theory has provided a theoretical framework, the concept of the mixed strategy has not been realized in nature, and alternative strategies are very rare. Recent findings suggest that almost all alternative reproductive phenotypes within the sexes are due to alternative tactics within a conditional strategy, and, as such, while the average fitnesses of the alternative phenotypes are unequal, the strategy is favoured in evolution. Proximate mechanisms that underlie alternative phenotypes may have many similarities with those operating between the sexes.     

PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya

SUMMARY: With increasing numbers of eukaryotic genome sequences, phylogenetic profiles of eukaryotic genes are becoming increasingly informative. Here, we introduce a new web-tool Phylopro (http://compsysbio.org/phylopro/), which uses the 120 available eukaryotic genome sequences to visualize the evolutionary trajectories of user-defined subsets of model organism genes. Applied to pathways or complexes, PhyloPro allows the user to rapidly identify core conserved elements of biological processes together with those that may represent lineage-specific innovations. PhyloPro thus provides a valuable resource for the evolutionary and comparative studies of biological systems.     

The mitochondrial control region of Cervidae: evolutionary patterns and phylogenetic content

The mitochondrial control region (CR) sequence, also known as the D- loop, has been determined for six Cervidae (Artiodactyla, Ruminantia): the red and fallow deers (subfamily Cervinae), the brocket deer and two roe deers (subfamily Odocoileinae), and the Chinese water deer (Hydropotinae). These new sequences have been aligned with available cervid and bovid orthologues. Comparative analyses indicate that the 5'- peripheral domain exhibits a 75-bp length polymorphism near sequences associated with the termination of the H-strand replication. The New World Odocoileinae possess the longest cervid CR due to the presence of an additional 47-bp tandem repeat, located in the 3'-peripheral domain, downstream of the initiation site for H-strand replication (OH) and the first conserved sequence block (CSB-1). This insertion represents a duplication spanning the OH to CSB-1 region and constitutes an exclusive synapomorphy for New World Odocoileinae. Phylogenetic analyses of the complete CR support the paraphyly of antlered deers due to the nesting of the antlerless Hydropotes within Odocoileinae. Capreolus is the closest relative of Hydropotes, and the divergence of this Old World Odocoileinae clade may have occurred between 8.7 and 10.4 MYA. The conserved central domain of CR can be aligned across ungulates and indicates the Pecora monophyly, their close association with cetaceans, and the earlier emergence of suiformes.      

cki-1 links cell division and cell fate acquisition in the C. elegans somatic gonad

The formation of a complex multicellular organism requires the precise specification of many diverse cell types at the correct time and position throughout development. This may be achieved by coordinating cell fate specification processes with progression through the cell cycle. Here, we show that the extra distal tip cells (DTCs) associated with the loss of cki-1, a Caenorhabditis elegans homologue of the cyclin-dependent kinase inhibitor p27, do not arise from duplications of pre-existing DTCs, but that they are formed from another cell type within the somatic gonad. Results from our laser microsurgery experiments suggest that the extra DTCs are caused by aberrant somatic gonadal precursor cell divisions in the absence of cki-1, resulting in abnormal daughter cell fates. cki-1(RNAi) animals also possess extra anchor cells and ectopic gonad arms with variable sheath cell numbers and positioning. In addition, cki-1(RNAi) animals display an endomitotic oocyte (Emo) phenotype. Our results uncover a novel role of this CKI in cell fate acquisition, either by directly influencing specification, or through a more conventional role in appropriately linking cell cycle phase with this process.     

Body-plan evolution in the Bilateria: early antero-posterior patterning and the deuterostome-protostome dichotomy

Recent molecular analyses reveal common themes in early antero-posterior patterning in the four major groups of invertebrate deuterostomes and vertebrates in spite of large differences in the mode of gastrulation. Comparisons with Drosophila and Cnidarians suggest a scheme for evolution of the Bilaterian body plan and emphasize the pressing need for similar studies in a wider variety of organisms, especially more basal protostomes.