Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)

Drosophila is the genus responsible for the birth of experimental genetics, but the taxonomy of drosophilids is difficult because of the overwhelming diversity of the group. In this study, we assembled sequences for 358 species (14 genera, eight subgenera, 57 species groups, and 65 subgroups) to generate a maximum‐likelihood topology and a Bayesian timescale. In addition to sampling an unprecedented diversity of Drosophila lineages, our analyses incorporated a geographical perspective because of the high levels of endemism. In our topology, Drosophila funebris (Fabricius, 1787) (the type species of Drosophila) is tightly clustered with the pinicola subgroup in a North American clade within subgenus Drosophila. The type species of other drosophilid genera fall within the Drosophila radiation, presenting interesting prospects for the phylogenetic taxonomy of the group. Our timescale suggests that a few drosophilid lineages survived the Cretaceous–Palaeogene (K‐Pg) extinction. The drosophilid diversification began during the Palaeocene in Eurasia, but peaked during the Miocene, an epoch of drastic climatic changes. The most recent common ancestor of the clades corresponding to subgenera Sophophora and Drosophila lived approximately 56 Mya. Additionally, Hawaiian drosophilids diverged from an East Asian lineage approximately 26 Mya, which is similar to the age of the oldest emerging atoll in the Hawaiian–Emperor Chain. Interestingly, the time estimates for major geographical splits (New World versus Asia and Africa versus Asia) were highly similar for independent lineages. These results suggest that vicariance played a significant role in the radiation of fruit flies. © 2013 The Linnean Society of London     

The Archaeal Diversity and Population in a Drained Alkaline Saline Soil of the Former Lake Texcoco (Mexico)

Draining soil of the former Lake Texcoco, Mexico with pH > 10.0 and electrolytic conductivity (EC) > 100 dS m^?1 for 17 years has reduced pH to 7.8 and EC to 0.68 dS m^?1. Metagenomic DNA from the archaeal community was extracted directly from this soil and used as template to amplify the 16S ribosomal genes by PCR to construct gene libraries. Most of the cloned Archaea were related to mesophilic crenarchaeota and were not-yet-cultured. Sequence and phylogenetic analyses of these clones identified a group of Archaea with close affiliation to the ammonia-oxidizing Archaea. The cloned sequences from the drained soil diverged clearly from Haloarchaea found in the undrained soil from the lake.     

Bacterial Populations (First Record) at Two Shallow Hydrothermal Vents of the Mexican Pacific West Coast

Thermophilic and metal-oxidizing bacteria were identified in shallow hydrothermal vents on the western Mexican coast. The role of these bacteria in biomineralization processes observed in the vents is explained, and the effect of the vents on biodiversity of prokaryotes is discussed. Research was done at two shallow hydrothermal vent sites: Bahía Concepción (BC) in the Baja California Peninsula and Punta Mita (PM), on the central Pacific coast. Temperature at the sediments proximal to the vents was similar, but the redox potentials (0.5 V in BC and ?0.3 V in PM) and pH (6.2 in BC and as low as 4.5 in PM) differed. The composition of the discharged water ranged from nearly seawater to lower-salinity fluids, and the gas phase was mainly CO₂ at BC and N₂ and CH₄ at PM. The study focuses on the biogeochemical processes related to the different species of bacteria present in the studied sites, which are involved in the anaerobic oxidation of methane (AOM), seawater sulfate reduction, and metal oxidation. The detected bacterial lineages represented typical deep vent species, which disproves a previous hypothesis that proposed that different consortia were populating deep and shallow hydrothermal vents. The results obtained here show that the main parameter affecting the bacterial groups present in shallow vents was the redox potential: gamma-, delta-, and epsilon proteobacteria as well as Bacteriodetes are present under the oxidizing conditions of BC, and Thermotogae, Aquificae, and Planctomycetes are present in PM. Sunlight abundance favored the prevalence of halophilic and Chlorofleaxae bacteria in both areas.     

Microbial Diversity and Community Structure on Corroding Concretes

The objective of this study was to analyze bacterial diversity in two different concrete samples to understand the dominant types of bacteria that may contribute to concrete corrosion. Two concrete samples, HN-1 from the sunny side and HN-2 from dark and damp side, were collected from Zijin Mountain in Nanjing and genomic DNA was extracted. The partial bacterial 16S rRNA gene fragment was PCR amplified and two clone libraries were constructed. Amplified ribosomal DNA restriction analysis (ARDRA) was performed by digestion of the 16S rRNA gene and each unique restriction fragment polymorphism pattern was designated as an operational taxonomic unit (OTU). Phylogenetic trees of bacterial 16S rDNA nucleotide sequences were constructed. Sample HN-1 and HN-2 contained 21 OTUs and 26 OTUs, respectively. Proteobacteria and Planctomycetes were the predominant bacteria in both samples, and they are distributed among Herbaspirillum, Archangium, Phyllobacteriaceae and Planctomycetaceae. Cyanobacteria and Rubrobacter sp. are dominant in HN-1; while Acidobacteriaceae, Adhaeribacter sp. and Nitrospira sp. are predominant in HN-2. This distribution pattern was consistent with local environmental conditions of these two samples. The inferred physiological characteristics of these bacteria, based on relatedness of the DNA clone sequences to cultivated species, revealed different mechanisms of concrete corrosion depending on the local environmental conditions.     

Diversity of Ferrous Iron-Oxidizing,Nitrate-Reducing Bacteria and their Involvement in Oxygen-Independent Iron Cycling

In previous studies, three different strains (BrG1, BrG2, and BrG3) of ferrous iron-oxidizing, nitrate-reducing bacteria were obtained from freshwater sediments. All three strains were facultative anaerobes and utilized a variety of organic substrates and molecular hydrogen with nitrate as electron acceptor. In this study, analyses of 16S rDNA sequences showed that strain BrG1 was affiliated with the genus Acidovorax, strain BrG2 with the genus Aquabacterium, and strain BrG3 with the genus Thermomonas. Previously, bacteria similar to these three strains were detected with molecular techniques in MPN dilution series for ferrous iron-oxidizing, nitrate-reducing bacteria inoculated with different freshwater sediment samples. In the present study, further molecular analyses of these MPN cultures indicated that the ability to oxidize ferrous iron with nitrate is widespread amongst the Proteobacteria and may also be found among the Gram-positive bacteria with high GC content of DNA. Nitrate-reducing bacteria oxidized ferrous iron to poorly crystallized ferrihydrite that was suitable as an electron acceptor for ferric iron-reducing bacteria. Biologically produced ferrihydrite and synthetically produced ferrihydrite were both well suited as electron acceptors in MPN dilution cultures. Repeated anaerobic cycling of iron was shown in a coculture of ferrous iron-oxidizing bacteria and the ferric iron-reducing bacterium Geobacter bremensis. The results indicate that iron can be cycled between its oxidation states +II and +III by microbial activities in anoxic sediments.     

New family characters of larval Plecoptera,with an analysis of the Chloroperlidae: Paraperlinae

Larval structures diagnostic of several Plecoptera families, subfamilies or genera are described and illustrated. They concern the following: distinction of larval Leuctridae from Capniidae; an additional apomorphy of Nemouridae; a synapomorphy of Perlidae and Perlodidae; monophyly of each of the two subfamilies of Chloroperlidae, and the generic limits among Chloroperlidae: Paraperlinae. Paraperla lepnevae Zhiltzova is transferred to Utaperla. Some comments on Notonemouridae are included.     

Birding and DNA: species for the new millennium

Capsule Based on the 1999 Witherby Memorial Lecture – reviews how developments in molecular and population genetics have led to a reappraisal of species limits in birds.

The taxonomy of birds of the West Palearctic has moved from the comparative stability of the ‘Voous List’ into a period of serious activity, with new data emerging in almost every issue of every evolutionary and avian journal! This activity comes from two directions. Firstly, developments in population genetics, molecular biology, acoustics, behaviour and distributional studies have opened new avenues to measuring differentiation among groups of birds. This, in turn, has led to the recognition that earlier views of what constitutes a ‘species’ are in need of modification (‘improvement’), and the emergence of the ‘lineage concept’ of species. I review some of the species concepts most relevant to avian studies, and attempt to show how and why this change has happened, and its consequences for taxonomy and species limits. Examples are given in the form of ‘case studies’, and include Carrion/Hooded Crows Corvus corone/cornix, Green-winged/Eurasian Teals Anas carolinensis/crecca and Phylloscopus warblers.     

DISENTANGLING EVOLUTIONARY CAUSE‐EFFECT RELATIONSHIPS WITH PHYLOGENETIC CONFIRMATORY PATH ANALYSIS

Confirmatory path analysis is a statistical technique to build models of causal hypotheses among variables and test if the data conform with the causal model. However, classical path analysis techniques ignore the nonindependence of observations due to phylogenetic relatedness among species, possibly leading to spurious results. Here, we present a simple method to perform phylogenetic confirmatory path analysis (PPA). We analyzed simulated datasets with varying amounts of phylogenetic signal in the data and a known underlying causal structure linking the traits to estimate Type I error and power. Results show that Type I error for PPA appeared to be slightly anticonservative (range: 0.047–0.072) but path analysis models ignoring phylogenetic signal resulted in much higher Type I error rates, which were positively related to the amount of phylogenetic signal (range: 0.051 for λ= 0 to 0.916 for λ= 1). Further, the power of the test was not compromised when accounting for phylogeny. As an example of the application of PPA, we revisit a study on the correlates of aggressive broodmate competition across seven avian families. The use of PPA allowed us to gain greater insight into the plausible causal paths linking species traits to aggressive broodmate competition.     

ELEVATED RATES OF MORPHOLOGICAL AND FUNCTIONAL DIVERSIFICATION IN REEF‐DWELLING HAEMULID FISHES

The relationship between habitat complexity and species richness is well established but comparatively little is known about the evolution of morphological diversity in complex habitats. Reefs are structurally complex, highly productive shallow‐water marine ecosystems found in tropical (coral reefs) and temperate zones (rocky reefs) that harbor exceptional levels of biodiversity. We investigated whether reef habitats promote the evolution of morphological diversity in the feeding and locomotion systems of grunts (Haemulidae), a group of predominantly nocturnal fishes that live on both temperate and tropical reefs. Using phylogenetic comparative methods and statistical analyses that take into account uncertainty in phylogeny and the evolutionary history of reef living, we demonstrate that rates of morphological evolution are faster in reef‐dwelling haemulids. The magnitude of this effect depends on the type of trait; on average, traits involved in the functional systems for prey capture and processing evolve twice as fast on reefs as locomotor traits. This result, along with the observation that haemulids do not exploit unique feeding niches on reefs, suggests that fine‐scale trophic niche partitioning and character displacement may be driving higher rates of morphological evolution. Whatever the cause, there is growing evidence that reef habitats stimulate morphological and functional diversification in teleost fishes.     

Microhabitat Variation Explains Local‐scale Distribution of Terrestrial Amazonian Lizards in Rondônia,Western Brazil

We investigate the role of ecology and phylogeny in the association between lizard abundance and microhabitat variables in an Amazon rain forest site. Using pitfall trap arrays, we collected data from 349 individuals belonging to 23 lizard species. After accounting for spatial autocorrelation and using a canonical correspondence analysis (CCA), we found that lizard captures were significantly associated with microhabitat variables, which accounted for 48 percent of the observed variation. Furthermore, a canonical phylogenetic ordination (CPO) indicated that microhabitat variables are more important in determining the distribution of lizard species than phylogenetic relationships among species. Termite nests, canopy openness, and tree circumference were strongly associated with the number of captures of certain lizard species. Our results confirm autecology studies of individual lizard species for which data are available. We suggest that maintaining heterogeneous forested microhabitats should be a central goal for sustaining a high lizard biodiversity in Amazon rain forests.