Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the discrete gamma model, uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates falling in the category. The performance of this method is found to be quite good, and four such categories appear to be sufficient to produce both an optimum, or near-optimum fit by the model to the data, and also an acceptable approximation to the continuous distribution. The second method, called fixed-rates model, classifies sites into several classes according to their rates predicted assuming the star tree. Sites in different classes are then assumed to be evolving at these fixed rates when other tree topologies are evaluated. Analyses of the data sets suggest that this method can produce reasonable results, but it seems to share some properties of a least-squares pairwise comparison; for example, interior branch lengths in nonbest trees are often found to be zero. The computational requirements of the two methods are comparable to that of Felsenstein's (1981, J Mol Evol 17:368–376) model, which assumes a single rate for all the sites.     

Jumping and gliding rodents: Mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach

An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes + Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.     

Congruence between nuclear and mitochondrial genes in Demospongiae: a new hypothesis for relationships within the G4 clade (Porifera: Demospongiae)

The current morphological classification of the Demospongiae G4 clade was tested using large subunit ribosomal RNA (LSU rRNA) sequences from 119 taxa. Fifty-three mitochondrial cytochrome oxidase 1 (CO1) barcoding sequences were also analysed to test whether the 28S phylogeny could be recovered using an independent gene. This is the largest and most comprehensive study of the Demospongiae G4 clade. The 28S and CO1 genetrees result in congruent clades but conflict with the current morphological classification. The results confirm the polyphyly of Halichondrida, Hadromerida, Dictyonellidae, Axinellidae and Poecilosclerida and show that several of the characters used in morphological classifications are homoplasious. Robust clades are clearly shown and a new hypothesis for relationships of taxa allocated to G4 is proposed.     

Plant morphometric traits and climate gradients in northern China: a meta-analysis using quadrat and flora data

Background and Aims

The collection of field data on plant traits is time consuming and this makes it difficult to examine changing patterns of traits along large-scale climate gradients. The present study tests whether trait information derived from regional floras can be used in conjunction with pre-existing quadrat data on species presence to derive meaningful relationships between specific morphometric traits and climate.

Methods

Quadrat records were obtained for 867 species in 404 sites from northern China (38–49°N, 82–132°E) together with information on the presence/absence of key traits from floras. Bioclimate parameters for each site were calculated using the BIOME3 model. Principal component analysis and correlation analysis were conducted to determine the most important climate factors. The Akaike Information Criterion was used to select the best relationship between each trait and climate. Canonical correspondence analysis was used to explore the relationships between climate and trait occurrence.

Key Results

The changing abundance of life form, leaf type, phenology, photosynthetic pathway, leaf size and several other morphometric traits are determined by gradients in plant-available moisture (as measured by the ratio of actual to potential evapotranspiration: α), growing-season temperature (as measured by growing degree-days on a 0 ° base: GDD₀) or a combination of these. Different plant functional types (PFTs, as defined by life form, leaf type and phenology) reach maximum abundance in distinct areas of this climate space: for example, evergreen trees occur in the coldest, wettest environments (GDD₀ < 2500 °Cd, α > 0·38), and deciduous scale-leaved trees occur in drier, warmer environments than deciduous broad-leaved trees. Most leaf-level traits show similar relationships with climate independently of PFT: for example, leaf size in all PFTs increases as the environment becomes wetter and cooler. However, some traits (e.g. petiole length) display different relationships with climate in different PFTs.

Conclusions

Based on presence/absence species data and flora-based trait assignments, the present study demonstrates ecologically plausible trends in the occurrence of key plant traits along climate gradients in northern China. Life form, leaf type, phenology, photosynthetic pathway, leaf size and other key traits reflect climate. The success of these analyses opens the possibility of using quadrat- and flora-based trait analyses to examine climate–trait relationships in other regions of the world.     

Multimodel inference in ecology and evolution: challenges and solutions

Information theoretic approaches and model averaging are increasing in popularity, but this approach can be difficult to apply to the realistic, complex models that typify many ecological and evolutionary analyses. This is especially true for those researchers without a formal background in information theory. Here, we highlight a number of practical obstacles to model averaging complex models. Although not meant to be an exhaustive review, we identify several important issues with tentative solutions where they exist (e.g. dealing with collinearity amongst predictors; how to compute model-averaged parameters) and highlight areas for future research where solutions are not clear (e.g. when to use random intercepts or slopes; which information criteria to use when random factors are involved). We also provide a worked example of a mixed model analysis of inbreeding depression in a wild population. By providing an overview of these issues, we hope that this approach will become more accessible to those investigating any process where multiple variables impact an evolutionary or ecological response.     

A comparison of the 16S ribosomal RNAs from mesophilic and thermophilic bacilli: Some modifications in the sanger method for RNA sequencing

Summary Two modifications in the Sanger two dimensional electrophoretic procedure for RNA analysis are reported. One increases resolution on the primary fingerprint to the point that digests of large RNAs, of the size 1500–3000 nucleotides yield well resolved fingerprint patterns. The other is a novel endonucleolytic procedure that proves useful in determining sequences of the large oligonucleotides produced by T1 ribonuclease.These modifications have been used in determining the catalogs of oligomers produced by T1 ribonuclease digestion of 16S rRNAs from three related organisms,Bacillus subtilis, B.pumilus andB.stearothermophilus. The possible effects of adaptation to a thermophilic niche on ribosomal RNA primary structure and the phylogenetic relatedness of the two mesophilic Bacilli are discussed.This is contribution No.6 in a series on procaryote phylogeny.     

Phylogenetic relationships and rates of evolution in primates: Allozymic data from catarrhine and platyrrhine species

The genetic electrophoretic variation at up to 43 protein loci was studied in four hominoid, three cercopithecoid, and three ceboid species. Phylogenetic reconstructions based on genetic distances show that the two chimpanzee species are closest to humans, while the gorilla diverged earlier than the split between humans and the chimpanzee. Within the cercopithecoids the green monkey apparently diverged earlier than the macaques, and within the ceboids, the owl monkey is only distantly related to the capuchin and squirrel monkeys. The hypothesis that rates of evolution at the level of protein electrophoretic variation are equal both among the groups, as well as within each group, could not be rejected.     

The phylogenetic history of Selaginellaceae based on DNA sequences from the plastid and nucleus: extreme substitution rates and rate heterogeneity

Molecular phylogenetic research on Selaginellaceae has focused on the plastid gene rbcL, which in this family has unusually high substitution rates. Here we develop a molecular data set from the nuclear 26S ribosomal DNA gene with the aim of evaluating and extending the results of previous phylogenetic research. The 26S rDNA and the rbcL regions were sequenced for a sample of 23 species, which represent the main elements of species diversity in the family. The data were analysed independently and in combination using both maximum parsimony and Bayesian inference. Although several between genome differences were found, the general pattern of relationships uncovered by all analyses was very similar. Results corroborate the previous study supporting new groupings not previously recognised on morphological grounds. Substitution rates in the 26S rDNA were also found to be high (26% informative) for the region analysed, but lower than for rbcL (37% informative). These data indicate that high substitution rates might be widespread in all three genomes (i.e., plastid, mitochondrion, and nucleus).     

Inflorescence diversification in the panicoid "bristle grass" clade (Paniceae, Poaceae): evidence from molecular phylogenies and developmental morphology

Grasses exhibit a great variety of inflorescence forms and these appear homoplasious when mapped onto cladograms. The overall pattern is sufficiently complex that it is difficult to analyze inflorescence evolution. We have reduced the complexity of the problem by examining one group of grasses, the panicoid "bristle clade," which exhibits a less complex pattern of variation. The clade is morphologically defined by inflorescences bearing both spikelets and sterile bristles and is monophyletic in both morphological and molecular phylogenetic analyses. We have constructed a chloroplast DNA phylogeny of the three main genera, which finds three well-supported clades, two comprising species placed in Setaria and one of Pennisetum + Cenchrus. In this tree Cenchrus is monophyletic, but both Setaria and Pennisetum are paraphyletic. Developmental morphology of these groups is very similar at early stages. Changes in axis ramification, primordial differentiation, and axis elongation account for most variation in mature inflorescence morphology. Characters derived from comparisons of developmental sequences were optimized onto one of the most parsimonious trees. Most developmental characters were congruent with the molecular phylogeny except for three reversals in the subclade containing S. barbata, S. palmifolia, and two accessions of S. poiretiana. Changes in just a handful of developmental events account for inflorescence evolution in the bristle clade, and similar changes may account for inflorescence diversity in the grasses as a whole.     

Spatial and temporal variability of net ecosystem production in a tropical forest: testing the hypothesis of a significant carbon sink

Tropical forest ecosystems play an important role in the global carbon balance. Depending on age and land use, they can act as carbon sources, sinks, or be in approximate balance, but it is uncertain if global environmental changes are forcing these ecosystems outside their natural range of variation. We asked the question of whether or not the net carbon flux of a tropical primary forest, which should be in balance over the long term, is within the expected range of natural variation. A simple Bayesian hypothesis testing method was used to address this question for primary forests in the Porce region of Colombia. Net ecosystem production (NEP) was measured in this forest in a set of 33 permanent plots from 2000 to 2002 in 2, 1‐year intervals. Our estimate of NEP ranged between −4.03 and 2.22 Mg C ha⁻¹ yr⁻¹ for the two intervals. This range was compared with a priori defined range of natural variation estimated from the ecosystem model STANDCARB, which estimated spatial and temporal variation due to gap dynamics. The prior range of variation was estimated between −1.5 and 1.5 Mg C ha⁻¹ yr⁻¹. The observed data on NEP did not provide sufficient evidence to reject the null hypothesis that these forests are in C balance. We concluded that the ecosystem is likely behaving within its range of natural variation, but measurement uncertainties were a major limitation to finding evidence to reject the null hypothesis. A literature review of C flux studies in the tropics revealed that about half of the observations could be explained by gap dynamics alone, while significant C sinks have only been observed during La Niña years, with contrasting results in other tropical forests. In conclusion, observational data of carbon fluxes do not appear to provide direct evidence for a significant carbon sink in some sites in the tropics.     

On the distribution of temporal variations in allele frequency: consequences for the estimation of effective population size and the detection of loci undergoing selection

The effective population size (Ne) is frequently estimated using temporal changes in allele frequencies at neutral markers. Such temporal changes in allele frequencies are usually estimated from the standardized variance in allele frequencies (Fc). We simulate Wright-Fisher populations to generate expected distributions of Fc and of Fc (Fc averaged over several loci). We explore the adjustment of these simulated Fc distributions to a chi-square distribution and evaluate the resulting precision on the estimation of Ne for various scenarios. Next, we outline a procedure to test for the homogeneity of the individual Fc across loci and identify markers exhibiting extreme Fc-values compared to the rest of the genome. Such loci are likely to be in genomic areas undergoing selection, driving Fc to values greater (or smaller) than expected under drift alone. Our procedure assigns a P-value to each locus under the null hypothesis (drift is homogeneous throughout the genome) and simultaneously controls the rate of false positive among loci declared as departing significantly from the null. The procedure is illustrated using two published data sets: (i) an experimental wheat population subject to natural selection and (ii) a maize population undergoing recurrent selection.     

Hydrologic and geologic factors that influenced spatial variations in loess deposition in China during the last interglacial-glacial cycle: results from proxy climate and GCM analyses

Results from climate proxy and General Circulation Model (GCM) analyses suggest that variations in soil moisture and desert expansion are key hydrologic and geologic factors, respectively, influencing temporal and spatial variations in loess texture and distribution in the Loess Plateau of China. During the last glacial period a reduction in soil moisture led to dune destabilization and a southward expansion of the desert (the source of loess) toward the Loess Plateau. Changes in soil moisture in East Asia may have been influenced by the size and extent of the Fennoscandian ice sheet, and the atmospheric circulation pattern that it induced downstream. These results suggest that both regional factors (i.e. changes in soil moisture and the position of the desert margin) and hemispherical factors (i.e. changes in the size and extent of the Eurasian ice sheets) have influenced loess deposition on the Loess Plateau of China.     

Allele frequency estimation from ambiguous data: using resampling schema in validating frequency estimates and in selective neutrality testing

The development of molecular typing techniques applied to the study of population genetic diversity originates data with increasing precision but at the cost of some ambiguities. As distinct techniques may produce distinct kinds of ambiguities, a crucial issue is to assess the differences between frequency distributions estimated from data produced by alternative techniques for the same sample. To that aim, we developed a resampling scheme that allows evaluating, by statistical means, the significance of the difference between two frequency distributions. The same approach is then shown to be applicable to test selective neutrality when only sample frequencies are known. The use of these original methods is presented here through an application to the genetic study of a Munda human population sample, where three different HLA loci were typed using two different molecular methods (reverse PCR-SSO typing on microbeads arrays based on Luminex technology and PCR-SSP typing), as described in details in the companion article by Riccio et al. [The Austroasiatic Munda population from India and its enigmatic origin: An HLA diversity study. Hum. Biol. 38:405-435 (2011)]. The differences between the frequency estimates of the two typing techniques were found to be smaller than those resulting from sampling. Overall, we show that using a resampling scheme in validating frequency estimates is effective when alternative frequency estimates are available. Moreover, resampling appears to be the unique way to test selective neutrality when only frequency data are available to describe the genetic structure of populations.     

Comment arising from a paper by Wittmer et al.: hypothesis testing for top-down and bottom-up effects in woodland caribou population dynamics

Asexual fungal endophytes, which do not produce reproductive structures, spread in host populations only vertically via the propagules of their hosts. With such a close relationship between the fitness of the asexual endophyte and that of the host, the relationship is traditionally thought to be mutualistic. Here we present data showing that the positive effect of asexual endophytes may concern only a short period of the host’s life and that its lifetime reproductive success may be reduced. We followed 180 individuals of a perennial grass, Puccinellia distans, for the first 3 years of their growth both in the field and in a common garden experiment. In the first 2 years, infected individuals produced more generative shoots with longer inflorescences. Three-year-old individuals produced significantly fewer generative shoots with shorter inflorescences when infected with the fungus Epichloë typhina. Moreover, the dry mass of above- and belowground parts after three seasons was significantly lower in infected individuals. We suggest that if the endophyte retains control over plant reproduction and if shorter generation time is more crucial for the fungus than for the perennial host, then the fungus should stimulate plant reproduction early in life even though infection incurs a future cost. This reasoning suggests that discovering an endophyte’s beneficial effect on its perennial host in one season provides insufficient grounds for concluding that a mutualistic relationship exists.     

Comment arising from a paper by Wittmer et al.: hypothesis testing for top-down and bottom-up effects in woodland caribou population dynamics

Conservation strategies for populations of woodland caribou Rangifer tarandus caribou frequently emphasize the importance of predator–prey relationships and the availability of lichen-rich late seral forests, yet the importance of summer diet and forage availability to woodland caribou survival is poorly understood. In a recent article, Wittmer et al. (Can J Zool 83:407–418, 2005b) concluded that woodland caribou in British Columbia were declining as a consequence of increased predation that was facilitated by habitat alteration. Their conclusion is consistent with the findings of other authors who have suggested that predation is the most important proximal factor limiting woodland caribou populations (Bergerud and Elliot in Can J Zool 64:1515–1529, 1986; Edmonds in Can J Zool 66:817–826, 1988; Rettie and Messier in Can J Zool 76:251–259, 1998; Hayes et al. in Wildl Monogr 152:1–35, 2003). Wittmer et al. (Can J Zool 83:407–418, 2005b) presented three alternative, contrasting hypotheses for caribou decline that differed in terms of predicted differences in instantaneous rates of increase, pregnancy rates, causes of mortality, and seasonal vulnerability to mortality (Table 1, p 258). These authors rejected the hypotheses that food or an interaction between food and predation was responsible for observed declines in caribou populations; however, the use of pregnancy rate, mortality season and cause of mortality to contrast the alternative hypotheses is problematic. We argue here that the data employed in their study were insufficient to properly evaluate a predation-sensitive foraging hypothesis for caribou decline. Empirical data on seasonal forage availability and quality and plane of nutrition of caribou would be required to test the competing hypotheses. We suggest that methodological limitations in studies of woodland caribou population dynamics prohibit proper evaluation of the mechanism of caribou population declines and fail to elucidate potential interactions between top-down and bottom-up effects on populations. An erratum to this article can be found at     

Genetic and electron-microscopic characterization of Rickettsiella bacteria from the manuka beetle, Pyronota setosa (Coleoptera: Scarabaeidae)

Larvae of manuka beetles, Pyronota spp. (Coleoptera: Scarabaeidae) cause pasture damage in New Zealand by feeding on the roots of grasses. Surveys for potential biocontrol agents revealed a putative disease, expressed as whitened larvae of one of the outbreak species, Pyronota setosa. Microbial diagnosis indicated an intracoelomic, intracellular infection, and intracellular bacteria have been identified with subcellular structures characteristic of infection by Rickettsiella-like microorganisms. These bacteria were rod-shaped, often slightly bent with a mean of 628 nm in length and 220 nm in width. Numerous associated protein crystals of variable size and shape occurred within round to oval shaped “giant bodies” either singly or as clusters of smaller crystals. Molecular phylogenetic analysis based on 16S ribosomal RNA and signal recognition particle receptor (FtsY) encoding sequences demonstrates that the manuka beetle pathogen belongs to the taxonomic genus Rickettsiella. Therefore, the pathotype designation ‘Rickettsiella pyronotae’ is proposed to refer to this organism. Moreover, genetic analysis makes it likely that - on the basis of the currently accepted organization of the genus Rickettsiella - this new pathotype should be considered a synonym of the nomenclatural type species, Rickettsiella popilliae.     

Molecular and structural analysis of C4-specific PEPC isoform from Pennisetum glaucum plays a role in stress adaptation

As an activator of adenylate cyclase, the neuropeptide Pituitary Adenylate Cyclase Activating Peptide (PACAP) impacts levels of cyclic AMP, a key second messenger available in brain cells. PACAP is involved in certain adult behaviors. To elucidate PACAP interactions, a compendium of microarrays representing mRNA expression in the adult mouse whole brain was pooled from the Phenogen database for analysis. A regulatory network was computed based on mutual information between gene pairs using gene expression data across the compendium. Clusters among genes directly linked to PACAP, and probable interactions between corresponding proteins were computed. Database “experts” affirmed some of the inferred relationships. The findings suggest ADCY7 is probably the adenylate cyclase isoform most relevant to PACAP's action. They also support intervening roles for kinases including GSK3B, PI 3-kinase, SGK3 and AMPK. Other high-confidence interactions are hypothesized for future testing. This new information has implications for certain behavioral and other disorders.