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May 29, 2015

00:06

As humans migrated around the world, they came to inhabit environments that differ widely in the soil levels of certain micronutrients, including selenium (Se). Coupled with cultural variation in dietary practices, these migrations have led to a wide range of Se intake levels in populations around the world. Both excess and deficiency of Se in the diet can have adverse health consequences in humans, with severe Se deficiency resulting in diseases of the bone and heart. Se is required by humans mainly due to its function in selenoproteins, which contain the amino acid selenocysteine as one of their constituent residues. To understand the evolution of the use of this micronutrient in humans, we surveyed the patterns of polymorphism in all selenoprotein genes and genes involved in their regulation in 50 human populations. We find that single nucleotide polymorphisms from populations in Asia, particularly in populations living in the extreme Se-deficient regions of China, have experienced concerted shifts in their allele frequencies. Such differentiation in allele frequencies across genes is not observed in other regions of the world and is not expected under neutral evolution, being better explained by the action of recent positive selection. Thus, recent changes in the use and regulation of Se may harbor the genetic adaptations that helped humans inhabit environments that do not provide adequate levels of Se in the diet.

00:06

Influenza A virus (IAV) has a segmented genome that allows for the exchange of genome segments between different strains. This reassortment accelerates evolution by breaking linkage, helping IAV cross species barriers to potentially create highly virulent strains. Challenges associated with monitoring the process of reassortment in molecular detail have limited our understanding of its evolutionary implications. We applied a novel deep sequencing approach with quantitative analysis to assess the in vitro temporal evolution of genomic reassortment in IAV. The combination of H1N1 and H3N2 strains reproducibly generated a new H1N2 strain with the hemagglutinin and nucleoprotein segments originating from H1N1 and the remaining six segments from H3N2. By deep sequencing the entire viral genome, we monitored the evolution of reassortment, quantifying the relative abundance of all IAV genome segments from the two parent strains over time and measuring the selection coefficients of the reassorting segments. Additionally, we observed several mutations coemerging with reassortment that were not found during passaging of pure parental IAV strains. Our results demonstrate how reassortment of the segmented genome can accelerate viral evolution in IAV, potentially enabled by the emergence of a small number of individual mutations.

00:06

Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-gatherers known as Jomon, who are assumed to have originated in southeast Asia and lived in the Japanese archipelago greater than 10,000 years ago, admixed with an agricultural people known as Yayoi, whom were migrants from the East Asian continent 2,000–3,000 years ago. Meanwhile, some anthropologists propose that rather, morphological differences between the Jomon and Yayoi people can be explained by microevolution following the lifestyle change. To resolve this controversy, we compared three demographic models by approximate Bayesian computation using genome-wide single nucleotide polymorphism (gwSNP) data from the Ainu people who are thought to be direct descendants of indigenous Jomon. If we assume Chinese people sampled in Beijing from HapMap have the same ancestry as Yayoi, then the hybridization model is predicted to be between 29 and 63 times more likely than the replacement and transformation models, respectively. Furthermore, our data provide strong support for a model in which the Jomon lineages had population structure diversified in local areas before the admixture event. Initial divergence between the Jomon and Yayoi ancestries was dated to late Pleistocene, followed by the divergence of Jomon lineages at early Holocene. These results suggest gwSNP data provides a detailed picture of the complex hybridization model for Japanese population history.

00:06

Adaptation drives genomic changes; however, evidence of specific adaptations in humans remains limited. We found that inhabitants of the northern Argentinean Andes, an arid region where elevated arsenic concentrations in available drinking water is common, have unique arsenic metabolism, with efficient methylation and excretion of the major metabolite dimethylated arsenic and a less excretion of the highly toxic monomethylated metabolite. We genotyped women from this population for 4,301,332 single nucleotide polymorphisms (SNPs) and found a strong association between the AS3MT (arsenic [+3 oxidation state] methyltransferase) gene and mono- and dimethylated arsenic in urine, suggesting that AS3MT functions as the major gene for arsenic metabolism in humans. We found strong genetic differentiation around AS3MT in the Argentinean Andes population, compared with a highly related Peruvian population (FST = 0.014) from a region with much less environmental arsenic. Also, 13 of the 100 SNPs with the highest genome-wide Locus-Specific Branch Length occurred near AS3MT. In addition, our examination of extended haplotype homozygosity indicated a selective sweep of the Argentinean Andes population, in contrast to Peruvian and Colombian populations. Our data show that adaptation to tolerate the environmental stressor arsenic has likely driven an increase in the frequencies of protective variants of AS3MT, providing the first evidence of human adaptation to a toxic chemical.

00:06

The "developmental hourglass" concept suggests that intermediate developmental stages are most resistant to evolutionary changes and that differences between species arise through divergence later in development. This high conservation during middevelopment is illustrated by the "waist" of the hourglass and it represents a low probability of evolutionary change. Earlier molecular surveys both on animals and on plants have shown that the genes expressed at the waist stage are more ancient and more conserved in their expression. The existence of such a developmental hourglass has not been explored in fungi, another eukaryotic kingdom. In this study, we generated a series of transcriptomic data covering the entire lifecycle of a model mushroom-forming fungus, Coprinopsis cinerea, and we observed a molecular hourglass over its development. The "young fruiting body" is the stage that expresses the evolutionarily oldest (lowest transcriptome age index) transcriptome and gives the strongest signal of purifying selection (lowest transcriptome divergence index). We also demonstrated that all three kingdoms—animals, plants, and fungi—display high expression levels of genes in "information storage and processing" at the waist stages, whereas the genes in "metabolism" become more highly expressed later. Besides, the three kingdoms all show underrepresented "signal transduction mechanisms" at the waist stages. The synchronic existence of a molecular "hourglass" across the three kingdoms reveals a mutual strategy for eukaryotes to incorporate evolutionary innovations.

00:06

Persistent adaptive challenges are often met with the evolution of novel physiological traits. Although there are specific examples of single genes providing new physiological functions, studies on the origin of complex organ functions are lacking. One such derived set of complex functions is found in the Lepidopteran bursa copulatrix, an organ within the female reproductive tract that digests nutrients from the male ejaculate or spermatophore. Here, we characterized bursa physiology and the evolutionary mechanisms by which it was equipped with digestive and absorptive functionality. By studying the transcriptome of the bursa and eight other tissues, we revealed a suite of highly expressed and secreted gene products providing the bursa with a combination of stomach-like traits for mechanical and enzymatic digestion of the male spermatophore. By subsequently placing these bursa genes in an evolutionary framework, we found that the vast majority of their novel digestive functions were co-opted by borrowing genes that continue to be expressed in nonreproductive tissues. However, a number of bursa-specific genes have also arisen, some of which represent unique gene families restricted to Lepidoptera and may provide novel bursa-specific functions. This pattern of promiscuous gene borrowing and relatively infrequent evolution of tissue-specific duplicates stands in contrast to studies of the evolution of novelty via single gene co-option. Our results suggest that the evolution of complex organ-level phenotypes may often be enabled (and subsequently constrained) by changes in tissue specificity that allow expression of existing genes in novel contexts, such as reproduction. The extent to which the selective pressures encountered in these novel roles require resolution via duplication and sub/neofunctionalization is likely to be determined by the need for specialized reproductive functionality. Thus, complex physiological phenotypes such as that found in the bursa offer important opportunities for understanding the relative role of pleiotropy and specialization in adaptive evolution.

00:06

Males and females often have marked phenotypic differences, and the expression of these dissimilarities invariably involves sex differences in gene expression. Sex-biased gene expression has been well characterized in animal species, where a high proportion of the genome may be differentially regulated in males and females during development. Male-biased genes tend to evolve more rapidly than female-biased genes, implying differences in the strength of the selective forces acting on the two sexes. Analyses of sex-biased gene expression have focused on organisms that exhibit separate sexes during the diploid phase of the life cycle (diploid sexual systems), but the genetic nature of the sexual system is expected to influence the evolutionary trajectories of sex-biased genes. We analyze here the patterns of sex-biased gene expression in Ectocarpus, a brown alga with haploid sex determination (dioicy) and a low level of phenotypic sexual dimorphism. In Ectocarpus, female-biased genes were found to be evolving as rapidly as male-biased genes. Moreover, genes expressed at fertility showed faster rates of evolution than genes expressed in immature gametophytes. Both male- and female-biased genes had a greater proportion of sites experiencing positive selection, suggesting that their accelerated evolution is at least partly driven by adaptive evolution. Gene duplication appears to have played a significant role in the generation of sex-biased genes in Ectocarpus, expanding previous models that propose this mechanism for the resolution of sexual antagonism in diploid systems. The patterns of sex-biased gene expression in Ectocarpus are consistent both with predicted characteristics of UV (haploid) sexual systems and with the distinctive aspects of this organism's reproductive biology.

00:06

Despite Cnidaria (sea anemones, corals, jellyfish, and hydroids) being the oldest venomous animal lineage, structure–function relationships, phyletic distributions, and the molecular evolutionary regimes of toxins encoded by these intriguing animals are poorly understood. Hence, we have comprehensively elucidated the phylogenetic and molecular evolutionary histories of pharmacologically characterized cnidarian toxin families, including peptide neurotoxins (voltage-gated Na+ and K+ channel-targeting toxins: NaTxs and KTxs, respectively), pore-forming toxins (actinoporins, aerolysin-related toxins, and jellyfish toxins), and the newly discovered small cysteine-rich peptides (SCRiPs). We show that despite long evolutionary histories, most cnidarian toxins remain conserved under the strong influence of negative selection—a finding that is in striking contrast to the rapid evolution of toxin families in evolutionarily younger lineages, such as cone snails and advanced snakes. In contrast to the previous suggestions that implicated SCRiPs in the biomineralization process in corals, we demonstrate that they are potent neurotoxins that are likely involved in the envenoming function, and thus represent the first family of neurotoxins from corals. We also demonstrate the common evolutionary origin of type III KTxs and NaTxs in sea anemones. We show that type III KTxs have evolved from NaTxs under the regime of positive selection, and likely represent a unique evolutionary innovation of the Actinioidea lineage. We report a correlation between the accumulation of episodically adaptive sites and the emergence of novel pharmacological activities in this rapidly evolving neurotoxic clade.

00:06

Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice.

00:06

The wealth of phylogenetic information accumulated over many decades of biological research, coupled with recent technological advances in molecular sequence generation, presents significant opportunities for researchers to investigate relationships across and within the kingdoms of life. However, to make best use of this data wealth, several problems must first be overcome. One key problem is finding effective strategies to deal with missing data. Here, we introduce Lasso, a novel heuristic approach for reconstructing rooted phylogenetic trees from distance matrices with missing values, for data sets where a molecular clock may be assumed. Contrary to other phylogenetic methods on partial data sets, Lasso possesses desirable properties such as its reconstructed trees being both unique and edge-weighted. These properties are achieved by Lasso restricting its leaf set to a large subset of all possible taxa, which in many practical situations is the entire taxa set. Furthermore, the Lasso approach is distance-based, rendering it very fast to run and suitable for data sets of all sizes, including large data sets such as those generated by modern Next Generation Sequencing technologies. To better understand the performance of Lasso, we assessed it by means of artificial and real biological data sets, showing its effectiveness in the presence of missing data. Furthermore, by formulating the supermatrix problem as a particular case of the missing data problem, we assessed Lasso’s ability to reconstruct supertrees. We demonstrate that, although not specifically designed for such a purpose, Lasso performs better than or comparably with five leading supertree algorithms on a challenging biological data set. Finally, we make freely available a software implementation of Lasso so that researchers may, for the first time, perform both rooted tree and supertree reconstruction with branch lengths on their own partial data sets.

00:06

OrthoAlign, an algorithm for the gene order alignment problem (alignment of orthologs), accounting for most genome-wide evolutionary events such as duplications, losses, rearrangements, and substitutions, was presented. OrthoAlign was used in a phylogenetic framework to infer the evolution of transfer RNA repertoires of 50 fully sequenced bacteria in the Bacillus genus. A prevalence of gene duplications and losses over rearrangement events was observed. The average rate of duplications inferred in Bacillus was 24 times lower than the one reported in Escherichia coli, whereas the average rates of losses and inversions were both 12 times lower. These rates were extremely low, suggesting a strong selective pressure acting on tRNA gene repertoires in Bacillus. An exhaustive analysis of the type, location, distribution, and length of evolutionary events was provided, together with ancestral configurations. OrthoAlign can be downloaded at: http://www.iro.umontreal.ca/~mabrouk/.

May 28, 2015

10:16

@karen_cranston wrote:

The FuturePhy folks have funds for (among other things) a series of hackathons. Given that focused events seem more productive than general "hacking on phylogenetics" events, what topics in phylogenetics could use a hackathon to move things forward?

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06:00
Background: Yeasts belonging to the subphylum Saccharomycotina have been used for centuries in food processing and, more recently, biotechnology. Over the past few decades, these yeasts have also been studied in the interest of their potential to produce oil to replace fossil resources. Developing yeasts for massive oil production requires increasing yield and modifying the profiles of the fatty acids contained in the oil to satisfy specific technical requirements. For example, derivatives of medium-chain fatty acids (MCFAs, containing 6–14 carbons) are used for the production of biodiesels, cleaning products, lubricants and cosmetics. Few studies are available in the literature on the production of MCFAs in yeasts. Results: We analyzed the MCFA content in Saccharomyces cerevisiae grown in various conditions. The results revealed that MCFAs preferentially accumulated when cells were grown on synthetic media with a high C/N ratio at low temperature (23 °C). Upon screening deletion mutant strains for genes encoding lipid droplet-associated proteins, we found two genes, LOA1 and TGL3, involved in MCFA homeostasis. A phylogenetic analysis on 16 Saccharomycotina species showed that fatty acid profiles differed drastically among yeasts. Interestingly, MCFAs are only present in post-whole genome duplication yeast species. Conclusions: In this study, we produced original data on fatty acid diversity in yeasts. We demonstrated that yeasts are amenable to genetic and metabolic engineering to increase their MCFA production. Furthermore, we revealed that yeast lipid biodiversity has not been fully explored, but that yeasts likely harbor as-yet-undiscovered strains or enzymes that can contribute to the production of high-value fatty acids for green chemistry.

May 27, 2015

06:25

@josephwb wrote:

Fellow phylo-dorks,

I was wondering if anyone had hard numbers (or a paper reference) for the energy consumption required by large phylogenetic analyses (or comparable computational problems from other fields). Perhaps @rdmpage, @ematsen, @alexei_drummond, @Alexis_RAxML, @mtholder, @phylorich, or @beerli might be able to help me out?

Thanks! JWB.

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May 26, 2015

22:30

Charles Darwin's most poetic published words concern his image of the Tree of Life. However, he did not claim to have originated the image. For example, Alfred Russel Wallace had already used it. Recently, the Natural History Apostilles blog has mentioned another important predecessor of both Englishmen, the Frenchman Charles Naudin, who deserves wider recognition.

Darwin's well-known words from On the Origin of Species (1859) are:
The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species ... As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.Wallace seems to have developed the Tree of Life metaphor quite independently (1855. On the law which has regulated the introduction of new species. Annals and Magazine of Natural History, 2nd series 16: 184-196):
"the analogy of a branching tree [is] the best mode of representing the natural arrangement of species ... a complicated branching of the lines of affinity, as intricate as the twigs of a gnarled oak ... we have only fragments of this vast system, the stem and main branches being represented by extinct species of which we have no knowledge, while a vast mass of limbs and boughs and minute twigs and scattered leaves is what we have to place in order, and determine the true position each originally occupied with regard to the others."Darwin freely admitted having read Wallace's work. Moreover, he was well aware of the other of his predecessors, Charles Naudin, because on p.167 of his 'Books Read' and 'Books to be Read' notebook of 1852-1860 (see Darwin Online CUL-DAR128) he recorded:
"Revue Horticol Imp. 1852. p. 102. Naudin Consid. Phil, sur l'espèce"Charles Naudin's words are these, roughly translated from the original French (1852. Considérations philosophiques sur l'espèce et la variété. Revue Horticole, 4th series 1: 102-109) [NB. the long convoluted sentences are in the original]:
This doctrine of inbreeding among organic beings of same family, the same class, and perhaps of the same kingdom, is not new; men of talent, both in France as well as abroad, among them our learned Lamarck, have supported it with all of the authority of their names. We do not deny that, on more than one occasion, they have reasoned upon assumptions which were not adequately supported by observation, that they did sometimes apply to the facts forced interpretations, that finally resulted in exaggerations that have mainly helped to push their ideas. But these defects in details do not diminish the greatness and perfect rationality of the whole system that, alone, reflects, by the community of origin, the great fact of the organizational community of the other living beings of the same kingdom, the primary basis of our rankings of species into genera, families, orders and phyla. In the opposing system now in vogue, in this system which involves many partial and independent creations we recognize or think we recognize as distinct species, one is forced to be logical, to admit the similarities exhibited by these species are only fortuitous coincidence, that is to say an effect without a cause, concluding that the reason is not acceptable. In our own [system], on the contrary, these similarities are both the consequence and proof of a relationship, not metaphorical, but real, that they hold a common ancestor, which they left at times more or less remote and through a series of intermediaries greater or fewer in number; so they express the true relationships between species by saying that the sum of their mutual similarities is the expression of their degree of relationship, as the sum of the differences is that of the distance they are from the common stock from which they derive their origin.Considered from this point of view, the plant kingdom would present, not as a linear series whose terms would increase or decrease in organizational complexity, according as we consider starting with one end or the other; it would not be more of a disordered tangle of intersecting lines, like a geographical map, whose regions, different in shape and size, would touch by a greater or lesser number of points; it would be a tree the roots of which, mysteriously hidden in the depths of cosmological time, would have given birth to a limited number of successively divided and subdivided stems. These first stems would represent the primordial types of the kingdom; their last ramifications would be the current species.It follows from there that a perfect and rigorous classification of the other organized beings of the same kingdom, of the same order, of the same family, if something other than the family tree even of the species, indicates the relative age of each, its degree of speciation and the line of ancestors from which it descended. Thereby would be represented, in a manner of some sort so palpable and material, the different degrees of relationship of the species, such as that of groups of varying degrees, dating back to the primordial kinds. Such a classification, summarized in a graphical table, would be seized with much facility by the mind through the eyes, and present the most beautiful application of this principle generally accepted by naturalists: that nature is avaricious [stingy?] of causes and prodigal of effects.This is quite clearly a description of a modern phylogenetic tree, and the taxonomic consequences of adopting that conception.

It is, however, rather a pity that he explicitly rejects a network ("a disordered tangle of intersecting lines") as a suitable model, along with the chain ("a linear series").

01:14
Genomics Week @ CIBIO-InBIO June 15-19, 2015 | CIBIO-InBIO, Vairao, Portugal >From June 15 to 19, CIBIO-InBIO will host a Genomics Week, taking place at Vairão Campus. The programme for this week includes: · on June 15-17, the advanced course “Genotyping by Sequencing (GBS): principles, approaches and applicationsâ€� [Registration required]; and · on June 18-19, a “Genomics Seminarâ€� [No registration required]. ADVANCED COURSE GENOTYPING BY SEQUENCING (GBS): PRINCIPLES, APPROACHES AND APPLICATIONS June 15-17, 2015 | Room 2 - Vairão Campus This course aims to give attendees a broad overview of Genotyping-by-Sequencing (GBS), including the principles of how data are obtained by the various different approaches, and their advantages and disadvantages. There will be a question and answer session to help determine the right approach for different study systems or special cases, such as degraded DNA. There will also be practical data-analysis sessions, where attendees will be guided through example data processing with various analysis tools. INTENDED AUDIENCE The course will be open to a maximum number of 20 participants. Priority will be given to: I. 1st year PhD students attending the BIODIV Doctoral Programme; II. Other BIODIV PhD students; III. PhD students attending other courses; IV. Other candidates. REGISTRATION Registration deadline: June 4, 2015 GENOMICS SEMINAR June 18-19, 2015 | Auditorium - Vairão Campus During this two-day seminar, five major topics in genomics research will be covered: 1. Environmental Genomics; 2. Phylogenomics; 3. Conservation/Population Genomics; 4. AgriGenomics; One Health Genomics. Participation in this seminar is free and the number of attendees is limited to the capacity of the auditorium. To know more about this event, please visit CIBIO-InBIO’s website [http://bit.ly/1SzFZf5]. References 1. mailto:divulgacao@cibio.up.pt 2. http://cibio.up.pt/ 3. http://on.fb.me/1Ecb3H2 CIBIO Divulgação via Gmail
Source: EVOLDIR