news aggregator

August 20, 2015

06:00
Background: Butterflies of the subtribe Mycalesina have radiated successfully in almost all habitat types in Africa, Madagascar, the Indian subcontinent, Indo-China and Australasia. Studies aimed at understanding the reasons behind the evolutionary success of this spectacular Old World butterfly radiation have been hampered by the lack of a stable phylogeny for the group. Here, we have reconstructed a robust phylogenetic framework for the subtribe using 10 genes from 195 exemplar taxa. Results: We recovered seven well supported clades within the subtribe corresponding to the five traditional genera (Lohora, Heteropsis, Hallelesis, Bicyclus, Mycalesis), one as recently revised (Mydosama) and one newly revised genus (Culapa). The phylogenetic relationships of these mycalesine genera have been robustly established for the first time. Within the proposed phylogenetic framework, we estimated the crown age of the subtribe to be 40 Million years ago (Mya) and inferred its ultimate origin to be in Asia. Our results reveal both vicariance and dispersal as factors responsible for the current widespread distribution of the group in the Old World tropics. We inferred that the African continent has been colonized at least twice by Asian mycalesines within the last 26 and 23 Mya. In one possible scenario, an Asian ancestor gave rise to Heteropsis on continental Africa, which later dispersed into Madagascar and most likely back colonised Asia. The second colonization of Africa by Asian ancestors resulted in Hallelesis and Bicyclus on continental Africa, the descendants of which did not colonise other regions but rather diversified only in continental Africa. The genera Lohora and Mydosama are derivatives of ancestors from continental Asia. Conclusion: Our proposed time-calibrated phylogeny now provides a solid framework within which we can implement mechanistic studies aimed at unravelling the ecological and evolutionary processes that culminated in the spectacular radiation of mycalesines in the Old World tropics.
06:00
Background: Despite their abundance, unspliced EST data have received little attention as a source of information on non-coding RNAs. Very little is know, therefore, about the genomic distribution of unspliced non-coding transcripts and their relationship with the much better studied regularly spliced products. In particular, their evolution has remained virtually unstudied. Results: We systematically study the evidence on unspliced transcripts available in EST annotation tracks for human and mouse, comprising 104,980 and 66,109 unspliced EST clusters, respectively. Roughly one third of these are located totally inside introns of known genes (TINs) and another third overlaps exonic regions (PINs). Eleven percent are “intergenic”, far away from any annotated gene. Direct evidence for the independent transcription of many PINs and TINs is obtained from CAGE tag and chromatin data. We predict more than 2000 3’UTR-associated RNA candidates for each human and mouse. Fifteen to twenty percent of the unspliced EST cluster are conserved between human and mouse. With the exception of TINs, the sequences of unspliced EST clusters evolve significantly slower than genomic background. Furthermore, like spliced lincRNAs, they show highly tissue-specific expression patterns. Conclusions: Unspliced long non-coding RNAs are an important, rapidly evolving, component of mammalian transcriptomes. Their analysis is complicated by their preferential association with complex transcribed loci that usually also harbor a plethora of spliced transcripts. Unspliced EST data, although typically disregarded in transcriptome analysis, can be used to gain insights into this rarely investigated transcriptome component. The frequently postulated connection between lack of splicing and nuclear retention and the surprising overlap of chromatin-associated transcripts suggests that this class of transcripts might be involved in chromatin organization and possibly other mechanisms of epigenetic control.
00:35
POST-DOCTORAL POSITIONS Two post-doctoral positions are available in the research groups led by Francesca Luca and Roger Pique-Regi, at the Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI. The research focus of the groups is on the genetic and molecular characterization of gene regulation from an evolutionary and functional perspective. Examples of collaborative projects include: characterizing variation in the response to hormonal and environmental stimuli at the individual and population level; identifying tissue-specific cis-regulatory modules with ATAC-seq and footprinting analysis; detecting signals of selection and adaptation in gene regulatory regions. The ultimate aim is to learn about the genetic and evolutionary basis of disease susceptibility and response to treatment. We have a strong record in using both functional and evolutionary genomics approaches. We use a combination of high throughput experimental platforms and computational/statistical tools. We seek applicants who are very creative, energetic, and can work independently. We operate relatively small but well-funded and intense laboratories. The goal is that everyone should have the resources, support and mentorship needed to be successful and become an independent investigator. The two positions are intended for applicants with complementary expertise. Specifically we are looking for talented individuals with either a strong experimental and/or computational background that will contribute to create a team jointly supervised by Dr. Luca and Dr. Pique-Regi. The experimentalist position would be under the direct supervision of Dr. Luca, and requires experience in collecting genome-scale data, in mammalian cell and tissue culture techniques and in functional genomics techniques. Familiarity with the quantitative skills required for the analysis of genomic data (e.g., Python, R, scripts for setting up an analysis pipeline) is also required. For the computational position (under the direct supervision of Dr. Pique-Regi), applicants should have a strong background in quantitative/statistical skills, and a very strong interest in biological applications. A background in genomics, gene regulation or statistical genetics is an advantage, although we will consider outstanding candidates with quantitative degrees (e.g. in Statistics, CS, or Engineering) For more information please contact: Francesca Luca, PhD e-mail: fluca@wayne.edu website: http://bit.ly/1PnyILU Roger Pique-Regi, PhD e-mail: rpique@wayne.edu Francesca Luca via Gmail
Source: EVOLDIR

August 19, 2015

23:30

The Department of Biosciences, University of Helsinki invites applications for a TWO-YEAR POST DOCTORAL RESEARCHER POSITION in the research group of Assistant Professor Arild Husby. The successful applicant will be part of the Centre of Excellence in Metapopulation Research at the Department of Biosciences, University of Helsinki (http://bit.ly/1TXQfvn). The main goal of the post doc project is to examine the epigenetic basis of avian timing of breeding using the great tit (Parus major) as a model species. The successful candidate will examine DNA methylation patterns using targeted bisulphite sequencing of previously identified candidate genes. DNA methylation levels will be compared among two groups of extreme phenotypes using blood samples already collected. In addition, the candidate will be involved in some field work to collect additional data to examine trans-generational DNA methylation patterns. The work will be performed in close collaboration with Prof. Marcel Visser and Dr Kees van Oers at the Netherlands Institute of Ecology (http://bit.ly/1Lm1s9Q). Fieldwork will be carried out in the Hoge Veluwe national park near Wageningen, The Netherlands and close to Viikki campus, Helsinki, Finland. The successful candidate should have PhD / postdoctoral experience within the fields of evolutionary genetics/genomics with previous experience in sequence based analysis of DNA methylation data. Previous experience working on birds is not necessary. Excellent written and verbal communication skills in English are required and you must also demonstrate ability to work as part of a team. The position will have a probationary period of four months. The starting date is flexible but at latest 1st January 2016. The salary will be based on level 5 of the demands level chart for teaching and research personnel in the salary system of Finnish universities. In addition, the appointee will be paid a salary component based on personal work performance. The total minimum salary at the beginning of the employment is 3311,17 €/month. To apply, please send, in a single pdf file, your CV with publications included and a letter (max 2 pages) with a description of your research interests and, in particular, why you would be a suitable candidate for the project. The application letter should also contain possible starting dates and contact details of three references. The applicatiions are to be addressed to Dr Arild Husby and submitted to biotiede-mrg@helsinki.fi by 1st October 2015 at 15.45 local Helsinki time. For more information about this position, please contact Dr Arild Husby (arild.husby@helsinki.fi), see also our lab website: http://bit.ly/1yT0ny7 via Gmail

Source: EVOLDIR
08:44

@rdmpage wrote:

This may seem like a strange question, but here goes. I'm looking for a computationally efficient way to represent a set of sequences in a 2D space. For example, imagine that we have 10,000 DNA barcodes. I could compute a tree, but (a) that get's computationally hard (if it doesn't seem hard, make it 100,000, or 1M), and (b) a tree drawing isn't stable in the sense that there's no global coordinate system that helps us compare trees for different subsets of data.

I thought about using something like DNA walks, where we start at 0,0 in a x-y graph, walk along a sequence, and make moves -1, 1 in the x or y direction depending on the next base in the sequence. For example, we could plot the final x,y coordinates at the end of the walk, and we'd have a simple to compute measure that depends solely on the sequence at hand, and which locates a sequence in a shared coordinate space. What I'd really like are broad-brush clusters that are recognisable enough to say "OK, over there are fish, these are insects, that cluster is molluscs"). I'm guessing this might work if there are clade-specific sequence properties such as base-composition, etc., otherwise, not so much.

Hope this doesn't sound to ridiculous. I'm curious as to whether there's a method for getting a quick sense of the taxonomic composition of a large set of N sequences that doesn't require the N^2 comparisons needed to compare the sequences in order to build a tree.

Posts: 4

Participants: 3

Read full topic

00:13

Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence–absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica—a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga.

00:13

Cellular Ca2+ homeostasis is tightly regulated and is pivotal to life. Inositol 1,4,5-trisphosphate receptors (IP3Rs) and ryanodine receptors (RyRs) are the major ion channels that regulate Ca2+ release from intracellular stores. Although these channels have been extensively investigated in multicellular organisms, an appreciation of their evolution and the biology of orthologs in unicellular organisms is largely lacking. Extensive phylogenetic analyses reveal that the IP3R gene superfamily is ancient and diverged into two subfamilies, IP3R-A and IP3R-B/RyR, at the dawn of Opisthokonta. IP3R-B/RyR further diversified into IP3R-B and RyR at the stem of Filozoa. Subsequent evolution and speciation of Holozoa is associated with duplication of IP3R-A and RyR genes, and loss of IP3R-B in the vertebrate lineages. To gain insight into the properties of IP3R important for the challenges of multicellularity, the IP3R-A and IP3R-B family orthologs were cloned from Capsaspora owczarzaki, a close unicellular relative to Metazoa (designated as CO.IP3R-A and CO.IP3R-B). Both proteins were targeted to the endoplasmic reticulum. However, CO.IP3R-A, but strikingly not CO.IP3R-B, bound IP3, exhibited robust Ca2+ release activity and associated with mammalian IP3Rs. These data indicate strongly that CO.IP3R-A as an exemplar of ancestral IP3R-A orthologs forms bona fide IP3-gated channels. Notably, however, CO.IP3R-A appears not to be regulated by Ca2+, ATP or Protein kinase A-phosphorylation. Collectively, our findings explore the origin, conservation, and diversification of IP3R gene families and provide insight into the functionality of ancestral IP3Rs and the added specialization of these proteins in Metazoa.

00:13

Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, are extremely diverse and universally present in traditional societies. A major focus of research in the early decades of modern anthropology, marriage rules impose social and economic forces that help structure societies and forge connections between them. However, in those early anthropological studies, the biological benefits or disadvantages of marriage rules could not be determined. We revisit this question by applying a novel simulation framework and genome-wide data to explore the effects of Asymmetric Prescriptive Alliance, an elaborate set of marriage rules that has been a focus of research for many anthropologists. Simulations show that strict adherence to these marriage rules reduces genetic diversity on the autosomes, X chromosome and mitochondrial DNA, but relaxed compliance produces genetic diversity similar to random mating. Genome-wide data from the Indonesian community of Rindi, one of the early study populations for Asymmetric Prescriptive Alliance, are more consistent with relaxed compliance than strict adherence. We therefore suggest that, in practice, marriage rules are treated with sufficient flexibility to allow social connectivity without significant degradation of biological diversity.

00:13

The high regulatory complexity of vertebrates has been related to two rounds of whole genome duplication (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families originated during the 2R-WGD contains LCRs. The number of gene duplicates with LCRs is 155 out of 550 analyzed (28%), about twice as many as the number of single copy genes with LCRs (15 out of 115, 13%). In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.

00:13

For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.

00:13

Environmental control of flowering allows plant reproduction to occur under optimal conditions and facilitates adaptation to different locations. At high latitude, flowering of many plants is controlled by seasonal changes in day length. The photoperiodic flowering pathway confers this response in the Brassicaceae, which colonized temperate latitudes after divergence from the Cleomaceae, their subtropical sister family. The CONSTANS (CO) transcription factor of Arabidopsis thaliana, a member of the Brassicaceae, is central to the photoperiodic flowering response and shows characteristic patterns of transcription required for day-length sensing. CO is believed to be widely conserved among flowering plants; however, we show that it arose after gene duplication at the root of the Brassicaceae followed by divergence of transcriptional regulation and protein function. CO has two close homologs, CONSTANS-LIKE1 (COL1) and COL2, which are related to CO by tandem duplication and whole-genome duplication, respectively. The single CO homolog present in the Cleomaceae shows transcriptional and functional features similar to those of COL1 and COL2, suggesting that these were ancestral. We detect cis-regulatory and codon changes characteristic of CO and use transgenic assays to demonstrate their significance in the day-length-dependent activation of the CO target gene FLOWERING LOCUS T. Thus, the function of CO as a potent photoperiodic flowering switch evolved in the Brassicaceae after gene duplication. The origin of CO may have contributed to the range expansion of the Brassicaceae and suggests that in other families CO genes involved in photoperiodic flowering arose by convergent evolution.

00:13

In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA "superbarcodes" for testing hypotheses regarding global patterns of diversity.

00:13

How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations.

00:13

Contrasting with birds and mammals, poikilothermic vertebrates often have homomorphic sex chromosomes, possibly resulting from high rates of sex-chromosome turnovers and/or occasional X–Y recombination. Strong support for the latter mechanism was provided by four species of European tree frogs, which inherited from a common ancestor (~5 Ma) the same pair of homomorphic sex chromosomes (linkage group 1, LG1), harboring the candidate sex-determining gene Dmrt1. Here, we test sex linkage of LG1 across six additional species of the Eurasian Hyla radiation with divergence times ranging from 6 to 40 Ma. LG1 turns out to be sex linked in six of nine resolved cases. Mapping the patterns of sex linkage to the Hyla phylogeny reveals several transitions in sex-determination systems within the last 10 My, including one switch in heterogamety. Phylogenetic trees of DNA sequences along LG1 are consistent with occasional X–Y recombination in all species where LG1 is sex linked. These patterns argue against one of the main potential causes for turnovers, namely the accumulation of deleterious mutations on nonrecombining chromosomes. Sibship analyses show that LG1 recombination is strongly reduced in males from most species investigated, including some in which it is autosomal. Intrinsically low male recombination might facilitate the evolution of male heterogamety, and the presence of important genes from the sex-determination cascade might predispose LG1 to become a sex chromosome.

00:13

Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears (Ursus americanus) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central Interior Highlands, Great Lakes, Northeast, Southeast), and western (Alaska-West, West, Pacific Coast, Southwest). We estimated that the western cluster diverged 67 ka, before eastern and Alaskan divergence 31 ka; these divergence dates contrasted with those from the mitochondrial genome where clades A and B diverged 1.07 Ma, and clades A-east and A-west diverged 169 ka. We combined estimates of divergence timing with hindcast species distribution models to infer glacial refugia for the species in Beringia, Pacific Northwest, Southwest, and Southeast. Our results show a complex arrangement of admixture due to expansion out of multiple refugia. The delineation of the genomic population clusters was inconsistent with the ranges for 16 previously described subspecies. Ranges for U. a. pugnax and U. a. cinnamomum were concordant with admixed clusters, calling into question how to order taxa below the species level. Additionally, our finding that U. a. floridanus has not diverged from U. a. americanus also suggests that morphology and genetics should be reanalyzed to assess taxonomic designations relevant to the conservation management of the species.

00:13

Polyploidy provides evolutionary and morphological novelties in many plants and some animals. However, the role of genome dosage and composition in gene expression changes remains poorly understood. Here, we generated a series of resynthesized Arabidopsis tetraploids that contain 0–4 copies of Arabidopsis thaliana and Arabidopsis arenosa genomes and investigated ploidy and hybridity effects on gene expression. Allelic expression can be defined as dosage dependent (expression levels correlate with genome dosages) or otherwise as dosage independent. Here, we show that many dosage-dependent genes contribute to cell cycle, photosynthesis, and metabolism, whereas dosage-independent genes are enriched in biotic and abiotic stress responses. Interestingly, dosage-dependent genes tend to be preserved in ancient biochemical pathways present in both plant and nonplant species, whereas many dosage-independent genes belong to plant-specific pathways. This is confirmed by an independent analysis using Arabidopsis phylostratigraphic map. For A. thaliana loci, the dosage-dependent alleles are devoid of TEs and tend to correlate with H3K9ac, H3K4me3, and CG methylation, whereas the majority of dosage-independent alleles are enriched with TEs and correspond to H3K27me1, H3K27me3, and CHG (H = A, T, or C) methylation. Furthermore, there is a parent-of-origin effect on nonadditively expressed genes in the reciprocal allotetraploids especially when A. arenosa is used as the pollen donor, leading to metabolic and morphological changes. Thus, ploidy, epigenetic modifications, and cytoplasmic-nuclear interactions shape gene expression diversity in polyploids. Dosage-dependent expression can maintain growth and developmental stability, whereas dosage-independent expression can facilitate functional divergence between homeologs (subfunctionalization and/or neofunctionalization) during polyploid evolution.