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February 14, 2015
Ph.D. applications to work with the wild (feral) horses of Sable Island, Nova Scotia: focus on ecology and evolution and/or conservation. Location: University of Saskatchewan, Saskatoon, Saskatchewan, Canada Closing: Will need to contact me as soon as possible to put together an application for internal scholarship, due Thursday, March 5, 2015. Start date is negotiable, but ideally students would be available July 1 or August 1 for immediate field work. Application for the scholarship will require an application to the U of S College of Graduate Studies and Research (online) well ahead of time, and to meet the deadline for the scholarship applications should be submitted asap (small online fee), i.,e., by early February. Students must have a record of publication in mainstream peer-reviewed journals and GPA of 3.8 or higher (to be competitive for this scholarship opportunity). Apply: Email me a CV and pdf copies of both undergrad and graduate transcripts. Email to firstname.lastname@example.org. Please write Sable Island PhD as the subject line. Description: We are developing a long-term, collaborative individual-based program of research into the ecology and evolution of the feral horses living on Sable Island, Nova Scotia. As part of this initiative, I am looking to recruit a Ph.D. student to ask fundamental questions of the population ecology, life history, behaviour, conservation, and/or evolution of the feral horse population. I am particularly looking for a mature M.Sc. student that is interested in developing a Ph.D. program that will contribute to and make use of the long-term dataset my lab is collecting on the life histories of the horses on the island, and collaborate with geneticists aligned with our program. This summer was the seventh year of data collection, which includes summer censusing and identification of all individuals on the island using digital photography, and documentation of individual life histories with the goal of constructing whole-island pedigrees. Sample sizes are large, with 552 horses alive on the island in Aug 2014. Ph.D. students with 2V3 years of further data collection will be in a position to ask interesting questions regarding the populations mating system, landscape and conservation genetics, individual-based dynamics, band dynamics and dispersal, behaviour and dominance, habitat selection, social networks, sex ratios and sexual selection, and questions involving traits such as intestinal parasite communities, body size and coloration patterns. Trends in the above will likely be related to a very strong and interesting gradient in habitat quality along the length of Sable Island from west to east, associated with availability of preferred forage and access to fresh water (horse density drops by half from west to east). We are also very interested in students with a background in conservation biology as we are currently developing a research theme examining the risks inherent to small populations like that on Sable, including inbreeding depression and demographic stochasticity. Field work on Sable Island is a team effort, and all students must be prepared to contribute to common aspects of field work and assist others with their projects in addition to working on their own research program. The former will include daily walking censuses and photography of horses, identifying individuals from digital photographs, database management, and collection of samples. All projects on the island flow from the individual- based study of the horse population, and contributing to the overall success of each field season is a requirement. For this particular application we are looking for a field team leader, and a demonstrated ability to fill such a role will be considered an asset. The successful student must work well in teams, deal well with life in a remote research station, be able to travel for field work for up to 2 months per summer by small airplane, fishing trawler, helicopter, or frigate; accept the limited diet available in remote field camps (with communal cooking), and be reasonably fit (as walking censuses require lots of hiking). Courses on first aid and driving All Terrain Vehicles will be provided prior to field work. Field work will occur principally in late summer on Sable Island; further information on this field site can be found at my lab website, http://bit.ly/1FK7niB It is important for applicants to be mature enough to develop their own insightful questions. That said, our lab is following several lines of research that potential students may want to build on. Current students are studying or have studied spatial heterogeneity in horse population growth on the island, stress as it relates to band structure and dynamics from cortisol (from hair), parasites, dispersal, body size, condition, patterns in vegetation and successional dynamics, and spatial heterogeneity in isotopic signatures from vegetation samples and animal tissues to develop isoscapes from seal and seabird transfer of marine-derived nutrients onto the island. Students can expect to publish outside of ones own thesis topic as part of whole-lab research questions. Preference will be given to students that aspire to a career in academia and who have a track record that reflects this career goal. In addition to obtaining scholarships, students will be expected to apply for and help secure research funding for their own projects. Students and post-docs with funding in-hand are always welcome. Interested applicants should contact me as soon as possible by email (email@example.com), and be prepared to submit a current CV with copies of transcripts. Website: http://bit.ly/1FK7niB Jocelyn Poissant via Gmail
Two postdoctoral research positions funded by the United States Department of Agriculture are available to work with Dr. Katrina Dlugosch (http://bit.ly/LzSdpW) and Dr. David Baltrus (http://bit.ly/1CrC9t6) at the University of Arizona on the ecological genomics of microbial interactions with the invasive plant yellow starthistle (Centaurea solstitialis). We are investigating the evolution of species interactions during range expansion and their impact on the spread of invading populations, and we are seeking postdoctoral researchers with interests and experience in these areas. One successful candidate will be responsible for next-generation genomic sequence generation and bioinformatic analyses, particularly by 1) surveying plant-associated microbial communities in the native (European) and invaded (North American) ranges of yellow starthistle, using 16S metagenomics and culture-based sequencing of field-collected specimens, and 2) quantifying rates of gene flow across the genome in invading plant populations using a high-throughput RADseq next-generation approach. Preferred start date in May 2015. To apply, submit a statement of interest and curriculum vitae to job #57623 at http://bit.ly/1mVZX4x A second successful candidate will be responsible for 1) mapping QTL associated with the genetic basis of variation in resistance to bacterial pathogens using large-scale greenhouse experiments and genome-wide RADseq markers, and 2) quantifying population-level impacts of infection using phenotypic data collection in combination with existing demographic models in collaboration with Dr. Sarah Swope (Mills College). Preferred start date in late 2015 or early 2016. To apply, submit a statement of interest and curriculum vitae to job #57624 at http://bit.ly/1mVZX4x Positions are for one year, with reappointment for up to two additional years subject to satisfactory performance. Review of applications will begin March 2, 2015 and continue until filled. Minimum qualifications *PhD in Biology or a related field *Authorship of peer-reviewed publications of research in a field related to the position *Strong communication skills *Ability to work independently and in a team Preferred Qualifications (Applicants without these skills will be considered): *Experience producing and analyzing molecular genetic data, particularly next-generation genomic data *Experience culturing bacterial colonies *Experience rearing plants under standard greenhouse conditions *Experience collecting and documenting field specimens Inquiries about the positions may be directed to Dr. Katrina Dlugosch (firstname.lastname@example.org). Katrina M. Dlugosch, Assistant Professor Ecology & Evolutionary Biology, University of Arizona email@example.com | http://bit.ly/LzSdpW firstname.lastname@example.org via Gmail
THE UNIVERSITY OF HUDDERSFIELD: DEPARTMENT OF BIOLOGICAL SCIENCES, SCHOOL OF APPLIED SCIENCES The Leverhulme Trust Doctoral Scholarship Centre in Evolutionary Genomics Supervisors: Professor Martin B. Richards, Dr Maria Pala, Dr Martin Carr, Dr Stefano Vanin Five PhD Studentships in Evolutionary Genomics Closing date for applications: March 31st, 2015 Funding availability: Funded PhD projects for UK/EU students We are seeking the first cohort of five PhD scholars in Evolutionary Genetics for the new Leverhulme Trust Centre at Huddersfield, to begin in October 2015. The scholars will receive training from leading experts in their respective fields and undertake cutting-edge research in archaeogenetics, palaeogenetics, bioinformatics, genomics, next-generation DNA sequencing, phylogenetics, population genetics, human evolution and forensic analysis. We envision openings this year in the archaeogenetics of Europe, Southeast Asia/ Pacific and Native Americans, working with mitochondrial DNA, Y-chromosome and genome-wide variation (including ancient DNA), and in forensic analysis on molecular insect identification from South American and European archaeological burials. In eukaryotic evolution, research work will include the evolution of fungal genomes and transposable element families. The students will work in the new molecular biology/ancient DNA facilities at Huddersfield, alongside existing students in all of these areas and two research fellows who will provide day to day guidance, along with the academic staff. Applicants should hold a good first degree (and preferably also an MSc or MA) in Genetics, Molecular Biology, Statistics, Computing, Bioarchaeology, Biological Anthropology, or other relevant subject, and ideally have experience of generic biological lab techniques such as DNA extraction and PCR. For the insect-related project, a general knowledge of general entomology/zoology and invertebrate morphology is required. Although training and hands-on supervision will be provided, it is essential that the candidates can operate independently and take the initiative to direct their research. The studentship will cover the full cost of tuition fees for UK/EU students, and will pay an annual tax-free bursary of 14,057 for three years (RCUK rates). There are additional funds available for laboratory consumables and travel for conferences, visits to collaborating laboratories and sample procurement. To apply, please go to: http://bit.ly/1zTzGKN and complete the on-line application, ensuring you select full-time PhD Biology. Please type ‘Leverhulme Trust’ in the ‘Personal Statement’ field. Please then email your CV, transcripts and two letters of recommendation in support of your application to Professor Richards (email: email@example.com). Please indicate in your email which supervisor and kind of project you are interested in, and why you believe you are well-qualified for that project. For informal enquiries please contact: Archaeogenetics: Professor Richards on +44 (0)1484 471676 (email firstname.lastname@example.org) or Dr Maria Pala on +44 1484 472273 (email@example.com) Eukaryotic evolution: Dr Martin Carr on +44 (0)1484 471608 (firstname.lastname@example.org) Forensic entomology/funerary archaeology: Dr Stefano Vanin on +44 (0)1484 473179 (email@example.com) Related web links: http://bit.ly/1zTzGKP http://bit.ly/174wf8R http://bit.ly/1zTzJWY University of Huddersfield inspiring tomorrow’s professionals. [http://bit.ly/1zTzJX0] This transmission is confidential and may be legally privileged. If you receive it in error, please notify us immediately by e-mail and remove it from your system. If the content of this e-mail does not relate to the business of the University of Huddersfield, then we do not endorse it and will accept no liability. via Gmail
—============_-788274450==_ma===========Content-Type: text/plain; charset=”iso-8859-1” ; format=”flowed” Content-Transfer-Encoding: quoted-printable Ph.D.: sexual selection in kangaroos. I am looking for a student interested in exploring the determinants of mating skew and reproductive success in male eastern grey kangaroos. The project will combine two three-months seasons of fieldwork in southern Victoria, Australia, with analysis of an existing 7-year database including ecological and morphological measurements and over 500 identified paternities in two populations. Over 1200 kangaroos have been marked and sampled, they are habituated and easy to observe. Nearly all individuals are recaptured each year, to measure changes in mass and size in this species with indeterminate growth. Applicants should have a M.Sc. degree, strong quantitative skills and experience in fieldwork. Previous experience with DNA analyses and quantitative genetics would be an asset. A scholarship of Can$ 19,000 a year for 3.5 years is available. Holders of or strong candidates for external scholarships will be preferred. The research will be conducted in collaboration with Dany Garant at the Universit de Sherbrooke and Graeme Coulson at the University of Melbourne. The Universit de Sherbrooke is a francophone institution, therefore either some knowledge of French or an interest in learning it are essential. If you are interested, e-mail me explaining why you want to do this research and why I should be interested in you, with a CV and the e-mails of two people able to evaluate your potential as a researcher. The program could start in May or in September 2015. Marco Festa-Bianchet m.festa@Usherbrooke.ca See http://bit.ly/1yAkux9 and http://bit.ly/1uTevIC for more information —============_-788274450==_ma===========Content-Type: text/html; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable
Graduate position in macro-evolution / systematics / macro-ecology in Zurich. The Cape flora of South Africa is arguably the most species-rich temperate flora, and this richness is expressed at both local (alpha-diversity) and regional (gamma-diversity) level. Much of this diversity was generated in a small number of radiations, consequently many closely related species co-exist. We will explore the traits that allow such co-existence. This research involves, inter alia, phylogeny reconstructions (in order to explore phylogenetic community assembly and phylogenetic beta-diversity), anatomical-morphological research (to compare the traits of co-existing species), eco-physiological experimentation, and field work. The work will be supervised by Peter Linder (firstname.lastname@example.org), and will be based in the Institute of Systematic Botany of the University of Zurich (http://bit.ly/1jNq6NX ). These projects are part of a research program using the Cape flora as test case to investigate the evolution of plant diversity. Successful candidates will have a Masters degree in botany / plant sciences and a valid drivers licence. Interested candidates should send Peter Linder their CV’s, the names of three potential referees, and a motivativion letter detailing why you are interested in this research. Peter Linder Institute of Systematic Botany University of Zurich Zollikerstrasse 107 CH-8008 Zurich Switzerland Email: email@example.com Peter Linder via Gmail
*Evolution and Cancer conference – Montpellier, March 19th 2015* Please join us at a one day conference on “Evolution and Cancer” at the Université de Montpellier 2. The conference is sponsored by the CNRS research consortium DarEvCan (http://bit.ly/1yXcGLl). The objective of the conference is to foster discussion on evolutionary perspectives to understanding cancer emergence, progression and therapies. The conference will include speakers from the Centre for Evolution and Cancer ( http://bit.ly/1F8WHNd and-cancer). The preliminary programme can be found at this link: *Programme* If you wish to attend, then please register by email (please put: “ Registration DarEvCan” in the subject header) to firstname.lastname@example.org -* Registration closes on February 16th.* Scientific committee: Pr Eric Solary (Institut Gustave Roussy), Pr. Ula Hibner (Institut de Génétique Moléculaire de Montpellier) and Pr. Michael Hochberg (Institut de Sciences de l’Evolution) Michael Hochberg via Gmail
February 13, 2015
The Ecology lab at the University of Konstanz (the group of Mark van Kleunen) and the lab of Biodiversity Research/Systematic Botany (the group of Jasmin Joshi) at the University of Potsdam are seeking to fill two 3-year PhD positions in a DFG-funded project on the role of epigenetic inheritance in rapid evolutionary adaptation of invasive plants. The PhD students will do common-garden experiments and molecular-marker studies using plants from invasive /Solidago canadensis /and /Solidago gigantea/ populations, and will do reciprocal transplant experiments with multiple invasive and native species. One of the PhD students will be based in Konstanz and the other one in Potsdam Applicants should have a deep interest in plant invasions, plant evolutionary ecology and evolution and hold a Master degree (or equivalent) in the relevant research fields (e.g. plant ecology, evolution). Applicants are expected to have relevant laboratory experience, and an interest in the design and analysis of ecological experiments. This position requires strong communication skills and strong writing and statistical skills (preferably in R).The salary will be at 65% of scale 13 TV-L. The latest starting date is 1 May 2015. The University of Konstanz is one of the Universities of Excellence in the Federal Republic of Germany, and is located on a small campus just outside the beautiful university town of Konstanz , which is at the shore of Lake Constance. The Ecology group is young and very international, and works on a diverse set of topics, including among others mating system evolution, plant responses to global change and determinants of plant invasiveness. The University of Potsdam is a young and dynamic university and an equal opportunity employer. Potsdam is a beautiful and green city close to the German capital of Berlin. The Biodiversiy Research/Systematic Botany group works on a diverse set of topics such as plant adaptation to novel environmental conditions, coexistence mechanisms in plant populations and the relationship between biodiversity and ecosystem functions. If equally qualified, disabled applicants will be considered preferentially. We aim at increasing the number of female researchers and encourage qualified women to apply. The University of Potsdam and the University of Konstanz make an effort to assist its members in family-related issues. The University of Potsdam has been repeatedly awarded the Total E-quality award, and the University of Konstanz has been certified by the Hertie Foundation to be a family-friendly institution. If you are interested in one of these positions, please, send a letter of motivation (also indicate whether you would prefer the position in Konstanz or the one in Potsdam or do not have a preference), a CV, a writing sample (for example part of your MSc or Bachelor thesis or a paper), and the contact details of two references to email@example.com. Please, merge all these documents into *a single PDF* file, and include your name in the file name. The *application deadline *is *15 March 2015*. Mark van Kleunen Mark van Kleunen via Gmail
Background: Sperm competition imposes a strong selective pressure on males, leading to the evolution of various physiological, morphological and behavioral traits. Sperm competition can be prevented by blocking or impeding the access to female genitalia by means of a mating plug. We investigated the factors responsible for plug production and function in the promiscuous female-cannibalistic spider Micaria sociabilis (Gnaphosidae). Results: We performed mating trials using females with and without a plug that consists of an amorphous mass. The mating trials demonstrated that the probability of male plugging increased non-linearly with the duration of copulation. Copulation duration and plug production seem to be controlled by the female. We found that females terminated matings later if males were fast at genital coupling. Whereas incomplete plugs had disappeared on the day following copulation, complete plugs persisted (40%). In matings with females with complete plugs, only a small proportion of males (7%) were able to remove the plug, indicating the high effectiveness of plugging. Moreover, males ceased attempts to copulate with plugged females with higher probability. 3D X-ray microscopy of the female and male genitalia showed that the plug material can extend far into the female genital tract and that the plug material is produced by a massive gland inside the palpal organ of the modified male pedipalps. Conclusions: Our study demonstrates that the mating plug in M. sociabilis constitutes an effective male strategy to avoid sperm competition that seems to be under female control.
Source: BMC Evolutionary Biology
Population Diversity and Adaptive Evolution in Keratinization Genes: Impact of Environment in Shaping Skin Phenotypes
Several studies have demonstrated the role of climatic factors in shaping skin phenotypes, particularly pigmentation. Keratinization is another well-designed feature of human skin, which is involved in modulating transepidermal water loss (TEWL). Although this physiological process is closely linked to climate, presently it is not clear whether genetic diversity is observed in keratinization and whether this process also responds to the environmental pressure. To address this, we adopted a multipronged approach, which involved analysis of 1) copy number variations in diverse Indian and HapMap populations from varied geographical regions; 2) genetic association with geoclimatic parameters in 61 populations of dbCLINE database in a set of 549 genes from four processes namely keratinization, pigmentation, epidermal differentiation, and housekeeping functions; 3) sequence divergence in 4,316 orthologous promoters and corresponding exonic regions of human and chimpanzee with macaque as outgroup, and 4) protein sequence divergence (Ka/Ks) across nine vertebrate classes, which differ in their extent of TEWL. Our analyses demonstrate that keratinization and epidermal differentiation genes are under accelerated evolution in the human lineage, relative to pigmentation and housekeeping genes. We show that this entire pathway may have been driven by environmental selection pressure through concordant functional polymorphisms across several genes involved in skin keratinization. Remarkably, this underappreciated function of skin may be a crucial determinant of adaptation to diverse environmental pressures across world populations.
Late Pleistocene Australian Marsupial DNA Clarifies the Affinities of Extinct Megafaunal Kangaroos and Wallabies
Understanding the evolution of Australia’s extinct marsupial megafauna has been hindered by a relatively incomplete fossil record and convergent or highly specialized morphology, which confound phylogenetic analyses. Further, the harsh Australian climate and early date of most megafaunal extinctions (39–52 ka) means that the vast majority of fossil remains are unsuitable for ancient DNA analyses. Here, we apply cross-species DNA capture to fossils from relatively high latitude, high altitude caves in Tasmania. Using low-stringency hybridization and high-throughput sequencing, we were able to retrieve mitochondrial sequences from two extinct megafaunal macropodid species. The two specimens, Simosthenurus occidentalis (giant short-faced kangaroo) and Protemnodon anak (giant wallaby), have been radiocarbon dated to 46–50 and 40–45 ka, respectively. This is significantly older than any Australian fossil that has previously yielded DNA sequence information. Processing the raw sequence data from these samples posed a bioinformatic challenge due to the poor preservation of DNA. We explored several approaches in order to maximize the signal-to-noise ratio in retained sequencing reads. Our findings demonstrate the critical importance of adopting stringent processing criteria when distant outgroups are used as references for mapping highly fragmented DNA. Based on the most stringent nucleotide data sets (879 bp for S. occidentalis and 2,383 bp for P. anak), total-evidence phylogenetic analyses confirm that macropodids consist of three primary lineages: Sthenurines such as Simosthenurus (extinct short-faced kangaroos), the macropodines (all other wallabies and kangaroos), and the enigmatic living banded hare-wallaby Lagostrophus fasciatus (Lagostrophinae). Protemnodon emerges as a close relative of Macropus (large living kangaroos), a position not supported by recent morphological phylogenetic analyses.
Trans-Splicing and Operons in Metazoans: Translational Control in Maternally Regulated Development and Recovery from Growth Arrest
Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced-leader (SL) RNA. Trans-splicing also occurs at monocistronic transcripts. The phlyogenetically sporadic appearance of trans-splicing and operons has made the driving force(s) for their evolution in metazoans unclear. Previous work has proposed that germline expression drives operon organization in Caenorhabditis elegans, and a recent hypothesis proposes that operons provide an evolutionary advantage via the conservation of transcriptional machinery during recovery from growth arrested states. Using a modified cap analysis of gene expression protocol we mapped sites of SL trans-splicing genome-wide in the marine chordate Oikopleura dioica. Tiled microarrays revealed the expression dynamics of trans-spliced genes across development and during recovery from growth arrest. Operons did not facilitate recovery from growth arrest in O. dioica. Instead, we found that trans-spliced transcripts were predominantly maternal. We then analyzed data from C. elegans and Ciona intestinalis and found that an enrichment of trans-splicing and operon gene expression in maternal mRNA is shared between all three species, suggesting that this may be a driving force for operon evolution in metazoans. Furthermore, we found that the majority of known terminal oligopyrimidine (TOP) mRNAs are trans-spliced in O. dioica and that the SL contains a TOP-like motif. This suggests that the SL in O. dioica confers nutrient-dependent translational control to trans-spliced mRNAs via the TOR-signaling pathway. We hypothesize that SL-trans-splicing provides an evolutionary advantage in species that depend on translational control for regulating early embryogenesis, growth and oocyte production in response to nutrient levels.
Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.
MicroRNAs (miRNAs) mediate gene regulation posttranscriptionally through pairing of their seed (2–7 nt) to 3'-untranslated regions (3'-UTRs) or coding regions (coding sequences [CDSs]) of their target genes. CDS target sites generally show weaker repression effects than 3'-UTR sites. However, little is known about the conservation of the function, that is, repression effect, for these two groups of target sites. In addition, no systematic analysis of the evolutionary constraint on CDS sites exists to date. To address these questions, we performed RNA-sequencing to quantify the regulatory effect of miR-15a/miR-16 and miR-92a on their CDS and 3'-UTR targets in human and macaque cells. These miRs were knocked down transiently so the repression effect could be tracked immediately. Although on average CDS targets are less derepressed than 3'-UTR targets in both species, both the 3'-UTR targets and the CDS targets are functionally conserved. The evolutionary analysis of miRNA target sites shows that CDS sites are more conserved than nontarget control, albeit to a lesser extent than 3'-UTR sites. In conclusion, CDS target sites are functional, even though they are subject to less functional constraint than 3'-UTR target sites.
Mitochondrial genomes of lycophytes are surprisingly diverse, including strikingly different transfer RNA (tRNA) gene complements: No mitochondrial tRNA genes are present in the spikemoss Selaginella moellendorffii, whereas 26 tRNAs are encoded in the chondrome of the clubmoss Huperzia squarrosa. Reinvestigating the latter we found that trnL(gag) and trnS(gga) had never before been identified in any other land plant mitochondrial DNA. Sensitive sequence comparisons showed these two tRNAs as well as trnN(guu) and trnS(gcu) to be very similar to their respective counterparts in chlamydial bacteria. We identified homologs of these chlamydial-type tRNAs also in other lycophyte, fern, and gymnosperm DNAs, suggesting horizontal gene transfer (HGT) into mitochondria in the early vascular plant stem lineages. These findings extend plant mitochondrial HGT to affect individual tRNA genes, to include bacterial donors, and suggest that Chlamydiae on top of their recently proposed key role in primary chloroplast establishment may also have participated in early tracheophyte genome evolution.
Zebrafish (Danio rerio) is an important model for vertebrate development, genomics, physiology, behavior, toxicology, and disease. Additionally, work on numerous Danio species is elucidating evolutionary mechanisms for morphological development. Yet, the relationships of zebrafish and its closest relatives remain unclear possibly due to incomplete lineage sorting, speciation with gene flow, and interspecies hybridization. To clarify these relationships, we first constructed phylogenomic data sets from 30,801 restriction-associated DNA (RAD)-tag loci (483,026 variable positions) with clear orthology to a single location in the sequenced zebrafish genome. We then inferred a well-supported species tree for Danio and tested for gene flow during the diversification of the genus. An approach independent of the sequenced zebrafish genome verified all inferred relationships. Although identification of the sister taxon to zebrafish has been contentious, multiple RAD-tag data sets and several analytical methods provided strong evidence for Danio aesculapii as the most closely related extant zebrafish relative studied to date. Data also displayed patterns consistent with gene flow during speciation and postspeciation introgression in the lineage leading to zebrafish. The incorporation of biogeographic data with phylogenomic analyses put these relationships in a phylogeographic context and supplied additional support for D. aesculapii as the sister species to D. rerio. The clear resolution of this study establishes a framework for investigating the evolutionary biology of Danio and the heterogeneity of genome evolution in the recent history of a model organism within an emerging model genus for genetics, development, and evolution.
Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale resequencing studies have shown an abundance of rare variation in humans, which may be particularly useful for making inferences of fine-scale population structure. To this end, we used an information theory framework and extensive coalescent simulations to rigorously quantify the informativeness of rare and common variation to detect signatures of fine-scale population structure. We show that rare variation affords unique insights into patterns of recent population structure. Furthermore, to empirically assess our theoretical findings, we analyzed high-coverage exome sequences in 6,515 European and African American individuals. As predicted, rare variants are more informative than common polymorphisms in revealing a distinct cluster of European–American individuals, and subsequent analyses demonstrate that these individuals are likely of Ashkenazi Jewish ancestry. Our results provide new insights into the population structure using rare variation, which will be an important factor to account for in rare variant association studies.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology