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April 22, 2014

10:18

Next-generation sequencing opened up new possibilities in phylogenetics; however, choosing an appropriate method of sample preparation remains challenging. Here, we demonstrate that restriction-site-associated DNA sequencing (RAD-seq) generates useful data for phylogenomics. Analysis of our RAD library using current bioinformatic and phylogenetic tools produced 400x more sites than our Sanger approach (2,262,825 nt/species), fully resolving relationships between 18 species of ground beetles (divergences up to 17 My). This suggests that RAD-seq is promising to infer phylogeny of eukaryotic species, though potential biases need to be evaluated and new methodologies developed to take full advantage of such data.

10:18

We present a new haplotype-based statistic (nSL) for detecting both soft and hard sweeps in population genomic data from a single population. We compare our new method with classic single-population haplotype and site frequency spectrum (SFS)-based methods and show that it is more robust, particularly to recombination rate variation. However, all statistics show some sensitivity to the assumptions of the demographic model. Additionally, we show that nSL has at least as much power as other methods under a number of different selection scenarios, most notably in the cases of sweeps from standing variation and incomplete sweeps. This conclusion holds up under a variety of demographic models. In many aspects, our new method is similar to the iHS statistic; however, it is generally more robust and does not require a genetic map. To illustrate the utility of our new method, we apply it to HapMap3 data and show that in the Yoruban population, there is strong evidence of selection on genes relating to lipid metabolism. This observation could be related to the known differences in cholesterol levels, and lipid metabolism more generally, between African Americans and other populations. We propose that the underlying causes for the selection on these genes are pleiotropic effects relating to blood parasites rather than their role in lipid metabolism.

10:18

We report metrics from complete genome capture of nuclear DNA from extinct mammoths using biotinylated RNAs transcribed from an Asian elephant DNA extract. Enrichment of the nuclear genome ranged from 1.06- to 18.65-fold, to an apparent maximum threshold of ~80% on-target. This projects an order of magnitude less costly complete genome sequencing from long-dead organisms, even when a reference genome is unavailable for bait design.

10:18

Genomic evolution can be highly heterogeneous. Here, we introduce a new framework to simulate genome-wide sequence evolution under a variety of substitution models that may change along the genome and the phylogeny, following complex multispecies coalescent histories that can include recombination, demographics, longitudinal sampling, population subdivision/species history, and migration. A key aspect of our simulation strategy is that the heterogeneity of the whole evolutionary process can be parameterized according to statistical prior distributions specified by the user. We used this framework to carry out a study of the impact of variable codon frequencies across genomic regions on the estimation of the genome-wide nonsynonymous/synonymous ratio. We found that both variable codon frequencies across genes and rate variation among sites and regions can lead to severe underestimation of the global dN/dS values. The program SGWE—Simulation of Genome-Wide Evolution—is freely available from http://code.google.com/p/sgwe-project/, including extensive documentation and detailed examples.

10:18

Mutation is the ultimate source of genetic variation and evolution. Mutation accumulation (MA) experiments are an alternative approach to study de novo mutation events directly. We have constructed a resource of Spontaneous Mutation Accumulation Lines (SMAL; http://cefg.uestc.edu.cn/smal), which contains all the current publicly available MA lines identified by high-throughput sequencing. We have relocated and mapped the mutations based on the most recent genome annotations. A total of 5,608 single base mutations and 540 other mutations were obtained and are recorded in the current version of the SMAL database. The integrated data in SMAL provide detailed information that can be used in new theoretical analyses. We believe that the SMAL resource will help researchers better understand the processes of genetic variation and the incidence of disease.

10:18

With genome sequence and composition highly analogous to human, rhesus macaque represents a unique reference for evolutionary studies of human biology. Here, we developed a comprehensive genomic framework of rhesus macaque, the RhesusBase2, for evolutionary interrogation of human genes and the associated regulations. A total of 1,667 next-generation sequencing (NGS) data sets were processed, integrated, and evaluated, generating 51.2 million new functional annotation records. With extensive NGS annotations, RhesusBase2 refined the fine-scale structures in 30% of the macaque Ensembl transcripts, reporting an accurate, up-to-date set of macaque gene models. On the basis of these annotations and accurate macaque gene models, we further developed an NGS-oriented Molecular Evolution Gateway to access and visualize macaque annotations in reference to human orthologous genes and associated regulations (www.rhesusbase.org/molEvo). We highlighted the application of this well-annotated genomic framework in generating hypothetical link of human-biased regulations to human-specific traits, by using mechanistic characterization of the DIEXF gene as an example that provides novel clues to the understanding of digestive system reduction in human evolution. On a global scale, we also identified a catalog of 9,295 human-biased regulatory events, which may represent novel elements that have a substantial impact on shaping human transcriptome and possibly underpin recent human phenotypic evolution. Taken together, we provide an NGS data-driven, information-rich framework that will broadly benefit genomics research in general and serves as an important resource for in-depth evolutionary studies of human biology.

05:02
Job Posting Number: 34886BR
Job Posting Title: Sr. Ontologist - GBS
Job Posting Category: Business Professional
Work Site: MN - Rochester
Department: Global Business Solutions - Ontology

Job Description
Provide leadership in the development, management and implementation of the Mayo Consumer Vocabulary to support navigation systems, search mechanisms, search engine optimization and personalized delivery of health information and services for Mayo Clinic Global Products and Services. Works collaboratively in cross functional teams to assess ontology needs to support product development across the department. Evaluates content domains, conducts content audits and analysis to inform the ongoing development of the Mayo Consumer Vocabulary. Supervises and directs ontology specialists and manages projects requiring substantial intra-organizational coordination.

Basic Qualifications:
Masters of Library and Information Science (MLIS) or comparable degree in areas such as information systems, knowledge management, or computer science is required. Five years experience in ontology/taxonomy development and management. Proven track record of leading ontology/taxonomy implementation for the complete life cycle of a web product or technology.

Other Qualifications:
Prefer experience with RDF/OWL, SKOS, and SPARQL. Experience evaluating effectiveness of taxonomies/ontologies in supporting products and services. Experience with taxonomy-management systems. Expertise in: information retrieval/search, information organization and classification, and content or entity extraction. Strong analytical skills; experience with both quantitative and qualitative methods desirable. Demonstrated leadership abilities for managing people and projects. Excellent communication and presentation skills.

License or Certification:


Benefit Eligible: Yes
Exemption Status: Exempt
Hours/Pay Period: Full time
Schedule Details:
Weekend Schedule:

Compensation Detail: Education, experience, and tenure may be considered along with internal equity when job offers are extended. The minimum salary every two weeks is approximately $2,551.20 based on a full-time position.

Staffing Specialist: Jessica Larson


Company Statement:
Mayo Clinic provides the highest quality patient care by placing the needs of the patient first. You'll discover a culture of teamwork, professionalism and mutual respect — and most importantly, a life-changing career. We invite you to join our diverse team as we provide health, hope and healing to people from all walks of life.


Mayo Clinic is an equal opportunity educator and employer (including veterans and persons with disabilities).
04:18
Complexity is an important aspect of evolutionary biology, but there are many reasonable concepts of complexity, and its objective measurement is an elusive matter. Here we develop a simple measure of complexity based on counts of elements, incorporating the hierarchical information as represented in anatomical ontologies. Neomorphic and transformational characters are used to identify novelties and individuated morphological regions, respectively. By linking the characters to terms in an anatomical ontology a node-driven approach is implemented, where a node ontology and a complexity score are inferred from the optimization of individual characters on each ancestral or terminal node. From the atomized vector of character scorings, the anatomical ontology is used to integrate the hierarchical structure of morphology in terminals and ancestors. These node ontologies are used to calculate a measure of complexity that can be traced on phylogenetic trees and is harmonious with usual phylogenetic operations. This strategy is compared with a terminal-driven approach, in which the complexity scores are calculated only for terminals, and optimized as a continuous character on the internal nodes. These ideas are applied to a real dataset of 166 araneomorph spider species scored for 393 characters, using Spider Ontology (SPD, https://bioportal.bioontology.org/ontologies/SPD); complexity scores and transitions are calculated for each node and branch, respectively. This result in a distribution of transitions skewed towards simplification; the transitions in complexity have no apparent correlation with character branch lengths. The node-driven and terminal-driven estimations are generally correlated in the complexity scores, but have higher divergence in the transition values. The structure of the ontology is used to provide complexity scores for organ systems and body parts of the focal groups.
Source: Cladistics
01:04
PhD opening The lab of Dr. Eric Hayden at Boise State University is seeking PhD students (and postdocs) to study the molecular evolution of non-protein-coding RNA molecules. Research topics include robustness and evolvability of RNA molecules, empirical RNA fitness landscapes, and experimental evolution of RNA. In addition to traditional molecular biology techniques, the research utilizes next-generation sequencing and provides opportunities for computational biology approaches. Students are encouraged to develop a project to match their learning and career objectives. Students will enter our interdisciplinary Biomolecular Science PhD program designed to offer students the opportunity to take classes and conduct research at the interfaces of Biology, Chemistry and Physics. Mentoring and resources are available from faculty in all three disciplines. Students and postdocs with an interest in developing skills around RNA molecular biology and sequence analysis/computational approaches are encouraged to apply. Previous experience with one of the approaches is preferred, but exceptional applicants without experience will be considered. PhD students will be guaranteed funding throughout their PhD based on a combination of Teaching assistantships and Research Assistantships. The city of Boise offers a unique combination of a very livable urban environment as well as access to numerous outdoor experiences, which landed it as #12 on the Best Places to Live in the U.S.A. (livability.com). Please email a brief description of why you are interested in the position and your past experiences to: erichayden@boisestate.edu Eric J. Hayden Assistant Professor Biological Sciences Boise State University Boise, Idaho, USA 83725 *Office Number*: 208-426-4625 *Office Fax*: 208-426-1040 Eric Hayden via Gmail
Source: EVOLDIR
00:34
HUXLEY FELLOW in ECOLOGY & EVOLUTION: The Ecology and Evolutionary Biology department of Rice University (http://eeb.rice.edu/) seeks to fill a Huxley Fellow position in ECOLOGY or EVOLUTION. The position is a two-year appointment with a third year extension possible, with a start date of July 1, 2014. Our prestigious Huxley Fellow Program aims to recruit outstanding researchers with a PhD and postdoctoral experience, who merge excellence in teaching (25%) and research (75%). The Huxley Fellows receive faculty status, employee benefits, competitive salary, and research funds for independent or collaborative research. Collaborative interests with the existing faculty are a plus and applicants are encouraged to identify a potential faculty host(s) within the EEB department. An application (curriculum vitae, statement of research interests and statement of teaching) and three letters of recommendation should be submitted via e-mail to Diane Hatton, rdh@rice.edu. Please write “Huxley Fellow Application” in the subject line. Application review will begin May, 9, 2014. For further questions and informal inquiries please contact Dr. Volker Rudolf (vr2@rice.edu), Huxley Fellow Search Committee Chair. Rice University is an Equal Opportunity/Affirmative Action Employer and values a diverse faculty. Women and minorities are encouraged to apply. Diane Hatton Project Coordinator Dept of Ecology and Evolutionary Biology Rice University Diane Hatton via Gmail
Source: EVOLDIR
00:04

—Apple-Mail=_03B0D558-7596-4468-A45A-F085144F55E1 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii TEXAS, COLLEGE STATION. Texas A&M University. The Department of Geography invites applications for a non-tenure track Visiting Assistant Professor in Geography with research and teaching interests in landscape genetics and spatial population genetics to begin 1 September 2014. The successful candidate will be required to teach two undergraduate classes per year in the Geography Department and the Environmental Studies Program at Texas A&M University. This position will be responsible for maintaining an active research agenda in coordination with the Biogeography Lab in the Department of Geography. This will include writing proposals, helping with the analysis of genetic/genomic data, and interacting with graduate students. Minimum qualifications include a Ph.D. in Genetics, Bioeography, Landscape Ecology or related discipline. Experience in ecological and landscape genetics and population genetics research is required. Familiarity with bioinformatics, genomics and speci fic software packages for genetics analysis are preferred (e.g. GeneLand, SPAGeDi, STRUCTURE, R). Preference will be given to candidates with experience working in plant population genetics, especially with conifers. The Biogeography Lab at TAMU (http://bit.ly/1jA7dP5) is engaged in using genetics/genomics techniques to investigate gene flow across topographically complex landscapes. One specific project aims to determine the importance of long distance dispersal to the migration potential of the alpine treeline in south central Alaska. More details regarding current and planned research projects are available from Dr. Cairns. The person hired for this position will be expected to work closely with Dr. Cairns to strengthen the landscape genetics research program. The Department of Geography has 20 faculty members with strengths in biogeography, climatology, geomorphology, human geography, human-environment relationships, geographic education and GIST (Geographic Information Science and Technology) (http://bit.ly/1kVjhgK). We are based in the College of Geosciences (http://bit.ly/1jA7e5R) with the Departments of Atmospheric Science, Geology & Geophysics, and Oceanogr aphy, and play a major role in the Environmental Programs in Geosciences. The College of Geosciences also includes Sea Grant, the Geochemical and Environmental Research Group (GERG), and the Integrated Ocean Drilling Program (IODP). Texas A&M University houses the Whole Systems Genomics Initiative (http://bit.ly/1kVjhgP) that provides an intellectually vibrant community and state-of-the-art resources for genomics and bioinformatics research. Texas A&M University, a land-,sea-, and space-grant university, is located in a metropolitan area with a dynamic and international community of 175,000 people. Candidates should submit a letter of application, curriculum vitae, and names and addresses (including e-mail addresses) of three referees to Dr. David Cairns (cairns@tamu.edu) Assistant Department Head, Department of Geography, Texas A&M University, College Station, TX, 77843-3147. We will begin reviewing applications immediately. Texas A&M University is an Affirmative Action/Equal Opportunity Employer committed to excellence through the recruitment and retention of a diverse faculty and student body and compliance with the Americans with Disabilities Act. The University is dedicated to the goal of building a culturally diverse and pluralistic faculty and staff committed to teaching and working in a multicultural environment. We strongly encourage applications from women, underrepresented ethnic groups, veterans, and individuals with disabilities. Texas A&M University also has a policy of being responsive to the needs of dual-career partners (http://bit.ly/1jA7dPj er.html). —Apple-Mail=_03B0D558-7596-4468-A45A-F085144F55E1 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii

TEXAS, COLLEGE STATION. Texas A&M University. The Department of Geography invites applications for a non-tenure track Visiting Assistant Professor in Geography with research and teaching interests in landscape genetics and spatial population genetics to begin 1 September 2014.  The successful candidate will be required to teach two undergraduate classes per year in the Geography Department and the Environmental Studies Program at Texas A&M University.  This position will be responsible for maintaining an active research agenda in coordination with the Biogeography Lab in the Department of Geography.  This will include writing proposals, helping with the analysis of genetic/genomic data, and interacting with graduate students.  Minimum qualifications include a Ph.D. in Genetics, Bioeography, Landscape Ecology or related discipline.  Experience in ecological and landscape genetics and population genetics research is required.  Familiarity with bioinformatics, genomics and specific software packages for genetics analysis are preferred (e.g. GeneLand, SPAGeDi, STRUCTURE, R).  Preference will be given to candidates with experience working in plant population genetics, especially with conifers.

 

The Biogeography Lab at TAMU (http://bit.ly/1jA7dP5) is engaged in using genetics/genomics techniques to investigate gene flow across topographically complex landscapes.  One specific project aims to determine the importance of long distance dispersal to the migration potential of the alpine treeline in south central Alaska.  More details regarding current and planned research projects are available from Dr. Cairns.  The person hired for this position will be expected to work closely with Dr. Cairns to strengthen the landscape genetics research program.  The Department of Geography has 20 faculty members with strengths in biogeography, climatology, geomorphology, human geography, human-environment relationships, geographic education and GIST (Geographic Information Science and Technology) (http://bit.ly/1kVjhgK). We are based in the College of Geosciences (http://bit.ly/1jA7e5R) with the Departments of Atmospheric Science, Geology & Geophysics, and Oceanography, and play a major role in the Environmental Programs in Geosciences. The College of Geosciences also includes Sea Grant, the Geochemical and Environmental Research Group (GERG), and the Integrated Ocean Drilling Program (IODP).  Texas A&M University houses the Whole Systems Genomics Initiative (http://bit.ly/1kVjhgP) that provides an intellectually vibrant community and state-of-the-art resources for genomics and bioinformatics research.  Texas A&M University, a land-,sea-, and space-grant university, is located in a metropolitan area with a dynamic and international community of 175,000 people.

 

Candidates should submit a letter of application, curriculum vitae, and names and addresses (including e-mail addresses) of three referees to Dr. David Cairns (cairns@tamu.edu) Assistant Department Head, Department of Geography, Texas A&M University, College Station, TX, 77843-3147. We will begin reviewing applications immediately. Texas A&M University is an Affirmative Action/Equal Opportunity Employer committed to excellence through the recruitment and retention of a diverse faculty and student body and compliance with the Americans with Disabilities Act. The University is dedicated to the goal of building a culturally diverse and pluralistic faculty and staff committed to teaching and working in a multicultural environment. We strongly encourage applications from women, underrepresented ethnic groups, veterans, and individuals with disabilities. Texas A&M University also has a policy of being responsive to the needs of dual-career partners (http://bit.ly/1kVjiBs).

 

 



—Apple-Mail=_03B0D558-7596-4468-A45A-F085144F55E via Gmail
Source: EVOLDIR

April 21, 2014

22:30

It is always interesting to see what the media make of scientific publications. Some time ago, several of us were involved in a paper in Trends in Genetics advocating the more widespread use of phylogenetic networks (Networks: expanding evolutionary thinking), which seemed mild enough. For example, the Idaho State University press release about the paper made it onto the Phys.Org news site reasonably accurately (Amending the Tree of Life).


However, the Intelligent Design site Evolution News and Views had a different take on things (Demolishing Darwin's Tree), reaching a series of conclusions that might surprise stun the authors of the original Trends in Genetics paper. You will need to read the ID commentary for yourself (and you should, if only for your own education), but the final set of conclusions will give you some of the flavour:
One can only welcome this paper's bold proposal to overturn entrenched dogma ... the "network" diagram seems conducive to ID research inasmuch as it calls into question universal common ancestry via natural selection (i.e., neo-Darwinism), and seeks to portray the evidence honestly ... It's too soon to tell if Darwin security forces will let this band of independent thinkers gather a following. If nothing else, it shows (notwithstanding the insistences of the National Center for Science Education) that insiders know about the fundamental controversies in evolutionary theory, and are calling for some of the same reforms that advocates of intelligent design do.I am not sure that all of these conclusions are logically consistent with the words of the original paper.

02:10
Some interesting threads in TAXACOM today (yes, really). The following article has appeared in Science:
Minteer, B. A., Collins, J. P., Love, K. E., & Puschendorf, R. (2014, April 18). Avoiding (Re)extinction. Science. American Association for the Advancement of Science (AAAS). doi:10.1126/science.1250953 (paywall)The authors argue that "The availability of adequate alternative methods of documentation, including high-resolution photography, audio recording, and nonlethal sampling, provide an opportunity to revisit and reconsider field collection practices and policies."

This has brought a swift response from Kevin Winkler
(Re)affirming the specimen gold standard who argues that physical specimens are vital for much of the science that museum collections support.

At the same time, David Schindel has posted on Minimum standards for e-voucher documentation, that is, DNA samples where no physical voucher exists (e.g., because the organism is a member of an endangered species, or still alive).
Source: iPhylo