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August 21, 2014
The Lakehead University Paleo-DNA Laboratory Practical DNA Training Program. Please post the following information about the training program on the EvolDir website and direct it towards evolutionary biologists: Practical DNA Training Program: A two-week (9 business days) intensive laboratory-based training program designed to teach participants the fundamentals of molecular techniques including DNA extraction, amplification (using PCR), sequencing and interpretation. This training program is offered at various times throughout the year and we will work with you to find a suitable time for training. The next two scheduled courses for the Practical DNA Training Program are October 14 - 24, 2014 and November 10 - 20, 2014. For more information please contact us at 807-343-8877 or firstname.lastname@example.org or visit our website www.ancientdna.com and click on ‘Training Programs’. Thank you. Karen. Karen Maa Administrative Assistant Paleo-DNA Laboratory 1294 Balmoral Street, 3rd Floor Thunder Bay, Ontario P7B 5Z5 Telephone: 1-866-DNA-LABS or 1-807-343-8616 Karen Maa via Gmail
The implications of a Silurian and other thylacocephalan crustaceans for the functional morphology and systematic affinities of the group
Background: Thylacocephala is a group of enigmatic extinct arthropods. Here we provide a full description of the oldest unequivocal thylacocephalan, a new genus and species Thylacares brandonensis, which is present in the Silurian Waukesha fauna from Wisconsin, USA. We also present details of younger, Jurassic specimens, from the Solnhofen lithographic limestones, which are crucial to our interpretation of the systematic position of Thylacocephala. In the past, Thylacocephala has been interpreted as a crustacean ingroup and as closely related to various groups such as cirripeds, decapods or remipeds. Results: The Waukesha thylacocephalan, Thylacares brandonensis n. gen. n. sp., bears compound eyes and raptorial appendages that are relatively small compared to those of other representatives of the group. As in other thylacocephalans the large bivalved shield encloses much of the entire body. The shield lacks a marked optical notch. The eyes, which project just beyond the shield margin, appear to be stalked. Head appendages, which may represent antennulae, antennae and mandibles, appear to be present. The trunk is comprised of up to 22 segments. New details observed on thylacocephalans from the Jurassic Solnhofen lithographic limestones include antennulae and antennae of Mayrocaris bucculata, and endites on the raptorial appendages and an elongate last trunk appendage in Clausocaris lithographica. Preserved features of the internal morphology in C. lithographica include the muscles of the raptorial appendage and trunk. Conclusions: Our results indicate that some ‘typical’ thylacocephalan characters are unique to the group; these autapomorphies contribute to the difficulty of determining thylacocephalan affinities. While the new features reported here are consistent with a eucrustacean affinity, most previous hypotheses for the position of Thylacocephala within Eucrustacea (as Stomatopoda, Thecostraca or Decapoda) are shown to be unlikely. A sister group relationship to Remipedia appears compatible with the observed features of Thylacocephala but more fossil evidence is required to test this assertion. The raptorial appendages of Thylacocephala most likely projected 45 degrees abaxially instead of directly forward as previously reconstructed. The overall morphology of thylacocephalans supports a predatory mode of life.
Source: BMC Evolutionary Biology
—_000_87FCC0D1FF47BB4E8B42E4989C746A862B9E0C80EXCHMBOX6exchuc_ Content-Type: text/plain; charset=”Windows-1252” Content-Transfer-Encoding: quoted-printable Position Description A postdoctoral position is available in the Department of Entomology at the University of California Riverside to work on the genetic and molecular basis of insecticide resistance in glassy winged sharpshooter (GWSS) - the primary vector of the bacteria Xylella fastidiosa, which causes Pierce’s Disease in grapevines. Recent insecticidal control failures and corresponding surges in GWSS numbers have raised serious concerns about the status of insecticide susceptibility in Californian populations of GWSS. The successful candidate will (1) determine the current resistance status of GWSS in California agricultural and nursery settings, (2) elucidate the genetic and molecular underpinnings of any resistance, and (3) design tools and assays for use in an integrated insecticide resistance management plan. Additionally, the postdoc is encouraged to develop new lines of work (e.g. population genomics, ecological modeling, etc.) on GWSS. The project, funded by the California Department of Food and Agriculture, is a collaborative effort headed by Drs. Frank Byrne, Rick Redak, and Bradley White. The postdoc will be supervised by Dr. White, but will also work closely with the other PIs. After completion of the project, the postdoc will have substantial experience designing and conducting bioassays, analyzing next-generation sequencing data, and communicating policy recommendations to growers. As such, the position represents an excellent opportunity to acquire a unique combination of skills that serve as good training for various positions in academia, industry, and government. We are looking for someone with expertise in evolutionary biology, insect ecology, vector biology, insect toxicology, and/or agricultural entomology. Familiarity with next-generation sequencing analysis is a positive, but not required. Regardless of prior experience, we expect the candidate to develop a wide-knowledge base and skillset. The position is for one year with the possibility of renewal for up to three years total. Salary will be commensurate with experience level. For additional information about the White Laboratory please navigate to http://bit.ly/17xDZQ5 To Apply A minimum qualification is a PhD or equivalent in Biology, Entomology, or a related discipline. Applicants with multiple, first-author publications are preferred. To apply, please send a brief description of previous research (1 page), a CV, and contact information for three references to email@example.com. A start date in Fall 2014 is ideal, but negotiable. Position is open until filled. Additional Information The White Lab is housed in the relatively new Entomology Building at UCR. We have access to state of the art genomic and bioinformatics core facilities and are part of the Center for Disease Vector Control (CDVR), which is composed of a diverse and highly talented group of scientists studying insect vectors of animal, human, and plant diseases. Substantial resources for field experiments are available through the Agricultural Experiment Station (AES) facilities. UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity. AA/EOE Bradley J. White Assistant Professor Center for Disease Vector Research Department of Entomology University of California Riverside, CA 92521 —_000_87FCC0D1FF47BB4E8B42E4989C746A862B9E0C80EXCHMBOX6exchuc_ Content-Type: text/html; charset=”Windows-1252” Content-Transfer-Encoding: quoted-printable
A postdoctoral position is available in the Department of Entomology at the University of California Riverside to work on the genetic and molecular basis of insecticide resistance in glassy winged sharpshooter (GWSS) - the primary vector of the bacteria Xylella fastidiosa, which causes Pierce’s Disease in grapevines. Recent insecticidal control failures and corresponding surges in GWSS numbers have raised serious concerns about the status of insecticide susceptibility in Californian populations of GWSS. The successful candidate will (1) determine the current resistance status of GWSS in California agricultural and nursery settings, (2) elucidate the genetic and molecular underpinnings of any resistance, and (3) design tools and assays for use in an integrated insecticide resistance management plan. Additionally, the postdoc is encouraged to develop new lines of work (e.g. population genomics, ecological modeling, etc.) on GWSS.
The project, funded by the California Department of Food and Agriculture, is a collaborative effort headed by Drs. Frank Byrne, Rick Redak, and Bradley White. The postdoc will be supervised by Dr. White, but will also work closely with the other PIs. After completion of the project, the postdoc will have substantial experience designing and conducting bioassays, analyzing next-generation sequencing data, and communicating policy recommendations to growers. As such, the position represents an excellent opportunity to acquire a unique combination of skills that serve as good training for various positions in academia, industry, and government.
We are looking for someone with expertise in evolutionary biology, insect ecology, vector biology, insect toxicology, and/or agricultural entomology. Familiarity with next-generation sequencing analysis is a positive, but not required. Regardless of prior experience, we expect the candidate to develop a wide-knowledge base and skillset. The position is for one year with the possibility of renewal for up to three years total. Salary will be commensurate with experience level.
For additional information about the White Laboratory please navigate to http://bit.ly/17xDZQ5
A minimum qualification is a PhD or equivalent in Biology, Entomology, or a related discipline. Applicants with multiple, first-author publications are preferred. To apply, please send a brief description of previous research (1 page), a CV, and contact information for three references to firstname.lastname@example.org. A start date in Fall 2014 is ideal, but negotiable. Position is open until filled.
The White Lab is housed in the relatively new Entomology Building at UCR. We have access to state of the art genomic and bioinformatics core facilities and are part of the Center for Disease Vector Control (CDVR), which is composed of a diverse and highly talented group of scientists studying insect vectors of animal, human, and plant diseases. Substantial resources for field experiments are available through the Agricultural Experiment Station (AES) facilities.
UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity. AA/EOE
Bradley J. White
Center for Disease Vector Research
Department of Entomology
University of California
Riverside, CA 92521—_000_87FCC0D1FF47BB4E8B42E4989C746A862B9E0C80EXCHMBOX6exchuc via Gmail
Postdoctoral position in Systematics and Evolution A two-year postdoctoral position in Systematics and Evolution is available in the Department of Zoology, Swedish Museum of Natural History, Stockholm. Project description “Species-level phylogeny and delimitation in a biodiversity hotspot” Madagascar is well known for its high level of endemism, basically across every organism group. The combination with severe habitat degradation has “rewarded” the island with a top placement among biodiversity hotspots. The increased evolutionary research interest last twenty years has focused on vertebrates and surprisingly little is yet known about the colonization and speciation history of most insect groups. Using Hydradephagan water beetles as model organisms this project will use dated phylogenetic frameworks to analyze colonization and speciation patterns across replicated endemic radiations and clades with representatives but seemingly without radiations. Intraspecific genetic variation will be sampled to estimate parameters in the multispecies coalescent model as a window into the speciation process. The project also includes evaluation of species delimitation methods on endemic radiations with non-reciprocally monophyletic species in gene-trees. Tasks The position is part of a research project and group (Bergsten Systematic Entomology Lab: http://bit.ly/1uZz1FZ) at the Swedish Museum of Natural History on the taxonomy, faunistics, phylogeny, colonization, speciation and evolutionary history of Hydradephagan water beetles on Madagascar. The work includes DNA labwork, fieldwork, data analyses, help with supervision of student projects, article- and grant writing. The DNA labwork will be conducted at the Molecular Systematics Laboratory at the Swedish Museum of Natural History. Qualifications To be qualified for the postdoctoral position the applicant needs to have a PhD degree (or have a PhD thesis ready with a date fixed within 2014 for thesis defense) in Systematics/Phylogenetics/Evolutionary Biology or similar direction of studies. The PhD degree should have been received no more than six years before the deadline for applications. Criteria for selection Among qualified applicants selection is made according to scientific merits, quality of the PhD thesis, personal skills, the applicant´s documented knowledge in subjects of relevance for the research area, ability to master English language (both spoken and written), analytical ability, creativity, initiative, independence, teamwork and ability to cooperate. Previous experience with molecular (DNA) lab work and knowledge of relevant theory and methods (phylogenetic, dating, species delimitation, biogeographic and diversification rate analyses) weigh heavily. Experience with entomological fieldwork, taxonomic work and French language (spoken in Madagascar) are consider as additional qualifications. Terms of employment The position is for two years full time. Start of position should be in 2014 but exact date up to negotiation with the successful candidate. The position is financed by a grant from the Swedish Research Council, VR. For more information, please contact Johannes Bergsten (email@example.com). Union representative is Bodil Kajrup, SACO-S. Both can be reached at telephone number + 46 8 519 540 00. To be included in the application Maximum one A4-page of personal presentation and your reasons for applying (letter of intent). Curriculum vitae with publication list. Copy of three selected publications. Copy of PhD thesis and PhD degree certificate or date of scheduled defense within 2014. Also provide a list of two persons who may act as references (with telephone numbers and e-mail addresses). Please send your application, marked with dnr 2.3.1-603-2014, to firstname.lastname@example.org or to Swedish Museum of Natural History, P. O. Box 50007, SE-104 05 Stockholm, Sweden, no later than September 9, 2014. Johannes Bergsten, PhD Senior Curator / Förste Intendent Research Division Swedish Museum of Natural History Box 50007 SE-104 05 Stockholm SWEDEN Visiting Address: Frescativägen 40 Phone: +46 8 5195 4192 Fax: +46 8 5195 4212 E-mail: email@example.com http://bit.ly/1AA3fQ2 Johannes Bergsten via Gmail
The Washington Area Phylogenetics Consortium is pleased to announce the Fourth annual Frontiers in Phylogenetics Symposium “Genome-Scale Phylogenetics: Analysing the Data” Sponsored by the National Museum of Natural History, Smithsonian Institution, and the Washington Area Phylogenetics Consortium Location: Warner Brothers Theatre, National Museum of American History, Washington, DC Time and Date: 9 AM to 5 PM, Monday September 15, 2014 REGISTRATION IS FREE BUT REQUIRED. Please visit the link below to register. http://bit.ly/FIPSymposium 8:00 Coffee and Continental Breakfast Service in Constitution Café 9:00 Introductions Michael Braun, National Museum of Natural History 9:05 Welcome to the Smithsonian John Kress, Interim Undersecretary for Science, Smithsonian Institution 9:15 Overview and Logistics Guillermo Ortí, George Washington University 9:25 Phylogenomics and Next-Generation Inferences: the Future of Phylogenetics in an Era of Big Data Lacey Knowles, University of Michigan 10:05 Break 10:30 Deep Metazoan Phylogeny and the Utility of Taxon-Specific Ortholog Sets Kevin Kocot, University of Queensland, Brisbane 11:10 A Phylogenomic View on the Early History of Gnasthostome Evolution: Is One Tree Enough? Ingo Ebersberger, Goethe University, Frankfurt 11:50 Lunch Break 1:30 Distinguishing Methodological and Biological Causes of Gene Tree Discordance in Phylogenomic Datasets Derrick Zwickl, University of Arizona 2:10 Filtering and Partitioning Strategies for Phylogenomic Analyses David Swofford, Duke University and National Evolutionary Synthesis Center 2:50 Break 3:10 Genome-scale Phylogenetics in the Presence of Hybridization and Incomplete Lineage Sorting Luay Nakhleh, Rice University 3:50 Joint Inference of Gene Trees and Species Trees at the Genomic Scale Bastien Boussau, University Claude Bernard, Lyon 4:30 Round Table Discussion With All Speakers Any questions or for more information contact Brian Coyle Coyleb@si.edu “Coyle, Brian J.” via Gmail
August 20, 2014
Dear EvolDir Community, We are pleased to announce the RNA-seqlopedia: http://bit.ly/1z4tj30 The RNA-seqlopedia is meant as a resource for researchers trying to utilize RNA-seq protocols for their research, including de novo assembly of transcriptomes as well as quantification of gene expression. The site focuses on multiple aspects of RNA-seq work including experimental design, molecular protocols, and bioinformatic analyses. We realize that the site does not yet cover all aspects of transcriptomic analysis, and undoubtedly contains errors or dated information that will be modified. We will continue to update the site and add to its content, particularly via input from the scientific community, so we request your input! We hope that the RNA-seqlopedia will prove to be a useful research resource for those interested in transcriptomic analyses using second (and third) generation sequencing. The site was made possible by a grant from the NIH National Center for Research Resources, and is being created and maintained by the Cresko Lab at the University of Oregon. If you have any feedback or suggestions, please write us. Sincerely, Clay Small Julian Catchen Susie Bassham Bill Cresko William A. Cresko, Ph.D. Associate Professor of Biology Director, Institute of Ecology and Evolution University of Oregon http://bit.ly/1pMIFIC; @wcresko firstname.lastname@example.org via Gmail
*Postdoctoral position in Evolutionary Genomics and Molecular and Cellular biology * */Molecular and cellular mechanisms of hyper-resistance to stress in the ameiotic bdelloid rotifer Adineta vaga/*** ** A 3-year postdoctoral research position is available in the group of Biochemistry, Biophysics and Molecular Genetics of Micro-organisms at the life Science Institute (ISV) of the Catholic University of Louvain (UCL, Belgium) to take part in a collaborative ARC research program with the Research Units in Environmental and Evolutionary Biology (URBE) and in Cellular Biology (URBC) at the University of Namur (UNamur, Be). This postdoc position is embedded within the research project entitled: /Asexuality and ‘immortality’, bdelloid rotifers as an evolutionary ‘scandal’ and a model system in biology. /This project is funded during 5 years and will start in October 2014. *Project:* Bdelloid rotifers are micro-organisms (animals) that have recently attracted much interest in the scientific community because of their ancient asexuality and their extreme resistance to stress, such as desiccation and high doses of ionizing radiation. They are capable to survive when their genome is shattered into small fragments and repair the DNA double strands breaks (DSBs) (see Hespeels et al., 2014). Repeated cycles of chromosomal repair are thought to promote allelic recombination and gene conversion in the absence of meiosis. Moreover desiccation and the induced DNA DSBs are also thought to provide a unique opportunity to acquire horizontally transferred genes, thereby contributing to the adaptive success of these organisms. In this project, the mechanisms that make bdelloid rotifers unique in terms of evolutionary strategy and hyper-resistance to stress will be investigated based on genomic data recently obtained by our consortium for the bdelloid rotifer /Adenita vaga/ (see Flot et al, 2013, Nature 500:453-7). Genomic approaches will be used to study the dynamics of /A. vaga/ genome during cycles of desiccation/rehydration/radiationand to decipher the genetic expression program that governs the different stages of its life-style. Molecular and cellular approaches will be developed to unveil and characterize the mechanisms that allow /A. vaga/ to repair its shattered chromosomes and generate genetic diversity,as well as its dependence with respect to oxidative stress response. Finally, conditions for horizontal gene transfer and RNA interference will be investigated, opening the way to the development of reverse genetic strategies. The ultimate prospect of the project is to establish bdelloid rotifers as a new model system for the understanding of fundamental biological processes such as DNA repair, cell survival and senescence. *PIs of the consortium:* Prof. Bernard Hallet (ISV, UCL), Prof. Karine Van Doninck (URBE, UNamur), Dr. Florence Debacq-Chainiaux (URBC, UNamur)** The involved consortium brings together experts in the fields of evolutionary biology and genomics (K. Van Doninck, URBE, UNamur), DNA recombination and genome plasticity (B. Hallet, ISV, UC) and oxidative stress response (F. Debacq-Chainiaux, URBC, UNamur). The appointed candidate will be expected to share its research time on both sites under the supervision of the three PIs of the consortium. The universities are at a distance of 35km from each other and easily connected by train. *Contacts:* Prof. Bernard Hallet, Bernard.email@example.com Universit Catholique de Louvain. Institut des Sciences de la Vie (ISV) http://bit.ly/1qTDNQl Prof. Karine Van Doninck, firstname.lastname@example.org University of Namur, Laboartory of Evolutionary Genetics and Ecology (http://bit.ly/1qTDQf8) *Qualifications:* We are looking for a post-doc with a strong interest and background in evolutionary genomics and molecular and cell biology. Expertise in the field of DNA repair and recombination, chromosome structure and dynamics, and/or genomics (NGS approach) is a valuable asset. Additional experience in cell biology techniques like DNA transfection, immuno-localization, fluorescence hybridization and microscopy will be a benefit. Priority will be given to candidates with a proven track record (with several publications as a first author) who will express their motivation in developing their autonomy and their interest for new challenges. *Application://* The position is available to both foreign nationals and Belgian citizens under ‘international mobility’ status, meaning that they may not have resided in Belgium for more than 12 months over the past 3 years preceding the appointment. The duration is for 2 years (with a possible 1-year renewal) starting on the *1^st of October 2014. *The closing date for applications is *^September 5th 2014.* Interested applicants should send a cover letter (briefly describing research experience, interests, and career goal), a curriculum vitae (with list of publications), and the names of three references (With address, phone number and E mail) to Bernard HALLET (Bernard.email@example.com) via Gmail
Postdoctoral Research Associate: Mechanistic Phylogenetic Models for Amino Acid Substitution Temple University An NSF-funded postdoctoral research position is available in the research group of David Liberles (Temple University from November, 2014; currently at University of Wyoming). The position is guaranteed for 1 year with the possibility of extension with successful performance. The successful candidate will be expected to relocate to Philadelphia, PA, USA and a start date as soon as possible after 11/1/14 is desired. The research project involves the construction and phylogenetic implementation of mechanistic models for amino acid substitution in C++. The ideal candidate will have a strong background in mathematics and statistics, strong C++ programming skills, and experience with phylogenetic methods. Knowledge of proteins and/or evolutionary biology is a plus. To apply, please send a cover letter that describes your background, motivation, and interests as well as a full CV to firstname.lastname@example.org. Please also arrange to have 3 letters of recommendation sent directly by the letter writer to the above email address as well. International applicants are encouraged to apply and will be given full consideration. “David A. Liberles” via Gmail
Ph.D. Student: Mechanistic Phylogenetic Models for Amino Acid Substitution Temple University An NSF-funded Ph.D. student position is available in the research group of David Liberles (Temple University from November, 2014; currently at University of Wyoming). The successful candidate will be expected to enroll in the Ph.D. program at Temple University in spring semester, 2015. The research project involves the construction and phylogenetic implementation of mechanistic models for amino acid substitution in C++. The ideal candidate will have prior programming coursework or experience, a strong background in mathematics, and interest in evolutionary biology. Students with any number of primary backgrounds, including biology and mathematics will be considered. To apply, please send a cover letter that describes your background, motivation, and interests as well as a full CV to email@example.com. I will guide the successful candidate through the Ph.D. application process at Temple University. International applicants are encouraged to apply and will be given full consideration. “David A. Liberles” via Gmail
Faculty Position in Genomics The Genome, Cell, and Developmental Biology Program at Indiana University invites applications for a tenured/tenure-track faculty position in Genomics at the level of assistant professor. Candidates should have well-developed research programs that apply cutting-edge genomic approaches to investigate the molecular mechanisms underlying important aspects of eukaryotic biology, including gene regulation, epigenetics, development, or evolution. More senior candidates with outstanding credentials in research and extramural funding may also be considered. The Department of Biology (http://bit.ly/1cfCtA9) and affiliated departments and programs represent more than 60 research labs housed in 3 adjacent buildings, providing ample opportunities for collaboration. The applicant will have access to outstanding resources including state-of-the-art facilities for genomics and bioinformatics, light and electron microscopy, flow cytometry, biophysical instrumentation, and computing. Applicants must hold a Ph.D. degree and have relevant postdoctoral experience with a strong record of research accomplishments. Faculty members are expected to establish vigorous well-funded research programs and to participate in undergraduate/graduate education. Applications received by October 15, 2014 will be assured of full consideration. Applicants should submit a cover letter, CV, research statement (past, present, and planned), up to three PDFs of re-prints/pre-prints, and arrange for three letters of references to be submitted at http://bit.ly/1n8sv7E. Please address inquires to Jennifer Tarter at 812-856-3984; firstname.lastname@example.org; 1001 E. Third Street, Bloomington, IN 47405-3700. Indiana University is an equal employment and affirmative action employer and a provider of ADA services. All qualified applicants will receive consideration for employment without regard to age, ethnicity, color, race, religion, sex, sexual orientation or identity, national origin, disability status or protected veteran status. Jennifer Tarter Administrative Assistant to the Chair Department of Biology Indiana University “Tarter, Jennifer A” via Gmail
"Open post-doc position on birds and climate change in University of Helsinki The Zoology Unit of the Finnish Museum of Natural History is inviting applications for a position of a Post-doctoral Researcher for a fixed term of 2 years and 8 months into the project The combined effect of climate change and habitat protection on population changes and range shifts in birds. The preferred starting time is 1 January 2015. More details can be found from this link: http://bit.ly/1ocfARV" Best wishes, Aleksi Lehikoinen Aleksi Lehikoinen, Docent, intendentti - curator Linnustonseuranta - Monitoring Team, The Helsinki Lab of Ornithology Luonnontieteellinen keskusmuseo - Finnish Museum of Natural History PL 17 - P.O. Box 17 00014 Helsingin yliopisto - University of Helsinki Finland puh. - tel. +358-9-19128851 mobile phone +358-45-1375732 email@example.com Aleksi Lehikoinen via Gmail
August 19, 2014
The Department of Biology at Stanford University invites applications for a tenure-track Assistant Professor in Evolution. We seek outstanding applicants engaged in answering broad basic questions in Evolution. We welcome a wide spectrum of applicants and will consider both theoretical and empirical evolutionary biologists. Applicants working at the interface of Evolution and Ecology and/or other areas of Biology are encouraged to apply. The successful candidate will hold a Ph.D., and is expected to develop a vigorous research program and to participate in the Department’s teaching activities at both the undergraduate and graduate levels. More information about the Department and the University can be found at http://stanford.io/1vfKoa3. All applicants should submit a cover letter, a curriculum vitae including publication list, a statement of research accomplishments and future plans, a description of teaching experience, and three letters of reference. All materials must be submitted electronically to AcademicJobsOnline . Inquiries may be directed to Faculty Searches, Dept. of Biology, 371 Serra Mall, Stanford, CA 94305, or to firstname.lastname@example.org. Applicant materials must be received by October 15, 2014. The appointment would begin September 1, 2015. Stanford University is an equal opportunity employer and is committed to increasing the diversity of its faculty. It welcomes nominations of and applications from women and members of minority groups, protected veterans and individuals with disabilities, as well as others who would bring additional dimensions to the universitys research, teaching, and clinical mission. email@example.com via Gmail
Phylogeneticists treat the tree image as having special meaning for themselves. Conceptually, the tree is used as a metaphor for phylogenetic relationships among taxa, and mathematically it is used as a model to analyze phenotypic and genotypic data to uncover those relationships. Irrespective of whether this metaphor / model is adequate or not, it has a long history as part of phylogenetics (Pietsch 2012). Of particular interest ihas been Charles Darwin's reference to the "Tree of Life" as a simile, since that is clearly the key to the understanding of phylogenetics by the general public.
The principle on which phylogenetic trees are based seems to be the same as that for human genealogies. That is, phylogenies are conceptually the between-species homolog of within-species genealogies. As far as Western thought is concerned, human genealogies make their first important appearance in the Bible, with a rather specific purpose. The Bible contains many genealogies, mostly presented as chains of fathers and sons. For example, Genesis 5 lists the descendants of Adam+Eve down to Noah and his sons, which can be illustrated as a pair of chains (as shown in the first figure); and the rest of Genesis gets from there down to Moses' family, for which the genealogy can be illustrated as a complex tree.
The genealogy as listed in Genesis 5.
Cain's lineage was terminated by the Flood.
However, the theologically most important genealogies are those of Jesus, as recorded in Matthew 1:2-16 and Luke 3:23-38. Matthew apparently presents the genealogy through Joseph, who was Jesus' legal father; and Luke apparently traces Jesus' bloodline through Mary's father, Eli. These two lineages coalesc in David+Bathsheba, and from there they have a shared lineage back to Abraham. Their importance lies in the attempt to substantiate that Jesus' ancestry fulfils the biblical prophecies that the Messiah would be descended from Abraham (Genesis 12:3) through Isaac (Genesis 17:21) and Jacob (Genesis 28:14), and that he would be from the tribe of Judah (Genesis 49:8), the family of Jesse (Isaiah 11:1) and the house of David (Jeremiah 23:5).
That is, these genealogies legitimize Jesus as the prophesied Messiah. Following this lead, subsequent use of genealogies has commonly been to legitimize someone as a monarch, so that royal genealogies have been of vital political and social importance throughout recorded history (see the example in the next figure). This importance was not lost on the rest of the nobility, either, so that documented genealogies of most aristocratic families allow us to identify the first-born son of the first-born son, etc, and thus legitimize claimants to noble titles — genealogies are a way for nobles to assert their nobility.
The genealogy of the current royal family of Sweden.
The lineage of the recent monarchs is highlighted as a chain, with an aborted side-branch dashed.
If we focus solely on the line of descent involved in legitimization, then genealogies can be represented as a chain (as shown in the genealogy above). However, if we include the rest of the paternal lines of descent then family genealogies can be represented as a tree. However, if we include some or all of the maternal lineages as well, then family genealogies can be represented as a network. For example, the biblical genealogies only rarely name women, but where females are specifically named the genealogies actually form a reticulated network. Jacob produced offspring with both Rachel and Leah, who were his first cousins; and Isaac and Rebekah were first cousins once removed. Even Moses was the offspring of parents who were, depending on the biblical source consulted, either nephew-aunt, first cousins, or first cousins once removed. These relationships cannot be represented in a tree. (See also the complex genealogy of the Spanish branch of the Habsburgs, who were kings of Spain from 1516 to 1700.)
This idea of genealogical chains, trees and networks was straightforward to transfer from humans to other species. Originally, biologists stuck pretty much to the idea of a chain of relationships among organisms, as presented in the early part of Genesis. Human genealogies were traced upwards to Adam and from there to God, and thus species relationships were traced upwards to God via humans. However, by the second half of the 1700s both trees and networks made their appearance as explicit suggestions for representing biological relationships. In particular, Buffon (1755) and Duchesne (1766) presented genealogical networks of dog breeds and strawberry cultivars, respectively.
However, these authors did not take the conceptual leap from within-species genealogies to between-species phylogenies. Indeed, they seem to have explicitly rejected the idea, confining themselves to relationships among "races". It was Charles Darwin and Alfred Russel Wallace, a century later, who first took this leap, apparently seeing the evolutionary continuum that connects genealogies to phylogenies. In this sense, they both took ideas that had been "in the air" for several decades, but previously applied only within species, and applied them to the origin of species themselves. [See the Note below.] Both of them, however, confined themselves to genealogical trees rather than using networks. It seems to me that it was Pax (1888) who first put the whole thing together, and produced inter-species phylogenetic networks (along with some intra-species ones).
In this sense, the biblical Tree of Life has only a peripheral relevance to phylogenetics. Darwin used it as a rhetorical device to arouse the interest of his audience (Hellström 2011), but it was actually the biblical genealogies that were of most practical importance to his evolutionary ideas. Apart from anything else, the original biblical tree was actually the lignum vitae (Tree of Eternal Life) not the arbor vitae (Tree of Life). Similarly, the tree from which Adam and Eve ate the forbidden fruit was the lignum scientiae boni et mali (Tree of Knowledge of Good and Evil), not the arbor scientiae (Tree of Knowledge) that was subsequently used as a metaphor for human knowledge.
Note. Along with phylogenetic trees, Darwin and Wallace did not actually originate the idea of natural selection, which had previously been discussed by people such as James Hutton (1794), William Charles Wells (1818), Patrick Matthew (1831), Edward Blyth (1835) and Herbert Spencer (1852). However, this discussion had been in relation to within-species diversity, whereas Wallace and Darwin applied the idea to the origin of between-species diversity (i.e. the origin of new species).
Buffon G-L de. 1755. Histoire naturelle générale et particulière, tome V. Paris: Imprimerie
Duchesne A.N. 1766. Histoire naturelle des fraisiers. Paris: Didot le Jeune & C.J. Panckoucke.
Hellström N.P. 2011. The tree as evolutionary icon: TREE in the Natural History Museum, London. Archives of Natural History 38: 1-17.
Pax F.A. 1888. Monographische übersicht über die arten der gattung Primula. Bot. Jahrb. Syst. Pflanzeng. Pflanzengeo. 10:75-241.
Pietsch T.W. 2012. Trees of life: a visual history of evolution. Baltimore: Johns Hopkins University Press.
Natural selection adapts organisms to their past environments and has no ability to foresee the future. When the environment changes, adaptations to past environments can misfire in the current environment, producing a mismatch that can only be solved by subsequent evolution or by modifying the current environment. Mismatches are an inevitable consequence of evolution in changing environments. They are especially relevant to human affairs, since modern human environments are so radically different from ancestral human environments. In addition, countless species are becoming mismatched to their environments thanks to anthropogenic environmental changes at a planetary scale. Waiting for subsequent genetic evolution to correct mismatches is not an option for problems requiring immediate solutions. This working group will develop a rigorous methodology for identifying evolutionary mismatches and finding the right environmental interventions, or âwhat to do about it,â in both humans and nonhuman species. The focus on mismatch emerged from the recent NESCent catalysis meeting titled âThe Nature of Regulation: How Evolutionary Theory Can Inform the Regulation of Large-scale Human Social Interactionsâ which was organized in collaboration with the Evolution Institute. The working group will continue the collaboration, including a novel organizational structure that nests the working group within larger groups that provide both an informed audience and enables meaningful input from a distance.
Simultaneous Bayesian Estimation of Alignment and Phylogeny under a Joint Model of Protein Sequence and Structure
For sequences that are highly divergent, there is often insufficient information to infer accurate alignments, and phylogenetic uncertainty may be high. One way to address this issue is to make use of protein structural information, since structures generally diverge more slowly than sequences. In this work, we extend a recently developed stochastic model of pairwise structural evolution to multiple structures on a tree, analytically integrating over ancestral structures to permit efficient likelihood computations under the resulting joint sequence–structure model. We observe that the inclusion of structural information significantly reduces alignment and topology uncertainty, and reduces the number of topology and alignment errors in cases where the true trees and alignments are known. In some cases, the inclusion of structure results in changes to the consensus topology, indicating that structure may contain additional information beyond that which can be obtained from sequences. We use the model to investigate the order of divergence of cytoglobins, myoglobins, and hemoglobins and observe a stabilization of phylogenetic inference: although a sequence-based inference assigns significant posterior probability to several different topologies, the structural model strongly favors one of these over the others and is more robust to the choice of data set.
Evidence for Increased Levels of Positive and Negative Selection on the X Chromosome versus Autosomes in Humans
Partially recessive variants under positive selection are expected to go to fixation more quickly on the X chromosome as a result of hemizygosity, an effect known as faster-X. Conversely, purifying selection is expected to reduce substitution rates more effectively on the X chromosome. Previous work in humans contrasted divergence on the autosomes and X chromosome, with results tending to support the faster-X effect. However, no study has yet incorporated both divergence and polymorphism to quantify the effects of both purifying and positive selection, which are opposing forces with respect to divergence. In this study, we develop a framework that integrates previously developed theory addressing differential rates of X and autosomal evolution with methods that jointly estimate the level of purifying and positive selection via modeling of the distribution of fitness effects (DFE). We then utilize this framework to estimate the proportion of nonsynonymous substitutions fixed by positive selection (α) using exome sequence data from a West African population. We find that varying the female to male breeding ratio (β) has minimal impact on the DFE for the X chromosome, especially when compared with the effect of varying the dominance coefficient of deleterious alleles (h). Estimates of α range from 46% to 51% and from 4% to 24% for the X chromosome and autosomes, respectively. While dependent on h, the magnitude of the difference between α values estimated for these two systems is highly statistically significant over a range of biologically realistic parameter values, suggesting faster-X has been operating in humans.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology