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August 15, 2014
Scott Nichols lab at the University of Denver is accepting applications from graduate students for admission in September 2015. We primarily use sponges and choanoflagellates as research models to address fundamental questions about early animal evolution. In particular, we are interested in questions related to the evolution of multicellularity and animal body plan diversification. Current projects range from studies of cell adhesion and developmental morphogenesis, to comparative genomics and gene expression. Students are encouraged to develop their own research ideas. The University of Denver (DU) is located minutes outside of the urban center of Denver, which is a vibrant city on the edge of the Rocky Mountains. Cultural, culinary, and outdoor opportunities abound. Many students choose to live within walking distance of the campus and there are excellent public transportation options including a municipal bus system and a light-rail system. The closest remote mountain areas and ski resorts are within a 45 minute drive. Students are guaranteed full tuition offset, health benefits, and a competitive living stipend for either two (MS) or five (PhD) years. Because DU is a private, non-profit institution, there are *no additional fees for out of state or international applicants*. Prospective applicants and first year students are also strongly encouraged to apply to the NSF predoctoral fellowship program (deadline Nov 4, 2014), and I am happy to discuss this option with you in advance. The Department of Biological Sciences offers both a Masters and PhD program, and students are invited to apply to either. The department does not offer a laboratory rotation system in the first year, instead successful applicants are admitted directly to the research laboratory where they will work. I often encourage students to enter the Masters program initially, because it is possible to transition to the PhD program at the end of the first year if desired. To learn more about the application process, please go to the Department of Biological Sciences homepage and read under Degree Programs . Applicants should contact Scott Nichols directly at firstname.lastname@example.org well before the January 1st (2015) application deadline. Please provide a brief description of your background and interests and your reasons for considering the Nichols lab for graduate training. Scott Nichols, Ph.D. Assistant Professor of Biological Sciences 2101 E. Wesley Ave SG Mudd #288 University of Denver Denver, CO 80208 email: email@example.com lab homepage: nicholslab.wikidot.com phone: 303-871-5658 Scott Nichols via Gmail
Chairperson, Department of Plant Biology Michigan State University Michigan State University invites applications and nominations for the position of Chairperson of the Department of Plant Biology. The Chair would lead an internationally recognized department with a long history of university commitment to excellence in the Plant Sciences. The Department has more than 30 faculty members, strong graduate and undergraduate programs, and a supportive administrative and technical staff. It is built on the concept of integrating all sub-disciplines of plant biology, ranging from evolution and ecology to cellular, molecular and genomic biology. Research is conducted in modern research facilities on campus and at field sites across Michigan and throughout the world. The department includes faculty affiliated with the Kellogg Biological Station, the MSU Department of Energy Plant Research Laboratory, and the Great Lakes Bioenergy Research Center. The Chair is expected to provide leadership and to promote a creative environment that fosters innovation and excellence in research and teaching/educational programs in Plant Biology. Candidates must possess an established record of strong scholarship in a relevant field, proven academic leadership, and strong interpersonal skills. Continuation of an active research program is encouraged and will be supported. Candidates should be qualified to hold the rank of tenured Full Professor. Applicants should submit: a complete curriculum vitae; a statement of interest highlighting specific strengths related to this position, including research and administrative experience and accomplishments; and the names of three references (who will be contacted only with your permission). Every effort will be made to maintain confidentiality until a list of candidates for interviewing is determined. All materials should be assembled into one PDF and uploaded to: https://jobs.msu.edu for position #9727. Review of applications will begin October 15, 2014, and will continue until the position is filled. Questions regarding the position may be sent to the Chair of the search committee, at PLBChairsearch@plantbiology.msu.edu. MSU is an affirmative-action, equal-opportunity employer and is committed to achieving excellence through diversity. The University actively encourages applications of women, persons of color, veterans, and persons with disabilities, and we endeavor to facilitate employment assistance to spouses or partners of candidates for faculty and academic staff positions. “LaClair, Stacy” via Gmail
Evolutionary Biologist: We invite applications for a tenure-track Assistant/Associate Professor of Biology in Evolutionary Biology to begin August 2015. We prefer taxonomic expertise in plants or fungi, but candidates with interests in other organisms will also be considered. Research interests should complement those of current faculty. This appointment will be at the rank of Assistant or Associate Professor (depending on qualifications). Applicants must have a Ph.D. in a relevant discipline (post-doctoral experience preferred), teaching experience, and demonstrated commitment to excellence in teaching as well as scholarship involving undergraduates. Teaching responsibilities will include lower division courses (introductory biology, or new sophomore level courses in genetics or cell biology), one or more upper division courses in area(s) of expertise, and departmental service courses for majors or non-majors. The average teaching load is 10-12 contact hours/semester (including labs); a common course load is 3 lectures and 4 labs per academic year. Faculty also mentor senior capstone projects (literature reviews or research projects). We seek a collegial scholar-teacher whose research interests complement existing expertise in the department. We expect the successful candidate to establish an active research program with undergraduates. The research program must be successful and feasible in our liberal arts college setting; it should also be attractive to our student body, which includes many preparing for professional school in the health professions (e.g., optometry, physical therapy, pharmacy) as well as some pursuing teaching, environmental biology, and other professional work in the life sciences. Our research facilities include a greenhouse, and start-up funds are provided. Pacific University is particularly interested in candidates who can contribute, through their research, teaching, or service, to the diversity and excellence of the academic community. Minimum requirements for the position include a Ph.D. In Biology, or equivalent terminal research-based degree; one academic year of college or university teaching experience (TA or instructor); and two years research experience in evolution. Education, teaching and research may be gained concurrently. Pacific University is an independent, comprehensive university in Forest Grove, Oregon (about 25 miles west of Portland). The Biology department is part of the College of Arts and Sciences (ca. 1700 students), a liberal arts undergraduate college where faculty and staff are committed to an intimate, personalized education. The University also includes a College of Health Professions (including Physical Therapy, Occupational Therapy, Physician Assistant Studies, Pharmacy, Dental Science and Professional Psychology), a College of Optometry, a College of Business, and a College of Education. The Biology Department currently has 10 permanent faculty members and 2 laboratory support staff. We are committed to learning through discovery in both the laboratory and the classroom. We graduate 35-50 majors each year. Many of our graduates pursue graduate or professional study in the health sciences or careers in teaching, biology research, or environmental biology. Application materials Please submit: 1. A cover letter that addresses your preparation/promise to teach in a liberal arts college with many pre-health professions students 2. CV 3. A teaching philosophy, with a separate section identifying courses you would feel qualified and comfortable teaching (upper and lower division) 4. A research statement, which should include a brief summary of prior research, a research plan for a liberal arts institution, and an argument for how your research program at Pacific would attract and involve undergraduates. Selection criteria will include feasibility of research plan and fit to our department and student body. 5. Unofficial graduate and undergraduate transcripts 6. Arrange for three letters of reference (at least one of which speaks directly to teaching ability and experience) to be submitted directly. 7. In October, candidates on our short list may be requested to submit evidence of teaching experience and excellence, such as teaching evaluations, reports from observers, or examples of teaching materials; please do not include these materials with your initial application. Please combine application materials 1-4 into a single file (.pdf or .doc), in the order listed above, with the following naming: Last name, First name, Evolution 2014. Send applications electronically to Patty Larkins (address below); put Evolutionary Biology 2014 as the subject in your e-mail. Patty Larkins, firstname.lastname@example.org Administrative Assistant, School of Natural Sciences, Pacific University Review of applications will begin October 3 and continue until the position is filled. Contact Dr. Stacey Halpern (Biology Department Chair) with questions. NOTICE OF NONDISCRIMINATION POLICY | It is the policy of Pacific University not to discriminate on the basis of sex, physical or mental disability, race, color, national origin, sexual orientation, age, religious preference or disabled veteran or Vietnam Era status in admission and access to, or treatment in employment, educational programs or activities as required by Title IX of the Education Amendments of 1972, section 504 of the Rehabilitation Act of 1973, Title VII of the Civil Rights Act of 1964, the Age Discrimination Act, the Americans with Disabilities Act of 1990, or any other classification protected under state or federal law, or city ordinance. Questions or complaints may be directed to the Vice President for Academic Affairs, 2043 College Way, Forest Grove, OR 97116, email@example.com. Patty Larkins | Administrative Assistant | School of Natural Sciences Pacific University | 2043 College Way | Forest Grove, OR 97116 p: 503.352.1492 | f: 503.352.2933 | firstname.lastname@example.org “Larkins, Patty” via Gmail
August 14, 2014
I am looking for an excellent candidate for a postdoc grant application to work on NZ manuka (Myrtaceae) population genetics. Please note this is not for a postdoc position for which I already have funding, however I need an applicant for a project proposal that is already written. In brief, I had a candidate until yesterday when this person was offered another position. I now have a well developed and exciting project proposal that just misses a strong candidate. The deadline for proposal in August 29th 2014, however I will be attending conferences from August 17th to 26th, so there is a bit of urgency (apologies for this). A summary of the proposal is below. I am looking for a candidate with strong leadership skills who completed a PhD and would be available in the next few months and for 2 to 3 years, with expertise in population genetics/genomics, molecular marker development and genome analysis, and plant biology. The quality of the applicant’s CV is crucial, so the usual criteria will apply (publications, awards and distinction etc…). Project summary Manuka honey is among New Zealand’s premium export products, largely due to the presence of the unique compound methylglyoxal (MG) which has strong, proven antimicrobial activity. A compound (dihydroxyacetone) present in the nectar is the precursor for MG. Manuka (Leptospermum scoparium) is a NZ native species found across a range of habitats, and key traits for manuka honey production are highly variable in natural populations. However, little is known about the interplay of manuka genetics, growth site and climate in regulating these traits. To address this lack of information, we will first determine genetic variability in manuka from sites around NZ, focussing our sampling on regions favoured by beekeepers. This will allow us to develop genetic markers for selection of plants and verification of population-of-origin of commercially available plants and future cultivars. Additionally, we will collect data on variability in key traits of interest, using replicates across multiple seasons and sites, to determine the interplay of genetic and environmental influences on trait variability. Using high-resolution genotyping, we will look for regions of the manuka genome associated with trait variation and develop genetic markers for desirable traits. A deeper understanding of the natural genetic resources available in manuka and of the relative influences of genetic and environmental factors on traits of interest to beekeepers will inform the choice of plants for plantations and assist in development of best management practices. If successful the postdoc will be based in Palmerston North, New Zealand at the New Zealand Institute for Plant & Food Research Ltd (Plant & Food Research). Thank you David David Chagné Scientist T: +64 6 953 7751 F: +64 6 953 7701 email@example.com http://bit.ly/1ozoWgc The New Zealand Institute for Plant & Food Research Limited Postal Address: Plant & Food Research Palmerston North Private Bag 11600, Manawatu Mail Centre, Palmerston North, 4442, New Zealand Physical Address: Plant & Food Research Palmerston North Batchelar Road, FISC Building, Palmerston North, 4474, New Zealand David Chagne via Gmail
Scott Handley wrote:
Hello Phylobabble community!
I am assisting in the organization of a Workshop on Molecular Evolution which will be held in Cesky Krumlov, Czech Republic in January 2015. I have helped to organize this event before, but this year we are renewing the program and I am working with several new people to design something that we believe will be of interest to many in the phyologenetics/molecular evolution communities. More details below!
We also organize a Workshop on Genomics immediately prior to the Molecular Evolution Workshop for those interested in those sorts of topics: http://evomics.org/workshops/workshop-on-genomics/2015-workshop-on-genomics-cesky-krumlov/
2015 Workshop on Molecular Evolution, Český Krumlov, Czech Republic
Dates: 25 January - 7 February, 2015
Application Deadline: 15 October, 2014 is the preferred application deadline, after which time people will be admitted to the course following application review by the admissions committee. However, later applications will certainly be considered for admittance or for placement on a waiting list.
Registration Fee: $1500 USD. Fee includes opening reception and access to all course material, but does not include other meals or housing. Special discounted pricing has been arranged for hotels, pensions and hostels. Information regarding housing and travel will be made to applicants following acceptance.
Useful Links: Direct Link to the Full Workshop Schedule: http://evomics.org/workshops/worksho...cesky-krumlov/ General Workshop information:http://evomics.org Frequently Asked Questions (FAQ) about the Workshop and Český Krumlov can be found here: http://evomics.org/workshops/faq/
The 2015 Workshop on Molecular Evolution brings together an international collection of faculty members and Workshop participants to study and discuss current ideas and techniques for exploring molecular evolution. The Workshop on Molecular Evolution consists of a series of lectures, demonstrations and computer laboratories that cover theoretical and conceptual aspects of molecular evolution with a strong emphasis on data analysis.
The Workshop has a strong focus on molecular phylogenetics, and covers all aspects of phylogenetic workflows, including marker selection, phylogeny reconstruction, time-calibration, as well as detection of natural selection, phylogeography, diversification rates, and trait evolution patterns. A majority of the schedule is dedicated to hands-on learning activities designed by faculty and the workshop team. This interactive experience provides Workshop participants with the practical experience required to meet the challenges presented by modern evolutionary sciences.
Co-directors: Walter Salzburger, Michael Matschiner, Jan Stefka and Scott Handley
For more information and online application see the Workshop web site - http://evomics.org
Update: Angelique Hjarding and her co-authors have responded in a guest post on iPhylo.
The quality and fitness for use of GBIF-mobilised data is a topic of interest to anyone that uses GBIF data. As an example, a recent paper on African chameleons comes to some rather alarming conclusions concerning the utility of GBIF data:
Hjarding, A., Tolley, K. A., & Burgess, N. D. (2014, July 10). Red List assessments of East African chameleons: a case study of why we need experts. Oryx. Cambridge University Press (CUP). doi:10.1017/s0030605313001427
Here's the abstract (unfortunately the paper is behind a paywall):
The IUCN Red List of Threatened Species uses geographical distribution as a key criterion in assessing the conservation status of species. Accurate knowledge of a species’ distribution is therefore essential to ensure the correct categorization is applied. Here we compare the geographical distribution of 35 species of chameleons endemic to East Africa, using data from the Global Biodiversity Information Facility (GBIF) and data compiled by a taxonomic expert. Data screening showed 99.9%of GBIF records used outdated taxonomy and 20% had no locality coordinates. Conversely the expert dataset used 100%up-to-date taxonomy and only seven records (3%) had no coordinates. Both datasets were used to generate range maps for each species, which were then used in preliminary Red List categorization. There was disparity in the categories of 10 species, with eight being assigned a lower threat category based on GBIF data compared with expert data, and the other two assigned a higher category. Our results suggest that before conducting desktop assessments of the threatened status of species, aggregated museum locality data should be vetted against current taxonomy and localities should be verified. We conclude that available online databases are not an adequate substitute for taxonomic experts in assessing the threatened status of species and that Red List assessments may be compromised unless this extra step of verification is carried out.
The authors used two data sets, one from GBIF, the other provided by an expert to compute the conservation status for each chameleon species endemic to Kenya and/or Tanzania. After screening the GBIF data for taxonomic and geographic issues, a mere 7% of the data remained - 93% of the 2304 records downloaded from GBIF were discarded.
This study raises a number of questions, some of which I will touch on here. Before doing so, it's worth noting that it's unfortunate that neither of the two data sets used in this study (the data downloaded from GBIF, and the expert data set assembled by Colin Tilbury) are provided by the authors, so our ability to further explore the results is limited. This is a pity, especially now that citable data repositories such as Dryad and Figshare are available. The value of this paper would have been enhanced if both datasets were archived.
Below is Table 1 from the paper, "Museums from which locality records for East African chameleons were obtained for the expert and GBIF datasets":
MuseumExpert datasetGBIFAfrika Museum, The NetherlandsxAmerican Museum of Natural History, USAxBishop Museum, USAxBritish Museum of Natural History, UKxBrussels Museum of Natural Sciences, BelgiumxCalifornia Academy of Sciences, USAxDitsong Museum, South AfricaxxLos Angeles County Museum of Natural History, USAxMuseum für Naturkunde, GermanyxMuseum of Comparative Zoology (Harvard University), USAxNaturhistorisches Museum Wien, AustriaxSmithsonian Institution, USAxSouth African Museum, South AfricaxTrento Museum of Natural Sciences, ItalyxUniversity of Dar es Salaam, TanzaniaxZoological Research Museum Alexander Koenig, Germanyx
It is striking that there is virtually no overlap in data sources available to GBIF and the sources used by the expert. Some of the museums have no presence in GBIF, including some major collections (I'm looking at you, The Natural History Museum), but some museums do contribute to GBIF, but not their herpetology specimens. So, GBIF has some work to do in mobilising more data (Why is this data not in GBIF? What are the impediments to that happening?). Then there are museums that have data in GBIF, but not in a form useful for this study. For example, the American Museum of Natural History has 327,622 herpetology specimens in GBIF, but not one of these is georeferenced! Given that there are records in GenBank for AMNH specimens that are georeferenced, I suspect that the AMNH collection has deliberately not made geographic coordinates available, which raises the obvious question - why?
I had a quick look at GBIF to get some idea of the geographic coverage of the relevant herpetology collections (or animal collections if herps weren't separated out). Below are maps for some of these collections. The AMNH is empty, as is the smaller Zoological Research Museum Alexander Koenig collection (which supplied some of the expert data).
American Museum of Natural History, USA
Bishop Museum, USA
California Academy of Sciences, USA
Ditsong Museum, South Africa
Los Angeles County Museum of Natural History, USA
Museum für Naturkunde, Germany
Museum of Comparative Zoology (Harvard University), USA
Smithsonian Institution, USA
Zoological Research Museum Alexander Koenig, Germany
Some collections are relevant, such as the California Academy of Sciences, but a number of the collections in GBIF simply don't have georeferenced data on chameleons. Then there are several museums that are listed as sources for the expert database and which contribute to GBIF, but haven't digitised their herp collections, or haven't made these available to GBIF.
The other issue encountered by Hjarding et al. 2014 is that the GBIF taxonomy for chameleons is out of date (2302 of 2304 GBIF-sourced records needed to be updated). Chameleons are a fairly small group, and it's not like there are hundreds of new species being discovered each year (see timeline in BioNames), 2006 was a bumper year with 12 new taxonomic names added. But there has been a lot of recent phylogenetic work which has clarified relationships, and as a result species get shuffled around different genera, resulting in a plethora of synonyms. GBIF's taxonomy has lagged behind current research, and also manages to horribly mangle the chameleon taxonomy is does have. For example, the genus Trioceros is not even placed within the chameleon family Chamaeleonidae but is simply listed as a reptile, which means anyone searching for data on the family Chamaeleonidae will all the Trioceros species.
The use case for this study seems one of the most basic that GBIF should be able to meet - given some distributions of organisms, compute an assessment of their conservation status. That GBIF-mobilised data is so patently not up to the task in this case is cause for concern.
However, I don't see this is simply a case of expert data set versus GBIF data, I think it's more complicated than that. A big issue here is data availability, and also the extent of data release (assuming that the AMNH is actively withholding geographic coordinates for some, if not most of its specimens). GBIF should be asking those museums that provide data why they've not made georeferenced data available, and if its because the museums simply haven't been able to do this, then how can it help this process? It should also be asking why museums which are part of GBIF haven't mobilised their herpetology data, and again, what can it do to help? Lastly, in an age of rapid taxonomic change driven by phylogenetic analysis, GBIF needs to overhaul the glacial pace at which it incorporates new taxonomic information.
Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3
We describe new methods for characterizing gene tree discordance in phylogenomic data sets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short arm of chromosome 3 in Oryza (rice) species, we applied these methods to identify the causes and consequences of differing patterns of discordance in the sets of gene trees inferred using a panel of 20 distinct analysis pipelines. We found that discordance patterns were strongly affected by aspects of data selection, alignment, and alignment masking. Unusual patterns of discordance evident when using certain pipelines were reduced or eliminated by using alternative pipelines, suggesting that they were the product of methodological biases rather than evolutionary processes. In some cases, once such biases were eliminated, evolutionary processes such as introgression could be implicated. Additionally, patterns of gene tree discordance had significant downstream impacts on species tree inference. For example, inference from supermatrices was positively misleading when pipelines that led to biased gene trees were used. Several results may generalize to other data sets: we found that gene tree and species tree inference gave more reasonable results when intron sequence was included during sequence alignment and tree inference, the alignment software PRANK was used, and detectable "block-shift" alignment artifacts were removed. We discuss our findings in the context of well-established relationships in Oryza and continuing controversies regarding the domestication history of O. sativa. [gene trees; multilocus data; Oryza; phylogenomics; phylogeny reconstruction; species trees.]
A Rich Fossil Record Yields Calibrated Phylogeny for Acanthaceae (Lamiales) and Evidence for Marked Biases in Timing and Directionality of Intercontinental Disjunctions
More than a decade of phylogenetic research has yielded a well-sampled, strongly supported hypothesis of relationships within the large ( > 4000 species) plant family Acanthaceae. This hypothesis points to intriguing biogeographic patterns and asymmetries in sister clade diversity but, absent a time-calibrated estimate for this evolutionary history, these patterns have remained unexplored. Here, we reconstruct divergence times within Acanthaceae using fossils as calibration points and experimenting with both fossil selection and effects of invoking a maximum age prior related to the origin of Eudicots. Contrary to earlier reports of a paucity of fossils of Lamiales (an order of ~23,000 species that includes Acanthaceae) and to the expectation that a largely herbaceous to soft-wooded and tropical lineage would have few fossils, we recovered 51 reports of fossil Acanthaceae. Rigorous evaluation of these for accurate identification, quality of age assessment and utility in dating yielded eight fossils judged to merit inclusion in analyses. With nearly 10 kb of DNA sequence data, we used two sets of fossils as constraints to reconstruct divergence times. We demonstrate differences in age estimates depending on fossil selection and that enforcement of maximum age priors substantially alters estimated clade ages, especially in analyses that utilize a smaller rather than larger set of fossils. Our results suggest that long-distance dispersal events explain present-day distributions better than do Gondwanan or northern land bridge hypotheses. This biogeographical conclusion is for the most part robust to alternative calibration schemes. Our data support a minimum of 13 Old World (OW) to New World (NW) dispersal events but, intriguingly, only one in the reverse direction. Eleven of these 13 were among Acanthaceae s.s., which comprises > 90% of species diversity in the family. Remarkably, if minimum age estimates approximate true history, these 11 events occurred within the last ~20 myr even though Acanthaceae s.s is over 3 times as old. A simulation study confirmed that these dispersal events were significantly skewed toward the present and not simply a chance occurrence. Finally, we review reports of fossils that have been assigned to Acanthaceae that are substantially older than the lower Cretaceous estimate for Angiosperms as a whole (i.e., the general consensus that has resulted from several recent dating and fossil-based studies in plants). This is the first study to reconstruct divergence times among clades of Acanthaceae and sets the stage for comparative evolutionary research in this and related families that have until now been thought to have extremely poor fossil resources. [Acanthaceae; BEAST; biogeography; calibration; clade age; comparative; Cretaceous; divergence time estimation; diversification; evolution; fossil; Jurassic; Lamiales; palynology; pollen; simulation; Triassic.]
A Generalized K Statistic for Estimating Phylogenetic Signal from Shape and Other High-Dimensional Multivariate Data
Phylogenetic signal is the tendency for closely related species to display similar trait values due to their common ancestry. Several methods have been developed for quantifying phylogenetic signal in univariate traits and for sets of traits treated simultaneously, and the statistical properties of these approaches have been extensively studied. However, methods for assessing phylogenetic signal in high-dimensional multivariate traits like shape are less well developed, and their statistical performance is not well characterized. In this article, I describe a generalization of the K statistic of Blomberg et al. that is useful for quantifying and evaluating phylogenetic signal in highly dimensional multivariate data. The method (Kmult) is found from the equivalency between statistical methods based on covariance matrices and those based on distance matrices. Using computer simulations based on Brownian motion, I demonstrate that the expected value of Kmult remains at 1.0 as trait variation among species is increased or decreased, and as the number of trait dimensions is increased. By contrast, estimates of phylogenetic signal found with a squared-change parsimony procedure for multivariate data change with increasing trait variation among species and with increasing numbers of trait dimensions, confounding biological interpretations. I also evaluate the statistical performance of hypothesis testing procedures based on Kmult and find that the method displays appropriate Type I error and high statistical power for detecting phylogenetic signal in high-dimensional data. Statistical properties of Kmult were consistent for simulations using bifurcating and random phylogenies, for simulations using different numbers of species, for simulations that varied the number of trait dimensions, and for different underlying models of trait covariance structure. Overall these findings demonstrate that Kmult provides a useful means of evaluating phylogenetic signal in high-dimensional multivariate traits. Finally, I illustrate the utility of the new approach by evaluating the strength of phylogenetic signal for head shape in a lineage of Plethodon salamanders. [Geometric morphometrics; macroevolution; morphological evolution; phylogenetic comparative method.]
Patterns of adaptation in response to environmental variation are central to our understanding of biodiversity, but predictions of how and when broad-scale environmental conditions such as climate affect organismal form and function remain incomplete. Succulent plants have evolved in response to arid conditions repeatedly, with various plant organs such as leaves, stems, and roots physically modified to increase water storage. Here, we investigate the role played by climate conditions in shaping the evolution of succulent forms in a plant clade endemic to Madagascar and the surrounding islands, part of the hyper-diverse genus Euphorbia (Euphorbiaceae). We used multivariate ordination of 19 climate variables to identify links between particular climate variables and three major forms of succulence—succulent leaves, cactiform stem succulence, and tubers. We then tested the relationship between climatic conditions and succulence, using comparative methods that account for shared evolutionary history. We confirm that plant water storage is associated with the two components of aridity, temperature, and precipitation. Cactiform stem succulence, however, is not prevalent in the driest environments, countering the widely held view of cactiforms as desert icons. Instead, leaf succulence and tubers are significantly associated with the lowest levels of precipitation. Our findings provide a clear link between broad-scale climatic conditions and adaptation in land plants, and new insights into the climatic conditions favoring different forms of succulence. This evidence for adaptation to climate raises concern over the evolutionary future of succulent plants as they, along with other organisms, face anthropogenic climate change. [Adaptation; climate; comparative analysis; Euphorbia; ordination; phylogeny.]
Public DNA databases are composed of data from many different taxa, although the taxonomic annotation on sequences is not always complete, which impedes the utilization of mined data for species-level applications. There is much ongoing work on species identification and delineation based on the molecular data itself, although applying species clustering to whole databases requires consolidation of results from numerous undefined gene regions, and introduces significant obstacles in data organization and computational load. In the current paper, we demonstrate an approach for species delineation of a sequence database. All DNA sequences for the insects were obtained and processed. After filtration of duplicated data, delineation of the database into species or molecular operational taxonomic units (MOTUs) followed a three-step process in which (i) the genetic loci L are partitioned, (ii) the species S are delineated within each locus, then (iii) species units are matched across loci to form the matrix L x S, a set of global (multilocus) species units. Partitioning the database into a set of homologous gene fragments was achieved by Markov clustering using edge weights calculated from the amount of overlap between pairs of sequences, then delineation of species units and assignment of species names were performed for the set of genes necessary to capture most of the species diversity. The complexity of computing pairwise similarities for species clustering was substantial at the cytochrome oxidase subunit I locus in particular, but made feasible through the development of software that performs pairwise alignments within the taxonomic framework, while accounting for the different ranks at which sequences are labeled with taxonomic information. Over 24 different homologs, the unidentified sequences numbered approximately 194,000, containing 41,525 species IDs (98.7% of all found in the insect database), and were grouped into 59,173 single-locus MOTUs by hierarchical clustering under parameters optimized independently for each locus. Species units from different loci were matched using a multipartite matching algorithm to form multilocus species units with minimal incongruence between loci. After matching, the insect database as represented by these 24 loci was found to be composed of 78,091 species units in total. 38,574 of these units contained only species labeled data, 34,891 contained only unlabeled data, leaving 4,626 units composed both of labeled and unlabeled sequences. In addition to giving estimates of species diversity of sequence repositories, the protocol developed here will facilitate species-level applications of modern-day sequence data sets. In particular, the L x S matrix represents a post-taxonomic framework that can be used for species-level organization of metagenomic data, and incorporation of these methods into phylogenetic pipelines will yield matrices more representative of species diversity. [Database partitioning; MOTU; multi-locus clustering; species delineation.]
Mixture Models of Nucleotide Sequence Evolution that Account for Heterogeneity in the Substitution Process Across Sites and Across Lineages
Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modeled accurately using the distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or underparameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10 000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42 337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these three sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modeled by a combination of eight edge-specific rate matrices (four for V1 and four for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the seven species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species. [Evolution; heterotachy; mixture model; non-homogeneous model; phylogeny; rate heterogeneity across sites; rate heterogeneity across lineages; yeast]
Competition between organisms influences the processes governing the colonization of new habitats. As a consequence, species or populations arriving first at a suitable location may prevent secondary colonization. Although adaptation to environmental variables (e.g., temperature, altitude, etc.) is essential, the presence or absence of certain species at a particular location often depends on whether or not competing species co-occur. For example, competition is thought to play an important role in structuring mammalian communities assembly. It can also explain spatial patterns of low genetic diversity following rapid colonization events or the "progression rule" displayed by phylogenies of species found on archipelagos. Despite the potential of competition to maintain populations in isolation, past quantitative analyses have largely ignored it because of the difficulty in designing adequate methods for assessing its impact. We present here a new model that integrates competition and dispersal into a Bayesian phylogeographic framework. Extensive simulations and analysis of real data show that our approach clearly outperforms the traditional Mantel test for detecting correlation between genetic and geographic distances. But most importantly, we demonstrate that competition can be detected with high sensitivity and specificity from the phylogenetic analysis of genetic variation in space. [Competition; dispersal; phylogeography.]
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution. [Computation; graphical models; inference; modularization; statistical phylogenetics; tree plate.]
The reconstruction of a central tendency "species tree" from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all taxa are present in every gene tree. Here, we list four apparently desirable properties that a method for estimating a species tree from gene trees could have (the strongest property states that building a species tree from input gene trees and then pruning leaves gives a tree that is the same as, or more resolved than, the tree obtained by first removing the taxa from the input trees and then building the species tree). We show that although it is technically possible to simultaneously satisfy these properties when taxon coverage is complete, they cannot all be satisfied in the more general supertree setting. In part two, we discuss a concordance-based consensus method based on Baum's "plurality clusters", and an extension to concordance supertrees. [Concordance; consensus tree; phylogenetics; plurality cluster; supertree.]
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology