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June 16, 2015
On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods
The estimation of species trees using multiple loci has become increasingly common. Because different loci can have different phylogenetic histories (reflected in different gene tree topologies) for multiple biological causes, new approaches to species tree estimation have been developed that take gene tree heterogeneity into account. Among these multiple causes, incomplete lineage sorting (ILS), modeled by the multi-species coalescent, is potentially the most common cause of gene tree heterogeneity, and much of the focus of the recent literature has been on how to estimate species trees in the presence of ILS. Despite progress in developing statistically consistent techniques for estimating species trees when gene trees can differ due to ILS, there is substantial controversy in the systematics community as to whether to use the new coalescent-based methods or the traditional concatenation methods. One of the key issues that has been raised is understanding the impact of gene tree estimation error on coalescent-based methods that operate by combining gene trees. Here we explore the mathematical guarantees of coalescent-based methods when analyzing estimated rather than true gene trees. Our results provide some insight into the differences between promise of coalescent-based methods in theory and their performance in practice.
Most existing methods for modeling trait evolution are univariate, although researchers are often interested in investigating evolutionary patterns and processes across multiple traits. Principal components analysis (PCA) is commonly used to reduce the dimensionality of multivariate data so that univariate trait models can be fit to individual principal components. The problem with using standard PCA on phylogenetically structured data has been previously pointed out yet it continues to be widely used in the literature. Here we demonstrate precisely how using standard PCA can mislead inferences: The first few principal components of traits evolved under constant-rate multivariate Brownian motion will appear to have evolved via an "early burst" process. A phylogenetic PCA (pPCA) has been proprosed to alleviate these issues. However, when the true model of trait evolution deviates from the model assumed in the calculation of the pPCA axes, we find that the use of pPCA suffers from similar artifacts as standard PCA. We show that data sets with high effective dimensionality are particularly likely to lead to erroneous inferences. Ultimately, all of the problems we report stem from the same underlying issue—by considering only the first few principal components as univariate traits, we are effectively examining a biased sample of a multivariate pattern. These results highlight the need for truly multivariate phylogenetic comparative methods. As these methods are still being developed, we discuss potential alternative strategies for using and interpreting models fit to univariate axes of multivariate data.
A postdoctoral position in evolutionary genomics is available in the Vicoso group at the Institute of Science and Technology, Austria. The general focus of the lab is the evolution of sex chromosomes, which we investigate using a combination of experimental and computational approaches. Questions that motivate our research include: why do some Y/W chromosomes degenerate while other remain homomorphic? What forces drive some species to acquire global dosage compensation, while others only compensate specific genes? What are the frequency and molecular dynamics of sex-chromosome turnover? The successful applicant will apply comparative genomics analyses to a wide variety of species, and combine them with population DNA and gene expression data, to achieve a better understanding of the evolutionary and molecular forces driving sex chromosome differentiation. Candidates wishing to work on a specific project in sex chromosome evolution are also encouraged to apply. Applicants should have obtained, or anticipate obtaining by the start date, a PhD in biology, genetics, bioinformatics, or a related field. A strong background in one or more the following areas is highly desired: • comparative genomics • molecular evolution • population genetics • bioinformatics The initial appointment is for two years, with the possibility of extension and a minimum salary of 49,070 Euros per year (gross). IST Austria (www.ist.ac.at) is a young and vibrant institute dedicated to basic research, with a strong focus on evolutionary biology (other EB groups include those of Nick Barton, Jonathan Bollback, and Sylvia Cremer) and ties to several evolutionary groups in the area (http://bit.ly/1pSDzd6). We are located on the outskirts of Vienna, and the official language of the institute is English. To apply, send a short summary of research interests, a CV, up to three relevant publications/manuscripts, and the names and contact information for three references to Beatriz Vicoso (email@example.com). The review of applications will start on July 1st and continue until the position is filled. The start date is flexible, but an earlier start would be preferable. More information on the lab is available at: http://bit.ly/1QAnLvawww.ist.ac.at) is a young and vibrant institute dedicated to basic research, with a strong focus on evolutionary biology (other EB groups include those of Nick Barton, Jonathan Bollback, and Sylvia Cremer) and ties to several evolutionary groups in the area (http://bit.ly/1pSDzd6). We are located on the outskirts of Vienna, and the official language of the institute is English. To apply, send a short summary of research interests, a CV, up to three relevant publications/manuscripts, and the names and contact information for three references to Beatriz Vicoso (firstname.lastname@example.org). The review of applications will start on July 1st and continue until the position is filled. The start date is flexible, but an earlier start would be preferable. More information on the lab is available at: http://bit.ly/1QAnLva Beatriz Vicoso via Gmail
June 15, 2015
*Laboratory technician in population genomics* *Louis Calder Center, Fordham University* *Armonk, NY 10504* *DUTIES & RESPONSIBILITIES* The Munshi-South Lab at the Louis Calder Center, Fordham Universitys biological field station, is looking for a lab technician to join a dynamic research group and contribute to a number of projects that use population genomic tools to address fundamental questions about the evolution of urban wildlife. The research technician will be involved in collecting and analyzing molecular datasets, with a particular emphasis on RAD-Seq and whole genome resequencing. Particular molecular techniques will include DNA extraction, DNA quantification, restriction digests, ligations, and gel electrophoresis. Running and maintenance of a liquid handling robotic platform will also be part of the technicians duties. The technician will share responsibility for day-to-day lab operations including laboratory administration, sample and data organization, and mentoring undergraduate researchers. The position may also include occasional assistance with field work, including trapping and sample collection from mammals, amphibians, and insects. More information about research activities in the Munshi-South Lab is available at http://bit.ly/1Ca7jGg *QUALIFICATIONS:* *Required:* Bachelor’s degree in Biology (or related field) with at least six months of experience with molecular wet-lab research, and excellent organizational skills. Ability to communicate clearly, work independently, and interact collaboratively is essential. *Preferred: *Experience with RADSeq or SNP genotyping; familiarity with Geneious, R, or programming languages (e.g. Python / PERL). *SALARY & APPOINTMENT INFORMATION* The initial term of appointment is for one year, with renewal for a second year contingent on satisfactory progress. The pay rate is $17.50 / hour for up to 35 hours / week (i.e. $32,000 annually). The Calder Center is located 25 miles north of New York City, and has the advantages of an idyllic, forested setting and potential for subsidized housing. *APPLICATION PROCEDURES* To apply for this position, please send application materials as a single PDF to Jason Munshi-South at email@example.com. A complete application will include a cover letter explaining your research interests and qualifications for the position, a CV, and contact information for up to three professional references. Full consideration will be given to complete applications received by *13 July 2015*. Jason Munshi-South, Ph.D. Associate Professor Louis Calder Center & Dept of Biological Sciences Fordham University Armonk, NY 10504 firstname.lastname@example.org (914) 273-3078 ext 20 http://bit.ly/1Ca7jGg email@example.com via Gmail
I am looking for a postdoctoral researcher to join my lab at the University of Missouri - St. Louis. The project involves constructing a species-level phylogeny for the Neotropical genus Burmeistera (Campanulaceae) using next-generation sequencing approaches (‘Hyb-Seq’, targeting low-copy nuclear regions with enrichment probes and genome-skimming for plastomes). Results will be used to test the relative roles of pollinator-mediated reproductive isolation and gametic isolation (post-pollination yet prezygotic) in the diversification of Burmeistera. Candidates should have experience with plant molecular phylogenetics, including labwork and bioinformatics analysis of next-gen data, and an interest in plant speciation and/or pollination biology. Successful applicants will also be encouraged to also carry out his or her own research projects related to work done in the Muchhala Lab (see http://bit.ly/1JSD39j). The start date for the position is flexible, from August of 2015 to January 2016. Funding is available for one year with renewal for a second year given satisfactory progress. St. Louis is a vibrant Midwestern city that boasts an exceptional quality of life, combining a low cost of living with a variety of cultural attractions including parks, museums, and lively music and art scenes. The University of Missouri - St. Louis has strong local ties with the Missouri Botanical Garden, the Saint Louis Zoo, Washington University, St. Louis University, and the Donald Danforth Plant Science Center, and annual retreats (sleec.weebly.com) bring together ecologists and evolutionary biologists from these and other local institutions. The Department also houses the Whitney R. Harris World Ecology Center, established to promote international research, particularly in tropical regions. Review of applications will begin on July 15th. Informal inquiries should be emailed to firstname.lastname@example.org (I will also be at Evolution 2015 in Brazil if you want to discuss in person). Submission online at http://www.umsl.jobs. Applicants must combine application materials, including 1) a short statement (one to two pages) on previous experience, research interest, and motivation for applying, and 2) a curriculum vitae, into a single PDF or Microsoft Word document and upload as a resume attachment. Additionally, have three recommendation letters sent to email@example.com. For questions about how to apply, please call (314) 516-5258, or if you are experiencing technical problems, please email firstname.lastname@example.org. UMSL is an Equal Opportunity/Access/Affirmative Action/Pro Disabled & Veteran Employer via Gmail
*Postdoctoral researcher in population genomics* *Department of Biological Sciences* *Fordham University, Bronx, NY * A postdoctoral position is available in the lab of Jason Munshi-South at Fordham University to work on a NSF-funded study examining population genomics, adaptive evolution, and global phylogeography of wild brown rats (*Rattus norvegicus*). The project aims to understand how demographic history and natural selection have influenced genomic variation in the New York City rat population since the mid 18th century. A parallel effort will investigate origins of and admixture between brown rat populations from around the world. The postdoc will also be encouraged to pursue extensions to these projects in line with their own interests. *DUTIES & RESPONSIBILITIES* The successful candidate will lead computational analyses of genome-wide SNP datasets and whole-genome sequences to investigate historical demography, selection, and phylogeography of rats. The postdoc may also be involved in museum genomics and the development of genomic technologies for rats, such as SNP chips or capture arrays. The postdoc will work with the PI and other lab members to produce manuscripts for publication, give presentations at professional meetings, and mentor graduate and undergraduate students. *QUALIFICATIONS* *Required*: Ph.D. in biology, bioinformatics, or similar field; experience with population genetic analysis; record of publication in peer-reviewed journals *Preferred*: Research experience with population genomics, particularly demographic modeling and parameter estimation, selection scans, and admixture analyses from genome-scale datasets. Experience with SNP genotyping, SNP chip / array design, or similar. Work with genomic datasets from humans, domesticated animals, or invasive species would be particularly relevant. *SALARY & APPOINTMENT INFORMATION* The initial term of appointment is for one year, with renewal for a second year contingent on satisfactory progress. The start date is negotiable, but preferably by January 2016. The position is open until filled. Annual salary for this position is $48,000. The successful applicant has the choice of being based out of the biology department at the Bronx campus (Rose Hill) of Fordham University, or the Louis Calder Center in Armonk, NY. The Calder Center is located 25 miles north of the Bronx, and has the advantages of an idyllic, forested setting and potential for subsidized housing. Some travel between the two sites will be necessary; Fordham provides a free shuttle. *APPLICATION PROCEDURES* To apply for this position, please send application materials as a single PDF to Jason Munshi-South at email@example.com. A complete application will include a cover letter explaining your research interests and qualifications for the position, a CV, contact information for three professional references, and up to three PDF reprints of relevant publications. Full consideration will be given to complete applications received by *13 July 2015*. via Gmail
June 14, 2015
Dear Evoldir Community, We’ve had some very interesting responses to our problem regarding our disappearing DNA. Below, please find all responses on the matter and more. Thanks to everyone for all their help, Nicole Foley *Original Query* Dear Evoldir Community, Recently in our lab we have been experiencing intermittent problems with long term DNA storage. The samples causing problems would have been extracted using a variety of different methods, stored at 4 degrees during use and then moved to -20 or -80 degrees for long term storage. These samples all have good nanodrop values and have been successfully PCR'ed. Once the samples are taken out of long term storage and are nanodropped again the DNA seems to have disappeared!!! The samples have been stored in a variety of plastic ware (different types of tubes and plates) all made from polypropylen. While it is possible that the DNA is somehow becoming stuck to the plastic, the fact that the problem is happening so infrequently makes us think it may be something else. Thankfully we have managed to recover the samples by heating and shaking at 60 degrees continuously for ~48 hours, but are puzzled as to why this is happening in the first place. Has anyone else experienced this before or have any insights into the causes? Thanks in advance for your help and I will of course re-post responses, Nicole Foley *Responses* It could simply be that the samples stored below -20C become insoluble and the DNA tends to crystallize to the walls of the tube. Thus you cannot pick up any signal on the nanodrop and when you re-suspend the DNA you find it again. Another cause could be the quality of the buffer you are using and the tubes you store the DNA in. You could either precipitate the samples and store them dry or just keep them at 4C - DNA is generally quite stable. Peter firstname.lastname@example.org Hi Nicole I have seen good DNA go bad but not since I started using low bind plastic. I use eppendorf lo-bind tubes and twin.tec plates. The plates are designed for PCR, but also work fine for DNA template storage. But I know from others that it is not always the solution. Sometimes DNA just mysteriously disappears. http://bit.ly/1efttlc There is an interesting paper by Gaillard and Strauss about this issue: international biotechnology laboratory / august 2000 Eliminating DNA loss & denaturation during storage in plastic microtubes good luck Arjen A.E.Van-T-Hof@liverpool.ac.uk My lab has experienced this from time to time with a small number of samples. In all cases, the DNA had been stored in water rather than a buffer like TE. DNA eventually denatures in water, especially if dilute. It can often be (partially) renatured by treatments similar to the one you used, and this can be facilitated by adding a small amount of concentrated TE (or that old standby, SSC) to the denatured DNA sample before heating. It is less successful if the storage water was acidic (below pH of about 6.0) to begin with or has become so with time or upon initial thawing from the freezer. Our Sanger sequencing facility on campus (like many others) requires samples to be submitted in water. There is a temptation therefore to elute our fish DNA samples from purification columns with water and then store them that way. If such samples are stored at - 20 or even -80 C for some time, we encounter the denaturation problem. So with precious samples we elute withTE (or with the elution soln. provided by the supplier of the columns, generally Qiagen or Zymo) and then repurify an aliquot and elute with water for sequencing. Bruce Turner email@example.com Dear Nicole Foley, I would like to share with you my experience: nanodrop measurements are not very reliable. Sometimes at all. I dont know how old are your DNAs, however, my DNAs were PCRable after 4 years of -20 storage (very good amplification at variable loci). Another option might be to lyophilisate DNA for long-term storage and keep it at -20 or - 80 C. Then dilute when you will need this DNA again. Just an idea. Nothing really new from my site, perhaps others will have bigger expertise in DNA storage. All the best, Josef Janouek Mendel University in Brno, Czech Republic firstname.lastname@example.org Hi Nicole, How was the DNA extracted and what is it stored in (e.g. TE, water, etc)? Some extraction methods such as boiling are good for short term yield, but can damage the DNA. Similarly some may leave other compounds in the solution that degrade the DNA. The final solution it is stored in is also important as it needs some buffering capacity. Theresa email@example.com Dear Nicole That’s not a big problem at all, we know DNA is a macro molecule and has a density more than water. Since we are storing these DNA micro centrifuge tubes (or any other) for years in a vertical position all the DNA may have settled down. You might have thawed and checked the nano drop reading again, but the quantity we generally load on nanodrop is to less and there is a possibility that it has not become an uniform DNA solution with simple thawing or vortexing. It’s good to hear that you managed to recover them by mixing and heating which also suggest us that the DNA has gone no where….!!! Keep posting these interesting observations!!! Cheers Pranay firstname.lastname@example.org Hi Nicole, Thanks for posting about your problem on the Evoldir weblist. I work with conifer DNA and this problem happens to me too. My DNA is stored at -20 degC all the time. When I extracted it it was in high concentration but a few month later there was only a little left in all of the tubes… I thought it was due to contaminants degrading the DNA in some way (conifer cells are full of crap!) … But the fact that it happened to you (What organism are you working with?) and especially the fact that you recovered it by heating and shaking makes me reconsider my interpretation! Also it might mean that it is a more common problem than I previously thought… Did you get replies other than mine? Also, If you need to continue investigating these kind of issues in the future, I would suggest you use the Qubit concentration reading method, more accurate in reading DNA or RNA concentration… it is more expensive than the nanodrop though, as it uses special reagents. Thank you, good luck, and all the best for your research! Joane email@example.com I hope you’ll post your answers I’ve actually had the strange result that DNA stored in the fridge fared better than DNA in the -80. I had purified plasmid DNA in water, stored for about 4 years - i was able to sequence the plasmids stored in the fridge, but those stored in the -80 failed. I know that frequent freezing and thawing of genomic DNA tends to shear the DNA, so I keep any working solutions in the fridge, but these samples were only frozen once. Of course it could be some other difference in the template that cause the frozen ones to fail.. best wishes diana firstname.lastname@example.org Hello Nicole, I am TA in the Meyerlab. I heard that you have problems with your DNA. I found a video from the Company Biomatrica maybe it could be a solution for you. https://www.youtube.com/watch?v=3DyJTcHgEZaKg You can ask this company why you have this problem with the DNA. here an link from the Company Qiagen: http://bit.ly/1G6zvKN Have a nice day, Dominique email@example.com Nicole, We tend to only store RNA at -80, not DNA, because we have found that temperature to cause breaks in DNA. -20 seems fine for long-term storage, especially if your DNA is in TE or another buffer. I haven’t done anything rigorous to back this up, but that’s been our experience. Chris firstname.lastname@example.org Hi Nicole, Polypropylene plastic ware can certainly cause issues for long-term DNA storage, due to DNA adhering to the plastic surface. A commonly-used way to both prevent this and ‘rescue’ extracts for which this has already occurred, is to add a detergent, such as Tween-20, to the extract after elution for a final concentration of 0.05% Tween-20. Hope that helps! Cheers, Pete Heintzman email@example.com firstname.lastname@example.org via Gmail
Phylogenetic position of the house dust mite subfamily Guatemalichinae (Acariformes: Pyroglyphidae) based on integrated molecular and morphological analyses and different measures of support
Based on multilocus phylogenetic analyses (18S, 28S, EF1-α, SRP54, HSP70, CO1, 10 860 nt aligned), we show that the house dust mite subfamily Guatemalichinae is nested within non-onychalgine pyroglyphid mites and forms the sister group to the genus Sturnophagoides (bootstrap support 100, posterior probability 1.0). Because high bootstrap support values may be misleading in the presence of incongruence, we evaluate robustness of the Guatemalichinae+Sturnophagoides clade using: (1) internode certainty indices to estimate the frequency of conflicting bipartitions in maximum-likelihood bootstrap trees, (ii) consensus networks to investigate conflict among different loci; and (iii) statistical hypothesis testing based on information theory, both multi-scale and regular bootstrap. Results suggest that this grouping is very well supported given the data. The molecular analyses were integrated with detailed morphological study using scanning electron and light microscopy. We suggest that the subfamilial status of Guatemalichinae should be reconsidered, and this lineage should be placed within the subfamily Dermatophagoidinae. The latter subfamily is currently accepted in the literature as a monophyletic group but was here inferred as paraphyletic and was not supported by any morphological synapomorphy. The paraphyly involved the most species-rich and medically important genus, Dermatophagoides. Our findings suggest the need for a comprehensive revision of the higher-level relationships of pyroglyphid house dust mites using both DNA sequences and morphology coupled with a broad taxonomic sampling.
Background: Substrate, ocean current and freshwater discharge are recognized as important factors that control the larval dispersal and recruitment of intertidal species. Life history traits of individual species will determine the differential responses to these physical factors, and hence resulting in contrasting phylogeography across the same biogeographic barrier. To determine how these factors affect genetic structure of rocky shore species along the China coast, a comparative phylogeographic study of four intertidal and subtidal species was conducted using mitochondrial and nuclear DNA by combining new sequences from Siphonaria japonica with previously published sequences from three species (Cellana toreuma, Sargassum horneri and Atrina pectinata). Results: Analysis of molecular variance and pairwise ΦST revealed significant genetic differences between the Yellow Sea (YS) and the other two marginal seas (East China Sea, ECS and South China Sea, SCS) for rocky-shore species (S. japonica, C. toreuma, S. horneri), but not for muddy-shore species Atrina pectinata. Demographic history analysis proved that the population size of all these four species were persistent though the Last Glacial Maximum (LGM, ~20 ka BP). Migration analysis revealed that gene flow differentiated northward and southward migration for these four species. However, the inferred direction of gene flow using alternatively mitochondrial or nuclear markers was contradictory in S. japonica. Conclusions: It is concluded that there is a phylogeographical break at the Yangtze River estuary for the rocky shore species and the causation of the barrier is mainly due to the unsuitable substratum and freshwater discharge. All four intertidal and subtidal species appear to have persisted through the LGM in China, indicating the lower impact of LGM on intertidal and subtidal species than generally anticipated. The imbalanced gene flow between YS and ESCS groups for these four species could be explained by historical refugia. The discordance between mitochondrial and nuclear markers in the MIGRATE analysis of S. japonica prove the importance of employing multi-locus data in biogeographic study. Climate change, land reclamation and dam construction, which are changing substrate and hydrological conditions around Yangtze River estuary, will consequently affect the biogeographic pattern of intertidal species.
I have noted several times in this blog that it is not just biological organisms that can be considered to have a phylogenetic history. Many human artifacts also do, provided that their history results from diversification from a common ancestor. For example, there are blog posts about the following topics:
However, while all human artifacts have a history, not everything has a phylogenetic history. There can be transformational history, for example, where concepts simply change through time without diversifying. This can represented by a timeline rather than a phylogeny, as discussed in these blog posts:
There are also situations where artifacts simply cluster together, based on their similarity. This can be represented as a tree-like diagram or a network, but such a tree/network is not a phylogeny, because the clustering does not necessarily have anything to do with common ancestry. Examples discussed in this blog include:
The problem with this latter situation is that we can always mathematically measure the similarity between concepts or objects, and therefore we can always cluster them based on this similarity, even if the clusters have little meaning. I have previously discussed this issue in this blog, noting that if the similarity measure used does not model evolutionary patterns then it cannot be expected to produce a phylogeny (Non-model distances in phylogenetics).
Another case in point is the work of William Shakespeare. Can the plays, for example, be considered to have a phylogeny? Each play certainly has a phylogeny on its own, because the Shakespearean author is well known for having taken the ideas for the plays from previous sources. So, each play has a phylogeny (a reticulate history) based on the historical connections among its sources. However, the plays as a group do not have a phylogeny (not unless they have been plagiarized from each other, anyway). Does Othello really share a common ancestor with King Lear? It certainly has similarities, if only on the basis that it is one of the Tragedies (along with Macbeth, etc). But they are not phylogenetic similarities, and there is no common ancestral Shakespearean play.
As shown by the picture above, this point is not always appreciated. The alleged phylogeny is taken from a press release from the Lawrence Berkeley National Laboratory. The textual similarities among the plays are based on what are called "feature frequency profiles", which have nothing to do with evolutionary history. So, while the data analysis may or may not be helpful for identifying the author(s) of the so-called Shakespearean plays, it is not much help for constructing a phylogeny.
The data analysis is discussed in more detail by:
June 13, 2015
Reminder: Call for 2016 SSB Symposia The Society for Systematic Biologists invites proposals for symposia at the 2016 SSB meeting in Austin, Texas from June 17-21st. The meeting will be held jointly with the American Society of Naturalists (ASN) and the Society for the Study of Evolution (SSE). Proposals should include (1) a descriptive title, (2) one or two paragraphs explaining the purpose of the symposium and its relevance to systematics, (3) a list of presentations including proposed speakers, their institutions or affiliations, and their presentation titles, and (4) an indication of whether the speakers have been invited and whether they have agreed to participate. Symposia are restricted to half-day sessions (typically 6 half hour talks). The society is particularly interested in symposia whose topics do not overlap with those from previous meetings, that introduce new ideas or synthesize important concepts, or those that are particularly good examples of the analysis of empirical data. Proposals that unite systematics with other fields are also desirable. We encourage participation from young investigators and others typically under-represented in symposia. Limited funding is available. The deadline for full consideration is June 23, 2015. Proposals should be emailed (Word or PDF format) to the Program Chairperson, Stacey D. Smith, email@example.com. Please use the subject heading: SSB Symposium Proposal. The program chair will confirm receipt of submitted proposals; please inquire if you do not receive email confirmation. The proposals will be considered by the SSB Council, and the two selected symposia will receive funds to partially defer participant costs. firstname.lastname@example.org via Gmail
Background: The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be. Results: After using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree. Conclusions: Although it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.
Background: Host-parasite coevolution is predicted to result in changes in the virulence of the parasite in order to maximise its reproductive success and transmission potential, either via direct host-to-host transfer or through the environment. The majority of coevolution experiments, however, do not allow for environmental transmission or persistence of long lived parasite stages, in spite of the fact that these may be critical for the evolutionary success of spore forming parasites under natural conditions. We carried out a coevolution experiment using the red flour beetle, Tribolium castaneum, and its natural microsporidian parasite, Paranosema whitei. Beetles and their environment, inclusive of spores released into it, were transferred from generation to generation. We additionally took a modelling approach to further assess the importance of transmissive parasite stages on virulence evolution. Results: In all parasite treatments of the experiment, coevolution resulted in extinction of the host population, with a pronounced increase in virulence being seen. Our modelling approach highlighted the presence of environmental transmissive parasite stages as being critical to the trajectory of virulence evolution in this system. Conclusions: The extinction of host populations was unexpected, particularly as parasite virulence is often seen to decrease in host-parasite coevolution. This, in combination with the increase in virulence and results obtained from the model, suggest that the inclusion of transmissive parasite stages is important to improving our understanding of virulence evolution.
June 12, 2015
Experimental Evolution in Drosophila A postdoctoral position is available at the Institute of Population Genetics, Vetmeduni Vienna (Austria). The research focus of the Institute of Population Genetics is on understanding the genetics of adaptation. This central question in evolutionary biology is being tackled using up-to-date methods and a variety of approaches, including experimental evolution, quantitative genetics, functional genetics, empirical population genetics, bioinformatics and statistics. The successful candidate will be part of a team of scientists studying adaptation of experimental Drosophila populations to temperature stress. Since our experimental evolution study is performed under controlled environmental conditions with a high level of replication we have a powerful system to successfully employ a combination of DNA sequencing, RNA-Seq and Chip-Seq to characterize the architecture of adaptation in an out-crossing species. With some of our populations having already evolved up to 100 generations, this project provides the opportunity to follow adaptive trajectories through time. We are looking for a candidate with a good quantitative training and experience in handling large data sets. A background in population genetics and/or experience with the analysis of RNA-Seq and Pool-Seq data are a bonus. The positions are available for at least two years starting August 2015, but the exact starting date is negotiable. The application should be emailed to email@example.com as a single pdf containing CV, list of publications, a statement of research interests, and the names of three references with contact details. While the search will continue until the position is filled, applications should be received by 1.7.2015 to ensure full consideration. Background: 1: Franssen, S.U.*, et al.* (2015) Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental *Drosophila melanogaster* populations. *Molecular Biology and Evolution* 32, 495-509 2: Orozco-terWengel, P.*, et al.* (2012) Adaptation of *Drosophila* to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. *Molecular Ecology* 21, 4931-4941 3: Schltterer, C.*, et al.* (2015) Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. *Heredity* 114, 431-440 4: Schltterer, C.*, et al.* (2014) Sequencing pools of individuals - mining genome-wide polymorphism data without big funding. *Nature Reviews. Genetics* 15, 749-763 5: Tobler, R.*, et al.* (2013) Massive habitat-specific genomic response in* D. melanogaster* populations during experimental evolution in hot and cold environments. *Molecular Biology and Evolution* 31, 364-375 Christian Schltterer Institut fr Populationsgenetik Vetmeduni Vienna Veterinrplatz 1 1210 Wien Austria/Europe phone: +43-1-25077-4300 fax: +43-1-25077-4390 http://bit.ly/QNzHfP Vienna Graduate School of Population Genetics http://bit.ly/1eUheEt SMBE 2015 in Vienna *http://smbe2015.at* Christian Schltterer via Gmail
PhD position in molecular ecology: Inquiries are invited for a PhD assistantship to examine the effects of the Deepwater Horizon oil spill on marsh rice rats in Louisiana. Research would include examining the relationship between genetic variation at immune genes and bayou virus infection on oiled and unoiled plots. Additional work could include gene methylation or other measures of response to PAH exposure depending on the candidate’s experience and interest. Work will include a lab and a field component. Qualifications: experience with genetic analyses (lab and statistical), experience coordinating and collecting field data (particularly handling rodents and operating boats), excellent writing and organizational skills, and ability to work in a large collaborative group. Salary for the position is $22K/year. Interested candidates are welcome to contact Dr. Sabrina Taylor, School of Renewable Natural Resources, Louisiana State University, staylor at lsu.edu, 225-578-4137. To apply, send a cover letter, CV, and a list of 3 references (with phone #s and/or email addresses). Equal Employment Opportunity applies to this position. With best wishes, Sabrina Sabrina Taylor Assistant Professor School of Renewable Natural Resources 227 RNR Bldg. (Office 331) Louisiana State University and AgCenter Baton Rouge, LA 70803 USA 225-578-4137, fax 4227 http://bit.ly/1C2pOfK “Taylor, Sabrina S” via Gmail
POST-DOCTORAL RESEARCH ASSOCIATE POSITION IN REGENERATIVE GENOMICS The School of Life Sciences at Arizona State University invites applications for a postdoctoral position working in regenerative genomics and bioinformatics. ASU is a dynamic and progressive university dedicated to interdisciplinary collaborations and integrating excellence in research and teaching. The School of Life Sciences at ASU contains over 100 faculty members who foster a culture of basic research and teaching with an eye toward applicability. Duties will include generation and analysis of differential gene expression in regeneration (RNA-Seq and proteomic data analysis using tools such as TopHat, Bowtie, Cuffdiff, and DESeq), transcriptome assembly (using tools such as Trinity), whole genome assembly and annotation (using tools such as ABySS, DISCOVAR, and MAKER). Position will entail studies of regeneration using genomic and bioinformatic approaches. Qualifications: Candidates must have earned a doctoral degree in genomics, bioinformatics, genetics, regenerative medicine, or developmental biology, or in a related field prior to appointment; candidate must not currently hold a permanent faculty position. Those with a demonstrated productive and innovative research experience will be given preference. Background in bioinformatics, mathematical biology, or computer science is desired but not essential. To apply: Send cover letter summarizing your qualifications and interests, curriculum vitae, and names and email addresses of three professional references to Dr. Kenro Kusumi, School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287-4501, Email: firstname.lastname@example.org. The initial closing date for receipt of applications is June 15, 2015; applications will be reviewed weekly thereafter until the search is closed. The search will be closed on August 1, 2015. A background check is required for employment. Arizona State University is an equal opportunity/affirmative action employer committed to excellence through diversity. Women and minorities are encouraged to apply. For additional information on this position and the School of Life Sciences, please visit http://bit.ly/HpWIBn. via Gmail
PhD position (FPI fellowship) at the Doñana Biological Station in Seville (ver debajo versión en castellano) We are seeking a highly motivated PhD candidate to apply for a FPI fellowship associated with the recently granted project “Patterns and processes of genomic divergence along the speciation continuum in two recent evolutionary radiations: a multidisciplinary and integrative approach” (DIVERGEN). The project will integrate genomic and phenotypic data for taxonomic delimitation in two species complexes of montane orthoptera and analyze the evolutionary and demographic trajectories of the delimited species in relation to landscape heterogeneity and past environmental changes. These questions will be addressed combining genomic data obtained using high-throughput DNA sequencing techniques, morphometric geometrics and species distribution modelling, among other analytical approaches. The PhD will be developed under the supervision of Joaquín Ortego and Anna Papadopoulou at Estación Biológica de Doñana (EBD-CSIC, Seville, Spain), a reference center for ecological and evolutionary research. For more information about this center and our research group visit: http://bit.ly/1zgCIUH, http://bit.ly/1qSZO44, and http://bit.ly/1GBBsp1 Although the official call will open in the next days, the deadline for submitting applications is expected to be around the end of June. The candidates should fulfil the requirements of the call (i.e., to hold a master degree and have been admitted in a PhD program from a Spanish university). A background in molecular techniques, bioinformatics, population genetics, phylogenetics and/or biogeography will be positively evaluated. Candidates should send their CV and a letter of motivation stating their interest in DIVERGEN to Joaquín Ortego (email@example.com) Best, Joaquín Ortego – via Gmail
POSTDOCTORAL FELLOW at Carnegie Museum of Natural History, Pittsburgh A one-year NSF-funded postdoctoral fellowship is available immediately and provides taxonomic, systematic, and curatorial training in entomology at the Carnegie Museum of Natural History in Pittsburgh, Pennsylvania, USA. We are seeking a highly motivated, well organized, and creative individual to conduct original systematic research on a targeted insect lineage, so as to enable imaging and data capture as specified by our NSF-funded project. The individual will work directly with one or more curators in the Section of Invertebrate Zoology , who will serve as supervisors and mentors throughout the term of the fellowship. * Fellowship Term.- The fellowship period is for one (1) year, starting on July 1, 2015 thru June 30, 2016. * Eligibility.- Candidate must possess a doctoral degree (or international equivalent) in entomology or a related field and must be able to conduct original research that will lead to the advancement of scientific knowledge at the Carnegie Museum of Natural History. Research interests should focus on collection- based, field-oriented studies in systematics that will have broad applications and impacts in theory, conservation, evolution, and/or biogeography. The candidate must have a publication record in international journals demonstrating her/his adequacy for the position offered. * Knowledge, Skills, Abilities.- The candidate must have prior graduate training in entomology with an emphasis on lineages that are well-represented but under-worked in the CMNH collection, including Siphonaptera, Mecoptera, Odonata, Hymenoptera, Heteroptera, and others (less emphasis on Coleoptera, Lepidoptera, Diptera, and Homoptera). The capacity to talk with and engage public audiences about her/his research while participating in public events at the museum is highly encouraged, as is participation as a lecturer in museum-sponsored scientific seminars. The appropriate skills, experience, and education of the Fellow will be determined by the curators, with emphasis placed on a postdoctoral program to train early career Ph.D. scientists, helping them to acquire scientific training under the tutelage of Carnegie curators to further their academic and/or research careers. * Funding.- The fellow will receive an annual salary of $38,000, plus fringe benefits. Funding is provided by the InvertNet Project (http://bit.ly/1Iyn3aW), which is a project funded through the NSF Advancing Digitization of Biological Collections (ADBC) program and nationally coordinated by the iDigBio Team (www.idigbio.org). A review of applications will begin on June 25th but applications will be accepted until the position is filled. The start date planned for this position is July 1, 2015. Applications should be completed online at http://bit.ly/1Iyn4LY (search for “Postdoctoral” and select Requisition ID #1020). Then create a profile and follow the on-screen instructions. The following items should be submitted as part of the application: 1) a CV, 2) a short statement of research interests, and 3) names and contact information for three references familiar with the candidate and his/her research. Questions about the position should be directed to either James Fetzner (FetznerJ@CarnegieMNH.Org) or John Rawlins (RawlinsJ@CarnegieMNH.Org), or Bob Davidson (DavidsonR@CarnegieMNH.Org). The information contained in this message and/or attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities othewww.idigbio.org). A review of applications will begin on June 25th but applications will be accepted until the position is filled. The start date planned for this position is July 1, 2015. Applications should be completed online at http://bit.ly/1Iyn4LY (search for “Postdoctoral” and select Requisition ID #1020). Then create a profile and follow the on-screen instructions. The following items should be submitted as part of the application: 1) a CV, 2) a short statement of research interests, and 3) names and contact information for three references familiar with the candidate and his/her research. Questions about the position should be directed to either James Fetzner (FetznerJ@CarnegieMNH.Org) or John Rawlins (RawlinsJ@CarnegieMNH.Org), or Bob Davidson (DavidsonR@CarnegieMNH.Org). The information contained in this message and/or attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any system and destroy any copies. Any views expressed in this message are those of the individual sender. “Fetzner, Jim” via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology