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February 11, 2015
**ESEB Outreach Fund** The European Society for Evolutionary Biology (ESEB) welcomes applications to the ESEB Outreach Fund for projects that promote evolution-related activities. The goal of this initiative is to improve public knowledge about evolution globally. Applications for funding will be accepted for educational initiatives that promote evolution, development of evolutionary material (books, films, web sites) intended for a general audience, public outreach seminars, public exhibitions, etc. While most projects will be financed for a sum between 1000-1500 Euros, exceptions can be made if a strong argument is provided for additional funds. The application form can be found on www.eseb.org (click on the “Outreach Fund” link). Applications will be accepted twice yearly (deadlines March 15, September 15) and should be submitted by email to Ute Friedrich (email@example.com; Subject: Outreach). Dr. Ute Friedrich ESEB Office Manager Email: firstname.lastname@example.org European Society for Evolutionary Biology - www.eseb.org email@example.com via Gmail
First phylogenetic analysis of the tribe Phyllotini (Rodentia: Sigmodontinae) combining morphological and molecular data
Previous phylogenetic analyses of the tribe Phyllotini, one of the largest components of the subfamily Sigmodontinae, have been based on a single source of evidence. In particular, morphological analyses were largely based on craniodental data, almost neglecting the potential phylogenetic information present in the postcranium. Despite the significant advances made in relation to the knowledge of phyllotine phylogeny in recent times, there are several unsolved issues that highlight the importance of a phylogenetic analysis that integrates multiple sources of evidence, including previously considered sources as well as new sources of data. We present here the first combined phylogenetic analysis (morphological and molecular) of phyllotines, which includes the widest taxon and character sampling to date. Our dataset includes 164 morphological characters, of which 83 are postcranial characters, plus 3561 molecular characters, scored for 52 species from 34 genera of Oryzomyalia. In this study 75 postcranial characters not previously considered in this group are thoroughly described, and their utility for solving the relationships within Phyllotini is evaluated by means of different complementary analyses. Phyllotini was retrieved as a monophyletic clade in the combined analysis, with a composition that matches that obtained in most other recent analyses. All genera of phyllotines were monophyletic and show high support values. Abrotrichini, Akodontini and Oryzomyini were also monophyletic. The inclusion of postcranial data appears to be of limited utility to solve the phylogenetic relationships within Phyllotini.
—Apple-Mail=_F6523B27-4F90-4BBE-9B0F-51BE0E32209A Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 The University of Virginia’s Mountain Lake Biological Station (MLBS) in the southern Appalachians is excited to offer a limited number of fellowships to support station and residency costs for researchers to explore new projects or collect preliminary data. This is a rare opportunity to make an extended stay of up to 2 months at one of North America’s premier field stations at no cost to the researcher. Preference will be given to individuals and projects with the potential to develop into long-term research activities at the Station. We especially encourage applications from individuals in the postdoctoral or early faculty phases of their careers, but will not exclude other individuals from consideration. For more information about the fellowship program, research opportunities or Mountain Lake Biological Station (mlbs.org), please contact the Director ” Butch Brodie (firstname.lastname@example.org ). Interested individuals should submit a single pdf file including CV and a 2-3 pp proposal outlining the proposed research and planned dates of residence (or duration of stay) to MLBS@virginia.edu . Review of proposals will begin March 20, 2015. —Apple-Mail=_F6523B27-4F90-4BBE-9B0F-51BE0E32209A Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
The University of Virginia’s Mountain Lake Biological Station (MLBS) in the southern Appalachians is excited to offer a limited number of fellowships to support station and residency costs for researchers to explore new projects or collect preliminary data. This is a rare opportunity to make an extended stay of up to 2 months at one of North America’s premier field stations at no cost to the researcher. Preference will be given to individuals and projects with the potential to develop into long-term research activities at the Station. We especially encourage applications from individuals in the postdoctoral or early faculty phases of their careers, but will not exclude other individuals from consideration.
Interested individuals should submit a single pdf file including CV and a 2-3 pp proposal outlining the proposed research and planned dates of residence (or duration of stay) to MLBS@virginia.edu. Review of proposals will begin March 20, 2015.—Apple-Mail=_F6523B27-4F90-4BBE-9B0F-51BE0E32209 via Gmail
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via Gmail
I am looking for one or two PhD or MSc students or a post-doctoral fellow to join my research team studying adaptation in seabirds. We have two main study systems: 1) Band-rumped storm-petrels represent an exciting case of repeated parallel evolution of sympatric allochronic races (populations separated by breeding time - basically, feathered sticklebacks). Initial studies in my lab documented the pattern of divergence. We are now investigating the mechanisms of parallel adaptation and speciation using genomic methods. The new project will entail combination of molecular data with an existing large data set to estimate heritability of various morphological and life history traits. Other projects within this study system are possible. Field work on barren tropical islands will be required. 2) Thick-billed Murres breed throughout the north Atlantic, Pacific and Arctic Oceans, and are increasingly challenged by climate change. The need, and the potential, for a species to adapt to anthropogenic change depends on the plasticity of key traits such as breeding time and heat tolerance. I am looking for a new student to combine genetic data with an existing large dataset to study the fitness effects and heritabilities of several physiological and life history traits. Field work on a remote arctic island will be required. This student will be co- supervised by Dr. Kyle Elliott (McGill University). Applicants must have some background in evolutionary genetics. Practical experience with genomics and bioinformatics is an asset. The successful applicant(s) will join a dynamic group of faculty and students studying ecology and evolution at Queen’s University. Please send a resume or curriculum vitae, informal transcript, and contact information for two academic references to Dr. Vicki Friesen (address below). Acceptance is conditional on scholarship funding through either Queen’s University or an external agency. Positions are not restricted to Canadians. Please contact email@example.com for further information. Dr. Vicki Friesen, Professor Department of Biology, 4443 Biosciences, 116 Barrie Street, Queen’s University, Kingston, ON K7L 3N6, Canada Tel: 613-533-6156 Fax: 613-533-6617 Haida Saying: Treat the Earth well: it is not given to us by our parents, it is loaned to us by our children. Vicki Friesen via Gmail
—001a113f8f8a7c61bf050ec39d49 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable The American Society of Naturalists Call for Symposia ASN meeting at Asilomar, California 10-14 Jan 2016 A stand-alone meeting of ASN will be held at Asilomar in Monterey, California 10-14 January 2016. The Executive Council of the Society invites proposals for two half-day symposia to be held at the meeting. Proposals should include (1) a title; (2) a description of the symposium topic (one page); (3) a tentative list of six speakers, including institutional affiliations; (4) a justification for the symposium explaining why the topic and speakers are appropriate for an ASN meeting, keeping in mind the broader goals of the society ( http://bit.ly/1CU61n7); and (5) a statement that all proposed invited speakers have agreed to participate. Proposals must be submitted by midnight Eastern Standard Time on March 31, 2015 by email (firstname.lastname@example.org) as a single pdf attachment, under subject heading: ASN Asilomar Symposium Proposal. Proposals that include women, young investigators and individuals from underrepresented groups are especially encouraged. Please note that as with the 2014 Asilomar meeting, ASN does not have funding allocated to support these symposia, although there may be opportunities to seek external symposium funding. Speakers should assume that they are likely to have to cover their own travel costs. The Society’s selection committee will evaluate proposals based on the likelihood of attracting a substantial audience, the significance and timeliness of the topic, and on it being substantively different from recent symposia sponsored by the Society. All applicants will be notified of the decision by late April 2015. —001a113f8f8a7c61bf050ec39d49 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable The American Society of NaturalistsCall for SymposiaASN meeting at Asilomar, California10-14 Jan 2016A stand-alone meeting of ASN will be held at Asilomar in Monterey, California 10-14 January 2016. The Executive Council of the Society invites proposals for two half-day symposia to be held at the meeting.Proposals should include (1) a title; (2) a description of the symposium topic (one page); (3) a tentative list of six speakers, including institutional affiliations; (4) a justification for the symposium explaining why the topic and speakers are appropriate for an ASN meeting, keeping in mind the broader goals of the society (http://bit.ly/1CU61n7); and (5) a statement that all proposed invited speakers have agreed to participate.Proposals must be submitted by midnight Eastern Standard Time on March 31, 2015 by email (email@example.com) as a single pdf attachment, under subject heading: ASN Asilomar Symposium Proposal. Proposals that include women, young investigators and individuals from underrepresented groups are especially encouraged.Please note that as with the 2014 Asilomar meeting, ASN does not have funding allocated to support these symposia, although there may be opportunities to seek external symposium funding. Speakers should assume that they are likely to have to cover their own travel costs.The Society’s selection committee will evaluate proposals based on the likelihood of attracting a substantial audience, the significance and timeliness of the topic, and on it being substantively different from recent symposia sponsored by the Society. All applicants will be notified of the decision by late April 2015. —001a113f8f8a7c61bf050ec39d4 via Gmail
"The least cost path from landscape genetics to landscape genomics: challenges and opportunities to explore NGS data in a spatially explicit context" is the title of a Research Topic for Frontiers in Ecology and Evolution to explore a number of critical challenges and opportunities for the transition from landscape genetics to landscape genomics. We invite the submission of papers (original research, general commentary, opinion article, etc.**) related to the transition from landscape genetics to landscape genomics. The papers may include : a) data and analysis of spatial analysis of empirical NGS data to identify markers under selection and quantify effects of environmental factors and heterogeneity on gene flow and selection; b) simulation and modeling to explore the application of spatially explicit, individual-based modeling in a NGS context; c) experimental genomics in common garden and gene-line selection experiments to discuss the challenges and opportunities of integrating experimental genetics with emerging genomic data; See the full text of the call for papers here: http://bit.ly/1zKpZhC Deadline for abstract: March 27, 2015 (declaration of intent, not compulsory) *Deadline for submission: September 25, 2015* The topic editors, Samuel Cushman, Andrew Shirk, Glenn Howe, Melanie Murphy, Rodney Dyer, Stéphane Joost **More information on Frontiers Research Topics: http://bit.ly/16QWL5h via Gmail
Dear all: We would like to draw your attention to up to 3 postdoctoral positions available in the Institute of Population Genetics at the Vetmeduni in Vienna. The positions are for up to 4 years, and are awarded on a competitive basis by the university. The groups at the Institute of Population Genetics comprise an international group of researchers applying cutting-edge statistical and molecular methods to evolutionary questions, including using experimental evolution to uncover the nature of genetic basis of adaptive phenotypic variation, population genetic inferences about the process of adaptation, and phylogenetic tree reconstruction. English is the common language spoken at the institute. Potential supervisors are Christian Schltterer, Carolin Kosiol, and Andrea Betancourt: See http://bit.ly/1Fxrxwi for additional information on their research interests, and http://bit.ly/1Fxrwsc for proposed research topics and other details. Informal inquires can be directed to the potential supervisor directly at (first name).(last name) at vetmeduni.ac.at (with Schltterer spelled ‘schloetterer’ in this case). Formal applications should be sent directly to the university, following the instructions here: http://bit.ly/1Fxrwsc Vienna provides and excellent environment for young researchers. It is home to a number of research groups working in population genetics and related areas (see http://bit.ly/1pSDzd6 ), many of whom participate in a training grant funding Ph.D. students working in population genetics http://bit.ly/1eUheEt Vienna is particularly attractive to Drosophila researchers, as it is home to the VDRC Stock Center, and a high-profile Drosophila research community, most notably at the IMP (http://bit.ly/1IG0bG7) and the IMBA (http://bit.ly/1IG0dh8). In addition to a stimulating scientific environment, Vienna also offers an extraordinarily high quality of life. Affordable housing, excellent public transport, great restaurants, a range of international schools, two operas, two music centers, many theaters and museums in combination with a pleasant climate make Vienna one of the most attractive cities in Europe. Cheers, Christian Schltterer, Carolin Kosiol, and Andrea Betancourt via Gmail
** *Summer 2015 REU Opportunities Mountain Lake Biological Station www.MLBS.org* ** Dear Colleagues and Friends, *Mountain Lake Biological Station* (University of Virginia) announces its 2015 summer *NSF REU undergraduate research internship program*,**now in its 23^th year.** ** REU participants are recruited from around the country for a unique 10-week learning and living research experience in the southern Appalachian Mountains. Students conduct independent research in field ecology, evolution, behavior and physiology under the supervision of station scientists. REUs are paid internships that include all station costs, travel, and a *$5,250 stipend*. *Application deadline February 20.* ** *2015 REU Internships:http://bit.ly/1Fxrxwd Please forward this information to colleagues or students you think might be interested. Thanks for your help! *//* */**** Learn all about Mountain Lake opportunities at www.MLBS.org ****/* ** *Eric Nagy*, Associate Director and REU Coordinator via Gmail
A fully funded PhD opportunity is available in the lab of Dr Casper J. Breuker (Oxford Brookes University):”How does a butterfly embryo cope with environmental stress?” (Breuker lab: http://bit.ly/1Fxrxw4) Collaboration with Dr Melanie Gibbs Centre for Ecology and Hydrology (Wallingford) Relevant Recent blogpost about our butterfly embryo research: http://bit.ly/1Fxrxw8 For enquiries about the position please email Casper Breuker: firstname.lastname@example.org Details: Full details (and how to apply) can be found at: http://bit.ly/1IRhuaG stress? at Oxford Brookes University Funding notes: Competitive three year full time studentship Eligibility: Only(!) UK/EU applicants can apply Closing date for applications: 15th March 2015 Start Date: 14th September 2015Value p.a.: Bursary of 13,863 for 2015/16 & fees EU ApplicantsRequire IELTS certificate minimum score level 6 in each of the four areas of reading, writing, listening and speaking with overall minimum score 7.0. Or undergraduate degree awarded by UK university both not older than two years. Applicants required a good Honours degree level equivalent to a UK degree BSc (minimum 2.1 or higher) Please download application form at: http://bit.ly/16tzqWT Applications will only be accepted by email to the ResearchAdministrator at the following address:email@example.com firstname.lastname@example.org via Gmail
—_000_CY1PR0801MB0986F625EEBEF8AE9ED6213BEA240CY1PR0801MB0986_ Content-Type: text/plain; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable Hello all, I am writing to ask a favor of you in distributing the following information. We are currently offering a Specialty Course titled Ecology and Evolution of Coleoptera. Although the deadline has passed, we are still have some spaces available. Ecology and Evolution of Coleoptera (Beetles) This three week course is oriented towards graduate students interested in intense training in the collection, identification and inquiry-based research on the largest order of insects, Coleoptera. Single site diversity in tropical rain forests, such as those in Costa Rica, has been estimated to be as high as 14,000 species. The study of beetles (including some of the largest and most beautiful of all insects) is not only fascinating, but economically important because the order includes numerous harmful as well as beneficial species that affect agriculture, forestry and man. Coordinators: Christopher Carlton, Richard Leschen, Nathan Lord, and Victoria Bayless. Course duration: 3 weeks (June 5-24, 2015) Credits: 2.0 Application Deadline: February 3, 2015 for priority consideration, followed by rolling admission until fully enrolled. Thank you, Andrs Santana Graduate Program Coordinator Organization for Tropical Studies San Pedro, Costa Rica. 676-2050 (506) 2524-0607 ext. 1511 Skype: andres.santana_otscro www.ots.ac.cr twitter: @ots_tropicaledu —_000_CY1PR0801MB0986F625EEBEF8AE9ED6213BEA240CY1PR0801MB0986_ Content-Type: text/html; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable
Two Graduate Student Positions (MSc or PhD) in Comparative and Population Genomics of Symbiotic and Pathogenic Fungi - Corradi Lab The Corradi Lab is currently seeking two talented graduate students (MSc or PhD level). Students will be supervised by Dr. Nicolas Corradi within a CIFAR (Canadian Institute for Advanced Research) - affiliated laboratory located in the Department of Biology of the University of Ottawa, Canada. Lab Website: http://bit.ly/OBmsOV The candidates are expected to contribute to some of the ongoing large-scale projects that focus on the Comparative and Population Genomics of two evolutionary unrelated groups of fungi: the Arbuscular Mycorrhizal Fungi (AMF) and the Microsporidia. Enquiries about specific projects can be sent to Dr. Nicolas Corradi (email@example.com). Applicants are expected to have some background in comparative genomics or populations genetics/genomics. Prior experience in either Population Genetics, Environmental Genomics, Metagenomics, genome annotation, Environmental Sampling and Strain cultivation (AMF spores), Fungal taxonomy and programming will be seen as an asset for the final selection of the candidate. Basic knowledge of Linux is desired. The lab is bilingual (English and French). For international applicants, fluency in French is considered as an asset, but is not required. A complete application package includes 1) a CV, 2) a short description of past research accomplishments and future goals, and 3) the names and e-mail addresses of at least 2 references. Evaluation of applications starts immediately and suitable candidates are expected to join the lab before September of 2015. The University of Ottawa is a large, research-intensive university, hosting over 40.000 students and located in the downtown core area of Canada’s capital city (http://bit.ly/OBmsOT). Ottawa is a vibrant, multicultural city with a very high quality of life (http://bit.ly/1dxMqIo) Applications can be sent to Dr. Nicolas Corradi (firstname.lastname@example.org). Representative publications: - Parisot N. *, Pelin A. * et al. 2014.. Microsporidian genomes harbour a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoa. Genome Biology and Evolution. 6 (9): 2289-2300. *Contributed equally. - Riley R. et al. 2014. Extreme Diversification of the MATA-HMG Gene Family in the Plant - Associated Arbuscular Mycorrhizal Fungi. New Phytologist. 201: 254-268 - James T.Y et al. 2013. Shared signatures of parasitism and phylogenomics unite the Cryptomycota and Microsporidia. Current Biology. 23 (16), 1548-1553 - Tisserant E. et al. The arbuscular mycorrhizal Glomus genome provides insights into the evolution of the oldest plant symbiosis. Proceedings of the National Academy of Sciences - USA. 110 (50), 20117-20122R576-R577 - Pombert J.F. *, Selman M.* et al. 2012. Gain and loss of multiple functionally- related horizontally transferred genes in the reduced genomes of two microsporidian parasites. Proceedings of the National Academy of Sciences - USA 109(31):12638-43 - Selman M. et al. 2011. Acquisition of an animal gene by two microsporidia. 2011. Current Biology 21: R576-R577 Nicolas Corradi Professeur Agrégé / Associate Professor Boursier de l’Institut canadien en recherches avancées / Fellow of the Canadian Institute for Advanced Research Université d’Ottawa / University of Ottawa Département de biologie / Department of Biology Pavillon Gendron / Gendron Hall Bureau 257 / Room 257 30 Marie Curie Priv. Ottawa ON Canada K1N 6N5 Tel. +1 (613) 5625800 # 6563 Website:http://bit.ly/OBmsOV Nicolas Corradi via Gmail
Dear evolDir community, one last unforeseen chance to submit your abstract to be considered for an oral contribution at SMBE 2015 in Vienna (July 12-16): The abstract system caused delays due to the required separate registration. Therefore, we will accept submissions for oral contributions until Sunday, Feb 15! Register for SBME 2015 here: http://bit.ly/14mz3wB Please register separately for the abstract system (the link to abstract submission will be sent to you in the conference registration confirmation). The Local Organising Committee is looking forward to welcome you to Vienna in July! A few meeting highlights: - All posters will be on display throughout the entire meeting. - At least four poster sessions - 27 symposia on cutting edge topics suggested by SMBE members and one Open Symposium for which 5 featured speakers will be selected though the Local Organising Committee (LOC). - Plenary speakers: Doris Bachtrog (UC Berkeley), Joe Felsenstein (Univ. of Washington), Johanna Schmitt (UC Davis) and Diethard Tautz (MPI for Evolutionary Biology). - Heavily subsidized child care - many awards (http://bit.ly/1yG2HVK): via Gmail
February 10, 2015
Recently, a number of computer programs have been released that are intended to produce phylogenetic networks representing introgression (or admixture) (see Admixture graphs – evolutionary networks for population biology).
A recent example of the use of these programs is presented by:
Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L (2014) Speciation with gene flow in equids despite extensive chromosomal plasticity. Proceedings of the National Academy of Sciences of the USA 111: 18655-18660.This study presents a phylogenetic analysis of the extant genomes of the genus Equus, the horses, asses and zebras. This analysis leads the authors to the conclusion that there is "evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs." The gene flow is indicated by the light-blue reticulations in the first diagram.
One important issue with these types of analyses is the logic on which the procedure is based. Programs like TreeMIx (used in this analysis) were developed to allow modelling of gene flow across the branches of trees at a microevolutionary (population) scale. Specifically, the graph generated by TreeMix models singular (pulse) introgression events in phylogenetic history.
The issue is that a tree is produced first, and then reticulations are added to it. The tree represents descent and the reticulations represent gene flow. But how do we produce a tree from a dataset that contains evidence of both descent and gene flow? The authors' initial tree is shown below.
The procedural logic works as follows:
(i) we assume that the traditionally recognized species exist
(ii) we assume that we have a representative sample of them, with one genome each
(iii) we construct a tree based on the assumption that there is no gene flow among the species
(iv) we then assess the species for gene flow, and discover it.
Isn't this rather circular? Surely (iv) invalidates the assumptions inherent in (i)-(iii)? How can we then assess the reliability of the sampling in (ii) and the analyses in (iii)? Why have we made assumption (i)? At best the species are fuzzy groups to one extent or another, and we do not know where we have sampled within the probabilistic space assigned to the groups.
This seems like a very poor way to go about studying the interaction between descent and gene flow. First we assume descent only, and then we assess gene flow. When we find gene flow we continue to accept the results of the initial analyses based on descent alone.
I would hate to have to justify this philosophy to someone outside phylogenetics, because I have a horrible feeling that they would either smile tolerantly or laugh outright.
This between-species situation is even more extreme for those within-species patterns where groups are recognized. Human races and domesticated breeds are two concepts that have received constant criticism. Neither races nor breeds form clear-cut groups, as there are no sharp boundaries between them, due to gene flow. Their "central locations" in genotype space are usually very different, however. Therefore it is quite possible to perform a tree-based analysis of samples from the central locations, and this would tell us a lot about descent. But it would tell us almost nothing about gene flow; and we would have a very distorted view of the phylogenetic history.
A working group to solve problems in model selection and phylogeny in mixed multi-factor meta-analysis
Meta-analysis is a statistical technique used for syntheses of results from numerous independent studies. Increasingly, evolutionary biologists need to perform meta-analysis in which the effects of numerous explanatory variables on a response variable of interest are considered, taking into account the evolutionary history of the species in the dataset. However, such analyses require analysis of numerous complex statistical models, and methods for such analyses have not been previously developed. Our working group is developing these methods and applying them to understand local adaptation, context-dependency, and the influence of evolutionary relationships on outcomes of symbiosis between plants and mycorrhizal fungi.
Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae
Background: Two non-homologous, isofunctional enzymes catalyze the penultimate step of chlorophyll a synthesis in oxygenic photosynthetic organisms such as cyanobacteria, eukaryotic algae and land plants: the light-independent (LIPOR) and light-dependent (POR) protochlorophyllide oxidoreductases. Whereas the distribution of these enzymes in cyanobacteria and land plants is well understood, the presence, loss, duplication, and replacement of these genes have not been surveyed in the polyphyletic and remarkably diverse eukaryotic algal lineages. Results: A phylogenetic reconstruction of the history of the POR enzyme (encoded by the por gene in nuclei) in eukaryotic algae reveals replacement and supplementation of ancestral por genes in several taxa with horizontally transferred por genes from other eukaryotic algae. For example, stramenopiles and haptophytes share por gene duplicates of prasinophytic origin, although their plastid ancestry predicts a rhodophytic por signal. Phylogenetically, stramenopile pors appear ancestral to those found in haptophytes, suggesting transfer from stramenopiles to haptophytes by either horizontal or endosymbiotic gene transfer. In dinoflagellates whose plastids have been replaced by those of a haptophyte or diatom, the ancestral por genes seem to have been lost whereas those of the new symbiotic partner are present. Furthermore, many chlorarachniophytes and peridinin-containing dinoflagellates possess por gene duplicates.In contrast to the retention, gain, and frequent duplication of algal por genes, the LIPOR gene complement (chloroplast-encoded chlL, chlN, and chlB genes) is often absent. LIPOR genes have been lost from haptophytes and potentially from the euglenid and chlorarachniophyte lineages. Within the chlorophytes, rhodophytes, cryptophytes, heterokonts, and chromerids, some taxa possess both POR and LIPOR genes while others lack LIPOR. The gradual process of LIPOR gene loss is evidenced in taxa possessing pseudogenes or partial LIPOR gene compliments. No horizontal transfer of LIPOR genes was detected. Conclusions: We document a pattern of por gene acquisition and expansion as well as loss of LIPOR genes from many algal taxa, paralleling the presence of multiple por genes and lack of LIPOR genes in the angiosperms. These studies present an opportunity to compare the regulation and function of por gene families that have been acquired and expanded in patterns unique to each of various algal taxa.
Spatiotemporal abnormality dynamics of the pale grass blue butterfly: three years of monitoring (2011¿2013) after the Fukushima nuclear accident
Background: Long-term monitoring of the biological impacts of the radioactive pollution caused by the Fukushima nuclear accident in March 2011 is required to understand what has occurred in organisms living in the polluted areas. Here, we investigated spatial and temporal changes of the abnormality rate (AR) in both field-caught adult populations and laboratory-reared offspring populations of the pale grass blue butterfly, Zizeeria maha, which has generation time of approximately one month. We monitored 7 localities (Fukushima, Motomiya, Hirono, Iwaki, Takahagi, Mito, and Tsukuba) every spring and fall over 3 years (2011–2013). Results: The adult ARs of these localities quickly increased and peaked in the fall of 2011, which was not observed in non-contaminated localities. In the offspring generation, the total ARs, which include deaths at the larval, prepupal, and pupal stages and morphological abnormalities at the adult stage, peaked either in the fall of 2011 or in the spring of 2012, with much higher levels than those of the parent field populations, suggesting that high incidence of deaths and abnormalities might have occurred in the field populations. Importantly, the elevated ARs of the field and offspring populations settled back to a normal level by the fall of 2012 and by the spring of 2013, respectively. Similar results were obtained not only in the spatiotemporal dynamics of the number of individuals caught per minute but also in the temporal dynamics of the correlation coefficient between the adult abnormality rate and the ground radiation dose or the distance from the Power Plant. Conclusions: These results demonstrated an occurrence and an accumulation of adverse physiological and genetic effects in early generations, followed by their decrease and leveling off at a normal level, providing the most comprehensive record of biological dynamics after a nuclear accident available today. This study also indicates the importance of considering generation time and adaptive evolution in evaluating the biological impacts of artificial pollution in wild organisms.
The alveolate translation initiation factor 4E family reveals a custom toolkit for translational control in core dinoflagellates
Background: Dinoflagellates are eukaryotes with unusual cell biology and appear to rely on translational rather than transcriptional control of gene expression. The eukaryotic translation initiation factor 4E (eIF4E) plays an important role in regulating gene expression because eIF4E binding to the mRNA cap is a control point for translation. eIF4E is part of an extended, eukaryote-specific family with different members having specific functions, based on studies of model organisms. Dinoflagellate eIF4E diversity could provide a mechanism for dinoflagellates to regulate gene expression in a post-transcriptional manner. Accordingly, eIF4E family members from eleven core dinoflagellate transcriptomes were surveyed to determine the diversity and phylogeny of the eIF4E family in dinoflagellates and related lineages including apicomplexans, ciliates and heterokonts. Results: The survey uncovered eight to fifteen (on average eleven) different eIF4E family members in each core dinoflagellate species. The eIF4E family members from heterokonts and dinoflagellates segregated into three clades, suggesting at least three eIF4E cognates were present in their common ancestor. However, these three clades are distinct from the three previously described eIF4E classes, reflecting diverse approaches to a central eukaryotic function. Heterokonts contain four clades, ciliates two and apicomplexans only a single recognizable eIF4E clade. In the core dinoflagellates, the three clades were further divided into nine sub-clades based on the phylogenetic analysis and species representation. Six of the sub-clades included at least one member from all eleven core dinoflagellate species, suggesting duplication in their shared ancestor. Conservation within sub-clades varied, suggesting different selection pressures. Conclusions: Phylogenetic analysis of eIF4E in core dinoflagellates revealed complex layering of duplication and conservation when compared to other eukaryotes. Our results suggest that the diverse eIF4E family in core dinoflagellates may provide a toolkit to enable selective translation as a strategy for controlling gene expression in these enigmatic eukaryotes.
Automatic selection of partitioning schemes for phylogenetic analyses using iterative k -means clustering of site rates
Background: Model selection is a vital part of most phylogenetic analyses, and accounting for the heterogeneity in evolutionary patterns across sites is particularly important. Mixture models and partitioning are commonly used to account for this variation, and partitioning is the most popular approach. Most current partitioning methods require some a priori partitioning scheme to be defined, typically guided by known structural features of the sequences, such as gene boundaries or codon positions. Recent evidence suggests that these a priori boundaries often fail to adequately account for variation in rates and patterns of evolution among sites. Furthermore, new phylogenomic datasets such as those assembled from ultra-conserved elements lack obvious structural features on which to define a priori partitioning schemes. The upshot is that, for many phylogenetic datasets, partitioned models of molecular evolution may be inadequate, thus limiting the accuracy of downstream phylogenetic analyses. Results: We present a new algorithm that automatically selects a partitioning scheme via the iterative division of the alignment into subsets of similar sites based on their rates of evolution. We compare this method to existing approaches using a wide range of empirical datasets, and show that it consistently leads to large increases in the fit of partitioned models of molecular evolution when measured using AICc and BIC scores. In doing so, we demonstrate that some related approaches to solving this problem may have been associated with a small but important bias. Conclusions: Our method provides an alternative to traditional approaches to partitioning, such as dividing alignments by gene and codon position. Because our method is data-driven, it can be used to estimate partitioned models for all types of alignments, including those that are not amenable to traditional approaches to partitioning.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology