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July 17, 2015

06:25

Many protein sequences have distinct domains that evolve with different rates, different selective pressures, or may differ in codon bias. Instead of modeling these differences by more and more complex models of molecular evolution, we present a multipartition approach that allows maximum-likelihood phylogeny inference using different codon models at predefined partitions in the data. Partition models can, but do not have to, share free parameters in the estimation process. We test this approach with simulated data as well as in a phylogenetic study of the origin of the leucin-rich repeat regions in the type III effector proteins of the pythopathogenic bacteria Ralstonia solanacearum. Our study does not only show that a simple two-partition model resolves the phylogeny better than a one-partition model but also gives more evidence supporting the hypothesis of lateral gene transfer events between the bacterial pathogens and its eukaryotic hosts.

July 15, 2015

00:53
Despite its ubiquity in the natural world, polymorphism is commonly disregarded or poorly sampled in phylogenetic analyses due to deliberate sampling strategy, inadequate sampling effort and limited specimen availability. Poor sampling of intraspecific variation engenders differential sampling of morphs within polymorphic species, which could generate conflicting tree topologies by altering the character-based affinity among taxa. To assess the potential magnitude of this impact, Polymorphic Entry Replacement Data Analysis (PERDA) was developed as a new script for the TNT phylogenetic program. This script simulates poor sampling of polymorphic taxa on a matrix of discrete characters by iteratively replacing each polymorphic state (e.g. [01]) with a randomly selected single state included in the original polymorphic coding (e.g. 0 or 1). The trees recovered from these subsampled data sets provide a distribution of tree distances, which indicates the level of incongruent trees resulting from different combinations of single states. Performing PERDA on empirical data sets shows alarming frequencies and magnitudes of conflicting tree topologies, demonstrating that poor sampling within polymorphic taxa could yield highly incompatible trees in many data sets. This troubling outcome undermines phylogenetic inferences based on data with poor intraspecific sampling, which is typical for palaeontological studies. With trees obtained from subsampled data sets, PERDA also generates a metaconsensus tree revealing interspecific relationships that become ambiguous due to documented levels of intraspecific variation. These collapsed clades point to taxa for which evidence should be sought to justify their taxonomic classification.
Source: Cladistics

July 14, 2015

22:30

Some years ago I came across this paper in the arXiv:
David Chavalarias and Jean-Philippe Cointet (2010) The reconstruction of science phylogeny. arXiv:0904.3154v3I was intrigued by what they could possibly mean by "science phylogeny". The abstract contains this information:
We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of scientific landscape evolution. Capitalizing on formerly introduced science mapping methods with overlapping clustering, we propose methods to reconstruct phylogenetic networks from successive science maps, and give insight into the various dynamics of scientific domains ... These results suggest that there exist regular patterns in the “life cycle” of scientific fields. The reconstruction of science phylogeny should improve our global understanding of science evolution and pave the way toward the development of innovative tools for our daily interactions with its productions. Over the long run, these methods should lead quantitative epistemology up to the point to corroborate or falsify theoretical models of science evolution based on large-scale phylogeny reconstruction from databases of scientific literature.The only actual description of phylogenetic methods is this:
The core question is: How can we reconstruct science dynamics through automated bottom-up analysis of scientific publications? ... The reconstruction of these inheritance patterns will be very useful to get a global overview of the activity and evolution of large scientific domains. Moreover, contrary to what is often encountered in biology, we should expect some hybridization events be- tween fields of research, which requires switching from phylogenetic trees to phylogenetic networks. Reconstructing the phylogenetic network of science consists in answering this simple question: given a scientific field CT' at period T' and a period T prior to T', from which fields at T does CT' derives its conceptual legacy? To achieve inter-temporal matching between fields, we have to find for each field at T the field or union of fields from which it inherits.When the authors formally published their work, the literature had changed, and the reference to phylogenetic networks had been replaced:
David Chavalarias, Jean-Philippe Cointet (2013) Phylomemetic patterns in science evolution — the rise and fall of scientific fields. PLOS One 8: e54847.The abstract contains this information:
We introduce an automated method for the bottom-up reconstruction of the cognitive evolution of science, based on big-data issued from digital libraries, and modeled as lineage relationships between scientific fields. We refer to these dynamic structures as phylomemetic networks or phylomemies, by analogy with biological evolution; and we show that they exhibit strong regularities, with clearly identifiable phylomemetic patterns.The explanation of phylomemetics is this:
[The] evolution of science, featuring innovations, cross-fertilization and selection, is suggestive of an analogy with the evolution of living organisms. We propose an adaptation of the concept of the phylogenetic tree, and combine it with the Richard Dawkins intuition of meme, to refer to phylomemetic networks (or phylomemy), which describes the complex dynamic structure of transformation of relations between terms. The concept of "phylomemetic network" is used by analogy to biological phylogenetic trees, which account for evolutionary relationships between genes. We do not make any assumption concerning the type of dynamics underlying the evolution and diffusion of terms. As such, contrarily to previous works in line with the memetics theory [9], which have already coined the term, we do not claim that cultural entities (memes) evolve following the same laws of selection as biological replicators (genes) do.The term "phylomemetics" was coined by:
Christopher J. Howe and Heather F. Windram (2011) Phylomemetics — evolutionary analysis beyond the gene. PLoS Biology 9: e1001069.However, you should note that Chavalarias & Cointet explicitly distance themselves from Howe & Windram's claim that cultural entities (memes) evolve following the same laws of selection as biological replicators (genes) do. They also insist upon a network representation rather than Howe & Windram's use of a tree.

The resulting networks are rather odd looking things, with multiple roots occurring at different times. There is one network for each of the selected fields of science (defined by their use of specific terminology). This is the one for the term "Gap junctions":


18:00
Background: Gene duplication provides raw material for the evolution of functional innovation. We recently developed a phylogenetic method that classifies evolutionary processes driving the retention of duplicate genes by quantifying divergence between their spatial gene expression profiles and that of their single-copy orthologous gene in a closely related sister species. Results: Here, we apply our classification method to pairs of duplicate genes in eight mammalian genomes, using data from 11 tissues to construct spatial gene expression profiles. We find that young mammalian duplicates are often functionally conserved, and that expression divergence rapidly increases over evolutionary time. Moreover, expression divergence results in increased tissue specificity, with an overrepresentation of expression in male kidney, underrepresentation of expression in female liver, and strong underrepresentation of expression in testis. Thus, duplicate genes acquire a diversity of new tissue-specific functions outside of the testis, possibly contributing to the origin of a multitude of complex phenotypes during mammalian evolution. Conclusions: Our findings reveal that mammalian duplicate genes are initially functionally conserved, and then undergo rapid functional divergence over evolutionary time, acquiring diverse tissue-specific biological roles. These observations are in stark contrast to the much faster expression divergence and acquisition of broad housekeeping roles we previously observed in Drosophila duplicate genes. Due to the smaller effective population sizes of mammals relative to Drosophila, these analyses implicate natural selection in the functional evolution of duplicate genes.
05:07
Although 11 studies have addressed the systematics of the four families and 281 fish species of the ecomorphologically diverse Anostomoidea, none has proposed a global hypothesis of relationships. We synthesized these studies to yield a supermatrix with 463 morphological characters among 174 ingroup species, and inferred phylogeny with parsimony and Bayesian optimization. We evaluated the applicability of the supermatrix approach to morphological datasets, tested its sensitivity to missing data, determined the impact of homoplastic characters on phylogenetic resolution, and determined the distribution of homologies and homoplasies on the topology. Despite more than 60% missing data, analyses supported the monophyly of all families, and phylogenetic structure degraded only with inclusion of species with high percentages of missing data and in analyses limited to homoplasies. The latter differs modestly from the full matrix indicating phylogenetic signal in homoplastic characters. Character distributions differ across the phylogeny, with a greater prevalence of homologies at deeper nodes and homoplasies nearer the tips than expected by chance. This may suggest early diversification into distinct bauplans with subsequent diversification of faster evolving character systems. The morphological supermatrix approach is powerful and allows integration of classical data with modern methods to examine the evolution of multiple character systems.
Source: Cladistics
05:07
Orthoptera have been used for decades for numerous evolutionary questions but several of its constituent groups, notably crickets, still suffer from a lack of a robust phylogenetic hypothesis. We propose the first phylogenetic hypothesis for the evolution of crickets sensu lato, based on analysis of 205 species, representing 88% of the subfamilies and 71% tribes currently listed in the database Orthoptera Species File (OSF). We reconstructed parsimony, maximum likelihood and Bayesian phylogenies using fragments of 18S, 28SA, 28SD, H3, 12S, 16S, and cytb (~3600 bp). Our results support the monophyly of the cricket clade, and its subdivision into two clades: mole crickets and ant-loving crickets on the one hand, and all the other crickets on the other (i.e. crickets sensu stricto). Crickets sensu stricto form seven monophyletic clades, which support part of the OSF families, “subfamily groups”, or subfamilies: the mole crickets (OSF Gryllotalpidae), the scaly crickets (OSF Mogoplistidae), and the true crickets (OSF Gryllidae) are recovered as monophyletic. Among the 22 sampled subfamilies, only six are monophyletic: Gryllotalpinae, Trigonidiinae, Pteroplistinae, Euscyrtinae, Oecanthinae, and Phaloriinae. Most of the 37 tribes sampled are para- or polyphyletic. We propose the best-supported clades as backbones for future definitions of familial groups, validating some taxonomic hypotheses proposed in the past. These clades fit variously with the morphological characters used today to identify crickets. Our study emphasizes the utility of a classificatory system that accommodates diagnostic characters and monophyletic units of evolution. Moreover, the phylogenetic hypotheses proposed by the present study open new perspectives for further evolutionary research, especially on acoustic communication and biogeography.
Source: Cladistics
02:41
The phylogeny of the superfamily Pamphilioidea is reconstructed using morphology and DNA sequence data of living and fossil taxa by employing two phylogenetic methods (maximum parsimony and Bayesian inference). Based on our results, the monophyly of Pamphilioidea and Pamphiliidae are corroborated, whereas two extinct families, Xyelydidae and Praesiricidae, are not monophyletic. Because members of Praesiricidae together with Megalodontes form a monophyletic group, we propose that the paraphyletic Praesiricidae is synonymized under Megalodontesidae (syn. nov.). The origin of Pamphilioidea is hypothesized to be as early as the Early Jurassic. To better understand morphological evolution in the early lineages of Pamphilioidea, ancestral states of the first flagellomere and the first and second abdominal terga are reconstructed on the morphology-based tree. In addition, three new genera (Medilyda, Brevilyda, Strenolyda) with five new species (Medilyda procera, M. distorta, Brevilyda provecta, Strenolyda marginalis and S. retrorsa) are described based on well-preserved xyelydid fossils from the Middle Jurassic Jiulongshan Formation of north-eastern China.
Source: Cladistics
02:40
We here argue that data from comparative studies of genome size and karyotypes provide important information for planning comparative research on genome evolution. We document for 39 species of sepsids that there is a four-fold difference in genome size (151–618 Mbp). Mapping genome sizes onto a phylogenetic hypothesis identifies that this range is the result of five genome expansions and four genome contractions that we here define as changes in genome size of more than 50 Mbp. We then generate karyotype data for 10 species and find no changes in chromosome number. The study reveals that the “Oriental” clade of sepsids is a promising system for studying genome evolution because it has experienced three genome expansion events. These events can be compared with an expansion in the “Neotropical” clade in order to reveal the mechanisms that underlie genome expansion in Sepsidae. A review of the literature on genome sizes and karyotypes reveals that they have been poorly documented in Metazoa. This means that researchers interested in the evolution of genome expansions and contractions are currently not being able to identify appropriate target taxa for genome sequencing. We thus argue for more comparative research on genome sizes and karyotypes and point out that historically species were chosen for genome sequencing for reasons not related to genome evolution (e.g. small genome size, model species status, phylogenetic position, interesting phenotypes). We believe that it is now time to use a more genome-centric selection criterion, where species for whole genome sequencing are selected based on their importance for understanding genome evolution.
Source: Cladistics
00:36
The Faculty of Sciences, Department Biology-Ethology of the University of Antwerp seeks to fill the following vacancy (m/f): Ph.D. student in Behavioural Ecology Job description: Parental care increases offspring survival, but entails fitness costs for the parents too. The resulting trade-off between investing in current offspring or in self-maintenance is a central tenet of life-history theory. But these costs and benefits vary with multiple environmental factors. When adjusting their level of investment, parents therefore have to respond to multiple cues from their ecological and social environment. Phenotypic plasticity, the ability of an individual to alter trait expression in function of the environment, plays therefore a central role. However, flexibility in parenting may sometimes be constrained, e.g. because of consistent individual differences in behavior, such as any form of foraging specialization. Moreover, parental decisions will also depend on the contribution to care by the partner. Parental responsiveness is likely to affect the efficiency of cooperation within pairs, and therewith ultimately reproductive success. In the proposed project we will apply sophisticated cross-fostering experiments in a wild population of individually marked Lesser black-backed gulls, a long-lived migratory species breeding in a heterogeneous environment. We will make use novel GPS tracking devices to investigate parental care in great detail, which we aim to combine with large scale behavioral observations and state-of-the-art physiological measures. We will apply recently developed behavioral reaction norm concepts in order to capture the multidimensional complexity of parental care. Profile and requirements: . You have a Master degree in Biology or an equivalent degree in life sciences. . You are an enthusiastic and motivated student with a strong interest in Behavioral and Evolutionary Ecology, who likes working in the field under at times harsh conditions. Preferentially you have already experience in fieldwork, but this is not essential. . You have good organizational, writing and presentation skills and should be able to work well both independently and in a team environment. We offer: . A doctoral scholarship for a period of two years, with the possibility of renewal for a further two-year period after positive evaluation, the starting date is between 1 October 2015 and 1 January 2016. . The successful applicant will join a young, dynamic and stimulating group of researchers working on all 4 major aspects of animal behaviour (causation, development, function, evolution), with particular emphasis on bird family life (maternal effects, phenotypic plasticity, parent-offspring conflict & co-adaptation) (see http://bit.ly/JzPMCb) . During fieldwork, you will form part of a small research team (2-4 PhD students, 2 field assistants) studying different aspects of gull ecology. . The project is part of an ongoing collaboration with Ghent University (Prof. Luc Lens, Dr. Liesbeth de Neve, http://bit.ly/1jgRMzy). Interested? . Applications may only be submitted online http://bit.ly/1K3yfQa , until the closing date August 9th 2015. The interviews will take place from August 17th until September 11th 2015 . For more information, contact Prof. Wendt Mller (Wendt.Mueller@uantwerpen.be) Kind regards, Josie Meaney-Ward Josie via Gmail
Source: EVOLDIR

July 12, 2015

16:30

When I was young, my siblings and I used to go to the movies regularly with my father. One of the movies I remember well, even after more than 40 years, was Jacques Tati's final cinema release, Trafic.

Tati made only five cinema features, plus several short movies, and one final made-for-TV movie (made in Sweden in 1974):
  • Jour de Fête (1949)
  • Les Vacances de Monsieur Hulot (1953)
  • Mon Oncle (1958)
  • Playtime (1967)
  • Trafic (1971)
All of them were originally in French, and were released internationally with subtitles. However, Tati came from the world of mime, and so his movies had very little dialg anyway, relying instead on the "moving picture" aspect of film making.


In spite of his small output, Tati managed to have a large impact on world cinema. His movies won several awards, notably at the Cannes Film Festival and the Venice Film Festival, and Mon Oncle won the Academy Award for Best Foreign-Language Film (and Les Vacances de Monsieur Hulot received a nomination for Best Screenplay). His movies regularly appear in "Top 50" and "Top 100" lists. Many people have acknowledged his influence, and Rowan Atkinson's character Mr Bean is basically an updated English-language version of Tati's character M. Hulot (even to the extent of making Mr Bean's Holiday). There is even a small homage to Mon Oncle near the beginning of The Blues Brothers.

Not unexpectedly, then, Tati's movies continue to attract the attention of the critics. At the aggregator site Rotten Tomatoes, his movies have 100% positive reviews, except for Mon Oncle which unexpectedly has only 92%. There are a total of 89 critics listed as having written reviews about at least one of Tati's movies, although only 28 of them have reviewed more than one of the films. Indeed, only four critics have provided individual reviews all five movies (and a few others have reviewed them collectively).

The fact that so few of the movie reviewers compare Tati's movies can be used to illustrate the dangers of assessing things in isolation. If we average the reviewer's scores for the movies, then we get this (standardized to a scale of 0-1):
Movie
Jour de Fête
Les Vacances de Monsieur Hulot
Mon Oncle
Playtime
Trafic No. reviewers
21
33
25
43
18Average score
0.833
0.879
0.833
0.920
0.782 Clearly, Playtime is the favorite, with Trafic trailing the field (although still with a good score).

On the other hand, this pattern is not quite repeated when we consider only those reviewers who provided scores for more than one movie. That is, we do not see quite the same pattern when we assess the pairwise preferences of those critics who scored at least two of the films.

Sometimes, the overall pattern is repeated. For example, you will note that Les Vacances de Monsieur Hulot scored higher than the other movies except for Playtime. Of the reviewers who also scored Les Vacances, 5 preferred Playtime, 4 scored them as equal, and 1 preferred Les Vacances, so that Playtime is clearly preferred. Similarly, 4 critics preferred Les Vacances to Trafic, 3 scored them as equal, and no-one preferred Trafic.

However, overall Les Vacances de Monsieur Hulot scored higher than Mon Oncle, which also reflects the latter's 92% "fresh" rating noted above, but this pattern is not repeated for the pairwise comparisons. If we look at the 10 reviewers who scored both of these movies, then 4 preferred Les Vacances to Mon Oncle, 3 scored them as equal, and 3 preferred Mon Oncle, thus showing little preference for one film over the other.

So, direct comparisons can be more important than independent assessments.

As usual, we can use a phylogenetic network as a form of exploratory data analysis, to compare all five movies in a single diagram. I first used the gower similarity to calculate the similarity of the five movies based on those 20 reviewers who scored more than one movie. This was followed by a Neighbor-net analysis to display the between-film similarities as a phylogenetic network. So, films that are closely connected in the network are similar to each other based on their scores, and those that are further apart are progressively more different from each other.


Clearly, the movies are not really very different from each other in score, and there is little preference for one over another for these 20 critics. This contrasts with the scores from all 89 critics.

The "audience score" at Rotten Tomatoes differs somewhat from the critics' scores. They score Playtime (90%) and Mon Oncle (89%) at the top, followed by Les Vacances de M. Hulot (86%) and Jour de Fête (85%), and finally Trafic (77%). In spite of this, I still have a soft spot for Trafic, although Mon Oncle is my personal favourite.

July 11, 2015

02:23

–_000_016E5005C6D68045B5294CF56C223027163D475FCNMB02WVPcorere_ Content-Type: text/plain; charset=“iso-8859-1” Content-Transfer-Encoding: quoted-printable Opportunities available to participate in an ongoing project at the CNRS in Moulis, France, investigating aggressive and social behavior in wild and captive blue and great tits. We are seeking two motivated volunteer research assistants to help with behavioral analysis from videos recorded at winter feeders and in captivity. Volunteers may also conduct analyses of ornamental patches from photos and feather samples via spectrophotometry. The positions are most suitable for graduates looking for a PhD position and seeking to gain further research experience. Good organizational skills, commitment and attention to details are required; previous experience with video analyses would also be desirable though not necessary. Positions start as soon as possible and will continue into Summer/Fall (dates flexible). Ideally, volunteers will spend at least a few days at the lab to get acquainted with analyses protocols, while subsequent work may be conducted remotely. Applicants should send a cover letter and CV, including names and e-mail addresses of three potential referees, as soon as possible. For further information and applications, please contact Enrico Sorato: enrico.sorato@ecoex-moulis.cnrs.fr or Alexis Chaine: Alexis.CHAINE@ecoex-moulis.cnrs.fr –_000_016E5005C6D68045B5294CF56C223027163D475FCNMB02WVPcorere_ Content-Type: text/html; charset=“iso-8859-1” Content-Transfer-Encoding: quoted-printable

Opportunities available to participate in an ongoing project at the CNRS in Moulis, France, investigating aggressive and social behavior in wild and captive blue and great tits. We are seeking two motivated volunteer research assistants to help with behavioral analysis from videos recorded at winter feeders and in captivity. Volunteers may also conduct analyses of ornamental patches from photos and feather samples via spectrophotometry.  The positions are most suitable for graduates looking for a PhD position and seeking to gain further research experience. Good organizational skills, commitment and attention to details are required; previous experience with video analyses would also be desirable though not necessary. Positions start as soon as possible and will continue into Summer/Fall (dates flexible). Ideally, volunteers will spend at least a few days at the lab to get acquainted with analyses protocols, while subsequent work may be conducted remotely. Applicants should send a cover letter and CV, including names and e-mail addresses of three potential referees, as soon as possible.  For further information and applications, please contact Enrico Sorato: enrico.sorato@ecoex-moulis.cnrs.fr  or Alexis Chaine: Alexis.CHAINE@ecoex-moulis.cnrs.fr –_000_016E5005C6D68045B5294CF56C223027163D475FCNMB02WVPcorere via Gmail
Source: EVOLDIR
02:07
2 PhD opportunities to study virulence of chytridiomycosis at James Cook University, Townsville, Queensland, Australia Chytridiomycosis has caused amphibian declines and extinctions globally as it has spread through naïve populations. It is now endemic in much of its suitable range in Australia where it still causes high mortality rates and threatens amphibian biodiversity. We have funds to investigate mechanisms of virulence and how virulence of Batrachochytrium dendrobatidis (Bd) is evolving as it adapts to new habitats. One project is focussed on how Bd causes disease and will involve bioassays, toxin identification and possibly gene knockouts. The second project involves comparing Australian Bd strains to assess growth characteristics and virulence. Both projects may involve frog transmission experiments. The students will be able to pursue areas of interest within this framework. The candidates will be part of the enthusiastic and supportive One Health Research Group at JCU, see http://bit.ly/1dRQdGR 7907.html and Facebook:http://on.fb.me/1M1pO8B. The projects are multidisciplinary and involve collaborators such as Qld Institute of Medical Research in Brisbane. The outcomes of the projects are likely to lead to the improved conservation of amphibian biodiversity and may contribute to theories on host/pathogen dynamics. The selected applicants would need to apply for an APA or international PhD scholarship (due 31 Aug). Please see http://bit.ly/1dRQbyS Ideal PhD candidates will have: 1^ st class honours or equivalent research credentials in a relevant discipline such as biology or veterinary science majoring in microbiology, biochemistry, molecular biology or pathology. 2. Demonstrated publication record in high impact journals 4. Demonstrated interpersonal and communication skills. Please send CV, cover letter and 2 reference letters to Lee.Berger@jcu.edu.au and Alex.Roberts@jcu.edu.au. Assessments of submissions begin 15 July. Thank you, Tiffany Tiffany A. Kosch Postdoctoral Research Fellow College of Public Health, Medical, and Veterinary Sciences James Cook University Townsville, QLD 4811 AUS Tel: +61 89 360 6600 Email: tiffany.kosch@gmail.com Tiffany Kosch via Gmail
Source: EVOLDIR
02:07

Field assistant: butterfly behaviour, Gamboa, Panama Salary: $800/month Dates: October 1st, 2015 - March 31st, 2016, with possibility of extension Description: We are seeking a field assistant for a research project on Heliconius butterfly behaviour and genetics at the Smithsonian Tropical Research Institute in Gamboa, Panama. Primary duties will be day-to-day maintenance of captive butterfly populations (including feeding butterflies and caterpillars, managing host plants, and assisting with insectary maintenance) and assistance with behavioural experiments on butterflies. Work will take place weekdays (up to 8 hours/day) and two weekends per month, with additional time off by arrangement with the supervisor. The field assistant will live in STRI housing in Gamboa, Panama, which is about 1 hour from Panama City. Rent, generally $220-240/month in Gamboa, is not provided. Note that STRI requires that all researchers have health coverage, and this is not provided but can be purchased through STRI relatively cheaply. Financial assistance with transportation to Gamboa may be available to those with financial need. Applicants should have training in biology or a related field, and/or have experience working in a field research setting. The ability to work independently and in a somewhat remote environment is crucial. Fluency in Spanish, experience working with butterflies or doing behavioural research, and experience living in tropical environments would be assets for this position, but are not required. Interested applicants should send a cover letter, CV/resume, and contact information for up to three references to southcott@uchicago.edu by August 1st, 2015. via Gmail

Source: EVOLDIR
02:07

–Apple-Mail=_AC9C8554-7DA3-4EA2-8D7B-5F6CB9F89BC6 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Dear Brian Golding, You will find as attached file a text describing an open PhD position available at the Musum National d'Histoire Naturelle (Paris, France). Please could you put it on EvolDir ? Thank you in advance for your help ! Best regards, Alexandre Alexandre Hassanin Musum national d'Histoire naturelle Institut de Systmatique, Evolution, Biodiversit (ISYEB) UMR 7205 MNHN CNRS UPMC 55, rue Buffon - CP N 51 75005 Paris - France Tel: 33 (0)1 40 79 56 93 Fax: 33 (0)1 40 79 30 63 hassanin@mnhn.fr http://bit.ly/1UHWZRl –Apple-Mail=_AC9C8554-7DA3-4EA2-8D7B-5F6CB9F89BC6 Content-Type: multipart/mixed; boundary=“Apple-Mail=_13C03319-D90E-40AD-9D39-CCC7ECB9F4B4” –Apple-Mail=_13C03319-D90E-40AD-9D39-CCC7ECB9F4B4 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252

Dear Brian Golding,You will find as attached file a text describing an open PhD position available at the Musum National d'Histoire Naturelle (Paris, France). –Apple-Mail=_13C03319-D90E-40AD-9D39-CCC7ECB9F4B4 Content-Disposition: attachment; filename=MNHNParis.GiraffaEvolution.txt Content-Type: text/plain; name=“MNHNParis.GiraffaEvolution.txt” Content-Transfer-Encoding: quoted-printable A 3-year Phd position on “Comparative genomics of extant and past populations of giraffesâ€
Source: EVOLDIR
01:51
On behalf of our research training group GRK 2010 RESPONSE - Biological Responses to Novel and Changing Environments (http://bit.ly/1KWxecX) I would like to anounce that we will organise a Summer School on Phenotypic Plasticity from 14th to 18th September, 2015 at the Ernst-Moritz-Arndt University of Greifswald, Germany. The summer school is open to a limited number of external graduate / PhD students. Michael G. Schöner M.A. Coordinator GRK 2010 RESPONSE Zoological Institute and Museum Johann-Sebastian-Bach-Str. 11/12 D - 17489 Greifswald Tel.: +49 (0)3834 86-4273 Fax.: +49 (0)3834 86-4252 schoenerm@uni-greifswald.de Safe trees - think twice before printing Michael Schner via Gmail
Source: EVOLDIR
00:32
Please submit an abstract for our bacterial evolution super-brainstorm http://bit.ly/1RpAnWr Thank you! Daniel Daniel Falush via Gmail
Source: EVOLDIR
00:32
Dear All, We are happy to announce an “Advanced course in RADSeq analyses and data interpretation, 5-9 October 2015, Lund University (Sweden). Course leaders: Julian Catchen (University of Illinois) William Cresko (University of Oregon) Dag Ahrn (Lund University) More info and application form: http://bit.ly/1RpAq4M Please spread among colleagues and PhDs! Best regards, GENECO Research School http://bit.ly/15PE0x1 Bengt Hansson (PhD, Associate Professor) Department of Biology, Lund University Ecology Building, SE-22362 Lund, Sweden Bengt Hansson via Gmail
Source: EVOLDIR
00:01
The Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e. V. (www.izw-berlin.de) together with the Research Institute of Wildlife Ecology (FIWI) at the University of Veterinary Medicine, Vienna (http://bit.ly/1GmIHjw), the Weierstra Institute for Applied Analysis and Stochastics (WIAS, www.wias-berlin.de), the Institut for Virology of the Freie Universitt Berlin (FU, http://bit.ly/17TQXsy) and the Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB, www.igb-berlin.de) have formed a consortium to implement the AQUAVIR project funded by the Leibniz Association. Water is required for life. We have accumulated evidence suggesting it may be an overlooked viral vector. In climatic zones with seasonally limited precipitation such as east Africa and central Asia, animals congregate at high densities at scarce water sources. We hypothesize that viruses shed in water in this ecological setting would gain a fitness advantage if they evolved traits permitting the retention of their infectivity in water and a reduction in host specificity. The AQUAVIR project will determine whether water is a significant viral vector and how viruses behave mechanistically in such settings, and develop mathematical models to understand the epidemiology and evolution of this phenomenon. We therefore seek to fill the following position: doctoral student in evolutionary disease ecology: African waterholes Specific tasks: Determine the distribution, persistence and species usage of transient water sources; determine the effect of water source characteristics on virus presence; non-invasively determine if physiological stress, reproduction or lactation are correlated with virus excretion in zebras; analyse environmental DNA of water samples to compare genetic diversity of potential viral host sequence diversity obtained directly from animals compared to their drinking sources. This is a team project consisting of 2 doctoral students and 2 postdoctoral researchers with the overall goal of understanding the potential role of water as a viral vector. However, each position represents an independent project. Though independent, the successful candidate will be expected to collaborate intensively with all members of the team. Requirements: A completed master’s/diploma degree in biological sciences; clean driver’s licence; competence in statistical methods; ability to work independently in challenging environments and to interact with scientists from a wide variety of fields; strong interest in wildlife, conservation and evolutionary biology; a background in ecology. Those candidates with previous experience with wildlife, experience in field research and off-road driving experience will have an advantage. The position will be supervised by Prof Alex Greenwood (IZW Dept of Wildlife Diseases) and Dr Marion L East (IZW Dept of Evolutionary Ecology). Applications and working environment In our consortium we offer state-of-the-art methodology and a stimulating international research environment within an interdisciplinary, collaborative context. The doctoral positions are initially limited to two years, with the possibility for extension to a maximum of three years. The position will start on September 1, 2015. Salary is according to TVD (65%). As a member of the Leibniz Association, and lead institution of the AQUAVIR consortium, the IZW is an equal opportunity employer, determined to increase the proportion of women in successful scientific careers, and particularly encourages women to apply. Preference will be given to disabled applicants with the same qualifications. Enquiries or questions should be directed to Prof. Alex Greenwood, email: greenwood@izw-berlin.de or Dr. Marion East, email: east@izw-berlin.de. Please email complete application documents as a single pdf-file including a letter of motivation, CV, copies of relevant degrees, and names and contact details of two referees as soon as possible but no later than August 17, 2015 via the IZW’s online-job-market (button “Apply online”). Stephanie Vollberg Personalsachbearbeiterin Abteilung Verwaltung/Technische Dienste/Bibliothek Leibniz-Institut fr Zoo- und Wildtierforschung (IZW) im Forschungsverbund Berlin e.V. Alfred-Kowalke-Str. 17 10315 Berlin DEUTSCHLAND Postfach 70 04 30, 10324 Berlin Tel.: + 49 - 30 - 5168107 Fax.: + 49 - 30 - 5126104 http://bit.ly/1xBHEqwwww.izw-berlin.de) together with the Research Institute of Wildlife Ecology (FIWI) at the University of Veterinary Medicine, Vienna (http://bit.ly/1GmIHjw), the Weierstra Institute for Applied Analysis and Stochastics (WIAS, www.wias-berlin.de), the Institut for Virology of the Freie Universitt Berlin (FU, http://bit.ly/17TQXsy) and the Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB, www.igb-berlin.de) have formed a consortium to implement the AQUAVIR project funded by the Leibniz Association. Water is required for life. We have accumulated evidence suggesting it may be an overlooked viral vector. In climatic zones with seasonally limited precipitation such as east Africa and central Asia, animals congregate at high densities at scarce water sources. We hypothesize that viruses shed in water in this ecological setting would gain a fitness advantage if they evolved traits permitting the retention of their infectivity in water and a reduction in host specificity. The AQUAVIR project will determine whether water is a significant viral vector and how viruses behave mechanistically in such settings, and develop mathematical models to understand the epidemiology and evolution of this phenomenon. We therefore seek to fill the following position: doctoral student in evolutionary disease ecology: African waterholes Specific tasks: Determine the distribution, persistence and species usage of transient water sources; determine the effect of water source characteristics on virus presence; non-invasively determine if physiological stress, reproduction or lactation are correlated with virus excretion in zebras; analyse environmental DNA of water samples to compare genetic diversity of potential viral host sequence diversity obtained directly from animals compared to their drinking sources. This is a team project consisting of 2 doctoral students and 2 postdoctoral researchers with the overall goal of understanding the potential role of water as a viral vector. However, each position represents an independent project. Though independent, the successful candidate will be expected to collaborate intensively with all members of the team. Requirements: A completed master’s/diploma degree in biological sciences; clean driver’s licence; competence in statistical methods; ability to work independently in challenging environments and to interact with scientists from a wide variety of fields; strong interest in wildlife, conservation and evolutionary biology; a background in ecology. Those candidates with previous experience with wildlife, experience in field research and off-road driving experience will have an advantage. The position will be supervised by Prof Alex Greenwood (IZW Dept of Wildlife Diseases) and Dr Marion L East (IZW Dept of Evolutionary Ecology). Applications and working environment In our consortium we offer state-of-the-art methodology and a stimulating international research environment within an interdisciplinary, collaborative context. The doctoral positions are initially limited to two years, with the possibility for extension to a maximum of three years. The position will start on September 1, 2015. Salary is according to TVD (65%). As a member of the Leibniz Association, and lead institution of the AQUAVIR consortium, the IZW is an equal opportunity employer, determined to increase the proportion of women in successful scientific careers, and particularly encourages women to apply. Preference will be given to disabled applicants with the same qualifications. Enquiries or questions should be directed to Prof. Alex Greenwood, email: greenwood@izw-berlin.de or Dr. Marion East, email: east@izw-berlin.de. Please email complete application documents as a single pdf-file including a letter of motivation, CV, copies of relevant degrees, and names and contact details of two referees as soon as possible but no later than August 17, 2015 via the IZW’s online-job-market (button “Apply online”). Stephanie Vollberg Personalsachbearbeiterin Abteilung Verwaltung/Technische Dienste/Bibliothek Leibniz-Institut fr Zoo- und Wildtierforschung (IZW) im Forschungsverbund Berlin e.V. Alfred-Kowalke-Str. 17 10315 Berlin DEUTSCHLAND Postfach 70 04 30, 10324 Berlin Tel.: + 49 - 30 - 5168107 Fax.: + 49 - 30 - 5126104 http://bit.ly/1xBHEqw :: Forschung fr den Artenschutz :: “Vollberg, Stephanie” via Gmail
Source: EVOLDIR