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August 22, 2015
Dear colleagues, Registration is open for the course “Using Phytools (and other R packages) to Study Macroevolution on Phylogenies”, taught by Dr. Liam Revell (University of Massachusetts Boston, USA), developer of Phytools. Dates: March 14th-17th, 2016. PLACE: Facilities of the Centre de Restauraci i Interpretaci Paleontologica, Els Hostalets de Pierola, Barcelona (Spain). Registration and more info: http://bit.ly/1h2AtTr PROGRAM: 1. Introduction to phylogenies & the comparative method. 2. Introduction the basics of the R statistical computing environment. 3. Introduction to reading, writing, manipulating, & visualizing phylogenies and comparative data in R. 4. Models of phenotypic trait evolution on trees: Brownian motion. 5. Simulating Brownian motion on trees using R. 6. Introduction to the phylogenetic comparative method: Phylogenetic independent contrasts. 7. Phylogenetic independent contrasts & exploring the properties of contrasts regression using simulation in R. 8. Phylogenetic generalized least squares regression & phylogenetic generalized ANOVA. 9. Multivariate statistical methods with phylogenies: Phylogenetic principal components analysis, canonical correlation analysis, & other approaches. 10. Phylogenetic PCA & phylogenetic CCA in R. 11. Continuous character models of trait evolution on phylogenies. 12. Fitting continuous character models to univariate trait data in R. 13. Ancestral state reconstruction I: Continuous characters. 14. Reconstructing ancestral states for continuous traits on phylogenies using R. 15. Ancestral state reconstruction II: Discrete characters. 16. Reconstructing ancestral states for discrete traits on phylogenies using R. 17. Exploring the limitations of ancestral state reconstruction for continuous & discrete characters on phylogenies using R. 18. Testing for the influence of one discrete character on a second using Pagels (1994) method. 19. Exploring the promise & limitations of the Pagel (1994) method using R. 20. Analyzing discrete character coevolution, and the evolution of discrete & continuous characters using the threshold model. 21. Fitting models of discrete & continuous character evolution on trees using the threshold model. 22. Multi-rate, multi-regime, & multivariate models of character evolution on phylogenies. 23. Fitting multi-regime & multivariate models for continuous character evolution in R. 24. Visualizing tr ees & phylogenetic comparative data. 25. Plotting phylogenies & comparative data using R. 26. Wrap-up & optional additional exercise or lecture. Knowledge of R is required. This course is organized by Transmitting Science, the Institut Catal de Paleontologia and the Centre de Restauraci i Interpretaci Paleontologica. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban-Trivigno, Ph.D. Course Coordinator firstname.lastname@example.org Transmitting Science http://bit.ly/1gdSpYn email@example.com via Gmail
Laboratory Technician Position Our lab at the University of California Santa Cruz is searching for a full-time lab technician with experience in biological research for a project investigating the interaction of marine phytoplankton and zooplankton and their respective microbiome. The position is supported until 2017 with renewal every year contingent of funding availability. Santa Cruz California is a beautiful place surrounded by redwoods and beautiful beaches and offers a lot of outdoor activities. For more details on the position, please see the posting on UCSC HR site, http://bit.ly/1Eb3h72 or email firstname.lastname@example.org. Essential Functions and Responsibilities: The laboratory technician will assist in the development of gnotobiotic systems on zooplankton and phytoplankton with a focus on studying the ecology, evolution and mechanisms of microbiome-phytoplankton/zooplankton interactions. The technician will be responsible for overseeing daily workings of the lab, conducting experiments and maintaining zooplankton and phytoplankton stocks. The applicant must be willing to work independently and communicate effectively with the principal investigator (PI). The technician will be working alongside undergraduate students, and will be expected to assist the PI in delegating tasks. Excellent skills in organization and communication, clear attention to details with accurate record keeping are therefore essential. Qualifications: Applicants should have a minimum of a bachelors degree in biology, microbiology, molecular biology or related subject with experience working in a research laboratory setting and is capable of going out on boats for ocean sampling. The technician will be trained on how to do microscopy for FISH bacterial probing and assist in preparation of samples for transcriptomics and metagenomics. Proficiency with computers and Microsoft Excel is required. The technician will also be taught on how to analyze next-gen sequences using bioinformatics tools. Preferred Qualifications: - Experience with molecular biology and microbiology methods including PCR, qPCR, RNA and DNA extractions and sequence data analysis. - Knowledge of marine biology, microbiology, evolution or ecology Interested candidates should submit a letter of interest, resume and the names and contact information of three professional references to email@example.com. Marilou P. Sison-Mangus Assistant Professor, Ocean Sciences University of California Santa Cruz 1156 High Street, Santa Cruz, CA 95064 Phone: 831-459-5563 Fax Main Office: 831-459-4882 firstname.lastname@example.org via Gmail
August 21, 2015
EVOLUTION AND ECOLOGY JUNIOR SPECIALIST POSITION AVAILABLE The Wainwright lab at the University of California, Davis, seeks a junior specialist to assist with research on the functional morphology and evolution of fishes. This person will organize and oversee the use of the laboratory by lab members, maintain live fishes in the laboratory, and conduct studies on their feeding and locomotion functional morphology. Additional responsibilities are managing a research collection of preserved and cleared and stained fish specimens and assisting other lab members with research projects. Requirements: Bachelor’s degree in biological sciences or related field required. Some previous experience in the field is required. The applicant must possess excellent written and oral communication skills. The ideal applicant will have a strong interest in fishes, functional morphology and phylogenetics, or some combination of these topics, and will have ambitions to go on to graduate school in the next couple of years. This is a full time, 40 hour per week position. Starting date can be immediately but before mid-October, with a proposed duration of one year with possibility of extension. Salary: $36,984 annually plus health benefits Application: please submit by email a letter of interest, CV, and contact information for 3 references to: Peter Wainwright email@example.com Peter Wainwright via Gmail
PhD Position in the research unit “Evolutionary Ecology of Marine Fishes” at GEOMAR Helmholtz Centre for Ocean Research Kiel The PhD student will be employed on the research project “implications of anthropogenic stressors on rapid co-adaptation in a tripartite species interaction”. The research program is embedded in the DFG funded priority programme “Rapid Evolutionary Adaptation: Potential and Constraints” (SPP1819), which consists of a group of experts working on rapid adaptation distributed all over Germany. Regular meetings with all experts guarantee a unique opportunity to establish a solid network and to discuss research ideas and data. The project leader is Dr. Carolin Wendling (GEOMAR, Kiel) in collaboration with Dr. Olivia Roth (GEOMAR, Kiel) and Dr. Heiko Liesegang (University of Göttingen). A close cooperation with a second PhD student from the University of Göttingen in the same project is expected. Project description: The project aims on investigating rapid evolutionary adaptation in response to anthropogenic stressors in a three-way host-parasite interaction. The work will be conducted on an established model system consisting of pipefish Syngnathus typhle (i.e the final animal host), bacteria of the genus Vibrio, and their associated temperate phages (i.e. viruses that infect Vibrio bacteria). In a unique research approach we will address (1) the implications of bioinvasion (2) the effects of temperature heterogeneity and (3) the exposure to antibiotics on the coevolutionary dynamics between the three players. In each of the three goals the empirical approach will consist of an in vitro evaluation of local adaptation among the players involved. We will then use evolution experiments and whole genome sequencing to investigate how each of the anthropogenic stressors affects phage-bacteria adaptation in vitro and how this correlates with bacterial virulence against local pipefish in vivo. The GEOMAR, the University of Kiel and the Max Planck Institute for Evolutionary Biology in Plön offer a stimulating research environment with focus on evolutionary biology. The PhD student will have the possibility to join one of our two graduate schools, either the International Max-Planck-Research School (IMPRS) “Evolutionary Biology” or the “Integrated School of Ocean Sciences” (ISOS). Kiel is the capital of the most Northern state of Germany, directly located at the coast of the Baltic Sea. The town offers many opportunities for leisure activities; in particular people enjoying water sports will love the environment. Qualification The successful candidate is required to have a Master or Diploma in Biology or related topics. We expect a motivated PhD student with a high commitment to science that has a strong background in evolutionary biology, preferably experimental evolution and/or skills in applied bioinformatics to analyse NGS-generated high-throughput genomic data. Knowledge of microbiological and molecular biology methods as well as applied bioinformatics is desired. In addition, the PhD student should have good English language skills and the ability to work in team. Furthermore, the candidate is expected to spend some time in the cooperating group at the University of Göttingen (Dr. Liesegang). The position is available for a 3-year funding. The salary will be 65% according to class E13 TVöD of the German tariff for public employees. The GEOMAR | Helmholtz Centre for Ocean Research is an equal opportunity employer and encourages female scientists and scientists with disabilities to apply. Applications including a one-page statement of research interests and motivation, CV and contact details of 2 referees should be sent as a single PDF file (max size 1MB) no later than 20^. September 2015 to the following e-mail address with a single pdf file, using the keyword “Rapid Evolution”: firstname.lastname@example.org For further information do not hesitate to contact Carolin Wendling (email@example.com) or visit the webpage: http://bit.ly/1NJa33J Dr. Carolin Wendling PostDoc GEOMAR | Helmholtz-Zentrum für Ozeanforschung Kiel Düsternbrooker Weg 20 24105 Kiel, Germany Tel.: 0431 600 4569 Fax: 0431 600 4553 firstname.lastname@example.org Carolin Wendling via Gmail
PhD projects@JCU on Advanced Shrimp Breeding and Evolutionary Genomics As part of a large collaborative project in Advanced Shrimp Breeding and Genomics, we are looking for various motivated students with skills in genomics, transcriptomics and evolutionary bioinformatics for the following projects: Project 1 Comparative, evolutionary and functional genomics of the black tiger prawn (James Cook University & University of Sydney) This project will be a component of the full genome assembly of an inbred black tiger prawn (Penaeus monodon) based on a combination of short-read sequences and standard mate-pair end Illumina together with the use of long-read sequencing data based on PacBio, HiC, Nanopore platforms for improved hybrid assembly (scaffold/chromosome level). After genome annotation, the project will aim to find syntenies and reconstruct the evolutionary history of Decapods/crustaceans by comparing the P. monodon genome to the genomes of Daphnia, Artemia, Litopenaeus vannamei and potentially other decapods/crustaceans. Project 2 â€“ Functional transcriptomics of viral infection in the black tiger prawn (James Cook University and CSIRO) This project will examine whether the manner in which a black tiger prawn (Penaeus monodon) is challenged with Gill-associated virus (GAV) affects what defence response pathways can be activated to protect the prawn against infection/disease. Essential components of the project will be GAV challenge trials in P. monodon and the generation and interrogation of RNAseq data to identify/predict genes and gene pathways activated in response to GAV challenge via the various infection routes examined. Silencing of gene expression using RNA interference (RNAi) will also be employed to further explore the functioning of genes predicted to have pivotal roles in the prawn defense response. Requirements The desired candidates will preferably have a background in molecular genetics (mainly for project 2) complemented with proven skills in next-generation sequencing approaches and computational analyses (project 1 and 2). Successful candidates will either be enrolled through James Cook University (or University of Sydney), and will work embedded or alongside partners of the ARC Research Hub for Advanced Prawn Breeding depending on the project (ie CSIRO, AGRF). The student will need to obtain an Australian Postgraduate Award (APA) or a JCU PGRS award for national/international students through James Cook University; therefore a first class Honours or Masters Degree and/or evidence of publishing in international peer-reviewed scientific journals are highly recommended. About James Cook University James Cook University is one of Australia’s most distinctive universities with a focus on creating a brighter future for life in the tropics worldwide. The University is located in the vibrant regional community of tropical Queensland, which has one of the fastest growing economies in Australia, adjacent to the Great Barrier Reef and Wet Tropics World Heritage Areas. The University’s internationally recognized research is matched by strong commitment to its region, partners and teaching. For more information on additional PhD opportunities, including what the Hub will achieve and partners please visit http://bit.ly/1PpnAhm For further details on projects and information on how to apply, please contact Professor Dean Jerry (email@example.com), Director ARC Hub for Advanced Prawn Breeding, Townsville, Australia. Gregory Maes, Ph.D. Lecturer in Evolutionary and Applied Genetics Centre for Sustainable Tropical Fisheries and Aquaculture School of Marine and Tropical Biology James Cook University Ph: +61 (0)7 4781 4790; E-mail: firstname.lastname@example.org Office: ATSIP DB145-314 (Molecular Ecology and Evolution Laboratory) Personal webpage: http://bit.ly/1eWCsAh School webpage: http://bit.ly/1eWCsAj “Maes, Gregory” via Gmail
Dear Members, Do you take nice walks along the coast? If so, we are after powdery mildew samples from Sea beet (Beta maritima) from around the world. If not, do you take nice walks in the countryside? If so, we are after powdery mildew samples from Sugar beet (Beta vulgaris) from around the world. Our focus for the project is primarily the UK and if you can send us a leaf we would be most grateful. If you are outside the UK we must ask that you do a DNA extraction (sample the leaf and please get in touch). If you are out and about and you identify a whitish dusty coating on the leaf of a Beta species (coastal species look like dock (Rumex)) if you can snip the leaf record your location and get in touch that would be great! Please contact email@example.com Lawrence.Percival-Alwyn@tgac.ac.uk for more information: if you have snipped a leaf, if you would like to know how to identify beets or if you just want to know more about the project. Best, Mark Dr Mark McMullan Postdoctoral Research Associate The Genome Analysis Centre Norwich Research Park Twitter: mcmullan0 Skype: mark.mcmullan http://bit.ly/1Lo7VBc “Mark McMullan (TGAC)” via Gmail
August 20, 2015
What triggers colour change? Effects of background colour and temperature on the development of an alpine grasshopper
Background: Colour polymorphisms are a fascinating facet of many natural populations of plants and animals, and the selective processes that maintain such variation are as relevant as the processes which promote their development. Orthoptera, the insect group that encompasses grasshoppers and bush crickets, includes a particularly large number of species that are colour polymorphic with a marked green-brown polymorphism being particularly widespread. Colour polymorphism has been associated with the need for crypsis and background matching and background-dependent homochromy has been described in a few species. However, when and how different environmental conditions influence variation in colour remains poorly understood. Here we test for effects of background colour and ambient temperature on the occurrence of colour morph switches (green to brown or brown to green) and developmental darkening in the alpine dwelling club-legged grasshopper Gomphocerus sibiricus. Results: We monitored individually housed nymphae across three of their four developmental stages and into the first week after final ecdysis. Our data show an absence of colour morph switches in G. sibiricus, without a single switch observed in our sample. Furthermore, we test for an effect of temperature on colouration by manipulating radiant heat, a limiting factor in alpine habitats. Radiant heat had a significant effect on developmental darkening: individuals under low radiant heat tended to darken, while individuals under high radiant heat tended to lighten within nymphal stages. Young imagoes darkened under either condition. Conclusions: Our results indicate a plastic response to a variable temperature and indicate that melanin, a multipurpose pigment responsible for dark colouration and presumed to be costly, seems to be strategically allocated according to the current environmental conditions. Unlike other orthopterans, the species is apparently unable to switch colour morphs (green/brown) during development, suggesting that colour morphs are determined genetically (or very early during development) and that other processes have to contribute to crypsis and homochromy in this species.
Systematics and historical biogeography of the old world butterfly subtribe Mycalesina (Lepidoptera: Nymphalidae: Satyrinae)
Background: Butterflies of the subtribe Mycalesina have radiated successfully in almost all habitat types in Africa, Madagascar, the Indian subcontinent, Indo-China and Australasia. Studies aimed at understanding the reasons behind the evolutionary success of this spectacular Old World butterfly radiation have been hampered by the lack of a stable phylogeny for the group. Here, we have reconstructed a robust phylogenetic framework for the subtribe using 10 genes from 195 exemplar taxa. Results: We recovered seven well supported clades within the subtribe corresponding to the five traditional genera (Lohora, Heteropsis, Hallelesis, Bicyclus, Mycalesis), one as recently revised (Mydosama) and one newly revised genus (Culapa). The phylogenetic relationships of these mycalesine genera have been robustly established for the first time. Within the proposed phylogenetic framework, we estimated the crown age of the subtribe to be 40 Million years ago (Mya) and inferred its ultimate origin to be in Asia. Our results reveal both vicariance and dispersal as factors responsible for the current widespread distribution of the group in the Old World tropics. We inferred that the African continent has been colonized at least twice by Asian mycalesines within the last 26 and 23 Mya. In one possible scenario, an Asian ancestor gave rise to Heteropsis on continental Africa, which later dispersed into Madagascar and most likely back colonised Asia. The second colonization of Africa by Asian ancestors resulted in Hallelesis and Bicyclus on continental Africa, the descendants of which did not colonise other regions but rather diversified only in continental Africa. The genera Lohora and Mydosama are derivatives of ancestors from continental Asia. Conclusion: Our proposed time-calibrated phylogeny now provides a solid framework within which we can implement mechanistic studies aimed at unravelling the ecological and evolutionary processes that culminated in the spectacular radiation of mycalesines in the Old World tropics.
Background: Despite their abundance, unspliced EST data have received little attention as a source of information on non-coding RNAs. Very little is know, therefore, about the genomic distribution of unspliced non-coding transcripts and their relationship with the much better studied regularly spliced products. In particular, their evolution has remained virtually unstudied. Results: We systematically study the evidence on unspliced transcripts available in EST annotation tracks for human and mouse, comprising 104,980 and 66,109 unspliced EST clusters, respectively. Roughly one third of these are located totally inside introns of known genes (TINs) and another third overlaps exonic regions (PINs). Eleven percent are “intergenic”, far away from any annotated gene. Direct evidence for the independent transcription of many PINs and TINs is obtained from CAGE tag and chromatin data. We predict more than 2000 3’UTR-associated RNA candidates for each human and mouse. Fifteen to twenty percent of the unspliced EST cluster are conserved between human and mouse. With the exception of TINs, the sequences of unspliced EST clusters evolve significantly slower than genomic background. Furthermore, like spliced lincRNAs, they show highly tissue-specific expression patterns. Conclusions: Unspliced long non-coding RNAs are an important, rapidly evolving, component of mammalian transcriptomes. Their analysis is complicated by their preferential association with complex transcribed loci that usually also harbor a plethora of spliced transcripts. Unspliced EST data, although typically disregarded in transcriptome analysis, can be used to gain insights into this rarely investigated transcriptome component. The frequently postulated connection between lack of splicing and nuclear retention and the surprising overlap of chromatin-associated transcripts suggests that this class of transcripts might be involved in chromatin organization and possibly other mechanisms of epigenetic control.
POST-DOCTORAL POSITIONS Two post-doctoral positions are available in the research groups led by Francesca Luca and Roger Pique-Regi, at the Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI. The research focus of the groups is on the genetic and molecular characterization of gene regulation from an evolutionary and functional perspective. Examples of collaborative projects include: characterizing variation in the response to hormonal and environmental stimuli at the individual and population level; identifying tissue-specific cis-regulatory modules with ATAC-seq and footprinting analysis; detecting signals of selection and adaptation in gene regulatory regions. The ultimate aim is to learn about the genetic and evolutionary basis of disease susceptibility and response to treatment. We have a strong record in using both functional and evolutionary genomics approaches. We use a combination of high throughput experimental platforms and computational/statistical tools. We seek applicants who are very creative, energetic, and can work independently. We operate relatively small but well-funded and intense laboratories. The goal is that everyone should have the resources, support and mentorship needed to be successful and become an independent investigator. The two positions are intended for applicants with complementary expertise. Specifically we are looking for talented individuals with either a strong experimental and/or computational background that will contribute to create a team jointly supervised by Dr. Luca and Dr. Pique-Regi. The experimentalist position would be under the direct supervision of Dr. Luca, and requires experience in collecting genome-scale data, in mammalian cell and tissue culture techniques and in functional genomics techniques. Familiarity with the quantitative skills required for the analysis of genomic data (e.g., Python, R, scripts for setting up an analysis pipeline) is also required. For the computational position (under the direct supervision of Dr. Pique-Regi), applicants should have a strong background in quantitative/statistical skills, and a very strong interest in biological applications. A background in genomics, gene regulation or statistical genetics is an advantage, although we will consider outstanding candidates with quantitative degrees (e.g. in Statistics, CS, or Engineering) For more information please contact: Francesca Luca, PhD e-mail: firstname.lastname@example.org website: http://bit.ly/1PnyILU Roger Pique-Regi, PhD e-mail: email@example.com Francesca Luca via Gmail
August 19, 2015
The Department of Biosciences, University of Helsinki invites applications for a TWO-YEAR POST DOCTORAL RESEARCHER POSITION in the research group of Assistant Professor Arild Husby. The successful applicant will be part of the Centre of Excellence in Metapopulation Research at the Department of Biosciences, University of Helsinki (http://bit.ly/1TXQfvn). The main goal of the post doc project is to examine the epigenetic basis of avian timing of breeding using the great tit (Parus major) as a model species. The successful candidate will examine DNA methylation patterns using targeted bisulphite sequencing of previously identified candidate genes. DNA methylation levels will be compared among two groups of extreme phenotypes using blood samples already collected. In addition, the candidate will be involved in some field work to collect additional data to examine trans-generational DNA methylation patterns. The work will be performed in close collaboration with Prof. Marcel Visser and Dr Kees van Oers at the Netherlands Institute of Ecology (http://bit.ly/1Lm1s9Q). Fieldwork will be carried out in the Hoge Veluwe national park near Wageningen, The Netherlands and close to Viikki campus, Helsinki, Finland. The successful candidate should have PhD / postdoctoral experience within the fields of evolutionary genetics/genomics with previous experience in sequence based analysis of DNA methylation data. Previous experience working on birds is not necessary. Excellent written and verbal communication skills in English are required and you must also demonstrate ability to work as part of a team. The position will have a probationary period of four months. The starting date is flexible but at latest 1st January 2016. The salary will be based on level 5 of the demands level chart for teaching and research personnel in the salary system of Finnish universities. In addition, the appointee will be paid a salary component based on personal work performance. The total minimum salary at the beginning of the employment is 3311,17 €/month. To apply, please send, in a single pdf file, your CV with publications included and a letter (max 2 pages) with a description of your research interests and, in particular, why you would be a suitable candidate for the project. The application letter should also contain possible starting dates and contact details of three references. The applicatiions are to be addressed to Dr Arild Husby and submitted to firstname.lastname@example.org by 1st October 2015 at 15.45 local Helsinki time. For more information about this position, please contact Dr Arild Husby (email@example.com), see also our lab website: http://bit.ly/1yT0ny7 via Gmail
This may seem like a strange question, but here goes. I'm looking for a computationally efficient way to represent a set of sequences in a 2D space. For example, imagine that we have 10,000 DNA barcodes. I could compute a tree, but (a) that get's computationally hard (if it doesn't seem hard, make it 100,000, or 1M), and (b) a tree drawing isn't stable in the sense that there's no global coordinate system that helps us compare trees for different subsets of data.
I thought about using something like DNA walks, where we start at 0,0 in a x-y graph, walk along a sequence, and make moves -1, 1 in the x or y direction depending on the next base in the sequence. For example, we could plot the final x,y coordinates at the end of the walk, and we'd have a simple to compute measure that depends solely on the sequence at hand, and which locates a sequence in a shared coordinate space. What I'd really like are broad-brush clusters that are recognisable enough to say "OK, over there are fish, these are insects, that cluster is molluscs"). I'm guessing this might work if there are clade-specific sequence properties such as base-composition, etc., otherwise, not so much.
Hope this doesn't sound to ridiculous. I'm curious as to whether there's a method for getting a quick sense of the taxonomic composition of a large set of N sequences that doesn't require the N^2 comparisons needed to compare the sequences in order to build a tree.
Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and Antarctic Micromonas Populations
Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence–absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica—a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga.
Tracing the Evolutionary History of Inositol, 1, 4, 5-Trisphosphate Receptor: Insights from Analyses of Capsaspora owczarzaki Ca2+ Release Channel Orthologs
Cellular Ca2+ homeostasis is tightly regulated and is pivotal to life. Inositol 1,4,5-trisphosphate receptors (IP3Rs) and ryanodine receptors (RyRs) are the major ion channels that regulate Ca2+ release from intracellular stores. Although these channels have been extensively investigated in multicellular organisms, an appreciation of their evolution and the biology of orthologs in unicellular organisms is largely lacking. Extensive phylogenetic analyses reveal that the IP3R gene superfamily is ancient and diverged into two subfamilies, IP3R-A and IP3R-B/RyR, at the dawn of Opisthokonta. IP3R-B/RyR further diversified into IP3R-B and RyR at the stem of Filozoa. Subsequent evolution and speciation of Holozoa is associated with duplication of IP3R-A and RyR genes, and loss of IP3R-B in the vertebrate lineages. To gain insight into the properties of IP3R important for the challenges of multicellularity, the IP3R-A and IP3R-B family orthologs were cloned from Capsaspora owczarzaki, a close unicellular relative to Metazoa (designated as CO.IP3R-A and CO.IP3R-B). Both proteins were targeted to the endoplasmic reticulum. However, CO.IP3R-A, but strikingly not CO.IP3R-B, bound IP3, exhibited robust Ca2+ release activity and associated with mammalian IP3Rs. These data indicate strongly that CO.IP3R-A as an exemplar of ancestral IP3R-A orthologs forms bona fide IP3-gated channels. Notably, however, CO.IP3R-A appears not to be regulated by Ca2+, ATP or Protein kinase A-phosphorylation. Collectively, our findings explore the origin, conservation, and diversification of IP3R gene families and provide insight into the functionality of ancestral IP3Rs and the added specialization of these proteins in Metazoa.
Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity
Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, are extremely diverse and universally present in traditional societies. A major focus of research in the early decades of modern anthropology, marriage rules impose social and economic forces that help structure societies and forge connections between them. However, in those early anthropological studies, the biological benefits or disadvantages of marriage rules could not be determined. We revisit this question by applying a novel simulation framework and genome-wide data to explore the effects of Asymmetric Prescriptive Alliance, an elaborate set of marriage rules that has been a focus of research for many anthropologists. Simulations show that strict adherence to these marriage rules reduces genetic diversity on the autosomes, X chromosome and mitochondrial DNA, but relaxed compliance produces genetic diversity similar to random mating. Genome-wide data from the Indonesian community of Rindi, one of the early study populations for Asymmetric Prescriptive Alliance, are more consistent with relaxed compliance than strict adherence. We therefore suggest that, in practice, marriage rules are treated with sufficient flexibility to allow social connectivity without significant degradation of biological diversity.
Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors
The high regulatory complexity of vertebrates has been related to two rounds of whole genome duplication (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families originated during the 2R-WGD contains LCRs. The number of gene duplicates with LCRs is 155 out of 550 analyzed (28%), about twice as many as the number of single copy genes with LCRs (15 out of 115, 13%). In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology