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Post-doc - Universidade de Goias

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Post-Doctoral Research position in Goiania, Brazil with a competitive salary (49,200 BRL a year) for one year, extendable to second based on performance, focusing on developing next-generation sequence data and comparing it to fossil pollen data for a population genomics study.

Applicants must have experience in population genomics or phylogenomics, as well as a strong interest in evolutionary biology and ecology. Programming skills are important and should include proficiency working in the Unix environment as well as experience with R, Python/Perl and/or standard sequence analysis tools. Highly enthusiastic applicants with a strong disposition to learn the needed tools to succeed are also encouraged to apply.

Informal inquiries as well as applications (including a CV, copies of relevant publications, and two names of recommenders) should be emailed to Christine Bacon (christinedbacon@gmail.com) prior to May 15th, 2014.

Starting date: July 1st, 2014, or upon agreement

Project: The de-evolution of diversity in Amazonia
Tropical America (the Neotropics) is recognized as harboring biodiversity hotspots, such as Amazonia, but there are some areas where diversity has decreased over time, particularly in oligarchic (monodominant) forests. This project aims to understand the evolutionary origins and maintenance of oligarchic forests in the context of geologic change and historical climate, thereby improving our predictions of how organisms, habitats, and Neotropical biomes may respond to comparable changes in the face of climate change. The genus Mauritia (Arecaceae, the palm family) presents an ideal system for investigating the evolution of oligarchic forests, or the de-evolution of Amazonian biodiversity. The genus has a rich pollen record, the taxonomy of palms is well known, and next- generation sequencing techniques, gene capture probes, have been developed specifically for palms that are appropriate for investigating demographic structure on both ecological and evolutionary time-scales. Furthermore, Mauritia is the most widely used and economically important native South American palm. We hypothesize that historical extinctions in Mauritia correlate with increased diversification rates in eudicotyledonous plants, the expansion of South American savannas, and/or the constriction of lowland rainforests during the Neogene. The inference of biogeography and diversification is an integral window into the past that enables the investigation of how geographic regions, biomes, and communities assembled through time and how they may evolve in the future. By integrating data across fields, for example from geology, genetics, fossils, species distribution and abundance, and morphology, we can reach a more comprehensive framework for the understanding of biome evolution and extinction.

Keywords: Amazon, biodiversity, fossil, next-generation sequencing, palms, pollen

Institution: Laboratory of Genetics and Biodiversity, Universidad Federal de Goias, Goiania, GO, Brazil (http://lgbio.icb.ufg.br/pages/33272-lgbio)

Remuneration: Monthly, untaxed salary is 4,100.00 Brazilian Reais per month. Moving costs and health insurance are not included. The position is for one year, extendable to two years based on a performance evaluation at the end of the first year. The position is funded by the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq; the Brazilian National Science Foundation). The post-doc position includes funding for travel abroad or within Brazil for project development, either for conferences, workshops, or training visits. One trip to the Antonelli Lab at the University of Gothenburg, Sweden is planned for early 2015.

The research project team: The Laboratory of Genetics and Biodiversity at the Universidad Federal de Goias is actively working on various next-generation sequencing projects of key plant taxa from the Cerrado, as well as other organisms (herpetofauna, ichtyofauna, etc.). The core supervisor for this position is Rosane Collevatti (http://scholar.google.com/citations?user=ChqtpzkAAAAJ&hl=en), known for her breadth of research on phylogeography and population genomics. The co-PI on the CNPq grant is Christine Bacon (http://scholar.google.com/citations?user=_p4DcHgAAAAJ&hl=en), who studies evolution and biogeography in palms (Arecaceae). Christine is based on Santander, Colombia and will be at UFG working on the project 1-3 months per year for the duration of the grant. Other associates of the project are Thiago Rangel (http://scholar.google.com/citations?user=EHbuZpYAAAAJ&hl=en) and Alexandre Jose Diniz Filho (http://scholar.google.com/citations?user=scYHGuQAAAAJ&hl=en), both well-known for their contributions to macroecology.

Post-doctoral researcher tasks: The post-doc will sequence the Mauritia flexuosa transciptome and annotate it using reference genomes in the Arecaceae (http://www.ncbi.nlm.nih.gov/assembly/?term=txid4710%5bOrganism:exp%5d). Using the annotated transciptome and palm genomic resources, putatively single-copy orthogroup targets will be identified for probe design (Mycroarray;http://www.mycroarray.com/mybaits/MYbaits+sequence+capture+target+enrichment+kit.html). Target sequencing using a Mauritia flexuosa-specific bait kit will be used to amplify variable sites in Mauritia flexuosa from populations across its biogeographic distribution in the Amazon Basin. After hybrid capture, Illumina sequencing reads will be filtered, paralogs will be removed, nuclear reads will be assembled and extended into contigs and alignments will be made. Nuclear gene trees will be built, age estimation will be inferred, and phylgeographic models will be implemented (e.g., Bayesian Skyline Plots, Drummond et al. 2005;http://mbe.oxfordjournals.org/content/22/5/1185.full).

Optional tasks include leading or participating in field work aimed at collecting leaf and pollen samples in the field. Two regions of particular interest are near Belem, Brasil and near Pucallpa and the Parque Nacional Alto Purus in Peru. Involvement with the fossil team and collaboration with Carina Hoorn (http://scholar.google.com/citations?user=yECQupMAAAAJ) on the integration of genetic and pollen data. Co-supervise a PhD student at the Universidade de Goiania on their project development and research.

Goiania: A safe, affordable, medium-sized city in the Cerrado –
http://en.wikipedia.org/wiki/Goiânia
http://aoprals.state.gov/web920/per_diem_action.asp?MenuHide=1&CountryCode=1042
http://thebrazilbusiness.com/article/cheapest-cities-to-live-in-brazil
http://www.numbeo.com/cost-of-living/city_result.jsp?country=Brazil&city=Goiania
http://en.wikipedia.org/wiki/Cerrado

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