rominassbatista / neotropics-thrushes-project Goto Github PK

¹Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, PPG (GCBEV) - Instituto Nacional de Pesquisas da Amazônia - INPA (INPA) Campus II. Av. André Araújo, 2936 – Petrópolis - CEP 69067-375, Manaus, AM, Brazil

²Gothenburg Global Biodiversity Centre, (GGBC), Box 461, 405 30 Gothenburg, Sweden

³Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Gothenburg, Sweden

⁴Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014 Helsinki, Finland

⁵Royal Botanic Gardens, (Kew), Richmond, Surrey TW9 3AE, UK

⁶Department of Ornithology, (American Museum of Natural History), New York, NY, USA

⁷Instituto Nacional de Pesquisas da Amazônia - INPA (INPA) Campus II. Av. André Araújo, 2936 – Petrópolis - CEP 69067-375, Manaus, AM, Brazil

The genus Turdus (Aves, Turdidae) consists of 83 currently recognised species occurring throughout the world. Previous attempts to reconstruct phylogenies have proved extremely challenging due to short internal branches and low node support. South and Central America currently host the highest number of species (ca.30) in the genus Turdus (Aves: Turdidae). A recently study (Batista et al, 2020) suggest that dispersal from the Western Palaearctic via the Antilles to the Neotropics might have occurred in a single event, giving rise to the rich Neotropical diversity of Turdus observed today, with no reverse dispersals to the Palaearctic or Africa. Detailed biogeographic studies on a finer scale in South America are necessary to examine the evolutionary history for these taxa, as well as for revising current taxonomy.

The application of Ultraconserved Elements (UCEs) is currently one of the most popular methods for phylogenomics using reduced representation genomic datasets. UCEs are highly conserved across distantly related taxa and have variable flanking regions. These characteristics make UCEs useful genetic markers for both deep and shallow evolutionary timescales, and they have successfully been used to resolve challenging phylogenetic relationships among many taxa (eg. birds, turtles, fishes).

Here, we sequenced >2K UCEs loci for 142 individuals of 24 species of the genus Turdus sampled across South America.

• The Project was conceived and designed by Romina Batista, Urban Olsson, Alexandre Antonelli and Camila Ribas.

• Romina Batista extracted DNA and sent outsourcing (Rapid Genomics) to proceed with Library Preparation, Sequence Capture and Sequencing.

• Romina Batista processed the data.

• Romina Batista built this repository.

• Romina Batista is analysing the data, and leading manuscript preparation.

• All collaborators are involved in discussions, and interpreting results.

Funding for this project came from:

1. NATIONAL SCIENCE FOUNDATION and FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP: 2012/50260-6, TITLE OF THE PROJECT "ASSEMBLY AND EVOLUTION OF THE AMAZONIAN BIOTA AND ITS ENVIRONMENT: AN INTEGRATED APPROACH". Principal Investigators (PI): Lúcia Lohmann (IB-USP) e Joel Cracraft (AMNH).

2. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (CAPES), A Doctoral Fellowship for Internship abroad to Romina Batista.

3. The Antonelli Lab (funding provided to Alexandre Antonelli from the European Research Council under the European Union’s Seventh Framework Programme [FP/2007-2013, ERC Grant Agreement n. 331024], the Wallenberg Foundation for a Wallenberg Academy Fellowship, and the Swedish Research Council [2015-04857]).

4. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (CAPES-INPA proc. 88887477562/2020-00), a Post-Doctoral Fellowship to Romina Batista

We would like to thank the many institutions that provided tissue loans for this research:

• Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Brazil (INPA);

• Field Museum of Natural History, Louisiana State University Museum of Natural Science, Louisiana State, USA (LSU);

• Museu Paraense Emílio Goeldi, MPEG, Belém, PA, Brazil (MPEG);

• Laboratório de Genética e Evolução Molecular de Aves, LGEMA, Departamento de Genética e Biologia Evolutiva do Instituto de Biociências da Universidade de São Paulo-USP (LGEMA);

• Divisão de Aves do Museu de Zoologia da Universidade Estadual de Feira de Santana, DAMZFS, Feira de Santana, Bahia, Brazil;

• American Museum of Natural History, AMNH, New York, NY, USA (AMNH).

We also would like to thank Mats Töpel, for his support with bioinformatics computer cluster Albiorix at the Department of Biological and Environmental Sciences, University of Gothenburg and his constructive advice that greatly helped to improve this repository.

☁️ Data stored (21/08/2017). Moved to /proj/data14/romina/projects/turdus-targetcapture-backup-rawdata/data/Facilities/RapidGenomics/rawdata-sequences by Mats in October/2017. Albioix

🔛 Analyses running at /prj/scratch/biogeoam/romina.batista2/Assembly_Itero, SDumont

🔛 Analyses running Romina's local machine /Users/Romina/Dropbox (ecoevounifesp)/Postdoc_INPA_2020/1. Turdus_South_America/Data_and_Analyses

📝 scripts at /scratch/biogeoam/romina.batista2/scripts_jobs/Turdus_SouthAmerica/, SDumont

open 📓 working in progress... /Users/Romina/Dropbox (ecoevounifesp)/Postdoc_INPA_2020/1. Turdus_South_America/Documentation_Notebook_Jupyter/Workflow_UCE_Turdus_SouthAmerica.ipynb