lecture3.md

Introduction to molecular biodiversity

High-throughput sequencing

• Introduction to HTS (NGS) data formats and representations
• Data (pre-)processing workflow
• Case studies in genomics

Barcoding

• Data science tools: UNIX
• BOLD/barcoding workflows and MSA data
• Species delimitation

Metabarcoding

• General workflow of metabarcoding assays
• Case study metabarcoding: DNA WaterScan
• Case study metabarcoding: Kinabalu fungal biodiversity

Phylogenies

• Phylogenetic data formats and representations
• Data science tools: relational databases
• Large tree representations and traversals

Practical and homework

• Fetching, filtering, aligning BoLD sequences
• Analyzing Kinabalu metabarcoding data
• Reading OSODOS
• Reading journal article, preparing 5 min. standup

Journal club

• What does this paper say about the systematics of this species (i.e. in relation to others)?
• If the paper is unsuitable, suggest an alternative (paper or species)
• Prepare 3 slides max to present the paper
• Prepare a 5 min talk

1. Maize - Cereal: Zea mays subsp. mays. Teosintes are Z. m. huehuetenangensis, Z. m. mexicana, and Z. m. parviglumis (Poaceae)
   • Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms. (2003)
2. Rice - Cereal: Oryza sativa (Poaceae)
   • Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s. (2009)
3. Sorghum - Cereal: Sorghum bicolor (Poaceae)
   • Oligocene CO2 decline promoted C4 photosynthesis in grasses. (2008)
4. Teff - Cereal (Chloridoideae): Eragrostis tef (Poaceae)
   • The origin and evolution of Eragrostis tef (Poaceae) and related polyploids: evidence from nuclear waxy and plastid rps161. (2002)
5. Millet - Cereal (Chloridoideae): Eleusine coracana (Poaceae)
   • Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales 1 (2010)
6. Barley - Cereal (Triticeae): Hordeum vulgare, wild ancestor is H. vulgare subsp. spontaneum. Domesticate alternatively named H. vulgare subsp. vulgare (Poaceae)
   • Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. (2014)
7. Wheat - Cereal (Triticeae): Triticum aestivum (Poaceae)
   • Evidence for the origin of the B genome of bread wheat based on chloroplast DNA (2012)
8. Rye - Cereal (Triticeae): Secale cereale (Poaceae)
   • Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae). (2011)
9. Cassava - New World tuber: Also known as Manioc, i.e. Manihot esculenta (Euphorbiaceae)
   • Are spurred cyathia a key innovation? Molecular systematics and trait evolution in the slipper spurges (Pedilanthus clade: Euphorbia, Euphorbiaceae) (2009)
10. Potato - New World tuber: Solanum tuberosum (Solanales, Solanaceae)
    • Evolution of the inflated calyx syndrome in Solanaceae. (2007)
11. Sweet Potato - New World tuber: Ipomoea batatas (Solanales, Convolvulaceae)
    • Monophyly of the Convolvulaceae and circumscription of their major lineages based on DNA sequences of multiple chloroplast loci. (2002)
12. Taro - Old World root/tuber: Colocasia esculenta (Araceae)
    • Phylogenetic relationships of aroids and duckweeds (Araceae) inferred from coding and noncoding plastid DNA. (2008)
13. Yams - Old World root/tuber: Dioscorea rotundata (Dioscoreaceae), D. cayennensis, D. alata, D. polystachya, D. bulbifera, D. esculenta, D. dumetorum and D. trifida
    • A Plastid Gene Phylogeny of the Yam Genus, Dioscorea: Roots, Fruits and Madagascar (2005)
14. Bananas - Musaceae: Bananas & plantains are hybrids of Musa acuminata and Musa balbisiana resulting in Musa × paradisiaca L. (Musaceae)
    • Evolution of Endogenous Sequences of Banana Streak Virus: What Can We Learn from Banana (Musa sp.) Evolution? (2010)
15. Ensete - Musaceae: Ensete ventricosum (Musaceae)
    • Unraveling the evolutionary radiation of the families of the Zingiberales using morphological and molecular evidence. (2001)
16. Buckwheat - Pseudocereal: Fagopyrum esculentum and Fagopyrum tataricum (Polygonaceae)
    • Molecular phylogeny of Persicaria (Persicarieae, Polygonaceae) (2008)
17. Groundnut - New World staple: Arachis hypogaea (Fabaceae)
    • A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers (2013)
18. Squashes - New World staple: Domesticated as Cucurbita argyrosperma, C. ficifolia, C. maxima, C. moschata and C. pepo (Cucurbitaceae)
    • Chloroplast phylogeny of Cucurbita: Evolution of the domesticated and wild species (2013)
19. Breadfruit - Fruit tree: Artocarpus altilis (Moraceae)
    • Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot. (2010)
20. Mango - Fruit tree: Mangifera indica (Anacardiaceae)
    • Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. (2010)
21. Coconut - Palm: Cocos nucifera (Arecaceae)
    • A new subfamily classification of the palm family (Arecaceae): evidence from plastid DNA phylogeny (2006)
22. Dates - Palm: Phoenix dactylifera (Arecaceae)
    • DNA barcoding for species identification in the Palmae family. (2014)
23. Sago - Palm: Metroxylon sagu (Arecaceae)
    • Molecular phylogenetics of subfamily Calamoideae (Palmae) based on nrDNA ITS and cpDNA rps16 intron sequence data. (2000)