@florianschulz.org

Strategies to optimize the analysis of gene flow in speciation at the example of giraffes,
bears, whales and seals 

Axel Janke

SUMMARY
In this project, we will sequence the genomes from a number of mammals to study how species differ at the sequence level. In particular methods implemented in D-stat, Phylonet, D-foil, CoalHMM will show how past and current gene flow or the lack thereof affects speciation. Initially, we will focus on current projects in giraffe, bears and seals. For these taxonomic groups geneflow has been documented or is suspected. The new findings will also be studied and interpreted with the aid of alternative presentations like networks to depict of evolutionary processes . So far, comparative genomic studies have only been made involving few individuals, but the expected inflation of the number of genomes for numerous species will make it necessary to develop efficient procedures to involve even hundreds of species/individuals in such studies.

During the course of TBG we will also involve other taxonomic groups from which genomes will become available for comparative genomic studies.

TBG GENOMIC STATS:

De novo genomes 3
Re- sequenced genomes 6
Total genomes: 9
Total data: 0,751 Tera bases

 

SPECIES INVOLVED:

SPECIES: Date (due) NCBI Coverage Quality (planned)  
Giraffes: 01.01.18 Yes 15x re-sequence
Northern giraffe (Giraffa camelopardalis) Nubian 01.01.19 No (15x) re-sequence
Northern giraffe (G. camelopardalis) Rothschild’s 01.01.19 No (15x) re-sequence
Northern giraffe (G. camelopardalis) West African 01.01.19 No (15x) re-sequence
Reticulated giraffe (G. reticulata) 01.01.19 No (15x) re-sequence
Masai giraffe (Gi. tippelskirchi) Masai 01.01.19 No (15x) re-sequence
Masai giraffe (G. tippelskirchi) Luanga Valle NP 01.01.19 No (15x) re-sequence
Southern giraffe (G. giraffa) Angolan 01.01.19 No (100x) de-novo (gold)
Southern giraffe (G.a giraffa) South African 01.01.19 No (15x) re-sequence
Bears:        
Syrian brown bear (Ursus arctos syriacus) male 01.07.18 No (20x) re-sequence
Syrian brown bear (Ursus arctos syriacus) female 01.07.18 No (20x) re-sequence
Kamchatka brown bear (Ursus arctos beringianus) 01.07.18 No (20x) re-sequence
Wales:        
NA right whale  (Eubalena glacialis) 06.04.18 Yes (10x) re-sequence
Sei whale (Balaenoptera borealis) 06.04.18 Yes (10x) re-sequence
Sei whale (Balaenoptera borealis) 06.04.18 Yes (10x) re-sequence
Blue whale (Balaenoptera musculus) 06.04.18 Yes (30x) re-sequence
Humpback whale (Megaptera novaeangliae) 06.04.18 Yes (10x) re-sequence
Fin whale (Balaenoptera physalus) 06.04.18 Yes (100x) de-novo (gold)
Minke whale (Balaenoptera acutorostrata) 06.04.18 Yes (10x) re-sequence
Gray whale (Eschrichtius robustus) 06.04.18 Yes (10x) re-sequence
Gray whale (Eschrichtius robustus) 06.04.18 Yes (10x) re-sequence
         
Hippopotamus (Hippopotamus amphibius) 06.04.18 Yes (60x) de-novo gold