@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 |