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

SUMMARY

In this project, we are sequencing mammalian genomes to study how species differ at the sequence level. In particular methods implemented in D-stat, Phylonet, D-foil, CoalHMM show how past and current gene flow 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 from small scale studies. We are sequence entire genomes, often in a population genomic approach, to study the extend of geneflow arcoss the genome. Alternative presentations such as networks and circus plots will depict of evolutionary processes. The expected inflation of the number of genomes for numerous species will make it necessary to develop efficient procedures to involve hundreds of species/individuals. Due to changes of the PI, this project is behind schedule, but 50 giraffe genomes are sequenced and I gathered an international consortium to study geneflow in bears across their distribution range 

Highlights

Migration rates among four giraffe clades:

Circular migration plot of recent migration rates among four giraffe clades estimated by BayesAss and indicated by ribbons connecting one species to another. The color coding represents the four species.

Geneflow signals for baleen whales:

Geneflow signals for baleen whales inferred by PhyloNet.( Rooted networks with reticulations inferred from PhyloNet based on 34,192 20-kbp genome fragments. Reticulations are shown as blue arrows with inheritance probability denoted above or below.

TBG group members

  • Prof. Dr. Axel Janke
  • Dr. Stefan Prost
  • Dr. Menno de Jong
  • MSc Sven Winter
  • MSc Raphael Coimbra
  • MSc Magnus Wolf

Genomes Sequenced

1 — Giraffe de novo PacBio+OMNI-C+Illumina
50 — Giraffe Illumina 15x
3 — Whales de novo PacBio and 10XGenomics
50 — Whales Illumina 20x
50 – Bears Illumina 20x

Group expertise / Methods

Genome assembly tool, evolutionary network analyses,
gene flow D-stat and it derivatives

PUBLICATIONS

Árnason, Úlfur, et al. “Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow.” Science advances 4.4 (2018): eaap9873

Coimbra et al Whole-genome analysis of giraffe supports four distinct species. Current Biology submitted

TBG GENOMIC STATS:

De novo genomes3
Re- sequenced genomes6
Total genomes:9
Total data:0,751 Tera bases

 

SPECIES INVOLVED:

SPECIES:Date (due)NCBICoverage Quality (planned) 
Giraffes:01.01.18Yes15xre-sequence
Northern giraffe (Giraffa camelopardalis) Nubian01.01.19No(15x)re-sequence
Northern giraffe (G. camelopardalis) Rothschild’s01.01.19No(15x)re-sequence
Northern giraffe (G. camelopardalis) West African01.01.19No(15x)re-sequence
Reticulated giraffe (G. reticulata)01.01.19No(15x)re-sequence
Masai giraffe (Gi. tippelskirchi) Masai01.01.19No(15x)re-sequence
Masai giraffe (G. tippelskirchi) Luanga Valle NP01.01.19No(15x)re-sequence
Southern giraffe (G. giraffa) Angolan01.01.19No(100x)de-novo (gold)
Southern giraffe (G.a giraffa) South African01.01.19No(15x)re-sequence
Bears:    
Syrian brown bear (Ursus arctos syriacus) male01.07.18No(20x)re-sequence
Syrian brown bear (Ursus arctos syriacus) female01.07.18No(20x)re-sequence
Kamchatka brown bear (Ursus arctos beringianus)01.07.18No(20x)re-sequence
Wales:    
NA right whale  (Eubalena glacialis)06.04.18Yes(10x)re-sequence
Sei whale (Balaenoptera borealis)06.04.18Yes(10x)re-sequence
Sei whale (Balaenoptera borealis)06.04.18Yes(10x)re-sequence
Blue whale (Balaenoptera musculus)06.04.18Yes(30x)re-sequence
Humpback whale (Megaptera novaeangliae)06.04.18Yes(10x)re-sequence
Fin whale (Balaenoptera physalus)06.04.18Yes(100x)de-novo (gold)
Minke whale (Balaenoptera acutorostrata)06.04.18Yes(10x)re-sequence
Gray whale (Eschrichtius robustus)06.04.18Yes(10x)re-sequence
Gray whale (Eschrichtius robustus)06.04.18Yes(10x)re-sequence
     
Hippopotamus (Hippopotamus amphibius)06.04.18Yes(60x)de-novo gold