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Our paper on bean geese appeared in @HeredityJournal today! 
"Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation"
https://www.nature.com/articles/s41437-020-0322-z
A thread on #ornithology and #genomics
(1/9)
"Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation"
https://www.nature.com/articles/s41437-020-0322-z
A thread on #ornithology and #genomics
(1/9)
It is not always easy to tell the difference between Taiga and Tundra Bean Goose.
In general, the taiga type has a longer beak with a broad orange marking whereas the tundra type has a shorter beak with a reduced orange band on the bill.
But what about their genetics?
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In general, the taiga type has a longer beak with a broad orange marking whereas the tundra type has a shorter beak with a reduced orange band on the bill.
But what about their genetics?
(2/9)
We resequenced the whole genomes of 18 individuals (9 from each taxon) and performed some basic population genomic analyses.
PCA and Admixture analyses clearly differentiate between Taiga and Tundra Bean Goose.
Case closed? Not so quick!
(3/9)
PCA and Admixture analyses clearly differentiate between Taiga and Tundra Bean Goose.
Case closed? Not so quick!
(3/9)
More stringent filtering of the genomic data revealed an admixed pattern. Also, the principal components only explained a small percentage of the genetic variance.
What is going on here?
(4/9)
What is going on here?
(4/9)
Exploring the genomic landscape of differentiation (based on several summary statistics) revealed that divergence between Taiga and Tundra Bean Goose is concentrated in a few genomic regions, so-called islands of differentiation.
(5/9)
(5/9)
These genomic islands might contain genes contributing to reproductive isolation. For example, we found the gene KCNU1 which is involved in spermatogenesis. 
However, other evolutionary forces (such as background selection) can also give rise to these islands.
(6/9)
However, other evolutionary forces (such as background selection) can also give rise to these islands.
(6/9)
The largely undifferentiated genomic landscape suggests high levels of gene flow. But when did this occur?
Demographic modelling (using DADI) indicated that Taiga and Tundra Bean Goose diverged about 2.5 Mya and established secondary contact ca. 60,000 years ago.
(7/9)
Demographic modelling (using DADI) indicated that Taiga and Tundra Bean Goose diverged about 2.5 Mya and established secondary contact ca. 60,000 years ago.
(7/9)
Based on the ecological, morphological and genomic data, we also assessed the taxonomy of these birds. We constructed a decision tree to guide us:
1. Reproductive isolation is incomplete
2. Low genomic differentiation
3. No clear diagnostic features
Verdict: subspecies!
(8/9)
1. Reproductive isolation is incomplete
2. Low genomic differentiation
3. No clear diagnostic features
Verdict: subspecies!
(8/9)
But what about that other member of the Bean Goose complex, the Pink-footed Goose? Where does this goose fit in?
That, my friends, is work in progress. Stay tuned for more exciting goose genomics in the near future!
(9/9)
That, my friends, is work in progress. Stay tuned for more exciting goose genomics in the near future!
(9/9)
