Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps
Numerous studies of emerging species have identified genomic "islands" of elevated differentiation against a background of relative homogeneity. The causes of these islands remain unclear, however, with some signs pointing toward "speciation genes" that locally restrict gene flow and others suggesting selective sweeps that have occurred within nascent species after speciation. Here, we examine this question through the lens of genome sequence data for five species of southern capuchino seedeaters, finch-like birds from South America that have undergone a species radiation during the last ∼50,000 generations. By applying newly developed statistical methods for ancestral recombination graph inference and machine-learning methods for the prediction of selective sweeps, we show that previously identified islands of differentiation in these birds appear to be generally associated with relatively recent, species-specific selective sweeps, most of which are predicted to be soft sweeps acting on standing genetic variation. Many of these sweeps coincide with genes associated with melanin-based variation in plumage, suggesting a prominent role for sexual selection. At the same time, a few loci also exhibit indications of possible selection against gene flow. These observations shed light on the complex manner in which natural selection shapes genome sequences during speciation.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2020 |
|---|---|
| Erschienen: |
2020 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:117 |
|---|---|
| Enthalten in: |
Proceedings of the National Academy of Sciences of the United States of America - 117(2020), 48 vom: 01. Dez., Seite 30554-30565 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Hejase, Hussein A [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Ancestral recombination graph |
|---|
| Anmerkungen: |
Date Completed 25.01.2021 Date Revised 17.05.2021 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1073/pnas.2015987117 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM317669532 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM317669532 | ||
| 003 | DE-627 | ||
| 005 | 20231225163741.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231225s2020 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1073/pnas.2015987117 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1058.xml |
| 035 | |a (DE-627)NLM317669532 | ||
| 035 | |a (NLM)33199636 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Hejase, Hussein A |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps |
| 264 | 1 | |c 2020 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 25.01.2021 | ||
| 500 | |a Date Revised 17.05.2021 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Numerous studies of emerging species have identified genomic "islands" of elevated differentiation against a background of relative homogeneity. The causes of these islands remain unclear, however, with some signs pointing toward "speciation genes" that locally restrict gene flow and others suggesting selective sweeps that have occurred within nascent species after speciation. Here, we examine this question through the lens of genome sequence data for five species of southern capuchino seedeaters, finch-like birds from South America that have undergone a species radiation during the last ∼50,000 generations. By applying newly developed statistical methods for ancestral recombination graph inference and machine-learning methods for the prediction of selective sweeps, we show that previously identified islands of differentiation in these birds appear to be generally associated with relatively recent, species-specific selective sweeps, most of which are predicted to be soft sweeps acting on standing genetic variation. Many of these sweeps coincide with genes associated with melanin-based variation in plumage, suggesting a prominent role for sexual selection. At the same time, a few loci also exhibit indications of possible selection against gene flow. These observations shed light on the complex manner in which natural selection shapes genome sequences during speciation | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, N.I.H., Extramural | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Research Support, U.S. Gov't, Non-P.H.S. | |
| 650 | 4 | |a ancestral recombination graph | |
| 650 | 4 | |a machine learning | |
| 650 | 4 | |a speciation | |
| 650 | 4 | |a sweeps | |
| 700 | 1 | |a Salman-Minkov, Ayelet |e verfasserin |4 aut | |
| 700 | 1 | |a Campagna, Leonardo |e verfasserin |4 aut | |
| 700 | 1 | |a Hubisz, Melissa J |e verfasserin |4 aut | |
| 700 | 1 | |a Lovette, Irby J |e verfasserin |4 aut | |
| 700 | 1 | |a Gronau, Ilan |e verfasserin |4 aut | |
| 700 | 1 | |a Siepel, Adam |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Proceedings of the National Academy of Sciences of the United States of America |d 1915 |g 117(2020), 48 vom: 01. Dez., Seite 30554-30565 |w (DE-627)NLM000008982 |x 1091-6490 |7 nnns |
| 773 | 1 | 8 | |g volume:117 |g year:2020 |g number:48 |g day:01 |g month:12 |g pages:30554-30565 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1073/pnas.2015987117 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 117 |j 2020 |e 48 |b 01 |c 12 |h 30554-30565 | ||