---
_id: '14463'
abstract:
- lang: eng
  text: Inversions are thought to play a key role in adaptation and speciation, suppressing
    recombination between diverging populations. Genes influencing adaptive traits
    cluster in inversions, and changes in inversion frequencies are associated with
    environmental differences. However, in many organisms, it is unclear if inversions
    are geographically and taxonomically widespread. The intertidal snail, Littorina
    saxatilis, is one such example. Strong associations between putative polymorphic
    inversions and phenotypic differences have been demonstrated between two ecotypes
    of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion
    polymorphism currently exists across the species range. Using whole genome data
    from 107 snails, most inversion polymorphisms were found to be widespread across
    the species range. The frequencies of some inversion arrangements were significantly
    different among ecotypes, suggesting a parallel adaptive role. Many inversions
    were also polymorphic in the sister species, L. arcana, hinting at an ancient
    origin.
acknowledgement: We would like to thank members of the Littorina team for their advice
  and feedback during this project. In particular, we thank Alan Le Moan, who inspired
  us to look at heterozygosity differences to identify inversions, and Katherine Hearn
  for helping with the PCA scripts. We thank Edinburgh Genomics for library preparation
  and sequencing. Sample collections, sequencing and data preparation were supported
  by the European Research Council (ERC-2015-AdG-693030- BARRIERS) and the Natural
  Environment Research Council (NE/P001610/1). The analysis was supported by the Swedish
  Research Council (vetenskaprådet; 2018-03695_VR) and the Portuguese Foundation for
  Science and Technology (Fundación para a Ciência e Tecnologia) through a research
  project (PTDC/BIA-EVL/1614/2021) and CEEC contract (2020.00275.CEECIND).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: James
  full_name: Reeve, James
  last_name: Reeve
- first_name: Roger K.
  full_name: Butlin, Roger K.
  last_name: Butlin
- first_name: Eva L.
  full_name: Koch, Eva L.
  last_name: Koch
- first_name: Sean
  full_name: Stankowski, Sean
  id: 43161670-5719-11EA-8025-FABC3DDC885E
  last_name: Stankowski
- first_name: Rui
  full_name: Faria, Rui
  last_name: Faria
citation:
  ama: Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms
    are widespread across the species ranges of rough periwinkles (Littorina saxatilis
    and L. arcana). <i>Molecular Ecology</i>. 2023. doi:<a href="https://doi.org/10.1111/mec.17160">10.1111/mec.17160</a>
  apa: Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., &#38; Faria, R. (2023).
    Chromosomal inversion polymorphisms are widespread across the species ranges of
    rough periwinkles (Littorina saxatilis and L. arcana). <i>Molecular Ecology</i>.
    Wiley. <a href="https://doi.org/10.1111/mec.17160">https://doi.org/10.1111/mec.17160</a>
  chicago: Reeve, James, Roger K. Butlin, Eva L. Koch, Sean Stankowski, and Rui Faria.
    “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges
    of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” <i>Molecular Ecology</i>.
    Wiley, 2023. <a href="https://doi.org/10.1111/mec.17160">https://doi.org/10.1111/mec.17160</a>.
  ieee: J. Reeve, R. K. Butlin, E. L. Koch, S. Stankowski, and R. Faria, “Chromosomal
    inversion polymorphisms are widespread across the species ranges of rough periwinkles
    (Littorina saxatilis and L. arcana),” <i>Molecular Ecology</i>. Wiley, 2023.
  ista: Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2023. Chromosomal inversion
    polymorphisms are widespread across the species ranges of rough periwinkles (Littorina
    saxatilis and L. arcana). Molecular Ecology.
  mla: Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across
    the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).”
    <i>Molecular Ecology</i>, Wiley, 2023, doi:<a href="https://doi.org/10.1111/mec.17160">10.1111/mec.17160</a>.
  short: J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology
    (2023).
date_created: 2023-10-29T23:01:17Z
date_published: 2023-10-16T00:00:00Z
date_updated: 2023-12-13T13:05:27Z
day: '16'
department:
- _id: NiBa
doi: 10.1111/mec.17160
external_id:
  isi:
  - '001085119000001'
  pmid:
  - '37843465'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1111/mec.17160
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Ecology
publication_identifier:
  eissn:
  - 1365-294X
  issn:
  - 0962-1083
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromosomal inversion polymorphisms are widespread across the species ranges
  of rough periwinkles (Littorina saxatilis and L. arcana)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14787'
abstract:
- lang: eng
  text: Understanding the phenotypic and genetic architecture of reproductive isolation
    is a long‐standing goal of speciation research. In several systems, large‐effect
    loci contributing to barrier phenotypes have been characterized, but such causal
    connections are rarely known for more complex genetic architectures. In this study,
    we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward
    an integrated understanding of speciation across a monkeyflower hybrid zone. Previous
    work suggests that pollinator visitation acts as a primary barrier to gene flow
    between two divergent red‐ and yellow‐flowered ecotypes of<jats:italic>Mimulus
    aurantiacus</jats:italic>. Several candidate isolating traits and anonymous single
    nucleotide polymorphism loci under divergent selection have been identified, but
    their genomic positions remain unknown. Here, we report findings from demographic
    analyses that indicate this hybrid zone formed by secondary contact, but that
    subsequent gene flow was restricted by widespread barrier loci across the genome.
    Using a novel, geographic cline‐based genome scan, we demonstrate that candidate
    barrier loci are broadly distributed across the genome, rather than mapping to
    one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals
    that most floral traits are highly polygenic, with little evidence that QTL colocalize,
    indicating that most traits are genetically independent. Finally, we find little
    evidence that QTL and candidate barrier loci overlap, suggesting that some loci
    contribute to other forms of reproductive isolation. Our findings highlight the
    challenges of understanding the genetic architecture of reproductive isolation
    and reveal that barriers to gene flow other than pollinator isolation may play
    an important role in this system.
acknowledgement: We thank Julian Catchen for making modifications to Stacks to aid
  this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and
  Nicholas H. Barton provided advice, stimulating discussion and critical feedback.
  The project was supported by National Science Foundation grant DEB-1258199.
article_processing_charge: No
article_type: original
author:
- first_name: Sean
  full_name: Stankowski, Sean
  id: 43161670-5719-11EA-8025-FABC3DDC885E
  last_name: Stankowski
- first_name: Madeline A.
  full_name: Chase, Madeline A.
  last_name: Chase
- first_name: Hanna
  full_name: McIntosh, Hanna
  last_name: McIntosh
- first_name: Matthew A.
  full_name: Streisfeld, Matthew A.
  last_name: Streisfeld
citation:
  ama: Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and
    bottom‐up approaches to understand the genetic architecture of speciation across
    a monkeyflower hybrid zone. <i>Molecular Ecology</i>. 2023;32(8):2041-2054. doi:<a
    href="https://doi.org/10.1111/mec.16849">10.1111/mec.16849</a>
  apa: Stankowski, S., Chase, M. A., McIntosh, H., &#38; Streisfeld, M. A. (2023).
    Integrating top‐down and bottom‐up approaches to understand the genetic architecture
    of speciation across a monkeyflower hybrid zone. <i>Molecular Ecology</i>. Wiley.
    <a href="https://doi.org/10.1111/mec.16849">https://doi.org/10.1111/mec.16849</a>
  chicago: Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld.
    “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture
    of Speciation across a Monkeyflower Hybrid Zone.” <i>Molecular Ecology</i>. Wiley,
    2023. <a href="https://doi.org/10.1111/mec.16849">https://doi.org/10.1111/mec.16849</a>.
  ieee: S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating
    top‐down and bottom‐up approaches to understand the genetic architecture of speciation
    across a monkeyflower hybrid zone,” <i>Molecular Ecology</i>, vol. 32, no. 8.
    Wiley, pp. 2041–2054, 2023.
  ista: Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down
    and bottom‐up approaches to understand the genetic architecture of speciation
    across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.
  mla: Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to
    Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid
    Zone.” <i>Molecular Ecology</i>, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:<a
    href="https://doi.org/10.1111/mec.16849">10.1111/mec.16849</a>.
  short: S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology
    32 (2023) 2041–2054.
date_created: 2024-01-10T10:44:45Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2024-01-16T10:10:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.16849
external_id:
  isi:
  - '000919244600001'
  pmid:
  - '36651268'
intvolume: '        32'
isi: 1
issue: '8'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2022.01.28.478139
month: '04'
oa: 1
oa_version: Preprint
page: 2041-2054
pmid: 1
publication: Molecular Ecology
publication_identifier:
  eissn:
  - 1365-294X
  issn:
  - 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Integrating top‐down and bottom‐up approaches to understand the genetic architecture
  of speciation across a monkeyflower hybrid zone
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '12159'
abstract:
- lang: eng
  text: The term “haplotype block” is commonly used in the developing field of haplotype-based
    inference methods. We argue that the term should be defined based on the structure
    of the Ancestral Recombination Graph (ARG), which contains complete information
    on the ancestry of a sample. We use simulated examples to demonstrate key features
    of the relationship between haplotype blocks and ancestral structure, emphasizing
    the stochasticity of the processes that generate them. Even the simplest cases
    of neutrality or of a “hard” selective sweep produce a rich structure, often missed
    by commonly used statistics. We highlight a number of novel methods for inferring
    haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate
    how they can be used to define haplotype blocks using an empirical data set. While
    the advent of new, computationally efficient methods makes it possible to apply
    these concepts broadly, they (and additional new methods) could benefit from adding
    features to explore haplotype blocks, as we define them. Understanding and applying
    the concept of the haplotype block will be essential to fully exploit long and
    linked-read sequencing technologies.
acknowledgement: 'We thank the Barton group for useful discussion and feedback during
  the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group,
  the tskit development team, editors and three reviewers greatly improved the manuscript.
  Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg
  Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant
  P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society
  and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Daria
  full_name: Shipilina, Daria
  id: 428A94B0-F248-11E8-B48F-1D18A9856A87
  last_name: Shipilina
  orcid: 0000-0002-1145-9226
- first_name: Arka
  full_name: Pal, Arka
  id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
  last_name: Pal
  orcid: 0000-0002-4530-8469
- first_name: Sean
  full_name: Stankowski, Sean
  id: 43161670-5719-11EA-8025-FABC3DDC885E
  last_name: Stankowski
- first_name: Yingguang Frank
  full_name: Chan, Yingguang Frank
  last_name: Chan
- first_name: Nicholas H
  full_name: Barton, Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
citation:
  ama: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure
    of haplotype blocks. <i>Molecular Ecology</i>. 2023;32(6):1441-1457. doi:<a href="https://doi.org/10.1111/mec.16793">10.1111/mec.16793</a>
  apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., &#38; Barton, N. H. (2023).
    On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. Wiley.
    <a href="https://doi.org/10.1111/mec.16793">https://doi.org/10.1111/mec.16793</a>
  chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and
    Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular
    Ecology</i>. Wiley, 2023. <a href="https://doi.org/10.1111/mec.16793">https://doi.org/10.1111/mec.16793</a>.
  ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the
    origin and structure of haplotype blocks,” <i>Molecular Ecology</i>, vol. 32,
    no. 6. Wiley, pp. 1441–1457, 2023.
  ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin
    and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.
  mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.”
    <i>Molecular Ecology</i>, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:<a href="https://doi.org/10.1111/mec.16793">10.1111/mec.16793</a>.
  short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology
    32 (2023) 1441–1457.
date_created: 2023-01-12T12:09:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:18:47Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16793
external_id:
  isi:
  - '000900762000001'
  pmid:
  - '36433653'
file:
- access_level: open_access
  checksum: b10e0f8fa3dc4d72aaf77a557200978a
  content_type: application/pdf
  creator: dernst
  date_created: 2023-08-16T08:15:41Z
  date_updated: 2023-08-16T08:15:41Z
  file_id: '14062'
  file_name: 2023_MolecularEcology_Shipilina.pdf
  file_size: 7144607
  relation: main_file
  success: 1
file_date_updated: 2023-08-16T08:15:41Z
has_accepted_license: '1'
intvolume: '        32'
isi: 1
issue: '6'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1441-1457
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
  grant_number: P32166
  name: The maintenance of alternative adaptive peaks in snapdragons
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
  grant_number: '101055327'
  name: Understanding the evolution of continuous genomes
publication: Molecular Ecology
publication_identifier:
  eissn:
  - 1365-294X
  issn:
  - 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '12166'
abstract:
- lang: eng
  text: Kerstin Johannesson is a marine ecologist and evolutionary biologist based
    at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated
    in the beautiful Kosterhavet National Park on the Swedish west coast. Her work,
    using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main
    model systems, has made a remarkable contribution to marine evolutionary biology
    and our understanding of local adaptation and its genetic underpinnings.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Anja M
  full_name: Westram, Anja M
  id: 3C147470-F248-11E8-B48F-1D18A9856A87
  last_name: Westram
  orcid: 0000-0003-1050-4969
- first_name: Roger
  full_name: Butlin, Roger
  last_name: Butlin
citation:
  ama: Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular
    Ecology Prize. <i>Molecular Ecology</i>. 2022;32(1):26-29. doi:<a href="https://doi.org/10.1111/mec.16779">10.1111/mec.16779</a>
  apa: Westram, A. M., &#38; Butlin, R. (2022). Professor Kerstin Johannesson–winner
    of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. Wiley. <a href="https://doi.org/10.1111/mec.16779">https://doi.org/10.1111/mec.16779</a>
  chicago: Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner
    of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>. Wiley, 2022. <a
    href="https://doi.org/10.1111/mec.16779">https://doi.org/10.1111/mec.16779</a>.
  ieee: A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the
    2022 Molecular Ecology Prize,” <i>Molecular Ecology</i>, vol. 32, no. 1. Wiley,
    pp. 26–29, 2022.
  ista: Westram AM, Butlin R. 2022. Professor Kerstin Johannesson–winner of the 2022
    Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.
  mla: Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of
    the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>, vol. 32, no. 1, Wiley,
    2022, pp. 26–29, doi:<a href="https://doi.org/10.1111/mec.16779">10.1111/mec.16779</a>.
  short: A.M. Westram, R. Butlin, Molecular Ecology 32 (2022) 26–29.
date_created: 2023-01-12T12:10:28Z
date_published: 2022-11-28T00:00:00Z
date_updated: 2023-08-04T09:09:15Z
day: '28'
department:
- _id: NiBa
doi: 10.1111/mec.16779
external_id:
  isi:
  - '000892168800001'
intvolume: '        32'
isi: 1
issue: '1'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1111/mec.16779
month: '11'
oa: 1
oa_version: Published Version
page: 26-29
publication: Molecular Ecology
publication_identifier:
  eissn:
  - 1365-294X
  issn:
  - 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2022'
...
---
_id: '10838'
abstract:
- lang: eng
  text: Combining hybrid zone analysis with genomic data is a promising approach to
    understanding the genomic basis of adaptive divergence. It allows for the identification
    of genomic regions underlying barriers to gene flow. It also provides insights
    into spatial patterns of allele frequency change, informing about the interplay
    between environmental factors, dispersal and selection. However, when only a single
    hybrid zone is analysed, it is difficult to separate patterns generated by selection
    from those resulting from chance. Therefore, it is beneficial to look for repeatable
    patterns across replicate hybrid zones in the same system. We applied this approach
    to the marine snail Littorina saxatilis, which contains two ecotypes, adapted
    to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous
    hybrid zones between ecotypes offered the opportunity to test for the repeatability
    of genomic architectures and spatial patterns of divergence. We sampled and phenotyped
    snails from seven replicate hybrid zones on the Swedish west coast and genotyped
    them for thousands of single nucleotide polymorphisms. Shell shape and size showed
    parallel clines across all zones. Many genomic regions showing steep clines and/or
    high differentiation were shared among hybrid zones, consistent with a common
    evolutionary history and extensive gene flow between zones, and supporting the
    importance of these regions for divergence. In particular, we found that several
    large putative inversions contribute to divergence in all locations. Additionally,
    we found evidence for consistent displacement of clines from the boulder–rock
    transition. Our results demonstrate patterns of spatial variation that would not
    be accessible without continuous spatial sampling, a large genomic data set and
    replicate hybrid zones.
acknowledgement: "We thank everyone who helped with fieldwork, snail processing and
  DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise
  Liabot, Mark Ravinet, Irena Senčić and Zuzanna Zagrodzka. We are also grateful to
  Edinburgh Genomics for library preparation and sequencing, to Stuart Baird and Mark
  Ravinet for helpful discussions, and to three anonymous reviewers for their constructive
  comments. This work was supported by the Natural Environment Research Council (NE/K014021/1),
  the European Research Council (AdG-693030-BARRIERS), Swedish Research Councils Formas
  and Vetenskapsrådet through a Linnaeus grant to the Centre for Marine Evolutionary
  Biology (217-2008-1719), the European Regional Development Fund (POCI-01-0145-FEDER-030628),
  and the Fundação para a iência e a Tecnologia,\r\nPortugal (PTDC/BIA-EVL/\r\n30628/2017).
  A.M.W. and R.F. were\r\nfunded by the European Union’s Horizon 2020 research and
  innovation\r\nprogramme under Marie Skłodowska-Curie\r\ngrant agreements\r\nno.
  754411/797747 and no. 706376, respectively."
article_processing_charge: No
article_type: original
author:
- first_name: Anja M
  full_name: Westram, Anja M
  id: 3C147470-F248-11E8-B48F-1D18A9856A87
  last_name: Westram
  orcid: 0000-0003-1050-4969
- first_name: Rui
  full_name: Faria, Rui
  last_name: Faria
- first_name: Kerstin
  full_name: Johannesson, Kerstin
  last_name: Johannesson
- first_name: Roger
  full_name: Butlin, Roger
  last_name: Butlin
citation:
  ama: Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones
    to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>.
    2021;30(15):3797-3814. doi:<a href="https://doi.org/10.1111/mec.15861">10.1111/mec.15861</a>
  apa: Westram, A. M., Faria, R., Johannesson, K., &#38; Butlin, R. (2021). Using
    replicate hybrid zones to understand the genomic basis of adaptive divergence.
    <i>Molecular Ecology</i>. Wiley. <a href="https://doi.org/10.1111/mec.15861">https://doi.org/10.1111/mec.15861</a>
  chicago: Westram, Anja M, Rui Faria, Kerstin Johannesson, and Roger Butlin. “Using
    Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.”
    <i>Molecular Ecology</i>. Wiley, 2021. <a href="https://doi.org/10.1111/mec.15861">https://doi.org/10.1111/mec.15861</a>.
  ieee: A. M. Westram, R. Faria, K. Johannesson, and R. Butlin, “Using replicate hybrid
    zones to understand the genomic basis of adaptive divergence,” <i>Molecular Ecology</i>,
    vol. 30, no. 15. Wiley, pp. 3797–3814, 2021.
  ista: Westram AM, Faria R, Johannesson K, Butlin R. 2021. Using replicate hybrid
    zones to understand the genomic basis of adaptive divergence. Molecular Ecology.
    30(15), 3797–3814.
  mla: Westram, Anja M., et al. “Using Replicate Hybrid Zones to Understand the Genomic
    Basis of Adaptive Divergence.” <i>Molecular Ecology</i>, vol. 30, no. 15, Wiley,
    2021, pp. 3797–814, doi:<a href="https://doi.org/10.1111/mec.15861">10.1111/mec.15861</a>.
  short: A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021)
    3797–3814.
date_created: 2022-03-08T11:28:32Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-09-05T16:02:19Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1111/mec.15861
external_id:
  isi:
  - '000669439700001'
  pmid:
  - '33638231'
file:
- access_level: open_access
  checksum: d5611f243ceb63a0e091d6662ebd9cda
  content_type: application/pdf
  creator: dernst
  date_created: 2022-03-08T11:31:30Z
  date_updated: 2022-03-08T11:31:30Z
  file_id: '10839'
  file_name: 2021_MolecularEcology_Westram.pdf
  file_size: 1726548
  relation: main_file
  success: 1
file_date_updated: 2022-03-08T11:31:30Z
has_accepted_license: '1'
intvolume: '        30'
isi: 1
issue: '15'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 3797-3814
pmid: 1
publication: Molecular Ecology
publication_identifier:
  eissn:
  - 1365-294X
  issn:
  - 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using replicate hybrid zones to understand the genomic basis of adaptive divergence
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2021'
...
---
_id: '7421'
abstract:
- lang: eng
  text: X and Y chromosomes can diverge when rearrangements block recombination between
    them. Here we present the first genomic view of a reciprocal translocation that
    causes two physically unconnected pairs of chromosomes to be coinherited as sex
    chromosomes. In a population of the common frog (Rana temporaria), both pairs
    of X and Y chromosomes show extensive sequence differentiation, but not degeneration
    of the Y chromosomes. A new method based on gene trees shows both chromosomes
    are sex‐linked. Furthermore, the gene trees from the two Y chromosomes have identical
    topologies, showing they have been coinherited since the reciprocal translocation
    occurred. Reciprocal translocations can thus reshape sex linkage on a much greater
    scale compared with inversions, the type of rearrangement that is much better
    known in sex chromosome evolution, and they can greatly amplify the power of sexually
    antagonistic selection to drive genomic rearrangement. Two more populations show
    evidence of other rearrangements, suggesting that this species has unprecedented
    structural polymorphism in its sex chromosomes.
article_processing_charge: No
article_type: original
author:
- first_name: Melissa A
  full_name: Toups, Melissa A
  id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
  last_name: Toups
  orcid: 0000-0002-9752-7380
- first_name: Nicolas
  full_name: Rodrigues, Nicolas
  last_name: Rodrigues
- first_name: Nicolas
  full_name: Perrin, Nicolas
  last_name: Perrin
- first_name: Mark
  full_name: Kirkpatrick, Mark
  last_name: Kirkpatrick
citation:
  ama: Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation
    radically reshapes sex‐linked inheritance in the common frog. <i>Molecular Ecology</i>.
    2019;28(8):1877-1889. doi:<a href="https://doi.org/10.1111/mec.14990">10.1111/mec.14990</a>
  apa: Toups, M. A., Rodrigues, N., Perrin, N., &#38; Kirkpatrick, M. (2019). A reciprocal
    translocation radically reshapes sex‐linked inheritance in the common frog. <i>Molecular
    Ecology</i>. Wiley. <a href="https://doi.org/10.1111/mec.14990">https://doi.org/10.1111/mec.14990</a>
  chicago: Toups, Melissa A, Nicolas Rodrigues, Nicolas Perrin, and Mark Kirkpatrick.
    “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common
    Frog.” <i>Molecular Ecology</i>. Wiley, 2019. <a href="https://doi.org/10.1111/mec.14990">https://doi.org/10.1111/mec.14990</a>.
  ieee: M. A. Toups, N. Rodrigues, N. Perrin, and M. Kirkpatrick, “A reciprocal translocation
    radically reshapes sex‐linked inheritance in the common frog,” <i>Molecular Ecology</i>,
    vol. 28, no. 8. Wiley, pp. 1877–1889, 2019.
  ista: Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. 2019. A reciprocal translocation
    radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology.
    28(8), 1877–1889.
  mla: Toups, Melissa A., et al. “A Reciprocal Translocation Radically Reshapes Sex‐linked
    Inheritance in the Common Frog.” <i>Molecular Ecology</i>, vol. 28, no. 8, Wiley,
    2019, pp. 1877–89, doi:<a href="https://doi.org/10.1111/mec.14990">10.1111/mec.14990</a>.
  short: M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28
    (2019) 1877–1889.
date_created: 2020-01-30T10:33:05Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-09-06T15:00:13Z
day: '01'
department:
- _id: BeVi
doi: 10.1111/mec.14990
external_id:
  isi:
  - '000468200800004'
  pmid:
  - '30576024'
intvolume: '        28'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa_version: None
page: 1877-1889
pmid: 1
publication: Molecular Ecology
publication_identifier:
  eissn:
  - 1365-294X
  issn:
  - 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: A reciprocal translocation radically reshapes sex‐linked inheritance in the
  common frog
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2019'
...
---
_id: '6095'
abstract:
- lang: eng
  text: Both classical and recent studies suggest that chromosomal inversion polymorphisms
    are important in adaptation and speciation. However, biases in discovery and reporting
    of inversions make it difficult to assess their prevalence and biological importance.
    Here, we use an approach based on linkage disequilibrium among markers genotyped
    for samples collected across a transect between contrasting habitats to detect
    chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in
    a single locality for the coastal marine snail, Littorina saxatilis. Patterns
    of diversity in the field and of recombination in controlled crosses provide strong
    evidence that at least the majority of these rearrangements are inversions. Most
    show clinal changes in frequency between habitats, suggestive of divergent selection,
    but only one appears to be fixed for different arrangements in the two habitats.
    Consistent with widespread evidence for balancing selection on inversion polymorphisms,
    we argue that a combination of heterosis and divergent selection can explain the
    observed patterns and should be considered in other systems spanning environmental
    gradients.
article_processing_charge: No
author:
- first_name: Rui
  full_name: Faria, Rui
  last_name: Faria
- first_name: Pragya
  full_name: Chaube, Pragya
  last_name: Chaube
- first_name: Hernán E.
  full_name: Morales, Hernán E.
  last_name: Morales
- first_name: Tomas
  full_name: Larsson, Tomas
  last_name: Larsson
- first_name: Alan R.
  full_name: Lemmon, Alan R.
  last_name: Lemmon
- first_name: Emily M.
  full_name: Lemmon, Emily M.
  last_name: Lemmon
- first_name: Marina
  full_name: Rafajlović, Marina
  last_name: Rafajlović
- first_name: Marina
  full_name: Panova, Marina
  last_name: Panova
- first_name: Mark
  full_name: Ravinet, Mark
  last_name: Ravinet
- first_name: Kerstin
  full_name: Johannesson, Kerstin
  last_name: Johannesson
- first_name: Anja M
  full_name: Westram, Anja M
  id: 3C147470-F248-11E8-B48F-1D18A9856A87
  last_name: Westram
  orcid: 0000-0003-1050-4969
- first_name: Roger K.
  full_name: Butlin, Roger K.
  last_name: Butlin
citation:
  ama: Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in
    a hybrid zone between Littorina saxatilis ecotypes. <i>Molecular Ecology</i>.
    2019;28(6):1375-1393. doi:<a href="https://doi.org/10.1111/mec.14972">10.1111/mec.14972</a>
  apa: Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon,
    E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid
    zone between Littorina saxatilis ecotypes. <i>Molecular Ecology</i>. Wiley. <a
    href="https://doi.org/10.1111/mec.14972">https://doi.org/10.1111/mec.14972</a>
  chicago: Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon,
    Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements
    in a Hybrid Zone between Littorina Saxatilis Ecotypes.” <i>Molecular Ecology</i>.
    Wiley, 2019. <a href="https://doi.org/10.1111/mec.14972">https://doi.org/10.1111/mec.14972</a>.
  ieee: R. Faria <i>et al.</i>, “Multiple chromosomal rearrangements in a hybrid zone
    between Littorina saxatilis ecotypes,” <i>Molecular Ecology</i>, vol. 28, no.
    6. Wiley, pp. 1375–1393, 2019.
  ista: Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović
    M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal
    rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular
    Ecology. 28(6), 1375–1393.
  mla: Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between
    Littorina Saxatilis Ecotypes.” <i>Molecular Ecology</i>, vol. 28, no. 6, Wiley,
    2019, pp. 1375–93, doi:<a href="https://doi.org/10.1111/mec.14972">10.1111/mec.14972</a>.
  short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon,
    M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin,
    Molecular Ecology 28 (2019) 1375–1393.
date_created: 2019-03-10T22:59:21Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-24T14:50:27Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.14972
external_id:
  isi:
  - '000465219200013'
file:
- access_level: open_access
  checksum: f915885756057ec0ca5912a41f46a887
  content_type: application/pdf
  creator: dernst
  date_created: 2019-03-11T16:12:54Z
  date_updated: 2020-07-14T12:47:19Z
  file_id: '6097'
  file_name: 2019_MolecularEcology_Faria.pdf
  file_size: 1510715
  relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: '        28'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1375-1393
publication: Molecular Ecology
publication_identifier:
  eissn:
  - 1365-294X
  issn:
  - 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
  record:
  - id: '9837'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis
  ecotypes
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 28
year: '2019'
...
---
_id: '7739'
abstract:
- lang: eng
  text: Currently, there is much debate on the genetic architecture of quantitative
    traits in wild populations. Is trait variation influenced by many genes of small
    effect or by a few genes of major effect? Where is additive genetic variation
    located in the genome? Do the same loci cause similar phenotypic variation in
    different populations? Great tits (Parus major) have been studied extensively
    in long‐term studies across Europe and consequently are considered an ecological
    ‘model organism’. Recently, genomic resources have been developed for the great
    tit, including a custom SNP chip and genetic linkage map. In this study, we used
    a suite of approaches to investigate the genetic architecture of eight quantitative
    traits in two long‐term study populations of great tits—one in the Netherlands
    and the other in the United Kingdom. Overall, we found little evidence for the
    presence of genes of large effects in either population. Instead, traits appeared
    to be influenced by many genes of small effect, with conservative estimates of
    the number of contributing loci ranging from 31 to 310. Despite concordance between
    population‐specific heritabilities, we found no evidence for the presence of loci
    having similar effects in both populations. While population‐specific genetic
    architectures are possible, an undetected shared architecture cannot be rejected
    because of limited power to map loci of small and moderate effects. This study
    is one of few examples of genetic architecture analysis in replicated wild populations
    and highlights some of the challenges and limitations researchers will face when
    attempting similar molecular quantitative genetic studies in free‐living populations.
article_processing_charge: No
article_type: original
author:
- first_name: Anna W.
  full_name: Santure, Anna W.
  last_name: Santure
- first_name: Jocelyn
  full_name: Poissant, Jocelyn
  last_name: Poissant
- first_name: Isabelle
  full_name: De Cauwer, Isabelle
  last_name: De Cauwer
- first_name: Kees
  full_name: van Oers, Kees
  last_name: van Oers
- first_name: Matthew Richard
  full_name: Robinson, Matthew Richard
  id: E5D42276-F5DA-11E9-8E24-6303E6697425
  last_name: Robinson
  orcid: 0000-0001-8982-8813
- first_name: John L.
  full_name: Quinn, John L.
  last_name: Quinn
- first_name: Martien A. M.
  full_name: Groenen, Martien A. M.
  last_name: Groenen
- first_name: Marcel E.
  full_name: Visser, Marcel E.
  last_name: Visser
- first_name: Ben C.
  full_name: Sheldon, Ben C.
  last_name: Sheldon
- first_name: Jon
  full_name: Slate, Jon
  last_name: Slate
citation:
  ama: Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic
    architecture of quantitative traits in two wild great tit populations. <i>Molecular
    Ecology</i>. 2015;24:6148-6162. doi:<a href="https://doi.org/10.1111/mec.13452">10.1111/mec.13452</a>
  apa: Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R.,
    Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture
    of quantitative traits in two wild great tit populations. <i>Molecular Ecology</i>.
    Wiley. <a href="https://doi.org/10.1111/mec.13452">https://doi.org/10.1111/mec.13452</a>
  chicago: Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers,
    Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser,
    Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture
    of Quantitative Traits in Two Wild Great Tit Populations.” <i>Molecular Ecology</i>.
    Wiley, 2015. <a href="https://doi.org/10.1111/mec.13452">https://doi.org/10.1111/mec.13452</a>.
  ieee: A. W. Santure <i>et al.</i>, “Replicated analysis of the genetic architecture
    of quantitative traits in two wild great tit populations,” <i>Molecular Ecology</i>,
    vol. 24. Wiley, pp. 6148–6162, 2015.
  ista: Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen
    MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic
    architecture of quantitative traits in two wild great tit populations. Molecular
    Ecology. 24, 6148–6162.
  mla: Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of
    Quantitative Traits in Two Wild Great Tit Populations.” <i>Molecular Ecology</i>,
    vol. 24, Wiley, 2015, pp. 6148–62, doi:<a href="https://doi.org/10.1111/mec.13452">10.1111/mec.13452</a>.
  short: A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L.
    Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology
    24 (2015) 6148–6162.
date_created: 2020-04-30T10:51:01Z
date_published: 2015-12-10T00:00:00Z
date_updated: 2021-01-12T08:15:12Z
day: '10'
doi: 10.1111/mec.13452
extern: '1'
intvolume: '        24'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1111/mec.13452
month: '12'
oa: 1
oa_version: Published Version
page: 6148-6162
publication: Molecular Ecology
publication_identifier:
  issn:
  - 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Replicated analysis of the genetic architecture of quantitative traits in two
  wild great tit populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '7745'
abstract:
- lang: eng
  text: The underlying basis of genetic variation in quantitative traits, in terms
    of the number of causal variants and the size of their effects, is largely unknown
    in natural populations. The expectation is that complex quantitative trait variation
    is attributable to many, possibly interacting, causal variants, whose effects
    may depend upon the sex, age and the environment in which they are expressed.
    A recently developed methodology in animal breeding derives a value of relatedness
    among individuals from high‐density genomic marker data, to estimate additive
    genetic variance within livestock populations. Here, we adapt and test the effectiveness
    of these methods to partition genetic variation for complex traits across genomic
    regions within ecological study populations where individuals have varying degrees
    of relatedness. We then apply this approach for the first time to a natural population
    and demonstrate that genetic variation in wing length in the great tit (Parus
    major) reflects contributions from multiple genomic regions. We show that a polygenic
    additive mode of gene action best describes the patterns observed, and we find
    no evidence of dosage compensation for the sex chromosome. Our results suggest
    that most of the genomic regions that influence wing length have the same effects
    in both sexes. We found a limited amount of genetic variance in males that is
    attributed to regions that have no effects in females, which could facilitate
    the sexual dimorphism observed for this trait. Although this exploratory work
    focuses on one complex trait, the methodology is generally applicable to any trait
    for any laboratory or wild population, paving the way for investigating sex‐,
    age‐ and environment‐specific genetic effects and thus the underlying genetic
    architecture of phenotype in biological study systems.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
  full_name: Robinson, Matthew Richard
  id: E5D42276-F5DA-11E9-8E24-6303E6697425
  last_name: Robinson
  orcid: 0000-0001-8982-8813
- first_name: Anna W.
  full_name: Santure, Anna W.
  last_name: Santure
- first_name: Isabelle
  full_name: DeCauwer, Isabelle
  last_name: DeCauwer
- first_name: Ben C.
  full_name: Sheldon, Ben C.
  last_name: Sheldon
- first_name: Jon
  full_name: Slate, Jon
  last_name: Slate
citation:
  ama: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic
    variation across the genome using multimarker methods in a wild bird population.
    <i>Molecular Ecology</i>. 2013;22(15):3963-3980. doi:<a href="https://doi.org/10.1111/mec.12375">10.1111/mec.12375</a>
  apa: Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., &#38; Slate,
    J. (2013). Partitioning of genetic variation across the genome using multimarker
    methods in a wild bird population. <i>Molecular Ecology</i>. Wiley. <a href="https://doi.org/10.1111/mec.12375">https://doi.org/10.1111/mec.12375</a>
  chicago: Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon,
    and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker
    Methods in a Wild Bird Population.” <i>Molecular Ecology</i>. Wiley, 2013. <a
    href="https://doi.org/10.1111/mec.12375">https://doi.org/10.1111/mec.12375</a>.
  ieee: M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning
    of genetic variation across the genome using multimarker methods in a wild bird
    population,” <i>Molecular Ecology</i>, vol. 22, no. 15. Wiley, pp. 3963–3980,
    2013.
  ista: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning
    of genetic variation across the genome using multimarker methods in a wild bird
    population. Molecular Ecology. 22(15), 3963–3980.
  mla: Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across
    the Genome Using Multimarker Methods in a Wild Bird Population.” <i>Molecular
    Ecology</i>, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:<a href="https://doi.org/10.1111/mec.12375">10.1111/mec.12375</a>.
  short: M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular
    Ecology 22 (2013) 3963–3980.
date_created: 2020-04-30T11:00:15Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1111/mec.12375
extern: '1'
intvolume: '        22'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3963-3980
publication: Molecular Ecology
publication_identifier:
  issn:
  - 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Partitioning of genetic variation across the genome using multimarker methods
  in a wild bird population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '7746'
abstract:
- lang: eng
  text: Clutch size and egg mass are life history traits that have been extensively
    studied in wild bird populations, as life history theory predicts a negative trade‐off
    between them, either at the phenotypic or at the genetic level. Here, we analyse
    the genomic architecture of these heritable traits in a wild great tit (Parus
    major) population, using three marker‐based approaches – chromosome partitioning,
    quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS).
    The variance explained by each great tit chromosome scales with predicted chromosome
    size, no location in the genome contains genome‐wide significant QTL, and no individual
    SNPs are associated with a large proportion of phenotypic variation, all of which
    may suggest that variation in both traits is due to many loci of small effect,
    located across the genome. There is no evidence that any regions of the genome
    contribute significantly to both traits, which combined with a small, nonsignificant
    negative genetic covariance between the traits, suggests the absence of genetic
    constraints on the independent evolution of these traits. Our findings support
    the hypothesis that variation in life history traits in natural populations is
    likely to be determined by many loci of small effect spread throughout the genome,
    which are subject to continued input of variation by mutation and migration, although
    we cannot exclude the possibility of an additional input of major effect genes
    influencing either trait.
article_processing_charge: No
article_type: original
author:
- first_name: Anna W.
  full_name: Santure, Anna W.
  last_name: Santure
- first_name: Isabelle
  full_name: De Cauwer, Isabelle
  last_name: De Cauwer
- first_name: Matthew Richard
  full_name: Robinson, Matthew Richard
  id: E5D42276-F5DA-11E9-8E24-6303E6697425
  last_name: Robinson
  orcid: 0000-0001-8982-8813
- first_name: Jocelyn
  full_name: Poissant, Jocelyn
  last_name: Poissant
- first_name: Ben C.
  full_name: Sheldon, Ben C.
  last_name: Sheldon
- first_name: Jon
  full_name: Slate, Jon
  last_name: Slate
citation:
  ama: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic
    dissection of variation in clutch size and egg mass in a wild great tit (Parus
    major) population. <i>Molecular Ecology</i>. 2013;22(15):3949-3962. doi:<a href="https://doi.org/10.1111/mec.12376">10.1111/mec.12376</a>
  apa: Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C.,
    &#38; Slate, J. (2013). Genomic dissection of variation in clutch size and egg
    mass in a wild great tit (Parus major) population. <i>Molecular Ecology</i>. Wiley.
    <a href="https://doi.org/10.1111/mec.12376">https://doi.org/10.1111/mec.12376</a>
  chicago: Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn
    Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch
    Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” <i>Molecular
    Ecology</i>. Wiley, 2013. <a href="https://doi.org/10.1111/mec.12376">https://doi.org/10.1111/mec.12376</a>.
  ieee: A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and
    J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild
    great tit (Parus major) population,” <i>Molecular Ecology</i>, vol. 22, no. 15.
    Wiley, pp. 3949–3962, 2013.
  ista: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013.
    Genomic dissection of variation in clutch size and egg mass in a wild great tit
    (Parus major) population. Molecular Ecology. 22(15), 3949–3962.
  mla: Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and
    Egg Mass in a Wild Great Tit (Parus Major) Population.” <i>Molecular Ecology</i>,
    vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:<a href="https://doi.org/10.1111/mec.12376">10.1111/mec.12376</a>.
  short: A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J.
    Slate, Molecular Ecology 22 (2013) 3949–3962.
date_created: 2020-04-30T11:00:32Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1111/mec.12376
extern: '1'
intvolume: '        22'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3949-3962
publication: Molecular Ecology
publication_identifier:
  issn:
  - 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Genomic dissection of variation in clutch size and egg mass in a wild great
  tit (Parus major) population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
