ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids

Heredia, Unai López de; Mora‐Márquez, Fernando; Goicoechea, P. G.; Guillardín-Calvo, Laura; Simeone, Marco Cosimo; Soto, Álvaro

doi:10.3389/fpls.2020.564414

Cited by 22 publications

(28 citation statements)

References 83 publications

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“…These shifts left imprints in the genetic signature of the family recording ancient and recent gene flow between lineages that diverged tens of millions of years ago (e.g. López de Heredia et al., 2020; McVay et al., 2017). These characteristics may have contributed to the success story of these trees, but at the same time complicated phylogenetic reconstructions.…”

Section: Discussionmentioning

confidence: 99%

5S‐IGS rDNA in wind‐pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species

et al. 2021

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SUMMARY Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind‐pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi‐copy, potentially multi‐locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra‐genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high‐throughput sequencing (HTS) of the 5S intergenic spacers (5S‐IGS) for a lineage of wind‐pollinated subtropical to temperate trees, the Fagus crenata – F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4963 unique 5S‐IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra‐genomic competition between two or more paralogous‐homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.

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Section: Discussionmentioning

confidence: 99%

5S‐IGS rDNA in wind‐pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species

et al. 2021

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“…The second is directional selection, which promotes identical allele frequencies under similar ecological/climatic circumstances, but differentiates populations in contrasting ecological circumstances, consequently favouring the two cluster scenario. Hybridisation between Q. suber and both Q. ilex and Q. cerris is indeed known to occur in the western and eastern ranges of the species’ distribution, respectively ( Lumaret et al, 2005 ; Magri et al, 2007 ; Lumaret & Jabbour-Zahab, 2009 ; López de Heredia, Sanchez & Soto, 2018 ; López de Heredia et al., 2020 ). Introgression from related Quercus species may have contributed to the survival of Q. suber through glaciation periods ( López de Heredia, Vázquez & Soto, 2017 ) and may also have influenced the number of private alleles of certain populations.…”

Section: Discussionmentioning

confidence: 99%

Population structure in Quercus suber L. revealed by nuclear microsatellite markers

Sousa

Costa

Ribeiro

et al. 2022

PeerJ

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Quercus suber L. is a sclerophyllous tree species native to the western Mediterranean, a region that is considered highly vulnerable to increased temperatures and severe dry conditions due to environmental changes. Understanding the population structure and demographics of Q. suber is essential in order to anticipate whether populations at greater risk and the species as a whole have the genetic background and reproductive dynamics to enable rapid adaptation. The genetic diversity of Q. suber has been subject to different studies using both chloroplast and nuclear data, but population structure patterns remain unclear. Here, we perform genetic analyses on Q. suber using 13 nuclear microsatellite markers, and analysed 17 distinct locations across the entire range of the species. Structure analyses revealed that Q. suber may contain three major genetic clusters that likely result from isolation in refugia combined with posterior admixture and putative introgression from other Quercus species. Our results show a more complex structure scenario than previously inferred for Q. suber using nuclear markers and suggest that different southern populations contain high levels of genetic variation that may contribute to the resilience of Q. suber in a context of environmental change and adaptive pressure.

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“…At the same time, species boundaries remain permeable: Fagaceae are known for both ancient and recent gene flow between lineages that diverged tens of millions of years ago (e.g. McVay et al, 2017;López-Heredia et al, 2020). Phases of area expansion likely led to secondary contacts and lineage mixing.…”

Section: Discussionmentioning

confidence: 99%

5S-IGS rDNA in wind-pollinated trees (FagusL.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species

Cardoni

Piredda

Denk

et al. 2021

Preprint

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Standard models of speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality is more complex: plant species can evolve from other species via isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi–copy, potentially multi–locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Here, we provide the first high-throughput sequencing (HTS) 5S intergenic spacer (5S – IGS) data for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata – F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4,963 unique 5S – IGS variants reflect a long history of repeated incomplete lineage sorting and lineage mixing since the early Cenozoic of two or more paralogous-homoeologous 5S rDNA lineages. Extant species of Fagus are genetic mosaics and, at least to some part, of hybrid origin.

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ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids

Abstract: Ló pez de Heredia et al. ddRADseq Analysis of Q. ilex-Q. suber Hybridization

Cited by 22 publications

References 83 publications

5S‐IGS rDNA in wind‐pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species

5S‐IGS rDNA in wind‐pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species

Population structure in Quercus suber L. revealed by nuclear microsatellite markers

5S-IGS rDNA in wind-pollinated trees (FagusL.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species

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