Multi‐locus phylogenetics, lineage sorting, and reticulation in <i>Pinus</i> subsection <i>Australes</i>

Gernandt, David S.; Dugua, Xitlali Aguirre; Vázquez‐Lobo, Alejandra; Willyard, Ann; Letelier, Alejandra Moreno; Rosa, Jorge A. Pérez de la; Piñero, Daniel; Liston, Aaron

doi:10.1002/ajb2.1052

Cited by 57 publications

(37 citation statements)

References 76 publications

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“…These results add to the growing number of studies that have formally evaluated the role of introgression in generating phylogenetic incongruence between plant nuclear and organellar genomes (e.g. Winkler et al ., ; Folk et al ., ; García et al ., ; Morales‐Briones et al ., ; Gernandt et al ., ). What has emerged is the robust detection of cytoplasmic introgression in diverse taxa representing both angiosperms and gymnosperms.…”

Section: Discussionmentioning

confidence: 97%

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)

et al. 2018

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Cytonuclear discordance is commonly observed in phylogenetic studies, yet few studies have tested whether these patterns reflect incomplete lineage sorting or organellar introgression. Here, we used whole-chloroplast sequence data in combination with over 1000 nuclear single-nucleotide polymorphisms to clarify the extent of cytonuclear discordance in wild annual sunflowers (Helianthus), and to test alternative explanations for such discordance. Our phylogenetic analyses indicate that cytonuclear discordance is widespread within this group, both in terms of the relationships among species and among individuals within species. Simulations of chloroplast evolution show that incomplete lineage sorting cannot explain these patterns in most cases. Instead, most of the observed discordance is better explained by cytoplasmic introgression. Molecular tests of evolution further indicate that selection may have played a role in driving patterns of plastid variation - although additional experimental work is needed to fully evaluate the importance of selection on organellar variants in different parts of the geographic range. Overall, this study represents one of the most comprehensive tests of the drivers of cytonuclear discordance and highlights the potential for gene flow to lead to extensive organellar introgression in hybridizing taxa.

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Section: Discussionmentioning

confidence: 97%

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)

et al. 2018

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“…DNA was quantified with a Qubit fluorometer kit (Life Technologies, Carlsbad, CA, USA) and shipped to Arbor Biosciences (Ann Arbor, MI, USA) for preparation of genomic libraries, and enrichment of low copy nuclear DNA genes using the combined target capture and genome skimming Hyb‐Seq method (Weitemier et al., ). A more detailed description of DNA extraction and sequencing methods is described elsewhere (Gernandt et al., ). Sequences were generated with an Illumina HiSeq 2000 (San Diego, CA, USA) with 100‐bp paired‐end reads.…”

Section: Methodsmentioning

confidence: 99%

Incorporating fossils into the Pinaceae tree of life

Gernandt

Arias

Terrazas

et al. 2018

American J of Botany

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“…The high degree of introgression can be explained by the relatively recent diversification of species in the subsection Australes and the very weak reproductive barriers between them (Little & Righter, 1965;Garrett, 1979;Dvorak et al, 2000;Vargas-Mendoza et al, 2011;Gernandt et al, 2018). Similar weak reproductive barriers and high recent speciation rates have been recorded for madrones (Arbutus spp.)…”

Section: Discussionmentioning

confidence: 73%

“…Natural hybridization has also been observed in other Mexican pine species (Gernandt et al, 2018). Previous studies of the subsection Australes identified natural hybridization between P. oocarpa × Pinus caribaea and P. oocarpa × Pinus pringlei only by morphological traits (Styles & Stead, 1982;López-Upton et al, 2001).…”

Section: Discussionmentioning

confidence: 84%

“…The aim of the present study was therefore to use AFLP molecular markers and morphological traits to determine the degree of hybridization between P. herrerae and P. luzmariae in seed stands of each species located in the Sierra Madre Occidental mountain system, Durango, Mexico. Although P. herrerae and P. luzmariae are morphologically very different (Perry, 1991;Farjon & Styles, 1997;García-Arévalo & González-Elizondo, 2003;Pérez de la Rosa & Vargas Amado, 2009), they are genetically closely related and can thus, theoretically, easily hybridize with each other (Dvorak et al, 2000;Ortiz-Martínez & Gernandt, 2016;Gernandt et al, 2018). In addition, we tested the possible P. luzmariae hybrid individuals for clues of possible hybrid vigour (heterosis).…”

Section: Introductionmentioning

confidence: 99%

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TallPinus luzmariaetrees with genes fromP. herrerae

Wehenkel

Mariscal-Lucero

González‐Elizondo

et al. 2020

PeerJ

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Context Pinus herrerae and P. luzmariae are endemic to western Mexico, where they cover an area of more than 1 million hectares. Pinus herrerae is also cultivated in field trials in South Africa and South America, because of its considerable economic importance as a source of timber and resin. Seed quality, afforestation success and desirable traits may all be influenced by the presence of hybrid trees in seed stands. Aims We aimed to determine the degree of hybridization between P. herrerae and P. luzmariae in seed stands of each species located in the Sierra Madre Occidental, Durango, Mexico. Methods AFLP molecular markers from samples of 171 trees across five populations were analyzed with STRUCTURE and NewHybrids software to determine the degree of introgressive hybridization. The accuracy of STRUCTURE and NewHybrids in detecting hybrids was quantified using the software Hybridlab 1.0. Morphological analysis of 131 samples from two populations of P. herrerae and two populations of P. luzmariae was also conducted by Random Forest classification. The data were compared by Principal Coordinate Analysis (PCoA) in GenAlex 6.501. Results Hybridization between Pinus herrerae and P. luzmariae was observed in all seed stands under study and resulted in enhancement of desirable silvicultural traits in the latter species. In P. luzmariae, only about 16% molecularly detected hybrids correspond to those identified on a morphological basis. However, the morphology of P. herrerae is not consistent with the molecularly identified hybrids from one population and is only consistent with 3.3 of those from the other population. Conclusions This is the first report of hybrid vigour (heterosis) in Mexican pines. Information about hybridization and introgression is essential for developing effective future breeding programs, successful establishment of plantations and management of natural forest stands. Understanding how natural hybridization may influence the evolution and adaptation of pines to climate change is a cornerstone to sustainable forest management including adaptive silviculture.

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Multi‐locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes

Abstract: Our analyses document cytonuclear discordance in Pinus subsection Australes. We attribute this discordance to ancient and recent introgression and present a phylogenetic hypothesis in which mostly hierarchical relationships are overlain by gene flow.

Cited by 57 publications

References 76 publications

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)

Incorporating fossils into the Pinaceae tree of life

TallPinus luzmariaetrees with genes fromP. herrerae

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