Genomic landscape of the global oak phylogeny

New Phytologist, Journal Year: 2019, Volume and Issue: 226(4), P. 1198 - 1212

Published: Oct. 14, 2019

Summary The tree of life is highly reticulate, with the history population divergence emerging from populations gene phylogenies that reflect histories introgression, lineage sorting and divergence. In this study, we investigate global patterns oak diversity test hypothesis there are regions genome broadly informative about phylogeny. We utilize fossil data restriction‐site associated DNA sequencing ( RAD ‐seq) for 632 individuals representing nearly 250 Quercus species to infer a time‐calibrated phylogeny world's oaks. use reversible‐jump Markov chain Monte Carlo method reconstruct shifts in diversification rates, accounting among‐clade sampling biases. then map > 20 000 ‐seq loci back an annotated genomic distribution introgression phylogenetic support across Oak lineages have diversified among geographic regions, followed by ecological within Americas Eurasia. Roughly 60% traces four clades experienced increases net diversification, probably response climatic transitions or opportunity. strong contrasts high heterogeneity signal introgression. Oaks phylogenomic mosaics, their may fact depend on flow shapes genome.

Language: Английский

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Oaks: an evolutionary success story

New Phytologist, Journal Year: 2019, Volume and Issue: 226(4), P. 987 - 1011

Published: Oct. 20, 2019

Summary The genus Quercus is among the most widespread and species‐rich tree genera in northern hemisphere. extraordinary species diversity America Asia together with continuous continental distribution of a limited number European raise questions about how macro‐ microevolutionary processes made an evolutionary success. Synthesizing conclusions reached during past three decades by complementary approaches phylogenetics, phylogeography, genomics, ecology, paleobotany, population biology quantitative genetics, this review aims to illuminate leading radiation expansion oaks. From opposing scales time geography, we converge on four overarching explanations success oaks: accumulation large reservoirs within populations species; ability for rapid migration contributing ecological priority effects lineage diversification; high rates divergence clades combined convergent solutions problems across clades; propensity hybridization, adaptive introgression facilitating migration. Finally, explore potential future research avenues, emphasizing integration macroevolutionary perspectives.

Language: Английский

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Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: March 14, 2022

Northern Hemisphere forests changed drastically in the early Eocene with diversification of oak family (Fagaceae). Cooling climates over next 20 million years fostered spread temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses nuclear plastid genomes to investigate timing pattern major macroevolutionary events ancient genome-wide signatures hybridization across Fagaceae. Innovation related seed dispersal is implicated triggering waves continental radiations beginning rapid lineages resulting unparalleled transformation forest dynamics within 15 following K-Pg extinction. We detect introgression at multiple time scales, including predating origination genus-level diversity. As moved into newly available habitats Miocene, secondary contact between previously isolated species occurred. This resulted adaptive introgression, which may have further amplified white Eurasia.

Language: Английский

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Regionalización biogeográfica y evolución biótica de México: encrucijada de la biodiversidad del Nuevo Mundo

Revista Mexicana de Biodiversidad, Journal Year: 2019, Volume and Issue: 90(0)

Published: Nov. 8, 2019

La increíble diversidad específica y ecosistémica sitúan a México entre los países megadiversos del planeta. Los patrones biogeográficos de taxones país también muestran una notable complejidad. parte norte se sitúa en la región Neártica, mientras que austral pertenece Neotropical. Entre ambas, principalmente las sierras Madre Faja Volcánica Transmexicana, mezcla neárticos neotropicales determina Zona Transición Mexicana. Esta encrucijada biótica hace sea tan interesante, no solo términos sus especies endémicas, sino cuanto variadas relaciones filogenéticas hipótesis han formulado para explicar cómo orígenes diversos, ensamblado Adicionalmente, el posee casi todos tipos vegetación, con desiertos, bosques tropicales templados, pastizales yermos alta montaña. Se revisa regionalización biogeográfica país, reconociéndose 2 regiones, 1 zona transición, 14 provincias 42 distritos.

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Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)

New Phytologist, Journal Year: 2019, Volume and Issue: 226(4), P. 1158 - 1170

Published: April 9, 2019

Botanists have long recognised interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterised and the complex genomic signals resulting from combination of vertical horizontal transmission may confound phylogenetic inference obscure our ability to accurately infer deep evolutionary history oaks. Using anchored enrichment, we obtained phylogenomic dataset consisting hundreds single-copy nuclear loci. Concatenation, species-tree network analyses were carried out in an attempt uncover signal ancient introgression divergent topology for oak clade. Locus site-level likelihood comparisons then conducted further explore introgressed dataset. Historical, intersectional is suggested occurred between ancestor Eurasian Roburoid lineage Quercus pontica North American Dumosae Prinoideae lineages. Despite extensive time past, approach proved successful detecting signature introgression. Our results, highlight importance sampling use plurality analytical tools methods sufficiently datasets, this signal, history.

Language: Английский

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An Updated Infrageneric Classification of the North American Oaks (Quercus Subgenus Quercus): Review of the Contribution of Phylogenomic Data to Biogeography and Species Diversity

Forests, Journal Year: 2021, Volume and Issue: 12(6), P. 786 - 786

Published: June 15, 2021

The oak flora of North America north Mexico is both phylogenetically diverse and species-rich, including 92 species placed in five sections subgenus Quercus, the clade centered on Americas. Despite phylogenetic taxonomic progress genus over past 45 years, classification at subsectional level remains unchanged since early treatments by WL Trelease, AA Camus, CH Muller. In recent work, we used a RAD-seq based phylogeny 250 sampled from throughout Americas Eurasia to reconstruct timing biogeography American radiation. This work demonstrates that comprises mostly regional radiations with limited affinities Mexican clades, two sister group connections Eurasia. Using this framework, describe patterns diversity within formally classify 62 into nine major subsections Lobatae (the red oaks) Quercus white oaks), largest Quercus. We also distill emerging evolutionary biogeographic impact phylogenomic data systematics multiple complexes instances hybridization.

Language: Английский

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Use of Genomic Resources to Assess Adaptive Divergence and Introgression in Oaks

Forests, Journal Year: 2021, Volume and Issue: 12(6), P. 690 - 690

Published: May 27, 2021

Adaptive divergence is widely accepted as a contributor to speciation and the maintenance of species integrity. However, mechanisms leading reproductive isolation, genes involved in adaptive divergence, traits that shape adaptation wild changes climate are still largely unknown. In studying role ecological interactions environment-driven selection, trees have emerged potential model organisms because their longevity large genetic diversity, especially natural habitats. Due recurrent gene flow among with different preferences, oaks arose early 1970s for understanding how can occur face interspecific flow, what we mean by “species” when geographically genomically heterogeneous introgression seems undermine species’ coherence. this review, provide an overview recent research into genomic underpinnings integrity flow. We review analytical tools instrumental better isolation oaks. evidence oak coherent entities, focusing on sympatric populations ongoing discuss hypotheses regarding linking isolation. As evolution drought- freezing-tolerance been key parallel diversification oaks, investigate question whether same or similar set drought stress tolerance across taxa sections. Finally, propose future directions hybridization change.

Language: Английский

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Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny

Molecular Phylogenetics and Evolution, Journal Year: 2020, Volume and Issue: 156, P. 107022 - 107022

Published: Nov. 24, 2020

Language: Английский

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Genomic Identity of White Oak Species in an Eastern North American Syngameon

Annals of the Missouri Botanical Garden, Journal Year: 2019, Volume and Issue: 104(3), P. 455 - 477

Published: Sept. 5, 2019

The eastern North American white oaks, a complex of approximately 16 potentially interbreeding species, have become classic model for studying the genetic nature species in syngameon. Genetic work over past two decades has demonstrated reality oak but gene flow between sympatric oaks raises question whether there are conserved regions genome that define species. Does homogenize entire genome? Do distinguish one part its range differ from it other parts range, where grows sympatry withdifferent species? Or relatively across ranges? In this study, we revisit seven syngameon using set 80 single-nucleotide polymorphisms (SNPs) selected previous study because they show differences among, and consistency within, We test hypothesis exist segments do not homogenized by repeated introgression, retain distinct alleles characteristic each undertake range-wide sampling to investigate SNPs appeared be fixed based on small sample our or nearly Each remains genetically given diagnostic markers, with few individuals exhibiting admixture multiple map back all 12 Quercus linkage groups (chromosomes) separated an average 7.47 million bp (± 8.74 bp, SD), significantly clustered relative random null distribution, suggesting SNP toolkit reflects genome-wide patterns divergence while being concentrated reflect higher-than-average history among-species divergence. This application DNA designed simple problem identifying field important implications. First, is composed entities most taxonomists would consider “good species.” Second, more fundamentally, coherent portions remain divergent despite introgression. Understanding conditions under which some loci diverge others introgress key understanding origins maintenance global tree diversity.

Language: Английский

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A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus)

American Journal of Botany, Journal Year: 2022, Volume and Issue: 109(10), P. 1596 - 1606

Published: Sept. 16, 2022

The true blueberries (Vaccinium sect. Cyanococcus; Ericaceae), endemic to North America, have been intensively studied for over a century. However, with species estimates ranging from nine 24 and much confusion regarding boundaries, this ecologically economically valuable group remains inadequately understood at basic evolutionary taxonomic level. As first step toward understanding the history taxonomy of complex, we present phylogenomic hypothesis known diploid blueberries.

Language: Английский

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