Generic and Subtribal relationShipS in neotropical cymbidieae (orchidaceae) baSed on matK/ycf1 plaStid data

Summary The Andean mountains of South America are the most species‐rich biodiversity hotspot worldwide with c. 15% of the world's plant species, in only 1% of the world's land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification.We address this knowledge gap by inferring the biogeographical history and diversification dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely sampled orchid phylogenies (including more than 400 newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets.We find that the majority of Andean orchid lineages only originated in the last 20–15 million yr. Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and recolonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales.Our study sheds new light on the timing and geography of a major Neotropical diversification, and suggests that mountain uplift promotes species diversification across all elevational zones.

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“…Trees were rooted on Calypso bulbosa (for Cymbidieae) and Arpophyllum giganteum (for Pleurothallidinae) following Whitten et al . ().…”

Section: Methodsmentioning

confidence: 97%

Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot

et al. 2017

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“…From the top 10 markers ranked in our list, just one (trnK/matK) has been used in more than one phylogenetic study in cacti (Nyffeler 2002;Edwards et al 2005 However, accD intergenic spacers, such as rbcL-accD and accD-psaI, have been much more widely used across disparate groups (Barfuss et al 2005;Miikeda et al 2006;Reginato et al 2010;Sun et al 2012;Michelangeli et al 2012). The ycf1 gene appears to be moderately used (Gernandt et al 2009;Guo et al 2012;Majure et al 2012;Whitten et al 2013;Shi et al 2013;Dastpak et al 2018), and increasingly reported to be a useful marker in phylogenetics inferences (Neubig et al 2009;Neubig and Abbott 2010;Dong et al 2012;Thomson et al 2018), and the most promising plastid DNA barcode of land plants (Dong et al 2015). The petD intron has been used Borsh et al 2009;Worberg et al 2007;Scataglini et al 2013), but in our analysis the entire gene was used (exon + intron) showing phylogenetic utility.…”

Section: Phylogenetically Informative Regionsmentioning

confidence: 92%

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Köhler

Reginato

et al. 2020

Preprint

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Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (~25 kb) and the ndh genes suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address 1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and 2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeats and the presence of all the ndh genes suite. An expansion of the large single copy unit and a reduction of the small single copy was observed, including translocations and inversion of genes as well as the putative pseudogenization of numerous loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in determining relationships among major clades and subclades within Opuntioideae, resolving three tribes with high support: Cylindropuntieae, Tephrocacteae and Opuntieae. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

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“…Our study builds-up upon previous DNA data matrices 43, 51, 63 . Genomic DNA was extracted from herbarium and fresh leaf material with the NucleoSpin plant kit (Macherey-Nagel; Düren, Germany).…”

Section: Methodsmentioning

confidence: 99%

Andean Mountain Building Did not Preclude Dispersal of Lowland Epiphytic Orchids in the Neotropics

Pérez‐Escobar

Gottschling

Chomicki

et al. 2017

Sci Rep

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The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical lineages. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) comprise ca 34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography of Cycnoches to better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models, we infer that the most recent common ancestor of Cycnoches originated in Amazonia ca 5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, these rare biological exchanges occurred well after major mountain building periods. The Andes have limited plant migration, yet it has seldom allowed episodic gene exchange of lowland epiphyte lineages such as orchids with great potential for effortless dispersal because of the very light, anemochorous seeds.

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Generic and Subtribal relationShipS in neotropical cymbidieae (orchidaceae) baSed on matK/ycf1 plaStid data

Cited by 27 publications

References 24 publications

Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot

Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Andean Mountain Building Did not Preclude Dispersal of Lowland Epiphytic Orchids in the Neotropics

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