Molecular phylogenetics and floral evolution of the Cirrhopetalum alliance (Bulbophyllum, Orchidaceae): Evolutionary transitions and phylogenetic signal variation

Hu, Aijun; Gale, Stephan W.; Liu, Zhong‐Jian; Suddee, Somran; Hsu, Tian‐Chuan; Fischer, Gunter A.; Saunders, Richard M.

doi:10.1016/j.ympev.2019.106689

Cited by 28 publications

(62 citation statements)

References 48 publications

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“…This modularization may be the result of selective pressures imposed by the visual preferences of pollinators and the need of consistency in pollinators visits to be efficient. In C. walkeriana, both the centripetal increase on color saturation and the yellow UV-absorbent patch of the labellum base create three different intrafloral color modules that are not entirely related to the morphological modules typically found in orchids (Hu et al, 2019). Such modules can be defined as: (1) the less saturated and variable color of sepals and petals, (2) the color of the labellum tip, which showed the highest color saturation, probably as an outcome of the selective pressure imposed by the innate preference of bees for centripetally color saturation in flowers (Lunau, 1990;Rohde et al, 2013), and (3) the color of the labellum base, which shows low hue variation among individuals and is probably an outcome of the selective pressure derived from the innate preference of bees for pollen-like colors (Lunau, 2000;Heuschen et al, 2005).…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, the overall similarity in sepals and lateral petals found here could be explained by the common expression of organ identity genes shared between sepals and petals (DEF-like classes 1 and 2) but not in labellum. Also, evidence from the literature shows that the labellum is under differential pollinator-mediated selection in relation to sepals and petals (Mondragón-Palomino and Theißen, 2009;Hu et al, 2019). This was especially strong for the labellum base color.…”

Section: Intrafloral Color Modularitymentioning

confidence: 97%

“…Given their potential different functions, sepals have evolved semi-independently from the petals, and the labellum has evolved semi-independently from petals (Mondragón-Palomino and Theißen, 2009). In addition, there was a phylogenetic conservatism during labellum evolution in comparison to the high lability of other petals and sepals in a specific orchid group (Cirrhopetalum alliance), revealing that pollinator-mediated selection could have a role in the modular evolution of orchid flowers (Hu et al, 2019), which could also influence intrafloral color patterns. Also, the hybrid orchid Cattleya "KOVA, " presents a spatiotemporal variation in pigments accumulation during floral development, regulated by three different transcription factors (Li et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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Intrafloral Color Modularity in a Bee-Pollinated Orchid

et al. 2020

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Flower color has been studied in different ecological levels of organization, from individuals to communities. However, it is unclear how color is structured at the intrafloral level. In bee-pollinated flowers, the unidirectional gradient in color purity and pollen mimicry are two common processes to explain intrafloral color patterns. Considering that floral traits are often integrated, usually reflecting evolutionary modules under pollinator-mediated selection, we hypothesize that such intrafloral color patterns are structured by intrafloral color modules as perceived by bee color vision system. Here, we studied the tropical bee-pollinated orchid Cattleya walkeriana , given its intrafloral color complexity and variation among individuals. Considering bee color vision, we investigated if intrafloral color modules arose among intrafloral patches (tip or base of the sepals, petals, and labellum). We expected a separate color module between the labellum patches (the main attractive structure in orchids) and petals and sepals. We measured the color reflectance and calculated the photoreceptor excitation, spectral purity, hue, and the chromatic contrast of the floral structures in the hexagon color model. Spectral purity (saturation) was higher in the labellum tip in comparison to petals and sepals, generating a unidirectional gradient. Labellum base presented a less saturated yellow UV-absorbing color, which may reflect a pollen mimicry strategy. C. walkeriana presented three intrafloral color modules corresponding to the color of petals and sepals, the color of the labellum tip, and the color of labellum base. These color modules were unrelated to the development of floral structures. Given the importance of intrafloral color patterns in bee attraction and guidance, our results suggest that intrafloral patterns could be the outcome of evolutionary color modularization under pollinator-mediated selection.

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Section: Resultsmentioning

confidence: 99%

Section: Intrafloral Color Modularitymentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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Intrafloral Color Modularity in a Bee-Pollinated Orchid

et al. 2020

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“…Given that many phylogenetic, phylogenomic and taxonomic uncertainties remain across this hyperdiverse family (e.g., Chen et al, 2019; Hu et al, 2020; Li et al, 2019; Mendoza et al, 2020; Perez‐Escobar et al, 2020; Salazar et al, 2018; Simo‐Droissart et al, 2018), the Orchidaceae is a prime candidate for wider testing of the phylogenetic and phylogenomic utility of targeted sequence capture methods. Beyond orchids, our findings indicate that by drawing on the increasing availability of transcriptomes, a customized multitiered sequence capture strategy, in combination with promising, yet underutilized phylogenomic approaches, will be effective for many plant groups.…”

Section: Discussionmentioning

confidence: 99%

A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids

Peakall

Wong

Phillips

et al. 2021

Molecular Ecology Resources

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With over 25,000 species, the drivers of diversity in the Orchidaceae remain to be fully understood. Here, we outline a multitiered sequence capture strategy aimed at capturing hundreds of loci to enable phylogenetic resolution from subtribe to subspecific levels in orchids of the tribe Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to give five target sequence sets aimed at the tribe (Sets 1 & 2), subtribe (Set 3), and within subtribe levels (Sets 4 & 5). Analysis included alternative de novo and reference‐guided assembly, before target sequence extraction, annotation and alignment, and application of a homology‐aware k‐mer block phylogenomic approach, prior to maximum likelihood and coalescence‐based phylogenetic inference. Our evaluation considered 87 taxa in two test data sets: 67 samples spanning the tribe, and 72 samples involving 24 closely related Caladenia species. The tiered design achieved high target loci recovery (>89%), with the median number of recovered loci in Sets 1–5 as follows: 212, 219, 816, 1024, and 1009, respectively. Interestingly, as a first test of the homologous k‐mer approach for targeted sequence capture data, our study revealed its potential for enabling robust phylogenetic species tree inferences. Specifically, we found matching, and in one case improved phylogenetic resolution within species complexes, compared to conventional phylogenetic analysis involving target gene extraction. Our findings indicate that a customized multitiered sequence capture strategy, in combination with promising yet underutilized phylogenomic approaches, will be effective for groups where interspecific divergence is recent, but information on deeper phylogenetic relationships is also required.

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“…Plastid sequences have been used in phylogenetic analyses based on their most nonrecombinant and uniparentally inherited and on their slower evolutionary rates than nuclear and mitochondrial genomes ( Wolfe, Li & Sharp, 1987 ; Birky, 1995 ). The plastid region of matK, rbcL and trnL-F have been used as genetic markers with great success in Orchidaceae ( Cameron et al, 1999 ; Salazar et al, 2017 ; Hu et al, 2020 ). However, the limited loci in phylogenetic inference are not powerful enough when closely related species are under consideration.…”

Section: Discussionmentioning

confidence: 99%

Plastome structure and adaptive evolution ofCalanthes.l. species

Chen

Zhong

Zhu

et al. 2020

PeerJ

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Calanthe s.l. is the most diverse group in the tribe Collabieae (Orchidaceae), which are pantropical in distribution. Illumina sequencing followed by de novo assembly was used in this study, and the plastid genetic information of Calanthe s.l. was used to investigate the adaptive evolution of this taxon. Herein, the complete plastome of five Calanthe s.l. species (Calanthe davidii, Styloglossum lyroglossa, Preptanthe rubens, Cephalantheropsis obcordata, and Phaius tankervilliae) were determined, and the two other published plastome sequences of Calanthe s.l. were added for comparative analyses to examine the evolutionary pattern of the plastome in the alliance. The seven plastomes ranged from 150,181 bp (C. delavayi) to 159,014 bp (C. davidii) in length and were all mapped as circular structures. Except for the three ndh genes (ndhC, ndhF, and ndhK) lost in C. delavayi, the remaining six species contain identical gene orders and numbers (115 gene). Nucleotide diversity was detected across the plastomes, and we screened 14 mutational hotspot regions, including 12 non-coding regions and two gene regions. For the adaptive evolution investigation, three species showed positive selected genes compared with others, C. obcordata (cemA), S. lyroglossa (infA, ycf1 and ycf2) and C. delavayi (nad6 and ndhB). Six genes were under site-specific positive selection in Calanthe s.l., namely, accD, ndhB, ndhD, rpoC2, ycf1, and ycf2, most of which are involved in photosynthesis. These results, including the new plastomes, provide resources for the comparative plastome, breeding, and plastid genetic engineering of orchids and flowering plants.

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Molecular phylogenetics and floral evolution of the Cirrhopetalum alliance (Bulbophyllum, Orchidaceae): Evolutionary transitions and phylogenetic signal variation

Cited by 28 publications

References 48 publications

Intrafloral Color Modularity in a Bee-Pollinated Orchid

Intrafloral Color Modularity in a Bee-Pollinated Orchid

A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids

Plastome structure and adaptive evolution ofCalanthes.l. species

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