<i>Caladenia</i> revisited: Results of molecular phylogenetic analyses of Caladeniinae plastid and nuclear loci

Clements, Mark A.; Howard, Christopher G.; Miller, Joseph T.

doi:10.3732/ajb.1500021

Cited by 12 publications

(12 citation statements)

References 54 publications

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“…While broadly recovering similar groupings of species and genera at the subtribe levels to Weston et al (2014) (c.f. Figures 2 and 6), our results indicate better resolution, particularly among closely related genera (e.g., among genera within the Drakaeinae, Megastylidinae, and Caladeniinae, see Clements et al, 2015; Miller & Clements, 2014; Weston et al, 2014)). However, our inability to resolve the relationships between the three major clades comprising the Prasophyllinae as Clade 1, Clade 2 as (Diuridinae(Cryptostylidinae(Thelymitrinae(Megastylidinae(Drakaeinae))))) and Clade 3 as (Acianthinae(Caladeniinae)), mirrors earlier findings (Clements et al, 2002; Kores et al, 2001; Weston et al, 2014, Figure 2), despite the very substantial increase in the number of loci.…”

Section: Discussionmentioning

confidence: 51%

“…One basis for sample inclusion in C72 was the requirement that two or more samples per species were successfully sequenced. Given a lack of species‐level resolution in previous molecular studies (Clements et al, 2015; Swarts et al, 2014), we reasoned that a first test of the effectiveness of Set 5 would be if the phylogenetic analysis could group individuals of the same species together. We also included examples of species that, based on morphology, appear to be closely allied as members of “species complexes” but can still be confidently distinguished in the field (Brown et al, 2013).…”

Section: Methodsmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 51%

Section: Methodsmentioning

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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“…However, we predict that this relationship is likely to be correlational rather than causal. While the sister clades to subgenera Calonema and Phlebochilus are pollinated primarily by food deception of nectar foraging insects (Phillips et al ., ; see Clements, Howard & Miller, , for phylogenetic data), these subgenera contain a large number of species pollinated by sexual deception of thynnine wasps (Phillips et al ., ), a strategy that appears to be associated with relatively rapid speciation (Cozzolino & Widmer, ; Peakall et al ., ). Further, sampling of genera allied to Caladenia may serve to erode this trend of low specificity in species‐poor clades.…”

Section: Discussionmentioning

confidence: 99%

Geographical range and host breadth ofSebacinaorchid mycorrhizal fungi associating withCaladeniain south-western Australia

et al. 2016

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Specialized mycorrhizal interactions have the potential to limit the geographical range of plant species and contribute to reproductive isolation. We investigated these predictions in Caladenia (Orchidaceae) from south‐western Australia, a group known to have specialized mycorrhizal associations with the genus Sebacina s.l. Sequencing of fungal isolates from 47 of the 136 species of Western Australian Caladenia was undertaken to resolve the geographical range and habitat preferences of mycorrhizal fungal operational taxonomic units (OTUs) and their host breadth in Caladenia. Eight different fungal OTUs were used by Caladenia, with the more frequently detected OTUs occurring in a wide range of habitats and geographical regions. Given the comparatively narrow geographical ranges of most Western Australian Caladenia taxa, this suggests that the geographical ranges of fungal OTUs are unlikely to limit the geographical range of Caladenia spp. Extensive sharing of fungal OTUs between closely related orchid species was detected, suggesting that in the main there is little potential for mycorrhizal fungi to contribute to reproductive isolation between Caladenia spp. Our data mostly support previous work suggesting high mycorrhizal specificity in Caladenia, but this may not be the case in all subgenera, highlighting that Caladenia may offer powerful opportunities for investigating the evolution of specialized mycorrhizal associations.

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“…Drakaea and Caladenia belong to different subtribes of the Diurideae (Drakaeinae and Caladeniinae; Kores et al 2001). No detailed phylogeny is available for Caladenia below the level of subgenus (see Clements et al 2015), but based on morphology, our study species Caladenia decora, C. procera and C. pectinata are believed to be closely related and may well be sister species (Hopper and Brown 2001; Fig. 1).…”

Section: Study Speciesmentioning

confidence: 97%

Convergent evolution of sexual deception via chromatic and achromatic contrast rather than colour mimicry

2016

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The Orchidaceae is characterised by the repeated evolution of sexual deception, one of the most specialised pollination strategies. In orchids, sexual deception involves long-range pollinator attraction via mimicry of female insect sex pheromones. At close range, visual signals involving colour mimicry, contrast to the background, and exploitation of pollinator sensory biases could attract pollinators, but remain largely untested. Here we focus on a remarkable system in which species from two only distantly related sexually deceptive orchid genera with strikingly different flowers (Drakaea livida and three species of Caladenia) share the same pollinator, males of the thynnine wasp Zaspilothynnus nigripes. We used spectral reflectance measurements and modelling to investigate pollinator perception of colour, including the first examination of overall colour patterns in flowers via colour pattern geometry analyses. Rather than closely matching the colours of female Z. nigripes, these orchids had strong chromatic and achromatic contrast against their backgrounds. For Caladenia, the sepals and petals show high contrast, while in D. livida, which has diminutive petals and sepals, it is the labellum that contrasts strongly against the background. Despite varying in colour, the Caladenia species all had strong withinflower contrast between a UV-bright central target (column and labellum) and a corolla of radiating stripes (petals and sepals). The colour pattern geometry analyses also indicated that the orchids' overall colour patterns are highly conspicuous against their backgrounds. Contrast, UV, and target patterns could all enhance detection, and exploit pollinators' innate preferences. Since colour contrast may function with a range of colours and floral forms, attracting pollinators via contrast rather than visual mimicry may be a critical but previously overlooked process facilitating the evolution of sexual deception.

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Caladenia revisited: Results of molecular phylogenetic analyses of Caladeniinae plastid and nuclear loci

Cited by 12 publications

References 54 publications

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

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

Geographical range and host breadth ofSebacinaorchid mycorrhizal fungi associating withCaladeniain south-western Australia

Convergent evolution of sexual deception via chromatic and achromatic contrast rather than colour mimicry

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