Speciation via floral heterochrony and presumed mycorrhizal host switching of endemic butterfly orchids on the Azorean archipelago

Ecological divergence of sibling allopolyploid marsh orchids is associated with species specific plasticity and distinct fungal communities

Phenotypic plasticity, the dynamic adjustment of traits to environmental variations, is crucial for enabling species to exploit broader niches and withstand suboptimal conditions. This adaptability is particularly relevant for newly formed allopolyploids, which possess redundant gene copies and must become established in diverse environments distinct from their parents and other relatives. By evaluating gene expression and root mycobiome among two ecologically divergent sibling allopolyploid marsh orchids (Dactylorhiza majalis and D. traunsteineri) in reciprocal transplants at localities where both species are native, we aimed to understand the drivers of species persistence in the face of interspecific gene flow. Despite consistent abiotic differences characterising the alternative environments at each locality, the majority of gene expression differences between the allopolyploids appears to be plastic. Ecologically relevant processes, such as photosynthesis and transmembrane transport, include some genes that are differentially expressed between the two orchids regardless of the environment, while others change their activity plastically in one species or the other. This suggests that although plasticity helps define the specific ecological range of each sibling allopolyploid, it also mediates gene flow between them, thereby preventing differentiation. Extending our investigations to the root mycobiome, we uncover more diverse fungal communities for either species when grown in the environment with nutrient-poor soils, indicating that both abiotic and biotic factors drive the distribution of sibling marsh orchids. Altogether, our results indicate that plasticity can simultaneously promote diversification and homogenisation of lineages, influencing the establishment and persistence of recurrently formed allopolyploid species.

Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis

BACKGROUND

The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid.

RESULTS

In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89.

CONCLUSION

Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.

Plant morpho evo-devo

Evo-devo is often thought of as being the study of which genes underlie which phenotypes. However, evo-devo is much more than this, especially in plant science. In leaf scars along stems, cell changes across wood growth rings, or flowers along inflorescences, plants trace a record of their own development. Plant morpho evo-devo provides data that genes could never furnish on themes such as heterochrony, the evolution of temporal phenotypes, modularity, and phenotype-first evolution. As plant science surges into increasingly -omic realms, it is essential to keep plant morpho evo-devo in full view as an honored member of the evo-devo canon, ensuring that plant scientists can, wherever they are, generate fundamental insights at the appropriate level of biological organization.

Morphological Continua Make Poor Species: Genus-Wide Morphometric Survey of the European Bee Orchids (Ophrys L.)

Despite (or perhaps because of) intensive multidisciplinary research, opinions on the optimal number of species recognised within the Eurasian orchid genus Ophrys range from nine to at least 400. The lower figure of nine macrospecies is based primarily on seeking small but reliable discontinuities in DNA 'barcode' regions, an approach subsequently reinforced and finessed via high-throughput sequencing studies. The upper figure of ca. 400 microspecies reflects the morphological authoritarianism of traditional taxonomy combined with belief in extreme pollinator specificity caused by reliance on pollination through pseudo-copulation, enacted by bees and wasps. Groupings of microspecies that are less inclusive than macrospecies are termed mesospecies. Herein, we present multivariate morphometric analyses based on 51 characters scored for 457 individual plants that together span the full morphological and molecular diversity within the genus Ophrys, encompassing 113 named microspecies that collectively represent all 29 mesospecies and all nine macrospecies. We critique our preferred morphometric approach of accumulating heterogeneous data and analysing them primarily using principal coordinates, noting that our conclusions would have been strengthened by even greater sampling and the inclusion of data describing pseudo-pheromone cocktails. Morphological variation within Ophrys proved to be exceptionally multidimensional, lacking strong directional trends. Multivariate clustering of plants according to prior taxonomy was typically weak, irrespective of whether it was assessed at the level of macrospecies, mesospecies or microspecies; considerable morphological overlap was evident even between subsets of the molecularly differentiable macrospecies. Characters supporting genuine taxonomic distinctions were often sufficiently subtle that they were masked by greater and more positively correlated variation that reflected strong contrasts in flower size, tepal colour or, less often, plant size. Individual macrospecies appear to represent morphological continua, within which taxonomic divisions are likely to prove arbitrary if based exclusively on morphological criteria and adequately sampled across their geographic range. It remains unclear how much of the mosaic of subtle character variation among the microspecies reflects genetic versus epigenetic or non-genetic influences and what proportion of any contrasts observed in gene frequencies can be attributed to the adaptive microevolution that is widely considered to dictate speciation in the genus. Moreover, supplementing weak morphological criteria with extrinsic criteria, typically by imposing constraints on geographic location and/or supposed pollinator preference, assumes rather than demonstrates the presence of even the weakest of species boundaries. Overall, it is clear that entities in Ophrys below the level of macrospecies have insufficiently structured variation, either phenotypic or genotypic, to be resolved into discrete, self-circumscribing ("natural") entities that can legitimately be equated with species as delimited within other less specialised plant genera. Our search for a non-arbitrary (meso)species concept competent to circumscribe an intermediate number of species has so far proven unsuccessful.

Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids

BACKGROUND AND AIMS

Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus.

METHODS

At least two accessions of each of the ten species groups previously circumscribed from large-scale cloned nuclear ribosomal internal transcibed spacer (nrITS) sequencing were subjected to restriction site-associated sequencing (RAD-seq). The resulting matrix of 4159 single nucleotide polymorphisms (SNPs) for 34 accessions was used to construct an unrooted network and a rooted maximum likelihood phylogeny. A parallel morphological cladistic matrix of 43 characters generated both polymorphic and non-polymorphic sets of parsimony trees before being mapped across the RAD-seq topology.

KEY RESULTS

RAD-seq data strongly support the monophyly of nine out of ten groups previously circumscribed using nrITS and resolve three major clades; in contrast, supposed microspecies are barely distinguishable. Strong incongruence separated the RAD-seq trees from both the morphological trees and traditional classifications; mapping of the morphological characters across the RAD-seq topology rendered them far more homoplastic.

CONCLUSIONS

The comparatively high level of morphological homoplasy reflects extensive convergence, whereas the derived placement of the fusca group is attributed to paedomorphic simplification. The phenotype of the most recent common ancestor of the extant lineages is inferred, but it post-dates the majority of the character-state changes that typify the genus. RAD-seq may represent the high-water mark of the contribution of molecular phylogenetics to understanding evolution within Ophrys; further progress will require large-scale population-level studies that integrate phenotypic and genotypic data in a cogent conceptual framework.

Characterization of sympatric Platanthera bifolia and Platanthera chlorantha (Orchidaceae) populations with intermediate plants

Platanthera bifolia and P. chlorantha are terrestrial and rewarding orchids with a wide Eurasian distribution. Although genetically closely related, they exhibit significant morphological, phenological and ecological differences that maintain reproductive isolation between the species. However, where both species co-occur, individuals with intermediate phenotypic traits, often considered as hybrids, are frequently observed. Here, we combined neutral genetic markers (AFLPs), morphometrics and floral scent analysis (GC-MS) to investigate two mixed Platanthera populations where morphologically intermediate plants were found. Self-pollination experiments revealed a low level of autogamy and artificial crossings combined with assessments of fruit set and seed viability, showed compatibility between the two species. The results of the genetic analyses showed that morphologically intermediate plants had similar genetic patterns as the P. bifolia group. These results are corroborated also by floral scent analyses, which confirmed a strong similarity in floral scent composition between intermediate morphotypes and P. bifolia. Therefore, this study provided a much more detailed picture of the genetic structure of a sympatric zone between two closely allied species and supports the hypothesis that intermediate morphotypes in sympatry could reflect an adaptive evolution in response to local pollinator-mediated selection.

The Times They Are A-Changin': Heterochrony in Plant Development and Evolution

Alterations in the timing of developmental programs during evolution, that lead to changes in the shape, or size of organs, are known as heterochrony. Heterochrony has been widely studied in animals, but has often been neglected in plants. During plant evolution, heterochronic shifts have played a key role in the origin and diversification of leaves, roots, flowers, and fruits. Heterochrony that results in a juvenile or simpler outcome is known as paedomorphosis, while an adult or more complex outcome is called peramorphosis. Mechanisms that alter developmental timing at the cellular level affect cell proliferation or differentiation, while those acting at the tissue or organismal level change endogenous aging pathways, morphogen signaling, and metabolism. We believe that wider consideration of heterochrony in the context of evolution will contribute to a better understanding of plant development.

Floral scent and species divergence in a pair of sexually deceptive orchids

Speciation is typically accompanied by the formation of isolation barriers between lineages. Commonly, reproductive barriers are separated into pre‐ and post‐zygotic mechanisms that can evolve with different speed. In this study, we measured the strength of different reproductive barriers in two closely related, sympatric orchids of the Ophrys insectifera group, namely Ophrys insectifera and Ophrys aymoninii to infer possible mechanisms of speciation. We quantified pre‐ and post‐pollination barriers through observation of pollen flow, by performing artificial inter‐ and intraspecific crosses and analyzing scent bouquets. Additionally, we investigated differences in mycorrhizal fungi as a potential extrinsic factor of post‐zygotic isolation. Our results show that floral isolation mediated by the attraction of different pollinators acts apparently as the sole reproductive barrier between the two orchid species, with later‐acting intrinsic barriers seemingly absent. Also, the two orchids share most of their fungal mycorrhizal partners in sympatry, suggesting little or no importance of mycorrhizal symbiosis in reproductive isolation. Key traits underlying floral isolation were two alkenes and wax ester, present predominantly in the floral scent of O. aymoninii. These compounds, when applied to flowers of O. insectifera, triggered attraction and a copulation attempt of the bee pollinator of O. aymoninii and thus led to the (partial) breakdown of floral isolation. Based on our results, we suggest that adaptation to different pollinators, mediated by floral scent, underlies species isolation in this plant group. Pollinator switches may be promoted by low pollination success of individuals in dense patches of plants, an assumption that we also confirmed in our study.

Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands

Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.

In situ morphometric survey elucidates the evolutionary systematics of the Eurasian Himantoglossum clade (Orchidaceae: Orchidinae)

Background and Aims

The charismatic Himantoglossum s.l. clade of Eurasian orchids contains an unusually large proportion of taxa that are of controversial circumscriptions and considerable conservation concern. Whereas our previously published study addressed the molecular phylogenetics and phylogeography of every named taxon within the clade, here we use detailed morphometric data obtained from the same populations to compare genotypes with associated phenotypes, in order to better explore taxonomic circumscription and character evolution within the clade.

Methods

Between one and 12 plants found in 25 populations that encompassed the entire distribution of the Himantoglossum s.l. clade were measured in situ for 51 morphological characters. Results for 45 of those characters were subjected to detailed multivariate and univariate analyses.

Key Results

Multivariate analyses readily separate subgenus Barlia and subgenus Comperia from subgenus Himantoglossum, and also the early-divergent H. formosum from the less divergent remainder of subgenus Himantoglossum. The sequence of divergence of these four lineages is confidently resolved. Our experimental approach to morphometric character analysis demonstrates clearly that phenotypic evolution within Himantoglossum is unusually multi-dimensional.

Conclusions

Degrees of divergence between taxa shown by morphological analyses approximate those previously shown using molecular analyses. Himantoglossum s.l. is readily divisible into three subgenera. The three sections of subgenus Himantoglossum—hircinum, caprinum and formosum—are arrayed from west to east with only limited geographical overlap. At this taxonomic level, their juxtaposition combines with conflict between contrasting datasets to complicate attempts to distinguish between clinal variation and the discontinuities that by definition separate bona fide species. All taxa achieve allogamy via food deceit and have only weak pollinator specificity. Artificial crossing demonstrates that intrinsic sterility barriers are weak. Although we have found evidence of gene flow among and within the three sections of subgenus Himantoglossum, reports of natural hybrids are surprisingly rare, probably because putative parents are sufficiently similar to questionably warrant the status of species. Phenological separation and increased xeromorphy characterise the origin of subgenus Barlia. Several individual morphological characters show evidence of parallel acquisition, and loss of features is especially frequent in floral markings among members of section caprinum. Detailed patterns of gain and loss demonstrate that several different categories of flower markings are inherited independently. Along with the dimensions of labellar lobes, these pigmentation characters have been over-emphasised in previous taxonomic treatments. Increased plant vigour was a crucial element of the origin of the genus, but vegetative characters underwent remarkably little subsequent evolution. Attempts to reconstruct hypothetical ancestors at internal nodes of the phylogeny are weakened by (a) uncertain placement of Steveniella as sister to Himantoglossum s.l. and (b) uncertain relationships among subtly different putative species within section caprinum. Nonetheless, heterochronic/allometric trends, ultimately limited by functional constraints, clearly dictate transitions between contrasting flower sizes and complex labellum shapes.

Mycorrhizal Fungal Diversity and Community Composition in Two Closely Related Platanthera (Orchidaceae) Species

While it is generally acknowledged that orchid species rely on mycorrhizal fungi for completion of their life cycle, little is yet known about how mycorrhizal fungal diversity and community composition vary within and between closely related orchid taxa. In this study, we used 454 amplicon pyrosequencing to investigate variation in mycorrhizal communities between pure (allopatric) and mixed (sympatric) populations of two closely related Platanthera species (Platanthera bifolia and P. chlorantha) and putative hybrids. Consistent with previous research, the two species primarily associated primarily with members of the Ceratobasidiaceae and, to a lesser extent, with members of the Sebacinales and Tulasnellaceae. In addition, a large number of ectomycorrhizal fungi belonging to various families were observed. Although a considerable number of mycorrhizal fungi were common to both species, the fungal communities were significantly different between the two species. Individuals with intermediate morphology showed communities similar to P. bifolia, confirming previous results based on the genetic architecture and fragrance composition that putative hybrids essentially belonged to one of the parental species (P. bifolia). Differences in mycorrhizal communities between species were smaller in mixed populations than between pure populations, suggesting that variation in mycorrhizal communities was largely controlled by local environmental conditions. The small differences in mycorrhizal communities in mixed populations suggests that mycorrhizal fungi are most likely not directly involved in maintaining species boundaries between the two Platanthera species. However, seed germination experiments are needed to unambiguously assess the contribution of mycorrhizal divergence to reproductive isolation.

Floral miniaturisation and autogamy in boreal-arctic plants are epitomised by Iceland's most frequent orchid, Platanthera hyperborea

Background and Aims. This paper concludes our series of publications comparing island and mainland speciation in European butterfly-orchids, by studying the morphology, phylogenetics and reproductive biology of the controversial circum-arctic species Platanthera (Limnorchis) hyperborea-the most frequent of seven Icelandic orchids. We draw particular attention to its phylogenetic placement, remarkable reproductive biology and morphological convergence on other Platanthera lineages through floral miniaturisation. Methods. Five populations of P. hyperborea in southwest Iceland were measured for 33 morphological characters and subjected to detailed multivariate and univariate analyses, supported by light and scanning electron microscopy of selected flowers. Representative samples from six populations were sequenced for nrITS and placed in a taxonomically broader phylogenetic matrix derived from previous studies. Key Results . Section Limnorchis consists of three distinct ITS-delimited clades based on P. stricta, P. sparsifolia-limosa-aquilonis and P. dilatata-hyperborea. Within the latter group, supposed species boundaries overlap; instead, the data indicate a crude stepwise series of ribotypic transitions extending eastward from North America to Iceland. Morphometric data failed to identify any taxonomically meaningful partitions among Icelandic P. hyperborea populations, despite the presence of a distinct and apparently plesiomorphic ribotype at the most glacially influenced habitat sampled. Microscopic study of the flowers revealed several distinguishing features (some not previously reported), including resupinate lateral sepals, toothed bract margins, club-shaped papillae shared by both the interior of the labellar spur and the stigmatic surface, and an exceptionally adhesive stigma that is reliably covered in disaggregated pollen masses prior to anthesis; auricles are absent. Conclusions. Ribotypes suggest that Icelandic P. hyperborea represents the terminus of a migration route that may have begun in East Asia before passing through North America and presumably Greenland. The incohesive pollinia, rapidly desiccating anther locules, weakly developed rostellum, exceptionally adhesive stigma and the close juxtaposition of compact male and female reproductive organs together conspire to cause routine autogamy and frequent cleistogamy, despite the continued production of substantial nectar reservoirs in the spur and consequent ongoing attraction to the flowers of insects, including mosquitoes. When considered in combination with independently derived lineages of Platanthera on the Azorean and Hawaiian archipelagos also bearing small green flowers, our observations show allometric and paedomorphic reductions in flower size as the primary evolutionary driver, but also indicate strong developmental and functional constraints.

Molecular phylogeny and evolutionary history of the Eurasiatic orchid genus Himantoglossum s.l. (Orchidaceae)

BACKGROUND AND AIMS

Lizard orchids of the genus Himantoglossum include many of Eurasia's most spectacular orchids, producing substantial spikes of showy flowers. However, until recently the genus had received only limited, and entirely traditional, systematic study. The aim of the current work was to provide a more robust molecular phylogeny in order to better understand the evolutionary relationships among species of particular conservation concern.

METHODS

All putative species of Himantoglossum s.l. were sampled across its geographical range. A large subsample of the 153 populations studied contributed to an initial survey of nuclear ribosomal internal transcribed spacer (nrITS) ribotypes. Smaller subsets were then sequenced for four plastid regions and the first intron of the low-copy-number nuclear gene LEAFY. Rooted using Steveniella as outgroup, phylogenetic trees were generated using parsimony and Bayesian methods from each of the three datasets, supplemented with a ribotype network.

KEY RESULTS

The resulting trees collectively determined the order of branching of the early divergent taxa as Himantoglossum comperianum > H. robertianum group > H. formosum, events that also involved significant morphological divergence. Relaxed molecular clock dating suggested that these divergences preceded the Pleistocene glaciations (the origin of the H. robertianum group may have coincided with the Messinian salinity crisis) and occurred in Asia Minor and/or the Caucasus. Among more controversial taxa of the H. hircinum-jankae clade, which are only subtly morphologically divergent, topological resolution was poorer and topological incongruence between datasets was consequently greater.

CONCLUSIONS

Plastid sequence divergence is broadly consistent with prior, morphologically circumscribed taxa and indicates a division between H. hircinum-adriaticum to the west of the Carpathians and H. jankae-caprinum (plus local endemics) to the east, a distinction also suggested by nrITS ribotypes. LEAFY phylogenies are less congruent with prior taxonomic arrangements and include one likely example of paralogy. Himantoglossum metlesicsianum fully merits its IUCN Endangered status. Potentially significant genetic variation was detected within Steveniella satyrioides, H. robertianum and H. hircinum. However, confident circumscription of the more derived species of Himantoglossum s.s., including local endemics of hybrid origin, must await future morphometric and population-genetic analyses.

Systematic revision of Platanthera in the Azorean archipelago: not one but three species, including arguably Europe's rarest orchid

Background and Aims. The Macaronesian islands represent an excellent crucible for exploring speciation. This dominantly phenotypic study complements a separate genotypic study, together designed to identify and circumscribe Platanthera species (butterfly-orchids) on the Azores, and to determine their geographic origin(s) and underlying speciation mechanism(s). Methods. 216 individuals of Platanthera from 30 Azorean localities spanning all nine Azorean islands were measured for 38 morphological characters, supported by light and scanning electron microscopy of selected flowers. They are compared through detailed multivariate and univariate analyses with four widespread continental European relatives in the P. bifolia-chlorantha aggregate, represented by 154 plants from 25 populations, and with the highly misleading original taxonomic descriptions. Physiographic and ecological data were also recorded for each study population. Key Results. Despite limited genetic divergence, detailed phenotypic survey reveals not one or two but three discrete endemic species of Platanthera that are readily distinguished using several characters, most floral: P. pollostantha (newly named, formerly P. micrantha) occupies the widest range of habitats and altitudes and occurs on all nine islands; P. micrantha (formerly P. azorica) occurs on eight islands but is restricted to small, scattered populations in laurisilva scrub; the true P. azorica appears confined to a single volcanigenic ridge on the central island of São Jorge. Conclusions. Although hybridity seems low, the excess of phenotypic over genotypic divergence suggests comparatively recent speciation. The most probable of several credible scenarios is that Azorean Platantheras represent a single migration to the archipelago of airborne seed from ancestral population(s) located in southwest Europe rather than North America, originating from within the P. bifolia-chlorantha aggregate. We hypothesise that an initial anagenetic speciation event, aided by the founder effect, was followed by the independent origins of at least one of the two rarer endemic species from within the first-formed endemic species, via a cladogenetic speciation process that involved radical shifts in floral development, considerable phenotypic convergence, and increased mycorrhizal specificity. The recent amalgamation by IUCN of Azorean Platantheras into a single putative species on their Red List urgently requires overruling, as (a) P. azorica is arguably Europe's rarest bona fide orchid species and (b) the almost equally rare P. micrantha is one of the best indicators of semi-natural laurisilva habitats remaining on the Azores. Both species are threatened by habitat destruction and invasive alien plants. These orchids constitute a model system that illustrates the general advantages of circumscribing species by prioritising field-based over herbarium-based morphological approaches.