Hybridization and geographic distribution shapes the spatial genetic structure of two co-occurring orchid species

Phenotypic plasticity rather than ecotypic differentiation explains the broad realized niche of a Neotropical orchid species

Local adaptation is common in plant species, and knowing whether a population is locally adapted has fundamental and applied relevance. However, local adaptation in tropical plants remains largely less studied, and covering this gap is not simple since reciprocal transplantation - the gold standard for detecting local adaptation - is not feasible for most species. Here, we combined genetic, climatic and phenotypic data to investigate ecotypic differentiation, an important aspect of local adaptation, in coastal and inland populations of the orchid Epidendrum fulgens Brongn., a long-lived tropical plant for which reciprocal transplantation would not be feasible. We used nine microsatellite markers to estimate genetic divergence between inland and coastal populations. Moreover, occurrence data and climate data were used to test for differences in the realized niche of those populations. Finally, we assessed saturated water content, leaf specific area, height, and stomatal density in common garden and in situ to investigate the effects of ecotypic differentiation and plasticity on the phenotype. Coastal and inland groups' niches do not overlap, the former occupying a wetter and warmer area. However, this differentiation does not seem to be driven by ecotypic differentiation since there was no positive correlation between genetic structure and climate dissimilarity. Moreover, specific leaf area and leaf saturated water content, which are important phenotypic traits related to soil fertility and drought stress, were rather plastic. We conclude that ecotypic differentiation is absent, since phenotypic plasticity is an important mechanism explaining the niche broadness of this species.

The novel developed microsatellite markers revealed potential hybridization among Cymbidium species and the interspecies sub-division of C. goeringii and C. ensifolium

BACKGROUND

Orchids (Cymbidium spp.) exhibit significant variations in floral morphology, pollinator relations, and ecological habitats. Due to their exceptional economic and ornamental value, Cymbidium spp. have been commercially cultivated for centuries. SSR markers are extensively used genetic tools for biology identification and population genetics analysis.

RESULT

In this study, nine polymorphic EST-SSR loci were isolated from Cymbidium goeringii using RNA-Seq technology. All nine SSR loci showed transferability in seven other congeneric species, including 51 cultivars. The novel SSR markers detected inter-species gene flow among the Cymbidium species and intra-species sub-division of C. goeringii and C. ensifolium, as revealed by neighborhood-joining and Structure clustering analyses.

CONCLUSION

In this study, we developed nine microsatellites using RNA-Seq technology. These SSR markers aided in detecting potential gene flow among Cymbidium species and identified the intra-species sub-division of C. goeringii and C. ensifolium.

Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species

Epidendrum, one of the three largest genera of Orchidaceae, exhibits significant horticultural and ornamental value and serves as an important research model in conservation, ecology, and evolutionary biology. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete plastome of this genus (including five species) were firstly sequenced and assembled to explore their characterizations. The plastomes exhibited a typical quadripartite structure. The lengths of the plastomes ranged from 147,902 bp to 150,986 bp, with a GC content of 37.16% to 37.33%. Gene annotation revealed the presence of 78-82 protein-coding genes, 38 tRNAs, and 8 rRNAs. A total of 25-38 long repeats and 130-149 SSRs were detected. Analysis of relative synonymous codon usage (RSCU) indicated that leucine (Leu) was the most and cysteine (Cys) was the least. The consistent and robust phylogenetic relationships of Epidendrum and its closely related taxa were established using a total of 43 plastid genomes from the tribe Epidendreae. The genus Epidendrum was supported as a monophyletic group and as a sister to Cattleya. Meanwhile, four mutational hotspots (trnCGCA-petN, trnDGUC-trnYGUA, trnSGCU-trnGUCC, and rpl32-trnLUAG) were identified for further phylogenetic studies. Our analysis demonstrates the promising utility of plastomes in inferring the phylogenetic relationships of Epidendrum.

Genetic diversity and structure in two epiphytic orchids from the montane forests of southern Ecuador: The role of overcollection on Masdevallia rosea in comparison with the widespread Pleurothallis lilijae

Ecuador has a high diversity of orchids, but little is known about levels of genetic diversity for the great majority of species. Understanding how orchids might adapt to changes is crucial as deforestation and fragmentation of forest ecosystems threaten the survival of many epiphytic orchids that depend on other species, such as fungi and their host trees, for germination, growth, and establishment. Overcollection and the illegal trade are also major concerns for the survival of wild populations of orchids. Despite increasing awareness, effective interventions are often limited by a lack of data concerning the impacts that overexploitation might have. To fill this gap, we tested the effects of overcollection in the genetic diversity and structure of Masdevallia rosea, a narrow distributed epiphytic orchid historically collected in Ecuador, in comparison with the widely distributed Pleurothallis lilijae. Genotyping based on AFLPs showed reduced levels of diversity in wild populations but most especially in the overcollected, M. rosea. Overall, genetic admixture was high in P. lilijae segregating populations by altitude levels while fewer genetic groups were found in M. rosea. Genetic differentiation was low in both species. A spatial genetic structure was found in P. lilijae depending on altitude levels, while no spatial genetic structure was found in M. rosea. These results suggest different scenarios for the two species: while gene flow over long distance is possible in P. lilijae, the same seems to be unlikely in M. rosea possibly due to the low levels of individuals in the known populations. In situ and ex situ conservation strategies should be applied to protect the genetic pool in these epiphytic orchid species, and to promote the connectivity between wild populations. Adopting measures to reduce overexploitation and to understand the impacts of harvesting in wild populations are necessary to strengthen the legal trade of orchids.

Hybridization boosters diversification in a Neotropical Bulbophyllum (Orchidaceae) group

Genetic data shows that cryptic hybrids are more common than previously thought and that hybridization and introgression are widespread processes. Regardless, studies on hybridization are scarce for the highly speciose Bulbophyllum. The genus presents more than 2,200 species and many examples of recent radiations, in which hybridization is expected to be frequent. Currently, only four natural Bulbophyllum hybrids are recognized, all of them recently described based on morphological evidence. Here we test whether genomic evidence supports the hybrid status of two Neotropical Bulbophyllum species, while also evaluating the impact of this phenomenon on the genomes of the putative parental species. We also assess if there is evidence of hybridization among B. involutum and B. exaltatum, sister species that diverged recently. We leverage the power of next-generation sequence data, associated with model-based analysis for three systems putatively constituted by two parental species and one hybrid. All taxa belong to the Neotropical B. sect. Didactyle clade. We found evidence of hybridization in all studied systems. Despite the occurrence of hybridization, there are no signs of backcrossing. Because of the high propensity of hybridization across many taxa, the common occurrence of hybridization during the evolutionary history of B. sect. Didactyle means it is time to account for and examine its evolutionary role in these orchids.

Exploring island syndromes: Variable matrix permeability in Phalaenopsis pulcherrima (Orchidaceae), a specialist lithophyte of tropical Asian inselbergs

INTRODUCTION

Plants confined to island-like habitats are hypothesised to possess a suite of functional traits that promote on-spot persistence and recruitment, but this may come at the cost of broad-based colonising potential. Ecological functions that define this island syndrome are expected to generate a characteristic genetic signature. Here we examine genetic structuring in the orchid Phalaenopsis pulcherrima, a specialist lithophyte of tropical Asian inselbergs, both at the scale of individual outcrops and across much of its range in Indochina and on Hainan Island, to infer patterns of gene flow in the context of an exploration of island syndrome traits.

METHODS

We sampled 323 individuals occurring in 20 populations on 15 widely scattered inselbergs, and quantified genetic diversity, isolation-by-distance and genetic structuring using 14 microsatellite markers. To incorporate a temporal dimension, we inferred historical demography and estimated direction of gene flow using Bayesian approaches.

RESULTS

We uncovered high genotypic diversity, high heterozygosity and low rates of inbreeding, as well as strong evidence for the occurrence of two genetic clusters, one comprising the populations of Hainan Island and the other those of mainland Indochina. Connectivity was greater within, rather than between the two clusters, with the former unequivocally supported as ancestral.

DISCUSSION

Despite a strong capacity for on-spot persistence conferred by clonality, incomplete self-sterility and an ability to utilize multiple magnet species for pollination, our data reveal that P. pulcherrima also possesses traits that promote landscape-scale gene flow, including deceptive pollination and wind-borne seed dispersal, generating an ecological profile that neither fully conforms to, nor fully contradicts, a putative island syndrome. A terrestrial matrix is shown to be significantly more permeable than open water, with the direction of historic gene flow indicating that island populations can serve as refugia for postglacial colonisation of continental landmasses by effective dispersers.

Hybridization and introgression are prevalent in Southern European Erysimum (Brassicaceae) species

BACKGROUND AND AIMS

Hybridization is a common and important force in plant evolution. One of its outcomes is introgression - the transfer of small genomic regions from one taxon to another by hybridization and repeated backcrossing. This process is believed to be common in glacial refugia, where range expansions and contractions can lead to cycles of sympatry and isolation, creating conditions for extensive hybridization and introgression. Polyploidization is another genome-wide process with a major influence on plant evolution. Both hybridization and polyploidization can have complex effects on plant evolution. However, these effects are often difficult to understand in recently evolved species complexes.

METHODS

We combined flow cytometry, analyses of transcriptomic sequences and pollen tube growth assays to investigate the consequences of polyploidization, hybridization and introgression on the recent evolution of several Erysimum (Brassicaceae) species from the South of the Iberian Peninsula, a well-known glacial refugium. This species complex differentiated in the last 2 million years, and its evolution has been hypothesized to be determined mainly by polyploidization, interspecific hybridization and introgression.

KEY RESULTS

Our results support a scenario of widespread hybridization involving both extant and 'ghost' taxa. Several taxa studied here, most notably those with purple corollas, are polyploids, probably of allopolyploid origin. Moreover, hybridization in this group might be an ongoing phenomenon, as pre-zygotic barriers appeared weak in many cases.

CONCLUSIONS

The evolution of Erysimum spp. has been determined by hybridization to a large extent. Species with purple (polyploids) and yellow flowers (mostly diploid) exhibit a strong signature of introgression in their genomes, indicating that hybridization occurred regardless of colour and across ploidy levels. Although the adaptive value of such genomic exchanges remains unclear, our results demonstrate the significance of hybridization for plant diversification, which should be taken into account when studying plant evolution.

Neutral and outlier single nucleotide polymorphisms disentangle the evolutionary history of a coastal Solanaceae species

Speciation begins with the isolation of some individuals or subpopulations due to drivers promoting a diverging genetic distribution. Such isolation may occur, followed by different processes and pressures. Isolation-by-distance (IBD), isolation-by-adaptation (IBA), and isolation-by-colonization (IBC) have been recognized as the main divergence patterns. Still, it is not easy to distinguish which one is the main pattern as each one may act at different points in time or even simultaneously. Using an extensive genome coverage from a Petunia species complex with coastal and inland distribution and multiple analytical approaches on population genomics and phylogeography, we showed a complex interplay between neutral and selective forces acting on the divergence process. We found 18,887 SNPs potentially neutral and 924 potentially under selection (outlier) loci. All analyses pointed that each subspecies displays its own genetic component and evolutionary history. We suggested plausible ecologic drivers for such divergence in a southernmost South Atlantic coastal plain in Brazil and Uruguay and identified a connection between adaptation and environment heterogeneity.

Serendipita restingae sp. nov. (Sebacinales): an orchid mycorrhizal agaricomycete with wide host range

The Serendipitaceae family was erected in 2016 to accommodate the Sebacinales 'group B' clade, which contains peculiar species of cultivable root-associated fungi involved in symbiotic associations with a wide range of plant species. Here we report the isolation of a new Serendipita species which was obtained from protocorms of the terrestrial orchid Epidendrum fulgens cultivated in a greenhouse. This species is described based on phylogenetic analysis and on its microscopic and ultrastructural features in pure culture and in association with the host's protocorms. Its genome size was estimated using flow cytometry, and its capacity to promote the germination of E. fulgens seeds and to associate with roots of Arabidopsis thaliana was also investigated. Serendipita restingae sp. nov. is closely related to Serendipita sp. MAFF305841, isolated from Microtis rara (Orchidaceae), from which it differs by 14.2% in the ITS region and by 6.5% in the LSU region. It produces microsclerotia formed of non-monilioid hyphae, a feature that was not reported for the Sebacinales hitherto. Serendipita restingae promoted the germination of E. fulgens seeds, forming typical mycorrhizal pelotons within protocorm cells. It was also able to colonize the roots of Arabidopsis thaliana under in vitro conditions. Arabidopsis plants grown in association with S. restingae increased their biomass more than fourfold. Serendipita restingae is the first Serendipitaceae species described for the Americas.

Differential gene expression reveals mechanisms related to habitat divergence between hybridizing orchids from the Neotropical coastal plains

BACKGROUND

Closely related hybridizing species are ideal systems for identifying genomic regions underlying adaptive divergence. Although gene expression plays a central role in determining ecologically-based phenotypic differences, few studies have inferred the role of gene expression for adaptive divergence in Neotropical systems. In this study, we conduct genome-wide expression analysis alongside soil elemental analysis in sympatric and allopatric populations of Epidendrum fulgens and E. puniceoluteum (Orchidaceae), which occur in contrasting adjacent habitats in the Neotropical coastal plains.

RESULTS

These species were highly differentiated by their gene expression profiles, as determined by 18-21% of transcripts. Gene ontology (GO) terms associated with reproductive processes were enriched according to comparisons between species in both allopatric and sympatric populations. Species showed differential expression in genes linked to salt and waterlogging tolerance according to comparisons between species in sympatry, and biological processes related to environmental stimulus appeared as representative among those transcripts associated with edaphic characteristics in each sympatric zone. Hybrids, in their turn, were well differentiated from E. fulgens, but exhibited a similar gene expression profile to flooding-tolerant E. puniceolutem. When compared with parental species, hybrids showed no transcripts with additive pattern of expression and increased expression for almost all transgressive transcripts.

CONCLUSIONS

This study sheds light on general mechanisms promoting ecological differentiation and assortative mating, and suggests candidate genes, such as those encoding catalase and calcium-dependent protein kinase, underling adaptation to harsh edaphic conditions in the Neotropical coastal plains. Moreover, it demonstrates that differential gene expression plays a central role in determining ecologically-based phenotypic differences among co-occurring species and their hybrids.

Biased assessment of ongoing admixture using STRUCTURE in the absence of reference samples

Detection of hybridization and introgression is important in ecological research as in conservation and evolutionary biology. STRUCTURE is one of the most popular software to study introgression and allows estimating what proportion of the genome of each individual belongs to each ancestral population, even in cases where no reference sample from the ancestral nonadmixed populations is previously identified. In spite of its frequent use, some studies have indicated that ancestry estimates may not always be reliable. We simulated population data under different conditions with regard to the genetic differentiation between ancestral populations, number of loci considered, number of alleles per marker and hybridization rate, and analysed data with STRUCTURE. When reference samples were not included, the comparison of the known degree of admixture for each simulated individual and the value estimated with STRUCTURE revealed a strong underestimation of the level of introgression, classifying many admixed individuals as nonadmixed. This derives from an inaccurate estimation of the ancestral allele frequencies. When samples from the nonadmixed ancestral population were included as reference in the analyses, the bias in the estimations was reduced. The most accurate estimates were obtained when potentially admixed samples were few in relation to reference samples. Thus, whenever possible, a very large proportion of nonadmixed reference samples should be included in admixture assessments and different approaches should be combined. The misestimate of the amount of introgression can impair our understanding of the evolutionary history of species and misguide conservation efforts.