Orchid phylogenetics and evolution: history, current status and prospects.

Background: Orchidaceae are one of the two largest families of angiosperms; they exhibit a host of changes -- morphological, ecological and molecular -- that make them excellent candidates for evolutionary study. Such studies are most effectively performed in a phylogenetic context, which provides direction to character change. Understanding of orchid relationships began in the pre-evolutionary classification systems of the 1800's that were based solely on morphology, and now is largely based on genomic analysis.

Organellar phylogenomics at the epidendroid orchid base, with a focus on the mycoheterotrophic Wullschlaegelia.

Background And Aims: Heterotrophic plants have long been a challenge for systematists, exemplified by the base of the orchid subfamily Epidendroideae, which contains numerous mycoheterotrophic species.

Methods: Here we address the utility of organellar genomes in resolving relationships at the epidendroid base, specifically employing models of heterotachy, or lineage-specific rate variation over time. We further conduct comparative analyses of plastid genome evolution in heterotrophs and structural variation in matK.

Lineage and role in integrative taxonomy of a heterotrophic orchid complex.

Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries.

Relationships between Tertiary relict and circumboreal woodland floras: a case study in Chimaphila (Ericaceae).

Background And Aims: Tertiary relict and Arctic/circumboreal distributions are two major patterns of Northern Hemisphere intercontinental disjunctions with very different histories. Each has been well researched, but members of one biome have generally not been incorporated in the biogeographical analyses of the other, and links or transitions between these two biomes have rarely been addressed.

Methods: Phylogenies of Chimaphila were generated based on cpDNA and nuclear ITS, using Bayesian and maximum likelihood methods.

Lacunicambarus chimera: a new species of burrowing crayfish (Decapoda: Cambaridae) from Illinois, Indiana, Kentucky, and Tennessee.

Lacunicambarus diogenes (Girard 1852) was, until recently, considered to be one of the most widely distributed North American crayfish species, occurring in 31 U.S. States and one Canadian province east of the North American Rocky Mountains.

Total duplication of the small single copy region in the angiosperm plastome: Rearrangement and inverted repeat instability in Asarum.

Premise Of The Study: As more plastomes are assembled, it is evident that rearrangements, losses, intergenic spacer expansion and contraction, and syntenic breaks within otherwise functioning plastids are more common than was thought previously, and such changes have developed independently in disparate lineages. However, to date, the magnoliids remain characterized by their highly conserved plastid genomes (plastomes).

Methods: Illumina HiSeq and MiSeq platforms were used to sequence the plastomes of Saruma henryi and those of representative species from each of the six taxonomic sections of Asarum.

On the brink: the highly reduced plastomes of nonphotosynthetic Ericaceae.

Ericaceae (the heather family) is a large and diverse group of plants that forms elaborate symbiotic relationships with mycorrhizal fungi, and includes several nonphotosynthetic lineages. Using an extensive sample of fully mycoheterotrophic (MH) species, we explored inter- and intraspecific variation as well as selective constraints acting on the plastomes of these unusual plants. The plastomes of seven MH genera were analysed in a phylogenetic context with two geographically disparate individuals sequenced for Allotropa, Monotropa, and Pityopus.

Biodiversity and the Species Concept-Lineages are not Enough.

The nature and definition of species continue to be matters of debate. Current views of species often focus on their nature as lineages-maximal reproductive communities through time. Whereas many authors point to the Evolutionary Species Concept as optimal, in its original form it stressed the ecological role of species as well as their history as lineages, but most recent authors have ignored the role aspect of the concept, making it difficult to apply unambiguously in a time-extended way.

Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms.

While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data.

A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae).

Premise Of The Study: Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera.

Methods: Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data.

Phylogenetic relationships in Asarum: Effect of data partitioning and a revised classification.

Premise Of The Study: Generic boundaries and infrageneric relationships among the charismatic temperate magnoliid Asarum sensu lato (Aristolochiaceae) have long been uncertain. Previous molecular phylogenetic analyses used either plastid or nuclear loci alone and varied greatly in their taxonomic implications for the genus. We analyzed additional molecular markers from the nuclear and plastid genomes, reevaluated the possibility of a derived loss of autonomous self-pollination, and investigated the topological effects of matrix-partitioning-scheme choice.

Putative floral brood-site mimicry, loss of autonomous selfing, and reduced vegetative growth are significantly correlated with increased diversification in Asarum (Aristolochiaceae).

The drivers of angiosperm diversity have long been sought and the flower-arthropod association has often been invoked as the most powerful driver of the angiosperm radiation. We now know that features that influence arthropod interactions cannot only affect the diversification of lineages, but also expedite or constrain their rate of extinction, which can equally influence the observed asymmetric richness of extant angiosperm lineages. The genus Asarum (Aristolochiaceae; ∼100 species) is widely distributed in north temperate forests, with substantial vegetative and floral divergence between its three major clades, Euasarum, Geotaenium, and Heterotropa.

Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification.

Background And Aims: The largest subfamily of orchids, Epidendroideae, represents one of the most significant diversifications among flowering plants in terms of pollination strategy, vegetative adaptation and number of species. Although many groups in the subfamily have been resolved, significant relationships in the tree remain unclear, limiting conclusions about diversification and creating uncertainty in the classification. This study brings together DNA sequences from nuclear, plastid and mitochrondrial genomes in order to clarify relationships, to test associations of key characters with diversification and to improve the classification.

Phylogenetic relationships and character evolution in Heuchera (Saxifragaceae) on the basis of multiple nuclear loci.

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Premise Of The Study: The use of multiple genetic regions from the nuclear genome, including low-copy markers, has long been recognized as essential to robust phylogenetic construction, addressing gene tree incongruence, and allowing increased resolution to test current taxonomy and resolve basic hypotheses about character evolution, biogeography, and other organismal traits of interest to biologists. Heuchera, the largest genus of Saxifragaceae endemic to North America, has presented an unusually difficult case for systematists with limited sampling in previous molecular studies. We used morphological and multilocus molecular phylogenetic data to test the monophyly of Heuchera, better resolve hypotheses of relationships, and test hypotheses of character evolution, biogeography, and diversification rates.

Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms.

Parasitic organisms exemplify morphological and genomic reduction. Some heterotrophic, parasitic plants harbor drastically reduced and degraded plastid genomes resulting from relaxed selective pressure on photosynthetic function. However, few studies have addressed the initial stages of plastome degradation in groups containing both photosynthetic and nonphotosynthetic species.

Rangewide analysis of fungal associations in the fully mycoheterotrophic Corallorhiza striata complex (Orchidaceae) reveals extreme specificity on ectomycorrhizal Tomentella (Thelephoraceae) across North America.

Fully mycoheterotrophic plants offer a fascinating system for studying phylogenetic associations and dynamics of symbiotic specificity between hosts and parasites. These plants frequently parasitize mutualistic mycorrhizal symbioses between fungi and trees. Corallorhiza striata is a fully mycoheterotrophic, North American orchid distributed from Mexico to Canada, but the full extent of its fungal associations and specificity is unknown.

An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid.

In the spirit of recent calls for species delimitation studies to become more pluralistic, incorporating multiple sources of evidence, we adopted an integrative, phylogeographic approach to delimiting species and evolutionarily significant units (ESUs) in the Corallorhiza striata species complex. This rare, North American, mycoheterotrophic orchid has been a taxonomic challenge regarding species boundaries, displaying complex patterns of variation and reduced vegetative morphology. We employed plastid DNA, nuclear DNA and morphometrics, treating the C.

Molecular phylogenetics of Hypoxidaceae--evidence from plastid DNA data and inferences on morphology and biogeography.

Phylogenetic relationships of the monocot family Hypoxidaceae (Asparagales), which occurs mainly in the Southern Hemisphere, were reconstructed using four plastid DNA regions (rbcL, trnL intron, trnL-F intergenic spacer, and trnS-G intergenic spacer) for 56 ingroup taxa including all currently accepted genera and seven species of the closely related families Asteliaceae, Blandfordiaceae, and Lanariaceae. Data were analyzed by applying parsimony, maximum likelihood and Bayesian methods. The intergenic spacer trnS-G--only rarely used in monocot research--contributed a substantial number of potentially parsimony informative characters.

Branch support via resampling: an empirical study.

The success of resampling approaches to branch support depends on the effectiveness of the underlying tree searches. Two primary factors are identified as key: the depth of tree search and the number of trees saved per resampling replicate. Two datasets were explored for a range of search parameters using jackknifing.

Relationships and evolution of matK in a group of leafless orchids (Corallorhiza and Corallorhizinae; Orchidaceae: Epidendroideae).

Corallorhizinae are a small group of Old and New World temperate orchids of which a core monophyletic group comprises Govenia, Cremastra, Aplectrum, Oreorchis and the leafless Corallorhiza, and which according to phylogenetic analysis of nuclear ITS and plastid matK sequences, are related in this way: (Govenia (Cremastra (Aplectrum (Oreorchis (Corallorhiza))))). This hypothesis is consistent with the progressive deletion of the trnK intron and matK ORF. Frameshift-resulting indels yield a predicted loss of translation for the critical "domain X" region of matK and are evidence that matK is a probable pseudogene in Aplectrum, Oreorchis, and Corallorhiza.

Molecular evolution of rbcL in the mycoheterotrophic coralroot orchids (Corallorhiza Gagnebin, Orchidaceae).

The RuBisCO large subunit gene (rbcL) has been the focus of numerous plant phylogenetic studies and studies on molecular evolution in parasitic plants. However, there has been a lack of investigation of photosynthesis gene molecular evolution in fully mycoheterotrophic plants. These plants invade pre-existing mutualistic associations between ectomycorrhizal trees and fungi, from which they obtain fixed carbon and nutrients.

Report on the Ohio State University workshops in phylogenetic methods.

A three-part series of workshops in phylogenetic methods was held at the Ohio State University in September and December 2005. The first two were sponsored by the OSU Mathematical Biosciences Institute (MBI), and focused on phylogeography and phylogenetic data, and phylogenetic analysis of large data sets respectively. These workshops highlighted theoretical and practical aspects of phylogeographic inferences using model-based approaches (e.

Patterns of anomalous floral development in the Asian Passiflora (subgenus Decaloba: supersection Disemma).

Approximately 22 species of Passiflora are native to the Old World. All of these species are placed in subgenus Decaloba, supersection Disemma. Within Disemma, three species vary in stamen and carpel number (≤ eight stamens and five carpels).