Molecular and morphological phylogenetics of the digitate-tubered clade within subtribe Orchidinae s.s. (Orchidaceae: Orchideae)

The digitate-tubered clade (Dactylorhiza s.l. plus Gymnadenia s.l.) within subtribe Orchidinae is an important element of the North-temperate orchid flora and has become a model system for studying the genetic and epigenetic consequences of organism-wide ploidy change. Here, we integrate morphological phylogenetics with Sanger sequencing of nrITS and the plastid region trnL-F in order to explore phylogenetic relationships and phenotypic character evolution within the clade. The resulting morphological phylogenies are strongly incongruent with the molecular phylogenies, instead reconstructing through parsimony the genus-level boundaries recognised by traditional 20th Century taxonomy. They raise fresh doubts concerning whether Pseudorchis is sister to Platanthera or to Dactylorhiza plus Gymnadenia. Constraining the morphological matrix to the topology derived from ITS sequences increased tree length by 20%, adding considerably to the already exceptional level of phenotypic homoplasy. Both molecular and morphological trees agree that D. viridis and D. iberica are the earliest- diverging species within Dactylorhiza (emphasising the redundancy of the former genus Coeloglossum). Morphology and ITS both suggest that the former genus Nigritella is nested within (and thus part of) Gymnadenia, the Pyrenean endemic 'N.' gabasiana apparently forming a molecular bridge between the two radically contrasting core phenotypes. Comparatively short subtending molecular branches plus widespread (though sporadic) hybridisation indicate that Dactylorhiza and Gymnadenia approximate the minimum level of molecular divergence acceptable in sister genera. They share similar tuber morphologies and base chromosome numbers, and both genera are unusually prone to polyploid speciation. Another prominent feature of multiple speciation events within Gymnadenia is floral paedomorphosis. The 'traditional' morphological and candidate-gene approaches to phylogeny reconstruction are critically appraised.Peer reviewedFinal Published versio

The Good, The Bad, The Ugly: Using Naturally Occurring Terata to Distinguish the Possible from the Impossible in Orchid Floral Evolution

We interpret extensive field observations of terata in the context of recent insights into monocot phylogeny and evolutionary-developmental genetics to explore the evolution of the orchid flower. Our arguably typological classification of floral terata focuses on natural occurrences of three contrasting modes of peloria (restoration of actinomorphy in a formerly zygomorphic perianth) and three contrasting modes of pseudopeloria (lessening of the degree of zygomorphy shown by the evolutionarily preceding perianth). Dynamic evolutionary transitions in floral morphology are assigned to recently revised concepts of heterotopy (including homeosis: evolutionary transitions in position of expression) and heterochrony (evolutionary transitions in timing of expression), seeking patterns that delimit developmental constraints and allow inferences regarding underlying genetic controls. Lateral heterotopy, occurring within the whorl of three petals (including the labellum) or within the adjacent whorl of three sepals, is more frequent than acropetal heterotopy, and full basipetal heterotopy does not occur. Pseudopeloria is more likely than peloria to generate a radically altered yet functional perianth but is also more likely to cause acropetal modification of the fused filaments and style that constitute the characteristic gynostemium of orchids. We infer that at least one gene or gene complex controls stylestamen fusion, which requires the preadaptation of strongly developed epigyny, and another determines both stamen suppression and labellum formation adaxially. Our earlier hypothesis implicating genes of the TCP family has recently been challenged by empirical evidence of complex interactions between several MADS-box genes. Many transitions are highly iterative, and some are reversible (atavistic). Once heritability has been demonstrated, the most effective criteria for determining the most appropriate taxonomic status of a novel morph are the profundity of the phenotypic shift that it represents, the number and uniformity of the resulting populations, and whether the novel morph subsequently diversified to generate further morphs that retain the innovative features. Although morphological transitions attributable to heterochrony may be a more common driver of speciation than those attributable to heterotopy, we demonstrate that arguably all of the modes of instantaneous floral transition described in this paper have the ability to generate prospecies

Enhanced protein domain discovery using taxonomy

BACKGROUND: It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been incorporated into statistical methods for finding domains in sequences of amino acids. RESULTS: We show that by incorporating our understanding of the taxonomic distribution of specific protein domains, we can enhance domain recognition in protein sequences. We identify 4447 new instances of Pfam domains in the SP-TREMBL database using this technique, equivalent to the coverage increase given by the last 8.3% of Pfam families and to a 0.7% increase in the number of domain predictions. We use PSI-BLAST to cross-validate our new predictions. We also benchmark our approach using a SCOP test set of proteins of known structure, and demonstrate improvements relative to standard Hidden Markov model techniques. CONCLUSIONS: Explicitly including knowledge about the taxonomic distribution of protein domains can enhance protein domain recognition. Our method can also incorporate other context-specific domain distributions – such as domain co-occurrence and protein localisation

Pile Design Procedure for Stabilizing Channel Slopes

A case history is presented for slope stabilization of channels using piles. The Kansas City District, Corps of Engineers has used various pile designs and types of piles for projects along the Blue River Channel in Kansas City Missouri to stabilize sections of unstable channel slopes in previous slide areas, since June of 1986. Low existing soil shear strengths and limited rights-of-way precluded use of more conventional stabilizing methods. Although a pile analysis method had been used for initial projects, with several piles instrumented with slope indicator devices, an improved analysis method was needed. In July of 1994, through a design analysis, the Kansas City District, Corps of Engineers developed a pile design procedure for the stabilization of a failed slope, along the Blue River Channel, known as the Gregory Blvd Project. The method utilizes both Limit Equilibrium slope stability methods and P-Y curve methods for pile analysis, and takes into account earth pressure theory. The method includes a trial and error procedure for determining the driving forces from a sliding mass of soil. The driving forces were then calculated at a concentrated point on the slide plane, coincident with the location of the piles, or where the piles intersect the slide surface, using limit equilibrium procedures with the most critical slide surface and at the desired factor of safety for the stabilized slope. For projects discussed, shear strengths, were determined from a back analysis of the existing slopes at failure using F=1.0. Laboratory test results generally did not yield usable values. The slope stability computer programs UTEXAS2 and UTEXAS3, using Spencer\u27s Procedure was used in all analyses. The driving forces, thus determined, are then input into the pile analysis (LPILE) program, using both a triangular and a uniform load distribution along with the appropriate soil strength parameters for generating the P-Y curves within the program. Depth of pile embedment below the slip surface, size of the piles, position of the piles in the slope and the required spacing are then determined. Actual instrumented field data located on piles are presented as well as comparisons with predicted results, using the pile procedure analysis technique. The case studies demonstrate the importance of proper formulation of the analysis and of modeling the soil using the correct P-Y soil parameters for the pile

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

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Colorado River Basin Precipitation Anomalies: Relationships with Large-Scale Atmospheric Features and Connections with Water Management

Colorado River Basin (CRB) water management has become more challenging in recent years due to small supply changes and large demand changes. CRB supply is largely determined by the condition of Upper Colorado River Basin (UCRB) snowpack at the end of winter. This paper examines historical differences in precipitation between the Upper and Lower Colorado River Basin (LCRB) and the relationship between precipitation and large-scale atmospheric features, including circulation and vapor transport patterns during December-January-February from 1920-2009. Precipitation commonly occurs over most of the UCRB and LCRB during the same winter season. Precipitation over the northern third of the UCRB is more closely related to northwest US precipitation instead of the rest of the CRB, suggesting a northerly moisture pathway dependence. The remainder of the CRB accumulates precipitation when moisture is transported from the southwest of the region. Wet UCRB seasons depend on a northwest US-centered trough pattern, enhanced vapor transport from the southwest, and enhanced relative moisture content; opposite conditions result in dry UCRB seasons. The results of this study can be incorporated by water management as part of the Bureau of Reclamation’s ongoing use of an adaptive management approach. Increased understanding of the physical drivers of CRB precipitation can better equip water management decisions to make skillful seasonal water supply forecasts

Global Electric Circuit Implications of Combined Aircraft Storm Electric Current Measurements and Satellite-Based Diurnal Lightning Statistics

Using rotating vane electric field mills and Gerdien capacitors, we measured the electric field profile and conductivity during 850 overflights of thunderstorms and electrified shower clouds (ESCs) spanning regions including the Southeastern United States, the Western Atlantic Ocean, the Gulf of Mexico, Central America and adjacent oceans, Central Brazil, and the South Pacific. The overflights include storms over land and ocean, and with positive and negative fields above the storms. Over three-quarters (78%) of the land storms had detectable lightning, while less than half (43%) of the oceanic storms had lightning. Integrating our electric field and conductivity data, we determined total conduction currents and flash rates for each overpass. With knowledge of the storm location (land or ocean) and type (with or without lightning), we determine the mean currents by location and type. The mean current for ocean thunderstorms is 1.7 A while the mean current for land thunderstorms is 1.0 A. The mean current for ocean ESCs 0.41 A and the mean current for land ESCs is 0.13 A. We did not find any significant regional or latitudinal based patterns in our total conduction currents. By combining the aircraft derived storm currents and flash rates with diurnal flash rate statistics derived from the Lightning Imaging Sensor (LIS) and Optical Transient Detector (OTD) low Earth orbiting satellites, we reproduce the diurnal variation in the global electric circuit (i.e., the Carnegie curve) to within 4% for all but two short periods of time. The agreement with the Carnegie curve was obtained without any tuning or adjustment of the satellite or aircraft data. Given our data and assumptions, mean contributions to the global electric circuit are 1.1 kA (land) and 0.7 kA (ocean) from thunderstorms, and 0.22 kA (ocean) and 0.04 (land) from ESCs, resulting in a mean total conduction current estimate for the global electric circuit of 2.0 kA. Mean storm counts are 1100 for land thunderstorms, 530 for ocean ESCs, 390 for ocean thunderstorms, and 330 for land ESCs

Systematic reappraisal of marsh-orchids native to Scotland

© The Author(s), 2023.This article is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.Summary: The intensively studied Eurasian orchid genus Dactylorhiza has become a model system for exploring allopolyploid evolution, yet determining the optimal circumscriptions of, and most appropriate ranks for, its constituent taxa remain highly controversial topics. Here, novel allozyme data and detailed morphometric data for 16 Scottish marsh-orchid populations are interpreted in the context of recent DNA sequencing studies. Despite being derived from the same pair of parental species, the two allopolyploid species that currently occur in Scotland can reliably be distinguished using allozymes, haplotypes, ribotypes or sequences of nuclear genes. A modest range of diverse morphological characters are shown to distinguish the two molecularly-circumscribed species, but they have in the past been obscured by equivalent levels of infraspecific variation in characters rooted in anthocyanin pigments; these characters are better employed for distinguishing infraspecific taxa. Dactylorhiza francis-drucei (formerly D. traunsteinerioides) is confirmed as being distinct from the continental D. traunsteineri/lapponica, probably originating through allopatric isolation once the continental lineage reached Britain. All Scottish populations are attributed to the comparatively small-flowered, anthocyanin-rich subsp. francis-drucei, which includes as a variety the former D. 'ebudensis'; the less anthocyanin-rich subsp. traunsteinerioides is confined to Ireland, North Wales and northern England. In contrast with D. francis-drucei, only a minority of Scottish populations of D. purpurella are attributed to the anthocyanin-rich race, var. cambrensis. This species most likely originated through an allopolyploidy event that occurred comparatively recently within the British Isles, as it contains allozyme alleles distinctive of British rather than continental D. incarnata (its diploid pollen-parent). In contrast, the rare Scottish population of D. incarnata subsp. cruenta shares with its Irish counterparts a continental genotype, and is most likely a recent arrival in Scotland through long-distance dispersal. Among all European allotetraploid dactylorchids, D. purpurella is the species that most closely resembles D. incarnata, both molecularly and morphologically.Peer reviewe

Electric Field Measurements During the Genesis and Rapid Intensification Processes (GRIP) Field Program

During the Genesis and Rapid Intensification Processes (GRIP) field program, a system of 6 electric field mills was flown on one of NASA's Global Hawk aircraft. We placed several mills on the aircraft to enable us to measure the vector electric field. We created a distributed, ethernet-connected system so that each sensor has its own embedded Linux system, complete with web server. This makes our current generation system fully "sensor web enabled." The Global Hawk has several unique qualities, but relevant to quality storm electric field measurements are high altitude (20 km) and long duration (20-30 hours) flights. There are several aircraft participating in the GRIP program, and coordinated measurements are happening. Lightning and electric field measurements will be used to study the relationships between lightning and other storm characteristics. It has been long understood that lightning can be used as a marker for strong convective activity. Past research and field programs suggest that lightning flash rate may serve as an indicator and precursor for rapid intensification change in tropical cyclones and hurricanes. We have the opportunity to sample hurricanes for many hours at a time and observe intensification (or de-intensification) periods. The electrical properties of hurricanes during such periods are not well known. America