Left. No, Right! Development of the Frame of Reference Transformation Tool (FORT)

A computational model was developed to predict the spatial-cognitive difficulties imposed when the operator must transform information along up to 6 degrees of freedom between a display (viewed at different orientations), and either a cognitive understanding or a compensatory control. The model applies to pilots, robotics operators, navigators or surgeons using endoscopic procedures. Penalties (in workload, errors or time) in the frame of reference transformation (FORT) are based on psychological findings in spatial cognition, such as mental rotation, depth compression, population stereotypes and verbally mediated strategies. We present the graphical user interface for exercising the model; then show how we have applied it to an astronaut space-shuttle, Hubble rendezvous sequence. Finally we validate the model against two existing data sets, one for cognition and one for control. The model could be used as the basis for both a design analysis tool and a real-time operator aiding system.

Rotation rate and duration effects on the somatogyral illusion

INTRODUCTION

Aviation spatial disorientation mishaps remain a concern, especially due to their fatality rate. Some of the most insidious disorientations are due to vestibular stimuli in the absence of visual cues. A category of such disorientations are known as somatogyral illusions.

METHODS

To determine the effects of spin rate and duration on the perception of the somatogyral illusion, we examined the subjective response of pilots and non-pilots to rotation around the yaw axis in a flight simulator in a manner that would mimic two vestibular illusions found in flight: the washout of the semi-circular canals following sustained turns, and the illusory counter-rotation following return to straight and level flight. There were 29 subjects (14 pilots) who were seated blindfolded in a flight simulator which accelerated to constant plateau rotation rates of 20, 70, and 120 degrees x s(-1) and then decelerated to stationary; plateaus were 10, 20, or 40 s. Subjects reported 1) the time when the perception of rotation ceased (i.e., the subjective time until washout was reached); 2) the relative magnitude of the counter-rotation experienced; and 3) the time until the perception of counter-rotation ceased. Subjects also manipulated a slider to provide a continuous subjective measure of their experience of rotation.

RESULTS

The two time measures increased with increases in both the duration and magnitude of the spin. The increase in perceived washout time with spin rate was non-linear (geometric). There was an interaction between spin duration and spin rate on the experience of illusory counter-rotation magnitude such that at low rates, spin duration had no effect, but its effect increased at faster rates. The time constant of adaptation of the semicircular canals was estimated to be 8.3 s.

DISCUSSION

The effects were validated against a model of semicircular canal and cupola adaptation, which predicted the data with high accuracy. Pilots and non-pilots did not differ in their illusory experience.

Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium)

Nuclear-encoded genes exist in families of various sizes. To further our understanding of the evolutionary dynamics of nuclear gene families we present a characterization of the structure and evolution of the alcohol dehydrogenase (Adh) gene family in diploid and tetraploid members of the cotton genus (Gossypium, Malvaceae). A PCR-based approach was employed to isolate and sequence multiple Adh gene family members, and Southern hybridization analyses were used to document variation in gene copy number. Adh gene copy number varies among Gossypium species, with diploids containing at least seven Adh loci in two primary gene lineages. Allotetraploid Gossypium species are inferred to contain at least 14 loci. Intron lengths vary markedly between loci, and one locus has lost two introns usually found in other plant Adh genes. Multiple examples of apparent gene duplication events were observed and at least one case of pseudogenization and one case of gene elimination were also found. Thus, Adh gene family structure is dynamic within this single plant genus. Evolutionary rate estimates differ between loci and in some cases between organismal lineages at the same locus. We suggest that dynamic fluctuation in copy number will prove common for nuclear genes, and we discuss the implications of this perspective for inferences of orthology and functional evolution.

Phylogeny, duplication, and intraspecific variation of Adh sequences in New World diploid cottons (Gossypium l., malvaceae)

The 13 "D-genome"cotton species are a monophyletic assemblage of morphologically diverse diploids that inhabit arid to semiarid regions in Mexico, with 1 disjunct species each in Peru and the Galapagos Islands and 1 species whose range extends northward into Arizona. While these species lack commercially significant fiber (i. e., cotton), they are important in that they represent one of the parental genomes of the cultivated tetraploid cottons. To assess phylogenetic relationships among these species, we sequenced and analyzed a region of a nuclear-encoded alcohol dehydrogenase gene (AdhA). Phylogenetic analysis resulted in a topology that is generally consistent with current taxonomic alignment of the species, although the phylogeny based on AdhA sequences conflicts with those inferred from cpDNA and ITS data sets, most notably in the position of the anomalous species Gossypium gossypioides. In one lineage, we detected both gene duplication and sequence polymorphisms that transcend species boundaries; sequences in this lineage formed a monophyletic clade, yet no taxon within the clade contained a monophyletic collection of sequences. Potential explanations for this latter phenomenon, including gene duplication, gene flow, and lineage sorting, are discussed.

Duplicated genes evolve independently after polyploid formation in cotton

Of the many processes that generate gene duplications, polyploidy is unique in that entire genomes are duplicated. This process has been important in the evolution of many eukaryotic groups, and it occurs with high frequency in plants. Recent evidence suggests that polyploidization may be accompanied by rapid genomic changes, but the evolutionary fate of discrete loci recently doubled by polyploidy (homoeologues) has not been studied. Here we use locus-specific isolation techniques with comparative mapping to characterize the evolution of homoeologous loci in allopolyploid cotton (Gossypium hirsutum) and in species representing its diploid progenitors. We isolated and sequenced 16 loci from both genomes of the allopolyploid, from both progenitor diploid genomes and appropriate outgroups. Phylogenetic analysis of the resulting 73.5 kb of sequence data demonstrated that for all 16 loci (14.7 kb/genome), the topology expected from organismal history was recovered. In contrast to observations involving repetitive DNAs in cotton, there was no evidence of interaction among duplicated genes in the allopolyploid. Polyploidy was not accompanied by an obvious increase in mutations indicative of pseudogene formation. Additionally, differences in rates of divergence among homoeologues in polyploids and orthologues in diploids were indistinguishable across loci, with significant rate deviation restricted to two putative pseudogenes. Our results indicate that most duplicated genes in allopolyploid cotton evolve independently of each other and at the same rate as those of their diploid progenitors. These indications of genic stasis accompanying polyploidization provide a sharp contrast to recent examples of rapid genomic evolution in allopolyploids.

Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.)

Levels of genetic diversity within and among populations and species are shaped by both external (population-level) and internal (genomic and genic) evolutionary forces. To address the effect of internal pressures, we estimated nucleotide diversity for a pair of homoeologous Adh loci in an allotetraploid species, Gossypium hirsutum. These data represent the first such estimates for a pair of homoeologous nuclear loci in plants. Estimates of nucleotide diversity for AdhA in Gossypium are lower than those for any plant nuclear gene yet described. This low diversity appears to reflect primarily a history of repeated, severe genetic bottlenecks associated with both speciation and recent domestication, supplemented by an unusually slow nucleotide substitution rate and an autogamous breeding system. While not statistically supportable, the sum of the observations also suggest differential evolutionary dynamics at each of the homoeologous loci.

The mitochondrial genome of allotetraploid cotton (Gossypium L.)

Knowledge of patterns of organellar inheritance are crucial for analyses of organellar genetics and population or phylogenetic analyses based on organellar genes. While it has previously been shown that chloroplast DNA is maternally inherited in cotton (Gossypium L.), no, studies have assessed the mitochondrial genome complement of the allotetraploid species of cotton or addressed inheritance of mitochondrial DNA. In this article we report Southern hybridization analyses that indicate that the AD-genome allotetraploid species have an A-genome-like mitochondrial genome and provide evidence that mitochondrial genomes are also maternally inherited in cotton.

The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group

Phylogenetic resolution is often low within groups of recently diverged taxa due to a paucity of phylogenetically informative characters. We tested the relative utility of seven noncoding cpDNA regions and a pair of homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons (Gossypium) as a model system. The five tetraploid species of Gossypium are a monophyletic assemblage derived from an allopolyploidization event that probably occurred within the last 0.5-2 million years. Previous analysis of cpDNA restriction site data provided only partial resolution within this clade despite a large number of enzymes employed. We sequenced three cpDNA introns (rpl16, rpoC1, ndhA) and four cpDNA spacers (accD-psaI, trnL-trnF, trnT-trnL, atpB-rbcL) for a total of over 7 kb of sequence per taxon, yet obtained only four informative nucleotide substitutions (0.05%) resulting in incomplete phylogenetic resolution. In addition, we sequenced a 1.65-kb region of a homoeologous pair of nuclear-encoded alcohol dehydrogenase (Adh) genes. In contrast with the cpDNA sequence data, the Adh homoeologues yielded 25 informative characters (0.76%) and provided a robust and completely resolved topology that is concordant with previous cladistic and phenetic analyses. The enhanced resolution obtained using the nuclear genes reflects an approximately three- to sixfold increase in nucleotide substitution rate relative to the plastome spacers and introns.

Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets

The phylogeny of baobab trees was analyzed using four data sets: chloroplast DNA restriction sites, sequences of the chloroplast rpl16 intron, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA, and morphology. We sampled each of the eight species of Adansonia plus three outgroup taxa from tribe Adansonieae. These data were analyzed singly and in combination using parsimony. ITS and morphology provided the greatest resolution and were largely concordant. The two chloroplast data sets showed concordance with one another but showed significant conflict with ITS and morphology. A possible explanation for the conflict is genealogical discordance within the Malagasy Longitubae, perhaps due to introgression events. A maximum-likelihood analysis of branching times shows that the dispersal between Africa and Australia occurred well after the fragmentation of Gondwana and therefore involved overwater dispersal. The phylogeny does not permit unambiguous reconstruction of floral evolution but suggests the plausible hypothesis that hawkmoth pollination was ancestral in Adansonia and that there were two parallel switches to pollination by mammals in the genus.