Morpho-anatomical affinities and evolutionary relationships of three paleoendemic podocarp genera based on seed cone traits

Background and Aims The three relict genera Pherosphaera, Microcachrys and Saxegothaea in Podocarpaceae produce quite distinct seed cone types in comparison to other genera and does not form a clade along with Acmopyle. The detailed seed cone morpho-anatomy of these three relict genera and affinities with other podocarps are poorly known. This study aims to understand the seed cone morpho-anatomy and affinities among these three disjunct relict genera and with other podocarps. Methods We comparatively analysed the seed cone morpho-anatomical traits of the three podocarps genera and used ancestral state reconstruction to understand the evolution of these traits. Key Results We described the seed cone morpho-anatomical structures of the three relict genera in detail. The three genera produce aggregated multiovulate cones. Both Microcachrys and Saxegothaea has an asymmetrical free cup-like epimatium. Both species of Pherosphaera lack epimatium. The ancestral state reconstruction implies that the presence of epimatium is an ancestral trait in podocarps and independently lost in Pherosphaera and Phyllocladus. The seed cones are fleshy in Microcachrys and non-fleshy in Saxegothaea and Pherosphaera. The seed cone macrofossils of both extinct and living podocarps also show the presence of epimatium and fleshiness in podocarps. Conclusions Altogether, the morpho-anatomy suggests Pherosphaera, Microcachrys and Saxegothaea present affinities with each other and other podocarps but the reconstruction of ancestral seed cone in Podcarpaceae is quite complex due to multiple convergent evolutions of several structures. These structures (e.g. epimatium, aril, receptaculum) are of low taxonomic value but of great evolutionary and ecologically significance and are responsive adaptations to ever-changing environmental conditions.

The coracoscapular joint of neornithine birds—extensive homoplasy in a widely neglected articular surface of the avian pectoral girdle and its possible functional correlates

A survey is given of the morphological variation of the coracoscapular joint of neornithine birds. In Mesozoic stem group representatives, the coracoid exhibits a deeply concave cotyla scapularis, which articulates with a globose tuberculum coracoideum of the scapula. This morphology is likely to be functionally related to the development of a powerful supracoracoideus muscle and the formation of a triosseal canal as a pulley for the tendon of this muscle. In neornithine birds, the coracoid articulates with the scapula either via a concave cotyla or a flat facies articularis, with the latter largely restricting movements of the coracoid to the paramedian plane. Ancestral state reconstruction suggests that a cotyla scapularis is plesiomorphic for Neornithes and that a flat facies articularis scapularis evolved at least 13 times independently within the clade. For several lineages, the transition to a flat facies articularis scapularis can be traced in the fossil record, and the replacement of a cup-shaped cotyla by a flat articular facet seems to have been due to various functional demands. Often, a flat facies articularis scapularis is associated with reduced shafts of the furcula. A weakly developed furcula enables transverse movements of the coracoid and therefore enables a restriction of the mobility of the coracoscapular joint to the paramedian plane. In taxa with a large crop, a flat facies articularis scapularis is likely to be associated with a reorganization of the pectoral musculature, whereas in procellariiform birds, the transition from a cotyla to a facies articularis appears to have been correlated with the capacity for sustained soaring without wing flapping.

USING PHYLOGENETICS TO ACCURATELY INFER HIV-1 TRANSMISSION DIRECTION

Inferring the direction of transmission between linked individuals living with HIV provides unparalleled power to understand the epidemiology that determines transmission. State-of-the-art approaches to infer directionality use phylogenetic ancestral state reconstruction to identify the individual in whom the most recent common ancestor of the virus populations originated. However, these methods vary in their accuracy when applied to different datasets and it is currently unclear under what circumstances inferring directionality is inaccurate and when bias is more likely. To evaluate the performance of phylogenetic ancestral state reconstruction, we inferred directionality for 112 HIV transmission pairs where the direction of transmission was known, and detailed additional information was available. Next, we fit a statistical model to evaluate the extent to which epidemiological, sampling, genetic and phylogenetic factors influenced the outcome of the inference. Third, we repeated the analysis under real-life conditions when only routinely collected data are available. We found that the inference of directionality depends principally on the topology class and branch length characteristics of the phylogeny. Specifically, directionality is most correctly inferred when the phylogenetic diversity and the minimum root-to-tip distance in the transmitter is greater than that of the recipient partner and when the minimum inter-host patristic distance is large. Similarly, under real-life conditions, the probability of identifying the correct transmitter increases from 52%--when a monophyletic-monophyletic or paraphyletic-polyphyletic tree topology is observed, when the sample size in both partners is small and when the tip closest to the root does not agree with the state at the root--to 93% when a paraphyletic-monophyletic topology is observed, when the sample size is large and when the tip closest to the root agrees with the state at the root. Our results support two conclusions. First, that discordance between previous studies in inferring transmission direction can be explained by differences in key phylogenetic properties that arise due to different evolutionary, epidemiological and sampling processes; and second that easily calculated metrics from the phylogenetic tree of the transmission pair can be used to evaluate the accuracy of inferring directionality under real-life conditions for use in population-wide studies. However, given that these methods entail considerable uncertainty, we strongly advise against using these methods for individual pair-level analysis.

Evolutionary Change in Locomotion Close to the Origin of Amniotes Inferred From Trackway Data in an Ancestral State Reconstruction Approach

Among amniote and non-amniote tetrapod trackways from late Carboniferous to early Permian deposits, certain trackway measures vary notably. Some of this variability can be attributed to evolutionary changes in trackmaker anatomy and locomotion style close to the origin of amniotes. Here we demonstrate that steps in early amniote locomotion evolution can be addressed by applying methods of ancestral state reconstruction on trackway data – a novel approach in tetrapod ichnology. Based on (a) measurements of 186 trackways referred to the Carboniferous and early Permian ichnogenera Batrachichnus, Limnopus, Hylopus, Amphisauropus, Matthewichnus, Ichniotherium, Dimetropus, Tambachichnium, Erpetopus, Varanopus, Hyloidichnus, Notalacerta and Dromopus, (b) correlation of these ichnotaxa with specific groups of amphibian, reptiliomorph, synapsid, and reptilian trackmakers based on imprint morphology and (c) known skeletal-morphology-based phylogenies of the supposed trackmakers, we infer ancestral states for functionally controlled trackway measures in a maximum likelihood approach. The most notable finding of our analysis is a concordant change in trackway parameters within a series of ancestral amniote trackmakers, which reflects an evolutionary change in locomotion: In the ancestors of amniotes and diadectomorphs, an increase in body size was accompanied by a decrease in (normalized) gauge width and glenoacetabular length and by a change in imprint orientation toward a more trackway-parallel and forward-pointing condition. In the subsequent evolution of diadectomorph, synapsid and reptilian trackmakers after the diversification of the clades Cotylosauria (Amniota + Diadectomorpha) and Amniota, stride length increased whereas gauges decreased further or remained relatively narrow within most lineages. In accordance with this conspicuous pattern of evolutionary change in trackway measures, we interpret the body size increase as an underlying factor that triggered the reorganization of the locomotion apparatus. The secondary increase in stride length, which occurred convergently within distinct groups, is interpreted as an increase in locomotion capability when the benefits of reorganization came into effect. The track-trackmaker pair of Ichniotherium sphaerodactylum and Orobates pabsti from the early Permian Bromacker locality of the Thuringian Forest, proposed in earlier studies as a suitable ancestral amniote track-trackmaker model, fits relatively well with our modeled last common ancestor of amniotes – with the caveat that the Bromacker material is younger and some of the similarities appear to be due to convergence.

Structural Features of Carnivorous Plant (Genlisea, Utricularia) Tubers as Abiotic Stress Resistance Organs

Carnivorous plants from the Lentibulariaceae form a variety of standard and novel vegetative organs and survive unfavorable environmental conditions. Within Genlisea, only G. tuberosa, from the Brazilian Cerrado, formed tubers, while Utricularia menziesii is the only member of the genus to form seasonally dormant tubers. We aimed to examine and compare the tuber structure of two taxonomically and phylogenetically divergent terrestrial carnivorous plants: Genlisea tuberosa and Utricularia menziesii. Additionally, we analyzed tubers of U. mannii. We constructed phylogenetic trees using chloroplast genes matK/trnK and rbcL and used studied characters for ancestral state reconstruction. All examined species contained mainly starch as histologically observable reserves. The ancestral state reconstruction showed that specialized organs such as turions evolved once and tubers at least 12 times from stolons in Lentibulariaceae. Different from other clades, tubers probably evolved from thick stolons for sect. Orchidioides and both structures are primarily water storage structures. In contrast to species from section Orchidioides, G. tuberosa, U. menziesii and U. mannii form starchy tubers. In G. tuberosa and U. menziesii, underground tubers provide a perennating bud bank that protects the species in their fire-prone and seasonally desiccating environments.