Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci

Genetic divergence and gene flow among closely related populations are difficult to measure because mutation rates of most nuclear loci are so low that new mutations have not had sufficient time to appear and become fixed. Microsatellite loci are repeat arrays of simple sequences that have high mutation rates and are abundant in the eukaryotic genome. Large population samples can be screened for variation by using the polymerase chain reaction and polyacrylamide gel electrophoresis to separate alleles. We analyzed 10 microsatellite loci to quantify genetic differentiation and hybridization in three species of North American wolflike canids. We expected to find a pattern of genetic differentiation by distance to exist among wolflike canid populations, because of the finite dispersal distances of individuals. Moreover, we predicted that, because wolflike canids are highly mobile, hybrid zones may be more extensive and show substantial changes in allele frequency, relative to nonhybridizing populations. We demonstrate that wolves and coyotes do not show a pattern of genetic differentiation by distance. Genetic subdivision in coyotes, as measured by theta and Gst, is not significantly different from zero, reflecting persistent gene flow among newly established populations. However, gray wolves show significant subdivision that may be either due to drift in past Ice Age refugia populations or a result of other causes. Finally, in areas where gray wolves and coyotes hybridize, allele frequencies of gray wolves are affected, but those of coyotes are not. Past hybridization between the two species in the south-central United States may account for the origin of the red wolf.      

A functional phylogenomic view of the seed plants

A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification.     

Femoral vein thrombosis and total hip replacement.

Of 160 patients who underwent total hip replacement, 81 developed venographic evidence of thrombi in the operated leg. In 46 cases (57%) the thrombus originated from the femoral vein, and in 43 of these the exact site of origin was defined by venography. In 34 cases (74%) the thrombus arose from the wall of the femoral vein at the level of the lesser trochanter. This region was studied by intraoperative venography in eight patients undergoing total hip replacement, and in every case severe distortion of the common femoral vein was observed, producing almost total occlusion. We suggest that intraoperative damage to the femoral vein results from manipulation of the leg, and that this is one reason why the operation is followed by a high incidence of deep vein thrombosis in the upper femoral region.     

Evidence for active cyclic electron flow in twig chlorenchyma in the presence of an extremely deficient linear electron transport activity

Fast and slow chlorophyll fluorescence induction curves at high and low actinic visible light, post-illumination changes in fluorescence yield and reflectance changes at 820 nm induced by far-red light were used to characterize the state of PSII and PSI and their electron transport capabilities in chlorophyllous twig cortices of Eleagnus angustifolius L., while corresponding leaves served as controls. Twigs displayed low dark-adapted PSII photochemical efficiencies and particularly low linear electron transport rates when illuminated. In addition, their PSII population was characterized by a high proportion of inactive, non-Q_B-reducing centers and an incomplete quenching of fluorescence during the slow induction phase. It is suggested that PSII in twigs is an inefficient electron donor to PSI and/or the reductive pentose phosphate cycle. Yet, in spite of this apparent PSII deficiency, pools of intermediate electron carriers and potential PSI activity were more than sufficient to support the observed linear electron transport rates. Moreover, the rate of PSI reduction upon far-red/dark transitions and the magnitude of fluorescence yield increase upon white light/dark transitions were compatible with an efficient electron flow to PSI from stromal donors in the absence of PSII activity. We conclude that corticular chlorenchyma may be actively engaged in cyclic at the expense of a linear electron flow and discuss the possible physiological significance of this finding in conjunction with the particular microenvironmental conditions encountered within twigs.     

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of those sequences that maximize likelihood under the Jukes-Cantor model is uninformative in the worst possible sense. For all inputs, all trees optimize the likelihood score. Second, we show that a greedy heuristic that uses GTR+Gamma ML to optimize the alignment and the tree can produce very poor alignments and trees. Therefore, the excellent performance of SATé-II and SATé-I is not because ML is used as an optimization criterion for choosing the best tree/alignment pair but rather due to the particular divide-and-conquer realignment techniques employed.     

Light-adaptive state transitions in the Ross Sea haptophyte Phaeocystis antarctica and in dinoflagellate cells hosting kleptoplasts derived from it

Light state transitions (STs) is a reversible physiological process that oxygenic photosynthetic organisms use in order to minimize imbalances in the electronic excitation delivery to the reaction centers of Photosystems I and II, and thus to optimize photosynthesis. STs have been studied extensively in plants, green algae, red algae and cyanobacteria, but sparsely in algae with secondary red algal plastids, such as diatoms and haptophytes, despite their immense ecological significance. In the present work, we examine whether the haptophyte alga Phaeocystis antarctica, and dinoflagellate cells that host kleptoplasts derived from P. antarctica, both endemic in the Ross Sea, Antarctica, are capable of light adaptive STs. In these organisms, Chl a fluorescence can be excited either by direct light absorption, or indirectly by electronic excitation (EE) transfer from ultraviolet light absorbing mycosporine-like amino acids (MAAs) to Chl a (Stamatakis et al., Biochim. Biophys. Acta 1858 [2017] 189–195). Here we show that, on adaptation to PS II-selective light, dark-adapted P. antarctica cells shift from light state 1 (ST1; more EE ending up in PS II) to light state 2 (ST2; more EE ending up in PS I), as revealed by the spectral distribution of directly-excited Chl a fluorescence and by changes in the macro-organization of pigment-protein complexes evidenced by circular dichroism (CD) spectroscopy. In contrast, no STs are clearly detected in the case of the kleptoplast-hosting dinoflagellate cells, and in the case of indirectly excited Chls a, via MAAs, in P. antarctica cells.     

Screen-Based Sedentary Behavior,Physical Activity,and Muscle Strength in the English Longitudinal Study of Ageing

Background

Sarcopenia is associated with loss of independence and ill-health in the elderly although the causes remain poorly understood. We examined the association between two screen-based leisure time sedentary activities (daily TV viewing time and internet use) and muscle strength.

Methods and Results

We studied 6228 men and women (aged 64.9±9.1 yrs) from wave 4 (2008-09) of the English Longitudinal Study of Ageing, a prospective study of community dwelling older adults. Muscle strength was assessed by a hand grip test and the time required to complete five chair rises. TV viewing and internet usage were inversely associated with one another. Participants viewing TV ≥6hrs/d had lower grip strength (Men, B = −1.20 kg, 95% CI, −2.26, −0.14; Women, −0.75 kg, 95% CI, −1.48, −0.03) in comparison to <2hrs/d TV, after adjustment for age, physical activity, smoking, alcohol, chronic disease, disability, depressive symptoms, social status, and body mass index. In contrast, internet use was associated with higher grip strength (Men, B = 2.43 kg, 95% CI, 1.74, 3.12; Women, 0.76 kg, 95% CI, 0.32, 1.20). These associations persisted after mutual adjustment for both types of sedentary behaviour.

Conclusions

In older adults, the association between sedentary activities and physical function is context specific (TV viewing vs. computer use). Adverse effects of TV viewing might reflect the prolonged sedentary nature of this behavior.