Linking phylogenetics with population genetics to reconstruct the geographic origin of a species

Reconstructing ancestral geographic origins is critical for understanding the long-term evolution of a species. Bayesian methods have been proposed to test biogeographic hypotheses while accommodating uncertainty in phylogenetic reconstruction. However, the problem that certain taxa may have a disproportionate influence on conclusions has not been addressed. Here, we infer the geographic origin of Drosophila simulans using 2,014 bp of the period locus from 63 lines collected from 18 countries. We also analyze two previously published datasets, alcohol dehydrogenase related and NADH:ubiquinone reductase 75 kDa subunit precursor. Phylogenetic inferences of all three loci support Madagascar as the geographic origin of D. simulans. Our phylogenetic conclusions are robust to taxon resampling and to the potentially confounding effects of recombination. To test our phylogenetically derived hypothesis we develop a randomization test of the population genetics prediction that sequences from the geographic origin should contain more genetic polymorphism than those from derived populations. We find that the Madagascar population has elevated genetic polymorphism relative to non-Madagascar sequences. These data are corroborated by mitochondrial DNA sequence data.     

Prospects for inferring pairwise relationships with single nucleotide polymorphisms

An extraordinarily large number of single nucleotide polymorphisms (SNPs) are now available in humans as well as in other model organisms. Technological advancements may soon make it feasible to assay hundreds of SNPs in virtually any organism of interest. One potential application of SNPs is the determination of pairwise genetic relationships in populations without known pedigrees. Although microsatellites are currently the marker of choice for this purpose, the number of independently segregating microsatellite markers that can be feasibly assayed is limited. Thus, it can be difficult to distinguish reliably some classes of relationship (e.g. full-sibs from half-sibs) with microsatellite data alone. We assess, via Monte Carlo computer simulation, the potential for using a large panel of independently segregating SNPs to infer genetic relationships, following the analytical approach of Blouin et al. (1996). We have explored a 'best case scenario' in which 100 independently segregating SNPs are available. For discrimination among single-generation relationships or for the identification of parent-offspring pairs, it appears that such a panel of moderately polymorphic SNPs (minor allele frequency of 0.20) will provide discrimination power equivalent to only 16-20 independently segregating microsatellites. Although newly available analytical methods that can account for tight genetic linkage between markers will, in theory, allow improved estimation of relationships using thousands of SNPs in highly dense genomic scans, in practice such studies will only be feasible in a handful of model organisms. Given the comparable amount of effort required for the development of both types of markers, it seems that microsatellites will remain the marker of choice for relationship estimation in nonmodel organisms, at least for the foreseeable future.     

Reconstructed bone end loads on the canine forelimb during gait

The objective of this work was to determine bone loading conditions that, when applied to a finite element model, would best reproduce the in vivo strain field as measured by surface-mounted strain rosettes. The present study adopts the basic mathematical approach to load reconstruction introduced by Weinans and Blankevoort (J. Biomech. 28 (1995) 739) who determined the relationship between applied loads and bone strain distribution using ex vivo calibration testing. Our method eliminates the need for subsequent ex vivo calibration tests by instead substituting a computational calibration procedure. This first application of the method is with in vivo strains on the canine forelimb during gait (Coleman et al., J. Biomech. 35 (2002) 1677), but with further refinements the method could be used to reconstruct the in vivo loading conditions in living subjects.     

Electron microscopy of functional ribosome complexes

Cryoelectron microscopy has made a number of significant contributions to our understanding of the translation process. The method of single-particle reconstruction is particularly well suited for the study of the dynamics of ribosome-ligand interactions. This review follows the events of the functional cycle and discusses the findings in the context provided by the recently published x-ray structures.     

Arboreallty and morphological evolution in ground beetles (Carabidae: Harpalinae): testing the taxon pulse model

Abstract.— One-third to two-thirds of all tropical carabids, or ground beetles, are arboreal, and evolution of arboreality has been proposed to be a dead end in this group. Many arboreal carabids have unusual morphological features that have been proposed to be adaptations for life on vegetation, including large, hemispheric eyes; an elongated prothorax; long elytra; long legs; bilobed fourth tarsomeres; adhesive setae on tarsi; and pectinate claws. However, correlations between these features and arboreality have not been rigorously tested previously. I examined the evolution of arboreality and morphological features often associated with this habitat in a phylogenetic context. The number and rates of origins and losses of arboreality in carabids in the subfamily Harpalinae were inferred with parsimony and maximum-likelihood on a variety of phylogenetic hypotheses. Correlated evolution in arboreality and morphological characters was tested with concentrated changes tests, maximum-likelihood, and independent contrasts on optimal phylogenies. There is strong evidence that both arboreality and the morphological features examined originated multiple times and can be reversed, and in no case could the hypothesis of equal rates of gains and losses be rejected. Several features are associated with arboreality: adhesive setae on the tarsi, bilobed tarsomeres, and possibly pectinate claws and an elongated prothorax. Bulgy eyes, long legs, and long elytra were not correlated with arboreality and are probably not arboreal adaptations. The evolution of arboreal carabids has not been unidirectional. These beetles have experienced multiple gains and losses of arboreality and the morphological characters commonly associated with the arboreal habitat. The evolutionary process of unidirectional character change may not be as widespread as previously thought and reversal from specialized lifestyles or habitats may be common.     

Further evaluation of amniotic membrane banking for transplantation in ocular surface diseases

Objective: To define the best conditions foramniotic membrane preparation, storage and banking in its use for cornealreconstruction.Methods: Amniotic membrane pieces were prepared understerile conditions from placentas selected on the basis of donor medical andsocial history, serology, microbiological tests and histology. The pieces werekept at –140 °C but before grafting they werethawed and stored at 4 °C in RPMI medium, to have apreparation usable within 72 h. This procedure was validatedby testing its therapeutic effectiveness in 25 patients 13 of which had cornealulcers of various origin, 3 had sequelae of herpes simplex keratitis, 3 bandkeratopathy and 6 corneal stem cell deficiency due to chemical or thermalburns.Results: The preparation showed appreciableanti-inflammatory and analgesic effects. In the absence of corneal stem celldeficiency a stable re-epithelialisation was achieved in 15 out of 19 patients.When the limbus was lesioned, the amniotic membrane decreased vascularizationand increased the number of corneal epithelial cells only in 1 of the 6patients. No adverse reactions attributable to the tissue were recorded.Conclusions: A ready-to-use amniotic membrane preparationstored at 4 °C after cryopreservation has been tested incorneal reconstruction. Like the amniotic membrane thawed immediately beforegrafting, this preparation displayed full therapeutic effect in epithelialdefects with stromal ulceration but without severe limbal stem cell deficiency.In two years banking activity 463 pieces of the preparation were successfullydistributed to 90 Italian hospitals.     

A cytochrome b origin of photosynthetic reaction centers: an evolutionary link between respiration and photosynthesis

The evolutionary origin of photosynthetic reaction centers has long remained elusive. Here, we use sequence and structural analysis to demonstrate an evolutionary link between the cytochrome b subunit of the cytochrome bc(1) complex and the core polypeptides of the photosynthetic bacterial reaction center. In particular, we have identified an area of significant sequence similarity between a three contiguous membrane-spanning domain of cytochrome b, which contains binding sites for two hemes, and a three contiguous membrane-spanning domain in the photosynthetic reaction center core subunits, which contains binding sites for cofactors such as (bacterio)chlorophylls, (bacterio)pheophytin and a non-heme iron. Three of the four heme ligands in cytochrome b are found to be conserved with the cofactor ligands in the reaction center polypeptides. Since cytochrome b and reaction center polypeptides both bind tetrapyrroles and quinones for electron transfer, the observed sequence, functional and structural similarities can best be explained with the assumption of a common evolutionary origin. Statistical analysis further supports a distant but significant homologous relationship. On the basis of previous evolutionary analyses that established a scenario that respiration evolved prior to photosynthesis, we consider it likely that cytochrome b is the evolutionary precursor for type II reaction center apoproteins. With a structural analysis confirming a common evolutionary origin of both type I and type II reaction centers, we further propose a novel "reaction center apoprotein early" hypothesis to account for the development of photosynthetic reaction center holoproteins.     

The mitotic spindle and associated membranes in the closed mitosis of trichomonads

In the present work, we followed the several phases of Tritrichomonas foetus and Trichomonas vaginalis cell cycles using immunofluorescence, serial thin sections, three-dimensional (3D) reconstruction, and transmission electron microscopy. In motile trichomonad cells or in pseudocyst forms, the nuclear envelope persists throughout mitosis, and the spindle is extranuclear. We found three types of spindle microtubules: pole-to-nucleus microtubules which are attached to the nuclear envelope, pole-to-pole microtubules forming a cylindrical, cytoplasmic groove on the nuclear compartment in pseudocysts of T. foetus cells, and pole-to-cytosol microtubules which extend freely into the cytoplasm. We demonstrated that: (1) in T. foetus, the spindle is assembled from an MTOC located at the base of the costa, underneath one of the basal bodies; (2) the spindle presents an unusual arc shape during the initial phases of mitosis in motile trophozoites; (3) the spindle microtubules are glutamylated, but not acetylated; (4) several membranes similar to those of the endoplasmic reticulum follow the spindle microtubules; (5) finger-like projections extend from the nucleus towards the cell poles in pseudocysts and multinucleated cells; and (6) vesicles formed in between the two nuclear membranes are seen in the course of mitosis in both trophozoite and pseudocyst forms.