Framing the Salmonidae Family Phylogenetic Portrait: A More Complete Picture from Increased Taxon Sampling

Considerable research efforts have focused on elucidating the systematic relationships among salmonid fishes; an understanding of these patterns of relatedness will inform conservation- and fisheries-related issues, as well as provide a framework for investigating evolutionary mechanisms in the group. However, uncertainties persist in current Salmonidae phylogenies due to biological and methodological factors, and a comprehensive phylogeny including most representatives of the family could provide insight into the causes of these difficulties. Here we increase taxon sampling by including nearly all described salmonid species (n = 63) to present a time-calibrated and more complete portrait of Salmonidae using a combination of molecular markers and analytical techniques. This strategy improved resolution by increasing the signal-to-noise ratio and helped discriminate methodological and systematic errors from sources of difficulty associated with biological processes. Our results highlight novel aspects of salmonid evolution. First, we call into question the widely-accepted evolutionary relationships among sub-families and suggest that Thymallinae, rather than Coregoninae, is the sister group to the remainder of Salmonidae. Second, we find that some groups in Salmonidae are older than previously thought and that the mitochondrial rate of molecular divergence varies markedly among genes and clades. We estimate the age of the family to be 59.1 MY (CI: 63.2-58.1 MY) old, which likely corresponds to the timing of whole genome duplication in salmonids. The average, albeit highly variable, mitochondrial rate of molecular divergence was estimated as ∼0.31%/MY (CI: 0.27–0.36%/MY). Finally, we suggest that some species require taxonomic revision, including two monotypic genera, Stenodus and Salvethymus. In addition, we resolve some relationships that have been notoriously difficult to discern and present a clearer picture of the evolution of the group. Our findings represent an important contribution to the systematics of Salmonidae, and provide a useful tool for addressing questions related to fundamental and applied evolutionary issues.     

Architectural specialization of the intrinsic thoracic limb musculature of the American badger (Taxidea taxus)

Evaluation of the relationships between muscle structure and digging function in fossorial species is limited. Badgers and other fossorial specialists are expected to have massive forelimb muscles with long fascicles capable of substantial shortening for high power and applying high out‐force to the substrate. To explore this hypothesis, we quantified muscle architecture in the thoracic limb of the American badger (Taxidea taxus) and estimated the force, power, and joint torque of its intrinsic musculature in relation to the use of scratch‐digging behavior. Architectural properties measured were muscle mass, belly length, fascicle length, pennation angle, and physiological cross‐sectional area. Badgers possess hypertrophied shoulder flexors/humeral retractors, elbow extensors, and digital flexors. The triceps brachii is particularly massive and has long fascicles with little pennation, muscle architecture consistent with substantial shortening capability, and high power. A unique feature of badgers is that, in addition to elbow joint extension, two biarticular heads (long and medial) of the triceps are capable of applying high torques to the shoulder joint to facilitate retraction of the forelimb throughout the power stroke. The massive and complex digital flexors show relatively greater pennation and shorter fascicle lengths than the triceps brachii, as well as compartmentalization of muscle heads to accentuate both force production and range of shortening during flexion of the carpus and digits. Muscles of most functional groups exhibit some degree of specialization for high force production and are important for stabilizing the shoulder, elbow, and carpal joints against high limb forces generated during powerful digging motions. Overall, our findings support the hypothesis and indicate that forelimb muscle architecture is consistent with specializations for scratch‐digging. Quantified muscle properties in the American badger serve as a comparator to evaluate the range of diversity in muscle structure and contractile function that exists in mammals specialized for fossorial habits. J. Morphol. 2013. © 2012 Wiley Periodicals, Inc.     

Grouped sequential exploitation of food patches in a flock feeder,the feral pigeon

Feral and laboratory flocks of rock doves ($\text{Columba}$$\text{livia}$) show a pattern of grouped sequential exploitation when simultaneously presented with two dispersed, depleting patches of seed. This behavior contrasts with the ideal free distribution pattern shown when patches are small and concentrated. Grouped sequential exploitation consists of two phases: all pigeons first land together and feed at one patch, then leave one by one for the other patch. Departure times of individuals for the second patch are correlated with feeding rate at patch 1, which is in turn correlated with position in the dominance hierarchy. The decision to switch from patch 1 to patch 2 improves individual feeding rates in all cases, but is done slightly later than it should according to optimal foraging theory.     

Mitochondrial dynamics: quantifying mitochondrial fusion <Emphasis Type="Italic">in vitro</Emphasis>

Mitochondrial fusion is an essential process for preserving the integrity and stability of mitochondrial DNA; however, regulation of this process remains largely mysterious. In this issue of BMC Biology, Schauss and colleagues describe a simple, reliable, and robust novel assay that allows fusion of mammalian mitochondria to be quantified in vitro.     

Correlation of androgen-responsiveness of Shionogi mouse mammary carcinoma cell lines with binding of dihydrotestosterone to nuclear envelopes

Purified nuclear envelopes have been isolated from an androgen-responsive and two androgen-unresponsive cell lines of the Shionogi mouse mammary carcinoma. The binding of dihydrotestosterone to nuclear envelope fractions isolated from the three variant cell lines is correlated with the androgen-responsiveness of the cell line. Nuclear envelopes prepared from the two androgen-unresponsive cell lines did not bind dihydrotestosterone specifically following incubation with radioactive dihydrotestosterone from 2.5 to 45.0 nM at 20 degrees C for 18 h. Under the same binding conditions, nuclear envelopes prepared from the androgen-responsive cell line demonstrated saturable, specific binding of dihydrotestosterone. Scatchard analysis revealed a class of binding sites with an apparent Kd of 14.2 nM and a maximum binding capacity of 28.7 fmol/mg protein. Proteinase and heat treatments resulted in the complete loss of androgen-binding activity, whereas DNAase treatment resulted in the loss of 38% of the binding activity. The binding sites were specific for dihydrotestosterone. Testosterone was only a weak competitor and estradiol did not compete. Extraction with concentrations of KCl up to 1.0 M did not result in loss of androgen binding.     

Interaction of steroids with the nuclear envelope

Three approaches have been taken to determine the molecular mechanism by which steroid hormones traverse the nuclear envelope on their way to the genome. The first approach involved characterization of steroid binding to nuclear envelope preparations. We have characterized androgen binding to nuclear envelopes isolated from the rat ventral prostate, the rat liver, and androgen-responsive and androgen-unresponsive cell lines of the Shionogi mouse mammary carcinoma and glucocorticoid binding to rat liver. Relatively high affinity binding sites for steroids have been identified on nuclear envelopes. Importantly, the number and specificity of the sites correlates with the responsiveness of the tissue to the steroid. In the second approach, we have undertaken to identify the steroid binding site directly. As the characteristics of the rat ventral prostate site resembled those of the nuclear androgen receptor, we have begun purifying that receptor and have found fast protein liquid chromatography to be very effective. By affinity labelling studies, the dexamethasone binding site on the rat liver nuclear envelope has been identified as a peptide of molecular weight of approximately 90,000. The third approach we have used is to identify androgen-dependent peptides in nuclear envelope preparations. In both the rat ventral prostate and an androgen-responsive cell line of the Shionogi mouse mammary carcinoma, we have identified abundant androgen-dependent peptides. The relationship of these peptides to the binding sites identified by the first two approaches and their role in steroid transport is being investigated.     

Effect of somatostatin in the Syrian hamster bearing a transplantable islet-cell tumor.

The influence of somatostatin (SRIF) on blood glucose, plasma insulin and plasma glucagon was studied in hamsters bearing a transplantable islet-cell tumor secreting insulin and glucagon as well as in normal controls. Fed anesthetized animals were infused intraperitoneally either at a dose of 10 microgram in 15 min or of 150 microgram in 30 min, and intravenously at a dose of 250 microgram in 30 min. Blood was withdrawn from the jugular vein before and after infusion. Before the infusions, tumor bearing animals (TB) had lower blood glucose, markedly elevated plasma glucagon and slightly lower plasma insulin by comparison with normal hamsters (N). Both doses of somatostatin infused by the intraperitoneal route produced a slight but significant hypoglycemia in TB hamsters but not in normals. Ten microgram SRIF did not affect insulin and plasma glucagon levels whereas 150 microgram SRIF significantly depressed plasma insulin in both types of hamsters (N and TB). This latter dose of SRIF decreased plasma glucagon in normal but not in tumor-bearing hamsters. Intravenous infusion of 250 microgram SRIF did not reduce the hyperglucagonemia of TB hamsters either. These results indicate that somatostatin does not reduce the hyperglucagonemia due to the transplantable islet-cell tumor but nevertheless decreases blood glucose and plasma insulin.