Studies on neurotrophic factors in chick muscle.

Experiments have been performed in order to try to elucidate the biological function of intramuscular protein (IMP), a novel substance antigenically related to vasoactive intestinal polypeptide (VIP). IMP was previously shown to be present in chick skeletal muscle during a restricted phase of development and to be secreted by cultured myotubes. This evidence and other findings suggested that IMP might be a trophic factor for motoneurons, and it is this hypothesis which the thesis sets out to test. Immunocytochemistry showed that IMP is present in ciliary muscle over a time course related to that of naturally occurring cell death in the ciliary ganglion (CG) and raised the possibility that IMP may be a trophic factor for CG neurons in addition to spinal cord motoneurons. IMP for use in bioassays was partially purified from embryonic muscle extract and myotube conditioned medium (MCM) by column chromatography, using a modified VIP radioimmunoassay to assay for IMP concentration. The molecular weight of IMP in muscle extracted in a neutral buffer is ca. 120kD, but when extracted in acid the major form has a molecular weight of ca. 35kD. The major form of IMP in MCM also has a molecular weight of ca. 35kD. Fractions containing IMP were tested in in vitro bioassays on CG neurons and motoneurons. Many IMP-containing fractions had survival activity for CG neurons; activities in IMP-containing fractions were also identified which (i) increased ChAT activity of CG neurons, (ii) had a synergistic effect on survival of CG neurons in the presence of ciliary neurotrophic factor, and (iii) had survival activity for spinal cord motoneurons. The role of IMP in these bioactivities was assessed by using fractions that had been depleted of IMP by antibody affinity chromatography, and in no case was activity clearly attributable to IMP. Thus several, possibly novel, trophic activities were identified. In conclusion, the strong circumstantial evidence for IMP being a neurotrophic factor has not been supported thus far by experiments designed to test this idea in vitro

Population genetics of mouse lemur vomeronasal receptors: current versus past selection and demographic inference

Abstract Background A major effort is underway to use population genetic approaches to identify loci involved in adaptation. One issue that has so far received limited attention is whether loci that show a phylogenetic signal of positive selection in the past also show evidence of ongoing positive selection at the population level. We address this issue using vomeronasal receptors (VRs), a diverse gene family in mammals involved in intraspecific communication and predator detection. In mouse lemurs, we previously demonstrated that both subfamilies of VRs (V1Rs and V2Rs) show a strong signal of directional selection in interspecific analyses. We predicted that ongoing sexual selection and/or co-evolution with predators may lead to current directional or balancing selection on VRs. Here, we re-sequence 17 VRs and perform a suite of selection and demographic analyses in sympatric populations of two species of mouse lemurs (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. Results M. ravelobensis had consistently higher genetic diversity at VRs than M. murinus. In general, we find little evidence for positive selection, with most loci evolving under purifying selection and one locus even showing evidence of functional loss in M. ravelobensis. However, a few loci in M. ravelobensis show potential evidence of positive selection. Using mismatch distributions and expansion models, we infer a more recent colonisation of the habitat by M. murinus than by M. ravelobensis, which most likely speciated in this region earlier on. Conclusions These findings suggest that the analysis of VR variation is useful in inferring demographic and phylogeographic history of mouse lemurs. In conclusion, this study reveals a substantial heterogeneity over time in selection on VR loci, suggesting that VR evolution is episodic

The Mid-Infrared Extinction Law in the Ophiuchus, Perseus, and Serpens Molecular Clouds

We compute the mid-infrared extinction law from 3.6-24 microns in three molecular clouds: Ophiuchus, Perseus, and Serpens, by combining data from the "Cores to Disks" Spitzer Legacy Science program with deep JHKs imaging. Using a new technique, we are able to calculate the line-of-sight extinction law towards each background star in our fields. With these line-of-sight measurements, we create, for the first time, maps of the chi-squared deviation of the data from two extinction law models. Because our chi-squared maps have the same spatial resolution as our extinction maps, we can directly observe the changing extinction law as a function of the total column density. In the Spitzer IRAC bands, 3.6-8 microns, we see evidence for grain growth. Below $A_{K_s} = 0.5$, our extinction law is well-fit by the Weingartner & Draine (2001) $R_V = 3.1$ diffuse interstellar medium dust model. As the extinction increases, our law gradually flattens, and for $A_{K_s} >= 1$, the data are more consistent with the Weingartner & Draine $R_V = 5.5$ model that uses larger maximum dust grain sizes. At 24 microns, our extinction law is 2-4 times higher than the values predicted by theoretical dust models, but is more consistent with the observational results of Flaherty et al. (2007). Lastly, from our chi-squared maps we identify a region in Perseus where the IRAC extinction law is anomalously high considering its column density. A steeper near-infrared extinction law than the one we have assumed may partially explain the IRAC extinction law in this region.Comment: 38 pages, 19 figures in pre-print format. Accepted for publication in ApJ. A version with full-resolution figures can be found here: http://peggysue.as.utexas.edu/SIRTF

Evolutionary pathways to convergence in plumage patterns.

BACKGROUND: Avian plumage is ideal for investigating phenotypic convergence because of repeated evolution of the same within-feather patterns. In birds, there are three major types of regular patterns within feathers: scales, bars and spots. Existing models of within-feather pattern development suggest that scales have the simplest developmental mechanism, bars require more stringent regulation than scales, and spots have the strictest developmental parameters. We hypothesized that increasing stringency in the mechanism of pattern formation predicts the evolutionary trajectory of patterns, and hence scales should evolve first, followed by bars and finally spots. Here, using Bayesian phylogenetic modeling we reconstructed pattern evolution in the most spectacularly patterned avian clades - aquatic waterfowl (Anseriformes) and terrestrial gamebirds (Galliformes). RESULTS: Our analyses suggest that the ancestral state of plumage is an absence of patterns, but with some variability. Independent analyses of seven feather patches reveal that spots evolve after bars and scales. However, both scales and bars evolve frequently from an absence of patterns, contradicting our predictions. Over the whole body, many constraints are conserved from the level of patches, for example the largest number of steps from the ancestral state was required for spots to evolve. CONCLUSIONS: Overall there was remarkable similarity in the inferred evolutionary trajectories of plumage pattern evolution in Galliformes and Anseriformes, suggesting that developmental constraint is similar in these two orders, despite large ecological differences. These evolutionary transitions are largely congruent with a reaction-diffusion based model of pattern formation, but the evolution of bars from an unpatterned ancestor is more common than expected. Our study highlights the promise of testing models of development using comparative methods.A Cambridge International Scholarship, as well as grants from the Gardiner Fund and Pembroke College Cambridge to T-LG funded this research

Testing whether macroevolution follows microevolution: Are colour differences among swans (Cygnus) attributable to variation at the MC1R locus?

<p>Abstract</p> <p>Background</p> <p>The <it>MC1R </it>(melanocortin-1 receptor) locus underlies intraspecific variation in melanin-based dark plumage coloration in several unrelated birds with plumage polymorphisms. There is far less evidence for functional variants of <it>MC1R </it>being involved in interspecific variation, in which spurious genotype-phenotype associations arising through population history are a far greater problem than in intraspecific studies. We investigated the relationship between <it>MC1R </it>variation and plumage coloration in swans (<it>Cygnus</it>), which show extreme variation in melanic plumage phenotypes among species (white to black).</p> <p>Results</p> <p>The two species with melanic plumage, <it>C. atratus </it>and <it>C. melanocoryphus </it>(black and black-necked swans respectively), both have amino acid changes at important functional sites in MC1R that are consistent with increased MC1R activity and melanism. Reconstruction of MC1R evolution over a newly generated independent molecular phylogeny of <it>Cygnus </it>and related genera shows that these putative melanizing mutations were independently derived in the two melanic lineages. However, interpretation is complicated by the fact that one of the outgroup genera, <it>Coscoroba</it>, also has a putative melanizing mutation at MC1R that has arisen independently but has nearly pure white plumage. Epistasis at other loci seems the most likely explanation for this discrepancy. Unexpectedly, the phylogeny shows that the genus <it>Cygnus </it>may not be monophyletic, with <it>C. melanocoryphus </it>placed as a sister group to true geese (<it>Anser</it>), but further data will be needed to confirm this.</p> <p>Conclusion</p> <p>Our study highlights the difficulty of extrapolating from intraspecific studies to understand the genetic basis of interspecific adaptive phenotypic evolution, even with a gene whose structure-function relationships are as well understood as MC1R as confounding variation make clear genotype/phenotype associations difficult at the macroevolutionary scale. However, the identification of substitutions in the black and black-necked swan that are known to be associated with melanic phenotypes, suggests <it>Cygnus </it>may be another example where there appears to be convergent evolution at MC1R. This study therefore provides a novel example where previously described intraspecific genotype/phenotype associations occur at the macroevolutionary level.</p

The differential expression of MC1R regulators in dorsal and ventral quail plumages during embryogenesis:Implications for plumage pattern formation

Melanin pigmentation patterns are ubiquitous in animals and function in crypsis, physical protection, thermoregulation and signalling. In vertebrates, pigmentation patterns formed over large body regions as well as within appendages (hair/feathers) may be due to the differential distribution of pigment producing cells (melanocytes) and/or regulation of the melanin synthesis pathway. We took advantage of the pigmentation patterns of Japanese quail embryos (pale ventrum and patterned feathers dorsally) to explore the role of genes and their transcripts in regulating the function of the melanocortin-1-receptor (MC1R) via 1. activation: pro-opiomelanocortin (POMC), endoproteases prohormone convertase 1 (PC1) and 2(PC2), and 2. inhibition-agouti signaling and agouti-related protein (ASIP and AGRP, respectively). Melanocytes are present in all feather follicles at both 8 and 12 days post-fertilisation (E8/E12), so differential deposition of melanocytes is not responsible for pigmentation patterns in embryonic quail. POMC transcripts expressed were a subset of those found in chicken and POMC expression within feather follicles was strong. PC1 was not expressed in feather follicles. PC2 was strongly expressed in all feather follicles at E12. ASIP transcript expression was variable and we report four novel ASIP transcripts. ASIP is strongly expressed in ventral feather follicles, but not dorsally. AGRP expression within feather follicles was weak. These results demonstrate that the pale-bellied quail phenotype probably involves inhibition of MC1R, as found previously. However, quail may require MC1R activation for eumelanogenesis in dorsal feathers which may have important implications for an understanding of colour pattern formation in vertebrates.</p

Population genetics of mouse lemur vomeronasal receptors: current versus past selection and demographic inference.

BACKGROUND: A major effort is underway to use population genetic approaches to identify loci involved in adaptation. One issue that has so far received limited attention is whether loci that show a phylogenetic signal of positive selection in the past also show evidence of ongoing positive selection at the population level. We address this issue using vomeronasal receptors (VRs), a diverse gene family in mammals involved in intraspecific communication and predator detection. In mouse lemurs, we previously demonstrated that both subfamilies of VRs (V1Rs and V2Rs) show a strong signal of directional selection in interspecific analyses. We predicted that ongoing sexual selection and/or co-evolution with predators may lead to current directional or balancing selection on VRs. Here, we re-sequence 17 VRs and perform a suite of selection and demographic analyses in sympatric populations of two species of mouse lemurs (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. RESULTS: M. ravelobensis had consistently higher genetic diversity at VRs than M. murinus. In general, we find little evidence for positive selection, with most loci evolving under purifying selection and one locus even showing evidence of functional loss in M. ravelobensis. However, a few loci in M. ravelobensis show potential evidence of positive selection. Using mismatch distributions and expansion models, we infer a more recent colonisation of the habitat by M. murinus than by M. ravelobensis, which most likely speciated in this region earlier on. CONCLUSIONS: These findings suggest that the analysis of VR variation is useful in inferring demographic and phylogeographic history of mouse lemurs. In conclusion, this study reveals a substantial heterogeneity over time in selection on VR loci, suggesting that VR evolution is episodic

Multiple origins of melanism in two species of North American tree squirrel ( Sciurus )

Abstract: Background: While our understanding of the genetic basis of convergent evolution has improved there are still many uncertainties. Here we investigate the repeated evolution of dark colouration (melanism) in eastern fox squirrels (Sciurus niger; hereafter “fox squirrels”) and eastern gray squirrels (S. carolinensis; hereafter “gray squirrels”). Results: We show that convergent evolution of melanism has arisen by independent genetic mechanisms in two populations of the fox squirrel. In a western population, melanism is associated with a 24 bp deletion in the melanocortin-1-receptor gene (MC1RΔ24 allele), whereas in a south-eastern population, melanism is associated with a point substitution in the agouti signalling protein gene causing a Gly121Cys mutation. The MC1R∆24 allele is also associated with melanism in gray squirrels, and, remarkably, all the MC1R∆24 haplotypes are identical in the two species. Evolutionary analyses show that the MC1R∆24 haplotype is more closely related to other MC1R haplotypes in the fox squirrel than in the gray squirrel. Modelling supports the possibility of gene flow between the two species. Conclusions: The presence of the MC1R∆24 allele and melanism in gray squirrels is likely due to introgression from fox squirrels, although we cannot completely rule out alternative hypotheses including introgression from gray squirrels to fox squirrels, or an ancestral polymorphism. Convergent melanism in these two species of tree squirrels has evolved by at least two and probably three different evolutionary routes

Vegetation Changes in the Miombo Woodlands in Northwestern Zimbabwe: A Case Study of Nkayi District 1990 to 2017

The research applied Geographic Information Systems (GISs) and remote sensing tools in quantifying land cover changes in Nkayi District and assess the drivers for such changes. This was done to link the impacts of anthropogenic activities to change in the physical environment especially looking at ecosystem goods and services, which in turn reduce their productivity. Satellite images were analyzed for 1990, 2000, 2010, and 2017 in order to produce temporal land cover maps for Nkayi District and use them as tools for estimating the rates and the extent to which land cover has changed from 1990 to 2017. Four main land cover types were identified, namely woodland, deforested land, cultivated land, and water bodies. In 1990, woodland covered 58% of the total land area in Nkayi District, while deforested land, cultivated land, and water bodies covered 31, 11, and 0.2%, respectively. From 1990 to 2017, woodland declined to 47% in 2017, while deforested land and cultivated land increased to 14.9 and 36%, respectively. The major drivers of land cover changes were increase in household numbers, which were associated with woodland clearing for agriculture. The other drivers of land cover changes were soil infertility and overgrazing by livestock. The research was crucial in detecting the problems of forage shortages and poor rangeland conditions, mainly caused by expanding fields coupled with infertile Kalahari sands. The research highlighted the urgent need to manage the fragile miombo woodlands, which are being threatened by the increased demand for land for human settlements and cultivation. Alternatively, the research also highlights the need for farmers to produce more biomass in their fields in the form of high-value crop residues to cater for the loss of rangelands

Coloration and the Genetics of Adaptation

Coat color is often used as camouflage and so has evolutionary benefit. How is coat color determined