Effects of Mitochondrial DNA Rate Variation on Reconstruction of Pleistocene Demographic History in a Social Avian Species, Pomatostomus superciliosus

Mitochondrial sequence data is often used to reconstruct the demographic history of Pleistocene populations in an effort to understand how species have responded to past climate change events. However, departures from neutral equilibrium conditions can confound evolutionary inference in species with structured populations or those that have experienced periods of population expansion or decline. Selection can affect patterns of mitochondrial DNA variation and variable mutation rates among mitochondrial genes can compromise inferences drawn from single markers. We investigated the contribution of these factors to patterns of mitochondrial variation and estimates of time to most recent common ancestor (TMRCA) for two clades in a co-operatively breeding avian species, the white-browed babbler Pomatostomus superciliosus. Both the protein-coding ND3 gene and hypervariable domain I control region sequences showed departures from neutral expectations within the superciliosus clade, and a two-fold difference in TMRCA estimates. Bayesian phylogenetic analysis provided evidence of departure from a strict clock model of molecular evolution in domain I, leading to an over-estimation of TMRCA for the superciliosus clade at this marker. Our results suggest mitochondrial studies that attempt to reconstruct Pleistocene demographic histories should rigorously evaluate data for departures from neutral equilibrium expectations, including variation in evolutionary rates across multiple markers. Failure to do so can lead to serious errors in the estimation of evolutionary parameters and subsequent demographic inferences concerning the role of climate as a driver of evolutionary change. These effects may be especially pronounced in species with complex social structures occupying heterogeneous environments. We propose that environmentally driven differences in social structure may explain observed differences in evolutionary rate of domain I sequences, resulting from longer than expected retention times for matriarchal lineages in the superciliosus clade.

Contribution of objective and subjective attributes to the variation in the whiteness and brightness of commercial mohair sale lots

Colour properties are measured prior to the sale of merino wool as they are of commercial importance when greasy wool is sold and when wool is dyed. With the paucity of knowledge of the colour properties of commercial mohair, this study aimed to identify and quantify the factors affecting the brightness (Y) and yellowness (Y-Z) values of commercial lots of Australian mohair. The research database comprised 520 sale lots (>500,000 kg mohair), which had tristimulus tests, and was sold during the period 2001–2009. Mohair was subjectively classed and sale lots objectively tested using international standard methods for mean fibre diameter (MFD, μm), fibre diameter coefficient of variation (%), International Wool Testing Organization (IWTO) clean wool base (IWTO yield, %w/w), vegetable matter (VM, %w/w) and the tristimulus values X, Y and Z (T units). The tristimulus values of Australian mohair were affected by the objective measurements of MFD, VM%, the subjective classing of stain, cotting, kemp and length and by the year and selling season. Variation in Y was more easily predicted with 90.5% of variance explained by the best model compared with variation in Y-Z, where the best model explained 51.6% of the total variance. Visually assessed properties of the mohair were very important in separating mohair of different Y properties, accounting for almost 80% of the total variance, but were far less important in accounting for the variance in Y-Z, accounting for about 9–10% of the total variance. The most important effects on the Y of mohair were associated with subjectively determined fault categories determined before the sale of mohair. In particular, stain fault explained about two-thirds of the variance in brightness of mohair sale lots. Stained mohair had much lower brightness than mohair free of stain but stain fault explained very little of the variation in yellowness of mohair sale lots. The extent of the differences in tristimulus values between seasons and years were not large for Y but were more important for yellowness (Y-Z), and these effects are likely to be of commercial importance. Generally, brightness decreased and yellowness increased as MFD increased up to about 30 μm. Both cotting and kemp fault were associated with reduced brightness and increased yellowness. The effects of VM% on tristimulus values were small. IWTO yield was associated with changes in tristimulus values, but in the best model, IWTO yield was not a significant determinant. This study indicates that commercial Australian fleece (nonfaulted) mohair was essentially white. Faulted mohair on the other hand exhibited poorer colour characteristics. The mohair subjectively identified as stained prior to sale comprised all the mohair which would be regarded as not white, and this investigation indicates that the effect of staining is on the brightness of mohair rather than the Y-Z measurement. Unlike the situation with merino wool, there was little relationship between the naturally occurring contaminants, as measured by the IWTO washing yield, and either Y or Y-Z.

The effects of topographic variation and the fire regime on coarse woody debris: insights from a large wildfire

Coarse woody debris (CWD) is a common structural component of terrestrial ecosystems, and provides important habitat for biota. Fires modify the distribution of CWD, both spatially and temporally. Changes in fire regimes, such as those arising from prescribed burning and changing climatic conditions, make it critical to understand the response of this resource to fire. We created a conceptual model of the effects of fire on logs and dead trees in topographically diverse forests in which trees often survive severe fire. We then surveyed paired sites, in a damp gully and adjacent drier slope, ~3.5. years after a large wildfire in south-eastern Australia. Sites were stratified by fire severity (unburnt, understorey burnt and severely burnt), and fire history (burnt ≤3. years or ≥20. years prior to the wildfire). Both components of the fire regime influenced CWD availability in gullies. Severe wildfire and fire history ≤3. years reduced the volume of small logs (10-30. cm diameter) in gullies, while severe wildfire increased the number of large dead trees in gullies. CWD on slopes was not affected by fire severity or history at ~3.5. years post-fire. Log volumes on slopes may recover more quickly after wildfire through rapid collapse of branches and trees. Gullies generally supported more logs than slopes, but longer inter-fire intervals in gullies may allow fuel loads to accumulate and lead to comparatively larger fire impacts. Given that fire severity and fire interval are predicted to change in many fire-prone ecosystems in coming decades, this study highlights the importance of understanding the interacting effects of multiple components of the fire regime with landscape structure. In particular, variation in fire interval and fire severity in relation to topographic position will influence the pattern of accumulation of coarse woody debris across the landscape, and therefore the structure and quality of habitats for biota.

Weathering, fibre strength and colour properties of processed white cashmere

Weathering refers to the degradation of wool fibres that occur during growth from exposure of the fleece to sunlight, water and air. Weathering damage to Merino wool reduces quantities of fibre that are harvested, reduces length in both raw and processed wools, reduces spinning performance and dyeing outcomes. This work aimed to aimed to quantify if and to what extent weathering occurred in 38 lots of commercial dehaired white cashmere and cashmere top sourced from traditional and new origins of production and the extent of any association between weathering and tensile strength properties of the dehaired cashmere and cashmere top. The cashmere was tested for physical properties, bundle tenacity and extension, tristimulus values brightness (Y) and yellowness (Y-Z) and reflectance. Dye uptake was used as an index of weathering. Linear models, relating to weathering, bundle tenacity and Y-Z were fitted to origin and other objective measurements. Mean attributes (range) were: mean fibre diameter, 17.0 μm (13.5–21.3 μm); bundle tenacity of tops, 10.3 cN/tex (8.3–12.9 cN/tex), for dehaired fibre, 10.1 cN/tex (9.1–11.4 cN/tex). Stain uptake varied from 0.92 to 6.34 mg/g fibre indicating a six-fold variation in the extent of weathering. Both the extent of weathering and the bundle tenacity of commercial lots of cashmere were affected by the origin of the cashmere. Increased weathering reduced bundle tenacity, bundle extension, increased the yellowness and reduced reflectance of white cashmere. Bundle tenacity of cashmere declined as fibre diameter variability increased from 20 to 22.5%. For the samples tested, the cashmere from China, Mongolia, Afghanistan and Iran showed more weathering than cashmere from Australia, New Zealand and the USA. The differences in the extent of weathering and of bundle tenacity between cashmere from different origins were of commercial significance.

Variation in the host preferences and responses of Ascia monuste orseis Godart (Lepidoptera: Pieridae) to cultivars of collard greens Brassica oleracea (L.) var. acephala

This work evaluated the preference of Ascia monuste orseis among 29 cultivars of collard greens through free- and no-choice assays using female adults (attractiveness and oviposition) and third-instar larvae (feeding preference), in both laboratory and greenhouse conditions. In free-choice tests with female adults, the L, V, Y, H, A, and Z cultivars produced oviposition non-preference in butterflies. Cultivars R, P, C, and D produced feeding non-preference in third-instar larvae of A. monuste orseis in free- and no-choice tests. Our findings may be useful for genetic improvement focusing on the development of B. oleracea var. acephala cultivars resistant to A. monuste orseis.

Evidence that the Ceratobasidium-like white-thread blight and black rot fungal pathogens from persimmon and tea crops in the Brazilian Atlantic Forest agroecosystem are two distinct phylospecies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Temporal variation in the abundance of two species of thrushes in relation to fruiting phenology in the Atlantic rainforest

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Concordance between macroinvertebrate communities and the typological classification of white and clear-water streams in Western Brazilian Amazonia

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Environmental and genetic variation of the effective radiative properties of the coat of Holstein cows under tropical conditions

Morphological characteristics, coat effective radiative properties, and the percentage of white colour were measured in the coats of 973 Holstein cows, and estimates of the genetic parameters were obtained for these traits, except morphological characteristics. The results showed that white coats are more dense with long, thin hairs, while the black coats are less dense with short, thick hairs. Effective transmissivity is greater in the less-dense coats with short, thin hairs, independently of coat colour. Effective reflectivity depends more on the variation in the radiative properties of the coat and skin surface rather than on the morphological characteristics of the coat. Effective absorptivity is greater in black and dense coats with long, thick hairs, than in the white and less-dense coat with short, thin hairs. All heritability estimates were of low magnitude, except for the percentage of white coat colour.

Hematological and serum chemistry values for the ring-necked pheasant (Phasianus colchicus): Variation with sex and age

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Spatial and Temporal Spread of Bovine Tuberculosis in Wild White-Tailed Deer in Michigan

In 1975, a wild white-tailed deer infected with bovine tuberculosis was shot in the northeastern Lower Peninsula, Michigan. The shooting of a second infected deer in the same area in 1994 triggered ongoing disease surveillance in the region. By 2002, bovine tuberculosis had been confirmed in 12 Michigan counties: from 449 deer; two elk; 41 non-cervid wildlife; one captive cervid facility and 28 cattle herds. We analyzed geographic spread of disease since the surveillance began and investigated factors influencing the prevalence of disease within the infected area. These analyses reveal that 78 percent of tuberculous deer came from within a 1560 km2 'core' area, within which the prevalence of apparent disease averaged 2.5 percent. Prevalence declined dramatically outside of the core and was an order of magnitude lower 30 km from its boundary. This prevalence gradient was highly significant (P<0.0001) and did not alter over the 6 year surveillance period (P= 0.98). Within the core, deer density and supplemental feeding by hunters were positively and independently correlated with tuberculosis prevalence in deer. Together, these two factors explained 55 percent of the variation in prevalence. We conclude that bovine tuberculosis was already well established in the deer population in 1994, that the infected area has not expanded significantly since that time, and that deer over-abundance and food supplementation have both contributed to ongoing transmission of disease. Managers are currently enforcing prohibitions on deer feeding in the core and are working to lower deer numbers there through increased hunting pressure.

Potential effect of marine traffic on white-beaked dolphin (Lagenorhynchus albirostris) distribution and behaviour in Faxaflói Bay, southwest Iceland

Faxaflói bay is a short, wide and shallow bay situated in the southwest of Iceland. Although hosting a rather high level of marine traffic, this area is inhabited by many different species of cetaceans, among which the white-beaked dolphin (Lagenorhynchus albirostris), found here all year-round. This study aimed to evaluate the potential effect of increasing marine traffic on white-beaked dolphins distribution and behaviour, and to determine whether or not a variation in sighting frequencies have occurred throughout years (2008 – 2014). Data on sightings and on behaviour, as well as photographic one, has been collected daily taking advantage of the whale-watching company “Elding” operating in the bay. Results have confirmed the importance of this area for white-beaked dolphins, which have shown a certain level of site fidelity. Despite the high level of marine traffic, this dolphin appears to tolerate the presence of boats: no differences in encounter durations and locations over the study years have occurred, even though with increasing number of vessels, an increase in avoidance strategies has been displayed. Furthermore, seasonal differences in probabilities of sightings, with respect to the time of the day, have been found, leading to suggest the existence of a daily cycle of their movements and activities within the bay. This study has also described a major decline in sighting rates throughout years raising concern about white-beaked dolphin conservation status in Icelandic waters. It is therefore highly recommended a new dedicated survey to be conducted in order to document the current population estimate, to better investigate on the energetic costs that chronic exposure to disturbances may cause, and to plan a more suitable conservation strategy for white-beaked dolphin around Iceland.

Exploration Of Survival Traits In The White-Nose Syndrome-Affected Big Brown Bat (Eptesicus Fuscus)

The widespread mortality of hibernating bats is associated with the emerging infectious disease white-nose syndrome (WNS), and has provoked a strong interest in understanding which bats will survive, and why? The ability of infected bats to resist WNS may depend upon variation in the expression of different characteristics. In a captive colony of big brown bats, I sought to characterize the phenotypic variability, repeatability, and survivability for several key ¿survival¿ traits, including: torpor patterns, microclimate preferences, and wound healing capacity. Torpor patterns were profiled using temperature sensitive dataloggers throughout the hibernation season, while microclimate preferences were quantified by using temperature-graded boxes and thermal imaging. In order to assess wound healing capacity, small wing biopsies were obtained from each bat and healing progress was tracked for one month. Individuals exhibited a wide range of phenotypes that were significantly influenced by sex and body condition. Repeatability estimates suggest that there is not a strong genetic basis for the observed variation in torpor patterns or microclimate preferences. Certain phenotypes (e.g., BMI) were associated with an increased probability of overwinter survivorship, which suggests a basis for intra-species differences in WNS susceptibility. The results from this project provide novel insight into what we know about ¿who will survive,¿ and will influence the direction and implementation of future conservation and mitigation strategies.

Bioremediation with White-Rot Fungi at Fisherville Mill: Analyses of Gene Expression and Number 6 Fuel Oil Degradation

Extracellular enzymes that white-rot fungi secrete during lignin decay have been proposed as promising agents for oxidizing pollutants. We investigated the abilities of the white-rot fungi Punctularia strigosozonata, Irpex lacteus, Trichaptum biforme, Phlebia radiata, Trametes versicolor, and Pleurotus ostreatus to degrade Number 6 fuel oil in wood sawdust cultures. Our goals are to advise bioremediation efforts at a brownfield redevelopment site on the Blackstone River in Grafton, Massachusetts and to contribute to the understanding of decay mechanisms in white-rot fungi. All species tested degraded a C10 alkane. When cultivated for 6 months, Irpex lacteus, T. biforme, P. radiata, T. versicolor and P. ostreatus also degraded a C14 alkane and the polycyclic aromatic hydrocarbon phenanthrene. Gene expression analyses of P. strigosozonata indicate differential gene expression in the presence of Number 6 oil and on pine and aspen sawdust.

Allelic Heterogeneity at the Equine KIT Locus in Dominant White (W) Horses

White coat color has been a highly valued trait in horses for at least 2,000 years. Dominant white (W) is one of several known depigmentation phenotypes in horses. It shows considerable phenotypic variation, ranging from approximately 50% depigmented areas up to a completely white coat. In the horse, the four depigmentation phenotypes roan, sabino, tobiano, and dominant white were independently mapped to a chromosomal region on ECA 3 harboring the KIT gene. KIT plays an important role in melanoblast survival during embryonic development. We determined the sequence and genomic organization of the approximately 82 kb equine KIT gene. A mutation analysis of all 21 KIT exons in white Franches-Montagnes Horses revealed a nonsense mutation in exon 15 (c.2151C>G, p.Y717X). We analyzed the KIT exons in horses characterized as dominant white from other populations and found three additional candidate causative mutations. Three almost completely white Arabians carried a different nonsense mutation in exon 4 (c.706A>T, p.K236X). Six Camarillo White Horses had a missense mutation in exon 12 (c.1805C>T, p.A602V), and five white Thoroughbreds had yet another missense mutation in exon 13 (c.1960G>A, p.G654R). Our results indicate that the dominant white color in Franches-Montagnes Horses is caused by a nonsense mutation in the KIT gene and that multiple independent mutations within this gene appear to be responsible for dominant white in several other modern horse populations.