Genomic diversity is shaped by the interplay between mutation, genetic drift, recombination, and natural selection. A major goal of evolutionary biology is to understand the relative contribution of these different microevolutionary forces to patterns of genetic variation both within and across species. The advent of massive parallel sequencing technologies opened new avenues to investigate the extent to which alternative evolutionary mechanisms impact the genome and the footprints they leave. We can leverage genomic information to, for example, trace back the demographic trajectory of populations and to identify genomic regions underlying adaptive traits. In this dissertation, I employ genomic data to explore the role of demography and natural selection in two New World bird systems distributed along steep environmental gradients: the Altamira Ori-ole (Icterus gularis), a Mesoamerican bird that exhibits large variation in body size across its range, and the Hairy and Downy woodpecker (Dryobates villosus and D. pubescens), two sympatric species whose phenotypes vary extensively in response to environments in North America. In Chapter 1, I combine ecological niche model, phenotypic and ddRAD sequencing data from several individuals of I. gularis to investigate which spatial processes best explain geographic variation in phenotypes and alleles: (i) isolation by distance, (ii) isolation by history or (iii) isolation by environment. I find that the pronounced genetic and phenotypic variation in I. gularis are only partially correlated and differ regarding spatial predictors. Whereas genomic variation is largely explained by historical barriers to gene flow (IBH), variation in body size can be best predicted by contemporary environmental heterogeneity (IBE), which is consistent with a pattern produced by either natural selection or environmental plasticity. In Chapter 2, I conduct whole genome resequencing on 140 individuals of Downy and Hairy Woodpecker from across North America to more explicitly elucidate the impact of demography and natural selection on the genome. I find that despite spatial congruence in allele frequencies, population structure in these two species has been produced at different temporal scales. Whereas Hairy Woodpeckers were isolated into two east-west glacial refugia, Downy woodpecker populations seem to have expanded from a single ancestral refugium. Demographic analyses suggest large variation in Ne over the past one million years in both Hairy and Downy Woodpeckers, with repeated episodes of bottleneck followed by population expansion, consistent with the onset of the climatic oscillations of the Pleistocene. Nucleotide diversity in both species was positively correlated with recombination rate and negatively correlated with gene density, suggesting the effect of linked selection. The magnitude of this effect, however, seems to have been modulated by the individual demographic trajectory of populations and species. Nevertheless, patterns of nucleotide diversity along the genome are highly correlated between Hairy and Downy Woodpecker, which may be attributed to pervasive selection acting on a conserved genomic landscape of recombination. Finally, in Chapter 3, I use a suite of statistical methods to scan the genome of Hairy and Downy Woodpecker for signatures of natural selection associated with population-specific environmental differences. I test whether climatic adaptation was achieved through selection on the same loci in both species, which would indicate parallel genetic mechanisms for adaptation. I find limited evidence of genomic parallelism at the SNP level, but large parallelism at the gene level. Candidate genes were involved in a broad range of biological processes, including immune response, nutritional metabolism, mitochondrial respiration, and embryonic development. Lastly, I identify potential candidates for key phenotypic traits in Downy and Hairy Woodpecker, such as genes in the IGF signaling pathway, putatively linked to differences in body size, and the melanoregulin gene (MREG), potentially involved in plumage variation. Together, these findings highlight the significant role of demography and natural selection in shaping genomic variation.

Thesis (PHD)--University of Montana, 2009. / Contents viewed on April 30, 2010. Title from author supplied metadata. Includes bibliographical references.

Quantification of cavity excavation produced strong empirical support for the ecological constraints model for the evolution of delayed dispersal in the cooperatively breeding red-cockaded woodpecker. The long times required for cavity excavation select for competition over breeding vacancies in established territories and against excavation of cavities in unoccupied habitat. Duration of excavation varies between woodpecker populations, but may require over 13 years in longleaf pine and over 10 years in loblolly pine. Duration of excavation is extremely variable. Much of the variation is due to variation in effort by excavating woodpeckers, which is in turn partially related to the need for new cavities in relation to the number of available cavities on a territory. An average of only 11 % of an individual's time budget is devoted to excavation, and only one individual per group makes significant contributions to excavation. Once completed, cavities are used for periods that may exceed fifteen years. Cavities in longleaf pine are used for significantly longer periods than cavities in loblolly. Whereas cavities no longer used as nests are abandoned altogether in loblolly, they are still roosted in for many years in longleaf. Final abandonment of longleaf cavities appears to be related to cavity loss. Quantification of cavity turnover revealed that three of the study populations were stable in cavity numbers over the study period, while a fourth underwent alarming declines. The continued use of restrictors and artificial cavities, and the protection of old-growth upon which the woodpeckers depend for excavation, are recommended. / Master of Science

I studied nest characteristics, breeding dispersal, and nest defence behaviour of Northern Flickers (<i>Colaptes auratus</i>, hereafter flickers) in central interior British Columbia with respect to nest predation. My research focused on three questions: (1) Are there nest characteristics associated with the risk of nest predation and nest loss to European Starlings (<i>Sturnus vulgaris</i>)? (2) Does nest predation influence breeding dispersal? (3) Do parental attributes influence nest defence behaviour? <p> An examination of flicker nest-site characteristics at five spatial scales revealed that nests were safer from mammalian predators (N=81) when they were higher, concealed by vegetation, farther from continuous coniferous forest blocks, and contained fewer conifers within the nesting clump. Proximity to conifers increased predation risk, but nests safe from competitors (N=18) were closer to coniferous forest blocks and contained a higher percentage of conifers in the nesting clump. Flickers face a trade-off between being safe from predators and safe from competitors. <p> Nesting success did not influence between-year breeding dispersal by 159 male or 76 female flickers. Because nests and forest clumps were not predictably safe from predators, benefits of dispersing likely outweigh costs. Other factors such as mate-switching, nest ectoparasites, and a fluctuating food source may play larger roles in dispersal than nest predation. Within years, 73% of pairs switched nest sites after their first attempt failed due to predation (N=37); however, there was no reproductive advantage for these pairs compared to pairs that remained at their original nest. Stressful encounters with predators involving nest defence may trigger dispersal, although it seems to offer no greater nest success. Of 24 flicker pairs presented with a control model before egg-laying, 3 pairs abandoned their nest, whereas 4 out of 24 pairs presented with a squirrel model abandoned their nest. This suggests that a one-time encounter with a nest predator is not a sufficient deterrent against continued nesting. Rather, costs of finding and excavating or renovating a new cavity may cause individuals to tolerate some risk in nesting at a location with an active predator. <p> In experimental trials (N=94), intensity of nest defence behaviour against a model predator was not related to the sex, age, body size, and body condition of the defending adult(s). The sexes may have behaved similarly because they are similar in size and have similar survival patterns. Costs and benefits of nest defence for flickers of different ages may also be equal because flickers are relatively short-lived and their survival rate is not linked with age. Brood size of the defending adult was also unrelated to the intensity of nest defence. If flickers have adjusted their clutch size in relation to the number of young for which they can optimally provide care, then no effects of brood size on nest defence behaviour should be recorded, as was the case here.</p>

I studied nest characteristics, breeding dispersal, and nest defence behaviour of Northern Flickers (<i>Colaptes auratus</i>, hereafter flickers) in central interior British Columbia with respect to nest predation. My research focused on three questions: (1) Are there nest characteristics associated with the risk of nest predation and nest loss to European Starlings (<i>Sturnus vulgaris</i>)? (2) Does nest predation influence breeding dispersal? (3) Do parental attributes influence nest defence behaviour? <p> An examination of flicker nest-site characteristics at five spatial scales revealed that nests were safer from mammalian predators (N=81) when they were higher, concealed by vegetation, farther from continuous coniferous forest blocks, and contained fewer conifers within the nesting clump. Proximity to conifers increased predation risk, but nests safe from competitors (N=18) were closer to coniferous forest blocks and contained a higher percentage of conifers in the nesting clump. Flickers face a trade-off between being safe from predators and safe from competitors. <p> Nesting success did not influence between-year breeding dispersal by 159 male or 76 female flickers. Because nests and forest clumps were not predictably safe from predators, benefits of dispersing likely outweigh costs. Other factors such as mate-switching, nest ectoparasites, and a fluctuating food source may play larger roles in dispersal than nest predation. Within years, 73% of pairs switched nest sites after their first attempt failed due to predation (N=37); however, there was no reproductive advantage for these pairs compared to pairs that remained at their original nest. Stressful encounters with predators involving nest defence may trigger dispersal, although it seems to offer no greater nest success. Of 24 flicker pairs presented with a control model before egg-laying, 3 pairs abandoned their nest, whereas 4 out of 24 pairs presented with a squirrel model abandoned their nest. This suggests that a one-time encounter with a nest predator is not a sufficient deterrent against continued nesting. Rather, costs of finding and excavating or renovating a new cavity may cause individuals to tolerate some risk in nesting at a location with an active predator. <p> In experimental trials (N=94), intensity of nest defence behaviour against a model predator was not related to the sex, age, body size, and body condition of the defending adult(s). The sexes may have behaved similarly because they are similar in size and have similar survival patterns. Costs and benefits of nest defence for flickers of different ages may also be equal because flickers are relatively short-lived and their survival rate is not linked with age. Brood size of the defending adult was also unrelated to the intensity of nest defence. If flickers have adjusted their clutch size in relation to the number of young for which they can optimally provide care, then no effects of brood size on nest defence behaviour should be recorded, as was the case here.</p>

Woodpeckers can withstand 1200-1400 g of force during repetitive pecking. The forces a woodpecker’s skull and brain are subjected to warrants an in-depth investigation for the possible existence of neuro-trauma. Dr. Philip May and colleagues in 1976 published a paper titled “Woodpeckers and Head Injury” detailing two woodpeckers and one toucan control. The group utilized ferrocyanide staining, a general stain used for detecting iron deposits, on the sections. The results of these stains were not reported in Dr. May’s paper, yet he and his colleagues conclude that “clearly the woodpecker’s brain is protected somehow from impact and vibration injury.” Close to 115 journal articles have cited this one paper as the standard for woodpeckers not incurring brain injury during pecking. Due to limited studies on the woodpecker brain and the fact the woodpecker is a model for advancing helmet technology, we set out to study the woodpecker’s brain for signs of injury. Taking 10 different ethanol preserved woodpeckers from all parts of the world in different climates, and five non-woodpecker, ethanol preserved red-winged black bird experimental controls, paraffin embedded sections were cut and stained. A piece of human Alzheimer’s disease cortex was also used as a positive control. We utilized Gallyas silver stain for the study of neurofibrillary tangles and tauopathies as well as anti-phospho-tau and anti-glial fibrillary acidic protein (GFAP) immunostaining to detect tau protein and GFAP respectively. The results demonstrated perivascular silver-positive deposits in the superficial cortex and axonal tract injury of eight out of the 10 woodpeckers. The anti-phospho-tau immunostaining stained axonal tract injury in two of the three woodpeckers studied. The red-winged back birds demonstrated no positivity for all three stains. The Alzheimer’s positive control showed silver positive and phospho-tau positive staining as expected. This is the first study of this kind to discover and label potential brain injury in the woodpecker model. The negative staining of the red-winged black bird controls contrasted with the positive staining woodpecker sections suggest pecking in the woodpecker may induce brain injury. When addressing the development of safety equipment, the use of the woodpecker model should be approached with caution. Moving forward, research into different immunostaining molecular targets and an age controlled woodpecker and experimental control study should be performed to determine if the brain injury seen with our research is age-dependent.

This dissertation proposes engineering principles for stress wave dissipation found in woodpeckers. From the experimental study of a woodpecker’s beaks via electron microscopy and mechanical testing, the three main design factors were pointed out. First, a woodpecker’s beak has wavy lines inside of the beak for local shearing. The waviness of wavy lines found in the woodpecker’s beaks was 1 while chicken’s was 0.3, and toucan’s was 0.05. Second, the woodpecker showed elongated the keratin scales to the pecking direction with a dimension ratio of 3.67 (width/height) while chicken’s and toucan’s were 3 and 1, respectively. Third, a woodpecker’s beak bone was less porous for structural strength. The porosity of a woodpecker’s beak bone was about 9.9 % while chicken’s and toucan’s were 42.3 % and 61.5 %, respectively. Also, by using computational simulations, unique geometries including hyoid apparatus and suture interfaces found in woodpeckers were investigated to assess their damping capabilities. Surrounding a woodpecker’s head, the hyoid apparatus composed of core cartilage and muscle encasing a core cartilage. The spiral and thinning geometry of the hyoid apparatus converted the normal waves into shear waves. Then shear waves generated lateral displacement of the hyoid bone, and lateral displacement brought strain energy into surrounding muscle, in which energy loss occurred by viscoelastic behavior of the muscle. Quantitatively, as the stress wave traveled from the anterior to the posterior end of the hyoid apparatus, its pressure decreased 75 % and the impulse decreased 84 %. Suture interfaces, which is another unique feature observed from woodpecker’s beak, was investigated for their geometrical effects on the dynamic impact mitigation. A sinusoidal pattern of suture interfaces induced wave scattering at its boundary causing conversion of longitudinal waves into shear waves. The suture gap also brought pressure decay by storing strain energy in its viscoelastic material. As a result, a bar with a suture interface attenuated stress waves about 37 % more than a bar with a flat interface. Based on the results and ideas presented herein, one can develop bio-inspired material for energy absorbing.

Little is known about arthropod communities inhabiting longleaf pines in the southeastern United States. This information is of particular importance because arthropods serve as the food base for the federally endangered red-cockaded woodpecker (RCW). In a recent study, this arthropod community has been suggested to be the mechanism by which RCW reproductive success is linked to the groundcover composition of the forest (which is a reflection of the forest's fire history). This is possible because it has been shown that much of the arthropod community found on longleaf pines originates from the forest floor. If the arthropod community is the link between the ground cover and the RCWs' reproductive success then higher amounts of arthropods should be found in areas with groundcover that is indicative of frequent burning. I conducted a one year study at three sites containing RCWs to determine whether the ground cover of the forest influences the abundance and mass of the arthropod communities on longleaf pines. I focused on impacts of groundcover on arthropods by controlling for tree species, tree age, soil type, hardwood midstory density, and overstory basal area. My results show that arthropod biomass was positively and significantly correlated to the percent coverage of herbaceous and graminoid vegetation and was negatively and significantly correlated to the percent coverage of woody vegetation. Arthropod biomass and abundance was also observed to vary seasonally with a peak occurring during spring and summer. Additionally, prescribed fire was not found to have a negative short-term impact on arthropod biomass. / Master of Science

Thesis (Ph. D.)--Florida State University, 2004. / Advisor: Dr. Frances C. James, Florida State University, College of Arts and Science, Dept. of Biological Science. Title and description from dissertation home page (viewed June 16, 2004). Includes bibliographical references.

Parental care in animals can be costly and is shared between both parents in many bird species. Not surprisingly, most studies of how parental care is shared between the sexes are in sexually dimorphic species, and much less in known about sexually monomorphic species where sex cannot be determined in the field. This has prevented a full understanding of parental care behaviors – which are intrinsically linked to fitness – in species such as the Red-headed Woodpecker (Melanerpes erythrocephalus) that is experiencing population declines throughout much of its range. In this study we assessed whether Redheaded Woodpecker brooding time, nestling provisioning rates, and nest cleaning rates vary as a function of parent sex, habitat type (savanna and closed canopy forest), brood size, nestling age, temperature and/or date. We recorded and analyzed 128 hours of high-quality video from 21 broods at Fort A.P. Hill, Virginia where this species is relatively abundant. We captured and color-banded Red-headed Woodpeckers, taking breast feather samples for genetic sexing, and determined brood size and chick age of nests using an extendable pole camera. Using generalized linear mixed models, we found the best predictor of nestling provisioning was an interaction between chick age and date; older chicks were fed more frequently in early summer (before 7 July) compared to late summer. The seasonal reduction in provisioning could be related to a reduction in resource availability, but whether or not provisioning in later nests affects nestling survival warrants further study. We found chick age and parent sex to be the best predictors in brooding models, with females brooding more when chicks are less than 10 days old and males being the only parent to enter the cavity after 10 days. Additionally, males almost exclusively remove fecal sacs from nests, highlighting an observational method to determine sex of breeding adults in the field. Such division of reproductive roles is similar to what is known for dimorphic woodpecker species and likely indicates energetic constraints due to the need for high parental investment from both sexes. Parental care is inextricably linked with habitat quality and home range size. Parents will travel to obtain the resources necessary to provision their young, and larger home ranges during the demanding nestling provisioning stage may indicate increased effort resulting from fewer available resources near the nest. We estimated home range sizes of 25 breeding adult Red-headed Woodpeckers using PinPoint GPS tags and 95% kernel density estimates (KDEs) with plug-in smoothing factors. We modeled the effects of habitat, sex, nest stage, date, and distance to nearest neighbor on home range estimates. Red-headed Woodpecker males have larger home ranges than females, and late summer home ranges are smaller than those measured before 7 July. More study is needed to determine if sex or date is a stronger factor on home range, given our naive sampling which resulted in more females sampled in late summer and observations that did not continue to the end of the breeding season (late August). Since we found date to be an influential factor to both provisioning rate and home range size, it is possible that seasonal resource changes are an important, unstudied factor related to nationwide declines of this species.