Patterns of nucleotide sequence variation in <Emphasis Type="Italic">ICAM1</Emphasis> and <Emphasis Type="Italic">TNF</Emphasis> genes in twelve ethnic groups of India: roles of demographic history and natural selection

We have studied DNA sequence variation in and around the genes ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India, with a view to investigating the relative roles of demographic history and natural selection in shaping the observed patterns of variation. The total numbers of single nucleotide polymorphisms (SNPs) detected at the ICAM1 and TNF loci were 29 and 12, respectively. Haplotype and allele frequencies differed significantly across populations. The site frequency spectra at these loci were significantly different from those expected under neutrality, and showed an excess of intermediate-frequency variants consistent with balancing selection. However, as expected under balancing selection, there was no significant reduction of F _ST values compared to neutral autosomal loci. Mismatch distributions were consistent with population expansion for both loci. On the other hand, the phylogenetic network among haplotypes for the TNF locus was similar to expectations under population expansion, while that for the ICAM1 was as expected under balancing selection. Nucleotide diversity at the ICAM1 locus was an order of magnitude lower in the promoter region, compared to the introns or exons, but no such difference was noted for the TNF gene. Thus, we conclude that the pattern of nucleotide variation in these genes has been modulated by both demographic history and selection. This is not surprising in view of the known allelic associations of several polymorphisms in these genes with various diseases, both infectious and noninfectious.     

Modeling the Western Arctic Caribou Herd During a Positive Growth Phase: Potential Effects of Wolves and Radiocollars

ABSTRACT Population modeling exercises can lead to both expected and unexpected results useful for wildlife research and management, even though inferences must often be qualitative, given underlying assumptions. Our main objective was to use empirical data on wolf (Canis lupus) kill rates and growth of the Western Arctic caribou (Rangifer tarandus) herd (WAH) of Alaska, USA, to assess the potential for predator regulation. We used available data and published literature to construct a deterministic density-dependent population model fitted to trends of the WAH from 1976 through 2003. By increasing wolf densities in the baseline model, we failed to reject the hypothesis that wolves at a density of 6.5 wolves per 1,000 km² could regulate a caribou herd at a density of 0.4 caribou per km². In addition, our model may be conservative by underestimating the regulatory potential of wolves. We suggest that this relatively simple predator-preysystem shows signs of a predation—food 2-state model. Elasticities from matrix models may be deceiving. Although herd growth is most sensitive to changes in adult female survival, survival of younger cohorts may be more easily influenced by natural conditions or management action. Management of the WAH near maximum sustained yield may not be attainable if desired, but modeling exercises such as this elucidate options. In conducting this research, we also discovered by Monte Carlo simulation that survival and productivity data from radiocollared females and calves were negatively biased and failed to predict herd growth. Thus, researchers should consider potential effects of neck collars on vital rates of female tundra caribou and concomitant offspring when using sample data to model population dynamics or test hypotheses.     

Noninvasive Estimation of Black Bear Abundance Incorporating Genotyping Errors and Harvested Bear

ABSTRACT Estimating black bear (Ursus americanus) population size is a difficult but important requirement when justifying harvest quotas and managing populations. Advancements in genetic techniques provide a means to identify individual bears using DNA contained in tissue and hair samples, thereby permitting estimates of population abundance based on established mark-capture-recapture methodology. We expand on previous noninvasive population-estimation work by geographically extending sampling areas (36,848 km²) to include the entire Northern Lower Peninsula (NLP) of Michigan, USA. We selected sampling locations randomly within biologically relevant bear habitat and used barbed wire hair snares to collect hair samples. Unlike previous noninvasive studies, we used tissue samples from harvested bears as an additional sampling occasion to increase recapture probabilities. We developed subsampling protocols to account for both spatial and temporal variance in sample distribution and variation in sample quality using recently published quality control protocols using 5 microsatellite loci. We quantified genotyping errors using samples from harvested bears and estimated abundance using statistical models that accounted for genotyping error. We estimated the population of yearling and adult black bears in the NLP to be 1,882 bears (95% CI = 1,389-2,551 bears). The derived population estimate with a 15% coefficient of variation was used by wildlife managers to examine the sustainability of harvest over a large geographic area.     

Greater Sage-Grouse Population Response to Energy Development and Habitat Loss

ABSTRACT Modification of landscapes due to energy development may alter both habitat use and vital rates of sensitive wildlife species. Greater sage-grouse (Centrocercus urophasianus) in the Powder River Basin (PRB) of Wyoming and Montana, USA, have experienced rapid, widespread changes to their habitat due to recent coal-bed natural gas (CBNG) development. We analyzed lek-count, habitat, and infrastructure data to assess how CBNG development and other landscape features influenced trends in the numbers of male sage-grouse observed and persistence of leks in the PRB. From 2001 to 2005, the number of males observed on leks in CBNG fields declined more rapidly than leks outside of CBNG. Of leks active in 1997 or later, only 38% of 26 leks in CBNG fields remained active by 2004–2005, compared to 84% of 250 leks outside CBNG fields. By 2005, leks in CBNG fields had 46% fewer males per active lek than leks outside of CBNG. Persistence of 110 leks was positively influenced by the proportion of sagebrush habitat within 6.4 km of the lek. After controlling for habitat, we found support for negative effects of CBNG development within 0.8 km and 3.2 km of the lek and for a time lag between CBNG development and lek disappearance. Current lease stipulations that prohibit development within 0.4 km of sage-grouse leks on federal lands are inadequate to ensure lek persistence and may result in impacts to breeding populations over larger areas. Seasonal restrictions on drilling and construction do not address impacts caused by loss of sagebrush and incursion of infrastructure that can affect populations over long periods of time. Regulatory agencies may need to increase spatial restrictions on development, industry may need to rapidly implement more effective mitigation measures, or both, to reduce impacts of CBNG development on sage-grouse populations in the PRB.     

Synchrony in a Wild Turkey Population and its Relationship to Spring Weather

Abstract: Synchrony is an important component of wildlife population dynamics because it describes spatial pattern in temporal population fluctuations. The strength and spatial extent of synchrony can provide information about the extrinsic and intrinsic forces that shape population structure. Wild turkey (Meleagris gallopavo silvestris) populations undergo annual fluctuations, possibly due to variation in weather during the reproductive season. To determine if spring weather plays a role in synchronizing wild turkey populations, we used a modified Mantel-type spatial autocorrelation procedure to measure the synchrony in fall wild turkey harvest data collected in 443 townships from 1990 to 1995 and compared this to the pattern of synchrony in spring weather variables (May rainfall and temp) over the same period. We measured correlation using Spearman correlation coefficients between the total fall harvests from 1990 to 1995 for each pair of townships, and sorted pairs into 6 50-km distance intervals. We calculated a mean correlation coefficient for each interval and estimated its P-value using resampling. We found moderately significant synchrony in the fall harvest (r_s = 0.12-0.34, P < 0.008) among township pairs <150 km apart, but no significant synchrony beyond this distance. In contrast, both May temperature (r = 0.82-0.90, P < 0.001) and rainfall (r = 0.49-0.76, P < 0.001) were strongly synchronized across all 6 distance intervals. Visual inspection of time series in the wild turkey fall harvest suggests that populations may be synchronized in some years when weather promotes high reproductive success (i.e., a synchronized growth peak) and asynchronous in other years. Knowledge of the spatial dynamics of wild turkey populations will aid wildlife managers in estimating population change, setting harvest quotas, and managing habitat.     

Uneven Rates of Landscape Change as a Source of Bias in Roadside Wildlife Surveys

ABSTRACT Roadside survey data have been used frequently to assess species occurrence and population trends and to establish conservation priorities. However, most studies using such data assume that samples are representative of either the amount of habitat or its rate of change at larger spatial scales. We tested both of these assumptions for the Breeding Bird Survey (BBS) from 1974 to 2001 in New Brunswick, Canada. Our study focused on mature forest—a cover type that we predicted would be characterized by rapid change due to human activities and that is of high ecological importance. We also sought to determine whether land cover changes adjacent to BBS routes were related to bird population trends detected in BBS data. Within all 3 time periods examined (1970s, 1980s, and 1990s), the amount of mature forest adjacent to BBS routes was significantly lower than in surrounding 1° blocks of latitude and longitude. This could be problematic for studies that use roadside data to compare the relative abundance of species. On average, mature forest declined at a rate of-1.5% per year over the 28-year study period. We detected no significant difference in the rate of change between degree blocks and BBS routes over this time span. However, in the 1970s and 1980s, mature forest declined more rapidly in degree blocks (-2.7%/yr) than adjacent to BBS routes (-0.5/yr). We also found that the BBS trend for a mature forest-associated species, blackburnian warbler (Dendroica fusca), was correlated with the trend in mature forest along BBS routes. This, combined with slower rates of mature forest change along routes in the 1970s and 1980s, suggests that BBS data may have underestimated population declines during this period. It is important that research be conducted to test for potential biases in roadside surveys caused by uneven rates of landscape change, particularly in regions characterized by rapid habitat alteration.     

Survival of Rio Grande Wild Turkeys on the Edwards Plateau of Texas

Abstract: The southeastern portion of the Edwards Plateau of Texas, historically a stronghold of Rio Grande wild turkeys (Meleagris gallopavo intermedia), has seen a decline in turkey numbers since the 1970s. Because adult and juvenile survival are key parameters affecting turkey population dynamics, we used radiotagged individuals to compare Rio Grande wild turkey survival in areas of suspected decline versus stable portions of the Edwards Plateau during 2001–2003. Reproductive period (breeding or nonbreeding) had an impact on survival, but differences in age, sex, or region did not influence survival. Model averaged estimates of monthly survival were 0.97 (SE = 0.005) for nonbreeding periods and 0.96 (SE = 0.007) for breeding periods. Our results indicate juvenile and adult survival in the declining areas was similar to survival in the stable areas of the Edwards Plateau. This suggests causes of the decline might be associated with differences during other life-history stages, such as nest success or poult survival, although we cannot rule out the possibility juvenile or adult survival contributed to the decline in the past. This situation demonstrates why wildlife managers should be cognizant of the implications of initiating long-term monitoring programs after changes in population status occur, rather than initiating them in expectation of such changes.     

Sandhill Crane Abundance and Nesting Ecology at Grays Lake,Idaho

Abstract: We examined population size and factors influencing nest survival of greater sandhill cranes (Grus canadensis tabida) at Grays Lake National Wildlife Refuge, Idaho, USA, during 1997–2000. Average local population of cranes from late April to early May, 1998–2000, was 735 cranes, 34% higher than that reported for May 1970–1971. We estimated 228 (SE = 30) nests in the basin core (excluding renests), 14% higher than a 1971 estimate. Apparent nest success in our study (x̄ = 60%, n = 519 nests) was lower than reported for Grays Lake 30–50 years earlier. Daily survival rates (DSRs) of all nests averaged 0.9707 (41.2%). The best model explaining nest survival included year and water depth and their interaction. Nest survival was highest (DSR = 0.9827) in 1998 compared with other years (0.9698-0.9707). Nest survival changed little relative to water depth in 1998, when flooding was extensive and alternative prey (microtines) irrupted, but declined markedly with lower water levels in 2000, the driest year studied. Hypotheses relating nest survival to vegetation height, land use (idle, summer grazing, fall grazing), and date were not supported. In a before-after-control-impact design using 12 experimental fields, nest survival differed among years but not among management treatments (idle, fall graze, fall burn, and summer—graze—idle rotation), nor was there an interaction between year and treatments. However, DSRs in fall-burn fields declined from 0.9781 in 1997–1998 to 0.9503 in 1999–2000 (posttreatment). Changes in the predator community have likely contributed to declines in nest success since the 1950s and 1970s. Our results did not support earlier concerns about effects of habitat management practices on crane productivity. Nest survival could best be enhanced by managing spring water levels. Managers should continue censuses during late April to evaluate long-term relationships to habitat conditions and management.     

Estimating and Correcting for Bias in Population Assessments of Sooty Shearwaters

Abstract: We investigated the precision and accuracy of an infrared burrowscope for detecting sooty shearwater (Pufffinus griseus) chicks at 13 plots from 3 islands in southern New Zealand in 2003. We partially excavated burrows systems to reveal the entire burrow contents after 2 teams of observers had prospected all burrow entrances. Accuracy was similar between islands and observer teams at approximately 85%. The majority of the inaccuracy stemmed from failure to detect some chicks. Logistic regression modeling identified 4 burrow characteristics occurring between the entrance and the nest-site that influenced detection of burrow occupants. Detection was lower at nest-sites further from burrow entrances, in burrows with a high rate of burrow division, and in burrows with a high level of curvature. There was a positive relationship between the interaction of rate of division and curvature and detection of chicks. Distance from the burrow entrance was the only parameter that could be reliably used as a predictor of detection rate, so a reduced model containing only this variable was constructed to correct for burrowscope bias. The correction factor performed well on The Snares and Bench Island where predicted bias was very similar to observed levels (within 5%), but bias was overestimated on Putauhinu by up to 19.1%. Consistent bias, lack of damage to burrows from excavation, and the successful application of a correction factor all indicate the value of further testing burrowscope accuracy on other burrow-nesting seabird species.