Using Publicly Available Forest Inventory Data in Climate-Based Models of Tree Species Distribution: Examining Effects of True Versus Altered Location Coordinates

Species distribution models (SDMs) were built with US Forest Inventory and Analysis (FIA) publicly available plot coordinates, which are altered for plot security purposes, and compared with SDMs built with true plot coordinates. Six species endemic to the western US, including four junipers (Juniperus deppeana var. deppeana, J. monosperma, J. occidentalis, J. osteosperma) and two piñons (Pinus edulis, P. monophylla), were analyzed. The presence–absence models based on current climatic variables were generated over a series of species-specific modeling extents using Random Forests and applied to forecast climatic conditions. The distributions of predictor variables sampled with public coordinates were compared to those sampled with true coordinates using t tests with a Bonferroni adjustment for multiple comparisons. Public- and true-based models were compared using metrics of classification accuracy. The modeled current and forecast distributions were compared in terms of their overall areal agreement and their geographic mean centroids. Comparison of the underlying distributions of predictor variables sampled with true versus public coordinates did not indicate a significant difference for any species at any extent. Both the public- and true-based models had comparable classification accuracies across extent for each species, with the exception of one species, J. occidentalis. True-based models produced geographic distributions with smaller areas under current and future scenarios. The greatest areal difference occurred in the species with the lowest modeled accuracies (J. occidentalis), and had a forecast distribution which diverged severely. The other species had forecast distributions with similar magnitudes of modeled distribution shifts.     

Hybrid Speciation in a Marine Mammal: The Clymene Dolphin (Stenella clymene)

Natural hybridization may result in the exchange of genetic material between divergent lineages and even the formation of new taxa. Many of the Neo-Darwinian architects argued that, particularly for animal clades, natural hybridization was maladaptive. Recent evidence, however, has falsified this hypothesis, instead indicating that this process may lead to increased biodiversity through the formation of new species. Although such cases of hybrid speciation have been described in plants, fish and insects, they are considered exceptionally rare in mammals. Here we present evidence for a marine mammal, Stenella clymene, arising through natural hybridization. We found phylogenetic discordance between mitochondrial and nuclear markers, which, coupled with a pattern of transgressive segregation seen in the morphometric variation of some characters, support a case of hybrid speciation. S. clymene is currently genetically differentiated from its putative parental species, Stenella coerueloalba and Stenella longisrostris, although low levels of introgressive hybridization may be occurring. Although non-reticulate forms of evolution, such as incomplete lineage sorting, could explain our genetic results, we consider that the genetic and morphological evidence taken together argue more convincingly towards a case of hybrid speciation. We anticipate that our study will bring attention to this important aspect of reticulate evolution in non-model mammal species. The study of speciation through hybridization is an excellent opportunity to understand the mechanisms leading to speciation in the context of gene flow.     

Low Incidence of Chest Wall Pain with a Risk-Adapted Lung Stereotactic Body Radiation Therapy Approach Using Three or Five Fractions Based on Chest Wall Dosimetry

Purpose

To examine the frequency and potential of dose-volume predictors for chest wall (CW) toxicity (pain and/or rib fracture) for patients receiving lung stereotactic body radiotherapy (SBRT) using treatment planning methods to minimize CW dose and a risk-adapted fractionation scheme.

Methods

We reviewed data from 72 treatment plans, from 69 lung SBRT patients with at least one year of follow-up or CW toxicity, who were treated at our center between 2010 and 2013. Treatment plans were optimized to reduce CW dose and patients received a risk-adapted fractionation of 18 Gy×3 fractions (54 Gy total) if the CW V30 was less than 30 mL or 10–12 Gy×5 fractions (50–60 Gy total) otherwise. The association between CW toxicity and patient characteristics, treatment parameters and dose metrics, including biologically equivalent dose, were analyzed using logistic regression.

Results

With a median follow-up of 20 months, 6 (8.3%) patients developed CW pain including three (4.2%) grade 1, two (2.8%) grade 2 and one (1.4%) grade 3. Five (6.9%) patients developed rib fractures, one of which was symptomatic. No significant associations between CW toxicity and patient and dosimetric variables were identified on univariate nor multivariate analysis.

Conclusions

Optimization of treatment plans to reduce CW dose and a risk-adapted fractionation strategy of three or five fractions based on the CW V30 resulted in a low incidence of CW toxicity. Under these conditions, none of the patient characteristics or dose metrics we examined appeared to be predictive of CW pain.     

The hTH-GFP Reporter Rat Model for the Study of Parkinson's Disease

Parkinson disease (PD) is the second leading neurodegenerative disease in the US. As there is no known cause or cure for PD, researchers continue to investigate disease mechanisms and potential new therapies in cell culture and in animal models of PD. In PD, one of the most profoundly affected neuronal populations is the tyrosine hydroxylase (TH)-expressing dopaminergic (DA) neurons of the substantia nigra pars compacta (SNpc). These DA-producing neurons undergo degeneration while neighboring DA-producing cells of the ventral tegmental area (VTA) are largely spared. To aid in these studies, The Michael J. Fox Foundation (MJFF) partnered with Thomas Jefferson University and Taconic Inc. to generate new transgenic rat lines carrying the human TH gene promoter driving EGFP using a 11 kb construct used previously to create a hTH-GFP mouse reporter line. Of the five rat founder lines that were generated, three exhibited high level specific GFP fluorescence in DA brain structures (ie. SN, VTA, striatum, olfactory bulb, hypothalamus). As with the hTH-GFP mouse, none of the rat lines exhibit reporter expression in adrenergic structures like the adrenal gland. Line 12141, with its high levels of GFP in adult DA brain structures and minimal ectopic GFP expression in non-DA structures, was characterized in detail. We show here that this line allows for anatomical visualization and microdissection of the rat midbrain into SNpc and/or VTA, enabling detailed analysis of midbrain DA neurons and axonal projections after toxin treatment in vivo. Moreover, we further show that embryonic SNpc and/or VTA neurons, enriched by microdissection or FACS, can be used in culture or transplant studies of PD. Thus, the hTH-GFP reporter rat should be a valuable tool for Parkinson''s disease research.     

Positive Reinforcement Training for a Trunk Wash in Nepal's Working Elephants: Demonstrating Alternatives to Traditional Elephant Training Techniques

Many trainers of animals in the zoo now rely on positive reinforcement training to teach animals to voluntarily participate in husbandry and veterinary procedures in an effort to improve behavioral reliability, captive management, and welfare. However, captive elephant handlers in Nepal still rely heavily on punishment- and aversion-based methods. The aim of this project was to determine the effectiveness of secondary positive reinforcement (SPR) in training free-contact elephants in Nepal to voluntarily participate in a trunk wash for the purpose of tuberculosis testing. Five female elephants, 4 juveniles and 1 adult, were enrolled in the project. Data were collected in the form of minutes of training, number of offers made for each training task, and success rate for each task in performance tests. Four out of 5 elephants, all juveniles, successfully learned the trunk wash in 35 sessions or fewer, with each session lasting a mean duration of 12 min. The elephants' performance improved from a mean success rate of 39.0% to 89.3% during the course of the training. This study proves that it is feasible to efficiently train juvenile, free-contact, traditionally trained elephants in Nepal to voluntarily and reliably participate in a trunk wash using only SPR techniques.     

Species distribution models for invasive Eurasian watermilfoil highlight the importance of data quality and limitations of discrimination accuracy metrics

AimAvailability of uniformly collected presence, absence, and abundance data remains a key challenge in species distribution modeling (SDM). For invasive species, abundance and impacts are highly variable across landscapes, and quality occurrence and abundance data are critical for predicting locations at high risk for invasion and impacts, respectively. We leverage a large aquatic vegetation dataset comprising point‐level survey data that includes information on the invasive plant Myriophyllum spicatum (Eurasian watermilfoil) to: (a) develop SDMs to predict invasion and impact from environmental variables based on presence–absence, presence‐only, and abundance data, and (b) compare evaluation metrics based on functional and discrimination accuracy for presence–absence and presence‐only SDMs.LocationMinnesota, USA.MethodsEurasian watermilfoil presence–absence and abundance information were gathered from 468 surveyed lakes, and 801 unsurveyed lakes were leveraged as pseudoabsences for presence‐only models. A Random Forest algorithm was used to model the distribution and abundance of Eurasian watermilfoil as a function of lake‐specific predictors, both with and without a spatial autocovariate. Occurrence‐based SDMs were evaluated using conventional discrimination accuracy metrics and functional accuracy metrics assessing correlation between predicted suitability and observed abundance.ResultsWater temperature degree days and maximum lake depth were two leading predictors influencing both invasion risk and abundance, but they were relatively less important for predicting abundance than other water quality measures. Road density was a strong predictor of Eurasian watermilfoil invasion risk but not abundance. Model evaluations highlighted significant differences: Presence–absence models had high functional accuracy despite low discrimination accuracy, whereas presence‐only models showed the opposite pattern.Main conclusionComplementing presence–absence data with abundance information offers a richer understanding of invasive Eurasian watermilfoil''s ecological niche and enables evaluation of the model''s functional accuracy. Conventional discrimination accuracy measures were misleading when models were developed using pseudoabsences. We thus caution against the overuse of presence‐only models and suggest directing more effort toward systematic monitoring programs that yield high‐quality data.     

A Comparison of Leaf Anatomy in Field-grown Gossypium hirsutum and G. barbadense

Gossypium hirsutum L. (upland cotton) and G. barbadense L. (Pimacotton) are two of the most important fibre producing cottonspecies in cultivation. When grown side-by-side in the field,G.hirsutum has higher photosynthetic and transpiration rates (Luet al., 1997. Australian Journal of Plant Physiology24: 693–700).The present study was undertaken to determine if the differencesin physiology can be explained by leaf and canopy morphologyand anatomy. Scanning electron microscopy was used to comparethe leaf anatomy of field-grown upland (‘Delta’and ‘Pine Land 50’) and Pima (‘S6’)cotton. Compared to G. hirsutum, mature leaves of G. barbadenseare larger and thinner, with a thinner palisade layer. G. barbadenseleaves show significant cupping or curling which allows fora more even absorption of insolation over the course of theday and much more light penetration into the canopy. AlthoughG. barbadense leaves have a 70–78% higher stomatal densityon both the abaxial and the adaxial surfaces, its stomates areonly one third the size of those of G. hirsutum. This resultsin G. barbadense having only about 60% of the stomatal surfacearea per leaf surface area compared to G. hirsutum. These resultsare indicative of the anatomical and physiological differencesthat may limit the yield potential of G. barbadense in certaingrowing environments. Copyright 2000 Annals of Botany Company Cotton, leaf anatomy, leaf development, photosynthesis, Gossypium hirsutum, Gossypium barbadense, stomatal density     

REPRODUCTIVE RATES OF HUMPBACK WHALES OFF CALIFORNIA

From 1986 to 1996 we examined the reproductive rates, calving rates, and reproductive histories of mature females as part of photo-identification studies of humpback whales that feed off California, Oregon, and Washington during summer and fall. Annual reproductive rates were measured by two methods: proportion of all whales that were calves based on sightings (0.6%-5.9% per year, mean = 3.6%, SD = 1.6) and based on individually identified animals (1.1%-8.0% per year, mean = 4.1%, SD = 1.8). The reproductive rate based on sightings varied significantly by year ( G test, P < 0.001), region ( G test, P < 0.001), and by month ( G test, P < 0.05). Seventy-nine sexually mature females were identified with 97 calves out of a total of 844 known individuals over the 11-yr study. Mother-calf separation on the feeding grounds was recorded in several instances. The apparent reproductive rates of this population are considerably lower than rates of 4%–15% reported from other feeding areas for this species. Our estimates are likely biased downward because this population has been increasing at about 5% per year. Calves may have been missed due to early weaning and because of our sampling from small boats late in the season. We also found evidence of geographic segregation of mother-calf pairs within our large study area. Despite these factors, we conclude the reproductive rate of this population appears to be lower than has been reported in other areas.     

Health status among prehistoric Eskimos from Point Hope,Alaska

Using the protocol outlined in The Backbone of History: Health and Nutrition in the Western Hemisphere (BBH) (Steckel and Rose. 2002a. The backbone of history: health and nutrition in the Western Hemisphere. Cambridge: Cambridge University Press), this project compares the Mark I Health Index (MIHI) scores of the Ipiutak (n = 76; 100BCE–500CE) and Tigara (n = 298; 1200–1700CE), two samples of North American Arctic Eskimos excavated from Point Hope, Alaska. Macroscopic examination of skeletal remains for evidence of anemia, linear enamel hypoplasias (LEH), infection, trauma, dental health, and degenerative joint disease (DJD) was conducted to assess differences in health status resulting from a major economic shift at Point Hope. These data demonstrate that despite differences in settlement pattern, economic system, and dietary composition, the MIHI scores for the Ipiutak (82.1) and Tigara (84.6) are essentially equal. However, their component scores differ considerably. The Ipiutak component scores are suggestive of increased prevalence of chronic metabolic and biomechanical stresses, represented by high prevalence of nonspecific infection and high frequencies of DJD in the hip/knee, thoracic vertebrae, and wrists. The Tigara experienced more acute stress, evidenced by higher prevalence of LEH and trauma. Comparison of overall health index scores with those published in BBH shows the MIHI score for the Ipiutak and Tigara falling just above the average for sites in the Western Hemisphere, adding support to the argument that the human capacity for cultural amelioration of environmental hardships is quite significant. Am J Phys Anthropol, 2011. © 2011 Wiley‐Liss, Inc.