
Joseph A E StewartUniversity of California, Davis | UCD · Department of Plant Sciences
Joseph A E Stewart
PhD
About
57
Publications
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Introduction
I'm a quantitative conservation biologist with a special interest in biogeography, climate change, genetic-environment interactions, and prediction. My current projects focus on reforestation. Where and when is reforestation prudent after wildfires? When managers opt for reforestation what seed sources will be best adapted to current and future climates?
web: ReforestationTools.org | StewartEcology.org
Additional affiliations
September 2013 - August 2018
September 2011 - April 2013
Publications
Publications (57)
Aim
The American pika ( Ochotona princeps ) appears to have experienced climate‐mediated upslope range contraction in the Great Basin of North America, but this result has not yet been extended to other portions of the pika's range. Our goals were: first, to determine the environmental parameters that most influence current pika distribution within...
Extreme weather events can provide unique opportunities for testing models that predict the effect of climate change. Droughts of increasing severity have been predicted under numerous models, thus contemporary droughts may allow us to test these models prior to the onset of the more extreme effects predicted with a changing climate. In the third y...
Contemporary climate change has been widely documented as the apparent cause of range contraction at the edge of many species distributions but documentation of climate change as a cause of extirpation and fragmentation of the interior of a species’ core habitat has been lacking. Here, we report the extirpation of the American pika (Ochotona prince...
Large, severe fires are becoming more frequent in many forest types across the western United States and have resulted in tree mortality across tens of thousands of hectares. Conifer regeneration in these areas is limited because seeds must travel long distances to reach the interior of large burned patches and establishment is jeopardized by incre...
We used machine learning models to produce remotely sensed maps of aspen (Populus tremuloides) percent cover in the broader Lake Tahoe area (BLTA). Aspen is an important ecological and cultural resource both sensitive to and dependent on wildfire, and also vulnerable to climate change. Elsewhere in its range aspen declines have been well documented...
Declines and extirpations of American pika ( Ochotona princeps) populations at historically occupied sites started being documented in the literature during the early 2000s. Commensurate with global climate change, many of these losses at peripheral and lower elevation sites have been associated with changes in ambient air temperature and precipita...
Given increasing forest disturbances, novel solutions are needed to rapidly recover ecosystem services such as carbon storage, while bolstering climate change adaptation. Reforestation with single-species mixed-provenance plantings is an emerging strategy that may enhance stand productivity and disturbance resistance, while assisted gene flow is a...
Wildfires may facilitate climate tracking of forest species moving upslope or north in latitude. For subalpine tree species, for which higher elevation habitat is limited, accelerated replacement by lower elevation montane tree species following fire may hasten extinction risk. We used a dataset of postfire tree regeneration spanning a broad geogra...
Contemporary climate change is modifying the distribution, morphology, phenology, physiology, evolution, and interspecific interactions of species. Effects of climate change are mediated not only through the magnitude of change experienced (exposure) and an animal's sensitivity to such changes, but also through the ability of the population or spec...
The USDA Forest Service, in collaboration with the California Natural Resources Agency and other partners, is committed to increasing the “pace and scale” of forest treatments in California. Multiple federal and state initiatives in the last few years detail this commitment. The Forest Service developed the “Strategy for Shared Stewardship” (2018),...
High-resolution historical climate grids are readily available and frequently used as inputs for a wide range of regional management and risk assessments including water supply, ecological processes, and as baseline for climate change impact studies that compare them to future projected conditions. Because historical gridded climates are produced u...
As the world population grows, so does the demand for food, putting unprecedented pressure on agricultural lands. At the same time, climate change, soil degradation, and water scarcity mean that productivity of many of these lands is deteriorating. In many desert dryland regions, drinking wells are drying up and the land above them is sinking, soil...
Accounting for within-species variability in the relationship between occurrence and climate is essential to forecasting species’ responses to climate change. Few climate-vulnerability assessments explicitly consider intraspecific variation, and those that do typically assume that variability is best explained by genetic affinity. Here, we evaluate...
A recent global trend toward retirement of farmland presents opportunities to reclaim habitat for threatened and endangered species. We examine habitat restoration opportunities in one of the world’s most converted landscapes, California’s San Joaquin Desert (SJD). Despite the presence of 35 threatened and endangered species, agricultural expansion...
Summary of resurvey effort for two apparently extirpated historical record locations at or near the historical northern range margin of Gambelia sila.
(XLSX)
Comparison of realized climatic niches for Gambelia sila and all three species in the genus Gambelia.
Other members of the genus occupy hotter and drier environments than are available to G. sila in the San Joaquin Desert (see also S2 Fig). Occurrence data were thinned to one record per 30-arcsecond climate grid cell. Climate data were extracted fr...
Ensemble habitat suitability surfaces generated for this study.
Zipped file includes GeoTIFF files representing continuous and binary historical habitat suitability for Gambelia sila (see text).
(ZIP)
Discussion of potential impact of climate change.
(PDF)
Hours of restriction during the breeding season (left) and hours of activity during the active season (right). Hours of restriction are average number of hours per day during the breeding season (AMJJ) that operative environmental temperatures are too hot for Gambelia sila to be active above ground. Hours of activity are number of hours per day dur...
Modeled change in habitat suitability over time for four future climate scenarios.
Climate scenarios were selected to represent a range of potential future conditions, combining two global circulation models with two emission scenarios. The global circulation models predict either a relatively hot and dry future (MIROC-ESM) or a relatively warm and...
Change in climatic niche of Gambelia sila from the historical era to modern era with respect to actual evapotranspiration (AET).
The distribution of all distinct G. sila record locations on intact habitat has shifted toward sites with lower AET from the historical (pre-1960) to modern (1995 or after) periods.
(TIFF)
Threatened, endangered, extinct, and extirpated species of the San Joaquin Desert.
List includes 42 species with occurrence records that fall within the boundary of the San Joaquin Desert (sensu Germano et al., 2011). SSC indicates a California species of special concern.
(XLSX)
Locations of some recent Gambelia sila habitat destruction.
This list is by no means comprehensive. It is a partial list of locations where the authors and collaborators have observed habitat loss in the course of other work duties. Examining historical aerial imagery in the vicinity of many of these disturbances reveals additional instances of hab...
Density plots for 11 candidate predictor variables.
Shown are Gambelia sila occurrence locations and background sampling locations used for parameterizing our models. Occurrence data was thinned to one record per 1-km grid cell. Old locations on developed habitat were not included.
(TIFF)
Habitat suitability in the Westlands Water District peaks on alkaline soils located in the western portions of the district.
Under a settlement negotiated with the federal government at least 405 km2 of farmland in Westlands Water District will be permanently retired, including 70–210 km2 of formerly suitable habitat for Gambelia sila. The thick bo...
Biases and critiques of previous species distribution models for San Joaquin Desert species.
(XLSX)
Information on 11 candidate predictor variables evaluated for their strength in determining habitat quality and distribution.
(XLSX)
Locations of Gambelia sila occurrence observed on retired agricultural lands.
Scars from former ploughing are clearly visible on aerial imagery of these sites.
(XLSX)
A recent global trend toward retirement of farmland presents opportunities to reclaim habitat for threatened and endangered species. We examine habitat restoration opportunities in one of the world’s most converted landscapes, California’s San Joaquin Desert (SJD). Despite the presence of 35 threatened and endangered species, agricultural expansion...
A recent global trend toward retirement of farmland presents opportunities to reclaim habitat for threatened and endangered species. We examine habitat restoration opportunities in one of the world’s most converted landscapes, California’s San Joaquin Desert (SJD). Despite the presence of 35 threatened and endangered species, agricultural expansion...
The American pika (Ochotona princeps) is a temperature-sensitive lagomorph reported to be in decline in warmer sites in California, Nevada and portions of Utah. Talus is used for denning and retreat habitat by the species. Climate envelope modeling and climate projections suggest the species' distribution will retract in coming decades-but other st...
Aim: Habitat loss has been the greatest historical driver of species extinctions. A recent global trend toward retirement of marginally productive agricultural lands presents opportunities to reclaim critical habitat for endangered species. We examine habitat restoration opportunities in the context of historical sources of habitat loss, including...
The US and Mexico share a common history in many areas, including language and culture. They face ecological changes due to the increased frequency and severity of droughts and rising energy demands; trends that entail economic costs for both nations and major implications for human well being. We describe an ongoing effort by the Environment Worki...
Snow depth measurements for weather station at Tahoe City, CA, USA.
Snow depth has decreased significantly over the period of record for snowpack, 1911–2015 (Spearman’s test, p < 0.0005, N = 91), with significantly lower snow depth in the years following 1955 than the preceding years (Mann-Whitney test, p < 0.0005). The frequency of years with negl...
AICc model comparison for north Lake Tahoe area sites.
AICc model comparison of 10 models of pika site occupancy in the north Lake Tahoe area. MST_min_1k is minimum mean summer temperature within 1 km of the site centroid; log_talus_area is log transformed talus area within 1 km of the site centroid.
(XLSX)
Graphical comparison of pika occupancy models.
Formerly occupied Pluto triangle sites (N = 13) plotted against the California-wide model of pika occupancy (Stewart et al. [27]). Horizontal axis is refugial (minimum) MST within 1 km, following the California-wide model. Vertical axis is area of talus habitat within 1 km of the site centroid. Central...
Locations and data for north Lake Tahoe area talus surveys.
Pika sign abbreviations: A–audio detection, GH–green haypile, FP–fresh pellets, BP–buried pellets (found in accumulations of organic debris), SP–surface pellets, not fresh (found on rock surfaces below other rocks), V–visual detection. Occurrence coordinates for survey data provided by the...
Pika occupancy status at north Lake Tahoe area pika sites as a function of the best performing predictor variable.
North Lake Tahoe area pika sites are shown in Fig 1 and listed in S1 Table (N = 38). Extant and extirpated sites differentiate perfectly by this metric (Welch’s t-test, p < 0.005). Four kilometers represents a threshold above which pik...
Radiocarbon data for buried pika scat.
Uncertainty is expressed as standard deviation. Calibrated age ranges represent 95% confidence intervals.
(XLSX)
Recent climate change should result in expansion of species to northern or high elevation
range margins,
Recent climate change should result in expansion of species to northern or high elevation range margins, and contraction at southern and low elevation margins in the northern hemisphere,
because of local extirpations or range shifts or both. We combined museum occurrence records from both the continental U.S. and Mexico with a new eco-physiological...
Recent climate change should result in expansion of species to northern or high elevation range margins, and contraction at southern and low elevation margins due to extinction. Climate models predict dramatic extinctions and distributional shifts in the next century, but there are few ground-truths of these dire forecasts leading to uncertainty in...
We report findings from the first statistically representative, geospatially randomized assessment of high elevation species occupancy in the northern Sierra Nevada. We assessed species occupancy and habitat characteristics in three focal community types: meadows, talus, and conifer. We emphasized surveys for and analysis of three focal species tha...
Table of surveyed localities and winter precipitation.
Binary data in column titled “Neonates observed in 2014” indicates neonates observed (= 1) or not observed (= 0). “ns” indicates we found no record of surveys conducted for neonates in past 3 years.
(XLSX)
Table of data used in model selection analysis.
(XLSX)
The American pika (Ochotona princeps) appears to have experienced a substantial upslope range contraction in the Great Basin in response to climate warming. In California, models predict range contraction, but whether the species' lower elevational limit has already shifted remains unclear. We located and determined current occupancy at 19 historic...
Background/Question/Methods
The American pika (Ochotona princeps) has been flagged as a bellwether of climate warming. To determine if the species has suffered climate-mediated upslope range retreat in California, researchers have resurveyed historical pika record locations. However, historical pika surveys did not attempt to capture the species’...
Riparian Vegetation exists in a unique environment characterized by frequent disturbance, spatial and temporal environmental heterogeneity, and abundant water supply. Riparian areas are important due to their disproportionately strong influences on both in stream and terrestrial ecosystems. Because of the importance of riparian areas, scientists an...
Questions
Question (1)
I was recently surprised to discover that a research article published by a reputable journal had not undergone peer review--it was simply accepted by the associate editor without outside peer review. Furthermore, the lack of peer review is not identified or stated anywhere, leaving the unsuspecting reader to assume that the article underwent the same peer-review process as other articles published by the journal. The journal is part of Oxford University Press which is a member of the Committee on Publication Ethics (COPE). The Journal's website states that manuscripts "will be sent to one or more outside reviewers." The COPE code of conduct states that non-peer-reviewed sections of the journals should be clearly identified. So it seems the journal deviated from both their description of their peer review process and from the COPE code of conduct.
My questions are:
* How common is it for research papers to be published without peer review?
* When research papers are published without peer review is this fact usually clearly identified?