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Museum specimen data reveal emergence of a plant disease may be linked to increases in the insect vector population


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The emergence rate of new plant diseases is increasing due to novel introductions, climate change, and changes in vector populations, posing risks to agricultural sustainability. Assessing and managing future disease risks depends on understanding the causes of contemporary and historical emergence events. Since the mid-1990s, potato growers in the western United States, Mexico, and Central America have experienced severe yield loss from Zebra Chip disease and have responded by increasing insecticide use to suppress populations of the insect vector, the potato psyllid, Bactericera cockerelli (Hemiptera: Triozidae). Despite the severe nature of Zebra Chip outbreaks, the causes of emergence remain unknown. We tested the hypotheses that 1) B. cockerelli occupancy has increased over the last century in California and 2) such increases are related to climate change, specifically warmer winters. We compiled a dataset of 87,000 museum specimen occurrence records across the order Hemiptera collected between 1900 and 2014. We then analyzed changes in B. cockerelli distribution using a hierarchical occupancy model using changes in background species lists to correct for collecting effort. We found evidence that B. cockerelli occupancy has increased over the last century. However, these changes appear to be unrelated to climate changes, at least at the scale of our analysis. To the extent that species occupancy is related to abundance, our analysis provides the first quantitative support for the hypothesis that B. cockerelli population abundance has increased, but further work is needed to link B. cockerelli population dynamics to Zebra Chip epidemics. Finally, we demonstrate how this historical macro-ecological approach provides a general framework for comparative risk assessment of future pest and insect vector outbreaks. This article is protected by copyright. All rights reserved.
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Museum specimen data reveal emergence of a plant disease may
be linked to increases in the insect vector population
Berkeley Initiative for Global Change Biology, University of California Berkeley,
3101 Valley Life Sciences Building, Berkeley, California 94720 USA
Department of Environmental Science, Policy, and Management, University of California Berkeley,
130 Mulford Hall, Berkeley, California 94720 USA
Stony Brook University, 650 Life Sciences Building, Stony Brook, New York 11789 USA
Department of Mathematics and Statistics, Williams College, Williamstown, Massachusetts 01267 USA
Essig Museum of Entomology, University of California Berkeley, 1101 Valley Life Sciences Building, Berkeley, California 94720 USA
Abstract. The emergence rate of new plant diseases is increasing due to novel introduc-
tions, climate change, and changes in vector populations, posing risks to agricultural sustain-
ability. Assessing and managing future disease risks depends on understanding the causes of
contemporary and historical emergence events. Since the mid-1990s, potato growers in the
western United States, Mexico, and Central America have experienced severe yield loss from
Zebra Chip disease and have responded by increasing insecticide use to suppress populations
of the insect vector, the potato psyllid, Bactericera cockerelli (Hemiptera: Triozidae). Despite
the severe nature of Zebra Chip outbreaks, the causes of emergence remain unknown. We
tested the hypotheses that (1) B. cockerelli occupancy has increased over the last century in
California and (2) such increases are related to climate change, specifically warmer winters. We
compiled a data set of 87,000 museum specimen occurrence records across the order Hemi-
ptera collected between 1900 and 2014. We then analyzed changes in B. cockerelli distribution
using a hierarchical occupancy model using changes in background species lists to correct for
collecting effort. We found evidence that B. cockerelli occupancy has increased over the last
century. However, these changes appear to be unrelated to climate changes, at least at the scale
of our analysis. To the extent that species occupancy is related to abundance, our analysis pro-
vides the first quantitative support for the hypothesis that B. cockerelli population abundance
has increased, but further work is needed to link B. cockerelli population dynamics to Zebra
Chip epidemics. Finally, we demonstrate how this historical macro-ecological approach
provides a general framework for comparative risk assessment of future pest and insect vector
Key words: Bayesian analysis; Candidatus Liberibacter solanacearum; list length analysis; NIMBLE;
occupancy model; opportunistic ecological data.
The emergence rate of novel infectious diseases of
humans, wildlife, and plants has increased dramatically
in recent decades (Anderson et al. 2004, Jones et al.
2008). For plant diseases, the majority of recent out-
breaks have been caused by the introduction of patho-
gens into new areas, but climate change and agricultural
change have also been implicated in recent emergence
events (Anderson et al. 2004). For vector-borne plant
pathogens, these same processes could also cause disease
outbreaks indirectly through changes in vector popula-
tions: evolutionary, numerical, or both (Anderson et al.
2004, Canto et al. 2009, Fereres 2015). Improved under-
standing of the causes of disease outbreaks is critical for
managing current epidemics and for assessing risks of
future ones (Garrett et al. 2011).
Climate change has the potential to exacerbate agri-
cultural disease risk in the near future and has already
caused contemporary outbreaks (Anderson et al. 2004,
Garrett et al. 2011). Much of the work on agricultural
pest and disease risks from climate change has relied on
a combination of small-scale experiments and modeling
to extrapolate experimental findings to larger scales
(Juroszek and von Tiedemann 2013). However, the mul-
tiple dimensions of climate change and the multitude of
biotic interactions have led to concerns about the rele-
vance of small-scale experiments (Van Der Putten et al.
2010, Juroszek and von Tiedemann 2013). At the same
time, historical macro-ecological analyses using long-
term data sets can contribute critical insight into the
possible role that climate change plays in contemporary
outbreaks amid the complexity of climatic variation and
interacting species (Jeger and Pautasso 2008).
Manuscript received 7 November 2016; revised 2 March
2017; accepted 12 April 2017. Corresponding Editor: Matthew
P. Ay r e s .
Ecological Applications, 27(6), 2017, pp. 18271837
©2017 by the Ecological Society of America
Beginning in the mid-1990s, potato growers in western
United States, Mexico, and Central America saw wide-
spread losses from the emergence of Zebra Chip disease,
caused by infections of the bacterial pathogen Candida-
tus Liberibacter solanacearum (Lso; =C. L. psyllau-
rous) (Munyaneza et al. 2007, Hansen et al. 2008).
Zebra Chip disease symptoms include plant stunting,
leaf scorching, and tuber necrosis, progressing eventually
to plant decline and death (Sengoda et al. 2009). Lso
also causes severe losses in tomato and pepper produc-
tion (Liu and Trumble 2006, Brown et al. 2010). Since
its emergence, the management of Lso has primarily
involved suppression of its vector, Bactericera cockerelli
(Sulc) (Hemiptera: Triozidae) or potato psyllid, through
insecticide use (Butler and Trumble 2012, Guenthner
et al. 2012).
Despite increasing harm to agricultural production
and the environment from ongoing Lso outbreaks and
increasing insecticide applications (Rosson et al. 2006,
Guenthner et al. 2012), the causes of Lso emergence
remain largely unknown. While B. cockerelli is native to
the western United States and Mexico, Zebra Chip
disease was first described in 1994 and Lso in 2008
(Munyaneza et al. 2007, Hansen et al. 2008). And while
other hypotheses warrant further investigation (see
Discussion), one dominant hypothesis has emerged: that
greater overwintering survival of northern B. cockerelli
populations is causing Zebra Chip outbreaks.
Historically, the range of B. cockerelli was thought to
be largely confined by its relatively narrow thermal toler-
ance and the availability of host plants. Pletsch (1947)
and Wallis (1955) hypothesized that populations were
limited in northern latitudes by cold winter temperatures,
a lack of host plants during winter, or both; these regions
would be subsequently colonized by populations migrat-
ing from the south in springtime. Beginning in 2011, pop-
ulations of B. cockerelli were found overwintering in
Oregon, Washington, and Idaho (Horton et al. 2015),
well beyond the specieshypothesized historic northern
limits (Wallis 1955), although a lack of historical moni-
toring leaves it unclear whether this represents a recent
range expansion. Greater overwintering survival of north-
ern populations would likely cause much greater densities
in potato fields earlier in potato plant development, when
plants are most susceptible to Lso infection (Gao et al.
2009). More generally, climate change is expected to
increase overwintering survival of insect herbivores across
temperate regions (Bale et al. 2002, Klapwijk et al. 2012).
Ecological theory predicts that increases in vector den-
sity can drive outbreaks of endemic pathogens. While the
relationship between vector density and host infection
prevalence is complex and rarely linear, it is generally a
positive relationship (Madden et al. 2000). Vector-borne
pathogens that are persistently and vertically transmitted,
which includes Lso (Hansen et al. 2008, Sengoda et al.
2014), should exhibit distinct epidemic thresholds across
a range of vector population densities (Jeger et al. 1998),
with the pathogen maintaining low prevalence in the host
population until vector populations reach very high den-
sities (Madden et al. 2000). Early work has failed to find
a relationship between adult B. cockerelli density and Lso
infection prevalence, but has found positive relationships
between late-stage nymph density, adult infection preva-
lence, and Zebra Chip disease prevalence (Goolsby et al.
2012, Workneh et al. 2013). Furthermore, contemporary
Lso infection prevalence in B. cockerelli populations
midwestern and northwestern United States (Goolsby
et al. 2012, Swisher et al. 2013). At such low infection
rates, very large vector populations may be required to
cause a disease epidemic.
While Zebra Chip disease was first described in the
1990s, there is some evidence that Lso has coexisted with
B. cockerelli for much longer than Zebra Chip disease
has been recognized (see Discussion). Historically, Zebra
Chip may have been confused with pathological effects
of B. cockerelli saliva, known as Psyllid Yellows disease,
first described in the 1920s (Richards 1928). Given that
visual foliar symptoms of Psyllid Yellows and Zebra
Chip disease are quite similar (Munyaneza et al. 2007,
Sengoda et al. 2009) and that Lso is unculturable, earlier
researchers may have observed a combination of patho-
logical effects from B. cockerelli saliva and Lso infec-
tion. As a result, it is possible that Lso is endemic to
North America, has only occasionally erupted in out-
breaks, such as the Psyllid Yellows outbreaks of the
1920s and 1930s and the contemporary Zebra Chip out-
breaks, but remained largely undetected otherwise.
In the present paper, we tested whether numerical
changes in B. cockerelli populations could explain the
emergence of Zebra Chip disease. Specifically, we
hypothesize that (1) B. cockerelli populations have
increased over the last century in California, USA and
(2) such increases are related to climate change, specifi-
cally higher winter temperatures. We tested these
hypotheses by fitting museum specimen occurrence data
and historical climate projections to a hierarchical occu-
pancy model. Interest in historical ecological data, such
as that from natural history collections, has increased in
recent years due to their value in assessing impacts of cli-
mate change on disease dynamics and other ecological
processes (Tingley and Beissinger 2009). For example,
previous studies have used museum specimens to chart
invasion of the Lymes disease pathogen, Borrelia
burgdorferi, in tick vector specimens (Persing et al.
1990), changes in pathogenic fungal populations related
to air pollution in wheat specimens (Bearchell et al.
2005), and historical prevalence of chytrid fungus in
amphibian populations (Ouellet et al. 2005). At the
same time, museum specimens were often opportunisti-
cally collected by a diverse set of professional and citizen
naturalists with different levels of expertise and effort
(Isaac and Pocock 2015). They also represent presence-
only occurrence data, with little or no information about
where a species was searched for but not found. As a
result, museum specimen occurrence data are rife with
1828 ADAM R. ZEILINGER ET AL. Ecological Applications
Vol. 27, No. 6
biases, making rigorous ecological inference difficult
(Newbold 2010).
Hierarchical statistical models and Bayesian analytical
methods have facilitated the analysis of opportunistically
collected ecological data by explicitly modeling the
observation process separate from the ecological process
(Isaac et al. 2014). For example, occupancy models com-
bine an ecological sub-model, relating the presence and
absence, or occupancy, of a focal species to a set of
covariates, with a detection sub-model that relates detec-
tion to a distinct set of covariates. Following previous
work, we generated non-detection data (i.e., absence
data) for B. cockerelli and corrected for variation in col-
lecting effort using list length analysis (Phillips et al.
2009, Szabo et al. 2010). List length analysis involves
compiling lists of related species collected in the same
time and place and using the length of these lists as a
proxy for collecting effort. Some lists will contain the
focal species while many others will not; these later lists
constitute non-detection data. Because list length acts as
a proxy for overall collecting effort (Roberts et al. 2007),
incorporating list length as a covariate into a detection
sub-model provides estimates of detection probability
for the focal species, i.e., longer lists without the focal
species are more likely than shorter lists to represent true
absences. Similar analyses have been used to detect
trends in bird populations (Link et al. 2006, Szabo et al.
2010, Barnes et al. 2015), butterfly and dragonfly popu-
lations (Van Strien et al. 2010, Breed et al. 2012), and
changes in owl prey populations (Van Strien et al. 2015).
Here we show that the analysis of museum specimen
occurrence data using Bayesian hierarchical models can
provide insights into the causes of recent outbreaks of
agricultural pests and disease vectors. Additionally, in
the Discussion we outline how such a historical macro-
ecological approach to the analysis of disease vector and
pest outbreaks could facilitate development of risk
assessment frameworks for future outbreaks.
Compiling species occurrence records
We first collected, digitized, and georeferenced all
pinned museum specimens of B. cockerelli from six
major California natural history museums: Bohart
Museum of Entomology, University of California Davis;
California Academy of Science, San Francisco; Califor-
nia State Collection of Arthropods (CSCA), Plant Pest
Diagnostics Center, California Department of Agricul-
ture; Essig Museum of Entomology, UC Berkeley; Los
Angeles County Museum of Natural History; and UC
Riverside Entomology Research Museum. For each col-
lection, we identified B. cockerelli specimens that had
not yet been determined to the species level, housed in
the Undetermined Psyllidaeor Undetermined Triozi-
daesections of the collections. We identified undeter-
mined specimens using the morphological description for
Paratrioza (=Bactericera)cockerelli in Tuthill (1945). We
also verified identification of a random subset of speci-
mens previously identified as B. cockerelli; all were con-
firmed correctly identified. We digitized all B. cockerelli
specimens, and georeferenced them using the point-
radius method of (Wieczorek et al. 2004) and the
GEOLocate web application.
In addition to pinned spec-
imens, we also included slide-mounted nymph specimens
from the Bohart Museum and records of ethanol-
preserved specimens from the Essig Museum. All georefer-
enced specimens, except for ethanol-preserved specimens,
were uploaded to the Essig Museum online database.
Our data set of B. cockerelli museum specimens repre-
sented presence-only data. To generate non-detection
data, we used the target-group background approach of
Phillips et al. (2009). When using presence-only data,
species distribution modeling requires the selection of
non-detection data, also known as background or
quadrature points in the spatial statistical literature
(Renner et al. 2015). Often non-detection points are
selected randomly or uniformly over the geographical or
environmental space of interest. However, Phillips et al.
(2009) selected non-detection points by using the pres-
ence of a larger set of related taxa (i.e., target group),
effectively reducing bias in the species distribution esti-
mates compared to uniform or random non-detection
selection methods.
We chose as our target group all species in the order
Hemiptera, excluding families that were predominantly
aquatic or carnivorous. The excluded families were Antho-
coridae, Belostomatidae, Cimicidae, Corixidae, Gelasto-
coridae, Geocoridae, Gerridae, Hebridae, Hydrometridae,
Leptopodidae, Macroveliidae, Mesoveliidae, Nabidae,
Naucoridae, Nepidae, Notonectidae, Ochteridae, Phymati-
dae, Pieidae, Polyctenidae, Reduviidae, Saldidae, and
Veliidae. The remaining families of Hemiptera are pre-
dominately (though not exclusively) composed of terres-
trial piercing-sucking herbivores and are likely to be
collected by entomologists in similar manners.
To generate our target group data set, we compiled
digitized and georeferenced California records of our
selected hemipteran families from three sources: the
Global Biodiversity Information Facility (GBIF; which
includes all records from the Essig Museum online data-
base), the American Museum of Natural History
(AMNH), and the CSCA database. An initial explo-
ration of these databases returned only 25 records of
B. cockerelli, far too few for analysis and thus requiring
the digitization and georeferencing of additional speci-
mens described above. In the CSCA database, we
included only records that were opportunistically col-
lected, excluding those that reported trap monitoring for
specific pest species. The data from the CSCA were
biased toward agricultural areas; however, this partially
balanced biases against agricultural areas in the GBIF
and AMNH data sets. Occurrence records were included
in our data set if they were collected within California
between 1900 and 2014, included the full species name,
and were georeferenced.
From our compiled records, we generated lists of spe-
cies collected across the same time and area of our
B. cockerelli records. To do so, we divided California
into 15 915 km grid cells and combined all species
records collected within the same spatial cell, month,
and year. This spatial resolution was similar to that pre-
viously used by Hill et al. (1999) to model changes in
distribution of butterfly distribution under climate
change. We included only lists with three or more spe-
cies, following methods of Van Strien et al. (2013), and
lists in which at least one collector had also collected a
B. cockerelli specimen in our data set. By filtering lists to
a set of common collectors, we reduced the influence of
collectors focused on only a single family or other taxon,
a common concern in the analysis of opportunistically
collected data (Isaac and Pocock 2015).
Climate data
Our aim was to model the temporal trends in
B. cockerelli occupancy and to test if these trends could
be explained by local-scale climate change. As such, we
compiled estimates of historical climate from the Califor-
nia Basin Characterization Model (BCM), which pro-
vides estimates of a range of temperature- and
precipitation-derived climatic indices at 270 9270 m
grid resolution for much of California on a monthly basis
from 1895 to 2014 (Flint et al. 2013, Flint and Flint
2014). For each species occurrence record in a list, we
extracted estimates of actual evapotranspiration (AET)
in the month of collection, the water-year annual mini-
mum temperature (T
,°C), and the water-year annual
maximum temperature (T
,°C). For annual minimum
and maximum temperatures, we extracted the minimum
temperature occurring in the most recent winter (Decem-
berFebruary) and most recent summer (JuneSeptem-
ber), respectively. Because our species lists were compiled
at a larger spatial cell size than the BCM cells, we
extracted the climate values for each occurrence record
within a list and then averaged these estimates to obtain
a list-level estimate of climate. The standard deviations
of these averages across lists were small for each of the
three climate variables (AET mean SD =2.08; T
SD =0.17; T
mean SD =0.26) relative to their stan-
dard deviations across all specimen records in the data
set (AET =35.71, T
=4.01, T
=5.86), indicating
that our averaging of climate variables at the list level did
not neglect significant within-list climatic variation.
AET is an estimate of the water available for plant
growth; it is a function of precipitation and temperature,
and is more biologically relevant than raw precipitation
estimates (Rapacciuolo et al. 2014). AET has been used
previously to successfully model changes in herbivorous
insect distributions from climate change (Hill et al.
1999). Additionally, historical descriptions of the distri-
bution of B. cockerelli indicate that the species primarily
occurs in arid and semiarid climates of the southwestern
and Rocky Mountain regions of the United States (Wallis
1955), which would be captured by estimates of AET. We
also considered incorporating estimates of climate water
deficit (CWD); however, AET and CWD were highly neg-
atively correlated within our data set and we thus opted
for keeping the former only (Appendix S1: Fig. S1).
We included annual T
because the prevailing
hypothesis explaining the emergence of Zebra Chip Dis-
ease is that B. cockerelli populations at the northern lim-
its of the species range have increased due to greater
overwintering survival (Wallis 1955, Horton et al. 2015).
If true, then B. cockerelli occupancy should be positively
associated with annual T
. Finally, we included annual
because of historical descriptions of B. cockerelli
phenology suggesting that southern populations are extir-
pated due to high summer temperatures (Romney 1939).
Statistical analyses
We modeled B. cockerelli occupancy using a hierarchi-
cal occupancy model, also known as a binomialbino-
mial mixture model, as described in Royle and K
(2007). This model explicitly models the observation or
detection process separately from the ecological or occu-
pancy processes that give rise to species occupancy pat-
terns and corrects for zero-inflation in our data set
(Martin et al. 2005). Importantly, however, our data did
not include repeated visits to a site. Rather, by using
non-overlapping sets of covariates for the two sub-
models, the occupancy and detection latent states were
identifiable (S
olymos et al. 2012). For the occupancy sub-
model, we included the year collected, AET, T
and a quadratic form for month collected. For the detec-
tion sub-model, we included list length and the interac-
tion between list length and year collected. We included
the interaction between list length and year to correct for
changes in the relationship between list length and occu-
pancy over time due to, e.g., changing collecting and pre-
serving technologies and collector expertise. List length
was natural-log-transformed (Szabo et al. 2010) and all
continuous covariates were standardized around the
mean and divided by the standard deviation. To incorpo-
rate spatial autocorrelation, we included the 15 915 km
spatial grid cells used to construct species lists as a ran-
dom effect in the occupancy sub-model. In other words,
lists that originated from the same location (i.e., spatial
grid cell) were assigned the same intercept. According to
the simulations of Isaac et al. (2014), occupancy models
with list length and a spatial random effect can be slightly
conservative, but are overall more robust to bias in
opportunistic occurrence data than other models.
We fit the occupancy model using the Markov chain
Monte Carlo (MCMC) engine provided with the NIM-
BLE package (version 0.6-3) for R 3.3.2 (NIMBLE
Development Team 2015, De Valpine et al. 2016, R Core
1830 ADAM R. ZEILINGER ET AL. Ecological Applications
Vol. 27, No. 6
Team 2016). MCMC speed and convergence were expe-
dited by making use of the flexibility of NIMBLE algo-
rithms. Latent states representing true (unknown) site
occupancy were analytically removed from the model
formulation using a custom-specified distribution, as
described in Turek et al. (2016). Block sampling was
used to jointly sample the coefficients of each linear pre-
dictor term within each sub-model, since these will gen-
erally exhibit strong posterior correlation (Roberts and
Sahu 1997). In addition, the standard deviation of site
random effects was sampled on a logarithmic scale using
the generalized Gibbs sampling framework described in
Liu and Sabatti (2000). We used uninformative priors
and three MCMC chains each with 150,000 iterations
and a burn-in period of 50,000. Convergence was veri-
fied by calculating Gelman-Rubin diagnostic and effec-
tive sample size (Gelman and Rubin 1992, Brooks and
Gelman 1998). R code for fitting models is available in; additional code for compiling and filtering
data and analyzing model output can be found at (
Our final data set of specimen records included 87,035
records of 2,840 species from 73 families; it also included
613 records of B. cockerelli. Specimens of all selected
Hemiptera were collected throughout California, with
the greatest number collected in the 1930s, 1960s, and
1970s (Fig. 1). Specimens of B. cockerelli were concen-
trated in southern California and arid interior regions of
the state; the majority of specimens were collected from
1950 to 1970 with the first and last B. cockerelli speci-
men collected in 1908 and 2011, respectively (Fig. 1).
From this specimen data set, we assembled 900 species
lists, which ranged in length from 3 to 40 species, 36 of
which contained B. cockerelli (Appendix S1: Fig. S2).
The MCMC chains successfully converged. Estimates
of the Gelman-Rubin diagnostic for all parameters were
1.1 and effective sample sizes of all parameters were
>1,000 (Table 1).
For the detection sub-model, list length was margin-
ally significant and positively related to probability of
detection, as was the list length 9year interaction
(Table 1, Fig. 2). The marginally significant interaction
term was likely due to a small but significant decline in
list length over time (Appendix S1: Fig. S3).
For the occupancy sub-model, the year main effect
was significant and positive (Table 1). However, none of
the climate variables were significant. The model pre-
dicts an increase in B. cockerelli probability of occu-
pancy in the late autumn/early winter in the 1950s and
increases in B. cockerelli throughout all seasons begin-
ning in the 1990s, with particularly high occupancy rates
in summers (Fig. 2).
We generated maps of the estimated occupancy proba-
bility over three different time periods: 19201945,
19501975, and 19902015 (Fig. 3), covering the
historical Psyllid Yellows outbreak, a non-outbreak per-
iod, and the contemporary outbreak period, respectively.
Although recent data are sparse, the model predicts an
overall increase in occupancy probability in southern
California in more recent years, with greater variation in
occupancy in early time periods.
Since emergence in the early 1990s, Zebra Chip disease
has devastated potato production in epidemic areas of
the United States, Mexico, and Central America (Secor
and Rivera-Varas 2004, Rosson et al. 2006, Horton et al.
FIG. 1. (a) Spatial and (b) temporal distribution of all
museum records (gray points and bars) and of Bactericera cock-
erelli museum records (black points and bars).
2015). For example, whereas Texas potato growers tradi-
tionally used few or no insecticides, growers currently
average over seven applications annually as a direct result
of Zebra Chip emergence (Goolsby et al. 2012, Guenth-
ner et al. 2012). Yet the causes of these outbreaks remain
unknown. Using museum specimen occurrence data and
a Bayesian occupancy model, we showed that occupancy
probability of the vector, B. cockerelli, has increased in
California over the last century.
Our analysis showed increasing occupancy probability
over the last century through a significant and positive
year main effect. However, sparse data weaken further
inference. Despite our initial large data set (>87,000 hemi-
pteran records and >600 B. cockerelli records), our final
data set consisted of 900 total species lists with only 36
containing B. cockerelli. The sharp reduction in data when
constructing the lists was due to a large number of single
species lists and to a large number of duplicate records,
which in each case reduces to a single detection event.
The reduced spatial coverage and total number of lists
in more recent decades, particularly in northern Califor-
nia, prevented us from testing for a potential northward
range expansion of B. cockerelli (Fig. 3). However, we
do not expect this decline in the number of records to
have influenced our main result of an overall increase in
occupancy probability for B. cockerelli over time.
Despite there being fewer lists in recent decades, the
proportion of those lists containing B. cockerelli, the
speciesreporting rate (Szabo et al. 2010), increased
markedly (Appendix S1: Fig. S4). This trend persists
after correcting for overall collecting effort and changes
in collecting effort over time, which we accounted for by
including a list length main effect and a list-length 9
year interaction effect in the detection sub-model.
In epidemiology of vector-borne pathogens, patterns of
vector occupancy are less relevant than patterns of vector
population dynamics for determining pathogen spread.
Nonetheless, occupancy probability over large spatial
scales is positively related to abundance (Gaston et al.
2000, Oliver et al. 2012, Guti
errez et al. 2013) except
when species exhibit very low colonization ability (Freck-
leton et al. 2005). Evidence suggests that B. cockerelli
exhibits high colonization ability (Nelson et al. 2014).
Thus, a positive occupancyabundance relationship
should hold and the increases in occupancy probability
that we detected should generally be associated with
increases in vector abundance. In future analyses, it may
be possible to treat duplicate species records as count
data and directly model abundance within a list length
analysis framework. However, theory relating species list
lengths to count data has not been developed and would
likely require additional statistical assumptions.
We had hypothesized that occupancy should be posi-
tively related to T
based on the previous literature
(Wallis 1955). While we found no evidence for an associ-
ation between T
and B. cockerelli occupancy, climate
change could influence B. cockerelli populations and
Lso emergence through processes beyond our present
analysis. Changes in degree-days are often more relevant
for insect development rates than annual minimum or
maximum temperatures (Bale et al. 2002). Recently,
Tran et al. (2012) showed that nymphs of B. cockerelli
ceased development and ~90% of individuals died at a
constant 8°C under laboratory conditions. In our data
set, T
reached below 8°C in 98% of all lists and 97%
of lists containing B. cockerelli. This apparent discrep-
ancy may be because the duration of cold temperatures
or the temperatures experienced over the entire develop-
mental period, as captured in degree-days, are more
important than the minimum temperature experienced
at a single point in time. We hope to incorporate degree-
days into future analyses.
Climate change could also influence B. cockerelli
populations indirectly. We hypothesized that any rela-
tionship between AET and B. cockerelli occupancy
would be mediated through changes in host plant popu-
lations. However, we found no evidence of a relationship
between AET and B. cockerelli occupancy. Explicitly
TABLE 1. Estimates of the Gelman-Rubin diagnostic, ^
r(with 97.5% credible intervals, CI), effective sample size (ESS), and
posterior mean (with 95% CI) for linear coefficients for Bactericera cockerelli occupancy model.
Model term ^
r(97.5% CI) ESS Mean [2.5% CI, 97.5% CI]
Year 1 (1) 2,268.39 50.4 [16.1, 95.4]
Month 1 (1) 2,976.61 1.88 [48.7, 53.9]
1 (1) 3,536.05 9.12 [40.9, 57.9]
AET 1 (1) 3,068.94 22.7 [73, 31.3]
1 (1) 2,470.83 13.6 [62.7, 35.2]
1 (1) 2,579.5 11.6 [62.9, 41.5]
Detection sub-model intercept 1 (1) 7,144.72 2.41 [2.86, 1.97]
List length 1 (1) 24,529.71 0.283 [0.0478, 0.595]
List length 9year 1 (1) 24,186.37 0.332 [0.0172, 0.701]
1 (1) 5,088.08 11 [65.6, 48.1]
1 (1.01) 1,219.42 271 [57.4, 868]
Notes: AET, actual evapotranspiration; T
, water-year annual minimum temperature; T
, water-year annual maximum
temperature; l
, mean of the spatial cell random effect; r
, variance of the spatial cell random effect.
Significant at 90% CI; significant at 95% CI.
1832 ADAM R. ZEILINGER ET AL. Ecological Applications
Vol. 27, No. 6
modeling changes in host plant occupancy in relation to
climatic variation and then relating host plant occu-
pancy to B. cockerelli occupancy, perhaps through a
joint distribution model, would be a more robust test.
Finally, beyond any effects on B. cockerelli, climate
change could contribute to Lso outbreaks by directly
influencing Lso populations or the interactions between
host plant, vector, and pathogen (Garrett et al. 2006).
Separate from climate change, B. cockerelli popula-
tion abundances may have increased through other
mechanisms. Horton et al. (2015) have hypothesized that
the outbreaks in the northwestern United States are
caused by invasion of a nonnative host plant, Solanum
dulcamara (Solanaceae), and concomitant adaptation by
B. cockerelli populations. More broadly, the role of wild
host plants in B. cockerelli population dynamics and
distribution remains an important area for future
research. Additionally, population or genetic differences
in B. cockerelli reproduction, development, and insecti-
cide resistance have been described by previous authors,
any of which could contribute to Zebra Chip emergence
(Liu and Trumble 2007, Mustafa et al. 2015a, b).
In a review of plant disease emergence events by
Anderson et al. (2004), pathogen introduction was the
FIG. 2. Occupancy model results. (a) Relationships between occupancy model-predicted probability of detection and list length,
(b) between model-predicted probability of B. cockerelli occupancy and year collected, and (c) the relationships of occupancy prob-
ability, year collected, and month collected. Trend lines on scatterplots are linear model fits to model-predicted probabilities. For
the contour plot (c), grayscale values indicate probability of occupancy.
most common cause of emergence. For Zebra Chip dis-
ease, introduction of Lso into North America remains a
possible but unlikely explanation. Lso has recently been
detected in Europe and is associated with the triozid spe-
cies Bactericera trigonica and Trioza apicalis (Munyaneza
et al. 2010, Teresani et al. 2014). However, the European
isolates appear to be genetically distinct from the North
American isolates and infect primarily non-solanaceous
host plants (Nelson et al. 2011, Lin and Civerolo 2014).
We also constructed a cladogram of available 16S rDNA
sequences that supports previous assertions that an intro-
duction of Lso from Europe to North America has not
occurred recently (Appendix S2). Future genetic analyses
of historical and contemporary samples would provide
critical insight into the origins of Lso. Importantly, none
of the above possible causes are mutually exclusive.
Rather, multiple factors may be contributing to the emer-
gence of Lso-associated diseases and may differ in rela-
tive importance in different epidemic areas.
Understanding the causes of plant disease outbreaks is
critical for integrated management of pathogens and vec-
tors (Garrett et al. 2011). Our analysis has been the first
to show an increase in B. cockerelli occupancy over
relatively large spatial and temporal scales. However, more
work is needed to link B. cockerelli population dynamics
and distribution to Lso spread, especially given the diffi-
culty of detecting a relationship at smaller scales (Goolsby
et al. 2012, Workneh et al. 2013). Just as importantly,
future work on the underlying causes of B. cockerelli
population expansion will aid in identifying conditions
that generate the greatest risk of future epidemics.
The potential that climate change could reduce
agricultural sustainability through pests and disease out-
breaks, and resulting increases in pesticide use, has
become an increasing concern for growers, scholars, and
other stakeholders. As with ecological risk assessment of
other stressors, a key challenge in the analysis of outbreak
risks from climate change remains to identify which pest
or pathogen species are most likely to become more prob-
lematic and through which risk pathways (USEPA 1998,
Garrett et al. 2011). Most work to date has approached
the problem mechanistically, focused on predicting out-
break risks by testing for changes in particular biotic
interactions or responses from species with different life
history traits under a subset of predicted climatic changes
(Juroszek and von Tiedemann 2013). However, the
FIG. 3. Maps of estimated B. cockerelli occupancy across California, USA for three selected time periods, (a) 19201945, (b)
19501975, and (c) 19902015. Solid circles indicate species lists containing B. cockerelli (i.e., detection events); open circles indicate
non-detection events. The size of the circle indicates the estimated probability of occupancy, with larger circles representing greater
probabilities. Occupancy probabilities were averaged over years for each site. Map coordinates are the same as in Fig. 1a.
TABLE 2. Estimated posterior means (with 95% credible intervals) of linear coefficients for occupancy model of Lygus hesperus,
Myzus persicae, and Rhopalosiphum padi occurrence using the same model and data set as for B. cockerelli occupancy.
Model term Lygus hesperus Myzus persicae Rhopalosiphum padi
Year 52.8 [81.7, 23.1]7.91 [66.9, 54.3] 13.2 [54.9, 37.2]
Month 8.91 [4.72, 29.5] 24.1 [77, 32.1] 20.8 [67, 31.3]
11.2 [29.2, 8.53] 7.34 [49.8, 38.8] 38.1 [12.9, 82.9]
AET 15.7 [0.0975, 36.8]28.3 [28.2, 81.3] 21.4 [20.1, 72.2]
21.7 [53.4, 1.39]1.6 [57.3, 58.5] 8.37 [57.8, 42.1]
13.9 [8.16, 33.9] 1.94 [54.1, 49.2] 3.02 [56.4, 57]
Detection intercept 1.44 [1.63, 1.24]5.79 [1.79, 22.2] 2.13 [2.59, 1.71]
List length 0.29 [0.124, 0.456]24.2 [0.611, 64.7]0.299 [0.0439, 0.641]
List length 9year 0.0424 [0.188, 0.102] 19.7 [55.4, 0.753] 0.0141 [0.32, 0.35]
65.2 [33.1, 99.5] 16.4 [76.1, 49.2] 17.9 [42.6, 74.3]
63.5 [26, 121] 352 [79.7, 920] 362 [38, 944]
Note: MCMC convergence diagnostics showed similarly good convergence as for the B. cockerelli occupancy model.
Significant at 90% CI; significant at 95% CI.
1834 ADAM R. ZEILINGER ET AL. Ecological Applications
Vol. 27, No. 6
complexity of biological responses to climate change
limits the realism of small-scale mechanistic studies.
Our analysis points to an additional, complementary
approach. Modeling changes in occupancy for a range
of pest and vector species within our data set may pro-
vide valuable comparative insights into which species
pose the greatest risk. As an example, we applied the
same occupancy model to detection and non-detection
data for three pest species that were well represented in
the data set: Lygus hesperus (Hemiptera: Miridae), a pest
of strawberries and cotton; Myzus persicae (Hemiptera:
Aphididae), a vector of potato leafroll virus; and
Rhopalosiphum padi (Hemiptera: Aphididae), a vector of
barley yellow dwarf virus. Our analysis indicates that
L. hesperus occupancy probability has significantly
decreased in California over the last century, and is mar-
ginally related to changes in AET and T
. In contrast,
occupancy probabilities of M. persicae and R. padi have
shown no clear pattern of change (Table 2). Our results
for R. padi are in line with those of the analysis of Davis
et al. (2014) for populations in the northwestern United
States; in both cases, R. padi distribution showed little
temporal trend and no relationship to climatic variation.
Although our analysis is spatially and temporally
coarse and ignores the roles of biotic interactions and
agricultural change, comparisons among species, using a
common data set and model, could facilitate more fine-
grain investigations into the specific mechanisms that
underlie large-scale differences among pest species and
their relationships to climatic variation. Linking fine-
scale studies of biotic interactions and life history traits
to macro-ecological analyses will be necessary to develop
rigorous assessment frameworks for the future risks of
pest and pathogen outbreaks caused by climate change.
We thank those who assisted us in sorting through and bor-
rowing specimens from entomological collections: Norm Penny,
California Academy of Sciences; Doug Yanega, UC Riverside
Entomology Research Museum; Lynn Kimsey, UC Davis
Bohart Museum of Entomology; Weiping Xie, LA County Nat-
ural History Museum; and Jackie Kishmirian, California State
Collection of Arthropods. Stephen Gaimari and Katja Selt-
mann helped with access to and filtering of the Plant Pest Diag-
nostic Center data and Christine Johnson helped with data
access from the American Museum of Natural History. Naia
Morueta-Holme and David Ackerly provided BCM climate
data. Emily Yao, Arsene Gaude, K Kai Din, Gordon Nishida,
and Joyce Gross assisted with digitizing and georeferencing
museum specimens. Sean Prager, Jay Rosenheim, Matt Daugh-
erty, members of the Almeida Lab and the Gillespie/Roderick
EvoLab, and two anonymous reviewers provided helpful com-
ments on earlier drafts. This work was supported by the Berke-
ley Initiative for Global Change Biology and the Gordon and
Betty Moore Foundation.
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... Introduction 23 Marine microplastic debris (MMD; plastic particles <1 mm in diameter) is an emerg- 24 ing, human-induced threat to the world's seas and oceans [1]. Annual plastic production 25 continues to rise [2,3], and the continued degradation of larger plastic items [4] further 26 increases the abundance of MMD and therefore the risk of wildlife being exposed to it [5].The assessment and management of future disease risks depends on understanding 48 the causes of historical and contemporary disease emergence events [23]. ...
... The assessment and management of future disease risks depends on understanding 48 the causes of historical and contemporary disease emergence events [23]. However, 49 because MMD is a newly recognized form of environmental pollution, there is little 50 information on the historical prevalence of MMD. ...
Full-text available
Marine wildlife and aquaculture species can accumulate large amounts of marine microplastic debris (MMD) (<1 mm) carrying pathogens, thus threatening the health of marine ecosystems and posing a risk to food safety and human health. Here, we outline a theoretical three-perspective approach for studying the relationship between MMD and disease. First, we provide a framework for retrospective analysis of MMD and pathogen loads in marine animal tissues to assess the relationship between these and other environmental variables in order to decide whether a compound or pathogen should be considered an emerging substance or organism. Second, we describe an experimental design for testing the effects of a variety of microplastics on infection intensity in two model species (oysters and zebrafish). Finally, we create a theoretical susceptible–infected microplastic particle and pathogen transmission model for bivalves and fish. Overall, the experiments and models we propose will pave the way for future research designed to assess the role of MMD as a vector for marine and human pathogens. This multi-faceted approach needs to be an urgent priority of the EU Strategic Research Innovation Agenda for addressing marine disease challenges related to MMD.
... The first symptoms of zebra chip disease on potato were observed in the 1990s in America, although there is evidence that CLso has coexisted with the potato psyllid Bactericera cockerelli for a much longer time (Zeilinger et al., 2017). Zeilinger et al. (2017) have also shown that B. cockerelli population abundance in relation to other Hemiptera species has increased during the last century. ...
... The first symptoms of zebra chip disease on potato were observed in the 1990s in America, although there is evidence that CLso has coexisted with the potato psyllid Bactericera cockerelli for a much longer time (Zeilinger et al., 2017). Zeilinger et al. (2017) have also shown that B. cockerelli population abundance in relation to other Hemiptera species has increased during the last century. However, further work is needed to link this to the zebra chip outbreaks. ...
Carrot cultivation in Europe is suffering from infections with 'Candidatus Liberibacter solanacearum' (CLso), a psyllid‐transmitted bacterial pathogen. In this study field experiments were carried out in Finland to separately measure the effects of psyllid feeding damage and CLso infection on the carrot root growth and to reveal the dynamics of the spreading of CLso within the field. Most of the experiments were carried out during the summers 2016 and 2017, and a follow‐up sampling was done in 2018. Carrot psyllid (Trioza apicalis) flight activity was monitored and carrots were sampled at 25 points within the field. Early in the season a clear spatial correlation was found between the sampling sites showing the psyllid feeding damage, i.e. leaf‐curling, up to the range of 40–60 m, indicating aggregation behaviour of the psyllids. No CLso‐infections were detected in the first sampling, which was done before the psyllid flight peak in both years. Later, a positive correlation between the psyllid feeding damage and the CLso titre was observed. An increase in the CLso titre occurred approximately a month after the psyllid flight peak, and this increase correlated with the accumulating effective temperature sum. In 2016, both the psyllid feeding damage and CLso infection had a significant effect on the carrot root weight. The effect of CLso titre on root weight was non‐linear, i.e. it intensified rapidly at the highest bacterial titres. During the colder summer of 2017 the CLso titres did not reach high enough levels in the plants to cause substantial visible symptoms and root growth reduction. Thus, it seems that in the Nordic conditions the effect of CLso infection on carrot yield is strongly dependent on the weather conditions during the growing season. This article is protected by copyright. All rights reserved.
... However, estimating trends from museum records necessitates addressing issues of recording bias, since these records were often collected in an opportunistic manner largely contingent on the context of each recording event [46], [47]. One effective approach to statistically correct for uneven recorder effort in opportunistic data is to use the number of species recorded during each sampling visit (the list length, L; sensu [48] as a proxy for recorder effort (e.g., [49], [50], [51], [52], [53]). Adding a covariate for list length within models of temporal estimates may enable disentangling true absences from failures to detect and record given species, because list length is positively associated with recorder effort and therefore probability of detection [54], [55]. ...
... The inclusion of a year term in conjunction with list-based proxies for recorder effort has previously been reliably used to estimate species' trends from opportunistic data such as museum records (e.g. [49], [50], [51], [52], [53]). To examine the potential effects of climate on temporal trends, we also included a linear term for each of the bioclimatic variables examined. ...
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Increasing attention to pollinators and their role in providing ecosystem services has revealed a paucity of studies on long-term population trends of most insect pollinators in many parts of the world. Because targeted monitoring programs are resource intensive and unlikely to be performed on most insect pollinators, we took advantage of existing collection records to examine long-term trends in northeastern United States populations of 26 species of hawk moths (family Sphingidae) that are presumed to be pollinators. We compiled over 6,600 records from nine museum and 14 private collections that spanned a 112-year period, and used logistic generalized linear mixed models (GLMMs) to examine long-term population trends. We controlled for uneven sampling effort by adding a covariate for list length, the number of species recorded during each sampling event. We found that of the 22 species for which there was sufficient data to assess population trends, eight species declined and four species increased in detection probability (the probability of a species being recorded during each year while accounting for effort, climate, and spatial effects in the GLMMs). Of the four species with too few records to statistically assess, two have disappeared from parts of their ranges. None of the four species with diurnal adults showed a trend in detection probability. Two species that are pests of solanaceous crops declined, consistent with a seven-fold drop in the area planted in tobacco and tomato crops. We found some evidence linking susceptibility to parasitoidism by the introduced fly Compsilura concinnata (Tachinidae) to declines. Moths with larvae that feed on vines and trees, where available evidence indicates that the fly is most likely to attack, had a greater propensity to decline than species that use herbs and shrubs as larval host plants. Species that develop in the spring, before Compsilura populations have increased, did not decline. However, restricting the analysis to hawk moth records from areas outside of a “refuge” area where Compsilura does not occur did not significantly increase the intensity of the declines as would be predicted if Compsilura was the primary cause of declines. Forests have recovered over the study period across most of the northeastern U.S., but this does not appear to have been a major factor because host plants of several of the declining species have increased in abundance with forest expansion and maturation. Climate variables used in the GLMMs were not consistently related to moth detection probability. Hawk moth declines may have ecological effects on both the plants pollinated by these species and vertebrate predators of the moths.
... Marine diseases may emerge as a result of novel introductions, climate change, changes in vector populations, and the introduction of novel vectors. The assessment and management of future disease risks depends on understanding the causes of historical and contemporary disease emergence events [26]. However, because MMD is a newly recognized form of environmental pollution, there is little information on the historical prevalence of MMD. ...
Full-text available
Marine wildlife and aquaculture species can accumulate large amounts of marine microplastic debris (MMD) (<1 mm) carrying pathogens, thus threatening the health of marine ecosystems and posing a risk to food safety and human health. Here, we outline a theoretical three-perspective approach for studying the relationship between MMD and disease. First, we provide a framework for retrospective analysis of MMD and pathogen loads in marine animal tissues to assess the relationship between these and other environmental variables in order to decide whether a compound or pathogen should be considered an emerging substance or organism. Second, we describe an experimental design for testing the effects of a variety of microplastics on infection intensity in two model species (oysters and zebrafish). Finally, we create a theoretical susceptible–infected microplastic particle and pathogen transmission model for bivalves and fish. Overall, the experiments and models we propose will pave the way for future research designed to assess the role of MMD as a vector for marine and human pathogens. This multi-faceted approach needs to be an urgent priority of the EU Strategic Research Innovation Agenda for addressing marine disease challenges related to MMD.
... Brooks et al., 2014), morphology (MacLean et al., 2019), species interactions (Meineke et al., 2018;Miller-Struttmann et al., 2015), disease dynamics (e.g. Zeilinger et al., 2017) and trait evolution (Holmes et al., 2016). Recent increases in the digital accessibility of these data have generated new interest in the possibility of using NHCs to estimate both species' distributions in historical time periods as well as trends in either distributions or abundances, particularly over longer time horizons than what is currently possible with contemporary survey data (e.g. ...
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1. Natural history collections (NHC) provide a wealth of information that can be used to understand the impacts of global change on biodiversity. As such, there is growing interest in using NHC data to estimate changes in species’ distributions and abundance trends over historic time horizons when contemporary survey data are limited or unavailable. 2. However, museum specimens were not collected with the purpose of estimating population trends and thus can exhibit spatiotemporal and collector‐specific biases that can impose severe limitations to using NHC data for evaluating population trajectories. 3. Here we review the challenges associated with using museum records to track long‐term insect population trends, including spatiotemporal biases in sampling effort and sparse temporal coverage within and across years. We highlight recent methodological advancements that aim to overcome these challenges and discuss emerging research opportunities. 4. Specifically, we examine the potential of integrating museum records and other contemporary data sources (e.g., collected via structured, designed surveys and opportunistic citizen science programs) in a unified analytical framework that accounts for the sampling biases associated with each data source. The emerging field of integrated modeling provides a promising framework for leveraging the wealth of collections data to accurately estimate long‐term trends of insect populations and identify cases where that is not possible using existing data sources.
... Several approaches can be used to decide which additional species are relevant to inferences on a focal species when search lists are not explicitly recorded as metadata. A frequently used approach is to use all available observations from the higher taxon that encompasses all of the study species such as the study phylum or class (van Strien et al. 2013, Rapacciuolo et al. 2017, Young et al. 2017, Zeilinger et al. 2017, Mason et al. 2018, Powney et al. 2019, Outhwaite et al. 2019. However, depending on the diversity of the higher taxon and the resulting variation among species in their ecology and detectability, taxonomy-based search lists may not satisfy the assumption that all associated species share the same observation biases or are ecologically relevant to each other (Hill 2012). ...
Opportunistic and unstructured observations of biodiversity crowdsourced from volunteers, community, and citizen scientists make up an increasingly large proportion of our global biodiversity knowledge. This incredible wealth of information exists in real time at both high resolutions and large extents of space, time, and taxonomy, thus holding huge potential to fill gaps in global biodiversity monitoring coverage in a cost‐effective way. Yet, the full potential of these data to provide essential indicators of biodiversity change for both research and management remains mostly unrealized, in large part due to the prevailing perception that the lack of standardization presents an unsurmountable barrier. In this paper, we provide an overview of the main challenges of working with unstructured community‐contributed data and synthesize the four fundamental approaches to overcome these challenges and extract useful inferences of biodiversity change, namely: 1) reverse‐engineering survey structure; 2) borrowing strength across taxa; 3) modeling the observation process, and; 4) integrating standardized data sources. To illustrate each of these approaches, we provide examples comparing community‐contributed observations crowdsourced via iNaturalist with long‐term standardized monitoring surveys for a subset of rocky intertidal organisms on the California coast from 2010 to 2019. We conclude by highlighting ways forward for the successful integration of unstructured community‐contributed observations within the global ecosystem of biodiversity change monitoring tools. Our ultimate goal is to update the prevailing perception among researchers and practitioners that unstructured community‐contributed observations of biodiversity are too noisy to use, and help establish this data stream as a key tool for research and management.
... Effects of bias can be reduced for certain studies with higher numbers of records, by combining information from different institutions, and including observation records to supplement specimen data [8]. Newer statistical and modeling approaches to deal with biases in biodiversity data have also been developed [43,48,53,54]. However, it is unclear how often studies actually address issues of error and bias when using opportunistic records. ...
Full-text available
Our world is in the midst of unprecedented change-climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed. We found that the most common uses of online biodiversity databases have been to estimate species distribution and richness, to outline data compilation and publication, and to assist in developing species checklists or describing new species. Only 69% of papers in our dataset addressed one or more aspects of data quality, which is low considering common errors and biases known to exist in opportunistic datasets. Globally, we find that biodiversity databases are still in the initial stages of data compilation. Novel and integrative applications are restricted to certain taxonomic groups and regions with higher numbers of quality records. Continued data digitization, publication, enhancement, and quality control efforts are necessary to make biodiversity science more efficient and relevant in our fast-changing environment.
... Owing to their ability to account for different types of sampling bias, occupancy models are also becoming key to modeling longer-term data sources. For instance, the application of hierarchical occupancy models to museum specimens and historical observations can vastly improve our estimates of the influence of selection on assemblages at the centennial scale (Tingley and Beissinger 2009, Tingley et al. 2012, Iknayan et al. 2014, Rapacciuolo et al. 2017, Zeilinger et al. 2017. Although different approaches have traditionally been preferred to account for imperfect detection in paleoecological data (Alroy et al. 2001, Sugita 2007a, b, Pirzamanbein et al. 2014, hierarchical occupancy models are beginning to be applied to the fossil record for assemblage-level inference (Liow 2013). ...
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The difficulty of integrating multiple theories, data, and methods has slowed progress towards making unified inferences of ecological change generalizable across large spatial, temporal and taxonomic scales. However, recent progress towards a theoretical synthesis now provides a guiding framework for organizing and integrating all primary data and methods for spatiotemporal assemblage‐level inference in ecology. In this paper, we describe how recent theoretical developments can provide an organizing paradigm for linking advances in data collection and methodological frameworks across disparate ecological sub‐disciplines and across large spatial and temporal scales. First, we summarize the set of fundamental processes that determine change in multispecies assemblages across spatial and temporal scales by reviewing recent theoretical syntheses of community ecology. Second, we review recent advances in data and methods across the main sub‐disciplines concerned with ecological inference across large spatial, temporal and taxonomic scales, and organize them based on the primary fundamental processes they include, rather than the spatiotemporal scale of their inferences. Finally, we highlight how iteratively focusing on only one fundamental process at a time, but combining all relevant spatiotemporal data and methods, may reduce the conceptual challenges to integration among ecological sub‐disciplines. Moreover, we discuss a number of avenues for decreasing the practical barriers to integration among data and methods. We aim to reconcile the recent convergence of decades of thinking in community ecology and macroecology theory with the rapid progress in spatiotemporal approaches for assemblage‐level inference, at a time where a robust understanding of spatiotemporal change in ecological assemblages is more crucial than ever to conserve biodiversity. This article is protected by copyright. All rights reserved.
Occupancy models estimate presence and detection probability of species of interest of which they provide useful information and also contribute to decision making. In this proof-of-concept, we propose an approach to demonstrate the applicability of occupancy models in insect monitoring having as targets the spittlebug Philaenus spumarius, the main European vector of Xylella fastidiosa, and other spittlebugs. Surveys were performed in two different agricultural settings (olive orchards and vineyards) in Trentino (northern Italy). Philaenus spumarius was present in all surveyed sites and its detectability was significantly influenced by site covariates (i.e., forest and vineyard coverage, hours of sunlight) and plot covariates (i.e., weed height). Site covariates influenced the detection probability of other spittlebugs as well, while the co-occurrence of different species did not affect the P. spumarius occupancy. Our outcomes suggest that occupancy models are valuable tools that should support future studies aimed at estimating the presence and abundance of pest insects, especially when site covariates and/or sampling methods affect the detectability of a species.
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Traditional Markov chain Monte Carlo (MCMC) sampling of hidden Markov models (HMMs) involves latent states underlying an imperfect observation process, and generates posterior samples for top-level parameters concurrently with nuisance latent variables. When potentially many HMMs are embedded within a hierarchical model, this can result in prohibitively long MCMC runtimes. We study combinations of existing methods, which are shown to vastly improve computational efficiency for these hierarchical models while maintaining the modeling flexibility provided by embedded HMMs. The methods include discrete filtering of the HMM likelihood to remove latent states, reduced data representations, and a novel procedure for dynamic block sampling of posterior dimensions. The first two methods have been used in isolation in existing application-specific software, but are not generally available for incorporation in arbitrary model structures. Using the NIMBLE package for R, we develop and test combined computational approaches using three examples from ecological capture-recapture, although our methods are generally applicable to any embedded discrete HMMs. These combinations provide several orders of magnitude improvement in MCMC sampling efficiency, defined as the rate of generating effectively independent posterior samples. In addition to being computationally significant for this class of hierarchical models, this result underscores the potential for vast improvements to MCMC sampling efficiency which can result from combinations of known algorithms.
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The potato psyllid, Bactericera cockerelli (Sulc) (Hemiptera: Triozidae) is a small phloem-feeding insect that develops almost exclusively on plants within the Solanaceae (Fig. 1A). The psyllid was described in 1909 by Karel Sulc from specimens collected in Boulder, Colorado, and is found in Mexico, Central America, the western U.S., and southern Canada, and as an introduction in New Zealand (Wallis 1955, Teulon et al. 2009, Munyaneza 2012). Outbreaks of potato psyllid in North America occurred at regular intervals in potatoes, tomatoes, and peppers beginning in the late 1800s and extending into the mid-1900s, largely along a corridor on both sides of the Rocky Mountains. The outbreaks failed to extend into the Pacific Northwest. That pattern changed dramatically in 2011, when an outbreak of potato psyllid caused massive economic losses to potato growers in Washington, Oregon, and Idaho. Losses were due to a new tuber disorder (“zebra chip”; Fig. 1 B-C), now known to be associated with a bacterium that is vectored by potato psyllid. Fig. 1. (A) Adult potato psyllid. (B, C) Discoloration of infected fresh tubers and of tuber slices after frying. The historical absence of psyllid problems in the Pacific Northwest means that our understanding of psyllid biology under Pacific Northwest conditions is woefully lacking. The outbreak in 2011, coupled with our limited …
Two genetically distinct potato psyllid populations [Bactericera cockerelli (Sulc) (Homoptera: Psyllidae)] were identified in our previous study: native and invasive. The invasive population, ranging from Baja, Mexico to central California, was the result of a recent invasion, while the native population is endemic to Texas. The native (Texas) and invasive (California) populations were collected from tomato and pepper, respectively, and were examined on both hosts to test the comparative fitness of invasive populations. Our results indicated that on both plant hosts, psyllids from the native range demonstrated higher survivorship, a higher growth index, and shorter development times than the psyllids from invasive populations. The fecundity of the native-range psyllids also was significantly higher than that of invasive psyllids on tomato, but not on pepper. For the native population, host plant differences for all fitness measurements were not significant. However, within the invasive population, psyllids feeding on tomatoes showed consistently better survivorship and a higher growth index than those feeding on pepper, despite the decreased developmental time required on peppers. The LC50 values (concentrations causing 50% mortality) of both populations were determined for three pesticides. Resistance to two of these pesticides was found in the invasive population. Thus, the invasive quality of the California populations may be related to increased pesticide resistance. However, it is impossible to determine if the California population was preadapted to pesticide resistance, or if the resistance developed after the range expansion and is simply a contributing factor to maintaining the expansion.
The abundance of insects can change dramatically from generation to generation; these generational changes may occur within a growing season or over a period of years. Such extraordinary density changes or "outbreaks" may be abrupt and ostensibly random, or population peaks may occur in a more or less cyclic fashion. They can be hugely destructive when the insect is a crop pest or carries diseases of humans, farm animals, or wildlife. Knowledge of these types of population dynamics and computer models that may help predict when they occur are very important. This important new book revisits a subject not thoroughly discussed in such a publication since 1988 and brings an international scale to the issue of insect outbreaks. Insect Outbreaks Revisited is intended for senior undergraduate and graduate students in ecology, population biology and entomology, as well as government and industry scientists doing research on pests, land managers, pest management personnel, extension personnel, conservation biologists and ecologists, and state, county and district foresters.
The pathogenic 'Candidatus Liberibacter' species have caused tremendous economic losses to agricultural crops. Since these bacteria are, generally, not yet unculturable, information regarding genetics and pathogenesis of the pathogens is limited. Comparative analyses of multiple Liberibacter genomes provide unprecedented insights into the evolutionary history, phylogenetic diversity, and metabolomic capacities among pathogenic bacteria. In addition, genomic analyses of plant disease-associated Liberibacters have led to the identification of potential or putative pathogenicity and virulence factors, as well as biomarkers associated with Liberibacter-host plant interactions. The availability of specific biomarkers associated with Liberibacter-host plant interactions will aid in the development of improved, reliable diagnostic protocols for early (i.e., presymptomatic), rapid Liberibacter detection as part of disease management strategies. Since no host resistance has been found in Liberibacter-associated diseases, knowledge of specific Liberibacter genes and their products associated with pathogenicity and virulence, as well as interactions with psyllid vectors, will lead to the identification of potential targets for mitigating Liberibacter acquisition and transmission by psyllids, host plant infection, and disease development. Finally, genomics-based research will facilitate improved understanding of the complex and diverse mechanisms of Liberibacter-plant interactions. © 2014 Springer-Verlag Berlin Heidelberg (outside the USA). All rights reserved.