Field evaluation of abundance estimates under binomial and multinomial N-mixture models

Assessing and modelling abundance from animal count data is a very common task in ecology and management. Detection is arguably never perfect, but modern hierarchical models can incorporate detection probability and yield abundance estimates that are corrected for imperfect detection. Two variants of these models rely on counts of unmarked individuals, or territories (binomial N-mixture models, or binmix), and on detection histories based on territory-mapping data (multinomial N-mixture models or multimix). However, calibration studies which evaluate these two N-mixture model approaches are needed. We analysed conventional territory-mapping data (three surveys in 2014 and four in 2015) using both binmix and multimix models to estimate abundance for two common avian cavity-nesting forest species (Great Tit Parus major and Eurasian Blue Tit Cyanistes caeruleus). In the same study area, we used two benchmarks: occupancy data from a dense nestbox scheme and total number of detected territories. To investigate variance in estimates due to the territory assignment, three independent ornithologists conducted territory assignments. Nestbox occupancy yields a minimum number of territories, as some natural cavities may have been used, and binmix model estimates were generally higher than this benchmark. Estimates using the multimix model were slightly more precise than binmix model estimates. Depending on the person assigning the territories, the multimix model estimates became quite different, either overestimating or underestimating the ‘truth’. We conclude that N-mixture models estimated abundance reliably, even for our very small sample sizes. Territory-mapping counts depended on territory assignment and this carried over to estimates under the multimix model. This limitation has to be taken into account when abundance estimates are compared between sites or years. Whenever possible, accounting for such hidden heterogeneity in the raw data of bird surveys, via including a ‘territory editor’ factor, is recommended. Distributing the surveys randomly (in time and space) to editors may also alleviate this problem.     

Northern bobwhite response to Conservation Reserve Program habitat and landscape attributes

The northern bobwhite (Colinus virginianus; hereafter bobwhite) has experienced substantial population declines in recent decades in the United States, and especially in Maryland and Delaware. The United States Department of Agriculture's Conservation Reserve Program (CRP) could provide additional habitat for bobwhites, leading to an increase in bobwhite abundance. I investigated if bobwhite abundance was related to the percent cover of CRP land and landscape attributes in local landscapes on Maryland's Eastern Shore and Delaware. Observers conducted bobwhite point transect surveys at 113 locations during the breeding seasons of 2006–2007, and I calculated landscape metrics for 500-m radius landscapes centered on each point transect location. Most CRP land in the study landscapes was planted to herbaceous vegetation. Bobwhite abundance was strongly positively associated with percent cover of CRP land in the landscape but was not strongly related to percent cover of agriculture or forest or to landscape patch density. These results suggest that the CRP has created additional habitat for bobwhites in Maryland and Delaware and that landscapes with greater proportions of herbaceous CRP practices support more bobwhites. © 2012 The Wildlife Society.     

产生无标记农杆菌突变体方法的建立及优化

农杆菌已经用作许多生物过程研究的模型细菌,为了解析这些生物过程的分子机理,对农杆菌的某些基因进行突变就显得非常重要．以自杀性基因sacB作为反向可选择性标记基因,利用同源重组的原理,建立了一种可对农杆菌基因进行准确插入、删除和位点置换的突变方法,所获突变体不带任何不需要的外源DNA序列．通过详细研究同源序列的长度对农杆菌同源重组效率和突变体产生概率的影响,以及对农杆菌中的同源重组机理的分析,提出了优化该突变体产生方法的方案,即通过设计不等长的上下游同源序列和选择其中一种类型的单交换重组体来筛选二次交换重组体的方法,可以显著地提高理想突变体的产生概率．研究结果对如何提高突变体的产生概率和减少突变体筛选的工作量具重要的参考价值．利用该方法成功地获得了两个基因被同时删除而且不含抗性标记的农杆菌突变株．     

Estimating Abundance of an Unmarked,Low-Density Species using Cameras

Estimating abundance of wildlife populations can be challenging and costly, especially for species that are difficult to detect and that live at low densities, such as cougars (Puma concolor). Remote, motion-sensitive cameras are a relatively efficient monitoring tool, but most abundance estimation techniques using remote cameras rely on some or all of the population being uniquely identifiable. Recently developed methods estimate abundance from encounter rates with remote cameras and do not require identifiable individuals. We used 2 methods, the time-to-event and space-to-event models, to estimate the density of 2 cougar populations in Idaho, USA, over 3 winters from 2016–2019. We concurrently estimated cougar density using the random encounter model (REM), an existing camera-based method for unmarked populations, and genetic spatial capture recapture (SCR), an established method for monitoring cougar populations. In surveys for which we successfully estimated density using the SCR model, the time-to-event estimates were more precise and showed comparable variation between survey years. The space-to-event estimates were less precise than the SCR estimates and were more variable between survey years. Compared to REM, time-to-event was more precise and consistent, and space-to-event was less precise and consistent. Low sample sizes made the space-to-event and SCR models inconsistent from survey to survey, and non-random camera placement may have biased both of the camera-based estimators high. We show that camera-based estimators can perform comparably to existing methods for estimating abundance in unmarked species that live at low densities. With the time- and space-to-event models, managers could use remote cameras to monitor populations of multiple species at broader spatial and temporal scales than existing methods allow. © 2020 The Wildlife Society.     

Unmarked individuals in mark–recapture studies: Comparisons of marked and unmarked southern elephant seals at Marion Island

The presence of unmarked individuals is common in mark–recapture study populations; however, their origin and significance in terms of population dynamics remain poorly understood. At Marion Island, southern Indian Ocean, where virtually all southern elephant seal Mirounga leonina pups born annually (1983–2008) were marked in a long‐term mark–resight study, large numbers of unmarked seals occur. Unmarked seals originate either from marker (tag) loss or from immigration. We aimed to identify patterns in the occurrence of marked and unmarked individuals that will allude to the possible origin and significance of the untagged component of the population, predicting that tag loss will add untagged seals to mainly adult age categories whereas migrating untagged individuals will be mostly juveniles. We fitted a generalized linear model using the factors month, year and age‐class to explain the relative abundance of untagged seals (tag ratio) from 1997 to 2009. Site usage of untagged seals relative to tagged seals was assessed using a binomial test. Untagged seals, predominantly juveniles, were present in the highest proportions relative to tagged seals during the winter haulout (tagged seals/total seals less than 0.3) and the lowest proportion (approximately 0.5) during the female breeding haulout, increasing in relative abundance from 1997 to 2009. Untagged seals were distributed evenly across suitable haulout sites while tagged seals displayed high local site fidelity and occurred in greater numbers at or near large breeding beaches. Untagged seals are considered to be mostly migrant seals that disperse from other islands within the southern Indian Ocean and haul out at Marion Island during non‐breeding haulouts in particular. Some of these seals immigrate to the breeding population, which can be a key component of the local population dynamics. We emphasize the need for mark–recapture studies to evaluate the role of the unmarked component of a population, thereby inducing a more confident estimation of demographic parameters from the marked sample.     

Construction and immunogencity of a DeltaapxIC/DeltaapxIIC double mutant of Actinobacillus pleuropneumoniae serovar 1

The apxIC and apxIIC genes of the Actinobacillus pleuropneumoniae serovar 1 strain SLW01, encoding the ApxI- and ApxII-activating proteins, respectively, were deleted successively by a method involving sucrose counterselection. The resulting strain, SLW03, contained no foreign DNA and could secrete unactivated ApxIA and ApxIIA RTX toxins with complete antigenicity. Strain SLW03 was attenuated at least 1000-fold in Balb/C mice and caused no adverse effects in pigs at doses of up to 1 x 10(9) CFU mL(-1). SLW03 was able to induce a significant immune response and provide complete protection from clinical signs upon homologous (serovar 1) and heterologous (serovar 9) challenge of A. pleuropneumoniae. Pigs vaccinated via the intranasal (i.n.) route had significantly higher serum titers and fewer pulmonary lesions than pigs vaccinated via the intramuscular route postchallenge. These results suggest that the mutant strain SLW03 could be used as a candidate live vaccine that can induce reliable cross-serovar protection following i.n. immunization.     

Technical note: Different techniques,different results—a comparison of photogrammetric and caliper-derived measurements

The primary goal of our study was to compare photogrammetric measurements with caliper-derived measurements. We also looked at the difference between caliper-derived measurements that were taken with and without the landmarks marked. Thirteen facial measurements were repeated ten times on two adult subjects as follows: 1) Calipers were used to take the measurements before the landmarks were marked on each subject's face; 2) the landmarks were then marked with a black pencil, and the calipers were used to take the measurements again; and 3) images were taken of each subject with the markings left on the face, and the measurements were extracted from these images. Compared with the caliper-derived data taken with the landmarks marked, the photogrammetric means and standard deviations were typically larger, leading us to conclude that there was a systematic difference between the data. The generally greater variation in the photogrammetric measurements was ascribed to poor conditions, such as shadows, oblique markings, and unmarked landmarks. When the data gathered by caliper with and without the landmarks marked were compared, a systematic difference was suggested by the number of statistically significant t-test probabilities. Marking the landmarks reduced the standard deviations in some measurements by controlling two sources of variation: differing pressure on the skin and slippage of the calipers. Anthropologists, medical geneticists, and others who use measurements for diagnostic or classificatory purposes should be aware that data gathered by different techniques may yield different results. Am J Phys Anthropol 106:547–552, 1998. © 1998 Wiley-Liss, Inc.     

Mini-Tn7 vectors as genetic tools for gene cloning at a single copy number in an industrially important and phytopathogenic bacteria, Xanthomonas spp.

Transposon mini-Tn 7 vectors insert into the chromosome of several Gram-negative bacteria in a site-specific manner. Here, we showed the application of mini-Tn 7 as single copy site-specific integration vector system for Xanthomonas campestris pv. campestris . The transposition of the mini-Tn 7 into the bacterial genome was detected at a Tn 7 attachment ( att Tn 7 ) site located downstream of glmS1 . Furthermore, using a newly constructed vector pBBR1FLP2 containing the flipase (FLP) recombinase for site-specific excision of the sequence between the FLP recombinase target (FRT) sites, and a sacB counter selection marker, an unmarked mini-Tn 7 insertion mutant was created. Mini-Tn 7 insertion did not affect bacterial virulence on the tested plant. The mini-Tn 7 and FLP–FRT systems also work well in Xanthomonas oryzae pv. oryzae .     

Spatial capture–recapture with random thinning for unidentified encounters

1. Spatial capture–recapture (SCR) models have increasingly been used as a basis for combining capture–recapture data types with variable levels of individual identity information to estimate population density and other demographic parameters. Recent examples are the unmarked SCR (or spatial count model), where no individual identities are available and spatial mark–resight (SMR) where individual identities are available for only a marked subset of the population. Currently lacking, though, is a model that allows unidentified samples to be combined with identified samples when there are no separate classes of “marked” and “unmarked” individuals and when the two sample types cannot be considered as arising from two independent observation models. This is a common scenario when using noninvasive sampling methods, for example, when analyzing data on identified and unidentified photographs or scats from the same sites.
2. Here we describe a “random thinning” SCR model that utilizes encounters of both known and unknown identity samples using a natural mechanistic dependence between samples arising from a single observation model. Our model was fitted in a Bayesian framework using NIMBLE.
3. We investigate the improvement in parameter estimates by including the unknown identity samples, which was notable (up to 79% more precise) in low‐density populations with a low rate of identified encounters. We then applied the random thinning SCR model to a noninvasive genetic sampling study of brown bear (Ursus arctos) density in Oriental Cantabrian Mountains (North Spain).
4. Our model can improve density estimation for noninvasive sampling studies for low‐density populations with low rates of individual identification, by making use of available data that might otherwise be discarded.