Summary
1. Spatial analysis has become increasingly popular in the biological sciences, particularly in disciplines such as landscape ecology and landscape genetics. However, many statistical ...functions for performing spatial analysis are not readily available (except in the most limited manner) in common, easy‐to‐use statistical packages or geographic information systems (GIS) software.
2. Over the last decade, the software package Pattern Analysis, Spatial Statistics and Geographic Exegesis (PASSaGE) has been popular tool for conducting spatial statistics. PASSaGE is completely free and has a user‐friendly graphical user interface. A new version of PASSaGE, rewritten from the ground up, has now been released and is available for download.
3. PASSaGE 2 is significantly more user friendly than the original release and provides an excellent platform for both scientific analysis and classroom training. PASSaGE 2 includes a broad array of spatial statistical analyses not commonly found in other software packages or GIS software, all in an easy‐to‐use framework. It includes support for one‐, two‐ and three‐dimensional spatial analysis, including a number of unique and newly developed approaches.
Landscape features exist at multiple spatial and temporal scales, and these naturally affect spatial genetic structure and our ability to make inferences about gene flow. This article discusses how ...decisions about sampling of genotypes (including choices about analytical methods and genetic markers) should be driven by the scale of spatial genetic structure, the time frame that landscape features have existed in their current state, and all aspects of a species' life history. Researchers should use caution when making inferences about gene flow, especially when the spatial extent of the study area is limited. The scale of sampling of the landscape introduces different features that may affect gene flow. Sampling grain should be smaller than the average home-range size or dispersal distance of the study organism and, for raster data, existing research suggests that simplifying the thematic resolution into discrete classes may result in low power to detect effects on gene flow. Therefore, the methods used to characterize the landscape between sampling sites may be a primary determinant for the spatial scale at which analytical results are applicable, and the use of only one sampling scale for a particular statistical method may lead researchers to overlook important factors affecting gene flow. The particular analytical technique used to correlate landscape data and genetic data may also influence results; common landscape-genetic methods may not be suitable for all study systems, particularly when the rate of landscape change is faster than can be resolved by common molecular markers.
Abstract
Some large-seeded plants lack effective seed dispersal agents when they are introduced as ornamental plants to new areas, but can rapidly colonize a landscape if seed dispersal functions are ...restored. We examined whether Gopherus polyphemus (Gopher Tortoise) facilitated the spread of Chrysobalanus icaco (Cocoplum; Chrysobalanaceae) over a 14-year period in a suburban nature preserve (in Jupiter, FL, USA) by: (i) comparing germination patterns among gut-passed, hand-depulped and whole fruit treatments, and (ii) testing hypotheses about environmental predictors of the spatial distribution of C. icaco, including information about G. polyphemus movement pathways and burrow locations. While we did not find a significant difference in the total proportion of C. icaco seeds that germinated in each treatment, time to event analysis revealed that seeds that were found in faeces germinated significantly earlier than seeds that were hand-depulped or that were planted as whole fruits, supporting a lone scarification effect. Point process modeling revealed that the density of C. icaco bushes was higher near G. polyphemus movement pathways and was lower inside Serenoa repens (Saw Palmetto) patches, supporting a positive effect of tortoise movement patterns on plant distributions. The density of C. icaco increased from west to east, consistent with westward dispersal from the four founder bushes on the east side of the study area. After removal of outliers, we also detected a negative association between C. icaco spatial density and G. polyphemus burrow density that was presumably explained by the fact that seeds defecated deep within burrows were unlikely to germinate and establish without secondary movement. The results suggest that G. polyphemus contributed to the rapid dispersal of C. icaco by scatter dispersal of seeds (via faeces) in areas where tortoises were active and that movement pathways provided suitable conditions for colonization. The spread of C. icaco by G. polyphemus over a relatively short period of time provides a valuable window into the earliest stages of the colonization process and further supports the role of Chelonians as effective seed dispersal agents for large-seeded plants.
Plants that produce large, fleshy fruits are sometimes introduced to new areas for ornamental purposes, but may not spread further due to the absence of animals that are capable of dispersing their seeds. We examined a case where four cocoplum bushes were introduced to a suburban gopher tortoise refuge (in Jupiter, FL, USA) for aesthetic purposes and subsequently spread throughout the area, over a 14-year period. We found evidence that the gopher tortoise likely contributed to cocoplum expansion, by accelerating seed germination and by defecating seeds in areas, such as trails, that provided suitable locations for cocoplum establishment.
Gunnison's prairie dogs, Cynomys gunnisoni, frequently utter a repetitive series (a ‘bout’) of alarm calls (called ‘barks’) in response to a variety of terrestrial predators. Previous work has ...suggested that the structure of barks is finely tuned in ways that provide highly specific information about the identity of the predator. We re-evaluated these findings by presenting individually marked adult females with taxidermy mounts of three terrestrial predators of prairie dogs: a coyote, Canis latrans, a bobcat, Lynx rufus, and an American badger, Taxidea taxus, as well as one control stimulus (a cardboard box). Significant variation among individuals was evident from analyses of 10 measures associated with the general pattern of barking (e.g. latency to begin barking, bout duration, average number of barks/bout, overall bark rate, interbout interval) and also from eight structural features of individual barks (e.g. frequency and duration measures of the fundamental frequency band). When controlling for the identity of alarm callers, we found little evidence for differences in these same variables in response to different stimuli. We conclude that, like several other species of ground-dwelling squirrels, Gunnison's prairie dogs have an individually distinctive alarm call that does not differ for different predators. Our results conflict with earlier claims of extreme specificity in the alarm calls of Gunnison's prairie dogs.
•We tested whether Gunnison's prairie dog alarm calls show referential specificity.•Controlling for caller ID, we found little evidence of call variation to four stimuli.•However, individuals' alarm calls were distinct from one other.•Previous studies not considering individual variation need to be re-evaluated.
The nine-banded armadillo (Dasypus novemcinctus) is unique among mammals because females produce litters of genetically identical quadruplets via monozygotic polyembryony. This unusual form of ...reproduction could have profound impacts on the spatial genetic structure of populations of armadillos, but at present it is unclear whether littermates remain together as adults, or if sex-biased dispersal occurs. The goal of our study was to determine whether fine-scale spatial genetic structure (FSGS) within a population of armadillos diminishes with age (i.e., from juvenile to adult due to the dispersal of littermates away from one another), and if the degree of FSGS for a given age class differs between the sexes. We obtained genotype data at seven microsatellite DNA loci for 421 individuals in a wild population of armadillos inhabiting the Yazoo National Wildlife Refuge in western Mississippi. Correlogram analyses based on measures of spatial genetic autocorrelation showed weak but significant FSGS that was driven by positive spatial genetic autocorrelation among both male and female juveniles and adult males, but not adult females. Positive spatial genetic autocorrelation among adult males could be due to either female-biased dispersal or high variance in male reproductive success. Further work is required to discriminate between these two possibilities.
The nine-banded armadillo ( Dasypus novemcinctus ) is the only known nonhuman reservoir of Mycobacterium leprae , the causative agent of Hansen's disease or leprosy. We conducted a 6-yr study on a ...wild population of armadillos in western Mississippi that was exposed to M. leprae to evaluate the importance of demographic and spatial risk factors on individual antibody status. We found that spatially derived covariates were not predictive of antibody status. Furthermore, analyses revealed no evidence of clustering by antibody-positive individuals. Lactating females and adult males had higher odds of being antibody positive than did nonlactating females. No juveniles or yearlings were antibody positive. Results of these analyses support the hypothesis that M. leprae infection patterns are spatially homogeneous within this armadillo population. Further research related to movement patterns, contact among individuals, antibody status, and environmental factors could help address hypotheses related to the role of environmental transmission on M. leprae infection and the mechanisms underlying the differential infection patterns among demographic groups.
Informally gathered species lists are a potential source of data for conservation biology, but most remain unused because of questions of reliability and statistical issues. We applied two ...alternative analytical methods (contingency tests and occupancy modeling) to a 35-year data set (1973-2007) to test hypotheses about local bird extinction. We compiled data from bird lists collected by expert amateurs and professional scientists in a 2-km² fragment of lowland tropical forest in coastal Ecuador. We tested the effects of the following on local extinction: trophic level, sociality, foraging specialization, light tolerance, geographical range area, and biogeographic source. First we assessed extinction on the basis of the number of years in which a species was not detected on the site and used contingency tests with each factor to compare the frequency of expected and observed extinction events among different species categories. Then we defined four multiyear periods that reflected different stages of deforestation and isolation of the study site and used occupancy modeling to test extinction hypotheses singly and in combination. Both types of analyses supported the biogeographic source hypothesis and the species-range hypothesis as causes of extinction; however, occupancy modeling indicated the model incorporating all factors except foraging specialization best fit the data.
How habitat edges affect the spatial dynamics of snakes has become an increasingly popular subject because of a massive increase in anthropogenic edges in many landscapes. Here, we used a novel ...randomization-based procedure to examine patterns of edge association for the Timber Rattlesnake (Crotalus horridus) within upland forest in St. Louis County, Missouri. For each set of locations, the minimal distance from each location to the nearest edge feature was measured, averaged, and compared to an expected null distribution of average minimal distances (AMDs) under the assumption that points are randomly located with respect to edges. The significance of the observed value was estimated by determining the proportion of AMDs from the randomized set that were equal to or less than the observed average distance. Results indicated considerable variation from year to year in test results for individuals, resulting in variation in the results of combined significance tests for subgroups (i.e., males, females, and gravid females). Although results for different edge types were not compared statistically, our results indicated that individuals were found most frequently in nonrandom proximity to fence edges. In general, results were consistent with previous studies of habitat selection in midwestern snakes, which failed to find a consistent association between snakes and edges.
A major technology break in snake biology was the publication of surgical protocols for implanting radiotransmitters in the body cavities of snakes. While many researchers have reported using some ...variant of these protocols successfully, protocol details often vary from study to study and best-practice procedures are not easily determinable given the variety of circumstances over which studies occur. Although professional society standards and federal regulations make explicit recommendations about this surgical procedure, some of the nonstandard techniques recommended for this protocol may raise the eyebrows of institutional animal care and use committees. In this commentary we discuss regulatory and logistical aspects of the intracoelmic radiotransmitter implant procedure for snakes, and we provide a pragmatic framework for choosing among surgical variables.
Radiotelemetry and genetic markers have enabled herpetologists to test the hypothesis that gene flow is restricted among snake dens (a.k.a. “hibernacula”). In the present study, observations of ...movement and mating were compared to indirect inferences of gene flow based on genetic data (microsatellite DNA loci) for six neighboring hibernacula of the Timber Rattlesnake (Crotalus horridus) in western St. Louis County, Missouri. Behavioral results were consistent with previous findings for this species, with most individuals exhibiting high fidelity to hibernacula, and males exhibiting larger activity areas than females. Behavioral results also supported several long-standing assumptions: males tended to mate at longer distances from hibernacula than females and random pairing between males and females from different hibernacula could not be rejected. Some gravid females moved considerable distances between locations, but most returned to an area near their own hibernaculum to give birth, and birth distances tended to be shorter than the nearest-neighbor distance between hibernacula. Genetic results indicated that the observed number of heterozygotes did not deviate from Hardy-Weinberg expectations at the level of total sample population, but that a significant heterozygote excess was found within hibernacula. A small but significant proportion of the genetic variance in the total population was due to differences among hibernacula; however, Bayesian clustering algorithms could not sort individuals (or groups of hibernacula) into discrete demes. Results suggest that patterns of genetic differentiation observed among hibernacula of the Timber Rattlesnake are better explained by behavioral and demographic factors resulting in natal philopatry, sex-biased dispersal, and/or a limited number of breeding adults, than by the balance of gene flow and drift, per se.
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