Shirli Bar-David

Allelic richness following population founding events--a stochastic modeling framework incorporating gene flow and genetic drift.

Allelic richness (number of alleles) is a measure of genetic diversity indicative of a populations long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an alleles presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a populations allele frequency spectrum to provide predictions for allele recovery. The models analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the “One Migrant per Generation” rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution.

DYNAMICS AND MANAGEMENT OF INFECTIOUS DISEASE IN COLONIZING POPULATIONS

The introduction of chronic, infectious diseases by colonizing populations (invasive or reintroduced) is a serious hazard in conservation biology, threatening the original host and other spillover species. Most research on spatial invasion of diseases has pertained to established host populations, either at steady state or fluctuating through time. Within a colonizing population, however, the spread of disease may be influenced by the expansion process of the population itself. Here we explore the simultaneous expansion of a colonizing population and a chronic, nonlethal disease introduced with it, describing basic patterns in homogeneous and structured landscapes and discussing implications for disease management. We describe expected outcomes of such introductions for three qualitatively distinct cases, depending on the relative velocities at which the population and epidemic expand. (1) If transmissibility is low the disease cannot be sustained, although it may first expand its range somewhat around the point of introduction. (2) If transmissibility is moderate but the wave-front velocity for the population, vp, is higher than that for the disease, vd, the disease wave front lags behind that of the population. (3) A highly transmissible disease, with vd > vp, will invade sufficiently rapidly to track the spread of the host. To test these elementary theoretical predictions, we simulated disease outbreaks in a spatially structured host population occupying a real landscape. We used a spatially explicit, individual-based model of Persian fallow deer (Dama mesopotamica) reintroduced in northern Israel, considering a hypothetical introduction of bovine tuberculosis. Basic patterns of disease expansion in this realistic setting were similar to our conceptual predictions for homogeneous landscapes. Landscape heterogeneity, however, induced the establishment of population activity centers and disease foci within them, leading to jagged wave fronts and causing local variation in the relative velocities at which the population and epidemic expanded. Based on predictions from simple theory and simulations of managed outbreaks, we suggest that the relative velocities at which the population and epidemic expand have important implications for the impact of different management strategies. Recognizing which of our three general cases best describes a particular outbreak will aid in planning an efficient strategy to contain the disease.

Impact of repeated releases on space-use patterns of Persian fallow deer

The space-use patterns of reintroduced animals are not well studied. We studied the space-use patterns of reintroduced Persian fallow deer (Dama mesopotamica) to assess how repeated releases from a single habituation enclosure and the presence of conspecifics influence the establishment of home range. We released 52 animals (33 were radiocollared). Movements of 27 radiocollared animals (5 M, 22 F) and 20 uncollared subadult males were studied by radiotracking and direct observation for ≤2 years from the time of reintroduction. Deer were released from the same habituation enclosure on 4 occasions over 20 months. During the first 3-6 months after release, deer usually occupied a limited range within 500 m from the enclosure. Later, animals moved to 1 of 3 areas 0.5-1.5 km from the enclosure, forming 3 subpopulations. The subpopulations consisted of animals from all releases and both sexes. Home ranges of animals from the first and second releases stabilized 8-10 months after release. Animals from the third release appeared to establish a stable home range almost immediately. Home-range size between September 1997 and April 1998 (7-8 mo) ranged from 86 to 365 ha, with home ranges of females not differing significantly from those of males. Later releases had little effect on the home-range stability of animals from previous releases. Our results suggest that over the short term, repeated releases from a single enclosure have no detrimental effects and actually may enhance the establishment of females from later releases. Movement patterns of released Persian fallow deer in this reintroduction indicate a slow, gradual movement away from the release site and establishment of a home range within a year.

Seasonal and circadian changes in the home ranges of reintroduced Persian fallow deer

The Persian fallow deer (Dama mesopotamica)-among the rarest deer species in the world-has been gradually reintroduced, using individuals from a captive-bred population, in northern Israel since September 1996. As of October 2000, >80 animals were in the wild population. We studied seasonal and circadian attributes of deer home ranges to assess the success of the reintroduction in terms of behavioral adjustments to the wild. We used radiotelemetry to determine locations and analyzed home ranges with the adaptive kernel method. We defined 3 seasons: fawning (Mar-Jun), rut (Jul-Oct), and winter (Nov-Feb). For females (n = 16), rut home ranges were significantly larger than winter home ranges (449 ± 45 ha [mean ± SE] vs. 384 ± 36 ha, P 1,15 = 0.013). During fawning, female home ranges were intermediate (424 ± 51 ha). Males (n = 5) increased their home ranges in rut season (820 ± 162 ha [mean ± SE], P < 0.012) and shifted their locations toward the release point. In winter, males significantly decreased their home ranges (584 ± 158 ha, P < 0.012), shifted their locations away from the release point, and almost no overlap of core areas was noticeable (1.8% overlap). In fawning (the time of antler casting and regrowth), males continued to shift away from the release point and decreased home ranges (358 ± 66 ha, P= 0.049) with almost no overlapping of core areas (0.06% overlap). No statistically significant differences were found between day home ranges (males [n = 5]: 621 ± 220 ha [mean ± SD], females [n = 16]: 402 ± 164) and night home ranges (males: 482 ± 145, females: 389 ± 183), although day core areas tended to be larger (in all males and 12 of 16 females). All documented aspects of seasonally, in female and male home ranges are in accordance with the annual reproduction cycle, and are related to seasonal food availability. These results, combined with previous works, suggest that so far, the reintroduced Persian fallow deer have adjusted well to living in the wild and that the chances of achieving A self-wild population are good. However, further research for extended period should verify these conclusions.

Long-Distance Movements by Fire Salamanders (Salamandra Infraimmaculata) and Implications for Habitat Fragmentation

Dispersal may be particularly important for the regional persistence of metapopulations that experience local extinctions. Some amphibian species are structured as metapopulations. Long-term persistence of these species should depend on natural connections between local subpopulations through dispersal. We explored movement distances of fire salamander adults (Salamandra infraimmaculata), a locally endangered species, on Mt. Carmel, northern Israel, and investigated the implications of movement for persistence of populations. During the breeding seasons (November-March) of 1999-2000 and 2002-2006, capture-recapture surveys were conducted around four breeding sites and along unpaved roads connecting them. Out of 300 adult salamander captures, 72 cases were recaptures. Most of the recaptures were in the same site as the initial capture. In eight cases (11%), however, salamanders were recaptured at least 400 m away from the first site. The maximum direct distances between capture-recapture sites (1100-1300 m...

Recursive movement patterns: review and synthesis across species

Recursive movement—returns to previously visited areas—is a widespread phenomenon exhibited by a large range of species from bees and birds to primates and large felines, at different spatial scales. Nevertheless, the wide scope and generality of this phenomenon remain underestimated by the scientific community. This limited appreciation for the pervasiveness of recursive movement can be attributed to its study by parallel lines of research, with different methodologies and nomenclature, and almost no cross referencing among them. Among these lines of studies are traplining behavior in foraging ecology, path recursions in movement ecology and the ecology of fear in predator–prey studies. We synthesize these three lines of research, to underline the mechanisms driving these patterns and create a conceptual model for recursive movement behavior across species and spatio-temporal scales. The emergence and complexity of recursive movement patterns are determined by the rate of resource recovery, environmental...

A factorial design experiment as a pilot study for noninvasive genetic sampling

Noninvasive genetic sampling has increasingly been used in ecological and conservation studies during the last decade. A major part of the noninvasive genetic literature is dedicated to the search for optimal protocols, by comparing different methods of collection, preservation and extraction of DNA from noninvasive materials. However, the lack of quantitative comparisons among these studies and the possibility that different methods are optimal for different systems make it difficult to decide which protocol to use. Moreover, most studies that have compared different methods focused on a single factor – collection, preservation or extraction – while there could be interactions between these factors. We designed a factorial experiment, as a pilot study, aimed at exploring the effect of several collection, preservation and extraction methods, and the interactions between them, on the quality and amplification success of DNA obtained from Asiatic wild ass (Equus hemionus) faeces in Israel. The amplification success rates of one mitochondrial DNA and four microsatellite markers differed substantially as a function of collection, preservation and extraction methods and their interactions. The most efficient combination for our system integrated the use of swabs as a collection method with preservation at −20 °C and with the Qiagen DNA Stool Kit with modifications as the DNA extraction method. The significant interaction found between the collection, preservation methods and the extraction methods reinforces the importance of conducting a factorial design experiment, rather than examining each factor separately, as a pilot study before initiating a full‐scale noninvasive research project.

Inference and Analysis of Population Structure Using Genetic Data and Network Theory

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition’s modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/).

Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass

Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re‐introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re‐introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re‐introduced populations genetic diversity could have significant consequences for the long‐term persistence of the population in the Negev. The stochastic modelling approach and the use of allele‐frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited.

Characterizing wild ass pathways using a non-invasive approach: applying least-cost path modelling to guide field surveys and a model selection analysis

Movement of animals is a key process affecting population dynamics. Information on factors that affect pathway use is essential for identifying and protecting pathways, and important for maintaining connectivity among populations. We present an innovative, non-invasive, approach for predicting pathways of reintroduced Asiatic wild ass (Equus hemionus) in Israel, which is based on understanding the effects of landscape factors on pathways use. The approach includes: Predicting pathways, by employing a least cost pathway (LCP) GIS models based on several landscape factors, so as to efficiently direct a field survey and explore the wild ass’s general preferences of pathway types; Collecting empirical data by surveying the dung density of wild ass along each of the predicted pathways and using the data as an index of pathway use; Evaluating the predicted pathways against the empirical data collected, to estimate the general pathway preferences of the wild ass; and Developing and evaluating alternative generalized linear models, according to a priori hypotheses based on empirical data so as to quantify the effect of different landscape factors on pathway use. The analyses were conducted for the entire landscape, and then for two distinct landscape types, open landscape and landscape-barriers (mountain ridges), as subsets of the entire landscape. There were clear differences in the mean number of faeces counts between the LCPs, indicating that the wild ass prefers certain pathway types as a function of landscape features. We further found that the factors affecting E. hemionus pathway usage—vegetation; slopes; canyons; and 4-wheel drive routes—varied largely between the two major landscape types studied, demonstrating the importance of studying space use patterns at different landscape terrains. This information can be applicable to landscape planning measures that aim to enhance protection of the species. This approach provides a framework for studying animal space-use patterns of a variety of species, including elusive species, in a heterogeneous landscape.