[MARMAM] UPDATE: SOCPROG 2.6, and generalized affiliation indices
SOCPROG is a set of programs for analyzing the social systems (as well as movements and populations) of animals. It has been used often for cetacean studies. A new and updated version of SOCPROG, SOCPROG2.6 (both compiled and uncompiled downloads) is available at: http://myweb.dal.ca/hwhitehe/social.htm. This version includes new a network diagram drawing routine, and calculates and analyzes generalized affiliation indices, which I think may be of value to some users (see below). The new version is compatible with MATLAB2015a and also fixes a few bugs. I hope this helps. Let me know about any problems that remain, or have been introduced. Thanks Hal Hal Whitehead (hwhit...@dal.ca) Dalhousie University Whitehead, H. and R. James. 2015. Generalized affiliation indices extract affiliations from social network data. Methods in Ecology and Evolution Available at: http://whitelab.biology.dal.ca/labpub.htm Summary 1. In the analysis of animal social networks, a common challenge has been distinguishing affiliations - active preferences of pairs of individuals to interact or associate with one another - from other, structural, causes of association or interaction. Such structural factors can include patterns of use of the habitat in time and space, gregariousness and differential association rates among age/sex classes. 2. In an approach with similarities to the multiple regression quadratic assignment procedures test, we suggest calculating generalized affiliation indices as the residuals from a regression of the measures of association or interaction on structural predictor variables, such as gregariousness and spatiotemporal overlap. If the original data are association indices or counts of interactions, then generalized linear models with binomial or Poisson error structures, respectively, can be used in place of linear regression. Anscombe or deviance residuals can be used to assess the significance of particular affiliation indices. 3. Generalized affiliation indices can be used as the weights of links in a social network representation. They can then be portrayed in network diagrams or cluster diagrams and used to calculate network statistics, to delineate communities by maximizing modularity and to test for overall affiliation using data-stream permutation tests. 4. We evaluate the effectiveness of such generalized affiliation indices using simulated and real association data, finding that the method removes much of the effect of structural variables on association patterns, revealing real affiliations. While the approach is very promising, it is limited by the extent to which the input predictor variables represent important structural factors. ___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
[MARMAM] Paper: Conflicting rates of increase in the sperm whale population of the eastern Caribbean
We would like to announce the publication of the following paper: H. Whitehead and S. Gero (2015) Conflicting rates of increase in the sperm whale population of the eastern Caribbean: positive rates do not reflect a healthy population. Endangered Species Research 27: 207–218 Abstract: Observed rates of increase calculated from trends in the numbers of animals present in a population should generally agree with those estimated from life-history data. However, for a small population of individually identified sperm whales Physeter macrocephalus occupying the waters of the eastern Caribbean there is a discrepancy. Using a mark-recapture analysis that included heterogeneity in identification, the population, numbering about 156 adults (95% CI 126−195) in 1998, has been increasing at 3.4% yr−1(95% CI: 1.0−5.7% yr-1). However, a 2-stage matrix population model including unweaned calves and adults (and excluding mature males), whose parameters were estimated directly from empirical data, gave a projected rate of increase of −2.7% yr−1(95% CI: −5.4 to −0.4% yr−1). This estimate is primarily sensitive to calculated adult mortality. The discrepancy between the observed and projected rates of increase for this population may be explained by a high, probably anthropogenic, mortality of sperm whales in the eastern Caribbean, coupled with immigration from surrounding regions, so the area becomes an attractive sink (ecological trap). The analysis emphasizes the fragility of sperm whale populations. More generally, our analysis of this population shows that a positive observed rate of increase is not necessarily a sign of a healthy population. This case study highlights the importance of analysing populations of endangered species using multiple methodologies and with a solid base of individual-level empirical data based on longitudinal monitoring. The paper is Open Access at: http://www.int-res.com/articles/esr2015/27/n027p207.pdf Hal Whitehead Dalhousie University hwhit...@dal.ca ___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
[MARMAM] Inferring Animal Densities from Tracking Data Using Markov Chains
MARMAM readers may be interested in this paper: Whitehead H, Jonsen ID (2013) Inferring Animal Densities from Tracking Data Using Markov Chains. PLoS ONE 8(4): e60901. doi:10.1371/journal.pone.0060901 Available at: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.006 0901 Abstract: The distributions and relative densities of species are keys to ecology. Large amounts of tracking data are being collected on a wide variety of animal species using several methods, especially electronic tags that record location. These tracking data are effectively used for many purposes, but generally provide biased measures of distribution, because the starts of the tracks are not randomly distributed among the locations used by the animals. We introduce a simple Markov-chain method that produces unbiased measures of relative density from tracking data. The density estimates can be over a geographical grid, and/or relative to environmental measures. The method assumes that the tracked animals are a random subset of the population in respect to how they move through the habitat cells, and that the movements of the animals among the habitat cells form a time-homogenous Markov chain. We illustrate the method using simulated data as well as real data on the movements of sperm whales. The simulations illustrate the bias introduced when the initial tracking locations are not randomly distributed, as well as the lack of bias when the Markov method is used. We believe that this method will be important in giving unbiased estimates of density from the growing corpus of animal tracking data. Abstract ___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
[MARMAM] Status of northern bottlenose whale
We have just published a paper entitled "Uncertain status of the northern bottlenose whale Hyperoodon ampullatus: population fragmentation, legacy of whaling and current threats". It is available on Open Access at: http://www.int-res.com/abstracts/esr/v19/n1/p47-61/ The abstract is below. Hal Whitehead (hwhit...@dal.ca) and Sascha Hooker. Whitehead, H. and S.K. Hooker. 2012. Uncertain status of the northern bottlenose whale (Hyperoodon ampullatus): population fragmentation, legacy of whaling, and current threats. Endangered Species Research 19: 47-61. ABSTRACT: The northern bottlenose whale Hyperoodon ampullatus is the best-known beaked whale species, but its conservation status remains very uncertain. A medium-sized cetacean that lives in the deeper waters of the northern North Atlantic, it is remarkable for its deep dives and inquisitiveness towards ships. There seem to have been of the order of 10 whales prior to 40 yr of intense whaling beginning in the 1880s, and this population was undoubtedly heavily reduced by 1920. The effects of a second phase of whaling between 1937 and 1973 are contentious, and current abundance estimates are patchy. There are suggestions of metapopulation structure (even at the scale of 50 km) in the western Atlantic among populations that do not appear to migrate. In the eastern Atlantic, data on population structure and migrations are few and confusing. Whales are incidentally caught in fishing gear and interact with fisheries off Labrador, Canada. They may also be affected by underwater noise. However, the population consequences of these and other anthropogenic stressors, particularly within this unknown metapopulation structure, are very uncertain. In some respects, such as the paucity of sightings on major whaling grounds off mainland Norway and Labrador, the picture that we have is disturbing. Analyses of genes, contaminants and vocalizations, as well as photoidentification and satellite tag data, can inform about population structure, migrations, life history parameters, current population sizes, and threats. ___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
[MARMAM] Industrial Research Chairs in Marine Animal Tracking
Dalhousie University, Faculty of Science, Department of Biology. The Department of Biology at Dalhousie University (http://biology.dal.ca) is accepting applications for two Industrial Research Chairs, a Senior and an Associate Chair, both to work in collaboration with AMIRIX-VEMCO (http://www.vemco.ca). The successful candidates will be expected to go through the proposal and peer review process run by NSERC (http://www.nserc-crsng.gc.ca/Professors-Professeurs/CFS-PCP/IRC- PCI_eng.asp). The appointment of a Senior Chair will be at the tenured, full Professor level; the appointment of an Associate Chair will be at the probationary tenure-track Assistant or Associate Professor level. A PhD is required for both positions. The successful candidate for the Senior Chair will be an internationally recognized, outstanding scientist with demonstrated success in research, graduate training and undergraduate teaching, as well as in service to the academic community. The successful candidate for the Associate Chair will be a scientist with demonstrated potential to become an internationally recognized and outstanding scientist. One of the appointments is for a FIELD-ORIENTED MARINE BIOLOGIST with expertise and interest in the use of acoustic tracking, telemetry and bio- logging approaches as a backbone for interdisciplinary studies linking organism condition, behaviour and other attributes with the environment. The other appointment is for a QUANTITATIVE ECOLOGIST with expertise and interest in advancing the analysis of electronic tracking data to assist in the understanding of marine animal movement patterns, behaviour, and distribution in conservation and resource management contexts. For more information, see: http://www.ecoevo.ca/common/AD%20IRC%20FINAL%20OCT%206%2020 10.doc Posted by Hal Whitehead, Dalhousie University ___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
[MARMAM] ABSTRACT: Estimating Abundance From One-Dimensional Passive Acoustic Surveys
The following paper may be of interest. A .pdf of this paper (and others) is available at: http://whitelab.biology.dal.ca/labpub.htm Hal Whitehead Estimating Abundance From One-Dimensional Passive Acoustic Surveys ABSTRACT Conventional distance sampling, the most-used method of estimating animal density and abundance, requires ranges to detected individuals, which are not easily measured for vocalizations. However, in some circumstances the sequential pattern of detection of vocalizations along a transect line gives information about the range of detection. Thus, from a one-dimensional acoustic point-transect survey (i.e., records of vocalizations detected or not detected at regularly spaced listening stations) it is possible to obtain a useful estimate of density or abundance. I developed equations for estimation of density for one- dimensional surveys. Using simulations I found that for the method to have little bias when both range of detection and rate of vocalization need to be estimated, stations needed to be spaced at 30-80% of the range of detection and the rate of vocalization should be >0.7. If either the range of detection or rate of vocalization is known, conditions are relaxed, and when both parameters are known the method works well almost universally. In favorable conditions for one-dimensional methods, estimated abundances have overall errors not much larger than those from conventional line-transect distance sampling. The methods appeared useful when applied to real acoustic data from whale surveys. The techniques may also be useful in surveys with nonacoustic detection of animals. JOURNAL OF WILDLIFE MANAGEMENT 73(6):1000-1009; 2009 DOI: 10.2193/2008-303 HAL WHITEHEAD, Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada ___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
[MARMAM] Abstract: Diversity of deep-water cetaceans and global warming
The following paper has recently been published: Whitehead, H., B. McGill and B. Worm. 2008. Diversity of deep- water cetaceans in relation to temperature: implications for ocean warming. Ecology Letters 11: 1198-1207. Abstract: Understanding the effects of natural environmental variation on biodiversity can help predict response to future anthropogenic change. Here we analyse a large, long-term data set of sightings of deep-water cetaceans from the Atlantic, Pacific and Indian Oceans. Seasonal and geographic changes in the diversity of these genera are well predicted by a convex function of sea- surface temperature peaking at c. 21 oC. Thus, diversity is highest at intermediate latitudes an emerging general pattern for the pelagic ocean. When applied to a range of Intergovernmental Panel on Climate Change global change scenarios, the predicted response is a decline of cetacean diversity across the tropics and increases at higher latitudes. This suggests that deep-water oceanic communities that dominate > 60% of the planet's surface may reorganize in response to ocean warming, with low-latitude losses of diversity and resilience. There is a .pdf at http://whitelab.biology.dal.ca/labpub.htm. Hal Whitehead Department of Biology Dalhousie University ___ MARMAM mailing list MARMAM@lists.uvic.ca https://lists.uvic.ca/mailman/listinfo/marmam
