Estimation of bowhead whale (Balaena mysticetus) population density using spatially explicit capture-recapture (SECR) methods

Tese de mestrado em Bioestatística, Universidade de Lisboa, Faculdade de Ciências, 2019Management and conservation of wildlife populations is a major concern. Population density is a key ecological variable when making adequate decisions about them. A variety of methods can be used for estimating density. Capture-recapture (CR, also known as mark- recapture) methods are a popular choice, but ignoring the spatial component of captures has historically led to problems with resulting inferences on abundance. Spatially explicit capture- recapture (SECR) methods use the spatial information to solve two key problems of classical CR: defining a precise study area where captures occur over and reducing un modeled heterogeneity in capture probabilities. Arrays of Directional Autonomous Sea floor Acoustic Recorders (DASARs) recorded calls from the Bearing-Chukchi-Beaufort (BCB) population of bowhead whales during the autumn migration. The available passive acoustic data set was collected over 5 sites (with 3–13 sensors per site) and 8 years (2007–2014), and then processed via both automated and manual procedures. The automated procedure involved computer-processing by a multi-stage detection, classification and localization algorithm. In the manual procedure, calls were detected and classified by trained staff who manually listened to the recordings and examined spectrograms. The resulting manual data presents some pitfalls for density estimation, including non-independence among sensors caused by human intervention. The non-independence leads to an excess of calls being detected in all DASARs on a site. Data from the automated procedure does not suffer the non-independence issue, but the amount of ’singletons’ is approximately 15 times higher than in the manual data. ’Singletons’ are calls detected exclusively in one sensor and we assume they mostly comprise false positives. False positives are sounds classified as coming from the species of interest, but in reality are something else. Considering only automated data from 2013 and 2014, several approaches were performed to solve the excess of singletons. Density estimation with a standard SECR analysis was conducted according to the following approaches: i)ignoring the singletons problem and analyzing all calls; ii) removing the singletons; and iii) discarding a proportion of 1 – p false positives from the singletons. Simulated results were compared to verify the best approach. We also discuss a new approach by developing a SECR likelihood function that accommodates truncation of certain acoustic cues, specifically singletons. We have laid foundations for the analysis of this data set, but there are other possible research avenues to explore. Our next steps would include embedding additional information (like received levels and bearing angle) in the SECR formulation

Historical food-web changes in invaded fish communities in the lower Guadiana basin

Freshwater ecosystems are increasingly being reshaped by biological invasions, leading to biotic homogenization and biodiversity loss. However, the extent to which novel species may drive changes in food-web structure over time remains poorly understood. Clarifying changes in historical ecological processes is critical to inform conservation and restoration efforts in recipient ecosystems. Here, we address food-web changes associated with fish invasions in the Lower Guadiana Basin (LGB) over the past 40 years, by contrasting feeding relationships between museum-archived and contemporary specimens, using stable carbon (δ13C) and nitrogen (δ15N) ratios. Specifically, trophic niches of museum-archived fishes sampled throughout 1978–1987 and 1999–2004 corresponding to the initial establishment and spread of non-native fishes, respectively, were compared with those of fishes sampled in 2019, characterizing the integration of non-native species in the recipient ecosystem. We focused on five native species (Anaecypris hispanica, Cobitis paludica, Iberochondrostoma lemmingii, Squalius pyrenaicus and Squalius alburnoides) and four non-native species (Lepomis gibbosus, Australo heros facetus, Micropterus salmoides and Gambusia holbrooki) with potential to cover multiple trophic positions in the food-webs. We approached historical baseline resources using prey items in gut con tents of the museum-archived fishes and characterized primary producers and macroinvertebrates in 2019. Prior to analysis, samples were normalized for high lipid content and corrected for preservation. We found considerable asymmetries in niche partitioning among species as invasion progressed. Over time, native species tended to be displaced to lower trophic levels, while non-native species showed significantly higher trophic niches, driven mainly by increases in trophic (δ15N) range. Our study highlights that stable isotopes may provide important insights on historical food-web structure and particularly on processes underpinning ecological changes associated with anthropogenetic pressures on freshwater ecosystems.info:eu-repo/semantics/publishedVersio

Accommodating false positives within acoustic spatial capture–recapture, with variable source levels, noisy bearings and an inhomogeneous spatial density

Funding: Tiago Marques was partly supported by CEAUL (funded by FCT - Fundação para a Ciência e a Tecnologia, Portugal, through the project UIDB/00006/2020).Passive acoustic monitoring is a promising method for surveying wildlife populations that are easier to detect acoustically than visually. When animal vocalisations can be uniquely identified on an array of sensors, the potential exists to estimate population density through acoustic spatial capture–recapture (ASCR). However, sound classification is imperfect, and in some situations, a high proportion of sounds detected on just a single sensor (‘singletons’) are not from the target species. We present a case study of bowhead whale calls (Baleana mysticetus) collected in the Beaufort Sea in 2010 containing such false positives. We propose a novel extension of ASCR that is robust to false positives by truncating singletons and conditioning on calls being detected by at least two sensors. We allow for individual-level detection heterogeneity through modelling a variable sound source level, model inhomogeneous call spatial density, and include bearings with varying measurement error. We show via simulation that the method produces near-unbiased estimates when correctly specified. Ignoring source-level variation resulted in a strong negative bias, while ignoring inhomogeneous density resulted in severe positive bias. The case study analysis indicated a band of higher call density approximately 30 km from shore; 59.8% of singletons were estimated to have been false positives.Publisher PDFPeer reviewe