Phylogeographic Triangulation: Using Predator-Prey-Parasite Interactions to Infer Population History from Partial Genetic Information

Phylogeographic studies, which infer population history and dispersal movements from intra-specific spatial genetic variation, require expensive and time-consuming analyses that are not always feasible, especially in the case of rare or endangered species. On the other hand, comparative phylogeography of species involved in close biotic interactions may show congruent patterns depending on the specificity of the relationship. Consequently, the phylogeography of a parasite that needs two hosts to complete its life cycle should reflect population history traits of both hosts. Population movements evidenced by the parasite’s phylogeography that are not reflected in the phylogeography of one of these hosts may thus be attributed to the other host. Using the wild rabbit (Oryctolagus cuniculus) and a parasitic tapeworm (Taenia pisiformis) as an example, we propose comparing the phylogeography of easily available organisms such as game species and their specific heteroxenous parasites to infer population movements of definitive host/predator species, independently of performing genetic analyses on the latter. This may be an interesting approach for indirectly studying the history of species whose phylogeography is difficult to analyse directly

Phylogenetic triangulation: Using predator-prey-parasite interactions to infer population history from partial genetic information

Phylogeographic studies, which infer population history and dispersal movements from intra-specific spatial genetic variation, require expensive and time-consuming analyses that are not always feasible, especially in the case of rare or endangered species. On the other hand, comparative phylogeography of species involved in close biotic interactions may show congruent patterns depending on the specificity of the relationship. Consequently, the phylogeography of a parasite that needs two hosts to complete its life cycle should reflect population history traits of both hosts. Population movements evidenced by the parasite's phylogeography that are not reflected in the phylogeography of one of these hosts may thus be attributed to the other host. Using the wild rabbit (Oryctolagus cuniculus) and a parasitic tapeworm (Taenia pisiformis) as an example, we propose comparing the phylogeography of easily available organisms such as game species and their specific heteroxenous parasites to infer population movements of definitive host/predator species, independently of performing genetic analyses on the latter. This may be an interesting approach for indirectly studying the history of species whose phylogeography is difficult to analyse directly

Multiplicative random walk Metropolis-Hastings on the real line

In this article we propose multiplication based random walk Metropolis Hastings (MH) algorithm on the real line. We call it the random dive MH (RDMH) algorithm. This algorithm, even if simple to apply, was not studied earlier in Markov chain Monte Carlo literature. The associated kernel is shown to have standard properties like irreducibility, aperiodicity and Harris recurrence under some mild assumptions. These ensure basic convergence (ergodicity) of the kernel. Further the kernel is shown to be geometric ergodic for a large class of target densities on $\mathbb{R}$. This class even contains realistic target densities for which random walk or Langevin MH are not geometrically ergodic. Three simulation studies are given to demonstrate the mixing property and superiority of RDMH to standard MH algorithms on real line. A share-price return data is also analyzed and the results are compared with those available in the literature

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

A comparison of three methods for estimating call densities of migrating bowhead whales using passive acoustic monitoring

TAM thanks partial support by Centro de Estatistica e Aplicações, Universidade de Lisboa (funded by FCT—Fundação para a Ciência e a Tecnologia, Portugal, through the project UID/MAT/00006/2013).Various methods for estimating animal density from visual data, including distance sampling (DS) and spatially explicit capture-recapture (SECR), have recently been adapted for estimating call density using passive acoustic monitoring (PAM) data, e.g., recordings of animal calls. Here we summarize three methods available for passive acoustic density estimation: plot sampling, DS, and SECR. The first two require distances from the sensors to calling animals (which are obtained by triangulating calls matched among sensors), but SECR only requires matching (not localizing) calls among sensors. We compare via simulation what biases can arise when assumptions underlying these methods are violated. We use insights gleaned from the simulation to compare the performance of the methods when applied to a case study: bowhead whale call data collected from arrays of directional acoustic sensors at five sites in the Beaufort Sea during the fall migration 2007–2014. Call detections were manually extracted from the recordings by human observers simultaneously scanning spectrograms of recordings from a given site. The large discrepancies between estimates derived using SECR and the other two methods were likely caused primarily by the manual detection procedure leading to non-independent detections among sensors, while errors in estimated distances between detected calls and sensors also contributed to the observed patterns. Our study is among the first to provide a direct comparison of the three methods applied to PAM data and highlights the importance that all assumptions of an analysis method need to be met for correct inference.Publisher PDFPeer reviewe

Application of asymptotic expansions of maximum likelihood estimators errors to gravitational waves from binary mergers: the single interferometer case

In this paper we describe a new methodology to calculate analytically the error for a maximum likelihood estimate (MLE) for physical parameters from Gravitational wave signals. All the existing litterature focuses on the usage of the Cramer Rao Lower bounds (CRLB) as a mean to approximate the errors for large signal to noise ratios. We show here how the variance and the bias of a MLE estimate can be expressed instead in inverse powers of the signal to noise ratios where the first order in the variance expansion is the CRLB. As an application we compute the second order of the variance and bias for MLE of physical parameters from the inspiral phase of binary mergers and for noises of gravitational wave interferometers . We also compare the improved error estimate with existing numerical estimates. The value of the second order of the variance expansions allows to get error predictions closer to what is observed in numerical simulations. It also predicts correctly the necessary SNR to approximate the error with the CRLB and provides new insight on the relationship between waveform properties SNR and estimation errors. For example the timing match filtering becomes optimal only if the SNR is larger than the kurtosis of the gravitational wave spectrum

Stochastically Consistent Caching and Dynamic Duty Cycling for Erratic Sensor Sources

We present a novel dynamic duty cycling scheme to maintain stochastic consistency for caches in sensor networks. To reduce transmissions, base stations often maintain caches for erratically changing sensor sources. Stochastic consistency guarantees the cache-source deviation is within a pre-specified bound with a certain confidence level. We model the erratic sources as Brownian motions, and adaptively {\it predict} the next cache update time based on the model. By piggybacking the next update time in each regular data packet, we can dynamically adjust the relaying nodes' duty cycles so that they are awake before the next update message arrives, and are sleeping otherwise. Through simulations, we show that our approach can achieve very high source-cache fidelity with low power consumption on many real-life sensor data. On average, our approach consumes 4-5 times less power than GAF~\cite{gaf}, and achieves 50\% longer network lifetime

A beamforming video recorder for integrated observations of dolphin behavior and vocalizations

Author Posting. © Acoustical Society of America, 2005. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 117 (2005): 1005-1008, doi:10.1121/1.1831284.In this Letter we describe a beamforming video recorder consisting of a video camera at the center of a 16 hydrophone array. A broadband frequency-domain beamforming algorithm is used to estimate the azimuth and elevation of each detected sound. These estimates are used to generate a visual cue indicating the location of the sound source within the video recording, which is synchronized to the acoustic data. The system provided accurate results in both lab calibrations and a field test. The system allows researchers to correlate the acoustic and physical behaviors of marine mammals during studies of social interactions.This research was funded by NSF Ocean Sciences CAREER award 9733391

Aspectos associados à degradação ambiental e ao uso de efluentes na agricultura do Brasil.

A exploração dos recursos naturais ao longo da história desconsiderou os impactos causados sobre a sua continuidade no atendimento às necessidades humanas. A água apresenta a maior preocupação a nível mundial, e a sua escassez torna o uso racional uma atitude inevitável. A utilização de efluentes na agricultura pode contribuir na redução da exploração dos recursos hídricos. Esse estudo apresentou uma discussão e levantamento bibliográfico sobre reaproveitamento de resíduo - efluente/água residuária na agricultura - utilizando como ferramentas: o histórico da exploração e a degradação dos recursos naturais em áreas urbanas e rurais; e um panorama do uso de efluentes na agricultura. Conclui-se que a degradação dos recursos naturais, aliada as mudanças climáticas e ao constante aumento da população e de suas necessidades, são os subsídios básicos para que se estimulem as pesquisas quanto ao uso de efluentes, na agricultura e atividades afins

Estado actual de la investigación arqueometalúrgica prehistórica en la provincia de Málaga

The lack of data on prehistoric metallurgical activities in Málaga made local prehistorians think that all the metal artefacts recovered in the province were of non-local origin. As a result of a project funded by the Junta de Andalucía, new data have been collected and we can begin to outline the development and socioeconomic importance that metal technologies have in different parts of Málaga throughout prehistory.La práctica inexistencia de datos sobre actividades metalúrgicas prehistóricas en Málaga y el vacío investigador que sobre este aspecto existía en la provincia habían creado un estado de opinión entre los prehistoriadores locales tendente a considerar como de origen extraprovincial la totalidad de los artefactos metálicos prehistóricos recuperados. Como resultado de un proyecto subvencionado por la Junta de Andalucía, estos datos que faltaban comienzan ahora a ser recuperados, y se puede empezar a trazar un esbozo general del desarrollo e importancia socieconómica que este grupo de tecnologías tuvieron en los diversos ambientes geográficos de la provincia de Málaga durante la prehistoria