Conservation of the critically endangered frog Telmatobufo bullocki in fragmented temperate forests of Chile : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Conservation Biology at Massey University, Albany, New Zealand

Amphibians are currently facing several threats and are suffering severe population declines and extinction worldwide. Telmatobufo bullocki (Anura: Calyptocephalellidae) is one of the rarest and most endangered amphibian species in Chile's temperate forests. It is the fifth most evolutionarily distinct and globally endangered (EDGE) amphibian in the world, and one of the world's top 100 priority species for conservation (Zoological Society of London, 2011).This stream-breeding frog is micro-endemic to the coastal Nahuelbuta mountain range in central-south Chile (37°C - 38°50' S), a hot-spot for conservation. This area has suffered severe loss and fragmentation of native forest, which has been replaced by extensive commercial plantations of exotic pines and eucalyptus. Despite its potential detrimental effects, the impact of native forest loss on this species has not been studied before. Furthermore, few historical observations exist, and the ecology and behaviour of the species is poorly known. In addition, current status and location of extant populations are uncertain, which makes conservation and targeted habitat protection difficult. Through the use of different approaches and modern conservation tools this thesis aims to make a significant contribution to the conservation of T.bullocki and its habitat. Historical and new locations were surveyed to identify extant populations. A distribution modeling approach (i.e. Maxent) was used to infer the species’ distribution within Nahuelbuta, generate a predictive habitat suitability map, identify important environmental associations, and assess the impact of main environmental threats (i.e. native forest loss, climate change).Field-based research (e.g. surveys, radio-tracking) was done to extend the ecological and behavioural knowledge of the species (e.g. movement patterns and habitat use), and identify critical aquatic and terrestrial habitat for protection (i.e. core habitat). Mitochondrial and specifically developed microsatellite genetic markers were used to measure levels of intra-specific genetic variability, define genetic population structure and connectivity, infer evolutionary history (phylogeography), estimate effective population size and detect demographic changes (e.g. bottlenecks). Finally, a landscape genetics approach was used to relate landscape characteristics to contemporary patterns of gene flow, and identify important landscape features facilitating (i.e. corridors) or hindering (i.e. barriers) genetic connectivity between populations. Telmatobufo bullocki was found in nine basins within Nahuelbuta, including historic and new locations. Presence of T. bullocki was positively related to the amount of native forests in the landscape. However, some populations persist in areas dominated by exotic plantations. Some frogs were found living under mature pine plantation adjacent to native forest, but no frogs were found in core plantation areas.T. bullocki makes extensive use of terrestrial habitat adjacent to breeding streams during the post-breeding season, moving up to 500 m away from streams. A core terrestrial habitat of at least 220 m from streams is proposed for the protection of populations. Population genetics and phylogeography revealed significant population structure. The northernmost and disjunct population of Chivilingo is geographically and genetically isolated from all other sampled populations and was identified as a separate evolutionary significant unit (ESU). The population of Los Lleulles was also identified as a separate management unit, while the remaining populations were grouped into two clusters forming a larger and more connected metaC population. Connectivity within groups was high, suggesting individuals are able to disperse between neighbouring basins. Levels of genetic diversity were not homogeneous, and were lowest at Los Lleulles and highest at Caramávida. Results suggest disjunct populations are at highest risk and should be prioritised for restoration and habitat protection, while management of metaCpopulations should aim at maintaining and improving connectivity among basins. Landscape genetic results identified streams and riparian habitat as dispersal pathways, and least-cost-path analysis was used to identify a potential connectivity network

A hierarchical model to estimate the abundance and biomass of salmonids by using removal sampling and biometric data from multiple locations

We present a Bayesian hierarchical model to estimate the abundance and the biomass of brown trout (Salmo trutta fario) by using removal sampling and biometric data collected at several stream sections. The model accounts for (i) variability of the abundance with fish length (as a distribution mixture), (ii) spatial variability of the abundance, (iii) variability of the catchability with fish length (as a logit regression model), (iv) spatial variability of the catchability, and (v) residual variability of the catchability with fish. Model measured variables are the areas of the stream sections as well as the length and the weight of the caught fish. We first test the model by using a simulated dataset before using a 3-location, 2-removal sampling dataset collected in the field. Fifteen model alternatives are compared with an index of complexity and fit by using the field dataset. The selected model accounts for variability of the abundance with fish length and stream section and variability of the catchability with fish length. By using the selected model, 95% credible interval estimates of the abundances at the three stream sections are (0.46,0.59), (0.90,1.07), and (0.56,0.69) fish/m2. Respective biomass estimates are (9.68, 13.58), (17.22, 22.71), and (12.69, 17.31) g/m2

Geoadditive Regression Modeling of Stream Biological Condition

Indices of biotic integrity (IBI) have become an established tool to quantify the condition of small non-tidal streams and their watersheds. To investigate the effects of watershed characteristics on stream biological condition, we present a new technique for regressing IBIs on watershed-specific explanatory variables. Since IBIs are typically evaluated on anordinal scale, our method is based on the proportional odds model for ordinal outcomes. To avoid overfitting, we do not use classical maximum likelihood estimation but a component-wise functional gradient boosting approach. Because component-wise gradient boosting has an intrinsic mechanism for variable selection and model choice, determinants of biotic integrity can be identified. In addition, the method offers a relatively simple way to account for spatial correlation in ecological data. An analysis of the Maryland Biological Streams Survey shows that nonlinear effects of predictor variables on stream condition can be quantified while, in addition, accurate predictions of biological condition at unsurveyed locations are obtained

Sequential Bayesian updating for Big Data

The velocity, volume, and variety of big data present both challenges and opportunities for cognitive science. We introduce sequential Bayesian updat-ing as a tool to mine these three core properties. In the Bayesian approach, we summarize the current state of knowledge regarding parameters in terms of their posterior distributions, and use these as prior distributions when new data become available. Crucially, we construct posterior distributions in such a way that we avoid having to repeat computing the likelihood of old data as new data become available, allowing the propagation of information without great computational demand. As a result, these Bayesian methods allow continuous inference on voluminous information streams in a timely manner. We illustrate the advantages of sequential Bayesian updating with data from the MindCrowd project, in which crowd-sourced data are used to study Alzheimer’s Dementia. We fit an extended LATER (Linear Ap-proach to Threshold with Ergodic Rate) model to reaction time data from the project in order to separate two distinct aspects of cognitive functioning: speed of information accumulation and caution

Attentive monitoring of multiple video streams driven by a Bayesian foraging strategy

In this paper we shall consider the problem of deploying attention to subsets of the video streams for collating the most relevant data and information of interest related to a given task. We formalize this monitoring problem as a foraging problem. We propose a probabilistic framework to model observer's attentive behavior as the behavior of a forager. The forager, moment to moment, focuses its attention on the most informative stream/camera, detects interesting objects or activities, or switches to a more profitable stream. The approach proposed here is suitable to be exploited for multi-stream video summarization. Meanwhile, it can serve as a preliminary step for more sophisticated video surveillance, e.g. activity and behavior analysis. Experimental results achieved on the UCR Videoweb Activities Dataset, a publicly available dataset, are presented to illustrate the utility of the proposed technique.Comment: Accepted to IEEE Transactions on Image Processin

Inferring the Andromeda Galaxy's mass from its giant southern stream with Bayesian simulation sampling

M31 has a giant stream of stars extending far to the south and a great deal of other tidal debris in its halo, much of which is thought to be directly associated with the southern stream. We model this structure by means of Bayesian sampling of parameter space, where each sample uses an N-body simulation of a satellite disrupting in M31's potential. We combine constraints on stellar surface densities from the Isaac Newton Telescope survey of M31 with kinematic data and photometric distances. This combination of data tightly constrains the model, indicating a stellar mass at last pericentric passage of log(M_s / Msun) = 9.5+-0.1, comparable to the LMC. Any existing remnant of the satellite is expected to lie in the NE Shelf region beside M31's disk, at velocities more negative than M31's disk in this region. This rules out the prominent satellites M32 or NGC 205 as the progenitor, but an overdensity recently discovered in M31's NE disk sits at the edge of the progenitor locations found in the model. M31's virial mass is constrained in this model to be log(M200) = 12.3+-0.1, alleviating the previous tension between observational virial mass estimates and expectations from the general galactic population and the timing argument. The techniques used in this paper, which should be more generally applicable, are a powerful method of extracting physical inferences from observational data on tidal debris structures.Comment: 27 pages, 10 figures. Accepted by MNRA