Contamination source inference in water distribution networks

We study the inference of the origin and the pattern of contamination in water distribution networks. We assume a simplified model for the dyanmics of the contamination spread inside a water distribution network, and assume that at some random location a sensor detects the presence of contaminants. We transform the source location problem into an optimization problem by considering discrete times and a binary contaminated/not contaminated state for the nodes of the network. The resulting problem is solved by Mixed Integer Linear Programming. We test our results on random networks as well as in the Modena city network

An effective and efficient method for identification of contamination sources in water distribution systems based on manual grab‐sampling

This is the author accepted manuscript. The final version is available from American Geophysical Union via the DOI in this recordData Availability Statement: The data will eventually be deposited in the general repository Zenodo by the time the article is accepted, and the data are now available as Supporting Information for review purpose.Most of the contamination source localization methods for water distribution systems (WDSs) assume the availability of accurate water quality models and multi-parameter online sensors, which are often out of reach of many water utilities. To address this, a novel manual grab-sampling method (MGSM) is developed to effectively and efficiently locate continuous contamination sources in a WDS using a dynamic and cyclical sampling strategy. The grab samples are collected at a pre-specified number of hydrants by the corresponding teams followed by laboratory tests. The MGSM optimizes the sampling plan at each cycle by making the probability of contamination source(s) in each sub-network as equal as possible, where sub-networks are determined by the selected hydrants and current flow pipe directions. The CS's size is reduced at each cycle by exploiting sample testing results obtained in the previous cycle until there are no further hydrants to sample from. Two real-world WDSs are used to demonstrate the effectiveness of the proposed MGSM. The results obtained show that the MGSM can significantly reduce the spatial range of the CS (to about 5% of the entire WDS) for a range of scenarios including multiple contamination sources and pipe flow direction changes. We found that an optimal number of sampling teams exists for a given WDS, representing a balanced trade-off between detection efficiency and sampling/testing budgets. Due to its relative simplicity, the proposed MGSM can be used in engineering practice straightaway and it represents a viable alternative to the methods associated with water quality models and sensors.Excellent Youth Natural Science Foundation of Zhejiang Province, ChinaNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaHong Kong Research Grants CouncilEuropean Research Counci

A Partition-Based Random Search Method for Multimodal Optimization

Practical optimization problems are often too complex to be formulated exactly. Knowing multiple good alternatives can help decision-makers easily switch solutions when needed, such as when faced with unforeseen constraints. A multimodal optimization task aims to find multiple global optima as well as high-quality local optima of an optimization problem. Evolutionary algorithms with niching techniques are commonly used for such problems, where a rough estimate of the optima number is required to determine the population size. In this paper, a partition-based random search method is proposed, in which the entire feasible domain is partitioned into smaller and smaller subregions iteratively. Promising regions are partitioned faster than unpromising regions, thus, promising areas will be exploited earlier than unpromising areas. All promising areas are exploited in parallel, which allows multiple good solutions to be found in a single run. The proposed method does not require prior knowledge about the optima number and it is not sensitive to the distance parameter. By cooperating with local search to refine the obtained solutions, the proposed method demonstrates good performance in many benchmark functions with multiple global optima. In addition, in problems with numerous local optima, high-quality local optima are captured earlier than low-quality local optima

Evolutionary Inference from Admixed Genomes: Implications of Hybridization for Biodiversity Dynamics and Conservation

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population persistence in a shifting adaptive landscape. Chapter I employed population genomic approaches to examine potential effects of habitat modification on species boundary stability in co-occurring endemic fishes of the Colorado River basin (Gila robusta and G. cypha). Results showed how one potential outcome of hybridization might drive species decline: via a breakdown in selection against interspecific heterozygotes and subsequent genetic erosion of parental species. Chapter II explored long-term contributions of hybridization in an evolutionarily recent species complex (Gila) using a combination of phylogenomic and phylogeographic modelling approaches. Massively parallel computational methods were developed (and so deployed) to categorize sources of phylogenetic discordance as drivers of systematic bias among a panel of species tree inference algorithms. Contrary to past evidence, we found that hypotheses of hybrid origin (excluding one notable example) were instead explained by gene-tree discordance driven by a rapid radiation. Chapter III examined patterns of local ancestry in the endangered red wolf genome (Canis rufus) – a controversial taxon of a long-standing debate about the origin of the species. Analyses show how pervasive autosomal introgression served to mask signatures of prior isolation—in turn misleading analyses that led the species to be interpreted as of recent hybrid origin. Analyses also showed how recombination interacts with selection to create a non-random, structured genomic landscape of ancestries with, in the case of the red wolf, the ‘original’ species tree being retained only in low-recombination ‘refugia’ of the X chromosome. The final three chapters present bioinformatic software that I developed for my dissertation research to facilitate molecular approaches and analyses presented in Chapters I–III. Chapter IV details an in-silico method for optimizing similar genomic methods as used herein (RADseq of reduced representation libraries) for other non-model organisms. Chapter V describes a method for parsing genomic datasets for elements of interest, either as a filtering mechanism for downstream analysis, or as a precursor to targeted-enrichment reduced-representation genomic sequencing. Chapter VI presents a rapid algorithm for the definition of a ‘most parsimonious’ set of recombinational breakpoints in genomic datasets, as a method promoting local ancestry analyses as utilized in Chapter III. My three case studies and accompanying software promote three trajectories in modern hybridization research: How does hybridization impact short-term population persistence? How does hybridization drive macroevolutionary trends? and How do outcomes of hybridization vary in the genome? In so doing, my research promotes a deeper understanding of the role that hybridization has and will continue to play in governing the evolutionary fates of lineages at both contemporary and historic timescales

Conservation genomics: speciation of the Neotropical damselfly species Megaloprepus caerulatus – as a model for insect speciation in tropical rainforests

The work presented in this thesis is located at the interface between ecology, evolution and developmental biology. It addresses theories and questions in population biology, phylogeography and speciation as well as methodological approaches for applying Next Generation Sequencing (NGS) data. In the center of this thesis stands the world’s largest extant damselfly, Megaloprepus caerulatus, as a model system for primary rainforests

Uncovering the genomic basis of an extraordinary plant invasion

Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant's remarkable success as an invasive species.Peer reviewe

Annotation of Non-Model Species’ Genomes

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population structure, and assess genetic health. In addition, researchers can examine unique features of genes related to the health of a threatened species, such as genes involved in immune function, reproduction, environmental response, as well as evolutionary trends and niche adaptations. Recent developments in sequencing and software also allow researchers to examine the noncoding- “ome”, providing a glimpse into gene regulation, developmental pathways, and response to viral sequences and mobile elements. Characterization of the biogenesis pathways of noncoding RNAs has facilitated the development of RNA interference strategies which are increasingly being used in therapeutics, agriculture, and pest control. The focus of this project is to use available sequencing technology and computational methods to annotate the genome and small RNA pathways of non-model organisms

Cães (Canis lupus familiaris) da Península Ibérica do período Calcolítico: uma abordagem genómica

Os cães existem na Península Ibérica pelo menos desde o Paleolítico Superior; o resto arqueológico mais antigo data há cerca de 16,000 AP (Erralla, Espanha). Existem diferentes teorias sobre a origem dos cães na Europa. Estudos anteriores indicam que os cães podem ter chegado à Europa a partir de uma população domesticada de lobos oriundos da Ásia Oriental, ou a partir de duas populações de lobos geneticamente distintas da Eurásia Oriental e Ocidental, domesticadas independentemente, e que mais tarde, a população de cães da Eurásia Oriental se espalhou e substituiu parcialmente a população da Eurásia Ocidental. Um estudo recente focando na composição genética de 6 cães Ibéricos do período Mesolítico, sugeriu que uma domesticação local na Península Ibérica pode ter ocorrido na Europa pré-Neolítica. Considerando o debate mantido sobre a origem dos cães, é crucial desvendar a composição genética de populações passadas e periféricas da Europa – usando métodos específicos para recuperar e analisar o DNA ancestral, de diferentes períodos, a fim de investigar a origem e a trajetória evolutiva dos cães no seu global. Nomeadamente, pode revelar-se importante por fornecer dados sobre uma possível contribuição do lobo Ibérico para a origem dos primeiros cães Ibéricos e informação genómica potencialmente útil para a detecção de eventos de hibridação histórica entre o cão e o seu parente selvagem, o lobo Ibérico – uma subespécie endêmica e atualmente considerada “Em perigo” de extinção. Esta informação pode ser englobada aquando a definição de medidas de gestão e conservação futuras para a espécie selvagem lobo Ibérico. Neste trabalho, uma abordagem genómica (Next Generation Sequencing, NGS) foi a escolhida para recuperar sequências do genoma mitocondrial (mt) e nuclear de Canis de três sítios arqueológicos Ibéricos datados do Calcolítico [ca. 5,000- 4,000 anos atrás]: dois cães de Leceia em Oeiras, Portugal; dois cães de Casetón de La Era em Valladolid, Espanha; e um lobo de Penedo de Lexim em Mafra, Portugal. Utilizando as ferramentas de bioinformática actuais, esses genomas foram identificados e compilados. Além disso, para entender a relação de populações passadas/modernas, construiu-se uma rede filogenética (baseada num fragmento parcial da região controlo do mtDNA) reunindo 254 sequências de Canis, bem como uma árvore filogenética de 23 mitogenomas de Canis disponíveis em bases dados públicos. Embora a recuperação e análise do genoma nuclear sejam um maior desafio se proveniente de amostras ancestrais, este foi investigado para a identificação do sexo molecular desses 5 espécimes. Relativamente ao estudo dos cães pré-históricos da Ibéria, esta é a primeira tentativa de aplicar com sucesso o método NGS para investigar a sua composição genética. Neste estudo, foi possível: gerar sequências do genoma mitocondrial (com 1x a 17x de cobertura) e recuperar entre 0.09% e 3.75% do genoma nuclear endógeno das 5 amostras do Calcolítico; identificar haplótipos de DNA mitocondrial e atribuí-los a dois (A e C) dos quatro principais haplogrupos descritos para os cães (A, B, C e D); gerar dados genómicos de um lobo Ibérico do Calcolítico que, tanto quanto investiguei, constituem os primeiros dados genómicos de um espécime de lobo da Ibéria e desta cronologia. Os resultados mostram que os cães Ibéricos do Calcolítico apresentavam a mesma frequência de haplótipos do Haplogrupo A (Hg anteriormente presente neste território, em contraste com as outras regiões da Europa), bem como do Haplogrupo C (já presente em outras regiões da Europa desde o Paleolítico).Domestic dogs exist in the Iberian Peninsula at least since the Upper Late Palaeolithic; the oldest remain dated to 16,000 BP years old (Erralla, Spain). There are different theories about the origins of European dogs. Previous studies indicated that dogs may arrived in Europe from an Eastern Asia domesticated population of wolves, or that two genetically distinct wolf populations in Eastern and Western Eurasia may have been independently domesticated, and that afterwards the Eastern dog population spread and partially replaced an indigenous Western Eurasian dog population. A recent study focusing in the genetic composition of 6 Mesolithic Iberian dogs reported that a local domestication in the Iberia Peninsula may have occurred in pre-Neolithic Europe. Considering the debated origin of Iberian dogs, it is crucial to unravel the genetic composition of past European peripheral populations - using specific methods to recover and analyse ancient DNA, from different periods in order to further investigate their origins and evolutionary trajectories. Additionally, it may prove important to provide data on a possible contribution of the Iberian wolf to the origin of the first Iberian dogs and genomic information potentially useful for the detection of historical hybridization events between the dog and its wild relative, the Iberian wolf – a subspecies and an endemism currently considered “Endangered”. This information can be included in the definition of future management and conservation measures for the wild Iberian wolf species. In this work, a genomic approach (Next Generation Sequencing, NGS) was carried out to recover mitogenome and nuclear genomic data of Canis from three Iberian archaeological sites dated to the Chalcolithic [ca. 5,000-4,000 years BP], in particular: two dogs from Leceia in Oeiras, Portugal; two dogs from Casetón de La Era in Valladolid, Spain; and one wolf from Penedo de Lexim in Mafra, Portugal. Using the most up-to-date bioinformatic tools, their mitochondrial (mt) and nuclear genomes were sequenced. In addition, to understand the relationship of past/extant populations, a phylogenetic network (based on a partial fragment of the mtDNA control region) comprising 254 Canis sequences, as well as a phylogenetic tree of 23 Canis mitogenomes, publicly available, were constructed. Furthermore, the nuclear genome, although more challenging to recover and analyse from ancient samples, was investigated to molecularly assess the sex of these 5 Canis specimens. Regarding ancient Iberian dogs, this is the first attempt to successfully apply NGS methods to investigate their genomic composition. In this study, it was possible to: generate the draft of mitochondrial genomes (coverages ranged between 1x and 17x) and recover between 0.09% and 3.75% of endogenous nuclear genomic data of these 5 Canis specimens; identify mitochondrial DNA haplotypes and assign those to 2 (A and C) of the four major dog haplogroups described (A, B C and D); generate genetic data from a Chalcolithic wolf - to the best of my knowledge this is the first genomic data available from an Iberian wolf specimen from this chronology. The results shown that the Chalcolithic Iberian dogs had about the same frequency of Haplogroup A (previously present in this territory, but contrasting with other European regions), as well as of the Haplogroup C (already present in other European regions since the Paleolithic).Mestrado em Ecologia Aplicad