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Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six- or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.

Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.

The etiologic agent of plague, Yersinia pestis, is a gramnegative coccobacillus and a facultative intracellular pathogen. Y. pestis exhibited the highest overall mortality rate of any infectious disease from its [...]

Space use is a fundamental characteristic that informs our knowledge of social relationships and the degree to which individuals are territorial. Until recently, relatively little was known about the spatial ecology and social organization of swift foxes (Vulpes velox (Say, 1823)). We investigated space use of swift foxes on shortgrass prairie in northeastern Colorado. Our first objective was to evaluate sizes of seasonal and annual home ranges and core areas of 13 radio-collared swift foxes monitored continuously for 2 years. Our second objective was to compare home-range and core-area overlap of breeding pairs to that of neighboring foxes, including male-male, female-female, and nonbreeding female-male dyads. Home-range size in our study population was among the smallest previously reported for swift foxes. Males tended to have slightly larger home ranges and core areas than females, and home-range size was significantly larger in the breeding season than in both the pup-rearing and the dispersal seasons; sizes of core areas did not differ seasonally. Spatial overlap between breeding pairs was substantial, whereas spatial overlap between neighbors, particularly males, was low, suggesting territoriality. Key words: Vulpes velox, home range, core area, seasonal, overlap, territoriality. L'utilisation de l'espace est une caracteristique fondamentale qui permet de connaitre les relations sociales et l'importance de la territorialite chez les individus. Jusqu'a recemment, on savait relativement peu de choses sur l'ecologie spatiale et l'organisation sociale des renards veloces (Vulpes velox (Say, 1823)). Nous avons etudie l'utilisation de l'espace chez les renards veloces dans la prairie d'herbes courtes du nord-est du Colorado. Notre premier objectif etait d'evaluer les domaines vitaux saisonniers et annuels et les aires centrales de 13 renards veloces porteurs de colliers radio suivis continuellement pendant 2 annees. Notre second objectif etait de comparer le chevauchement des domaines vitaux et des aires centrales des couples reproducteurs a celui de renards voisins, incluant des dyades male-male, femelle-femelle et femelle-male non reproducteurs. La taille du domaine vital observe dans la population etudiee est parmi les plus petites jamais signalees chez le renard veloce. Les males ont tendance a posseder un domaine vital et une aire centrale plus etendus que ceux des femelles; la taille du domaine vital est significativement plus grande durant la saison de reproduction que durant les deux saisons d' elevage des petits et de dispersion. La taille des aires centrales ne varie pas en fonction de la saison. Le chevauchement spatial est considerable entre les couples reproducteurs, alors que le chevauchement spatial entre les voisins, particulierement les males, est faible, ce qui laisse croire a l'existence de territorialite. Mots-cles : Vulpes velox, domaine vital, aire centrale, saisons, chevauchement, territorialite. [Traduit par la Redaction], Introduction Space use is a fundamental behavioral and ecological characteristic that informs our knowledge of an animal's interactions with its environment, including relationships with others in the population and the [...]

To assess the value of molted feathers as a noninvasive source of DNA for genetic studies of Northern Goshawks (Accipiter gentilis), we isolated and quantified DNA from molted feathers and compared yields across five feather types. We also compared PCR success across the same five feather types using five microsatellite genetic markers of varying size. In addition, we compared DNA yields from a commonly used extraction method versus one we modified to increase DNA yield. Results indicated molted feathers provided on average 24 ng [micro][l.sup.-1] of DNA, which is a relatively high DNA yield compared to other noninvasive tissue sources. Tail feathers yielded significantly more DNA than primary, secondary, and smaller feathers, yet all feather sizes produced equally high rates of PCR success. Although our modified extraction method increased the time required for processing feathers, it resulted in significantly higher yields of DNA as compared to the unmodified protocol. Key words: Accipiter gentilis, DNA extraction, DNA yield, molted feathers, noninvasive genetic sampling, Northern Goshawk. Con el objetivo de determinar el valor de las plumas mudadas como metodo no invasivo para obtener ADN en estudios de Accipiter gentilis, aislamos y cuantificamos ADN de plumas mudadas y comparamos la utilidad de cinco tipos de plumas. Tambien comparamos la amplificacion de ADN por PCR entre los cinco tipos de plumas usando como marcadores geneticos cinco micro-satelites de diferentes tamanos. Ademas, comparamos la cantidad de ADN obtenida con un metodo de extraccion comunmente usado con la incorporacion de una modificacion que proponemos para incrementar la concentracion de ADN obtenida de las muestras. Nuestros resultados sugieren que las plumas mudadas proveen en promedio 24 ng [micro]l-1 de ADN, lo cual es relativamente alto comparado con el uso de otros tejidos como fuente de obtencion no invasivos. Significativamente mayor cantidad de ADN fue extraido de las plumas de la cola que de las terneras primarias, secundarias y plumas mas pequenas. Sin embargo, todos los tipos de pluma resultaron en altos niveles de amplificacion por PCR. A pesar de que el metodo de extraccion que proponemos incrementa el tiempo necesario para procesar las plumas, resulta en un aumento significativo de la cantidad de ADN extraido, comparado con el metodo tradicional.

Recent interest in characterizing infectious agents associated with bioterrorism has resulted in the development of effective pathogen genotyping systems, but this information is rarely combined with phenotypic data. Yersinia pestis, the aetiological agent of plague, has been well defined genotypically on local and worldwide scales using multi-locus variable number tandem repeat analysis (MLVA), with emphasis on evolutionary patterns using old isolate collections from countries where Y. pestis has existed the longest. Worldwide MLVA studies are largely based on isolates that have been in long-term laboratory culture and storage, or on field material from parts of the world where Y. pestis has potentially circulated in nature for thousands of years. Diversity in these isolates suggests that they may no longer represent the wild-type organism phenotypically, including the possibility of altered pathogenicity. This study focused on the phenotypic and genotypic properties of 48 Y. pestis isolates collected from 10 plague foci in and bordering Kazakhstan. Phenotypic characterization was based on diagnostic tests typically performed in reference laboratories working with Y. pestis. MLVA was used to define the genotypic relationships between the central-Asian isolates and a group of North American isolates, and to examine Kazakh Y. pestis diversity according to predefined plague foci and on an intermediate geographical scale. Phenotypic properties revealed that a large portion of this collection lacks one or more plasmids necessary to complete the blocked flea/mammal transmission cycle, has lost Congo red binding capabilities ([Pgm.sup.-]), or both. MLVA analysis classified isolates into previously identified biovars, and in some cases groups of isolates collected within the same plague focus formed a clade. Overall, MLVA did not distinguish unique phylogeographical groups of Y. pestis isolates as defined by plague foci and indicated higher genetic diversity among older biovars.