Life Sciences Commons^™

Toward A Synthesis Of Conservation And Animal Welfare Science, David Fraser

David Fraser, PhD

Conservation biology and animal welfare science are multidisciplinary fields of research that address social concerns about animals. Conservation biology focuses on wild animals, works at the level of populations, ecological systems and genetic types, and deals with threats to biodiversity and ecological integrity. Animal welfare science typically focuses on captive (often domestic) animals, works at the level of individuals and groups, and deals with threats to the animals’ health and quality of life. However, there are many areas of existing or potential overlap: (i) many real-life problems, such as environmental contamination, urban development and transportation, create problems for animals that …

Rating Harms To Wildlife: A Survey Showing Convergence Between Conservation And Animal Welfare Views, S. Dubois, D. Fraser

David Fraser, PhD

Human activities may cause conservation concerns when animal populations or ecosystems are harmed and animal welfare concerns when individuals are harmed. In general, people are concerned with one or the other, as the concepts may be regarded as separate or even at odds. An online purposive survey of 339 British Columbians explored differences between groups that varied by gender, residency, wildlife engagement level and value orientation (conservation-oriented or animal welfare-oriented), to see how they rated the level of harm to wildlife caused by different human activities. Women, urban residents, those with low wildlife engagement, and welfare-orientated participants generally scored activities …

The Use Of Judgement Bias To Assess Welfare In Farm Livestock, L. Baciadonna, A. G. Mcelligott

Alan G. McElligott, PhD

The development of accurate measures of animal emotions is important for improving and promoting animal welfare. Cognitive bias indicates the effect of emotional states on cognitive processes, such as memory, attention, and judgement. Cognitive bias tests complement existing behavioural and physiological measures for assessing the valence of animal emotions indirectly. The judgement bias test has been used to assess emotional states in non-human animals; mainly in laboratory settings. The aim of this review is to summarise the findings on the use of the judgement bias test approach in assessing emotions in non-human animals, focusing in particular on farm livestock. The …

Fallow Deer Polyandry Is Related To Fertilization Insurance, Elodie F. Briefer, Mary E. Farrell, Thomas J. Hayden, Alan G. Mcelligott

Alan G. McElligott, PhD

Polyandry is widespread, but its adaptive significance is not fully understood. The hypotheses used to explain its persistence have rarely been tested in the wild and particularly for large, long-lived mammals. We investigated polyandry in fallow deer, using female mating and reproduction data gathered over 10 years. Females of this species produce a single offspring (monotocous) and can live to 23 years old. Overall, polyandry was evident in 12 % of females and the long-term, consistent proportion of polyandrous females observed, suggests that monandry and polyandry represent alternative mating strategies. Females were more likely to be polyandrous when their first …

Goats Favour Personal Over Social Information In An Experimental Foraging Task, Luigi Baciadonna, Alan G. Mcelligott, Elodie F. Briefer

Alan G. McElligott, PhD

Animals can use their environments more efficiently by selecting particular sources of information (personal or social), according to specific situations. Group-living animals may benefit from gaining information based on the behaviour of other individuals. Indeed, social information is assumed to be faster and less costly to use than personal information, thus increasing foraging efficiency. However, when food sources change seasonally or are randomly distributed, individual information may become more reliable than social information. The aim of this study was to test the use of conflicting personal versus social information in goats (Capra hircus), in a foraging task.We found that goats …

Assortative Mating In Fallow Deer Reduces The Strength Of Sexual Selection, Mary E. Farrell, Elodie Briefer, Alan G. Mcelligott

Alan G. McElligott, PhD

Background: Assortative mating can help explain how genetic variation for male quality is maintained even in highly polygynous species. Here, we present a longitudinal study examining how female and male ages, as well as male social dominance, affect assortative mating in fallow deer (Dama dama) over 10 years. Assortative mating could help explain the substantial proportion of females that do not mate with prime-aged, high ranking males, despite very high mating skew. We investigated the temporal pattern of female and male matings, and the relationship between female age and the age and dominance of their mates.

Results: The peak of …

Catalinia, A New Scorpion Genus From Southern California, Usa And Northern Baja California, Mexico (Scorpiones: Vaejovidae), Michael E. Soleglad, Richard F. Ayrey, Matthew R. Graham, Victor Fet

Victor Fet

Genus Catalinia, gen. nov. (Scorpiones: Vaejovidae) is described from southern California, USA and Baja California, Mexico. The genus is composed of four species formerly placed in Pseudouroctonus: Catalinia minima (Kraepelin, 1911), comb. nov. (type species), C. andreas (Gertsch et Soleglad, 1972), comb. nov., C. castanea (Gertsch et Soleglad, 1972), comb. nov., and C. thompsoni, comb. nov. (Gertsch et Soleglad, 1972). Major diagnostic characters of Catalinia include a carapace with a very weak anterior indentation, a very stout metasoma with little or no tapering from segment I to V, and a mating plug with two partial bases. Evidence is presented suggesting …

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, Catherine Putonti

Konstantin Läufer

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 …

Freshwater Metaviromics And Bacteriophages: A Current Assessment Of The State Of The Art In Relation To Bioinformatic Challenges, Katherine Bruder, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhan C. Watkins, Catherine Putonti

Catherine Putonti

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with …

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, Catherine Putonti

Catherine Putonti

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 …

Clusters Of Alpha Satellite On Human Chromosome 21 Are Dispersed Far Onto The Short Arm And Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering

Catherine Putonti

Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the …

18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti

Catherine Putonti

Despite their critical role in the aquatic food web and nutrient cycling, microeukaryotes within freshwater environments are under-studied. Herein we present the first high-throughput molecular survey of microeukaryotes within Lake Michigan. Every two weeks from May 13 to August 5, 2014, we collected surface water samples from the nearshore waters of four Chicago area beaches: Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach. Four biological replicates were collected for each sampling date and location, resulting in 112 samples. Eighty-nine of these samples were surveyed through targeted sequencing of the V7 and V8 regions of the 18S rDNA gene. …

Floristic Response To Urbanization: Filtering Of The Bioregional Flora In Indianapolis, Indiana, Usa, Rebecca W. Dolan, Myla F.J. Aronson, Andrew L. Hipp

Rebecca W. Dolan

PREMISE OF THE STUDY: Globally, urban plant populations are becoming increasingly important, as these plants play a vital role in ameliorating effects of ecosystem disturbance and climate change. Urban environments act as filters to bioregional flora, presenting survival challenges to spontaneous plants. Yet, because of the paucity of inventory data on plants in landscapes both before and after urbanization, few studies have directly investigated this effect of urbanization. METHODS: We used historical, contemporary, and regional plant species inventories for Indianapolis, Indiana USA to evaluate how urbanization filters the bioregional flora based on species diversity, functional traits, and phylogenetic community structure. …

The Second Record Of A Relict Akrav Israchanani Levy, 2007 (Scorpiones: Akravidae) From Levana Cave, Israel, Victor Fet, Michael E. Soleglad, Sergei L. Zonstein, Israel Naaman, Shlomi Lubaton, Boaz Langford, Amos Frumkin

Victor Fet

We report the remnants of five new scorpion specimens discovered dead in Levana Cave in Israel in December 2015. We confirm that they belong to the relict scorpion Akrav israchanani Levy, 2007 (Akravidae), famously described from the neighboring Ayyalon Cave, also from dead specimens. The details of morphology of the new specimens are given; they match completely the characters of A. israchanani redescribed by Fet, Soleglad & Zonstein (2011). This second record indicates a wider distribution of this unique cave scorpion, which, however, is extinct in both caves. There is still no evidence that live populations of this species exist.

2017_Murphy Et Al._Food Habits Of A Small Fl Bear Population In Endangered Ecosystem.Pdf, Sean M. Murphy, Wade A. Ulrey, Joseph M. Guthrie, David S. Maehr, Warren G. Abrahamson Ii, Sutton C. Maehr, John J. Cox

Warren G. Abrahamson, II

Genetic Demography At The Leading Edge Of The Distribution Of A Rabies Virus Vector, Antoinette J. Piaggio, Amy L. Russell, Ignacio A. Osorio, Alejandro J. Ramirez, Justin W. Fischer, Jennifer L. Neuwald, Annie E. Tibbels, Luis Lecuona, Gary F. Mccracken

Amy L. Russell

Hypogenic Versus Epigenic Subterranean Ecosystem: Lessons From Eastern Iberian Peninsula, Alberto Sendra, Policarp Garay, Vicente M. Ortuño, José D. Gilgado, Santiago Teruel, Ana Sofia P.S. Reboleira

Ana Sofia P.S. Reboleira

Over the last 40 years, hypogenic karst/caves have become well known and hypogene speleogenesis has been used to explain the formation of some of the largest subterranean maze caves. These hypogenic systems involve confined aquifers with upwards flow, responsible for their karstification. Such spaces begun and could be remain isolated from the surface and the contiguous subterranean habitats, including the shallow ones. We studied the invertebrate fauna and the geology/speleogenesis of two recently opened caves from Eastern Iberian Peninsula, which clearly showed features of hypogenic origin. Their scarce faunistic composition, formed by non cave-adapted fauna, is similar to other hypogenic …

African Penguins Follow The Gaze Direction Of Conspecifics, Christian Nawroth, Livio Favaro

Christian Nawroth, Ph.D.

Why Animal Welfarism Continues To Fail, Lori Marino

Lori Marino, PhD

Welfarism prioritizes human interests over the needs of nonhuman animals. Despite decades of welfare efforts other animals are mostly worse off than ever before, being subjected to increasingly invasive and harmful treatments, especially in the factory farming and biomedical research areas. A legal rights-based approach is essential in order for other animals to be protected from the varying ethical whims of our species.

Measuring Artificial Light Levels On Florida Sea Turtle Nesting Beaches From 1992 To 2013 Using Satellite Data, Ketaira Phillips

KeTaira Phillips

A Test Of An Antipredatory Function Of Conspicuous Plastron Coloration In Hatchling Turtles, Beth Reinke, Ryan Calsbeek, Devi Stuart-Fox

Beth Reinke

Competition And Propagule Density Affect Sexual And Clonal Propagation Of A Weed, Daniel Z. Atwater, Wonjae Kim, Daniel R. Tekiela, Jacob N. Barney

Wonjae Kim

A Sonic Net Excludes Birds From An Airfield: Implications For Reducing Bird Strike And Crop Losses, John P. Swaddle, Dana L. Moseley, Mark H. Hinders, Elizabeth P. Smith

John Swaddle

Collisions between birds and aircraft cause billions of dollars of damages annually to civil, commercial, and military aviation. Yet technology to reduce bird strike is not generally effective, especially over longer time periods. Previous information from our lab indicated that filling an area with acoustic noise, which masks important communication channels for birds, can displace European Starlings (Sturnus vulgaris) from food sources. Here we deployed a spatially controlled noise (termed a “sonic net”), designed to overlap with the frequency range of bird vocalizations, at an airfield. By conducting point counts, we monitored the presence of birds for four weeks before …

Acoustic Space Is Affected By Anthropogenic Habitat Features: Implications For Avian Vocal Communication, Caitlin R. Kight, Mark H. Hinders, John P. Swaddle

John Swaddle

Human-altered landscapes often include structural features, such as higher levels of impervious surface cover (ISC) and less vegetation, that are likely to affect the transmission of avian vocalizations. We investigated the relationships between human habitat modifications and signal transmission by measuring four acoustic parameters—persistence, reverberation, and signal-to-noise ratio (SNR) of broadcast tones, as well as absolute ambient noise level—in each of 39 avian breeding territories across an anthropogenic disturbance gradient. Using a geographic information system, we quantified the amounts of different habitat features (e.g., ISC, grass, trees) at each site; a principal component analysis was used to identify which of …

Experimental Exposure To Urban And Pink Noise Affects Brain Development And Song Learning In Zebra Finches (Taenopygia Guttata), Dominique A. Potvin, Michael T. Curcio, John P. Swaddle, Scott A. Macdougall-Shackleton

John Swaddle

Recently, numerous studies have observed changes in bird vocalizations—especially song—in urban habitats. These changes are often interpreted as adaptive, since they increase the active space of the signal in its environment. However, the proximate mechanisms driving cross-generational changes in song are still unknown. We performed a captive experiment to identify whether noise experienced during development affects song learning and the development of song-control brain regions. Zebra finches (Taeniopygia guttata) were bred while exposed, or not exposed, to recorded traffic urban noise (Study 1) or pink noise (Study 2). We recorded the songs of male offspring and compared these to fathers’ …

Blood Mercury Levels Of Zebra Finches Are Heritable: Implications For The Evolution Of Mercury Resistance, Kenton A. Buck, Claire W. Varian-Ramos, Daniel A. Cristol, John P. Swaddle

John Swaddle

Mercury is a ubiquitous metal contaminant that negatively impacts reproduction of wildlife and has many other sub-lethal effects. Songbirds are sensitive bioindicators of mercury toxicity and may suffer population declines as a result of mercury pollution. Current predictions of mercury accumulation and biomagnification often overlook possible genetic variation in mercury uptake and elimination within species and the potential for evolution in affected populations. We conducted a study of dietary mercury exposure in a model songbird species, maintaining a breeding population of zebra finches (Taeniopygia guttata) on standardized diets ranging from 0.0–2.4 μg/g methylmercury. We applied a quantitative genetics …

Reproductive Success Of Eastern Bluebirds (Siala Sialis) On Suburban Golf Courses, Kerri L. Cornell, Caitlin R. Kight, Ryan B. Burdge, Alex R. Gunderson, Joanna K. Hubbard, Allyson K. Jackson, Joshua E. Leclerc, Marie L. Pitts, John P. Swaddle, Daniel A. Cristol

John Swaddle

Understanding the role of green space in urban—suburban landscapes is becoming critical for bird conservation because of rampant habitat loss and conversion. Although not natural habitat, golf courses could play a role in bird conservation if they support breeding populations of some native species, yet scientists remain skeptical. In 2003–2009, we measured reproduction of Eastern Bluebirds (Siala sialis) in Virginia on golf courses and surrounding reference habitats, of the type that would have been present had golf courses not been developed on these sites (e.g., recreational parks, cemeteries, agriculture land, and college campus). We monitored >650 nest boxes …

Revbayes: Bayesian Phylogenetic Inference Using Graphical Models And An Interactive Model-Specification Language, Sebastian Höhna, Michael J. Landis, Tracy A. Heath, Nicolas Lartillot, Brian R. Moore, John P. Huelsenbeck, Fredrik Ronquist

Tracy Heath

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive …

Total-Evidence Dating Under The Fossilized Birth–Death Process, Chi Zhang, Tanja Stadler, Serena Klopfstein, Tracy A. Heath, Fredrik Ronquist

Tracy Heath

Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth–death (FBD) process, which has been used to model speciation, extinction, and fossilization rates that can vary over time …

Regressive Evolution In The Mexican Cave Tetra, Astyanax Mexicanus, Meredith E. Protas, Melissa Conrad, Joshua B. Gross, Clifford Tabin, Richard Borowsky

Meredith Protas

Cave adapted animals generally have reduced pigmentation and eyes, but the evolutionary forces driving the reductions are unknown; Darwin famously questioned the role of natural selection in eye loss in cave fishes; “As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse” [1]. We studied the genetic basis of this phenomenon in the Mexican cave tetra, Astyanax mexicanus, by mapping the quantitative trait loci (QTL) determining differences in eye/lens sizes and melanophore number between cave and surface fish. In addition, we mapped …