Digital Commons Network^™

Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner

Andrew Ozga

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon …

Decadal Effects Of Thinning On Understory Light Environments And Plant Community Structure In A Subtropical Forest, Ho-Chen Tsai, Jyh-Min Chiang, Ryan Mcewan, Teng-Chiu Lin

Ryan McEwan

Canopy-opening disturbance such as thinning has immediate and substantive effects on understory microclimate and therefore the establishment and growth of understory plants. A large number of studies have reported the effects of thinning on tree growth, but few studies have examined long-term effects of thinning on understory light environments and species and functional diversity of understory plants. Even less is known whether the change in understory plant community structure observed following canopy disturbance is short-lived and would diminish as the canopy closes or a long lasting due to legacy effects. We examined the effects of an experimental removal of 25% …

Five-Year Response Of Spontaneous Vegetation To Removal Of Invasive Amur Bush Honeysuckle Along An Urban Creek, Rebecca W. Dolan, Kelly H. Brown

Rebecca W. Dolan

Non-native invasive species have major impacts on landscapes worldwide, but their effects in urban areas are not well documented. We quantified the response of naturally regenerating vegetation along an urban creek to removal of the invasive shrub Lonicera maackii (Amur Bush Honeysuckle). Over the 5-year study, species richness more than doubled. Most new plants were native, disturbance-adapted, early successional species. Trend analysis of function traits revealed annuals that rely on seed dispersal by wind or externally on animals were significantly overrepresented among new plants in comparison to their proportion in the countywide species pool. Increased species richness did not result …

What Controls Tropical Reef Fish Populations: Recruitment Or Benthic Mortality? An Example In The Caribbean Reef Fish Haemulon Flavolineatum, M. J. Shulman, John C. Ogden

John Ogden

Recruitment from a planktonic larval stage has been proposed to be an important factor in limiting populations of marine organisms, particularly tropical reef fishes. We monitored recruitment and population densities of juvenile size classes In French grunt Haemulon flavolineatum (Haemulidae) from October 1978 through December 1980 In a portion of Tague Bay, St. Croix, U. S. Virgin Islands. Within our study area, 95 % of new recruits settled onto the sand and seagrass lagoon floor and within a few weeks migrated to nearby reefs; the remaining 5'10 settled directly onto reef structures. Mean annual recruitment rate was 1.8 recruits per …

Mode And Rate Of Evolution Of Haemosporidian Mitochondrial Genomes: Timing The Radiation Of Avian Parasites, Patricia Parker, M Andreína Pacheco, Nubia E. Matta, Gediminas Valkiūnas, Beatriz Mello, Craig E. Stanley Jr, Miguel Lentino, Maria Alexandra Garcia-Amado, Michael Cranfield, Sergei L Kosakovsky Pond, Ananias A. Escalante

Patricia Parker

Beyond Bivariate Correlations: Three-Block Partial Least Squares Illustrated With Vegetation, Soil, And Topography, Daehyun Kim, Thomas J. Dewitt, César S. B. Costa, John A. Kupfer, Ryan W. Mcewan, J. Anthony Stallins

Ryan McEwan

Ecologists, particularly those engaged in biogeomorphic studies, often seek to connect data from three or more domains. Using three-block partial least squares regression, we present a procedure to quantify and define bi-variance and tri-variance of data blocks related to plant communities, their soil parameters, and topography. Bi-variance indicates the total amount of covariation between these three domains taken in pairs, whereas tri-variance refers to the common variance shared by all domains. We characterized relationships among three domains (plant communities, soil properties, topography) for a salt marsh, four coastal dunes, and two temperate forests spanning several regions in the world. We …

The Friesner Herbarium (But) Of Butler University, Rebecca Dolan

Rebecca W. Dolan

The Friesner Herbarium (BUT) of Butler University is a collection of over 100,000 specimens built from the personal herbarium of Ray C. Friesner. He and other botanists at Butler amassed one of the largest and most complete collections of Indiana plants. Active exchange from the 1920’s through the 1940’s increased the holdings of plants from other states. Although the collection does not contain many type specimens, it is rich in vouchers from floristic and ecological studies conducted in the first half of the 20th century and published in the scientific journal,Butler University Botanical Studies.

From Shelf To Shelf: Assessing Historical And Contemporary Genetic Differentiation And Connectivity Across The Gulf Of Mexico In Gag, Mycteroperca Microlepis, Nathaniel Kenneth Jue, Thierry Brule, Felicia C. Coleman, Christopher C. Koenig

Nathaniel Jue

The Global Decline Of Reptiles, Deja’ Vu Amphibians, J. Whitfield Gibbons, David E. Scott, Travis J. Ryan, Kurt A. Buhlmann, Tracey D. Tiuberville, Brian S. Metts, Judith L. Greene, Tony Mills, Yale Leiden, Sean Poppy, Christopher T. Winne

Travis J. Ryan

Reptile species are declining on a global scale. Six significant threats to reptile populations are habitat loss and degradation, introduced invasive species, environmental pollution, disease, unsustainable use, and global climate change.

What Can We Learn From Confusing Olivella Columellaris And O. Semistriata (Olivellidae, Gastropoda), Two Key Species In Panamic Sandy Beach Ecosystems?, Alison I. Troost, Samantha D. Rupert, Ariel Z. Cyrus, Frank V. Paladino, Benjamin F. Dattilo, Winfried S. Peters

Benjamin F. Dattilo

Abstract: Olivella columellaris (Sowerby 1825) and O. semistriata (Gray 1839) are suspension-feeding, swash-surfing snails on tropical sandy beaches of the east Pacific. While they often are the numerically dominant macrofaunal element in their habitats, their biology is poorly understood; the two species actually have been confused in all of the few publications that address their ecology. Frequent misidentifications in publications and collections contributed also to an overestimation of the geographic overlap of the two species. To provide a sound taxonomic basis for further functional, ecological, and evolutionary investigations, we evaluated the validity of diagnostic traits in wild populations and museum …

Social Organization Of Neotoma Micropus, The Southern Plains Woodrat, Sarah A. Conditt, David O. Ribble

David O Ribble

This study described the social organization of Neotoma micropus, the southern plains woodrat, using radiotelemetry. We studied woodrats from September 1994 through April 1995 at the Urban Wilderness Reserve in S Bexar County, Texas. Sixteen individuals (three adult males, 11 adult females, and two subadult males) were radiocollared and located in the evening or early morning duringJanuary and February. Seventy-four percent of female radiolocations and 57% of male radiolocations were from their respective nests. No more than one adult individual was observed at any nest at the same time. Males had significantly larger (x = 1899 m2) home ranges than …

Social Organization Of Neotoma Micropus, The Southern Plains Woodrat, Sarah A. Conditt, David O. Ribble

David O Ribble

This study described the social organization of Neotoma micropus, the southern plains woodrat, using radiotelemetry. We studied woodrats from September 1994 through April 1995 at the Urban Wilderness Reserve in S Bexar County, Texas. Sixteen individuals (three adult males, 11 adult females, and two subadult males) were radiocollared and located in the evening or early morning duringJanuary and February. Seventy-four percent of female radiolocations and 57% of male radiolocations were from their respective nests. No more than one adult individual was observed at any nest at the same time. Males had significantly larger (x = 1899 m2) home ranges than …

Accounting For False Positive Detection Error Induced By Transient Individuals, Chris Sutherland, D Elston, X. Lambin

Chris Sutherland

The Role Of Tooth Enamel Mechanical Properties In Primate Dietary Adaptation, Paul J. Constantino, James Jw Lee, Yvonne Gerbig, Adam Hartstone-Rose, Mauricio Talebi, Brian Lawn, Peter Lucas

Paul J. Constantino

Primate teeth adapt to the physical properties of foods in a variety of ways including changes in occlusal morphology, enamel thickness, and overall size. We conducted a comparative study of extant primates to examine whether their teeth also adapt to foods through variation in the mechanical properties of the enamel. Nanoindentation techniques were used to map profiles of elastic modulus and hardness across tooth sections from the enamel-dentin junction to the outer enamel surface in a broad sample of primates including apes, Old World monkeys, New World monkeys, and lemurs. The measured data profiles feature considerable overlap among species, indicating …

Chapter 12 Evolutionary Conservation Biology, Sujan Henkanaththegedara, Craig Stockwell

Sujan Henkanaththegedara

From Structure To Function: The Ecology Of Host-Associated Microbial Communities, Courtney Jaime Robinson, Brendan J M Bohannan, Vincent Bensan Young

Courtney Robinson

Individual Differences In Exploratory And Antipredator Behaviour In Juvenile Smallmouth Bass (Micropterus Dolomieu), Kelly L. Smith, Jeffrey Gibson Miner, Daniel D. Wiegmann, Steven P. Newman

Jeffrey Gibson Miner

The correlation of individual behaviour in different contexts, known as a behavioural syndrome, constrains the optimization of behaviour within each context. Recent studies reveal that the strength of syndromes differs amongst populations and over individual ontogeny. In this study, exploratory behaviour in an unfamiliar environment and behavioural responses to a simulated predator attack in the presence of food were measured in juvenile smallmouth bass (Micropterus dolomieu). The results revealed a syndrome: individuals who actively explored the unfamiliar environment also behaved more boldly in the presence of the model predator. The syndrome implies a tradeoff between collecting information about one's environment …

Rules Of Engagement: Interspecies Interactions That Regulate Microbial Communities, Ainslie Little, Courtney Jaime Robinson, S Brook Peterson, Kenneth F. Raffa, Jo Handelsman

Courtney Robinson

Molecules, Morphology And Fossils: A Comprehensive Approach To Odonate Phylogeny And The Evolution Of The Odonate Wing, T. Heath Ogden

T. Heath Ogden

We undertook a comprehensive morphological and molecular phylogenetic analysis of dragonfly phylogeny, examining both extant and fossil lineages in simultaneous analyses. The legitimacy of higher-level family groups and the phylogenetic relationship between families were tested. Thirteen families were supported as monophyletic (Aeshnidae, Calopterygidae, Chlorocyphidae, Euphaeidae, Gomphidae, Isostictidae, Lestidae, Libellulidae, Petaluridae, Platystictidae, Polythoridae, Pseudostigmatidae and Synthemistidae) and eight as non-monophyletic (Amphipterygidae, Coenagrionidae, Corduliidae, Megapodagrionidae, Protoneuridae and Synlestidae), although Perilestidae and Platycnemididae were recovered as monophyletic under Bayesian analyses. Nine families were represented by one species, thus monophyly was not tested (Epiophlebiidae, Austropetaliidae, Chlorogomphidae, Cordulegastridae, Macromiidae, Chorismagrionidae, Diphlebiidae, Lestoideidae and Pseudolestidae). Epiprocta …

Esa And Environmental Justice, George Middendorf, Charles Nilon

George Middendorf

No abstract provided.

Evaluation Of Eelgrass Mitigation And Fishery Enhancement Structures In San Diego Bay, California, Daniel Pondella Ii

Daniel Pondella

To offset habitat loss and increase fishery production, an eelgrass mitigation habitat was completed in San Diego Bay, California in 1997. This mitigation effort consisted of the transplantation of eelgrass, Zostera marina L., in the western portion of the bay. In addition to the establishment of a new eelgrass bed, four enhancement reefs made of either quarry rock or concrete rubble were created to further enhance fishery stocks and the area's ecosystem. Two design criteria and a direct comparison between quarry rock and concrete reefs were examined in this 5-yr pilot program. The newly created eelgrass habitat quickly performed at …

Conservation Medicine On The Galápagos Islands: Partnerships Among Behavioral, Population, And Veterinary Scientists, Patricia G. Parker, Noah Kerness Whiteman, R. Eric Miller

Patricia Parker

No abstract provided.

Post-Fire Recovery Of Acorn Production By Four Oak Species In Southern Ridge Sandhill Association In South-Central Florida, Warren Abrahamson, J.N. Layne

Warren G. Abrahamson, II

No abstract provided.

Bird Distribution And Conservation In The Ailao Mountains, Yunnan, China, Zhijun Wang, Chris Carpenter, Stephen S. Young

Stephen Young

Factors Influencing Maternal Behaviour In A Burrower Bug, Sehirus Cinctus (Heteroptera: Cydnidae), Scott Kight

Scott Kight

Review Essay Of Two Books On The History Of Science, Charles Kay Smith

Charles Kay Smith

Contrary to what I was taught in high school in the mid-1940s, science is no longer defined as an inductive methodology for immaculately conceiving culture-free truth after sifting through a huge data base of objective facts. For without some prior hypothesis to guide her, a scientist would not be able to decide which facts were relevant. Nowadays hypotheses can come from anywhere in the imagination or culture within which the scientist is working. The importance of a scientific hypothesis is that it be framed in such a way that it can be falsified when tested. Science now has a history …