Life Sciences Commons^™

Convergence To Consensus In Heterogeneous Groups And The Emergence Of Informal Leadership, Sergey Gavrilets, Jeremy David Auerbach, Mark Van Vugt

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

When group cohesion is essential, groups must have efficient strategies in place for consensus decisionmaking. Recent theoretical work suggests that shared decision-making is often the most efficient way for dealing with both information uncertainty and individual variation in preferences. However, some animal and most human groups make collective decisions through particular individuals, leaders, that have a disproportionate influence on group decision-making. To address this discrepancy between theory and data, we study a simple, but general, model that explicitly focuses on the dynamics of consensus building in groups composed by individuals who are heterogeneous in preferences, certain personality traits (agreeability and …

Transatlantic Disjunction In Fleshy Fungi Iii: Gymnopus Confluens, Karen Hughes, Ronald H. Petersen

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Phylogeographic data indicate that DNA differences consistently exist between the North American and European allopatric populations of Gymnopus confluens. Conversely, pairing experiments show that collections from both populations were sexually compatible in vitro and detailed morphological examinations of numerous fresh and dried basidiomata do not produce qualitative differences. Percent ITS sequence divergence between Europe and North American collections of G. confluens was 3.25%. Species delineation metrics including Rosenberg’s P_AB statistic, P_ID metrics, R_RD ( randomly distributed) and PTP (Poisson Tree Processes ) gave mixed indications that North American and European populations were distinct at species rank. …

To Play Or Not To Play? That’S A Resource Abundance Question, Jeremy David Auerbach, Andrew R. Kanarek, Gordon M. Burghardt

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Although play occurs in a wide variety of animals, models of the origins of play behavior are lacking. We propose a novel computational model exploring the evolution of non-social frivolous play. Asexually reproducing semelparous animals can either rest or forage. Foraging occurs when an organism is below an energy threshold. Success is determined by the combination of skill and availability of resources, which declines over time but replenishes for each generation. Play was introduced as a mutant strategy: a frivolous activity that uses energy and increases the probability of dying over resting with no direct fitness benefit. Simulations show that …

Cloning Of Ribosomal Its Pcr Products Creates Frequent, Non-Random Chimeric Sequences – A Test Involving Heterozygotes Between Gymnopus Dichrous Taxa I And Ii., Karen Hughes, Samuel D. Morris, Ana L. Reboredo-Segovia

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Gymnopus dichrous exists in the southern Appalachians as two distinct entities with essentially identical nuclear ribosomal ITS1 sequences but differing ITS2 and LSU sequences (for convenience, called G. dichrous I and II). F₁ ITS heterozygotes between the two are routinely collected from nature. Cloning of ITS PCR products from F₁ heterozygotes produced sequences of both parental haplotypes but also numerous chimeric sequences (21.9%). The location of template switching was non-random leading to recovery of the same chimera several times and the chimeric region varied from 45bp to 300bp. By comparison, single-basidiospore isolates from heterozygote F₁ fruitbodies showed …

Two New Species Of Ramaria From Arkansas, Karen Hughes, Ronald H. Petersen, Jay Justice

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Two species of Ramaria from the Ozark region of Arkansas, USA, R. admiratia and R. calvodistalis, are proposed as new. They are described morphologically and placed molecularly within a large clade including taxa of ramarioid and cantharelloid fungi.

Iterates: An R Package For Implementing A Parametric Rate Comparison On Phylogenetic Trees, James A. Fordyce, Premal Shah, Benjamin M Fitzpatrick

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently used to infer historical, ecological, and evolutionary processes. The parametric rate comparison (PRC) is a method for detecting rate variation in trees that models branch lengths as random variables drawn from familiar statistical distributions. iteRates is a library of functions for the R statistical computing environment for implementing PRC on phylogenetic trees. Here, we describe some of the functions in iteRates for subtree identification, tree manipulation, applying the PRC and K-clades PRC analyses, and conducting a whole-tree randomization test.

Gymnopus Eneficola-Species Nova From Newfoundland, Ron Petersen, Karen Hughes, Andrus Voitk

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

In the course of a survey of dried collections of Gymnopus collected over some years in Newfoundland by AV and Foray Newfoundland & Labrador, a taxon was discovered which did not conform to other known eastern North American or European taxa of the genus. Occasional reports of taxa now placed in Gymnopus (formerly included in an expansive concept of Collybia) include those concerning Nova Scotia, summarized by Gourley, and Michigan, none of which, nor those of the even older publication by Coker and Beardslee circumscribed the proposed species from Newfoundland. In addition to morphological distinctions, DNA analysis also indicated that …

Meta-Analysis Reveals Evolution In Invasive Plant Species But Little Support For Evolution Of Increased Competitive Ability (Eica), E Felker-Quinn, J A. Schweitzer, J K. Bailey

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Ecological explanations for the success and persistence of invasive species vastly outnumber evolutionary hypotheses, yet evolution is a fundamental process in the success of any species. The Evolution of Increased Competitive Ability (EICA) hypothesis (Blossey and Nötzold 1995) proposes that evolutionary change in response to release from coevolved herbivores is responsible for the success of many invasive plant species. Studies that evaluate this hypothesis have used different approaches to test whether invasive populations allocate fewer resources to defense and more to growth and competitive ability than do source populations, with mixed results. We conducted a meta-analysis of experimental tests of …

Symbiote Transmission And Maintenance Of Extra-Genomic Associations, Benjuamin M. Fitzpatrick

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Symbiotes can be transmitted from parents to offspring or horizontally from unrelated hosts or the environment. A key question is whether symbiote transmission is similar enough to Mendelian gene transmission to generate and maintain coevolutionary associations between host and symbiote genes. Recent papers come to opposite conclusions, with some suggesting that any horizontal transmission eliminates genetic association. These studies are hard to compare owing to arbitrary differences in modeling approach, parameter values, and assumptions about selection. I show that associations between host and symbiote genes (extra-genomic associations) can be described by the same dynamic model as conventional linkage disequilibria between …

The Effects Of Insects, Nutrients, And Plant Invasion On Community Structure And Function Above- And Belowground, Phoebe Wright, Melissa A. Cregger, Lara Souza, Nathan J. Sanders, Aimee T. Classen

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Soil nutrient availability, invasive plants, and insect presence can directly alter ecosystem structure and function, but less is known about how these factors may interact. In this 6-year study in an old-field ecosystem, we manipulated insect abundance (reduced and control), the propagule pressure of an invasive nitrogen-fixing plant (propagules added and control), and soil nutrient availability (nitrogen added, nitrogen reduced and control) in a fully crossed, completely randomized plot design. We found that nutrient amendment and, occasionally, insect abundance interacted with the propagule pressure of an invasive plant to alter above- and belowground structure and function at our site. Not …

Explosive Diversification Following A Benthic To Pelagic Shift In Freshwater Fishes, Phillip R. Hollingsworth Jr., A M. Simons, J A. Fordyce, C D. Hulsey

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

BACKGROUND:

Interspecific divergence along a benthic to pelagic habitat axis is ubiquitous in freshwater fishes inhabiting lentic environments. In this study, we examined the influence of this habitat axis on the macroevolution of a diverse, lotic radiation using mtDNA and nDNA phylogenies for eastern North America's most species-rich freshwater fish clade, the open posterior myodome (OPM) cyprinids. We used ancestral state reconstruction to identify the earliest benthic to pelagic transition in this group and generated fossil-calibrated estimates of when this shift occurred. This transition could have represented evolution into a novel adaptive zone, and therefore, we tested for a period …

Fire Promotes Pollinator Visitation: Implications For Ameliorating Declines Of Pollination Services, Michael E. Van Nuland, Elliot N. Haag, Jessica Am Bryant, Quentin D. Read, Robert N. Klein, Morgan J. Douglas, Courtney E. Gorman, Trey D. Greenwell, Mark W. Busby, Jonathan Collins, Joseph T. Leroy, George Schuchmann, Jennifer A. Schweitzer, Joseph K. Bailey

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Pollinators serve critical roles for the functioning of terrestrial ecosystems, and have an estimated annual value of over $150 billion for global agriculture. Mounting evidence from agricultural systems reveals that pollinators are declining in many regions of the world, and with a lack of information on whether pollinator communities in natural systems are following similar trends, identifying factors which support pollinator visitation and services are important for ameliorating the effects of the current global pollinator crisis. We investigated how fire affects resource structure and how that variation influences floral pollinator communities by comparing burn versus control treatments in a southeastern …

Introgressive Hybridization In A Trophically Polymorphic Cichlid, C Darrin Hulsey, Francisco J. García-De-León

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Trophically polymorphic species could represent lineages that are rapidly diverging along an ecological axis or could phenotypically mark the collapse of species through introgressive hybridization. We investigated patterns of introgression between the trophically polymorphic cichlid fish Herichthys minckleyi and its relative H. cyanoguttatus using a combination of population genetics and species tree analyses. We first examined the distribution of mitochondrial haplotypes within the alternative H. minckleyi pharyngeal jaw morphotypes that are endemic to the small desert valley of Cuatro Ciénegas. We recovered two clusters of mitochondrial haplotypes. The first contained a number of slightly differentiated cytochrome b (cytb) …

Genetic Variation In Hippocampal Microrna Expression Differences In C57bl/6 J X Dba/2 J (Bxd) Recombinant Inbred Mouse Strains, Michael J. Parsons, Christina Grimm, Jose L. Paya-Cano, Cathy Fernandes, Lin Liu, Vivek M. Philip, Elissa J. Chesler, Wilfried Neitfeld, Hans Lehrach, Leonard C. Schalkwyk

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

miRNAs are short single-stranded non-coding RNAs involved in post-transcriptional gene regulation that play a major role in normal biological functions and diseases. Little is currently known about how expression of miRNAs is regulated. We surveyed variation in miRNA abundance in the hippocampus of mouse inbred strains, allowing us to take a genetic approach to the study of miRNA regulation, which is novel for miRNAs. The BXD recombinant inbred panel is a very well characterized genetic reference panel which allows quantitative trait locus (QTL) analysis of miRNA abundance and detection of correlates in a large store of brain and behavioural …

Frequency-Dependent Selection By Wild Birds Promotes Polymorphism In Model Salamanders, Benjamin M. Fitzpatrick, Kim Shook, Reuben Izally

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Co-occurrence of distinct colour forms is a classic paradox in evolutionary ecology because both selection and drift tend to remove variation from populations. Apostatic selection, the primary hypothesis for maintenance of colour polymorphism in cryptic animals, proposes that visual predators focus on common forms of prey, resulting in higher survival of rare forms. Empirical tests of this frequency-dependent foraging hypothesis are rare, and the link between predator behaviour and maintenance of variation in prey has been difficult to confirm. Here, we show that predatory birds can act as agents of frequency-dependent selection on terrestrial salamanders. Polymorphism for presence/absence of …

Belowground Interactions Shift The Relative Importance Of Direct And Indirect Genetic Effects, M A. Genung, J K. Bailey, J A. Schweitzer

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Intraspecific genetic variation can affect decomposition, nutrient cycling, and interactions between plants and their associated belowground communities. However, the effects of genetic variation on ecosystems can also be indirect, meaning that genes in a focal plant may affect ecosystems by altering the phenotype of interacting (i.e., neighboring) individuals. We manipulated genotype identity, species identity, and the possibility of belowground interactions between neighboring Solidago plants. We hypothesized that, because our plants were nitrogen (N) limited, the most important interactions between focal and neighbor plants would occur belowground. More specifically, we hypothesized that the genotypic identity of a plant's neighbor would have …

Alternative Forms For Genomic Clines, Benjamin M. Fitzpatrick

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Understanding factors regulating hybrid fitness and gene exchange is a major research challenge for evolutionary biology. Genomic cline analysis has been used to evaluate alternative patterns of introgression, but only two models have been used widely and the approach has generally lacked a hypothesis testing framework for distinguishing effects of selection and drift. I propose two alternative cline models, implement multivariate outlier detection to identify markers associated with hybrid fitness, and simulate hybrid zone dynamics to evaluate the signatures of different modes of selection. Analysis of simulated data shows that previous approaches are prone to false positives (multinomial regression) or …

Long-Term Insect Herbivory Slows Soil Development In An Arid Ecosystem, Aimee T. Classen, Samantha K. Chapman, Thomas G. Whitham, Stephen C. Hart, George W. Koch

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Although herbivores are well known to alter litter inputs and soil nutrient fluxes, their long-term influences on soil development are largely unknown because of the difficulty of detecting and attributing changes in carbon and nutrient pools against large background levels. The early phase of primary succession reduces this signal-to-noise problem, particularly in arid systems where individual plants can form islands of fertility. We used natural variation in tree-resistance to herbivory, and a 15 year herbivore-removal experiment in an Arizona piñon-juniper woodland that was established on cinder soils following a volcanic eruption, to quantify how herbivory shapes the development of soil …

Biogeography Of The Ecosystems Of The Healthy Human Body, Yanjiao Zhou, Hongyu Gao, Kathie A. Mihindukulasuriya, Patricio S. La Rosa, Kristine M. Wylie, Tatiana Vishnivetskaya, Mircea Podar, Barb Warner, Phillip I. Tarr, David E. Nelson, J. D. Fortenberry, Martin Holland, Sarah E. Burr, William D. Shannon, Erica Sodergren, George M. Weinstock

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Characterizing the biogeography of the microbiome of healthy humans is essential for understanding microbial associated diseases. Previous studies mainly focused on a single body habitat from a limited set of subjects. Here, we analyzed one of the largest microbiome datasets to date and generated a biogeographical map that annotates the biodiversity, spatial relationships, and temporal stability of 22 habitats from 279 healthy humans.

Results

We identified 929 genera from more than 24 million 16S rRNA gene sequences of 22 habitats, and we provide a baseline of inter-subject variation for healthy adults. The oral habitat has the most stable microbiota …

The Afterlife Of Interspecific Indirect Genetic Effects: Genotype Interactions Alter Litter Quality With Consequences For Decomposition And Nutrient Dynamics, Mark A. Genung, Joseph K. Bailey, Jennifer A. Schweitzer

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Aboveground-belowground linkages are recognized as divers of community dynamics and ecosystem processes, but the impacts of plant-neighbor interactions on these linkages are virtually unknown. Plant-neighbor interactions are a type of interspecific indirect genetic effect (IIGE) if the focal plant’s phenotype is altered by the expression of genes in a neighboring heterospecific plant, and IIGEs could persist after plant senescence to affect ecosystem processes. This perspective can provide insight into how plant-neighbor interactions affect evolution, as IIGEs are capable of altering species interactions and community composition over time. Utilizing genotypes of Solidago altissima and Solidago gigantea, we experimentally tested whether …

Transgressive Hybdrids As Hopeful Monsters, Dylan R. Dittrich-Reed, Benjamin M. Fitzpatrick

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

The origin of novelty is a critical subject for evolutionary biologists. Early geneticists speculated about the sudden appearance of new species via special macromutations, epitomized by Goldschmidt’s infamous “hopeful monster”. Although these ideas were easily dismissed by the insights of the Modern Synthesis, a lingering fascination with the possibility of sudden, dramatic change has persisted. Recent work on hybridization and gene exchange suggests an underappreciated mechanism for the sudden appearance of evolutionary novelty that is entirely consistent with the principles of modern population genetics. Genetic recombination in hybrids can produce transgressive phenotypes, “monstrous” phenotypes beyond the range of parental populations. …

Sharing And Re-Use Of Phylogenetic Trees (And Associated Data) To Facilitate Synthesis, Arlin Stoltzfus, Brian C. O'Meara, Jamie Whitacre, Ross Mounce, Emily L. Gillespie, Sudhir Kumar, Dan F. Rosauer, Rutger A. Vos

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use.

Findings

Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find …

Estimating Ancestry And Heterozygosity Of Hybrids Using Molecular Markers, Benjamin M. Fitzpatrick

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Hybridization, genetic mixture of distinct populations, gives rise to myriad recombinant genotypes. Characterizing the genomic composition of hybrids is critical for studies of hybrid zone dynamics, inheritance of traits, and consequences of hybridization for evolution and conservation. Hybrid genomes are often summarized either by an estimate of the proportion of alleles coming from each ancestral population or classification into discrete categories like F1, F2, backcross, or merely “hybrid” vs. “pure”. In most cases, it is not realistic to classify individuals into the restricted set of classes produced in the first two generations of admixture. However, the continuous ancestry index …

Litter, Color Variation, And Sex Effects On Feeding And Anti-Predator Behavior In Individual Thamnophis Sirtalis, Jennifer F. Porter, Gordon M. Burghardt

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

There are stark coloration differences within single populations of Thamnophis sirtalis such as the Isle Royale population. While these red color patterns cause the snakes to stand out, it is unsure if it is for some defensive purpose such as aposematic coloring. To see if this or other genetic factors, sex, and relatedness with litters, could influence behavior anti-predator and feeding tests were performed on 38 captive-born neonate T. sirtalis. The feeding experiment recorded the latency of feeding from placement of the piece of night crawler to food capture. The anti-predator experiment recorded reactions to a probe touching each snake …

Positive Interactions In Ecology: Filling The Fundamental Niche, Mariano A. Rodriguez-Cabal, M Noelia Barrios-Garcia, Martin A. Nuñez

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

The role of negative interactions in shaping ecological communities and the realized niches of species has been a focus of considerable research for at least decades. Traditionally, the discrepancy between the size of the fundamental and realized niche of a species was attributed to the effect of negative interactions, such that the realized niche is always smaller than the fundamental niche. However, in the last decade, a series of studies have highlighted the important role that positive interactions played in shaping the structure of communities. This renewed interest in positive interactions has led to a reconsideration of the niche concept. …

Underappreciated Consequences Of Phenotypic Plasticity For Ecological Speciation, Benjamin M. Ftizpatrick

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Phenotypic plasticity was once seen primarily as a constraint on adaptive evolution or merely a nuisance by geneticists. However, some biologists promote plasticity as a source of novelty and a factor in evolution on par with mutation, drift, gene flow, and selection. These claims are controversial and largely untested, but progress has been made on more modest questions about effects of plasticity on local adaptation (the first component of ecological speciation). Adaptive phenotypic plasticity can be a buffer against divergent selection. It can also facilitate colonization of new niches and rapid divergent evolution. The influence of non-adaptive plasticity has been …

Spatial Geographic Mosaic In An Aquatic Predator-Prey Network, Johel Chaves-Campos, Steven G. Johnson, C. Darrin Hulsey

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

The geographic mosaic theory of coevolution predicts 1) spatial variation in predatory structures as well as prey defensive traits, and 2) trait matching in some areas and trait mismatching in others mediated by gene flow. We examined gene flow and documented spatial variation in crushing resistance in the freshwater snails Mexipyrgus churinceanus, Mexithauma quadripaludium, Nymphophilus minckleyi, and its relationship to the relative frequency of the crushing morphotype in the trophically polymorphic fish Herichthys minckleyi. Crushing resistance and the frequency of the crushing morphotype did show spatial variation among 11 naturally replicated communities in the Cuatro Ciénegas …

Developmental Evolution Of Flowering Plant Pollen Tube Cell Walls: Callose Synthase (Cals) Gene Expression Patterns, Jason M. Abercrombie, Brian C. O'Meara, Andrew R. Moffatt, Joseph H. Williams

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

A number of innovations underlie the origin of rapid reproductive cycles in angiosperms. A critical early step involved the modification of an ancestrally short and slow-growing pollen tube for faster and longer distance transport of sperm to egg. Associated with this shift are the predominantly callose (1,3-β-glucan) walls and septae (callose plugs) of angiosperm pollen tubes. Callose synthesis is mediated by callose synthase (CalS). Of 12 CalS gene family members in Arabidopsis, only one (CalS5) has been directly linked to pollen tube callose. CalS5 orthologues are present in several monocot and eudicot genomes, but little is …

Population Growth Of Mexican Free-Tailed Bats (Tadarida Brasiliensis Mexicana) Predates Human Agricultural Activity, Amy Russell, Murray P. Cox, Veronica A. Brown, Gary F. Mccracken

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Human activities, such as agriculture, hunting, and habitat modification, exert a significant effect on native species. Although many species have suffered population declines, increased population fragmentation, or even extinction in connection with these human impacts, others seem to have benefitted from human modification of their habitat. Here we examine whether population growth in an insectivorous bat (Tadarida brasiliensis mexicana) can be attributed to the widespread expansion of agriculture in North America following European settlement. Colonies of T. b. mexicana are extremely large (~10⁶ individuals) and, in the modern era, major agricultural insect pests form an important …

Climate Change Alters Seedling Emergence And Establishment In An Old-Field Ecosystem, Aimée T. Classen, Richard J. Norby, Courtney E. Campany, Katherine E. Sides, Jake F. Weltzin

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Ecological succession drives large-scale changes in ecosystem composition over time, but the mechanisms whereby climatic change might alter succession remain unresolved. Here, we asked if the effects of atmospheric and climatic change would alter tree seedling emergence and establishment in an old-field ecosystem, recognizing that small shifts in rates of seedling emergence and establishment of different species may have long-term repercussions on the transition of fields to forests in the future.

Methodology/Principal Findings

We introduced seeds from three early successional tree species into constructed old-field plant communities that had been subjected for 4 years to altered temperature, precipitation, and …