42 Works

Data from: Historical environment is reflected in modern population genetics and biogeography of an island endemic lizard (Xantusia riversiana reticulata)

Iris A. Holmes, William J. Mautz & Alison R. Davis Rabosky
The restricted distribution and isolation of island endemics often produces unique genetic and phenotypic diversity of conservation interest to management agencies. However, these isolated species, especially those with sensitive life history traits, are at high risk for the adverse effects of genetic drift and habitat degradation by non-native wildlife. Here, we study the population genetic diversity, structure, and stability of a classic “island giant” (Xantusia riversiana, the Island Night Lizard) on San Clemente Island, California...

Data from: Assembling a species–area curve through colonization, speciation and human-mediated introduction

Evan P. Economo, Milan Janda, Benoit Guénard & Eli Sarnat
Aim: The fundamental biogeographical processes of colonization, speciation and extinction shape island biotas in space–time. On oceanic islands, area and isolation affect these processes and resulting biodiversity patterns. In the Anthropocene, a new human-mediated colonization dynamic is altering insular ecosystems world-wide. Here, we test predictions about the roles of archipelago area and isolation in structuring ant diversity patterns through effects on both natural and anthropogenic biogeographical processes. Location: Tropical Pacific islands. Methods: We compiled a...

Data from: Tests of species-specific models reveal the importance of drought in postglacial range shifts of a Mediterranean-climate tree: insights from integrative distributional, demographic and coalescent modelling and ABC model selection

Jordan B. Bemmels, Pascal O. Title, Joaquín Ortego & L. Lacey Knowles
Past climate change has caused shifts in species distributions and undoubtedly impacted patterns of genetic variation, but the biological processes mediating responses to climate change, and their genetic signatures, are often poorly understood. We test six species-specific biologically informed hypotheses about such processes in canyon live oak (Quercus chrysolepis) from the California Floristic Province. These hypotheses encompass the potential roles of climatic niche, niche multidimensionality, physiological trade-offs in functional traits, and local-scale factors (microsites and...

Data from: Do macrophylogenies yield stable macroevolutionary inferences? An example from squamate reptiles

Pascal O. Title & Daniel L. Rabosky
Advances in the generation, retrieval, and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These “macrophylogenies”—large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches—provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life. These trees are...

Data from: Preoperative falls predict postoperative falls and other adverse patient-reported outcomes

Vanessa L. Kronzer, Michelle R. Jerry, Arbi Ben Abdallah, Troy S. Wildes, Susan L. Stark, Sherry L. McKinnon, Daniel L. Helsten, Anshuman Sharma & Michael S. Avidan
BACKGROUND: Falls are common and linked to morbidity. Our objectives were to characterize postoperative falls, and determine whether preoperative falls independently predicted postoperative falls (primary outcome), functional dependence, quality of life, complications, and readmission. METHODS: This prospective cohort study included 7982 unselected patients undergoing elective surgery. Data were collected from the medical record, a baseline survey, and follow-up surveys approximately 30days and one year after surgery. RESULTS: Fall rates (per 100 person-years) peaked at 175...

Data from: The architecture of river networks can drive the evolutionary dynamics of aquatic populations

Andrea T. Thomaz, Mark R. Christie & L. Lacey Knowles
It is widely recognized that physical landscapes can shape genetic variation within and between populations. However, it is not well understood how riverscapes, with their complex architectures, affect patterns of neutral genetic diversity. Using a spatially explicit agent-based modeling (ABM) approach, we evaluate the genetic consequences of dendritic river shapes on local population structure. We disentangle the relative contribution of specific river properties to observed patterns of genetic variation by evaluating how different branching architectures...

Data from: Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges

Rob Massatti & L. Lacey Knowles
Deterministic processes may uniquely affect codistributed species’ phylogeographic patterns such that discordant genetic variation among taxa is predicted. Yet, explicitly testing expectations of genomic discordance in a statistical framework remains challenging. Here, we construct spatially and temporally dynamic models to investigate the hypothesized effect of microhabitat preferences on the permeability of glaciated regions to gene flow in two closely related montane species. Utilizing environmental niche models from the Last Glacial Maximum and the present to...

Data from: Fitness costs of herbicide resistance across natural populations of the common morning glory, Ipomoea purpurea

Megan L. Van Etten, Adam Kuester, Shu-Mei Chang & Regina S. Baucom
Although fitness costs associated with plant defensive traits are widely expected, they are not universally detected, calling into question their generality. Here we examine the potential for life history trade-offs associated with herbicide resistance by examining seed germination, root growth, and above-ground growth across 43 naturally occurring populations of Ipomoea purpurea that vary in their resistance to RoundUp®, the most commonly used herbicide worldwide. We find evidence for life history trade-offs associated with all three...

Data from: Herbivores control effects of algal species richness on community biomass and stability in a laboratory microcosm experiment

Chase Rakowski & Bradley J. Cardinale
Hundreds of studies that have explored how biodiversity affects the productivity and stability of ecosystems have produced a consensus that communities composed of more species tend to have higher biomass that is more stable through time. However, the majority of this work stems from studies performed using highly simplified food webs, often composed of just primary producers competing for inorganic resources in the absence of trophic interactions. When studies have incorporated trophic interactions, diversity-function relationships...

Data from: Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

Sergey A. Naumenko, Maria D. Logacheva, Nina V. Popova, Anna V. Klepikova, Aleksey A. Penin, Georgii A. Bazykin, Anna E. Etingova, Nikolai S. Mugue, Alexey S. Kondrashov & Lev Y. Yampolsky
Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two non-endemic outgroups, we report a revised phylogeny of this species flock, and analyze evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into...

Data from: Predation on feather stars by regular echinoids as evidenced by laboratory and field observations and its paleobiological implications

Angela Stevenson, Forest J. Gahn, Tomasz K. Baumiller & George D. Sevastopulo
Among extant crinoids, the feather stars are the most diverse and occupy the greatest bathymetric range, being especially common in reef environments. Feather stars possess a variety of morphological, behavioral and physiological traits that have been hypothesized to be critical to their success, especially in their ability to cope with predation. However, knowledge of their predators is exceptionally scant, consisting primarily of circumstantial evidence of attacks by fishes. In this study the question whether regular...

Data from: Parapatric genetic introgression and phenotypic assimilation: testing conditions for introgression between Hercules beetles (Dynastes, Dynastinae)

Jen-Pan Huang
The prevalence and consequences of genetic introgression between species have been intensively debated. I used Hercules beetles as examples to test for conditions that may be associated with the occurrence of introgression. RADseq data were used to reconstruct the species tree and history of introgression between Hercules beetles. Image data from museum specimens were used to investigate the phenotypic similarity of two adaptive traits between species from two distinct climatic realms (Nearctic vs. Neotropical). Genetic...

Data from: Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: a case-study in Carex sect. Racemosae

Rob Massatti, Anton A. Reznicek & L. Lacey Knowles
PREMISE OF THE STUDY: Relationships among closely related and recently diverged taxa can be especially difficult to resolve. Here we use both Sanger sequencing and next-generation RADseq data sets to estimate phylogenetic relationships among species of Carex section Racemosae (Cyperaceae), a clade largely restricted to high latitudes and elevations. Interest in relationships among these taxa derives from questions about the species’ biogeographic histories and possible links between diversification and Pleistocene glaciations. METHODS: A combination of...

Data from: Glacial refugia, recolonisation patterns, and diversification forces in Alpine-endemic Megabunus harvestmen

Gregor A. Wachter, Anna Papadopoulou, Christoph Muster, Wolfgang Arthofer, L. Lacey Knowles, Florian M. Steiner & Birgit C. Schlick-Steiner
The Pleistocene climatic fluctuations had a huge impact on all life-forms, and various hypotheses regarding the survival of organisms during glacial periods have been postulated. In the European Alps, evidence has been found in support of refugia outside the ice shield (massifs de refuge) acting as sources for postglacial recolonisation of inner-Alpine areas. In contrast, evidence for survival on nunataks, ice-free areas above the glacier, remains scarce. Here, we combine multivariate genetic analyses with ecological...

Data from: Habitat, predators, and hosts regulate disease in Daphnia through direct and indirect pathways

Alexander T. Strauss, Marta S. Shocket, David J. Civitello, Jessica L. Hite, Rachel M. Penczykowski, Meghan A. Duffy, Carla E. Cáceres & Spencer R. Hall
Community ecology can link habitat to disease via interactions among habitat, focal hosts, other hosts, their parasites, and predators. However, complicated food web interactions (i.e., trophic interactions among predators, and their impacts on host density and diversity) often obscure the important pathways regulating disease. Here, we disentangle community drivers in a case study of planktonic disease, using a two-step approach. In step one, we tested univariate field patterns linking community interactions to two disease metrics....

Data from: Coral snakes predict the evolution of mimicry across New World snakes

Alison R. Davis Rabosky, Christian L. Cox, Daniel L. Rabosky, Pascal O. Title, Iris A. Holmes, Anat Feldman & Jimmy A. McGuire
Batesian mimicry, in which harmless species (mimics) deter predators by deceitfully imitating the warning signals of noxious species (models), generates striking cases of phenotypic convergence that are classic examples of evolution by natural selection. However, mimicry of venomous coral snakes has remained controversial because of unresolved conflict between the predictions of mimicry theory and empirical patterns in the distribution and abundance of snakes. Here we integrate distributional, phenotypic and phylogenetic data across all New World...

Data from: Disentangling endogenous versus exogenous pattern formation in spatial ecology: a case study of the ant Azteca sericeasur in southern Mexico

Kevin Li, John H. Vandermeer & Ivette Perfecto
Spatial patterns in ecology can be described as reflective of environmental heterogeneity (exogenous), or emergent from dynamic relationships between interacting species (endogenous), but few empirical studies focus on the combination. The spatial distribution of the nests of Azteca sericeasur, a keystone tropical arboreal ant, is thought to form endogenous spatial patterns among the shade trees of a coffee plantation through self-regulating interactions with controlling agents (i.e. natural enemies). Using inhomogeneous point process models, we found...

Data from: X-rays and virtual taphonomy resolve the first Cissus (Vitaceae) macrofossils from Africa as early diverging members of the genus

Neil F. Adams, Margaret E. Collinson, Selena Y. Smith, Marion K. Bamford, Félix Forest, Panagiota Malakasi, Federica Marone, Dan Sykes, N. F. Adams, M. E. Collinson, D. Sykes, F. Forest, P. Malakasi, S. Y. Smith & M. K. Bamford
PREMISE OF THE STUDY: Fossilized seeds similar to Cissus (Vitaceae) have been recognized from the Miocene of Kenya, though some were previously assigned to the Menispermaceae. We undertook a comparative survey of extant African Cissus seeds to identify the fossils and consider their implications for the evolution and biogeography of Cissus and for African early Miocene paleoenvironments. METHODS: Micro-computed tomography (µCT) and synchrotron-based X-ray tomographic microscopy (SRXTM) were used to study seed morphology and anatomy....

Data from: Can longitudinal generalized estimating equation models distinguish network influence and homophily? an agent-based modeling approach to measurement characteristics

Kori Sauser Zachrison, Theodore J. Iwashyna, Achamyeleh Gebremariam, Meghan Hutchins & Joyce M. Lee
Background: Connected individuals (or nodes) in a network are more likely to be similar than two randomly selected nodes due to homophily and/or network influence. Distinguishing between these two influences is an important goal in network analysis, and generalized estimating equation (GEE) analyses of longitudinal dyadic network data are an attractive approach. It is not known to what extent such regressions can accurately extract underlying data generating processes. Therefore our primary objective is to determine...

Data from: Phylogenetic stability, tree shape, and character compatibility: a case study using early tetrapods

Massimo Bernardi, Kenneth D. Angielczyk, Jonathan S. Mitchell & Marcello Ruta
Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and...

Data from: Haplotype-phased synthetic long reads from short-read sequencing

James A. Stapleton, Jeongwoon Kim, John P. Hamilton, Ming Wu, Luiz C. Irber, Rohan Maddamsetti, Bryan Briney, Linsey Newton, Dennis R. Burton, C. Titus Brown, Christina Chan, C. Robin Buell & Timothy A. Whitehead
Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp) reads. We show that our method can construct 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic samples, full-length mRNA sequences...

Data from: Biotic and abiotic variables influencing plant litter breakdown in streams: a global study

Luz Boyero, Richard Pearson, Cang Hui, Mark Gessner, Javier Perez, Markos Alexandrou, Manuel Graça, Bradley Cardinale, Ricardo Albariño, M. Arunachalam, Leon Barmuta, Andrew Boulton, Andreas Bruder, Marcos Callisto, Eric Chauvet, Russell Death, David Dudgeon, Andrea Encalada, Veronica Ferreira, Ricardo Figueroa, Alex Flecker, , Julie Helson, Tomoya Iwata, Tajang Jinggut … & Catherine Yule
Plant litter breakdown is a key ecological process in terrestrial and freshwater ecosystems. Streams and rivers, in particular, have high rates of carbon dioxide evasion and they contribute substantially to global carbon fluxes. However, there is little information available on the relative roles of different drivers of plant litter breakdown in fresh waters, particularly at large scales. We present a global-scale study of litter breakdown in streams to compare the roles of biotic, climatic and...

Data from: Identifying targets of selection in mosaic genomes with machine learning: applications in Anopheles gambiae for detecting sites within locally adapted chromosomal inversions

Qixin He & L. Lacey Knowles
Chromosomal inversions are important structural changes that may facilitate divergent selection when they capture co-adaptive loci in the face of gene flow. However, identifying selection targets within inversions can be challenging. The high degrees of differentiation between heterokaryotypes, as well as the differences in demographic histories of collinear regions compared with inverted ones, reduce the power of traditional outlier analyses for detecting selected loci. Here, we develop a new approach that uses discriminant functions informed...

Data from: Powerful methods for detecting introgressed regions from population genomic data

Benjamin K. Rosenzweig, James B. Pease, Nora J. Besansky, Matthew H. Hahn & Matthew W. Hahn
Understanding the types and functions of genes that are able to cross species boundaries—and those that are not—is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next-generation sequencing data sets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the signature of such events. Here, we introduce a new summary...

Data from: Multi-scale heterogeneity in vegetation and soil carbon in exurban residential land of southeastern Michigan, USA

William S. Currie, Sarah Kiger, Joan I. Nassauer, Meghan Hutchins, Lauren L. Marshall, Daniel G. Brown, Rick L. Riolo, Derek T. Robinson & Stephanie K. Hart
Exurban residential land (one housing unit per 0.2–16.2 ha) is growing in importance as a human-dominated land use. Carbon storage in the soils and vegetation of exurban land is poorly known, as are the effects on C storage of choices made by developers and residents. We studied C storage in exurban yards in southeastern Michigan, USA, across a range of parcel sizes and different types of neighborhoods. We divided each residential parcel into ecological zones...

Registration Year

  • 2016
    42

Resource Types

  • Dataset
    42

Affiliations

  • University of Michigan-Ann Arbor
    42
  • University of Georgia
    4
  • Okinawa Institute of Science and Technology
    3
  • Purdue University
    2
  • Indiana University Bloomington
    2
  • University of Hong Kong
    2
  • Georgia Southern University
    2
  • University of the Basque Country
    1
  • University of Massachusetts Amherst
    1
  • Field Museum of Natural History
    1