627 Works

Data from: Bayesian species delimitation combining multiple genes and traits in a unified framework

Claudia Solís-Lemus, L. Lacey Knowles & Cécile Ané
Delimitation of species based exclusively on genetic data has been advocated despite a critical knowledge gap: how might such approaches fail because they rely on genetic data alone, and would their accuracy be improved by using multiple data-types. We provide here the requisite framework for addressing these key questions. Because both phenotypic and molecular data can be analyzed in a common Bayesian framework with our program iBPP, we can compare the accuracy of delimited taxa...

Data from: Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees

Daniel L. Rabosky
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model...

Data from: X-Ray computed tomography of two mammoth calf mummies

Daniel C. Fisher, Ethan A. Shirley, Christopher D. Whalen, Zachary T. Calamari, Adam N. Rountrey, Alexei N. Tikhonov, Bernard Buigues, Frédéric Lacombat, Semyon Grigoriev & Piotr A. Lazarev
Two female woolly mammoth neonates from permafrost in the Siberian Arctic are the most complete mammoth specimens known. Lyuba, found on the Yamal Peninsula, and Khroma, from northernmost Yakutia, died at ages of approximately one and two months, respectively. Both specimens were CT-scanned, yielding detailed information on the stage of development of their dentition and skeleton and insight into conditions associated with death. Both mammoths died after aspirating mud. Khroma's body was frozen soon after...

Data from: Model inadequacy and mistaken inferences of trait-dependent speciation

Daniel Rabosky, Emma E. Goldberg & Daniel L. Rabosky
Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, and other factors that affect rates of species proliferation. Recent methods for explicitly modeling the relationships among character states, speciation rates, and extinction rates on phylogenetic trees- BiSSE, QuaSSE, GeoSSE, and related models - have been widely used to test hypotheses about character state-dependent diversification rates. Here, we document the disconcerting ease with which neutral traits are...

Data from: Subtype diversity and reassortment potential for co-circulating avian influenza viruses at a diversity hot spot

Heather D. Barton, Pejman Rohani, David E. Stallknecht, Justin Brown & John M. Drake
1. Biological diversity has long been used to measure ecological health. While evidence exists from many ecosystems that declines in host biodiversity may lead to greater risk of disease emergence, the role of pathogen diversity in the emergence process remains poorly understood. Particularly, because a more diverse pool of pathogen types provides more ways in which evolutionary innovations may arise, we suggest that host–pathogen systems with high pathogen diversity are more prone to disease emergence...

Data from: The socio-genetics of a complex society: female gelada relatedness patterns mirror association patterns in a multi-level society.

Noah Snyder-Mackler, Susan C. Alberts & Thore J. Bergman
Multilevel societies with fission–fusion dynamics—arguably the most complex animal societies—are defined by two or more nested levels of organization. The core of these societies are modular social units that regularly fission and fuse with one another. Despite convergent evolution in disparate taxa, we know strikingly little about how such societies form and how fitness benefits operate. Understanding the kinship structure of complex societies could inform us about the origins of the social structure as well...

Data from: Plant-derived differences in the composition of aphid honeydew and their effects on colonies of aphid-tending ants

Elizabeth G. Pringle, Alexandria Novo, Ian Ableson, Raymond V. Barbehenn & Rachel L. Vannette
In plant–ant–hemipteran interactions, ants visit plants to consume the honeydew produced by phloem-feeding hemipterans. If genetically based differences in plant phloem chemistry change the chemical composition of hemipteran honeydew, then the plant's genetic constitution could have indirect effects on ants via the hemipterans. If such effects change ant behavior, they could feed back to affect the plant itself. We compared the chemical composition of honeydews produced by Aphis nerii aphid clones on two milkweed congeners,...

Data from: Reading the leaves: a comparison of leaf rank and automated areole measurement for quantifying aspects of leaf venation

Walton A. Green, Stefan A. Little, Charles A. Price, Scott L. Wing, Selena Y. Smith, Benjamin Kotrc & Gabriela Doria
The reticulate venation that is characteristic of a dicot leaf has excited interest from systematists for more than a century, and from physiological and developmental botanists for decades. The tools of digital image acquisition and computer image analysis, however, are only now approaching the sophistication needed to quantify aspects of the venation network found in real leaves quickly, easily, accurately, and reliably enough to produce biologically meaningful data. In this paper, we examine 120 leaves...

Data from: Response of stream ecosystem function and structure to sediment metal: context-dependency and variation among endpoints

David M. Costello & G. Allen Burton
Physicochemical and ecological attributes of ecosystems (i.e., environmental context) can modify the exposure and effects of metals, which presents a challenge for ecosystem management. Furthermore, the functional and structural attributes of an ecosystem may not respond equally to metals or be uniformly responsive to environmental context. We explored how physicochemical and ecological context modified sediment metal dose-response for a suite of functional and structural measures. Two sediments with high (HB) and low (LB) acid volatile...

Data from: Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway

James W. Horn, Zhenxiang Xi, Ricarda Riina, Jess A. Peirson, Ya Yang, Brian L. Dorsey, Paul E. Berry, Charles C. Davis & Kenneth J. Wurdack
The mid-Cenozoic decline of atmospheric CO2 levels that promoted global climate change was critical to shaping contemporary arid ecosystems. Within angiosperms, two CO2-concentrating mechanisms (CCMs)—CAM and C4—evolved from the C3 photosynthetic pathway, enabling more efficient whole-plant function in such environments. Many angiosperm clades with CCMs are thought to have diversified rapidly due to Miocene aridification, but links between this climate change, CCM evolution, and increased net diversification rates (r) remain to be further understood. Euphorbia...

Data from: Is recombination a problem for species-tree analyses?

Hayley C. Lanier & L. Lacey Knowles
As the field of phylogenetics transitions into phylogenomics it has spurred a shift in the general paradigm for data analysis whereby specific dataset attributes can now be considered in a model-based framework. Much effort has been put in to modeling the effects of nucleotide substitution within a genealogy (i.e., modeling mutations; Felsenstein 2005) and the sorting genes between lineages (i.e., coalescence; Knowles and Kubatko 2010), both of which are inherent properties of all species histories....

Data from: Fungal pathogen species richness: why do some plant species have more pathogens than others?

Zachariah J. Miller
Variation among plant species in the number of associated herbivore and pathogen species is predicted to fit a species-area relationship in which the area or biomass embodied by a plant species is a function of individual size and geographic range size. This hypothesis is tested using published estimates of geographic range, individual size, and species richness of fungal-pathogens for 490 plant species occurring in the United States and controlling for sampling intensity and phylogenetic effects....

Data from: Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays

John E McCormack, Joseph Heled, Kathleen S Delaney, A Townsend Peterson & L Lacey Knowles
Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma...

Data from: Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

Daniel L. Rabosky, Francesco Santini, Jonathan Eastman, Stephen A. Smtih, Brian Sidlauskas, Jonathan Chang & Michael E. Alfaro
Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+...

Data from: Diversity dynamics of mammals in relation to tectonic and climatic history: comparison of three Neogene records from North America

Catherine Badgley & John A. Finarelli
In modern ecosystems, regions of topographic heterogeneity, when compared with nearby topographically homogeneous regions, support high species densities of mammals and other groups. This biogeographic pattern could be explained by either greater diversification rates or greater accommodation of species in topographically complex regions. In this context, we assess the hypothesis that changes in landscape history have stimulated diversification in mammals. Landscape history includes tectonic and climatic processes that influence topographic complexity at regional scales. We...

Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands

Anna Papadopoulou & L. Lacey Knowles
Harnessing the power of genomic scans, we test the debated ‘species pump’ hypothesis that implicates repeated cycles of island connectivity and isolation as drivers of divergence. This question has gone understudied given the limited resolution of past molecular markers for studying such dynamic phenomena. With an average of 32000 SNPs from the genome of 136 individuals from ten populations of a Caribbean flightless ground cricket species (Amphiacusta sanctaecrucis) and a complementary set of statistical approaches,...

Data from: Habitat corridors facilitate genetic resilience irrespective of species dispersal abilities or population sizes

Mark R. Christie & L. Lacey Knowles
Corridors are frequently proposed to connect patches of habitat that have become isolated due to human-mediated alterations to the landscape. While it is understood that corridors can facilitate dispersal between patches, it remains unknown whether corridors can mitigate the negative genetic effects for entire communities modified by habitat fragmentation. These negative genetic effects, which include reduced genetic diversity, limit the potential for populations to respond to selective agents such as disease epidemics and global climate...

Data from: Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies

Patrick Venail, Kevin Gross, Todd H. Oakley, Anita Narwani, Eric Allan, Pedro Flombaum, Forest Isbell, Jasmin Joshi, Peter B. Reich, David Tilman, Jasper Van Ruijven & Bradley J. Cardinale
1.Hundreds of experiments have now manipulated species richness of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function...

Data from: Influence of introgression and geological processes on phylogenetic relationships of western North American mountain suckers (Pantosteus, Catostomidae)

Peter J. Unmack, Thomas E. Dowling, Nina J. Laitinen, Carol L. Secor, Richard L. Mayden, Dennis K. Shiozawa & Gerald R. Smith
Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western...

Data from: Altitudinal changes in malaria incidence in highlands of Ethiopia and Colombia

Amir S. Siraj, Mauricio Santos-Vega, Menno J. Bouma, Damtew Yadeta, Daniel Ruiz Carrascal & Mercedes Pascual
The impact of global warming on insect-borne diseases and on highland malaria in particular remains controversial. Temperature is known to influence transmission intensity through its effects on the population growth of the mosquito vector and on pathogen development within the vector. Spatiotemporal data at a regional scale in highlands of Colombia and Ethiopia supplied an opportunity to examine how the spatial distribution of the disease changes with the interannual variability of temperature. We provide evidence...

Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Stephen A. Smith, Ya Yang, Joseph W. Brown & Michael J. Moore
Background: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in...

Data from: The implications of stratigraphic compatibility for character integration among fossil taxa

Peter J. Wagner & George F. Estabrook
Two characters are stratigraphically compatible if some phylogenies indicate that their combinations (state-pairs) evolved without homoplasy and in an order consistent with the fossil record. Simulations assuming independent character change indicate that we expect approximately 95% of compatible character pairs to also be stratigraphically compatible over a wide range of sampling regimes and general evolutionary models. However, two general models of rate heterogeneity elevate expected stratigraphic incompatibility: “early burst” models, where rates of change are...

Data from: A robust semi-parametric test for detecting trait-dependent diversification

Daniel L. Rabosky & Huateng Huang
Rates of species diversification vary widely across the tree of life and there is considerable interest in identifying organismal traits that correlate with rates of speciation and extinction. However, it has been challenging to develop methodological frameworks for testing hypotheses about trait-dependent diversification that are robust to phylogenetic pseudoreplication and to directionally biased rates of character change. We describe a semi-parametric test for trait-dependent diversification that explicitly requires replicated associations between character states and diversification...

Data from: Feeding ecology and habitat preferences of top predators from two Miocene carnivore-rich assemblages

M. Soledad Domingo, Laura Domingo, Juan Abella, Alberto Valenciano, Catherine Badgley & Jorge Morales
Carnivoran-rich fossil sites are uncommon in the fossil record and, accordingly, provide valuable opportunities to study predators from vantages that are rarely applied to ancient faunas. Through stable isotopes of carbon and a Bayesian mixing model, we analyze time-successive (nearly contemporaneous), late Miocene carnivoran populations from two fossil sites (Batallones-1 and Batallones-3) from central Spain. Stable isotopes of carbon in tooth enamel provide a reliable and direct methodology to track ancient diets. These two carnivoran-dominated...

Data from: Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa

Lindy M Jensen, Jessica R Grant, , Laura A. Katz & Lindy Jensen
A sequestered germline in Metazoa has been argued to be an obstacle to lateral gene transfer (LGT), though few studies have specifically assessed this claim. Here we test the hypothesis that the origin of a sequestered germline reduced LGT events in Bilateria (i.e. triploblast lineages) as compared to early-diverging Metazoa (i.e. Ctenophora, Cnidaria, Porifera, and Placozoa). We analyze single-gene phylogenies generated with over 900 species, sampled from among Bacteria, Archaea and Eukaryota to identify well-supported...

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  • University of Michigan-Ann Arbor
  • University of Michigan–Ann Arbor
  • Fudan University
  • Huazhong University of Science and Technology
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Sun Yat-sen University
  • Nanjing Medical University
  • Chinese Academy of Sciences
  • Xiangya Hospital Central South University
  • Southern Medical University