687 Works

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: 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: Species-specific responses to island connectivity cycles: refined models for testing phylogeographic concordance across a Mediterranean Pleistocene Aggregate Island complex

Anna Papadopoulou & L. Lacey Knowles
The contribution of Pleistocene sea level changes to diversification patterns in archipelagos around the world, and specifically whether the repeated cycles of island connectivity and isolation acted as a ‘species pump’ is debated. The debate has been perpetuated in part because of the type of evidence used to evaluate the species-pump hypothesis. Specifically, existing tests of the ‘Pleistocene Aggregate Island Complex’ (PAIC) model of diversification interpret the lack of concordant divergence times among multiple codistributed...

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: Genetic basis of octanoic acid resistance in Drosophila sechellia: functional analysis of a fine-mapped region

Jose M. Andrade López, Stephen M. Lanno, Jeremy M. Auerbach, Eva C. Moskowitz, Laura A. Sligar, Patricia J. Wittkopp & Joseph D. Coolon
Drosophila sechellia is a species of fruit fly endemic to the Seychelles islands. Unlike its generalist sister species, D. sechellia has evolved to be a specialist on the host plant Morinda citrifolia. This specialization is interesting because the plant's fruit contains secondary defense compounds, primarily octanoic acid (OA), that are lethal to most other Drosophilids. Although ecological and behavioral adaptations to this toxic fruit are known, the genetic basis for evolutionary changes in OA resistance...

Data from: Multilevel and sex-specific selection on competitive traits in North American red squirrels.

David N. Fisher, Stan Boutin, Ben Dantzer, Murray M. Humphries, Jeffrey E. Lane & Andrew G. McAdam
Individuals often interact more closely with some members of the population (e.g. offspring, siblings or group members) than they do with other individuals. This structuring of interactions can lead to multilevel natural selection, where traits expressed at the group-level influence fitness alongside individual-level traits. Such multilevel selection can alter evolutionary trajectories, yet is rarely quantified in the wild, especially for species that do not interact in clearly demarcated groups. We quantified multilevel natural selection on...

Data from: Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration: a comment on Puttick et al

Joseph W. Brown, Caroline Parins-Fukuchi, Gregory W. Stull, Oscar M. Vargas & Stephen A. Smith
Puttick et al. (2017 Proc. R. Soc. B 284, 20162290 (doi:10.1098/rspb.2016.2290)) performed a simulation study to compare accuracy among methods of inferring phylogeny from discrete morphological characters. They report that a Bayesian implementation of the Mk model (Lewis 2001 Syst. Biol. 50, 913–925 (doi:10.1080/106351501753462876)) was most accurate (but with low resolution), while a maximum-likelihood (ML) implementation of the same model was least accurate. They conclude by strongly advocating that Bayesian implementations of the Mk model...

Data from: Use of continuous traits can improve morphological phylogenetics

Caroline Parins-Fukuchi
The recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modelling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modelling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character...

The effects of the Medicare NCS reimbursement policy: utilization, payments, and patient access

Evan Reynolds, Kevin Kerber, Chloe Hill, Lindsey De Lott, Brandon Magliocco, Gregory Esper & Brian Callaghan
Objective: To determine whether the 2013 nerve conduction study (NCS) reimbursement reduction changed Medicare utilization, payments, and patient access to Medicare physicians, we performed a retrospective analysis of Medicare data (2012-2016 fee-for-service data from the CMS Physician and Other Supplier Public Use File). Methods: Individual billable services were identified by Healthcare Common Procedure Coding System CPT and G codes. Medicare utilization and payments were stratified by specialty and type of service (electrodiagnostic tests, including NCS...

Data from: Stasis of functionally versatile specialists

Miriam L. Zelditch, Jingchun Li & Donald L. Swiderski
A classic hypothesis posits that lineages exhibiting long-term stasis are broadly adapted generalists that remain well-adapted despite environmental change. However, lacking constraints that steepen adaptive peaks and stabilize the optimum, generalists’ phenotypes might drift around a broad adaptive plateau. We propose that stasis would be likely for morphological specialists that behave as ecological generalists much of the time because specialists’ functional constraints stabilize the optimum, but those with a broad niche can, like generalists, persist...

Data from: Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

James B. Pease, Joseph W. Brown, Joseph F. Walker, Cody E. Hinchliff & Stephen A. Smith
Premise of the Study—Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As datasets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative. Methods— We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in...

Data from: Sex difference in prevalence of depression after stroke

Liming Dong, Brisa N. Sanchez, Lesli E. Skolarus, Eric Stulberg, Lewis B. Morgenstern & Lynda D. Lisabeth
Objective: This study investigated the sex difference in prevalence of depression at 90 days after first-ever stroke. Methods: Patients with first-ever stroke (n = 786) were identified from the population-based Brain Attack Surveillance in Corpus Christi project (2011–2016). Poststroke depressive symptoms were assessed by the 8-itemPatient Health Questionnaire, and prestroke depression status (history and medication use) was self-reported. Logistic regression was used to examine the association between sex and depression after stroke, and effect modification...

Data from: Detecting ancient co-dispersals and host shifts by double dating of host and parasite phylogenies: application in proctophyllodid feather mites associated with passerine birds

Pavel B. Klimov, Sergey V. Mironov & Barry M. OConnor
Inferring co-phylogeographic events requires matching the timing of these events on both host and symbiont (e.g., parasites) phylogenies because divergences of hosts and their symbionts may not temporally coincide, and host switches may occur. We investigate a large radiation of birds (Passeriformes) and their permanent symbionts, the proctophyllodid feather mites (117 species from 116 bird species; 6 genes, 11,468 nt aligned) using two time-calibration strategies for mites: fossils only and host phylogeography only. Out of...

Data from: Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties

Andrea T. Thomaz, Luiz R. Malabarba & L. Lacey Knowles
Past shifts in connectivity in riverine environments (for example, sea-level changes) and the properties of current drainages can act as drivers of genetic structure and demographic processes in riverine population of fishes. However, it is unclear whether the same river properties that structure variation on recent timescales will also leave similar genomic signatures that reflect paleodrainage properties. By characterizing genetic structure in a freshwater fish species (Hollandichthys multifasciatus) from a system of basins along the...

Data from: Daphniid zooplankton assemblage shifts in response to eutrophication and metal contamination during the Anthropocene

Mary Alta Rogalski, Peter R. Leavitt & David K. Skelly
Human activities during the Anthropocene result in habitat degradation that has been associated with biodiversity loss and taxonomic homogenization of ecological communities. Here we estimated effects of eutrophication and heavy metal contamination, separately and in combination, in explaining zooplankton species composition during the past 125–145 years using analysis of daphniid diapausing egg banks from four lakes in the northeastern USA. We then examined how these community shifts influenced patterns of diversity and homogenization. Analysis of...

Correlates of War, 1816-1997

J. David Singer & Melvin Small
This data collection is part of the Correlates of War (COW) Project at the University of Michigan under the guidance of J. David Singer and Melvin Small. The data contain statistics of extra-, inter-, and intra-state wars fought from 1816-1997. Variables for extra-state wars include name of war, name of participants, date ranges, victor designation, outside intervention, theater designation, and total battle deaths. Inter-state wars include date ranges, on which side the state intervened, if...

Comparable space use by lions between hunting concessions and national parks in West Africa

Kirby Mills, Yahou Harissou, Isaac Gnoumou, Yaye Abdel-Nasser, Benoit Doamba & Nyeema Harris
Spatially varied resources and threats govern the persistence of African lions across dynamic protected areas. An important precursor to effective conservation for lions requires assessing tradeoffs in space use due to heterogeneity in habitat, resources, and human presence between national parks and hunting areas, the dominant land-use classifications across their range. We conducted the largest camera survey in West Africa, encompassing 3 national parks and 11 hunting concessions in Burkina Faso and Niger, equating to...

Data from: Foliar damage beyond species distributions is partly explained by distance dependent interactions with natural enemies

Daniel S. W. Katz & Inés Ibáñez
Plant distributions are expected to shift in response to climate change, and range expansion dynamics will be shaped by the performance of individuals at the colonizing front. These plants will encounter new biotic communities beyond their range edges, and the net outcome of these encounters could profoundly affect colonization success. However, little is known about how biotic interactions vary across range edges and this has hindered efforts to predict changes in species distributions in response...

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...

Data from: Fine with heat, problems with water: microclimate alters water loss in a thermally adapted insular lizard

Anat Belasen, Kinsey Brock, Binbin Li, Dimitra Chremou, Efstratios Valakos, Panayiotis Pafilis, Barry Sinervo & Johannes Foufopoulos
Global change, including habitat isolation and climate change, has both short- and long-term impacts on wildlife populations. For example, genetic drift and inbreeding result in genetic impoverishment in small, isolated populations, while species undergo range shifts or adaptive phenotypic change in response to shifts in environmental temperatures. In this study, we utilize a model system in which Holocene landscape changes have occurred to examine long-term effects of population isolation. To examine how isolation may constrain...

Data from: Environmental filtering structures fungal endophyte communities in tree bark

Peter Pellitier, Donald Zak & Sydney Salley
The factors that control the assembly and composition of endophyte communities across plant hosts remains poorly understood. This is especially true for endophyte communities inhabiting inner tree bark, one of the least studied components of the plant microbiome. Here, we test the hypothesis that bark of different tree species acts as an environmental filter structuring endophyte communities, as well as the alternative hypothesis, that bark acts as a passive reservoir that accumulates a diverse assemblage...

The Flint MDT Study (March 2014- January 2016)

Robin Pott
The Flint MDT Study is one of the projects of the the National Quality Improvement Center on the Representation of Children in Child Welfare (QIC-ChildRep). The Study partnered with a group of five lawyers-guardian ad litem to observe and evaluate a multidisciplinary approach to representing children in child protection proceedings. The study provided the LGALs two social workers and randomly assigned cases to be either represented by the attorney/social worker team or by the attorney...

Data from: A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

Adam Kuester, Ariana Wilson, Shu-Mei Chang & Regina S. Baucom
Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection approach to examine the potential for genotypic and phenotypic evolution in Ipomoea purpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs. 2012), suggesting...

Data from: Bayesian model selection with BAMM: effects of the model prior on the inferred number of diversification shifts

Jonathan S. Mitchell & Daniel L. Rabosky
1. Understanding variation in rates of speciation and extinction -- both among lineages and through time -- is critical to the testing of many hypotheses about macroevolutionary processes. BAMM is a flexible Bayesian framework for inferring the number and location of shifts in macroevolutionary rate across phylogenetic trees and has been widely used in empirical studies. BAMM requires that researchers specify a prior probability distribution on the number of diversification rate shifts before conducting an...

A new species of croton (Euphorbiaceae) from a Madagascan lineage discovered in coastal Kenya

Veronicah Ngumbau, Mwadime Nyange, Neng Wei, Benjamin Van Ee, Paul Berry, Itambo Malombe, Guang-Wan Hu & Qing-Feng Wang
Croton kinondoensis, a new species from Kenya, is described and illustrated here with photographs. It is found in the sacred Kaya Kinondo Forest, one of the last remaining coastal forests patches in Kenya. Its morphology and systematic position based on ITS and trnL-F DNA sequence data clearly place it within the Adenophorus Group of Croton, a clade of ca. 15 species otherwise known only from Madagascar and the Comoros Archipelago. Its closest affinities appear to...

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  • University of Michigan-Ann Arbor
  • University of Michigan–Ann Arbor
  • Fudan University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Huazhong University of Science and Technology
  • Nanjing Medical University
  • Chinese Academy of Sciences
  • Sun Yat-sen University
  • Shanghai Jiao Tong University
  • Peking University