28 Works

Data From: Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)

Xuankun Li, Luisa C. Teasdale, Keith M. Bayless, Allan G. Ellis, Brian M. Wiegmann, Carlos José E. Lamas, Christine L. Lambkin, Neal L. Evenhuis, James A. Nicholls, Diana Hartley, Seunggwan Shin, Michelle Trautwein, Andreas Zwick, Bryan D. Lessard & David K. Yeates
Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the...

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

Data from: Using phylogenomics to resolve mega-families: an example from Compositae

Jennifer R. Mandel, Rebecca B. Dikow & Vicki A. Funk
Next-generation sequencing and phylogenomics hold great promise for elucidating complex relationships among large plant families. Here we performed targeted capture of low copy sequences followed by next-generation sequencing on the Illumina platform in the large and diverse angiosperm family Compositae (Asteraceae). The family is monophyletic based on morphology and molecular data, yet many areas of the phylogeny have unresolved polytomies and interpreting phylogenetic patterns has been historically difficult. In order to outline a method and...

Historical biogeography of New World Passalidae

Cristian Beza-Beza, Larry Jiménez-Ferbans & Duane McKenna
Aim: The fauna of Mesoamerica is extraordinarily species rich and exhibits a high degree of local, regional, and high-elevation endemism. Traditionally, this area has been seen as a transition zone between the Nearctic and Neotropical regions; in contrast, new data suggest Mesoamerica is a center of origin and taxonomic diversification. For example, the diversity of species and genera of Passalidae in Mesoamerica is concentrated in montane environments and there are many locally-endemic taxa; thus, Mesoamerica...

Data from: Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)

Stephanie Haddad, Seunggwan Shin, Alan R. Lemmon, Emily Moriarty Lemmon, Petr Svacha, Brian Farrell, Adam Ślipiński, Donald Windsor & Duane D. McKenna
Cerambycidae is a species-rich family of mostly wood-feeding (xylophagous) beetles containing nearly 35 000 known species. The higher-level phylogeny of Cerambycidae has never been robustly reconstructed using molecular phylogenetic data or a comprehensive sample of higher taxa, and its internal relationships and evolutionary history remain the subjects of ongoing debate. We reconstructed the higher-level phylogeny of Cerambycidae using phylogenomic data from 522 single copy nuclear genes, generated via anchored hybrid enrichment. Our taxon sample (31...

Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera

Hojun Song, Olivier Béthoux, Seunggwan Shin, Alexander Donath, Harald Letsch, Shanlin Liu, Duane D. McKenna, Guanliang Meng, Bernhard Misof, Lars Podsiadlowski, Xin Zhou, Benjamin Wipfler & Sabrina Simon
Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific...

Data from: Distribution and biogeography of Sanguina snow algae: fine-scale sequence analyses reveal previously unknown population structure

Shawn Brown
It has been previously suggested that snow algal species within the genus Sanguina (S. nivaloides and S. aurantia) show no population structure despite being found globally (S. nivaloides) or throughout the Northern Hemisphere (S. aurantia). However, systematic biogeographic research into global distributions is lacking due to few genetic and no genomic resources for these snow algae. Here, using all publicly available and previously unpublished Sanguina sequences of the Internal Transcribed Spacer 2 region, we investigate...

Phylogenomic data for hyperdiverse daisy tribes

Jennifer Mandel, Linda Watson & Carolina Siniscalchi
Asteraceae account for 10% of all flowering plant species, and 35-40% of these are in five closely-related tribes that total over 10,000 species. These tribes include Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae, which form one of two enormous clades within Subfamily Asteroideae. We took a phylogenomics approach to resolve evolutionary relationships among these five tribes. We sampled the nuclear and plastid genomes via HybSeq target enrichment and genome skimming, and recovered 74 plastid genes and...

Data from: An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

Katy E Jones, Tomáš Fér, Roswitha E Schmickl, Rebecca B Dikow, Vicki A Funk, Sonia Herrando-Moraira, Norbert Kilian, Carolina M Siniscalchi, Alfonso Susanna, Marek Slovák, Ramhari Thapa, Linda E Watson & Jennifer R Mandel
Premise of the study: Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq method and the outcomes of different phylogenetic analyses are assessed. Methods: Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, datasets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of the analyzing alternative...

Data from: The genetic basis of speciation in the Giliopsis lineage of Ipomopsis (Polemoniaceae)

Troy E. Wood, Takuya Nakazato & Loren H. Rieseberg
One of the most powerful drivers of speciation in plants is pollinator-mediated disruptive selection, which leads to the divergence of floral traits adapted to the morphology and behavior of different pollinators. Despite the widespread importance of this speciation mechanism, its genetic basis has been explored in only a few groups. Here, we characterize the genetic basis of pollinator-mediated divergence of two species in genus Ipomopsis, I. guttata and I. tenuifolia, using quantitative trait locus (QTL)...

Data from: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: a phylogenomic example from Heuchera (Saxifragaceae)

Ryan A. Folk, Jennifer R. Mandel & John V. Freudenstein
Premise of the study: Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera. Methods: Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data. Biotinylated probes were designed for enrichment of these loci. Reference-based...

Data from: Genomic and morphological evidence converge to resolve the enigma of Strepsiptera

Oliver Niehuis, Gerrit Hartig, Sonja Grath, Hans Pohl, Jörg Lehmann, Hakim Tafer, Alexander Donath, Veiko Krauss, Carina Eisenhardt, Jana Hertel, Malte Petersen, Christoph Mayer, Karen Meusemann, Ralph S. Peters, Peter F. Stadler, Rolf G. Beutel, Erich Bornberg-Bauer, Duane D. McKenna & Bernhard Misof
The phylogeny of insects, one of the most spectacular radiations of life on earth, has received considerable attention. However, the evolutionary roots of one intriguing group of insects, the twisted-wing parasites (Strepsiptera), remain unclear despite centuries of study and debate. Strepsiptera exhibit exceptional larval developmental features, consistent with a predicted step from direct (hemimetabolous) larval development to complete metamorphosis that could have set the stage for the spectacular radiation of metamorphic (holometabolous) insects. Here we...

Phylogenomics resolves the relationships within Antennaria (Asteraceae, Gnaphalieae) and yields new insights into its morphological character evolution and biogeography

Ramhari Thapa, Randall Bayer & Jennifer Mandel
Antennaria are dioecious perennial herbs distributed mainly in the Holarctic Region with their major center of diversity in the Rocky Mountains of Western North America. The genus comprises 33 known sexual diploid/tetraploid species and at least five polyploid agamic complexes which mostly reproduce by forming asexual seeds. We performed a phylogenetic reconstruction of the 31 sexually-reproducing Antennaria species using a novel target enrichment method that employs custom capture probes and is designed to work across...

Data from: Phylogenomics clarifies repeated evolutionary origins of inbreeding and fungus farming in bark beetles (Curculionidae, Scolytinae)

Andrew Johnson, McKenna, Bjarte H. Jordal, Anthony I. Cognato, Sarah M. Smith, Alan R. Lemmon, Emily L. Moriarty Lemmon & Jiri Hulcr
Bark and ambrosia beetles (Curculionidae, Scolytinae) display a conspicuous diversity of unusual genetic and ecological attributes and behaviors. Reconstructing the evolution of Scolytinae, particularly the large and ecologically significant tribe Cryphalini (pygmy borers), has long been problematic. These challenges have not adequately been addressed using morphological characters, and previous research has used only DNA sequence data from small numbers of genes. Through a combination of anchored hybrid enrichment, low-coverage draft genomes, and transcriptomes, we addressed...

Data from: Pre- and post-natal effects of experimentally manipulated maternal corticosterone on growth, stress reactivity, and survival of nestling house wrens

Beth M. Weber, E. Keith Bowers, Kimberly A. Terrell, Josephine F. Falcone, Charles F. Thompson & Scott K. Sakaluk
1. Corticosterone plays a central role in maintaining homeostasis, promoting energy acquisition, and regulating the stress response in birds. Exposure to elevated levels of corticosterone during development can profoundly alter offspring behaviour and physiology, but the effects of elevated maternal corticosterone on offspring development remain poorly understood. 2. We tested two competing hypotheses concerning the effect of maternally derived corticosterone on growth and development of free-living house wrens: i) elevated maternal corticosterone causes damaging effects...

Data from: Climate and host plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic

Harald Letsch, Brigitte Gottsberger, Christian Metzl, Jonas Astrin, Ariel Leib Leonid Friedman, Duane D. McKenna & Konrad Fiedler
Using molecular phylogenetic data and methods we infer divergence times and diversification patterns for the weevil subfamily Ceutorhynchinae in the context of host-plant associations and global climate over evolutionary time. We detected four major diversification shifts that correlate with both host shifts and major climate events. Ceutorhynchinae experienced an increase in diversification rate at ~53 Ma, during the Early Eocene Climate Optimum, coincident with a host shift to Lamiaceae. A second major diversification phase occurred...

Data from: Epigenome-wide association study of lung function level and its change

Medea Imboden, Matthias Wielscher, Faisal I Rezwan, Andre F S Amaral, Emmanuel Schaffner, Ayoung Jeong, Anna Beckmeyer-Borowko, Sarah E Harris, John M Starr, Ian J Deary, Claudia Flexeder, Melanie Waldenberger, Annette Peters, Holger Schulz, Su Chen, Shadia KHan Sunny, Wilfried J J Karmaus, Yu Jiang, Gertraud Erhart, Florian Kronenberg, Ryan Arathimos, Gemma C Sharp, Alexander John Henderson, Yu Fu, Paivi Piirila … & Nicole M Probst-Hensch
Previous reports link differential DNA methylation (DNAme) to environmental exposures which are associated with lung function. Direct evidence on lung function DNAme is however limited. We undertook an agnostic epigenome-wide association study (EWAS) on pre-bronchodilation lung function and its change in adults. In a discovery-replication EWAS design, DNAme in blood and spirometry were measured twice, six-to-15 years apart, in the same participants of three adult population-based discovery cohorts (n=2,043). Associated DNAme markers (P<5x10-7) were tested...

Data from: Resource constraints highlight complex microbial interactions during lake biofilm development

Kevin H. Wyatt, Rody C. Seballos, Maria N. Shoemaker, Shawn P. Brown, Sudeep Chandra, Kevin A. Kuehn, Allison R. Rober & Steven Sadro
Abstract 1. This study evaluated how the availability of nutrients and organic carbon interact to influence the associations between autotrophic and heterotrophic microorganisms during lake biofilm development. Considering that decomposers are often better competitors for nutrients than producers in aquatic environments, we hypothesized that heterotrophs would outcompete autotrophs for available nutrients unless heterotrophs were limited by organic carbon provided by autotrophs. 2. To test our hypothesis, we evaluated autotrophic (algae) and heterotrophic (fungi, bacteria) biomass...

Data from: Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)

Seunggwan Shin, Keith M. Bayless, Shaun L. Winterton, Torsten Dikow, Bryan D. Lessard, David K. Yeates, Brian M. Wiegmann & Michelle D. Trautwein
Early diverging brachyceran fly lineages underwent a rapid radiation approximately 180 million years ago, coincident in part with the origin of flowering plants. This region of the fly tree includes 25,000 described extant species with diverse ecological roles such as blood feeding (haematophagy), parasitoidism, predation, pollination, and wood feeding (xylophagy). Early diverging brachyceran lineages were once considered a monophyletic group of families called Orthorrhapha, based on the shared character of a longitudinal break in the...

Data from: Species characteristics affect local extinctions

Meredith Ann Zettlemoyer, Duane D. McKenna & Jennifer A. Lau
Premise of the study. Human activities threaten thousands of species with extinction. However, it remains difficult to predict extinction risk for many vulnerable species. Species characteristics help predict responses to anthropogenic environmental change and may help predict likelihood of extinction. Phylogenetic signatures of extinction can also provide insights into patterns of species loss. Historical data on species losses can allow for testing phylogenetic patterns in extinctions and identifying traits that influence species vulnerability to local...

Data from: A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae

Jennifer R. Mandel, Rebecca B. Dikow, Vicki A. Funk, Rishi R. Masalia, S. Evan Staton, Alex Kozik, Richard W. Michelmore, Loren H. Rieseberg & John M. Burke
Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous...

Data from: Phylogenomic data yield new and robust insights into the phylogeny and evolution of weevils

Seunggwan Shin, Dave J. Clarke, Alan R. Lemmon, Emily Moriarty Lemmon, Alexander L. Aitken, Stephanie Haddad, Brian D. Farrell, Adriana E. Marvaldi, Rolf G. Oberprieler & Duane D. McKenna
The phylogeny and evolution of weevils (the beetle superfamily Curculionoidea) has been extensively studied, but many relationships, especially in the large family Curculionidae (true weevils; > 50000 species), remain uncertain. We used phylogenomic methods to obtain DNA sequences from 522 protein coding genes for representatives of all families of weevils and all subfamilies of Curculionidae. Most of our phylogenomic results had strong statistical support, and the inferred relationships were generally congruent with those reported in...

Data from: A geology and geodesy based model of dynamic earthquake rupture on the Rodgers Creek-Hayward-Calaveras fault system, California

Michael Barall, Ruth Harris, David Lockner, Diane Moore, Ponce David, Russell Graymer, Gareth Funning, Carolyn Morrow, Christodoulos Kyriakopoulos & Donna Eberhart-Phillips
The Hayward fault in California's San Francisco Bay area produces large earthquakes, with the last occurring in 1868. We examine how physics-based dynamic rupture modeling can be used to numerically simulate large earthquakes on not only the Hayward fault, but also its connected companions to the north and south, the Rodgers Creek and Calaveras faults. Equipped with a wealth of images of this fault system, including those of its 3D geology and 3D geometry, in...

Variation in brown rat cranial shape shows directional selection over 120 years in New York City

Emily Puckett, Emma Sherratt, Matthew Combs, Elizabeth Carlen, William Harcourt-Smith & Jason Munshi-South
Urbanization exposes species to novel environments and selection pressures that may change morphological traits within a population. We investigated how the shape and size of crania and mandibles changed over time within a population of brown rats (Rattus norvegicus) living in Manhattan, New York, USA, a highly urbanized environment. We measured 3D landmarks on the cranium and mandible of 62 adult individuals sampled in the 1890s and 2010s. Static allometry explained approximately 22% of shape...

Bergmann's rule is followed at multiple stages of post-embryonic development in a long-distance migratory songbird

Joseph Youtz, Kelly Miller, Emerson Bowers, Samantha Rogers, Lesley Bulluck, Matthew Johnson, Brian Peer, Katie Percy, Erik Johnson, Elizabeth Ames, Christopher Tonra & Than Boves
Aim: We assessed the presence of Bergmann’s rule in a model migratory species across all life stages on their breeding grounds. We then compared historic and contemporary egg sizes to understand if the biogeographic patterns during this developmental life stage have changed over time. Location: Eastern North America. Time period: 1865 to 2019. Major taxa: Prothonotary warbler, Protonotaria citrea Methods: We measured the size of eggs, young and old nestlings, and adults (of two age...

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