13 Works

A target enrichment probe set for resolving the flagellate land plant tree of life

Jesse W. Breinholt, Sarah B. Carey, George P. Tiley, E. Christine Davis, Lorena Endara, Stuart F. McDaniel, Leandro Neves, Emily B. Sessa, Matt Von Konrat, Susan Fawcett, Stefanie M. Ickert-Bond, Paulo H. Labiak, Juan Larraín, Marcus Lehnert, Lily R. Lewis, Nathalie S. Nagalingum, Nikisha Patel, Stefan A. Rensing, Weston Testo, Alejandra Vasco, Juan Carlos Villarreal, Evelyn Webb Williams, J. Gordon Burleigh, Sahut Chantanaorrapint, Leandro G. Neves … & Stefanie M. Ickert‐Bond
Premise of the Study: New sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. Methods and Results: We leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target...

Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

Gustavo Bravo, Bret Whitney, Ricardo Belmonte-Lopes, Marcos Bornschein, Natalia Aristizabal, Renata Beco, Jaqueline Battilana, Luciano Naka, Alexandre Aleixo, Marcio Pie, Luis Silveira, Elizabeth Derryberry & Robb Brumfield
The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus...

Data for: Long-term surveys support declines in early-season forest plants used by bumble bees

John Mola, Leif Richardson, Greg Spyreas, David Zaya & Ian Pearse
Populations of bumble bees and other pollinators have declined over the past several decades due to numerous threats, including habitat loss and degradation. However, we can rarely investigate the role of resource loss due to a lack of detailed long-term records of forage plants and habitats. We use 22-year repeated surveys of more than 262 sites located in grassland, forest, and wetland habitats across Illinois, USA to explore how the abundance and richness of bumble...

Functional, temporal, and spatial complementarity in mammal-fungal spore networks enhances mycorrhizal dispersal following forest harvesting

Ryan Stephens, Serita Frey, Anthony D'Amato & Rebecca Rowe
Animals that disperse plant or fungal propagules following forest disturbances, including timber harvests, play an important role during forest regeneration by dispersing seeds or spores from intact communities to disturbed sites. Determining how complementary or redundant animal species are as dispersers of propagules is key to understanding the stability of dispersal dynamics and informing management practices. Here we examine the functional, temporal, and spatial components of mycorrhizal fungal spore dispersal by small mammals (rodents and...

Agriculture is adapting to phenological shifts caused by climate change, but grassland songbirds are not

Noah Perlut, Allan Strong & Maeve McGowan
Migratory birds time their migration based on cues that signal resource availability for reproduction. However, with climate change, the timing of seasonal events may shift, potentially inhibiting the ability of some species to use them as accurate cues for migration. We studied the relationship between phenological shifts and reproduction by long- and short-distance migratory songbirds—Bobolinks (Dolichonyx oryzivorus) and Savannah Sparrows (Passerculus sandwichensis). Our study population breeds in hayfields and pastures in Vermont, USA, where farmers...

Chemosensory genes in Leptinotarsa decemlineata

Sean Schoville, Yolanda Chen, Zach Cohen, Michael Crossley, Patamarerk Engsontia & Robert Mitchell
Plants and plant-feeding insects comprise the majority of global species diversity, and their coevolutionary dynamics provide an important window into the mechanisms that mediate niche evolution. In particular, there is considerable interest in understanding the nature of genetic changes that allow host-plant shifts to occur and to determine whether functional genomic diversity varies predictably in relation to host-plant breadth. Insect chemosensory proteins play a central role in mediating insect-plant interactions, as they directly influence plant...

Data from: Ecological genetics of Juglans nigra: differences in early growth patterns of natural populations

Laura Leites, Lauren Onofrio & Gary Hawley
Many boreal and temperate forest tree species distributed across large geographic ranges are composed of populations adapted to the climate they inhabit. Forestry provenance studies and common gardens provide evidence of local adaptation to climate when associations between fitness traits and the populations’ home climates are observed. Most studies that evaluate tree height as a fitness trait do so at a specific point in time. In this study, we elucidate differences in early growth patterns...

Date of planting and nitrogen management for malt barley production in the Northeast USA

Arthur Siller, Masoud Hashemi, Alexandra Smychkovich, Caroline Wise & Heather Darby

Winter malt barley growth, yield, and quality following leguminous cover crops in the Northeast United States

Arthur Siller, Heather Darby, Alexandra Smychkovich & Masoud Hashemi

Data for Manuscript: A desert songbird with no confamilials in the Western Hemisphere (Verdin, Auriparus flaviceps) investigates divergent conspecific songs

Emma Greig, Eva Kinnebrew, Max Witynski & Eric Larsen
This is the dataset that accompanies the manuscript: A desert songbird with no confamilials in the Western Hemisphere (Verdin, Auriparus flaviceps) investigates divergent conspecific songs, published in the journal Ornithology (2021). One spreadsheet is a dataset for analysis of Verdin song acoustic structure (“Supplementary Material Acoustic Data.xls”), one spreadsheet is a dataset for analysis of Verdin response to playbacks (“Supplementary Material Playback Data.xls”), and one spreadsheet is metadata about all the recordings used in the...

Effect of data source on estimates of regional bird richness in northeastern United States

Roi Ankori-Karlinsky, Ronen Kadmon, Michael Kalyuzhny, Katherine F. Barnes, Andrew M. Wilson, Curtis Flather, Rosalind Renfrew, Joan Walsh & Edna Guk
Standardized data on large-scale and long-term patterns of species richness are critical for understanding the consequences of natural and anthropogenic changes in the environment. The North American Breeding Bird Survey (BBS) is one of the largest and most widely used sources of such data, but so far, little is known about the degree to which BBS data provide accurate estimates of regional richness. Here we test this question by comparing estimates of regional richness based...

Natural disturbance impacts on trade-offs and co-benefits of forest biodiversity and carbon

Martin Mikoláš, Marek Svitok, Radek Bače, Garrett Meigs, William Keeton, Heather Keith, Arne Buechling, Volodymyr Trotsiuk, Kurt Bollmann, Krešimir Begovič, Vojtěch Čada, Oleh Chaskovskyy, Dheeraj Ralhan, Martin Dušátko, Matej Ferenčík, Michal Frankovič, Rhiannon Gloor, Jeňýk Hofmeister, Pavel Janda, Ondrej Kameniar, Daniel Kozák, Jana Lábusová, Linda Majdanová, Thomas Nagel, Jakob Pavlin … & Miroslav Svoboda
With accelerating environmental change, understanding the influence of forest disturbances and trade-offs between biodiversity and carbon dynamics is of high socio-economic importance. Most studies, however, have assessed immediate or short-term effects of disturbance, while long-term impacts remain poorly understood. Here, using a tree-ring-based approach, we modelled the effect of 250 years of disturbances on present-day biodiversity indicators and carbon dynamics in well-preserved European temperate primary forests. Our results indicated that disturbance legacies spanning centuries shaped...

A reassessment of the little-known Amazonian fern Diplazium praestans based on molecular and morphological evidence

Weston Testo, Lindsey Riibe, Michael Sundue & Emily Sessa
Family- and genus-level circumscription of ferns in the suborder Aspleniineae (eupolypods II) has long been controversial, due in part to confusion about the relationship among the families Aspleniaceae and Athyriaceae. Recent studies have demonstrated that character states traditionally used to infer a close relationship between these two families are either symplesiomorphic or homoplastic, and re-examination of numerous taxa has led to the recircumscription of several clades, and the description of several new families and genera....

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Vermont
  • University of Massachusetts Amherst
  • University of Florida
  • Prince of Songkla University
  • Federal University of Paraná
  • Sao Paulo State University
  • Columbia University
  • Technical University of Zvolen
  • University of Michigan-Ann Arbor
  • Field Museum of Natural History