18 Works

Data from: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Nicolás Mongiardino Koch, Jeffrey R Thompson, Avery S Hatch, Marina F McCowin, A Frances Armstrong, Simon E Coppard, Felipe Aguilera, Omri Bronstein, Andreas Kroh, Rich Mooi & Greg W Rouse
Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ eighteen novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise...

Recent dispersal and diversification within the clingfish genus Acyrtus (Actinopterygii: Gobiesocidae), with the description of a new western Atlantic species

Thais L. Quintão, João Luiz Gasparini, Jean-Christophe Joyeux, Luiz A. Rocha & Hudson T. Pinheiro
Abstract The genus Acyrtus (Gobiesocidae) is represented by four valid species distributed in the western Atlantic, and a recently described fifth species from the eastern Pacific. Here, we describe a new species endemic to Trindade Island, Brazil, and provide the first phylogenetic inference for the genus including all representatives. The new species can be distinguished from all its congeners by meristic and morphometric characters, as well as genetic differences. It presents low genetic diversity and,...

Ocular lens morphology is influenced by ecology and metamorphosis in frogs and toads

Kate Thomas, Amartya Mitra, Molly Womack, David Gower, Jeffrey Streicher, Brett Clark, Rayna Bell, Ryan Schott & Matthew Fujita
The shape and relative size of an ocular lens affects the focal length of the eye, with consequences for visual acuity and sensitivity. Lenses are typically spherical in aquatic animals with camera-type eyes and axially flattened in terrestrial species to facilitate vision in optical media with different refractive indices. Frogs and toads (Amphibia: Anura) are ecologically diverse, with many species shifting from aquatic to terrestrial ecologies during metamorphosis. We quantified lens shape and relative size...

Additional file 1 of Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik V. Scheller, Blake A. Simmons, Javier A. Ceja-Navarro & Steven W. Singer
Additional file 1: Supplementary Fig. 1. Residual dry weight biomass after a 56-day incubation. The figure shows that three incubations diverge in terms of biomass degradation. Supplementary Fig. 2. Phylogenetic tree reconstructed based on 49 core universal genes defined by Clusters of Orthologous Groups (COGs) using maximum likelihood. The tree was reconstructed on KBase. Supplementary Fig. 3. Gene proportion per MAG for selected GHs. MAGs with a completeness above 30% and contamination level lower than...

Recent dispersal and diversification within the clingfish genus Acyrtus (Actinopterygii: Gobiesocidae), with the description of a new western Atlantic species

Thais L. Quintão, João Luiz Gasparini, Jean-Christophe Joyeux, Luiz A. Rocha & Hudson T. Pinheiro
Abstract The genus Acyrtus (Gobiesocidae) is represented by four valid species distributed in the western Atlantic, and a recently described fifth species from the eastern Pacific. Here, we describe a new species endemic to Trindade Island, Brazil, and provide the first phylogenetic inference for the genus including all representatives. The new species can be distinguished from all its congeners by meristic and morphometric characters, as well as genetic differences. It presents low genetic diversity and,...

The global distribution of known and undiscovered ant biodiversity

Jamie Kass, Benoit Guénard, Kenneth Dudley, Clinton Jenkins, Fumika Azuma, Brian Fisher, Catherine Parr, Heloise Gibb, John Longino, Philip Ward, Anne Chao, David Lubertazzi, Michael Weiser, Walter Jetz, Robert Guralnick, Rumsaïs Blatrix, James Des Lauriers, David Donoso, Christos Georgiadis, Kiko Gomez, Peter Hawkes, Robert Johnson, John Lattke, Joe MacGown, William Mackay … & Evan Economo
Invertebrates constitute the majority of animal species and are critical for ecosystem functioning and services. Nonetheless, global invertebrate biodiversity patterns and their congruences with vertebrates remain largely unknown. We resolve the first high-resolution (~20-km) global diversity map for a major invertebrate clade, ants, using biodiversity informatics, range modeling, and machine learning to synthesize existing knowledge and predict the distribution of undiscovered diversity. We find that ants and different vertebrate groups have distinct features in their...

Data for: Phylogeography and populations genetics of a widespread cold-adapted ant, Prenolepis imparis

Maria Tonione, Ke Bi, Robert Dunn, Andrea Lucky, Dan Portik & Neil Tsutsui
Historical climate fluctuations have left genetic signatures on species and populations across North America. Here, we used phylogenetic and population genetic analyses from 1,402 orthologous sequences of 75 individuals obtained through sequencing of Ultraconserved Elements (UCEs) to identify population genetic structure and historical demographic patterns across the range of a widespread, cold-adapted ant, the winter ant, Prenolepis imparis. We relate the genomic patterns to those expected as a result of in situ diversification, maintained connectivity,...

Additional file 1 of Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik V. Scheller, Blake A. Simmons, Javier A. Ceja-Navarro & Steven W. Singer
Additional file 1: Supplementary Fig. 1. Residual dry weight biomass after a 56-day incubation. The figure shows that three incubations diverge in terms of biomass degradation. Supplementary Fig. 2. Phylogenetic tree reconstructed based on 49 core universal genes defined by Clusters of Orthologous Groups (COGs) using maximum likelihood. The tree was reconstructed on KBase. Supplementary Fig. 3. Gene proportion per MAG for selected GHs. MAGs with a completeness above 30% and contamination level lower than...

Additional file 2 of Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik V. Scheller, Blake A. Simmons, Javier A. Ceja-Navarro & Steven W. Singer
Additional file 2: Supplementary Table S1. MG_FC_annotations. Table with data for contigs, predicted genes, and feature count values for genes in the metagenomes. MG_metadata. Metadata for sequenced metagenomes. MT_FC_annotations. Table with data for contigs, predicted genes, and feature count values for genes in the metatranscriptomes. MT_metadata. Metadata for sequenced metatranscriptomes.

Systematic revision of the arboreal Neotropical ‘Thorellii’ clade of Centruroides Marx, 1890 bark scorpions (Buthidae c.l. Koch, 1837) with descriptions of six new species

Aaron Goodman, Lorenzo Prendini, Oscar Francke & Lauren Esposito
The arboreal Neotropical ‘thorellii’ clade of Centruroides Marx, 1890 bark scorpions (Buthidae C.L. Koch, 1837) is revised, using a novel approach to species delimitation. A phylogenetic analysis, based on 112 morphological characters and 1078 aligned DNA nucleotides from the mitochondrial Cytochrome c Oxidase Subunit I (COI) gene, provided the framework for placing singletons from geographically disparate localities (and often with suboptimal preservation) using COI minibarcodes, thereby enlarging the taxon sample for diagnosis and delimitation of...

Aposematic patterns shift continuously through the life of poison frogs

Michael Yuan, Catherine Jung, Rayna Bell & Jessica Nelson
Color and pattern are often dynamic traits that change throughout an individual’s lifetime. Still, long-term shifts in coloration have received limited attention. Dendrobatid poison frogs are a classical system in the study of color and pattern evolution in which both sexual selection and predation avoidance are thought to drive the evolution of color and pattern at the population and species level. Here, we highlight an overlooked axis of pattern diversity, within individual variation, using three...

Additional file 2 of Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik V. Scheller, Blake A. Simmons, Javier A. Ceja-Navarro & Steven W. Singer
Additional file 2: Supplementary Table S1. MG_FC_annotations. Table with data for contigs, predicted genes, and feature count values for genes in the metagenomes. MG_metadata. Metadata for sequenced metagenomes. MT_FC_annotations. Table with data for contigs, predicted genes, and feature count values for genes in the metatranscriptomes. MT_metadata. Metadata for sequenced metatranscriptomes.

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik V. Scheller, Blake A. Simmons, Javier A. Ceja-Navarro & Steven W. Singer
Abstract Background Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized...

The gut microbiome reflects ancestry despite dietary shifts across a hybrid zone

Danny Nielsen, Joshua Harrison, Nathan Byer, Trevor Faske, Thomas Parchman, W. Brian Simison & Marjorie Matocq
The microbiome is critical to an organism’s phenotype, and its composition is shaped by, and a driver of, eco-evolutionary interactions. We investigated how host ancestry, habitat, and diet shape gut microbial composition in a mammalian hybrid zone that occurs across an ecotone between distinct vegetation communities. We found that habitat is the primary determinant of diet, while host genotype is the primary determinant of the gut microbiome—a finding further supported by intermediate microbiome composition in...

Endemism, invasion, and overseas dispersal: The phylogeographic history of the Lesser Antillean frog, Eleutherodactylus johnstonei

Michael Yuan, Jeffrey Frederick, Jimmy McGuire, Rayna Bell, Struan Smith, Calvin Fenton, Jourdan Cassius, Rudell Williams, Ian Wang, Robert Powell & S. Blair Hedges
Cryptogenic species, those whose native and introduced ranges are unknown, pose a challenge not only to conservation but also to studies of ecology, biogeography, and evolution. One such species is the Lesser Antillean frog, Eleutherodactylus johnstonei, which is broadly distributed through the Caribbean and mainland South America. The Lesser Antilles pose a particular challenge with regard to cryptogenic species because these islands have been anthropogenically connected since before recorded history. We combined genetic (available on...

How the Easter Egg Weevils got their spots: Phylogenomics reveals Müllerian mimicry in Pachyrhynchus (Coleoptera, Curculionidae)

Matthew H. Van Dam
The evolutionary origins of mimicry in the Easter Egg weevil, Pachyrhynchus, have fascinated researchers since first noted more than a century ago by Alfred Russel Wallace. Müllerian mimicry, or mimicry in which two or more distasteful species look similar, is widespread throughout the animal kingdom. Given the varied but discrete color patterns in Pachyrhynchus, this genus presents one of the best opportunities to study the evolution of both perfect and imperfect mimicry. We analyzed more...

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik V. Scheller, Blake A. Simmons, Javier A. Ceja-Navarro & Steven W. Singer
Abstract Background Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized...

Vindication of Physcomitrium pygmaeum (Funariaceae), an elusive and endangered moss from North America’s Great Basin

Matthew Johnson, Rafael Medina, Nikisha Patel, Genevieve Tocci, David Toren & Bernard Goffinet
Physcomitrium pygmaeum is an ephemeral moss described in 1871 from a single collection from Utah, currently considered conspecific with Physcomitrium pyriforme. The interpretation of the taxon has been problematic due to its rarity in the field, the elusiveness of the type material, and an extremely scattered and inconsistent collection record. Here we present a comprehensive description and assessment of the taxon following the identification of the original material and lectotype designation, the examination of all...

Registration Year

  • 2022
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  • Dataset
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Affiliations

  • California Academy of Sciences
    18
  • University of California, Berkeley
    9
  • University of Oklahoma
    7
  • University of Adelaide
    6
  • The University of Texas at Austin
    6
  • Jilin University
    6
  • Karolinska University Hospital
    6
  • Huazhong University of Science and Technology
    6
  • Fudan University
    6
  • Bengbu Medical College
    6