99 Works

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.

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: Reed frog diversification in the Gulf of Guinea: overseas dispersal, the progression rule, and in situ speciation

Rayna C. Bell, Robert C. Drewes & Kelly R. Zamudio
Oceanic islands accumulate endemic species when new colonists diverge from source populations or by in situ diversification of resident island endemics. The relative importance of dispersal versus in situ speciation in generating diversity on islands varies with a number of archipelago characteristics including island size, age, and remoteness. Here we characterize inter-island dispersal and in situ speciation in frogs endemic to the Gulf of Guinea islands. Using mitochondrial sequence and genome-wide SNP data we demonstrate...

Data from: A passerine bird's evolution corroborates the geologic history of the island of New Guinea

Kristy Deiner, Alan R. Lemmon, Andrew L. Mack, Robert C. Fleischer & John P. Dumbacher
New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine patterns of phylogeographic variation of a common and widespread New Guinean bird species (Colluricincla megarhyncha). Specifically, we test the mechanisms hypothesized to cause geographic and genetic variation (e.g., vicariance, isolation...

Data from: Genomic signatures of geographic isolation and natural selection in coral reef fishes

Michelle R. Gaither, Moisés A. Bernal, Richard R. Coleman, Brian W. Bowen, Shelley A. Jones, Warren Brian Simison & Luiz A. Rocha
The drivers of speciation remain among the most controversial topics in evolutionary biology. Initially, Darwin emphasized natural selection as a primary mechanism of speciation, but the architects of the modern synthesis largely abandoned that view in favour of divergence by geographic isolation. The balance between selection and isolation is still at the forefront of the evolutionary debate, especially for the world's tropical oceans where biodiversity is high, but isolating barriers are few. Here, we identify...

Data from: Plant diversity and endemism in the California Floristic Province

Dylan O. Burge, James H. Thorne, Susan P. Harrison, Bart C. O'Brien, Jon P. Rebman, James R. Shevock, Edward R. Alverson, Linda K. Hardison, José Delgadillo-Rodríguez, Steven A. Junak, Thomas A. Oberbauer, Hugo Riemann, Sula E. Vanderplank & Teri Barry
The California Floristic Province (CFP) is an area of high biodiversity and endemism corresponding roughly to the portion of western North America having a Mediterranean-type climate. High levels of diversity and endemism in the CFP are attributed to the unique geo-climatic setting of the region. In recent years, much has been learned about the origins of plant diversity in western North America. This work, however, has been hindered by a focus on political rather than...

Data from: Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon)

Moises A. Bernal, Michelle R. Gaither, Warren Brian Simison & Luiz A. Rocha
Closely related marine species with large sympatric ranges provide opportunities to study the mechanisms of speciation, particularly when there is evidence of gene flow between the lineages. Here we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via Restriction-site Associated DNA Sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI...

Data from: Patterns of genomic divergence and signals of selection in sympatric and allopatric northeastern Pacific and Sea of Cortez populations of the sargo (Anisotremus davidsonii) and longjaw mudsucker (Gillichthys mirabilis)

Eric Garcia, Brian Simison & Giacomo Bernardi
Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, USA, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands...

Data from: Taxonomic revision of imitating carpenter ants, Camponotus subgenus Myrmopytia (Hymenoptera, Formicidae) of Madagascar, using morphometry and qualitative traits

Nicole Rasoamanana, Sándor Csősz & Brian L. Fisher
The ant genus Camponotus (Mayr, 1861) is one of the most abundant and species rich ant genera in the Malagasy zoogeographical region. Although this group is commonly encountered, its taxonomy is far from complete. Here, we clarify the taxonomy of the Malagasy-endemic Camponotus subgenus Myrmopytia (Emery, 1920). Species delimitation was based on traditional morphological characters and multivariate morphometric analyses, including exploratory Nest Centroid clustering and confirmatory cross-validated Linear Discriminant Analysis. Four species are recognized: Camponotus...

Do alignment and trimming methods matter for phylogenomic (UCE) analyses?

Daniel Portik & John Wiens
Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from dozens, hundreds, or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e. removing poorly...

Incipient speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

Kyle O'Connell, Ivan Prates, Lauren Scheinberg, Kevin Mulder & Rayna Bell
Secondary contact of lineages in the early stages of divergence can result in lineage fusion or promote reproductive isolation through reinforcement. While these processes are well studied in many taxonomic groups, we know little about their contribution to diversification of the secretive and enigmatic caecilians (Amphibia: Gymnophiona). Here, we combine genetic (mtDNA and genome-wide SNPs) and phenotypic data to investigate the divergence history of caecilians endemic to the oceanic island of São Tomé in the...

Speciation and gene flow across an elevational gradient in New Guinea kingfishers

Ethan Linck, Benjamin Freeman & John Dumbacher
Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks, and Timema stick insects, support for ecological speciation driven by other selective pressures has come...

Data from: Adaptation to reef habitats through selection on the coral animal and its associated microbiome

Madeleine J.H. Van Oppen, Pim Bongaerts, Pedro Frade, Lesa M. Peplow, Sarah E. Boyd, Hieu T. Nim, Line K. Bay & Madeleine J. H. Van Oppen
Spatially adjacent habitats on coral reefs can represent highly distinct environments, often harbouring different coral communities. Yet, certain coral species thrive across divergent environments. It is unknown whether the forces of selection are sufficiently strong to overcome the counteracting effects of the typically high gene flow over short distances, and for local adaptation to occur. We screened the coral genome (using restriction-site-associated sequencing [RAD-seq]), and characterized both the dinoflagellate photosymbiont and tissue-associated prokaryote microbiomes (using...

Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California

Yi-Ming Weng, Sean Schoville & David Kavanaugh
The evolutionary histories of alpine species are often directly associated with responses to glaciation. Deep divergence among populations and complex patterns of genetic variation have been inferred as consequences of persistence within glacier boundaries (i.e. on nunataks), while shallow divergence and limited genetic variation is assumed to result from expansion from large refugia at the edge of ice shields (i.e. massifs de refuge). However, for some species, dependence on specific microhabitats could profoundly influence their...

A high-quality carabid genome provides insights into beetle genome evolution and cold adaptation

Yi-Ming Weng, Charlotte Francoeur, Cameron Currie, David Kavanaugh & Sean Schoville
The hyper-diverse order Coleoptera comprises a staggering ~25% of known species on Earth. Despite recent breakthroughs in next generation sequencing, there remains a limited representation of beetle diversity in assembled genomes. Most notably, the ground beetle family Carabidae, comprising more than 40,000 described species, has not been studied in a comparative genomics framework using whole genome data. Here we generate a high-quality genome assembly for Nebria riversi, to examine sources of novelty in the genome...

Data from: High species richness and lineage diversity of reef corals in the mesophotic zone

Paul R. Muir, Carden C. Wallace, Michel Pichon & Pim Bongaerts
Coral reefs are increasingly threatened by thermal bleaching and tropical storm events associated with rising sea surface temperatures. Deeper habitats offer some protection from these impacts and may safeguard reef-coral biodiversity, but their faunas are largely undescribed for the Indo-Pacific. Here, we show high species richness of scleractinian corals in mesophotic habitats (30-125 m) for the northern Great Barrier Reef region that greatly exceeds previous records for mesophotic habitats globally. Overall, 45% of shallow reef...

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...

The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution

Matthew Van Dam, Analyn Anzano Cabras, James B. Henderson, Andrew J. Rominger, Cynthia Pérez Estrada, Arina D. Omer, Olga Dudchenko, Erez Lieberman Aiden & Athena W. Lam
Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale...

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...

Data from: Three-dimensional morphological variability of recent rhynchonellide brachiopod crura

Holly A. Schreiber, Peter D. Roopnarine & Sandra J. Carlson
Crura, the calcareous support structures of the lophophore in rhynchonellide brachiopods, have historically been used to justify higher-level rhynchonellide classification and reveal major evolutionary lineages within rhynchonellides. Seventeen crural types have been described and categorized into four groups based on variation in overall structure and cross-sectional shape, but not evaluated in a quantitative or comprehensive manner. Heterochrony has been hypothesized to play a role in the evolutionary transitions among some types, but the structural, developmental,...

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