44 Works

Data from: A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics

Katriina L. Ilves & Hernán López-Fernández
Cichlid fishes (family Cichlidae) are models for evolutionary and ecological research. Massively parallel sequencing approaches have been successfully applied to study relatively recent diversification in groups of African and Neotropical cichlids, but such technologies have yet to be used for addressing larger scale phylogenetic questions of cichlid evolution. Here we describe a process for identifying putative single-copy exons from five African cichlid genomes and sequence the targeted exons for a range of divergent (> tens...

Data from: Testing of the effect of missing data estimation and distribution in morphometric multivariate data analyses

Caleb Marshall Brown, Jessica H. Arbour & Donald A. Jackson
Missing data are an unavoidable problem in biological datasets and the performance of missing data deletion and estimation techniques in morphometric datasets are poorly understood. Here a novel method is used to measure the introduced error of multiple techniques on a representative sample. A large sample of extant crocodilian skulls was measured and analyzed with principal components analysis (PCA). Twenty-three different proportions of missing data were introduced into the dataset, estimated, analyzed, and compared to...

Data from: In and out of refugia: historical patterns of diversity and demography in the North American Caesar’s mushroom species complex

Santiago Sánchez-Ramirez, Rodham E. Tulloss, Laura Guzmán-Davalos, Joaquín Cifuentes-Blanco, Ricardo Valenzuela, Arturo Estrada-Torres, Felipe Ruán-Soto, Raúl Díaz-Moreno, Nallely Hernández-Rico, Mariano Torres-Gómez, Hugo León & Jean-Marc Moncalvo
Some of the effects of past climate dynamics on plant and animal diversity make-up have been relatively well studied, but to less extent in fungi. Pleistocene refugia are thought to harbor high biological diversity (i.e. phylogenetic lineages and genetic diversity), mainly as a product of increased reproductive isolation and allele conservation. In addition, high extinction rates and genetic erosion is expected in previously glaciated regions. Some of the consequences of past climate dynamics might involve...

Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics

Scott V. Edwards, Alison Cloutier & Allan J. Baker
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the...

Data from: The Collins’ monster, a spinous suspension-feeding lobopodian from the Cambrian Burgess Shale of British Columbia

Jean-Bernard Caron & Cédric Aria
Lobopodians, a paraphyletic group of Palaeozoic vermiform animals bearing metameric appendages, are key to the origin of extant panarthropods. First discovered in 1983 on Mount Stephen (Yoho National Park, British Columbia), the Cambrian (Wuliuan) Burgess Shale lobopodian nicknamed “Collins’ monster” is formally described as Collinsovermis monstruosus gen. et sp. nov. A formal systematic revision of the poorly known lobopodian Acinocricus stichus from Utah is also provided. The body of Collinsovermis is plump and compact, lacking...

Exceptional multifunctionality in the feeding apparatus of a mid-Cambrian radiodont

Joseph Moysiuk & Jean-Bernard Caron
Radiodonts (stem Euarthropoda) were ecologically diverse, but species generally displayed limited functional specialization of appendages along the body axis compared to crown group euarthropods. This is puzzling because such functional specialization is considered to have been an important driver of euarthropod ecological diversification. One way to circumvent this constraint could have been the functional specialization of different parts of the frontal appendages, known to have been ecologically important in radiodonts. This hypothesis has yet to...

Data from: Adaptive landscape and functional diversity of Neotropical cichlids: implications for the ecology and evolution of Cichlinae (Cichlidae; Cichliformes)

Jessica H. Arbour & Hernan López-Fernández
Morphological, lineage and ecological diversity can vary substantially even among closely related lineages. Factors that influence morphological diversification, especially in functionally relevant traits, can help to explain the modern distribution of disparity across phylogenies and communities. Multivariate axes of feeding functional morphology from 75 species of Neotropical cichlid and a stepwise-AIC algorithm were used to estimate the adaptive landscape of functional morphospace in Cichlinae. Adaptive landscape complexity and convergence, as well as the functional diversity...

Data from: Evolution of sexual dimorphism in phenotypic covariance structure in Phymata

David Punzalan & Locke Rowe
Sexual dimorphism is a consequence of both sex-specific selection and potential constraints imposed by a shared genetic architecture underlying sexually homologous traits. However, genetic architecture is expected to evolve to mitigate these constraints, allowing the sexes to approach their respective optimal mean phenotype. In additon, sex-specific selection is expected to generate sexual dimorphism of trait covariance structure (e.g. the phenotypic covariance matrix, P) but previous empirical work has not fully addressed this prediction. We compared...

Data from: Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses

Taylor Edwards, Marc Tollis, PingHsun Hsieh, Ryan N. Gutenkunst, Zhen Liu, Kenro Kusumi, Melanie Culver & Robert W. Murphy
Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus....

Data from: A new species of Peckoltia from the Upper Orinoco (Siluriformes: Loricariidae)

Jonathan Armbruster, Nathan Lujan, Jonathan W. Armbruster & Nathan K. Lujan
A new species of the suckermouth armored catfish genus Peckoltia is described from the lower Ventuari River, a tributary of the upper Orinoco River in Amazonas State, Venezuela. Specimens of this species were formerly included in the wide-ranging Amazonian species P. vittata, but a recent molecular phylogeny found Orinoco individuals to be distantly related to Amazon Basin individuals spanning the range of P. vittata syntypes. Detailed morphological examination confirmed distinctiveness of Orinoco specimens, and found...

Data from: A new family of Cambrian rhynchonelliformean brachiopods (Order Naukatida) with an aberrant coral-like morphology

Michael Streng, Aodhán D. Butler, John S. Peel, Russell J. Garwood & Jean-Bernard Caron
Tomteluva perturbata gen. et sp. nov. and Nasakia thulensis gen. et sp. nov., two new rhynchonelliformean brachiopod taxa, are described from carbonate beds from the lower middle Cambrian (Series 3, Stage 5) basinal Stephen Formation, Canada, and the upper lower Cambrian (Series 2, Stage 4) Henson Gletscher Formation, North Greenland, respectively. The two taxa are characterized by an unusual coral-like morphology typified by a high conical ventral valve with an anteriorly curved umbo and a...

Data from: Three new naraoiid species from the Burgess Shale, with a morphometric and phylogenetic reinvestigation of Naraoiidae

Benjamin Mayers, Cédric Aria & Jean-Bernard Caron
Naraoiids are non‐biomineralized euarthropods characterized by the complete fusion of post‐cephalic tergo‐pleurae into a single shield, as well as an extensively ramified digestive tract. Ranging from the early Cambrian to the late Silurian (Pridoli), these arthropods of simple appearance have traditionally been associated with the early diversification of trilobites and their close relatives, but the interrelationships and affinities of naraoiids within Artiopoda remain poorly characterized. Three new species from the Burgess Shale (middle Cambrian, Stage...

Data from: Earth history and the passerine superradiation

Carl H. Oliveros, Daniel J. Field, Daniel T. Ksepka, F. Keith Barker, Alexandre Aleixo, Michael J. Andersen, Per Alström, Brett W. Benz, Edward L. Braun, Michael J. Braun, Gustavo A. Bravo, Robb T. Brumfield, R. Terry Chesser, Santiago Claramunt, Joel Cracraft, Andrés M. Cuervo, Elizabeth P. Derryberry, Travis C. Glenn, Michael G. Harvey, Peter A. Hosner, Leo Joseph, Rebecca T. Kimball, Andrew L. Mack, Colin M. Miskelly, A. Townsend Peterson … & Brant C. Faircloth
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships...

Data from: Convergent regulatory evolution and loss of flight in palaeognathous birds

Timothy B. Sackton, Phil Grayson, Alison Cloutier, Zhirui Hu, Jun S. Liu, Nicole E. Wheeler, Paul P. Gardner, Julia A. Clarke, Allan J. Baker, Michele Clamp & Scott V. Edwards
A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which...

Data from: Landscape genetics of leaf-toed geckos in the tropical dry forest of northern Mexico

Christopher Blair, Victor H. Jiménez Arcos, Fausto R. Mendez De La Cruz & Robert W. Murphy
Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF) contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity...

Data from: Ontogeny, morphology and taxonomy of the soft-bodied Cambrian ‘mollusc’ Wiwaxia

Martin R. Smith
The soft-bodied Cambrian organism Wiwaxia poses a taxonomic conundrum. Its imbricated dorsal scleritome suggests a relationship with the polychaete annelid worms, whereas its mouthparts and naked ventral surface invite comparison with the molluscan radula and foot. 476 new and existing specimens from the 505-Myr-old Burgess Shale cast fresh light on Wiwaxia's sclerites and scleritome. My observations illuminate the diversity within the genus and demonstrate that Wiwaxia did not undergo discrete moult stages; rather, its scleritome...

Data from: Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites

Allan J. Baker, Oliver Haddrath, John D. McPherson & Alison Cloutier
One of the most startling discoveries in avian molecular phylogenetics is that the volant tinamous are embedded in the flightless ratites, but this topology remains controversial because recent morphological phylogenies place tinamous as the closest relative of a monophyletic ratite clade. Here, we integrate new phylogenomic sequences from 1,448 nuclear DNA loci totalling almost one million base pairs from the extinct little bush moa, Chilean tinamou and emu with available sequences from ostrich, elegant crested...

Data from: A new ankylosaurine dinosaur from the Judith River Formation of Montana, USA, based on an exceptional skeleton with soft tissue preservation

Victoria M. Arbour & David C. Evans
The terrestrial Judith River Formation of northern Montana was deposited over an approximately 4 Myr interval during the Campanian (Late Cretaceous). Despite having been prospected and collected continuously by palaeontologists for over a century, few relatively complete dinosaur skeletons have been recovered from this unit to date. Here we describe a new genus and species of ankylosaurine dinosaur, Zuul crurivastator, from the Coal Ridge Member of the Judith River Formation, based on an exceptionally complete...

Data from: Widespread generalist clones are associated with range and niche expansion in allopolyploids of Pacific Northwest Hawthorns (Crataegus L.)

Jennifer M. Coughlan, S. Han, Saša Stefanović & Timothy A. Dickinson
Range and niche expansion are commonly associated with transitions to asexuality, polyploidy, and hybridity (allopolyploidy) in plants. The ability of asexual polyploids to colonize novel habitats may be due to widespread generalist clones, multiple ecologically specialized clones, or may be a neutral byproduct of multiple, independent origins of asexual polyploids throughout the range. We have quantified niche size and divergence for hawthorns of the Pacific Northwest using data from herbarium vouchers with known cytotypes. We...

Data from: The strength of sex-specific selection in the wild

Amardeep Singh & David Punzalan
Anisogamy predisposes the sexes to very different patterns of selection on shared traits. Selective differences between the sexes may manifest as changes in the direction or strength of selection acting on shared phenotypes. Although previous studies have found evidence for widespread differences in the direction of selection between the sexes, surprisingly little is known regarding potential differences in the magnitude of selection and whether such differences might be confined to specific components of fitness. We...

Data from: Comparative phylogeography of mainland and insular species of Neotropical molossid bats (Molossus)

Livia O. Loureiro, Mark D. Engstrom & Burton K. Lim
Genetic structures, historical events, habitat preferences, and geographic barriers might result in distinct patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein we use a genotype by sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and...

The Burgess Shale paleocommunity with new insights from Marble Canyon, British Columbia

Karma Nanglu, Jean-Bernard Caron & Robert Gaines
The middle (Wuliuan Stage) Cambrian Burgess Shale is famous for its exceptional preservation of diverse and abundant soft-bodied animals through the “thick” Stephen Formation. However, with the exception of the Walcott Quarry (Fossil Ridge) and the stratigraphically older Tulip Beds (Mount Stephen) which are both in Yoho National Park (British Columbia), quantitative assessments of the Burgess Shale have remained limited. Here we first provide a detailed quantitative overview of the diversity and structure of the...

An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)

Jinmin Chen, Elizabeth Prendini, Yun-He Wu, Bao-Lin Zhang, Chatmongkon Suwannapoom, Hong-Man Chen, Jie-Qiong Jin, Emily Moriarty Lemmon, Alan R. Lemmon, Bryan L. Stuart, Christopher J. Raxworthy, Robert W. Murphy, Zhi-Yong Yuan & Jing Che
Rhacophoridae is one of the most speciose and ecologically diverse families of amphibians. Resolution of its evolutionary relationships is key to understanding the accumulation of biodiversity, yet previous hypotheses based on Sanger sequencing exhibit much discordance amongst generic relationships. This conflict precludes the making of sound macroevolutionary conclusions. Herein, we conduct the first phylogenomic study using broad-scale sampling and sequences of 352 nuclear DNA loci obtained using anchored hybrid enrichment targeted sequencing. The robust time-calibrated...

Foraging strategies, craniodental traits and interaction in the bite force of Neotropical frugivorous bats (Phyllostomidae: Stenodermatinae)

Leidy Viviana García Herrera, Leidy Azucena Ramírez Fráncel, Giovany Guevara Cardona, Gladys Reinoso Flórez, Alfonso Sánchez Hernández, Burton K. Lim & Sergio Losada Prado
1. Bats in the family Phyllostomidae exhibit great diversity in skull size and morphology that reflects the degree of resource division and ecological overlap in the group. In particular, the subfamily Stenodermatinae has high morphological diversification associated with cranial and mandibular traits that is associated with the ability to consume the full range of available fruits (soft and hard). 2. Was analyzed craniodental traits and their relationship to the bite force in 343 specimens distributed...

Data from: Systematics of spiny-backed treefrogs (Hylidae: Osteocephalus): an Amazonian puzzle

Karl-Heinz Jungfer, Julián Faivovich, José M. Padial, Santiago Castroviejo-Fisher, Mariana M. Lyra, Bianca Von Muller Berneck, Patricia P. Iglesias, Philippe J. R. Kok, Ross T. Macculloch, Miguel Trefaut Rodrigues, Vanessa K. Verdade, Claudia P. Torres Gastello, Juan Carlos Chaparro, Paula H. Valdujo, Steffen Reichle, Jiří Moravec, Václav Gvoždík, Giussepe Gagliardi-Urrutia, Raffael Ernst, Ignacio De La Riva, Donald Bruce Means, Albertina P. Lima, J. Celsa Señaris, Ward C. Wheeler & Célio F. B. Haddad
Spiny-backed tree frogs of the genus Osteocephalus are conspicuous components of the tropical wet forests of the Amazon and the Guiana Shield. Here, we revise the phylogenetic relationships of Osteocephalus and its sister group Tepuihyla, using up to 6134 bp of DNA sequences of nine mitochondrial and one nuclear gene for 338 specimens from eight countries and 218 localities, representing 89% of the 28 currently recognized nominal species. Our phylogenetic analyses reveal (i) the paraphyly...

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