21 Works

Data for: Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone

Erin Molloy, John Gatesy & Mark Springer
A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and...

Macroevolution of dimensionless life history metrics in tetrapods

Cecina Babich Morrow, S.K. Morgan Ernest & Drew Kerkhoff
Life history traits represent organisms’ strategies to navigate the fitness trade-offs between survival and reproduction. Eric Charnov developed three dimensionless metrics to quantify fundamental life history trade-offs. Lifetime reproductive effort (LRE), relative reproductive lifespan (RRL), and relative offspring size (ROS), together with body mass, can be used to classify life history strategies across the four major classes of tetrapods: amphibians, reptiles, mammals, and birds. First, we investigate how the metrics have evolved in concert with...

Anatomy of the nasal and auditory regions of the fossil lagomorph Palaeolagus haydeni: systematic and evolutionary implications

Łucja Fostowicz-Frelik, Irina Ruf & Jin Meng
Palaeolagus, a late Eocene to early Miocene North American lagomorph genus, represented by numerous and well-preserved specimens, has been long considered a basal leporid, although it is currently understood as a stem lagomorph. Based on micro-computed tomography (μCT) data and 3D reconstructions, here we present the first description of intracranial structures of the nasal and auditory regions of a complete skull of Palaeolagus haydeni from the early Oligocene of Nebraska. Although Palaeolagus haydeni shows a...

How to render species comparable taxonomic units through deep time: A case study on intraspecific osteological variability in extant and extinct Lacertid lizards

Emanuel Tschopp, James Napoli, Lukardis Wencker, Massimo Delfino & Paul Upchurch
Generally, the species is considered to be the only naturally occurring taxon. However, species recognised and defined using different species delimitation criteria cannot readily be compared, impacting studies of biodiversity through Deep Time. This comparability issue is particularly marked when comparing extant with extinct species, because the only available data for species delimitation in fossils is derived from their preserved morphology, which is generally restricted to osteology in vertebrates. Here, we quantify intraspecific, intrageneric, and...

Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome-wide SNP data from seven native species

Nathan Lujan, Jason Weir, Brice Noonan, Nathan Lovejoy & Nicholas Mandrak
Since the early Holocene, fish population genetics in the Laurentian Great Lakes have been shaped by the dual influences of habitat structure and post-glacial dispersal. Riverscape genetics theory predicts that longitudinal habitat corridors and unidirectional downstream water-flow drive the downstream accumulation of genetic diversity, whereas post-glacial dispersal theory predicts that fish genetic diversity should decrease with increasing distance from glacial refugia. This study examines populations of seven native fish species codistributed above and below the...

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge

Alisa Vershinina, Peter Heintzman, Duane Froese, Grant Zazula, Molly Cassatt-Johnstone, Love Dalén, Clio Der Sarkissian, Shelby Dunn, Luca Ermini, Cristina Gamba, Pamela Groves, Joshua Kapp, Daniel Mann, Andaine Seguin-Orlando, John Southon, Mathias Stiller, Matthew Wooller, Gennady Baryshnikov, Dmitry Gimranov, Eric Scott, Elizabeth Hall, Susan Hewitson, Irina Kirillova, Pavel Kosintsev, Fedor Shidlovsky … & Beth Shapiro
The Bering Land Bridge (BLB) last connected Eurasia and North America during the Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and...

Interrogating discordance resolves relationships in the rapid radiation of Old World fruit bats (Chiroptera: Pteropodidae)

Nicolas Nesi, Stephen Rossiter, Michael McGowen, Georgia Tsagkogeorga, Burton Lim, Susan Tsang, Violaine Nicolas, Aude Lalis, Silke Riesle Sbarbaro, Sigit Wiantoro, Alan Hitch, Javier Juste, Corinna Pinzari, Frank Bonaccorso, Nancy Simmons, Annette Scanlon & Christopher Todd
The family Pteropodidae (Old World fruit bats) comprises >200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with >50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the...

Datafile - In situ adaptation and ecological release facilitate the occupied niche expansion of an invasive Madagascan day gecko in Florida

Thomas Fieldsend, Nicolas Dubos, Kenneth Krysko, Christopher Raxworthy & Sparkle Malone
Aim To investigate whether the frequently advocated climate-matching species distribution modelling approach could predict the well-characterized colonization of Florida by the Madagascar giant day gecko Phelsuma grandis. Location Madagascar and Florida, USA. Methods To determine the climatic conditions associated with the native range of P. grandis, we used native-range presence-only records and Bioclim climatic data to build a Maxent species distribution model and projected the climatic thresholds of the native range onto Florida. We then...

High-density 3-D coordinate data of avian and non-avian dinosaur endocasts

Akinobu Watanabe, Amy Balanoff, Paul Gignac, M. Eugenia Gold & Mark Norell
How do large and unique brains evolve? Historically, comparative neuroanatomical studies have attributed the evolutionary genesis of highly encephalized brains to deviations along, as well as from, conserved scaling relationships among brain regions. However, the relative contributions of these concerted (integrated) and mosaic (modular) processes as drivers of brain evolution remain unclear, especially in non-mammalian groups. While proportional brain sizes have been the predominant metric used to characterize brain morphology to date, we perform a...

Volcanism and paleoclimate change drive diversification of world’s largest whip spider (Amblypygi)

Frederic Dominique Schramm, Alejandro Valdez-Mondragón & Lorenzo Prendini
The tropics contain many of the most biodiverse regions on Earth but the processes responsible for generating this diversity remain poorly understood. This study investigated the drivers of diversification in arthropods with stenotopic ecological requirements and limited dispersal capability using as model the monotypic whip spider (Amblypygi) genus Acanthophrynus, widespread in the tropical deciduous forests of Mexico. We hypothesized that for these organisms, the tropical deciduous forests serve as a conduit for dispersal, with their...

Ecological divergence and the history of gene flow in the Nearctic milksnakes (Lampropeltis triangulum complex)

Frank Burbrink
Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with the geographic space, contemporary and historical climate, and biogeographic barriers may have complex effects on population genetic structure and speciation. While allopatric speciation at biogeographic barriers is considered the primary mechanism for generating species, more recently it has been shown that parapatric modes of divergence may be...

Data For: The developing bird pelvis passes through ancestral Archosaurian and Dinosaurian conditions

Christopher Griffin, João Botelho, Michael Hanson, Matteo Fabbri, Daniel Smith-Paredes, Ryan Carney, Mark Norell, Shiro Egawa, Stephen Gatesy, Timothy Rowe, Ruth Elsey, Sterling Nesbitt & Bhart-Anjan Bhullar
Living birds (Aves) have bodies dramatically modified from the ancestral reptilian condition. The avian pelvis in particular experienced dramatic changes during the transition from early archosaurs to living birds. This stepwise transformation is well documented by an excellent fossil record; however, the ontogenetic alterations that underly it are less well-understood. We used embryological imaging techniques to examine the morphogenesis of avian pelvic tissues in three dimensions, allowing direct comparison with the fossil record. Many ancestral...

Phylogenetic results of 6 morphological character matrices

Congyu Yu
The construction of morphological character matrices is central to paleontological systematic study, which extracts paleontological information from fossils. Although the word information has been repeatedly mentioned in a wide array of paleontological systematic studies, its meaning has rarely been clarified and there has not been a standard to measure paleontological information due to the incompleteness of fossils, difficulty of recognizing homologous and homoplastic structures, etc. Here, based on information theory, we show the deep connections...

Ecological drivers of carnivoran body shape evolution

Chris Law
Morphological diversity is often attributed as adaptations to distinct ecologies. Although biologists have long hypothesized that distinct ecologies drive the evolution of body shape, these relationships are rarely tested across macroevolutionary scales in mammals. Here, I tested hypotheses that locomotor, hunting, and dietary ecologies influenced body shape evolution in carnivorans, a morphologically and ecologically diverse clade of mammals. I found that adaptive models with ecological trait regimes were poor predictors of carnivoran body shape and...

Incorporating hierarchical characters into phylogenetic analysis

Katherine St. John & Melanie Hopkins
Popular optimality criteria for phylogenetic trees focus on sequences of characters that are applicable to all the taxa. As studies grow in breadth, it can be the case that some characters are applicable for a portion of the taxa and inapplicable for others. Past work has explored the limitations of treating inapplicable characters as missing data, noting that this strategy may favor trees where interval nodes are assigned impossible states, where the arrangement of taxa...

Identifying traits that enable lizard adaptation to different habitats

Flávia Lanna, Guarino Colli, Frank Burbrink & Bryan Carstens
Aim: Species adapt differently to contrasting environments, such as open habitats with sparse vegetation and forested habitats with dense forest cover. We investigated colonization patterns in the open and forested environments in the Diagonal of Open Formations and surrounding rain forests (i.e., Amazon and Atlantic Forest) in Brazil, tested whether the diversification rates were affected by the environmental conditions, and identified traits that enabled species to persist in those environments. Location: South America, Brazil. Taxon:...

Community phylogeographic patterns reveal how a barrier filters and structures taxa in North American warm deserts

Kaiya Provost, Edward A. Myers & Brian Smith
Aim: The study of biogeographic barriers has been instrumental in understanding the evolution and distribution of taxa. With the increasing availability of empirical datasets, emergent patterns can be inferred from communities by synthesizing how barriers filter and structure populations across species. We assemble phylogeographic data across a barrier and perform spatially-explicit simulations to quantify spatiotemporal patterns of divergence, the influence of species traits on these patterns, and the statistical power needed to differentiate alternative diversification...

Data from: Accelerated diversification explains the exceptional species richness of tropical characoid fishes

Bruno Melo, Brian Sidlauskas, Thomas Near, Fabio Roxo, Ava Ghezelayagh, Luz Ochoa, Melanie Stiassny, Jairo Arroyave, Jonathan Chang, Brant Faircloth, Daniel MacGuigan, Richard Harrington, Ricardo Benine, Michael Burns, Kendra Hoekzema, Natalia Sanches, Javier Maldonado-Ocampo, Ricardo Castro, Fausto Foresti, Michael Alfaro & Claudio Oliveira
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1288 ultraconserved element loci spanning 293 species, 211...

Speciation in the abyss - genomics and morphology reveal a new species of beaked whale

Emma L. Carroll, Michael R. McGowen, Morgan L. McCarthy, Felix G. Marx, Natacha Aguilar De Soto, Merel L. Dalebout, Sascha Dreyer, Oscar E. Gaggiotti, Sabine S. Hansen, Anton Van Helden, Aubrie B. Onoufriou, Robin W. Baird, C. Scott Baker, Simon Berrow, Danielle Cholewiak, Diane Claridge, Rochelle Constantine, Nicholas J. Davison, Catarina Eira, R. Ewan Fordyce, John Gatesy, G. J. Greg Hofmeyr, Vidal Martin, James G. Mead, Antonio A. Mignucci-Giannoni … & Morten T. Olsen
Earth’s deep oceans remains less well understood than the surface of Mars. Beaked whales (ziphiids) are among the most visible inhabitants of the abyss, due to their large size and worldwide distribution, yet their diversity and ecology remain obscure. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari’s beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous people of the lands from which the species holotype and...

Data from: An Appalachian population of neochoristoderes (Diapsida: Choristodera) elucidated through fossil evidence and ecological niche modeling

Thomas Dudgeon, Zoe Landry, Wayne Callahan, Carl Mehling & Steven Ballwanz
Four neochoristoderan vertebral centra are described from the latest Cretaceous of New Jersey. One specimen was recovered from the basal transgressive lag of the Navesink Formation in the area of Holmdel Park, New Jersey, and two others were recovered nearby and likely were derived from the same horizon. The fourth was recovered from the Marshalltown sequence in the vicinity of the Ellisdale Dinosaur Site. These vertebrae expand the geographic range of Late Cretaceous neochoristoderes in...

Phylogenomics, origin and diversification of anthozoans (Phylum Cnidaria)

Catherine McFadden, Andrea Quattrini, Mercer Brugler, Peter Cowman, Luisa Dueñas, Marcelo Kitahara, David Paz-García, James Reimer & Estefania Rodríguez
Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, analyses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds...

Registration Year

  • 2021

Resource Types

  • Dataset


  • American Museum of Natural History
  • The Ohio State University
  • Oregon State University
  • Smithsonian Institution
  • National Autonomous University of Mexico
  • Canadian Museum of Nature
  • University of Copenhagen
  • University of California, Riverside
  • Yale University
  • City University of New York