28 Works

Hierarchical multi-grain models improve descriptions of species’ environmental associations, distribution, and abundance

Katherine Mertes, Marta Jarzyna & Walter Jetz
The characterization of species’ environmental niches and spatial distribution predictions based on them are now central to much of ecology and conservation, but implicitly requires decisions about the appropriate spatial scale (i.e. grain) of analysis. Ecological theory and empirical evidence suggest that range-resident species respond to their environment at two characteristic, hierarchical spatial grains: (i) response grain, the (relatively fine) grain at which an individual uses environmental resources, and (ii) occupancy grain, the (relatively coarse)...

Illuminating the impact of diel vertical migration on visual gene expression in deep-sea shrimp

Danielle DeLeo & Heather Bracken-Grissom
Diel vertical migration (DVM) of marine animals represents one of the largest migrations on our planet. Migrating fauna are subjected to a variety of light fields and environmental conditions that can have notable impacts on sensory mechanisms, including an organism’s visual capabilities. Among deep-sea migrators are oplophorid shrimp, that vertically migrate hundreds of meters to feed in shallow waters at night. These species also have bioluminescent light organs that emit light during migrations to aid...

Data from: Climate drives the geography of marine consumption by changing predator communities

Matthew Whalen, Ross Whippo & Emmett Duffy
The global distribution of primary production and consumption by humans (fisheries) is well-documented, but we have no map linking the central ecological process of consumption within food webs to temperature and other ecological drivers. Using standardized assays that span 105° of latitude on four continents, we show that rates of bait consumption by generalist predators in shallow marine ecosystems are tightly linked to both temperature and the composition of consumer assemblages. Unexpectedly, rates of consumption...

Alignments of Sequence Data for Phylogenetic Analysis of Damsel

Emily McFarland, Carole Baldwin, D Ross Robertson, Luiz Rocha & Luke Tornabene
Initially described in 1882, Chromis enchrysurus, the Yellowtail Reeffish, was redescribed in 1982 to account for an observed color morph that possesses a white tail instead of a yellow one, but morphological and geographic boundaries between the two color morphs were not well understood. Taking advantage of newly collected material from submersible studies of deep reefs and photographs from rebreather dives, we sought to determine whether the white-tailed Chromis is actually a color morph of...

Data from: Phylogenomic analyses of the Photinia complex support the recognition of a new genus Phippsiomeles and the resurrection of a redefined Stranvaesia in Maleae (Rosaceae)

Bin-Bin Liu, De-Yuan Hong, Shi-Liang Zhou, Chao Xu, Wen-Pan Dong, Gabriel Johnson & Jun Wen
Photinia and its morphologically similar allies in Maleae (Rosaceae) consist of five currently recognized genera: Aronia, Heteromeles, Photinia, Pourthiaea, and Stranvaesia, and 68 species, distributed in Asia and North & Central America. Despite previous efforts to clarify relationships in this group, the generic delimitations have remained uncertain. Our goals were to reconstruct a robust phylogeny of Photinia and its close allies to test the monophyly of the currently recognized genera, especially Photinia and Stranvaesia, and...

Data from: Life in the canopy: community trait assessments reveal substantial functional diversity among fern epiphytes

Joel H. Nitta, James E. Watkins & Charles C. Davis
The expansion of angiosperm-dominated forests in the Cretaceous and early Cenozoic had a profound effect on terrestrial biota by creating novel ecological niches. The majority of modern fern lineages are hypothesized to have arisen in response to this expansion, particularly fern epiphytes that radiated into the canopy. Recent evidence, however, suggests that epiphytism does not correlate with increased diversification rates in ferns, calling into question the role of the canopy habitat in fern evolution. To...

Data from: Morphology and performance of the trap-jaw cheliceral strikes in spiders (Araneae, Mecysmaucheniidae)

Hannah Wood
Mecysmaucheniidae spiders have evolved ultra-fast cheliceral strikes four times independently. The mechanism for producing these high-speed strikes is likely due to a latch/spring system that allows for stored energy to be rapidly released. This study examines two different sister-lineages: Zearchaea has ultra-fast cheliceral strikes and Aotearoa, based on external morphology, is hypothesized to have slower strikes. Using high-speed videography, I gather kinematic data on each taxon and test the hypothesis that external morphology predicts cheliceral...

Effects of snake fungal disease on short-term survival, behavior, and movement in free-ranging snakes

Steven Price, Jennifer McKenzie, Grant Connette, Simon Bonner & Jeffrey Lorch
Pathogenic fungi are increasingly associated with epidemics in wildlife populations. Snake fungal disease (SFD) is an emerging threat to snakes, taxa that are elusive and difficult to sample. Thus, assessments of the impacts of SFD on populations have rarely occurred. We used a field technique to enhance detection, Passive Integrated Transponder (PIT) telemetry, and a multistate capture-mark-recapture model to assess SFD effects on short-term (within-season) survival, movement, and surface activity of two wild snake species,...

Tracking the Near East origins and European dispersal of the house mouse

Thomas CUCCHI, Katerina Papayianni, Sophie Cersoy, Laetitia Aznar-Cormano, Antoine Zazzo, Régis Debruyne, Rémi Berthon, Adrian Bălășescu, Alan Simmons, François Valla, Yannis Hamilakis, Fanis Mavridis, Marjan Mashkour, Jamshid Darvish, Roohollah Siahsarvi, Fereidoun Biglari, Cameron A. Petrie, Lloyd Weeks, Alireza Sardari, Sepideh Maziar, Christiane Denys, David Orton, Emma Jenkins, Melinda Zeder, Jeremy B. Searle … & Jean-Denis Vigne
The house mouse (Mus musculus) is one of the most invasive mammals and an evolutionary model. However, the timing and components of its origin and dispersal remain poorly documented. To track its synanthropisation and subsequent biological invasion during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, dating between 40,000 and 3,000 cal. BP, combining geometric morphometris numerical taxonomy with ancient mitochondrial DNA...

The first specimen of Deinotherium indicum (Mammalia, Proboscidea, Deinotheriidae) from the late Miocene of Kutch, India

Ningthoujam Singh, Advait Jukar, Rajeev Patnaik, Kongrailatpam Sharma, Nongmaithem Singh & Yumlembam Singh
Deinotheriidae Bonaparte, 1845 are a family of browsing proboscideans which was widespread in the Old World during the Neogene. From Miocene deposits in the Indian Subcontinent, deinotheres are known largely from dental remains. Both large and small species have been described from the region. Previously, only small deinothere species have been identified from Kutch in western India. In the fossiliferous Tapar beds in Kutch, dental remains have been referred to the small species, Deinotherium sindiense...

The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases

Roger Close, Roger Benson, John Alroy, Matthew Carrano, Terri Cleary, Emma Dunne, Philip Mannion, Mark Uhen & Richard Butler
There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 38,711 fossil occurrences, we show that the spatial extent of the ‘global’ terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic, and that this spatial variation explains around 75% of the variation in known fossil species counts. Controlling for this bias, we find that regional-scale terrestrial...

Phylogenomics indicates Amazonia as the major source of Neotropical swarm-founding social wasp diversity

Rodolpho S.T. Menezes, Michael W. Lloyd & Seán G. Brady
The Neotropical realm harbors unparalleled species richness and hence has challenged biologists to explain the cause of its high biotic diversity. Empirical studies to shed light on the processes underlying biological diversification in the Neotropics are focused mainly on vertebrates and plants, with little attention to the hyperdiverse insect fauna. Here, we use phylogenomic data from ultraconserved element (UCE) loci to reconstruct for the first time the evolutionary history of Neotropical swarm-founding social wasps (Hymenoptera,...

Data from: Archaeological Central American maize genomes suggest ancient gene flow from South America

Logan Kistler, Heather B. Thakar, Amber M. VanDerwarker, Alejandra Domic, Anders Bergström, Richard J. George, Thomas K. Harper, Robin G. Allaby, Kenneth Hirth & Douglas J. Kennett
Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ~9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but...

The filtered VCF file containing SNPs detected from the Vitis bryoniifolia clade using RAD-seq.

Zhi-Yao Ma, Jun Wen, Jing-Pu Tian, Liu-Liu Gui & Xiu-Qun Liu
The grape genus (Vitis L.) is of great agronomic importance and represents an economically valuable resource. Researchers have explored the phylogenetic relationships of subgenus Vitis for decades. However, the evolutionary patterns of many morphological characters of subgenus Vitis have not yet been explored in the context of a robust phylogenetic framework. Within the East Asian clade, V. bryoniifolia and its closely related taxa form the V. bryoniifolia clade, which is taxonomically complex. The phylogenetic relationships...

Indo-Asian Eriolaena expanded to include two Malagasy genera, and other generic realignments based on molecular phylogenetics of Dombeyoideae (Malvaceae)

Laurence Dorr & Kenneth Wurdack
Molecular phylogenetic analyses of Malvaceae subfamily Dombeyoideae based on a 6-marker dataset sampling all 21 currently accepted genera (including extinct Astyria) yielded improved resolution and evidence for multiple generic circumscription problems. The taxonomy of the subfamily is adjusted with the synonymization of 10 genera (eight in current use) and the description of one new one, for a revised Dombeyoideae comprised of 14 genera and supported by morphological, anatomical, and/or palynological evidence. Eriolaena is expanded from...

Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation

Jason J. Kolbe, Richard E. Glor, Marta López‐Darias, C. Verónica Gómez Pourroy, Alexis S. Harrison, Kevin De Queiroz, Liam J. Revell, Jonathan B. Losos & Robert Graham Reynolds
Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis...

From Gondwana to GAARlandia: Evolutionary history and biogeography of ogre‐faced spiders (Deinopis)

Lisa Chamberland, Anne McHugh, Sarah Kechejian, Greta Binford, Jason Bond, Jonathan Coddington, Gaynor Dolman, Chris Hamilton, Mark Harvey, Matjaz Kuntner & Ingi Agnarsson
Aim We explore the evolutionary history of the ogre‐faced spiders (Deinopis) from their Early Cretaceous origins to present day. Specifically, we investigate how vicariance and dispersal have shaped distribution patterns of this lineage. Within the Caribbean, we test the role of GAARlandia, a hypothesized land bridge that connected South America to the Greater Antilles during the Eocene–Oligocene transition (~35–33 Ma), in the biogeography of Deinopis. Taxon Araneae: Deinopidae: Deinopis. Location Caribbean islands, with additional global...

The importance of nighttime length to latitudinal variation in avian incubation attentiveness

Helen Sofaer, Lauren Nagle, Scott Sillett, Jongmin Yoon & Cameron Ghalambor
Avian incubation provides an opportunity to test how parental behavior and ecological conditions interact to shape variation in offspring traits along geographic gradients. In particular, the duration of the incubation period is shorter at higher latitudes, but the degree to which this pattern arises from genetic divergence in rates of growth and development versus from parentally-mediated variation in egg temperatures is controversial. At higher latitudes parents have higher daytime incubation attentiveness, i.e., they spend a...

Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul

Edson F. Abreu-Jr, Silvia E. Pavan, Mirian T. N. Tsuchiya, Don E. Wilson, Alexandre Reis Percequillo & Jesus E. Maldonado
Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by phylogeneticists is likely a product of the scarcity or unavailability of fresh tissue samples for DNA sequencing. Lack of comprehensive phylogenies result in highly discrepant taxonomic arrangements that are based exclusively on morphological data—impressively, these are the only...

Data from: Fluid preservation causes minimal reduction of parasite detectability in fish specimens: a new approach for reconstructing parasite communities of the past?

Evan Fiorenza, Katie Leslie, Mark Torchin, Katherine Maslenikov, Luke Tornabene & Chelsea Wood
Long-term datasets are needed to evaluate temporal patterns in wildlife disease burdens, but historical data on parasite abundance are extremely rare. For more than a century, natural history collections have been accumulating fluid-preserved specimens, which should contain the parasites infecting the host at the time of its preservation. However, before this unique data source can be exploited, we must identify the artefacts that are introduced by the preservation process. Here, we experimentally address whether the...

Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian‐ eastern North American Nyssa (Nyssaceae)

Wenbin Zhou, Jun Wen & Qiuyun Xiang
Nyssa (Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian‐eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin...

Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)

Björn Stelbrink, Romy Richter, Frank Köhler, Frank Riedel, Ellen Strong, Bert Van Bocxlaer, Christian Albrecht, Torsten Hauffe, Timothy Page, David Aldridge, Arthur Bogan, Li-Na Du, Marivene Manuel-Santos, Ristiyanti Marwoto, Alena Shirokaya & Thomas Von Rintelen
The Viviparidae, commonly known as River Snails, is a dominant group of freshwater snails with a nearly worldwide distribution that reaches its highest taxonomic and morphological diversity in Southeast Asia. The rich fossil record is indicative of a probable Middle Jurassic origin on the Laurasian supercontinent where the group started to diversify during the Cretaceous. However, it remains uncertain when and how the biodiversity hotspot in Southeast Asia was formed. Here, we used a comprehensive...

Weda, a new genus with two new species of Euphorbiaceae-Crotonoideae from Halmahera (North Moluccas, Indonesia) and phylogenetic relationships of the Australasian tribe Ricinocarpeae

Peter Van Welzen, Susana Arias Guerrero, Deby Arifiani, Tjut Bangun, Roderick Bouman, Marcel Eurlings, Iska Gushilman, Peter Philipson, Iris Tabak, Esmée Winkel & Kenneth Wurdack
Two unknown Euphorbiaceae were discovered during the environmental impact study for a proposed nickel mine behind Weda Bay on Halmahera in the North Moluccas (Maluku Utara Province) of Indonesia. Morphological comparisons and molecular phylogenetic analyses using four markers (plastid trnL-F and rbcL, and nuclear ribosomal ITS and ETS) indicated they should be recognized as constituting a new, distinct genus of two species, which are described and illustrated here as Weda fragarioides and W. lutea. The...

Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes)

Adela Roa-Varon, Rebecca Dikow, Giorgio Carnevale, Luke Tornabene, Carole Baldwin, Chenhong Li & Eric Hilton
Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large datasets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or...

Disentangling interactions among mercury, immunity, and infection in a Neotropical bat community

Daniel Becker, Kelly Speer, Jennifer Korstian, Dmitriy Volokhov, Hannah Droke, Alexis Brown, Catherene Baijnauth, Ticha Padgett-Stewart, Hugh Broders, Raina Plowright, Thomas Rainwater, Brock Fenton, Nancy Simmons & Matthew Chumchal
Contaminants such as mercury are pervasive and can have immunosuppressive effects on wildlife. Impaired immunity could be important for forecasting pathogen spillover risks, as many land-use changes that generate mercury contamination also bring wildlife into close contact with humans and domestic animals. However, the interactions among contaminants, immunity, and infection are difficult to study in natural systems, and empirical tests of possible directional relationships remain rare. We capitalized on extreme mercury variation in a diverse...

Registration Year

  • 2020

Resource Types

  • Dataset


  • Smithsonian Institution
  • University of Washington
  • University of Cambridge
  • University of Sao Paulo
  • Indonesian Institute of Sciences
  • Harvard University
  • University of Oxford
  • University of Kansas
  • Ferdowsi University of Mashhad
  • Laboratoire des sciences de l'ingénieur de l'informatique et de l'imagerie