15 Works

The contribution of environmental and dispersal filters on beta diversity patterns in Amazonian tree communities

Juan Ernesto Guevara Andino, Nigel C.A. Pitman, Hans Ter Steege, Manuel Peralvo, Carlos Cerón & Paul V.A. Fine
Environmental filters (e.g. climate, geomorphology and soils) and dispersal filters are key determinants of species distributions of Amazonian tree communities. However, a comprehensive analysis of the role of environmental and dispersal filters is needed to understand the ecological and evolutionary processes that drive phylogenetic and taxonomic turnover of Amazonian tree communities. We compare measures of taxonomic and phylogenetic beta diversity in 40 one-hectare plots to test the relative importance of climate, soils, geology, geomorphology, pure...

WiBB: An integrated method for quantifying the relative importance of predictive variables

Qin Li & Xiaojun Kou
This dataset contains simulated datasets, empirical data, and R scripts described in the paper: “Li, Q. and Kou, X. (2021) WiBB: An integrated method for quantifying the relative importance of predictive variables. Ecography (DOI: 10.1111/ecog.05651)”. A fundamental goal of scientific research is to identify the underlying variables that govern crucial processes of a system. Here we proposed a new index, WiBB, which integrates the merits of several existing methods: a model-weighting method from information theory...

Pontocaspian habitat polygon shapefiles from: Decline of unique Pontocaspian biodiversity in the Black Sea Basin: a review

Aleksandre Gogaladze, Mikhail Son, Matteo Lattuada, Vitaliy Anistratenko, Vitaly Syomin, Ana Bianca Pavel, Oana Popa, Luis Popa, Jan-Johan Ter Poorten, Jacobus Biesmeijer, Niels Raes, Thomas Wilke, Arthur Francis Sands, Teodora Trichkova, Zdravko Hubenov, Maxim Vinarski, Olga Anistratenko, Tatiana Alexenko & Frank Wesselingh
The unique aquatic Pontocaspian (PC) biota of the Black Sea Basin (BSB) is in decline. The lack of detailed knowledge on the status and trends of species, populations and communities hampers a thorough risk assessment and precludes effective conservation. This paper reviews PC biodiversity trends in the BSB ( Bulgaria, Romania, Moldova, Ukraine and Russia) using endemic molluscs as a model group. We aim to assess changes in PC habitats, community structure and species distribution...

Plant DNA metabarcoding record from a sediment core from Lake Naleng, southeastern Tibetan Plateau

Sisi Liu, Stefan Kruse, Dirk Scherler, Richard H. Ree, Heike H. Zimmermann, Kathleen R. Stoof-Leichsenring, Laura S. Epp, Steffen Mischke & Ulrike Herzschuh
Here, we provide the raw plant DNA metabarcoding data archived in Lake Naleng sediment core spanning the late-glacial to the present (17,700 to 0 cal yr BP). Lake Naleng (31.10° N, 99.7°5 E, 4200 above sea level) is situated in a glacially-formed basin on the southeastern Tibetan Plateau. It is an alpine freshwater lake with a maximum water depth of 36.7 m, an open surface area of 1.7 km2, a specific conductivity of 0.045 mS/cm,...

Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: When data agree to disagree

Fernando Alda, William B. Ludt, Diego J. Elías, Caleb D. McMahan & Prosanta Chakrabarty
Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to...

Fossil-informed models reveal a Boreotropical origin and divergent evolutionary trajectories in the walnut family (Juglandaceae)

Qiuyue Zhang, Richard Ree, Nicolas Salamin, Yaowu Xing & Daniele Silvestro
Temperate woody plants in the Northern Hemisphere have long been known to exhibit high species richness in East Asia and North America and significantly lower diversity in Europe, but the causes of this pattern remain debated. Here, we quantify the roles of dispersal, niche evolution, and extinction in shaping the geographic diversity of the temperate woody plant family Juglandaceae (walnuts and their relatives). Integrating evidence from molecular, morphological, fossil, and (paleo)environmental data, we find strong...

OTU data and analysis files for interspecies comparison of Philippine terrestrial small mammal diets

Anna Petrosky, Dakota Rowsey & Lawrence Heaney
Island radiations represent unique evolutionary histories in unique ecological contexts. These radiations provide opportunities to investigate ecological diversification in groups that typically exhibit niche partitioning among their constituents, including partitioning of food resources. DNA metabarcoding produces finer levels of diet identification than traditional methods, allowing us to examine dietary niche partitioning in communities or clades in which species share superficially similar diets. Here we use DNA metabarcoding to investigate dietary niche partitioning in an endemic...

Functional biogeography of Neotropical moist forests: trait-climate relationships and assembly patterns of tree communities

Bruno Pinho, Marcelo Tabarelli, Cajo Ter Braak, S. J. Wright, Victor Arroyo-Rodriguez, Maíra Benchimol, Bettina Engelbrecht, Simon Pierce, Peter Hietz, Bráulio Santos, Carlos Peres, Sandra Müller, Ian Wright, Frans Bongers, Madelon Lohbeck, Ülo Niinemets, Martijn Slot, Steven Jansen, Davi Jamelli, Renato Augusto Ferreira De Lima, Nathan Swenson, Richard Condit, Jos Barlow, Ferry Slik, Manuel Hernández-Ruedas … & Felipe Melo
Aim: Here we examine the functional profile of regional tree species pools across the latitudinal distribution of Neotropical moist forests, and test trait-climate relationships among local communities. We expected opportunistic strategies (acquisitive traits, small seeds) to be overrepresented in species pools further from the equator due to long-term instability, but also in terms of abundance in local communities in currently wetter, warmer and more seasonal climates. Location: Neotropics. Time period: Recent. Major taxa studied: Trees....

Shallow population structure and shared phylogeographic and demographic patterns in seven Amazonian White-Sand ecosystems birds

João Marcos Guimarães Capurucho, Mary Ashley, Cintia Cornelius, Sérgio Borges, Camila Ribas & John Bates
White-sand ecosystems (WSE) have a patchy distribution throughout Amazonia and harbor a specialized community of birds. The patchiness of WSE lead to the expectation of highly fragmented and isolated populations across Amazonia. Additionally, the sandy substrate could render these ecosystems vulnerable climatic changes. We performed a comparative phylogeographic study of seven WSE birds using Ultra-conserved elements to evaluate their relation to Amazonian environmental and landscape history and the occurrence of shared patterns. Genetic structure varied...

Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families

Nicholas Crouch, Stewart Edie, Katie Collins, Rüdiger Bieler & David Jablonski
Analyses of evolutionary dynamics can be profoundly affected by age calibrations of phylogenetic nodes under different models of lineage branching. Most time-calibrated molecular phylogenies of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. Lineages can also split via budding, in which a parent lineage persists following the origin of a daughter lineage, and nodes are calibrated using the age...

A target enrichment probe set for resolving the flagellate land plant tree of life

Jesse W. Breinholt, Sarah B. Carey, George P. Tiley, E. Christine Davis, Lorena Endara, Stuart F. McDaniel, Leandro Neves, Emily B. Sessa, Matt Von Konrat, Susan Fawcett, Stefanie M. Ickert-Bond, Paulo H. Labiak, Juan Larraín, Marcus Lehnert, Lily R. Lewis, Nathalie S. Nagalingum, Nikisha Patel, Stefan A. Rensing, Weston Testo, Alejandra Vasco, Juan Carlos Villarreal, Evelyn Webb Williams, J. Gordon Burleigh, Sahut Chantanaorrapint, Leandro G. Neves … & Stefanie M. Ickert‐Bond
Premise of the Study: New sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. Methods and Results: We leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target...

Sizes and environmental variables to peccaries

Carla D. Hendges, Bruce D. Patterson & Nilton C. Cáceres
Aim: Bergmann's rule is an ecogeographical rule that describes a negative relationship between body size and temperature. Here, we used a multivariate measure of skull size (centroid size) as a proxy for body size to test the influence of temperature, precipitation, elevation, human influence and competition on size in Dicotyles tajacu and Tayassu pecari. Location: American tropics and sub-tropics. Taxon: Tayassuidae. Methods: Using geometric morphometric methods, we measured 426 adult skulls of both peccary species...

Relaxed feeding constraints facilitate the evolution of mouthbrooding in Neotropical cichlids

Hannah Weller, Hernán López-Fernández, Caleb McMahan & Elizabeth Brainerd
Multifunctionality is often framed as a core constraint of phenotypic evolution. Mouthbrooding, a form of parental care where offspring develop inside a parent’s mouth, increases multifunctionality by adding a major function (reproduction) to a structure already serving other vital functions (feeding and respiration). Despite increasing multifunctionality, mouthbrooding has evolved repeatedly from other forms of parental care in at least 7 fish families. We hypothesized that mouthbrooding is more likely to evolve in lineages with feeding...

Data and code from: Evolution of brilliant iridescent feather nanostructures

Klara Nordén, Chad Eliason & Mary Caswell Stoddard
The brilliant iridescent plumage of birds creates some of the most stunning color displays known in the natural world. Iridescent plumage colors are produced by nanostructures in feathers and have evolved in a wide variety of birds. The building blocks of these structures—melanosomes (melanin-filled organelles)—come in a variety of forms, yet how these different forms contribute to color production across birds remains unclear. Here, we leverage evolutionary analyses, optical simulations and reflectance spectrophotometry to uncover...

Data from: Morphology and distribution of scales, dermal ossifications, and other non-feather integumentary structures in non-avialan theropod dinosaurs

Christophe Hendrickx, Phil R. Bell, Michael Pittman, Andrew R. C. Milner, Elena Cuesta, Jingmai O'Connor, Mark Loewen, Philip J. Currie, Octávio Mateus, Thomas G. Kaye & Rafael Delcourt
Modern birds are typified by the presence of feathers, complex evolutionary innovations that were already widespread in the group of theropod dinosaurs (Maniraptoriformes) that include crown Aves. Squamous or scaly reptilian-like skin is, however, considered the plesiomorphic condition for theropods and dinosaurs more broadly. Here, we review the morphology and distribution of non-feathered integumentary structures in non-avialan theropods covering squamous skin and naked skin as well as dermal ossifications. The integumentary record of non-averostran theropods...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Field Museum of Natural History
  • Duke University
  • University of Chicago
  • Naturalis Biodiversity Center
  • Consortium for Sustainable Development of the Andean Ecoregion
  • Princeton University
  • National Academy of Sciences of Ukraine
  • University of Michigan-Ann Arbor
  • Institute of Oceanology. PP Shirshov Russian Academy of Sciences
  • University of Tennessee at Chattanooga