143 Works

Data from: Local endemism and within-island diversification of shrews illustrate the importance of speciation in building Sundaland mammal diversity

Terrence C. Demos, Anang S. Achmadi, Thomas C. Giarla, Heru Handika, , Kevin C. Rowe & Jacob A. Esselstyn
Island systems are important models for evolutionary biology because they provide convenient, discrete biogeographic units of study. Continental islands with a history of intermittent dry land connections confound the discrete definitions of islands and have led zoologists to predict (1) little differentiation of terrestrial organisms among continental shelf islands and (2) extinction, rather than speciation, to be the main cause of differences in community composition among islands. However, few continental island systems have been subjected...

Data from: Checkerboard score-area relationships reveal spatial scales of plant community structure

Gordon G. McNickle, Eric G. Lamb, Mike Lavender, , Brandon S. Schamp, Steven D. Siciliano, Richard Condit, Stephen P. Hubbell, Jennifer L. Baltzer & James F Cahill
Identifying the spatial scale at which particular mechanisms influence plant community assembly is crucial to understanding the mechanisms structuring communities. It has long been recognized that many elements of community structure are sensitive to area; however the majority of studies examining patterns of community structure use a single relatively small sampling area. As different assembly mechanisms likely cause patterns at different scales we investigate how plant species co-occurrence patterns change with sampling unit scale. We...

Data from: Microevolutionary processes impact macroevolutionary patterns

Jingchun Li, Jen-Pen Huang, Jeet Sukumaran & L Lacey Knowles
Background: Macroevolutionary modeling of species diversification plays important roles in inferring large-scale biodiversity patterns. It allows estimation of speciation and extinction rates and statistically testing their relationships with different ecological factors. However, macroevolutionary patterns are ultimately generated by microevolutionary processes acting at population levels, especially when speciation and extinction are considered protracted instead of point events. Neglecting the connection between micro- and macroevolution may hinder our ability to fully understand the underlying mechanisms that drive...

Data from: Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales: Jungermanniopsida), including two reinstated and five new species

Matt A. M. Renner, Nicolas Devos, Jairo Patiño, Elizabeth A. Brown, Andrew Orme, Michael Elgy, Trevor Wilson, Lindsey J. Gray, Matt J. Von Konrat, Lindsey Gray, Matt Renner, Elizabeth Brown & Matt Von Konrat
Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph....

Data from: Best practices for justifying fossil calibrations

James F. Parham, Philip C. J. Donoghue, Christopher J. Bell, Tyler D. Calway, Jason J. Head, Patricia A. Holroyd, Jun G. Inoue, Randall B. Irmis, Walter G. Joyce, Daniel T. Ksepka, José S. L. Patané, Nathan D. Smith, James E. Tarver, Marcel Van Tuinen, Ziheng Yang, Kenneth D. Angielczyk, Jenny M. Greenwood, Christy A. Hipsley, Jacobs Louis, Peter J. Makovicky, Johannes Müller, Krister T. Smith, Jessica M. Theodor, Rachel C. M. Warnock, Michael J. Benton … & Louis Jacobs
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates...

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...

Data from: Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

Rachel C. M. Warnock, James F. Parham, Walter G. Joyce, Tyler R. Lyson & Philip C. J. Donoghue
Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a...

Data from: Analysis of inbreeding depression in mixed-mating plants provides evidence for selective interference and stable mixed mating

Alice A Winn, Elizabeth Elle, Susan Kalisz, Pierre-Olivier Cheptou, Christopher G Eckert, Carol Goodwillie, Mark O. Johnston, David A Moeller, Richard H Ree, Risa D Sargent & Mario Vallejo-Marín
Hermaphroditic individuals can produce both selfed and outcrossed progeny, termed mixed mating. General theory predicts that mixed-mating populations should evolve quickly toward high rates of selfing, driven by rapid purging of genetic load and loss of inbreeding depression (ID), but the substantial number of mixed-mating species observed in nature calls this prediction into question. Greater average ID reported for selfing than for outcrossing populations is consistent with purging and suggests that mixed-mating taxa in evolutionary...

Data from: Phylogenetic inference of reciprocal effects between geographic range evolution and diversification

Emma E. Goldberg, Lesley T. Lancaster & Richard H. Ree
Geographic characters---traits relating to the spatial distribution of a species---may both affect and be affected by processes associated with lineage birth and death. This is potentially confounding to comparative analyses of species distributions because current models do not allow reciprocal interactions between the evolution of traits and the growth of phylogenetic trees. Here we introduce a likelihood-based approach to estimating region-dependent rates of speciation, extinction, and range evolution from a phylogeny, using a new model...

Data from: The cranial morphology, phylogenetic position and biogeography of the upper Permian dicynodont Compsodon helmoedi van Hoepen (Therapsida, Anomodontia)

Kenneth D. Angielczyk & Christian F. Kammerer
Compsodon helmoedi is an obscure dicynodont originally described based on a single specimen from the upper Permian of the Karoo Basin. The discovery of three new specimens of Compsodon from the Luangwa Basin of Zambia and two additional specimens from South African museum collections facilitates a reassessment of its cranial morphology and phylogenetic position. Compsodon is diagnosed by an autapomorphic secondary palate morphology: medial depression at anterior end of premaxillary secondary palate; medial anterior palatal...

Data from: The spatial structure of phylogenetic and functional diversity in the United States and Canada: an example using the sedge family (Cyperaceae)

Daniel Spalink, Jocelyn Pender, Marcial Escudero, Andrew L. Hipp, Eric H. Roalson, Julian R. Starr, Marcia J. Waterway, Lynn Bohs & Kenneth J. Sytsma
Systematically quantifying diversity across landscapes is necessary to understand how clade history and ecological heterogeneity contribute to the origin, distribution, and maintenance of biodiversity. Here, we chart the spatial structure of diversity among all species in the sedge family (Cyperaceae) throughout the USA and Canada. We first identify areas of remarkable species richness, phylogenetic diversity, and functional trait diversity, and highlight regions of conservation priority. We then test predictions about the spatial structure of this...

Data from: Defaunation increases the spatial clustering of lowland Western Amazonian tree communities

Robert Bagchi, Varun Swamy, Jean-Paul Latorre Farfan, John Terborgh, César I. A. Vela, Nigel C. A. Pitman & Washington Galiano Sanchez
1.Declines of large vertebrates in tropical forests may reduce dispersal of tree species that rely on them, and the resulting undispersed seedlings might suffer increased distance- and density- dependent mortality. Consequently, extirpation of large vertebrates may alter the composition and spatial structure of plant communities and impair ecosystem functions like carbon storage. 2.We analysed spatial patterns of tree recruitment within six forest plots along a defaunation gradient in western Amazonia. We divided recruits into two...

Data from: Patterns of nitrogen-fixing tree abundance in forests across Asia and America

Duncan N. L. Menge, Ryan A. Chisholm, Stuart J. Davies, Kamariah Abu Salim, David Allen, Mauricio Alvarez, Norm Bourg, Warren Y. Brockelman, Sarayudh Bunyavejchewin, Nathalie Butt, Min Cao, Wirong Chanthorn, Wei-Chun Chao, Keith Clay, Richard Condit, Susan Cordell, João Batista Da Silva, H. S. Dattaraja, Ana Cristina Segalin De Andrade, Alexandre A. Oliveira, Jan Den Ouden, Michael Drescher, Christine Fletcher, Christian P. Giardina, C. V. Savitri Gunatilleke … & Tak Fung
Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N‐fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N‐fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America...

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...

Data from: Multiple lines of evidence indicate ongoing allopatric and parapatric diversification in an Afromontane sunbird (Cinnyris reichenowi)

Jacob C. Cooper, J. Dylan Maddox, Kellie McKague & John M. Bates
Africa’s montane ecosystems are noteworthy not only for their isolation, but for their morphologically similar bird populations that inhabit geographically disparate localities. Many species possess range disjunctions in excess of 2,000 km and appear to represent populations that have been isolated since at least the last Ice Age, including the Northern Double-collared Sunbird (Cinnyris reichenowi). Recent work on other Afromontane birds has demonstrated substantial phylogeographic structure can exist in phenotypically similar populations, with cryptic species...

A shrewd inspection of vertebral regionalization in large shrews (Soricidae: Crocidurinae)

Stephanie M Smith & Kenneth D Angielczyk
The regionalization of the mammalian spinal column is an important evolutionary, developmental, and functional hallmark of the clade. Vertebral column regions are usually defined using transitions in external bone morphology, such as the presence of transverse foraminae or rib facets, or measurements of vertebral shape. Yet the internal structure of vertebrae, specifically the trabecular (spongy) bone, plays an important role in vertebral function, and is subject to the same variety of selective, functional, and developmental...

Data from: A new tusked cistecephalid dicynodont (Therapsida, Anomodontia) from the upper Permian Upper Madumabisa Mudstone Formation, Luangwa Basin, Zambia

Kenneth Angielczyk, Julien Benoit & Bruce Rubidge
Cistecephalids are among the most distinctive Permian dicynodonts because of their highly derived skulls and postcrania, which indicate a fossorial ecology. Four cistecephalid species have been described from India, South Africa, and Tanzania; a fifth putative species has been reported from the Luangwa Basin of Zambia but never formally described. Here we present a detailed description of the Luangwa Basin cistecephalid, which we name Kembawacela kitchingi gen. et. sp. nov. The most obvious diagnostic character...

Genital morphology and the mechanics of copulation in the millipede genus Pseudopolydesmus (Diplopoda: Polydesmida: Polydesmidae)

Xavier Zahnle, Petra Sierwald, Stephanie Ware & Jason Bond
Mate choice, copulation, genital morphology, and sperm storage are not very well understood in millipedes. The use of three-dimensional x-ray computed tomography (µCT) provides new morphological data regarding millipede reproductive systems in both the female and male, including chitinous sclerites and membranes, muscles, glands, oviducts, and sperm conduits. Here we present a complete integrated account of the morphology and function of the female genital organs in the family Polydesmidae (Diplopoda: Polydesmida) using µCT, UV fluorescence...

Data from: Tracing the diversification history of a Neogene rodent invasion into South America

Renan Maestri, Nathan S. Upham & Bruce D. Patterson
We investigated spatial patterns of evolutionary relatedness and diversification rates to test hypotheses about the historical biogeographic processes underlying the radiation of Neotropical rats and mice (Sigmodontinae, ~400 species). A negative correlation between mean phylogenetic distance and diversification rates of rodent assemblages reveals a pattern of species co-occurrence in which assemblages of closely related species are also the fastest diversifying ones. Subregions of the Neotropics occupied by distantly related species that are on average more...

Data from: Diversity, phylogeny and biogeography of the South American ‘cardiomyine’ rodents (Hystricognathi, Cavioidea) with a description of two new species

María E. Pérez, Cecilia M. Deschamps & María G. Vucetich
‘Cardiomyine’ rodents are extinct large terrestrial Caviidae closely related to capybaras, that inhabited large parts of South America during the middle Miocene and Pliocene. They are mostly preserved as isolated teeth, but also as skull and jaw fragments. Here we revise the taxonomy of this group and describe two new species, each pertaining to one of the two main late Miocene groups, represented by the genera Caviodon and Cardiomys. This suggests that the diversity of...

Data from: Is sexual selection driving diversification of the bioluminescent ponyfishes (Teleostei: Leiognathidae)?

Prosanta Chakrabarty, Matthew P Davis, W. Leo Smith, Zachary H Baldwin & John S Sparks
Sexual selection is a mechanism of speciation that theoretically could provide genetic isolation among populations and lead to an increase in diversification rates. In this study, we investigate the impact of potential sexual selection on the tempo and mode of ponyfish evolution. Ponyfishes (Leiognathidae) are bioluminescent marine fishes that exhibit sexually-dimorphic features of their unique light-organ system (LOS). Given that some leiognathid species have a sexually dimorphic LOS, whereas others do not, this family provides...

Data from: The ecology of a continental evolutionary radiation: Is the radiation of sigmodontine rodents adaptive?

Renan Maestri, Leandro Rabello Monteiro, Rodrigo Fornel, Nathan S. Upham, Bruce D. Patterson & Thales Renato Ochotorena De Freitas
Evolutionary radiations on continents are less well-understood and appreciated than those occurring on islands. The extent of ecological influence on species divergence can be evaluated to determine whether a radiation was ultimately the outcome of divergent natural selection or else arose mainly by nonecological divergence. Here, we used phylogenetic comparative methods to test distinct hypotheses corresponding to adaptive and nonadaptive evolutionary scenarios for the morphological evolution of sigmodontine rodents. Results showed that ecological variables (diet...

Data from: Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae)

Caleb D. McMahan, Prosanta Chakrabarty, John S. Sparks, Wm. Leo Smith & Matthew P. Davis
The contrasting distribution of species diversity across the major lineages of cichlids makes them an ideal group for investigating macroevolutionary processes. In this study, we investigate whether different rates of diversification may explain the disparity in species richness across cichlid lineages globally. We present the most taxonomically robust time-calibrated hypothesis of cichlid evolutionary relationships to date. We then utilize this temporal framework to investigate whether both species-rich and depauperate lineages are associated with rapid shifts...

Data from: Hidden diversity of African yellow house bats (Vespertilionidae, Scotophilus): insights from multilocus phylogenetics and lineage delimitation

Terrence C. Demos, Paul W. Webala, Michael Bartonjo & Bruce D. Patterson
The genus Scotophilus contains 21 currently recognized species ranging throughout Africa and Southeast Asia. Among the 13 species recognized from continental Africa, systematic relationships remain poorly understood. Taxonomic uncertainty regarding names, suggestions of polytypic species complexes, and undescribed cryptic diversity all contribute to the current confusion. To gain insights into the systematics of this group, we inferred single locus and multi-locus phylogenies and conducted lineage delimitation analyses using seven unlinked genes for specimens from across...

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