148 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: 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: 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: 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...

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...

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: 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: 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...

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: 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: 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: 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: 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...

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...

Dataset: Local hydrological conditions influence tree diversity and composition across the Amazon basin

Manuel J. Marca-Zevallos, Gabriel M. Moulatlet, Thaiane R. Sousa, Juliana Schietti, Luiz De Souza Coelho, José Ferreira Ramos, Diogenes De Andrade Lima Filho, Iêda Leão Amaral, Francisca Dionízia De Almeida Matos, Lorena M. Rincón, Juan David Cardenas Revilla, Marcelo Petratti Pansonato, Rogerio Gribel, Edelcilio Marques Barbosa, Ires Paula De Andrade Miranda, Luiz Carlos De Matos Bonates, Juan Ernesto Guevara, Rafael P. Salomão, Leandro Valle Ferreira, Dário Dantas Do Amaral, Nigel C.A. Pitman, Corine Vriesendorp, Tim R. Baker, Roel Brienen, Marcelo De Jesus Veiga Carim … & Flávia R.C. Costa
Tree diversity and composition in Amazonia are known to be strongly determined by the water supplied by precipitation. Nevertheless, within the same climatic regime, water availability is modulated by local topography and soil characteristics (hereafter referred to as local hydrological conditions), varying from saturated and poorly drained to well-drained and potentially dry areas. While these conditions may be expected to influence species distribution, the impacts of local hydrological conditions on tree diversity and composition remain...

Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves

Jingchun Li, Sarah Lemer, Lisa Kirkendale, Rudiger Bieler, Colleen Cavanaugh & Gonzalo Giribet
Background: Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily...

Data from: Step-wise evolution of complex chemical defenses in millipedes: a phylogenomic approach

Juanita Rodriguez, Tappey H. Jones, Petra Sierwald, Paul E. Marek, William A. Shear, Michael S. Brewer, Kevin M. Kocot & Jason E. Bond
With fossil representatives from the Silurian capable of respiring atmospheric oxygen, millipedes are among the oldest terrestrial animals, and likely the first to acquire diverse and complex chemical defenses against predators. Exploring the origin of complex adaptive traits is critical for understanding the evolution of Earth’s biological complexity, and chemical defense evolution serves as an ideal study system. The classic explanation for the evolution of complexity is by gradual increase from simple to complex, passing...

Data from: Comparative genomics reveals convergent rates of evolution in ant-plant mutualisms

Benjamin E. R. Rubin & Corrie S. Moreau
Symbiosis—the close and often long-term interaction of species—is predicted to drive genome evolution in a variety of ways. For example, parasitic interactions have been shown to increase rates of molecular evolution, a trend generally attributed to the Red Queen Hypothesis. However, it is much less clear how mutualisms impact the genome, as both increased and reduced rates of change have been predicted. Here we sequence the genomes of seven species of ants, three that have...

Data from: New insights into New World biogeography: an integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies

F. Keith Barker, Kevin J. Burns, John Klicka, Scott M. Lanyon & Irby J. Lovette
Understanding the biogeographic origins and temporal sequencing of groups within a region or of lineages within an ecosystem can yield important insights into evolutionary dynamics and ecological processes. Fifty years ago, Ernst Mayr generated comprehensive—if limited—inferences about the origins of the New World avifaunas, including the importance of pre-Isthmian dispersal between North and South America. Since then, methodological advances have improved our ability to address many of the same questions, but the phylogenies upon which...

Data from: Early and dynamic colonization of Central America drives speciation in Neotropical army ants

Max E. Winston, Daniel J. C. Kronauer & Corrie S. Moreau
The emergence of the Isthmus of Panama is one of the most important events in recent geological history, yet its timing and role in fundamental evolutionary processes remain controversial. While the formation of the isthmus was complete around 3 million years ago (Ma), recent studies have suggested prior intercontinental biotic exchange. In particular, the possibility of early intermittent land bridges facilitating colonization constitutes a potential mechanism for speciation and colonization before full closure of the...

Data from: The challenge of modeling niches and distributions for data-poor species: a comprehensive approach to model complexity

Peter J. Galante, Babatunde Alade, Robert Muscarella, Sharon A. Jansa, Steven M. Goodman & Robert P. Anderson
Models of species ecological niches and geographic distributions now represent a widely used tool in ecology, evolution, and biogeography. However, the very common situation of species with few available occurrence localities presents major challenges for such modeling techniques, in particular regarding model complexity and evaluation. Here, we summarize the state of the field regarding these issues and provide a worked example using the technique Maxent for a small mammal endemic to Madagascar (the nesomyine rodent...

Data from: Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis

Elizabeth G. Pringle & Corrie S. Moreau
Ants have long been renowned for their intimate mutualisms with trophobionts and plants and more recently appreciated for their widespread and diverse interactions with microbes. An open question in symbiosis research is the extent to which environmental influence, including the exchange of microbes between interacting macroorganisms, affects the composition and function of symbiotic microbial communities. Here we approached this question by investigating symbiosis within symbiosis. Ant–plant–hemipteran symbioses are hallmarks of tropical ecosystems that produce persistent...

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