46 Works

Data from: Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards

Sonal Singhal, Huateng Huang, Pascal O. Title, Stephen C. Donnellan, Iris Holmes & Daniel L. Rabosky
Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus. To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based...

Data from: History cleans up messes: the impact of time in driving divergence and introgression in a tropical suture zone

Sonal Singhal & Ke Bi
Contact zones provide an excellent arena in which to address questions about how genomic divergence evolves during lineage divergence. They allow us to both infer patterns of genomic divergence in allopatric populations isolated from introgression and to characterize patterns of introgression after lineages meet. Thusly motivated, we analyze genome-wide introgression data from four contact zones in three genera of lizards endemic to the Australian Wet Tropics. These contact zones all formed between morphologically cryptic lineage-pairs...

Data from: Stream nitrogen concentration, but not plant N-fixing capacity, modulates litter diversity effects on decomposition

Alan M. Tonin, Luz Boyero, Silvia Monroy, Ana Basaguren, Javier Perez, Richard G. Pearson, Bradley J. Cardinale, & Jesus Pozo
1. We are facing major biodiversity loss and there is evidence that such loss can alter ecosystem functioning. However, the effects of plant diversity on decomposition – a key component of the global carbon cycle – are still unclear. A recent study suggested that a plant trait – their nitrogen (N)-fixing capacity – could mediate effects of litter diversity on decomposition by means of a microbial transfer of N from N-fixers to non-fixers. 2. We...

Data from: Spinosity, regeneration, and targeting among Paleozoic crinoids and their predators

Valerie J.P. Syverson, Carlton E. Brett, Forest J. Gahn & Tomasz K. Baumiller
Evolving interactions between predators and prey constitute one of the major adaptive influences on marine animals during the Paleozoic. Crinoids and fish constitute a predator-prey system that may date back to at least the Silurian, as suggested by patterns of crinoid regeneration and spinosity in concert with changes in the predatory fauna. Here we present data on the frequency of breakage and regeneration in the spines of the Middle Devonian camerate Gennaeocrinus and Late Paleozoic...

Data from: A nutrient mediates intraspecific competition between rodent malaria parasites in vivo

Nina Wale, Derek G. Sim & Andrew F. Read
Hosts are often infected with multiple strains of a single parasite species. Within-host competition between parasite strains can be intense and has implications for the evolution of traits that impact patient health, such as drug resistance and virulence. Yet the mechanistic basis of within-host competition is poorly understood. Here, we demonstrate that a parasite nutrient, para-aminobenzoic acid (pABA), mediates competition between a drug resistant and drug susceptible strain of the malaria parasite, Plasmodium chabaudi. We...

Data from: Not all weeds are created equal: a database approach uncovers differences in the sexual system of native and introduced weeds

Megan L. Van Etten, Jeffrey K. Conner, Shu-Mei Chang & Regina S. Baucom
Weedy species provide excellent opportunities to examine the process of successful colonization of novel environments. Despite the influence of the sexual system on a variety of processes from reproduction to genetic structure, how the sexual system of species influences weediness has received only limited consideration. We examined the hypothesis that weedy plants have an increased likelihood of being self-compatible compared with nonweedy plants; this hypothesis is derived from Baker's law, which states that species that...

Data from: Suitability of Laurentian Great Lakes for invasive species based on global species distribution models and local habitat

Andrew M. Kramer, Gust Annis, Marion E. Wittmann, William L. Chadderton, Edward S. Rutherford, David M. Lodge, Lacey Mason, Dmitry Beletsky, Catherine Riseng & John M. Drake
Efficient management and prevention of species invasions requires accurate prediction of where species of concern can arrive and persist. Species distribution models provide one way to identify potentially suitable habitat by developing the relationship between climate variables and species occurrence data. However, these models when applied to freshwater invasions are complicated by two factors. The first is that the range expansions that typically occur as part of the invasion process violate standard species distribution model...

Data from: Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

Joseph F. Walker, Ya Yang, Moore J. Michael, Jessica Mikenas, Alfonso Timoneda, Samuel Frasier Brockington, Stephen Andrew Smith & Michael J. Moore
PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. METHODS: To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare...

Data from: Structure of FlgK reveals the divergence of the bacterial hook-filament junction of Campylobacter

Paula V. Bulieris, Nausad H. Shaikh, Peter L. Freddolino & Fadel A. Samatey
Evolution of a nano-machine consisting of multiple parts, each with a specific function, is a complex process. A change in one part should eventually result in changes in other parts, if the overall function is to be conserved. In bacterial flagella, the filament and the hook have distinct functions and their respective proteins, FliC and FlgE, have different three-dimensional structures. The filament functions as a helical propeller and the hook as a flexible universal joint....

Data from: Divergence of thermal physiological traits in terrestrial breeding frogs along a tropical elevational gradient

Rudolf Von May, Alessandro Catenazzi, Ammon Corl, Roy Santa-Cruz, Ana Carolina Carnaval & Craig Moritz
Critical thermal limits are thought to be correlated with the elevational distribution of species living in tropical montane regions, but with upper limits being relatively invariant compared to lower limits. To test this hypothesis, we examined the variation of thermal physiological traits in a group of terrestrial breeding frogs (Craugastoridae) distributed along a tropical elevational gradient. We measured the critical thermal maximum (CTmax; n = 22 species) and critical thermal minimum (CTmin; n = 14...

Data from: Experimental small-scale flower patches increase species density but not abundance of small urban bees

Maria-Carolina M. Simao, Jill Matthijs & Ivette Perfecto
1. Large flower plantings are often used to combat negative effects of habitat loss on pollinators, but whether these floral additions are effective at smaller scales remains unclear, particularly in urban settings. 2. To test the effectiveness of small-scale floral additions on enhancing urban bee populations, as well as their impact from one year to the next, different quantities of potted sweet alyssum (Lobularia maritima) flowers were placed across sites in Ann Arbor, Michigan for...

Data from: Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

Alison G. Nazareno, Jordan B. Bemmels, Christopher W. Dick & Lúcia G. Lohmann
High throughput DNA sequencing facilitates the analysis of large portions of the genome in non-model organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double digest restriction associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a non-model plant species for which no...

Data from: Daphniid zooplankton assemblage shifts in response to eutrophication and metal contamination during the Anthropocene

Mary Alta Rogalski, Peter R. Leavitt & David K. Skelly
Human activities during the Anthropocene result in habitat degradation that has been associated with biodiversity loss and taxonomic homogenization of ecological communities. Here we estimated effects of eutrophication and heavy metal contamination, separately and in combination, in explaining zooplankton species composition during the past 125–145 years using analysis of daphniid diapausing egg banks from four lakes in the northeastern USA. We then examined how these community shifts influenced patterns of diversity and homogenization. Analysis of...

Data from: From the track to the ocean: using flow control to improve marine bio-logging tags for cetaceans

Giovani Fiore, Erik Anderson, C. Spencer Garborg, Mark Murray, Mark Johnson, Michael J. Moore, Laurens Howle & K. Alex Shorter
Bio-logging tags are an important tool for the study of cetaceans, but superficial tags inevitably increase hydrodynamic loading. Substantial forces can be generated by tags on fast-swimming animals, potentially affecting behavior and energetics or promoting early tag removal. Streamlined forms have been used to reduce loading, but these designs can accelerate flow over the top of the tag. This non-axisymmetric flow results in large lift forces (normal to the animal) that become the dominant force...

Data from: Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration: a comment on Puttick et al

Joseph W. Brown, Caroline Parins-Fukuchi, Gregory W. Stull, Oscar M. Vargas & Stephen A. Smith
Puttick et al. (2017 Proc. R. Soc. B 284, 20162290 (doi:10.1098/rspb.2016.2290)) performed a simulation study to compare accuracy among methods of inferring phylogeny from discrete morphological characters. They report that a Bayesian implementation of the Mk model (Lewis 2001 Syst. Biol. 50, 913–925 (doi:10.1080/106351501753462876)) was most accurate (but with low resolution), while a maximum-likelihood (ML) implementation of the same model was least accurate. They conclude by strongly advocating that Bayesian implementations of the Mk model...

Data from: Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties

Andrea T. Thomaz, Luiz R. Malabarba & L. Lacey Knowles
Past shifts in connectivity in riverine environments (for example, sea-level changes) and the properties of current drainages can act as drivers of genetic structure and demographic processes in riverine population of fishes. However, it is unclear whether the same river properties that structure variation on recent timescales will also leave similar genomic signatures that reflect paleodrainage properties. By characterizing genetic structure in a freshwater fish species (Hollandichthys multifasciatus) from a system of basins along the...

Data from: Detecting ancient co-dispersals and host shifts by double dating of host and parasite phylogenies: application in proctophyllodid feather mites associated with passerine birds

Pavel B. Klimov, Sergey V. Mironov & Barry M. OConnor
Inferring co-phylogeographic events requires matching the timing of these events on both host and symbiont (e.g., parasites) phylogenies because divergences of hosts and their symbionts may not temporally coincide, and host switches may occur. We investigate a large radiation of birds (Passeriformes) and their permanent symbionts, the proctophyllodid feather mites (117 species from 116 bird species; 6 genes, 11,468 nt aligned) using two time-calibration strategies for mites: fossils only and host phylogeography only. Out of...

Data from: Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

James B. Pease, Joseph W. Brown, Joseph F. Walker, Cody E. Hinchliff & Stephen A. Smith
Premise of the Study—Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As datasets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative. Methods— We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in...

Data from: Linking micro- and macroevolutionary perspectives to evaluate the role of Quaternary sea-level oscillations in island diversification

Anna Papadopoulou & L. Lacey Knowles
With shifts in island area, isolation, and cycles of island fusion-fission, the role of Quaternary sea-level oscillations as drivers of diversification is complex and not well understood. Here we conduct parallel comparisons of population and species divergence between two island areas of equivalent size that have been affected differently by sea-level oscillations, with the aim to understand the micro- and macroevolutionary dynamics associated with sea-level change. Using genome-wide datasets for a clade of seven Amphiacusta...

Data from: Use of continuous traits can improve morphological phylogenetics

Caroline Parins-Fukuchi
The recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modelling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modelling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character...

Data from: Multilevel and sex-specific selection on competitive traits in North American red squirrels.

David N. Fisher, Stan Boutin, Ben Dantzer, Murray M. Humphries, Jeffrey E. Lane & Andrew G. McAdam
Individuals often interact more closely with some members of the population (e.g. offspring, siblings or group members) than they do with other individuals. This structuring of interactions can lead to multilevel natural selection, where traits expressed at the group-level influence fitness alongside individual-level traits. Such multilevel selection can alter evolutionary trajectories, yet is rarely quantified in the wild, especially for species that do not interact in clearly demarcated groups. We quantified multilevel natural selection on...

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  • University of Michigan-Ann Arbor
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