119 Works

Data from: A multi-tissue view on telomere dynamics and postnatal growth

Sarah Wolf & Kimberly Rosvall
Trade-offs between growth and self-maintenance are common in nature, such that early-life effects on growth can generate lasting consequences on survival and longevity. Telomeres – putative biomarkers of self-maintenance – may link early growth with these later phenotypic effects, but evidence for growth-telomere trade-offs is mixed. Null or even positive relationships between growth and telomeres may be driven by heterogeneity in resource availability or invariable allocation towards telomere maintenance within a population. We used nestling...

Genotypic variation in an ecologically important parasite is associated with host species, lake, and spore size

Clara Shaw, Rebecca Bilich, Bruce O'Brien, Carla Cáceres, Spencer Hall, Timothy James & Meghan Duffy
Genetic variation in parasites has important consequences for host-parasite interactions. Prior studies of the ecologically important parasite Metschnikowia bicuspidata have suggested low genetic variation in the species. Here, we collected M. bicuspidata from two host species (Daphnia dentifera and Ceriodaphnia dubia) and two regions (Michigan and Indiana, USA). Within a lake, outbreaks tended to occur in one host species but not the other. Using microsatellite markers, we identified six parasite genotypes grouped within three distinct...

Supplementary data, code, and information for ‘Interhemispheric antiphasing of neotropical precipitation during the past millennium’ (PNAS, Steinman et al. 2022)

B.A. Steinman, N. Stansall, M.E. Mann, C.A. Cooke, M.B. Abbott, M. Vuille, B.W. Bird, M.S. Lachniet & A. Fernandez
Uncertainty about the influence of anthropogenic radiative forcing on the position and strength of convective rainfall in the Intertropical Convergence Zone (ITCZ) inhibits our ability to project future tropical hydroclimate change in a warmer world. Paleoclimatic and modeling data inform on the timescales and mechanisms of ITCZ variability; yet a comprehensive, long-term perspective remains elusive. Here, we quantify the evolution of neotropical hydroclimate over the pre-industrial past millennium (850 to 1850 CE) using a synthesis...

A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes

Remi Ketchum, Phillip Davidson, Edward Smith, Gregory Wray, John Burt, Joseph Ryan & Adam Reitzel
Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for Echinometra sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an...

Traits of soil bacteria predict plant responses to soil moisture

Lana Bolin, Jennifer Lau & Jay Lennon
Microbes can promote beneficial plant and animal responses to abiotic environments, but the ecological drivers of this benefit remain elusive. Here we investigated byproduct benefits, which occur when traits that increase the fitness of one species provide incidental benefits to another species with no direct cost to the provider species. In experimental mesocosms, microbial traits predicted plant responses to soil moisture such that bacteria with self-beneficial traits in drought increased plant early growth, size at...

Data from: Reconciling extremely strong barriers with high levels of gene exchange in annual sunflowers

Julianno Bergoch Monteiro Sambatti, Jared L. Strasburg, Daniel Ortiz-Barrientos, Eric J. Baack & Loren Henry Rieseberg
In several cases, estimates of gene flow between species appears to be higher than predicted given the strength of interspecific barriers. However, as far as we are aware, detailed measurements of reproductive isolation have not previously been compared with a coalescent-based assessment of gene flow. Here, we contrast these two measures in two species of sunflower, Helianthus annuus and Helianthus petiolaris. We quantified the total reproductive barrier strength between these species by compounding the contributions...

Data from: Alternative paths to success in a parasite community: within-host competition can favor higher virulence or direct interference

Farrah Bashey-Visser, Hadas Hawlena & Curtis M. Lively
Selection imposed by coinfection may vary with the mechanism of within-host competition between parasites. Exploitative competition is predicted to favor more virulent parasites, while interference competition may result in lower virulence. Here, we examine whether exploitative or interference competition determines the outcome of competition between two nematode species (Steinernema spp.), which in combination with their bacterial symbionts (Xenorhabdus spp.), infect and kill insect hosts. Multiple isolates of each nematode species, carrying their naturally associated bacteria,...

Data from: A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait

Peter C. Zee, Helena Mendes-Soares, Yuen-Tsu Nicco Yu, Susanne A. Kraemer, Heike Keller, Stephan Ossowski, Korbinian Schneeberger & Gregory J. Velicer
While the importance of epistasis in evolution has long been recognized, remarkably little is known about the processes by which epistatic interactions evolve in real time in specific biological systems. Here, we have characterized how the epistatic fitness relationship between a social gene and an adapting genome changes radically over a short evolutionary time frame in the social bacterium Myxococcus xanthus. We show that a highly beneficial effect of this social gene in the ancestral...

Data from: The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen

Desiree E. Allen & Michael Lynch
Cyclical parthenogens are a valuable system in which to empirically test theoretical predictions as to the genetic consequences of sexual reproduction in natural populations, particularly if the frequency of sexual relative to asexual reproduction can be quantified. In this study we utilized a series of lake populations of the cyclical parthenogen, Daphnia pulicaria, that vary consistently in their investment in sexual reproduction, to address the questions of whether the ecological variation in investment in sex...

Data from: Population genomics of wild and laboratory zebrafish (Danio rerio)

Andrew R Whiteley, Anuradha Bhat, Emilia P Martins, Richard L Mayden, M Arunachalam, Silva Uusi-Heikkilä, A.T.A. Ahmed, Jiwan Shrestha, Matthew Clark, Derek Stemple & Louis Bernatchez
Understanding a wider range of genotype-phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1,832 polymorphic EST-based SNPs and the cytb mitochondrial gene in 13 wild populations and...

Data from: Wide variation in ploidy level and genome size in a New Zealand freshwater snail with coexisting sexual and asexual lineages

Maurine Neiman, Dorota Paczesniak, Deanna M Soper, Austin T Baldwin & Gery Hehman
Natural animal populations are rarely screened for ploidy-level variation at a scale that allows detection of potentially important aberrations of common ploidy patterns. This type of screening can be especially important for the many mixed sexual/asexual systems where sexuals are presumed to be dioecious diploids and asexuals are assumed to be triploid and all-female. For example, elevation of ploidy level above triploidy can be a source of genetic variation and raises the possibility of gene...

Data from: Global database of matched Plasmodium falciparum and P. vivax incidence and prevalence records from 1985–2013

Katherine E. Battle, Carlos A. Guerra, Nick Golding, Kirsten A. Duda, Ewan Cameron, Rosalind E. Howes, Iqbal R. F. Elyazar, J. Kevin Baird, , Peter W. Gething, David L. Smith & Simon I. Hay
Measures of clinical incidence are necessary to help estimate the burden of a disease. Incidence is a metric not commonly measured in malariology because the longitudinal surveys required are costly and labour intensive. This database is an effort to collate published incidence records obtained using active case detection for Plasmodium falciparum and Plasmodium vivax malaria. The literature search methods, data abstraction procedures and data processing procedures are described here. A total of 1,680 spatio-temporally unique...

Data from: Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals

Gregg W. C. Thomas & Matthew W. Hahn
Convergent evolution occurs when the same trait arises independently in multiple lineages. In most cases of phenotypic convergence such transitions are adaptive, so finding the underlying molecular causes of convergence can provide insight into the process of adaptation. Convergent evolution at the genomic level also lends itself to study by comparative methods, though molecular convergence can also occur by chance, adding noise to this process. Parker et al. (2013) studied convergence across the genomes of...

Data from: Joint effects of habitat, zooplankton, host stage structure and diversity on amphibian chytrid

Jessica L. Hite, Jaime Bosch, Saioa Fernández-Beaskoetxea, Daniel Medina & Spencer R. Hall
Why does the severity of parasite infection differ dramatically across habitats? This question remains challenging to answer because multiple correlated pathways drive disease. Here, we examined habitat–disease links through direct effects on parasites and indirect effects on parasite predators (zooplankton), host diversity and key life stages of hosts. We used a case study of amphibian hosts and the chytrid fungus, Batrachochytrium dendrobatidis, in a set of permanent and ephemeral alpine ponds. A field experiment showed...

Data from: The roles of compensatory evolution and constraint in aminoacyl tRNA synthetase evolution

Jeffrey R. Adrion, P. Signe White & Kristi L. Montooth
Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their nuclear-encoded counterparts, the cytoplasmic tRNAs (cyt-tRNAs). This dynamic predicts elevated rates of compensatory evolution of mt-aaRS that interact with mt-tRNAs, relative to aaRS that interact with cyt-tRNAs (cyt-aaRS). We find that mt-aaRS do evolve...

Data from: Gene-tree reconciliation with MUL-trees to resolve polyploidy events

Gregg W.C. Thomas, S. Hussain Ather & Matthew W. Hahn
Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids - autopolyploids and allopolyploids - differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together...

Data from: Habitat heterogeneity, host population structure and parasite local adaptation

Curtis M. Lively
Reciprocal-transplant experiments have proven to be a powerful tool for detecting local adaptation (LA). More recently, reciprocal cross-inoculation experiments have been used to evaluate adaptation by parasites to their local host populations. These experiments are conceptually similar to reciprocal-transplant experiments, except that the "environment" (the host population) may have evolved in response to changes in the parasite population. Here, I use analytical tools and computer simulations to determine when parasites would be expected to be...

Data from: Volatile fatty acid and aldehyde abundances evolve with behavior and habitat temperature in Sceloporus lizards

Stephanie Campos, Jake Pruett, Helena Soini, J. Jaime Zúñiga-Vega, Jay Goldberg, Cuauhcihuatl Vital-García, Milos Novotny, Diana Hews & Emília Martins
Animal signals evolve by striking a balance between the need to convey information through particular habitats and the limitations of what types of signals can most easily be produced and perceived. Here, we present new results from field measures of undisturbed behavior and biochemical analyses of scent marks from 12 species of Sceloporus lizards to explore whether evolutionary changes in chemical composition are better predicted by measures of species behavior , particularly those associated with...

Data from: Trait plasticity alters the range of possible coexistence conditions in a competition-colonization trade-off

Ranjan Muthukrishnan, Lauren L. Sullivan, Allison Shaw & James Forester
Most of the classical theory on species coexistence has been based on species-level competitive trade-offs. However, it is becoming apparent that plant species display high levels of trait plasticity. The implications of this plasticity are almost completely unknown for most coexistence theory. Here, we model a competition-colonization trade-off and incorporate trait plasticity to evaluate its effects on coexistence. Our simulations show that the classic competition-colonization trade-off is highly sensitive to environmental circumstances and coexistence only...

Seasonal patterns of melatonin alter aggressive phenotypes of female Siberian hamsters

Nikki Rendon, Christopher Petersen, Kathleen Munley, Andrea Amez, Daniel Boyes, Marcy Kingsbury & Gregory Demas
Many animal species exhibit year-round aggression, a behaviour that allows individuals to compete for limited resources in their environment (e.g., food and mates). Interestingly, this high degree of territoriality persists during the non-breeding season, despite low levels of circulating gonadal steroids (i.e., testosterone [T] and oestradiol [E2]). Our previous work suggests that the pineal hormone melatonin mediates a ‘seasonal switch’ from gonadal to adrenal regulation of aggression in Siberian hamsters (Phodopus sungorus); solitary, seasonally breeding...

The plot thickens: Haploid and triploid-like thalli, hybridization, and biased mating type ratios in Letharia

Sandra Lorena Ament-Velásquez, Veera Tuovinen, Linnea Bergström, Toby Spribille, Dan Vanderpool, Juri Nascimbene, Yoshikazu Yamamoto, Göran Thor & Hanna Johannesson
The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex and symbiotic lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we used genomic data from a pure culture and from thalli, together with a PCR survey of the MAT locus, to infer the genome organization and reproduction in Letharia. We found that the read count variation in...

A putative telomerase activator has tissue-specific effects on telomere length in a developing songbird

Sarah Wolf, Keegan Stansberry, Kristen Content & Kimberly Rosvall
There is good evidence that telomeres predict variation in health and longevity, yet it is unclear whether these patterns are causally derived from telomeres per se, in part because relatively little research directly manipulates telomere length during early life, when telomere shortening is most dynamic. Here, we test how the telomerase activator TA-65 (i.e., cycloastrogenol) affects telomere length in five tissues during the peak of growth in the wild tree swallow (Tachycineta bicolor). Following 8...

Supporting information for: The frequency and topology of pseudoorthologs

Megan Smith & Matthew Hahn
Phylogenetics has long relied on the use of orthologs, or genes related through speciation events, to infer species relationships. However, identifying orthologs is difficult because gene duplication can obscure relationships among genes. Researchers have been particularly concerned with the insidious effects of pseudoorthologs—duplicated genes that are mistaken for orthologs because they are present in a single copy in each sampled species. Because gene tree topologies of pseudoorthologs may differ from the species tree topology, they...

Data from: Signatures of north-eastern expansion and multiple refugia: Genomic phylogeography of the Pine Barrens Treefrog, Hyla andersonii (Anura: Hylidae)

Alexa Warwick, Lisa Barrow, Megan Smith, D. Bruce Means, Alan Lemmon & Emily Lemmon
Range fragmentation poses challenges for species persistence over time and may be caused by both historical and contemporary processes. We combined genomic data, phylogeographic model testing, and paleoclimate niche modeling to infer the evolutionary history of the Pine Barrens Treefrog (Hyla andersonii), a seepage bog specialist, in eastern North America to better understand the historical context of its fragmented distribution. We sampled H. andersonii populations across the three disjunct regions of the species’ range: Alabama/Florida...

The probability of being infected with haemosporidian parasites increases with host age

Samuel Slowinski, Aidan Geissler, Nicole Gerlach, Britt Heidinger & Ellen Ketterson
In vertebrates, disease susceptibility often varies with age. Older individuals may be more susceptible than younger individuals due to senescent declines in immune function. Alternatively, disease susceptibility may decrease with age if older individuals are more likely to have had prior exposures to parasites and acquired adaptive immune responses that allowed them to resist future infections. Disease susceptibility can also vary with reproductive state, and reproductive hormones have been shown to increase infection susceptibility. Here...

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  • Indiana University
  • Indiana University Bloomington
  • Stanford University
  • University of Michigan-Ann Arbor
  • University of Georgia
  • University of Minnesota
  • University of Melbourne
  • University of Massachusetts Amherst
  • University of Washington
  • New York University Abu Dhabi