22 Works

The Scathingly Brilliant Scholarship of Lisa Blomgren Amsler (Formerly Bingham)

Mariana Hernandez-Crespo, David Lipsky, Tina Nabatchi & Rosemary O'Leary

Preferential allocation of benefits and resource competition among recipients allows coexistence of symbionts within hosts

Shyamolina Ghosh, Daniel C. Reuman & James D. Bever
Functionally variable symbionts commonly co-occur including within the roots of individual plants, in spite of arguments from simple models of the stability of mutualism that predict competitive exclusion among symbionts. We explore this paradox by evaluating the dynamics generated by symbiont competition for plant resources, and the plant’s preferential allocation to the most beneficial symbiont, using a system of differential equations representing the densities of mutualistic and non-mutualistic symbionts and the level of preferentially allocated...

A phylogeny of white-eyes based on ultraconserved elements

Michael Andersen, Carl Oliveros & Robert Moyle
White-eyes are an iconic radiation of passerine birds that have been the subject of studies in evolutionary biology, biogeography, and speciation theory. Zosterops white-eyes in particular are thought to have radiated rapidly across continental and insular regions of the Afro- and Indo-Pacific tropics, yet, their phylogenetic history remains equivocal. Here, we sampled 77% of the genera and 47% of known white-eye species and sequenced thousands of ultraconserved elements to infer the phylogeny of the avian...

Data from: Ornithogenic vegetation: How significant has the seabird influence been on the Aleutian Island vegetation during the Holocene?

Olesya Smyshlyaeva, Elena Severova, Olga Krylovich, Evgeniya Kuzmicheva, Arkady Savinetsky, Dixie West & Virginia Hatfield
In the Aleutian Islands during the Holocene, terrestrial predators were actually absent; as a result, large seabird colonies thrived along the coasts or across entire islands. Bird guano enriches the soil with nitrogen, which can lead to the formation of highly modified ornithogenic (bird-formed) ecosystems. For a more detailed investigation of avian influence, we reconstructed more than 10,000-year-old vegetation dynamics of the coast of Shemya Island (Near Islands) by pollen analysis. At the initial stages...

Selenium-associated differentially expressed microRNAs and their targeted mRNAs across the placental genome in two U.S. birth cohorts

Fu-Ying Tian, Elizabeth M. Kennedy, Karen Hermetz, Amber Burt, Todd M. Everson, Tracy Punshon, Brian P. Jackson, Ke Hao, Jia Chen, Margaret R. Karagas, Devin C. Koestler & Carmen Marsit
Selenium is an important micronutrient for foetal development. MicroRNAs play an important role in the function of the placenta, in communication between the placenta and maternal systems, and their expression can be altered through environmental and nutritional cues. To investigate the associations between placental selenium concentration and microRNA expression in the placenta, our observational study included 393 mother-child pairs from the New Hampshire Birth Cohort Study (NHBCS) and the Rhode Island Child Health Study (RICHS)....

Geomorphology variables predict fish assemblages for forested and endorheic rivers

Mark Pyron, Robert Shields, Emily Arsenault, James Thorp, Mario Minder, Caleb Artz, John Costello, Amarbat Otgonganbat, Bud Mendsaikhan & Alain Maasri
This dataset contains data from field collections described in the paper: “Shields, R., Pyron, M., Arsenault, E., Thorp, J., Minder, M., Artz, C., Costello, J., Otgonganbat, A., Mendsaikhan, B., Maasri., A. (2022) Geomorphology variables predict fish assemblages for forested and endorheic rivers. Ecology and Evolution. ECE-2021-08-01367”. Stream fishes are restricted to specific environments with appropriate habitats for feeding and reproduction. Interactions between streams and surrounding landscapes influence the availability and type of fish habitat, nutrient...

Code and resulting candidate gene datasets from Anopheles genome environment association testing

Devon DeRaad
The concept of a fundamental ecological niche is central to questions of geographic distribution, population demography, species conservation, and evolutionary potential. But robust inference of genomic regions associated with evolutionary adaptation to particular environmental conditions remains difficult due to the myriad of potential confounding processes that can generate heterogeneous patterns of variation across the genome. Here, we interrogate the potential role of genome environment association (GEA) testing as an initial step in building an understanding...

Selenium-associated differentially expressed microRNAs and their targeted mRNAs across the placental genome in two U.S. birth cohorts

Fu-Ying Tian, Elizabeth M. Kennedy, Karen Hermetz, Amber Burt, Todd M. Everson, Tracy Punshon, Brian P. Jackson, Ke Hao, Jia Chen, Margaret R. Karagas, Devin C. Koestler & Carmen Marsit
Selenium is an important micronutrient for foetal development. MicroRNAs play an important role in the function of the placenta, in communication between the placenta and maternal systems, and their expression can be altered through environmental and nutritional cues. To investigate the associations between placental selenium concentration and microRNA expression in the placenta, our observational study included 393 mother-child pairs from the New Hampshire Birth Cohort Study (NHBCS) and the Rhode Island Child Health Study (RICHS)....

Inter- and intra-archipelago dynamics of population structure and gene flow in a Polynesian bird

Ethan Gyllenhaal, Xena Mapel, Tejashree Modak, Lucas DeCicco, Alivereti Naikatini, Ruth Utzurrum, Joshua Seamon, Jean-Claude Thibault, Alice Cibois, Michael Sorenson, Robert Moyle, Lisa Barrow & Michael Andersen
Islands are separated by natural barriers that prevent gene flow between terrestrial populations and promote allopatric diversification. Birds in the South Pacific are an excellent model to explore the interplay between isolation and gene flow due to the region’s numerous archipelagos and well-characterized avian communities. The wattled honeyeater complex (Foulehaio spp.) comprises three allopatric species that are widespread and common across Fiji, Tonga, Samoa, and Wallis and Futuna. Here, we explored patterns of diversification within...

Data from: Ecological factors influence balancing selection on leaf chemical profiles of a wildflower

Lauren Carley, Julius Mojica, Baosheng Wang, Chia-Yu Chen, Ya-Ping Lin, Kasavajhala Prasad, Emily Chan, Che-Wei Hsu, Rose Keith, Chase Nuñez, Carrie Olson-Manning, Catherine Rushworth, Maggie Wagner, Jing Wang, Pei-Min Yeh, Michael Reichelt, Kathryn Ghattas, Jonathan Gershenzon, Cheng-Ruei Lee & Thomas Mitchell-Olds
Balancing selection is frequently invoked as a mechanism to maintain variation within and across populations. However, rigorous tests demonstrating balancing selection operating in nature are scarce, particularly on complex traits, which frequently display high levels of variation. Leveraging a focal polymorphism, leaf chemical profile in a perennial wildflower (Boechera stricta, Brassicaceae), we investigated the ecological and genetic mechanisms that may influence the maintenance of variation in this trait. A suite of common garden and greenhouse...

Identification of Rad51 as a prognostic biomarker correlated with immune infiltration in hepatocellular carcinoma

Hao Xu, Chen Xiong, Yuan Chen, Chi Zhang & Dousheng Bai
Rad51, a DNA-repair-related gene, has been reported to be involved in multiple cancers. However, its link with immune infiltration in liver cancer still unknown. Therefore, more research into the roles and activities of Rad51 in hepatocellular carcinoma (HCC) is required. The International Cancer Genome Consortium (ICGC) was used to identify the DNA repair gene Rad51, and has been proved to be overexpressed in HCC patients. We plotted the Kapan-Meier curve, demonstrating that patients with high...

Identification of Rad51 as a prognostic biomarker correlated with immune infiltration in hepatocellular carcinoma

Hao Xu, Chen Xiong, Yuan Chen, Chi Zhang & Dousheng Bai
Rad51, a DNA-repair-related gene, has been reported to be involved in multiple cancers. However, its link with immune infiltration in liver cancer still unknown. Therefore, more research into the roles and activities of Rad51 in hepatocellular carcinoma (HCC) is required. The International Cancer Genome Consortium (ICGC) was used to identify the DNA repair gene Rad51, and has been proved to be overexpressed in HCC patients. We plotted the Kapan-Meier curve, demonstrating that patients with high...

A novel body plan alters diversification of body shape and genitalia in live-bearing fish

R. Brian Langerhans & Eduardo Rosa-Molinar
Major evolutionary innovations can greatly influence subsequent evolution. While many major transitions occurred in the deep past, male live-bearing fishes (family Poeciliidae) more recently evolved a novel body plan. This group possesses a three-region axial skeleton, with one region—the ano-urogenital region—representing a unique body region accommodating male genitalic structures (gonopodial complex). Here we evaluate several hypotheses for the evolution of diversity in this region and examine its role in the evolution of male body shape....

Contrasting patterns of phylogenetic diversity and alpine specialization across the alpine flora of the American mountain range system

Hector Fox Figueroa, Hannah E. Marx, Maria Beatriz De Souza Cortez, Charles J. Grady, Nicholas Engle-Wrye, Jim Beach, Aimee Stewart, Ryan A. Folk, Douglas E. Soltis, Pamela S. Soltis & Stephen A. Smith
Although mountainous habitats contribute substantially to global biodiversity, comparatively little is known about biogeographic patterns of distributions of alpine species across multiple mountain ranges. Here, we present a detailed analysis of the distributions and phylogenetic affinities of alpine seed plant lineages across North, Central, and South American mountain systems. Using a comprehensive dataset that characterized the elevational niches of American seed plants in a continuously valued way, we were able to quantitatively investigate how the...

Data from: Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

Heather E. Machado, Alan O. Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Iryna Kozeretska, Brian P. Lazzaro, Thomas JS Merritt, John E. Pool, Katherine O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri Petrov & Bernard Kim
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched at...

Code for: Environmental fluctuations dampen the effects of clonal reproduction on evolutionary rescue

James Peniston, Michael Barfield, Robert Holt & Maria Orive
Evolutionary rescue occurs when genetic change allows a population to persist in response to an environmental change that would otherwise have led to extinction. Most studies of evolutionary rescue assume that species have either fully clonal or fully sexual reproduction; however, many species have partially clonal reproductive strategies in which they reproduce both clonally and sexually. Furthermore, the few evolutionary rescue studies that have evaluated partially clonal reproduction did not consider fluctuations in the environment,...

Micro-CT data from: Maternal care in mid-Cretaceous lagonomegopid spiders

Xiangbo Guo, Paul Selden & Dong Ren
This dataset contains the raw Micro-CT data and a 3D CT reconstruction of a piece of Burmese amber CNU009432 from "Guo, X., Selden, P. and Ren, D. (2021) Maternal care in mid-Cretaceous lagonomegopid spiders. Proc. R. Soc. B.". These data shows the maternal care behaviour of an adult female lagonomegopid spider guarding her egg sac. Maternal care benefits the survival and fitness of offspring often at a cost to the mother's future reproduction and has...

Diet overlap among non-native trout species and native Cutthroat Trout (Oncorhynchus clarkii) in two U.S. ecoregions

Mario Minder, Emily Arsenault, Bolortsetesg Erdenee, Alain Maasri & Mark Pyron
The invasion of freshwater ecosystems by non-native species can constitute a significant threat to native species and ecosystem health. Non-native trouts have long been stocked in areas where native trouts occur and have negatively impacted native trouts through predation, competition, and hybridization. This study encompassed two seasons of sampling efforts across two ecoregions of the western United States: The Great Basin in summer 2016 and the Yellowstone River Basin in summer 2017. We found significant...

Population connectivity across a highly fragmented distribution: Phylogeography of the Chalcophaps doves

Devon DeRaad, Joseph Manthey, Emily Ostrow, Lucas DeCicco, Michael Andersen, Peter Hosner, Hannah Shult, Leo Joseph, John Dumbacher & Robert Moyle
Chalcophaps is a morphologically conserved genus of ground-walking doves distributed from India to mainland China, south to Australia, and across the western Pacific to Vanuatu. Here, we reconstruct the evolutionary history of this genus using DNA sequence data from two nuclear genes and one mitochondrial gene, sampled from throughout the geographic range of Chalcophaps. We find support for three major evolutionary lineages in our phylogenetic reconstruction, each corresponding to the three currently recognized Chalcophaps species....

Maximum clade credibility (MCC) tree of Argyrodes lanyuensis from Philippines and Orchid Island Taiwan using BEAST 1.10

Mae Responte, Yong-Chao Su, Po Peng, Yi-Fan Chiu, Rafe Brown & Chia-Yen Dai
Oceanic islands are unique geographic systems that promote local adaptations and allopatric speciation in many of their highly endemic taxa. This is a common case in the Philippine Archipelago, where numerous unrelated taxa on islands have been inferred to have diversified in isolation. However, few cases have been reported in invertebrates especially among parasitic organisms. Here, we tested for biogeographical structure in novel populations of the “generalist" kleptoparasitic spider, Argyrodes lanyuensis Yoshida, Tso & Severinghaus,...

Quantifying niche similarity among new world seed plants--Species Distribution Models (SDMs) & associated metadata

Hector Figueroa, Hannah Marx, CJ Grady, Jim Beach, Ryan Folk, Douglas Soltis, Pamela Soltis, Aimee Stewart & Stephen Smith
Niche shift and conservatism are often framed as mutually exclusive. However, both processes could contribute to biodiversity patterns. We tested this expectation by quantifying the degree of climatic niche similarity among New World seed plants. To incorporate the biological reality that species experience varied abiotic conditions across their range, we assembled distribution models and used these to characterize temperature, precipitation, and elevation niches for species as continuously-valued distributions. We then quantified niche similarity (distributional overlap)...

Identification of hepatocellular carcinoma-related genes associated with macrophage differentiation based on bioinformatics analyses

Jun Cao, Chi Zhang, Guo-Qing Jiang, Sheng-Jie Jin, Qian Wang, Ao-Qing Wang & Dou-Sheng Bai
Macrophage differentiation is associated with tumorigenesis, including the tumorigenesis of hepatocellular carcinoma (HCC). Herein, we explored the value of macrophage differentiation-associated genes (MDGs) in the prognosis of HCC using data from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) databases. We performed multivariate Cox regression analyses to identify the hub genes affecting HCC patient prognoses. The correlations between hub genes and macrophage differentiation and immune checkpoint inhibitors (PD-1, PD-L1, and CTLA4)...

Registration Year

  • 2021
    22

Resource Types

  • Dataset
    18
  • Text
    3
  • Image
    1

Affiliations

  • University of Kansas
    22
  • Central South University
    5
  • Nantong Tumor Hospital
    4
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    4
  • Sun Yat-sen University
    3
  • Zhejiang University
    3
  • Huazhong University of Science and Technology
    3
  • Wenzhou Medical University
    3
  • University of North Carolina at Chapel Hill
    3
  • Fudan University
    3