61 Works

Data from: Postglacial expansion pathways of red mangrove, Rhizophora mangle, in the Caribbean Basin and Florida

John Paul Kennedy, Maria W. Pil, C. Edward Proffitt, Walter A. Boeger, Alice M. Stanford & Donna J. Devlin
PREMISE OF THE STUDY: The Last Glacial Maximum (LGM) was a period of massive range contraction. Post-LGM, water-dispersed coastal species, including the red mangrove (Rhizophora mangle), expanded poleward as propagules were transported by ocean currents. We assessed postglacial marine expansion pathways for R. mangle within the Caribbean Basin and Florida. METHODS: Six microsatellite loci were used to genotype 237 individuals from nine R. mangle populations in the Caribbean, Florida, and Northwest Africa. We evaluated genetic...

Data from: Breeding sex ratio and population size of loggerhead turtles from Southwestern Florida

Jacob A. Lasala, Colin R. Hughes & Jeanette Wyneken
Species that display temperature-dependent sex determination are at risk as a result of increasing global temperatures. For marine turtles, high incubation temperatures can skew sex ratios towards females. There are concerns that temperature increases may result in highly female-biased offspring sex ratios, which would drive a future sex ratio skew. Studying the sex ratios of adults in the ocean is logistically very difficult because individuals are widely distributed and males are inaccessible because they remain...

A Document Analysis of Anti-Hazing Policy

Christobal Salinas, Michelle Boettcher & Jennifer Plagman-Galvin

Supplementary Materials from Genomic evidence for ancient human migration routes along South America's Atlantic coast

Andre Luiz Campelo dos Santos, Amanda Owings, Henry Socrates Lavalle Sullasi, Omer Gokcumen, Michael DeGiorgio & John Lindo
An increasing body of archaeological and genomic evidence has hinted to a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from...

Additional file 1 of Rheumatoid arthritis sera antibodies to citrullinated collagen type II bind to joint cartilage

Qixing Li, Yanpeng Li, Bibo Liang, Rui Xu, Bingze Xu, Erik Lönnblom, Hui Feng, Jing’an Bai, Roma Stawikowska, Changrong Ge, Aiping Lu, Gregg B. Fields, Lianbo Xiao & Rikard Holmdahl
Additional file 1: Supplementary Table S1. Cyclic human COL2 peptide sequences (ACC10 and their corresponding arginine peptides). Amino acids differing from mouse are indicated in italic. Supplementary Table S2. Detailed information of antibody response to ACC10 in different sera subset. Supplementary Table S3. Information of other antigen peptides. Supplementary Table S4. Triple-helical COL2 peptide sequences. Supplementary Table S5. Peptides to which private sera have specific responses. Fig. S1. Some characteristics from patients with promiscuous or...

Data from: Reconstruction of larval origins based on genetic relatedness and biophysical modeling

Iris Segura-García, Lysel Garavelli, Tringali Michael, Thomas Matthews, Laurent M. Chérubin, John Hunt & Stephen J. Box
The assessment of the mechanisms and patterns of larval connectivity between geographically separated populations leads to a better understanding of benthic marine population dynamics, especially in commercially valuable species. This study investigated for the first time the fine-scale temporal genetic variability of new settlers and their origins in a benthic marine organism with one of the longest pelagic larval phases, the Caribbean spiny lobster (Panulirus argus). We genotyped newly settled postlarvae in the Florida Keys...

Data from: Female zebra finches prefer the songs of males who quickly solve a novel foraging task to the songs of males unable to solve the task

Clara Howell, Rindy Anderson & Elizabeth Derryberry
Correlative evidence suggests that high problem-solving and foraging abilities in a mate are associated with direct fitness advantages, so it would benefit females to prefer problem-solving males. Recent work has also shown that females of several bird species who directly observe males prefer those that can solve a novel foraging task over those that cannot. In addition to or instead of direct observation of cognitive skills, many species utilize assessment signals when choosing a mate....

Identifying and classifying shared selective sweeps from multilocus data

Alexandre Harris & Michael DeGiorgio
Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can...

Supplementary figures for: Of traits and trees: probabilistic distances under continuous trait models for dissecting the interplay among phylogeny, model, and data

Richard Adams, Heath Blackmon & Michael DeGiorgio
Stochastic models of character trait evolution have become a cornerstone of evolutionary biology in an array of contexts. While probabilistic models have been used extensively for statistical inference, they have largely been ignored for the purpose of measuring distances between phylogeny-aware models. Recent contributions to the problem of phylogenetic distance computation have highlighted the importance of explicitly considering evolutionary model parameters and their impacts on molecular sequence data when quantifying dissimilarity between trees. By comparing...

Supplementary material from \"Genomic evidence for ancient human migration routes along South America's Atlantic coast\"

Andre Luiz Campelo dos Santos, Amanda Owings, Henry Socrates Lavalle Sullasi, Omer Gokcumen, Michael DeGiorgio & John Lindo
An increasing body of archaeological and genomic evidence has hinted to a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from...

Additional file 6 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 6

Additional file 1 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 1

Additional file 1 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 1

Additional file 2 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 2

Additional file 3 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 3

Data from: Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

Thomas J. Near, Alex Dornburg, Ron I. Eytan, Benjamin P. Keck, W. Leo Smith, Kristen L. Kuhn, Jon A. Moore, Samantha A. Price, Frank T. Burbrink, Matt Friedman & Peter C. Wainwright
Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at...

Data from: A test of the eavesdropping avoidance hypothesis as an explanation for the structure of low amplitude aggressive signals in the song sparrow

Joseph M. Niederhauser, Adrienne L. DuBois, William A. Searcy, Stephen Nowicki & Rindy C. Anderson
Low amplitude signals function in private exchanges of information between signalers and nearby receivers. The eavesdropping avoidance hypothesis proposes that selection favors quiet threat signals in order to avoid the costs of eavesdroppers. If true, then selection should favor other acoustic traits in addition to low amplitude that lead to quiet signals transmitting less effectively through the environment compared to broadcast signals. The “warbled” soft songs of male song sparrows differ from “crystallized” soft songs...

Nesting White Ibis prey use in Everglades National Park in 2017 and 2018

Tasso Cocoves
As avian reproductive success is generally prey limited, identifying important prey types or sizes, and understanding mechanisms governing prey availability are important objectives for avian conservation ecology. Irruptive White Ibis (Eudocimus albus) nesting at coastal colonies in the southern Everglades numbered over 100,000 nests in the 1930s. A century of drainage and altered hydrologic patterns reduced aquatic prey availability and eliminated large nesting events; nesting activity in recent decades has been typically <5% of historical...

A spatially aware likelihood test to detect sweeps from haplotype distributions

Zachary Szpiech & Michael DeGiorgio
The inference of positive selection in genomes is a problem of great interest in evolutionary genomics. By identifying putative regions of the genome that contain adaptive mutations, we are able to learn about the biology of organisms and their evolutionary history. Here we introduce a composite likelihood method that identifies recently completed or ongoing positive selection by searching for extreme distortions in the spatial distribution of the haplotype frequency spectrum along the genome relative to...

Disparate financial assistance support for small business owners

Sophia Fox-Ditchter, Daniel Auguste, Mathieu Despard & Michal Grinstein-Weiss

Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Abstract Background Aggression is observed across the animal kingdom, and benefits animals in a number of ways to increase fitness and promote survival. While aggressive behaviors vary widely across populations and can evolve as an adaptation to a particular environment, the complexity of aggressive behaviors presents a challenge to studying the evolution of aggression. The Mexican tetra, Astyanax mexicanus exists as an aggressive river-dwelling surface form and multiple populations of a blind cave form, some...

Additional file 6 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 6

Additional file 2 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 2

Additional file 4 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 4

Additional file 5 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 5

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