34 Works

A Document Analysis of Anti-Hazing Policy

Christobal Salinas, Michelle Boettcher & Jennifer Plagman-Galvin

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...

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...

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...

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....

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...

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

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...

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...

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...

Supplementary figures for SpeciesTopoTestR: likelihood-based tests of species trees

Richard Adams & Michael DeGiorgio
Likelihood-based tests of phylogenetic trees are a foundation of modern systematics, and examples of such tests are among the most widely-referenced scientific literature of all time. Over the past decade, an enormous wealth and diversity of model-based approaches have been developed for phylogenetic inference of both gene trees and species trees. However, while many techniques exist for conducting formal likelihood-based tests of gene trees, such frameworks are comparatively underdeveloped and underutilized for testing species-level hypotheses....

Data from: Assessment of mesophotic coral ecosystem connectivity for proposed expansion of a marine sanctuary in the northwest Gulf of Mexico: population genetics

Michael S. Studivan & Joshua D. Voss
While there are several areas containing shallow coral habitats in the Gulf of Mexico (GOM), the availability of suitable reef habitat at mesophotic depths (~30–150 m) along the continental shelf margin suggests the potential for ecologically connected coral populations across hundreds of kilometers in the northwest (NW) GOM. The NW GOM includes a relatively high proportion of mesophotic habitats, including salt diapirs in Flower Garden Banks National Marine Sanctuary (FGBNMS), Bright Bank, and McGrail Bank,...

Data from: The impact of shifts in marine biodiversity hotspots on patterns of range evolution: evidence from the Holocentridae (squirrelfishes and soldierfishes)

Alex Dornburg, Jon Moore, Jeremy Michael Beaulieu, Ron I. Eytan & Thomas J. Near
One of the most striking biodiversity patterns is the uneven distribution of marine species richness, with species diversity in the Indo-Australian Archipelago (IAA) exceeding all other areas. However, the IAA formed fairly recently, and marine biodiversity hotspots have shifted across nearly half the globe since the Paleogene. Understanding how lineages have responded to shifting biodiversity hotspots represents a necessary historic perspective on the formation and maintenance of global marine biodiversity. Such evolutionary inferences are often...

Data from: Genetic profiling links changing sea-ice to shifting beluga whale migration patterns

Gregory O'Corry-Crowe, Andrew R. Mahoney, Robert Suydam, Lori Quakenbush, Alex Whiting, Lloyd Lowry, Lois Harwood & Greg O'Corry-Crowe
There is increasing concern over how Arctic fauna will adapt to climate related changes in sea-ice. We used long-term sighting and genetic data on beluga whales (Delphinapterus leucas) in conjunction with multi-decadal patterns of sea-ice in the Pacific Arctic to investigate the influence of sea-ice on spring migration and summer residency patterns. Substantial variations in sea-ice conditions were detected across seasons, years and sub-regions, revealing ice–ocean dynamics more complex than Arctic-wide trends suggest. This variation...

Data from: Time-integrated habitat availability is a resource attribute that informs patterns of use in intertidal areas

Leonardo Calle, Lauri Green, Allan Strong & Dale E. Gawlik
In dynamic environments, resource availability may change by several orders of magnitude, over hours to months, but the duration of resource availability is not often included as a characteristic attribute of resources even though temporal resource dynamics might limit patterns of use. In our study of wading birds foraging in intertidal areas, tides cause large changes in the areal extent of shallow-water foraging habitat (i.e., the resource), but tides also constrain the duration of availability,...

Data from: The extension of internal humidity levels beyond the soil surface facilitates mound expansion in Macrotermes

Daniel S. Calovi, Paul Bardunias, Nicole Carey, Rupert Soar, Scott Turner, Radhika Nagpal & Justin Werfel
Termites in the genus Macrotermes construct large-scale soil mounds above their nests. The classic explanation for how termites coordinate their labour to build the mound, based on a putative cement pheromone, has recently been called into question. Here we present evidence for an alternate interpretation based on sensing humidity. The high humidity characteristic of the mound internal environment extends a short distance into the low-humidity external world, in a “bubble” that can be disrupted by...

Developmental changes in bone mechanics from Florida manatees (Trichechus manatus latirostris), obligate swimming mammals

Danielle Ingle
Mammals living in aquatic environments load their axial skeletons differently than their terrestrial counterparts. The structure and mechanical behavior of trabecular bone can be especially indicative of varying habitual forces. Here, we investigate vertebral trabecular bone mechanical properties (yield strength, stiffness, and toughness) throughout development in Florida manatees (Trichechus manatus latirostris), obligate undulatory swimmers. Thoracic, lumbar, and caudal vertebrae were dissected from manatees (N=20) during necropsies. We extracted 6 mm3 samples from vertebral bodies and...

Complex relationship between tunneling patterns and individual behaviors in termites

Nobuaki Mizumoto, Paul Bardunias & Stephen Pratt
The nests built by social insects are complex group-level structures that emerge from interactions among individuals following simple behavioral rules. Nest patterns vary among species, and the theory of complex systems predicts that there is no simple one-to-one relationship between variations in collective patterns and variation in individual behaviors. Therefore, a species-by-species comparison of the actual building process is essential to understand the mechanism producing diverse nest patterns. Here we compare tunnel formation of three...

Data from: VolcanoFinder: genomic scans for adaptive introgression

Derek Setter, Sylvain Mousset, Xiaoheng Cheng, Rasmus Nielsen, Michael DeGiorgio & Joachim Hermisson
Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method---VolcanoFinder---to detect recent events of adaptive introgression using polymorphism data...

Juvenile Bachman's sparrow audio

Hans Gonzembach, Heather Wolverton & Rindy Anderson
Vocal learning is a focal point of avian research, and can vary greatly across taxa. Different species may adapt to alternative learning strategies based on the timing of their sensitive periods, size of their repertoires, and social structure of their populations. Studying song learning in a broad range of species is essential for understanding how different factors may affect song learning. The Bachman’s Sparrow is a songbird with a large repertoire of primary songs and...

Data from: Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes

Jeanne Zeh, Maya Zawlodzki, Melvin Bonilla, Eleanor Su-Keene, Michael Padua & David Zeh
Maternal inheritance of mitochondria creates a sex-specific selective sieve through which mitochondrial mutations harmful to males but not females accumulate and contribute to sexual differences in longevity and disease susceptibility. Because eggs and sperm are under disruptive selection, sperm are predicted to be particularly vulnerable to the genetic load generated by maternal inheritance, yet evidence for mitochondrial involvement in male fertility is limited and controversial. Here, we exploit the coexistence of two divergent mitochondrial haplogroups...

Comparative morphology of shark pectoral fins

Sarah Hoffmann, Thaddaeus Buser & Marianne Porter
Sharks vary greatly in morphology, physiology, and ecology. Differences in whole body shape, swimming style, and physiological parameters have previously been linked to varied habitat uses. Along with whole body morphology, shark pectoral fins are also previously described to vary in both shape and skeleton; however, there are limited comparative data on external and skeletal morphology. Further, fins were previously categorized into two discrete groups based on the amount of skeletal support present: (1) aplesodic,...

Data from: Evaluating temporal and spatial transferability of a tidal inundation model for foraging waterbirds

Marisa Martinez, Leonardo Calle, Stephanie Romanach & Dale Gawlik
For ecosystem models to be applicable outside their context of development, temporal and spatial transferability must be demonstrated. This presents a challenge for modeling intertidal ecosystems where spatiotemporal variation arises at multiple scales. Models specializing in tidal dynamics are generally inhibited from having wider ecological applications by coarse spatiotemporal resolution or high user competency. The Tidal Inundation Model of Shallow-water Availability (TiMSA) uniquely simulates tides to empirically derive a time-integrated measure of availability for a...

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