Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Correcting spatial bias in wildlife citizen-surveys: Integrating manatee sighting reports with GPS tag data

<p>Poster created and presented in 2012</p> <p><strong>Abstract</strong></p> <p>Species occurrence data collected by citizen volunteers or mined from historical records can supplement species distribution studies by adding dimensions of spatial and temporal survey coverage that may not be cost-effective or even possible for researchers to obtain otherwise. In the absence of rigorous survey or quality assurance methods, most citizen-collected or historic occurrence data may be biased in space to favor human population centers: species in areas of high human activity may be oversampled, while species in relatively unpopulated areas may not be adequately accounted for. We gathered citizen-reported occurrence data for the West Indian manatee (Trichechus manatus) in coastal Alabama (AL), USA from 2007 to 2012. We found significant differences in spatial distribution between citizen-reported sightings and reference locations derived from GPS tag data from six manatees in the study area. To correct for potential spatial biases in the citizen-reported dataset, we weighted each sighting report using a) population density of closest US Census block (2010), and b) aquatic distance to closest boat ramp. After correcting for spatial bias, the spatial distribution of citizen-reported sightings was closer to reference GPS locations. These results provided a foundation to enhance our knowledge of manatee distribution in AL by supplementing GPS tag data with unbiased sighting report data not explicitly detected by GPS tags, such as manatee group size and behavior. These results demonstrate that species occurrence data collected under different methodologies may be corrected and integrated to form a more robust depiction of location and movement patterns for the species being surveyed.</p

Confirmation of significant sea turtle nesting activity on a remote island chain in the Gulf of Mexico

Abstract Globally, six of the seven sea turtle species are threatened or endangered and as such, monitoring reproductive activity for these species is necessary for effective population recovery. Remote beaches provide a challenge to conducting these surveys, which often results in data gaps that can hamper management planning. Throughout the summer of 2022, aerial surveys were conducted over the Chandeleur Islands in the Gulf of Mexico. Turtle crawls were photographed for subsequent review by 10 expert observers. Whenever possible, ground surveys were conducted, and samples of unhatched eggs or dead hatchlings were collected. A summary of historic reports of sea turtle nesting activity at this site was also compiled. On 11 days between May 4, 2022, and July 30, 2022, photographs of 55 potential sea turtle crawls were taken. Observers identified 54 of those as being made by a sea turtle. There was high‐to‐moderate certainty that 16 of those crawls were nests, that 14 were made by loggerheads, and that two were made by Kemp's ridleys. Observers were least certain of species identification when surveys were conducted during rainy weather. Genetic analyses based on mitochondrial and nuclear DNA were conducted on samples from five nests and those analyses confirmed that three nests were laid by Kemp's ridleys and two were laid by loggerheads. Historic records from the Chandeleur Islands substantiate claims that the Chandeleurs have supported sea turtle nesting activity for decades; however, the consistency of this activity remains unknown. Our aerial surveys, particularly when coupled with imaging, were a useful tool for documenting nesting activity on these remote islands. Future monitoring programs at this site could benefit from a standardized aerial survey program with a seaplane so trends in nesting activity could be determined particularly as the beach undergoes restoration

Exposure of Marine Turtle Nesting Grounds to Named Storms Along the Continental USA

Named storms can cause substantial impacts on the habitat and reproductive output of threatened species, such as marine turtles. To determine the impacts of named storms on marine turtles and inform management, it is necessary to determine the exposure of marine turtle nesting grounds to recent storm activities. To address this, remote sensing information of named storm tracks coupled with nesting ground data were used to investigate the temporal and spatial overlap between nesting grounds for four species of marine turtles in the continental United States of America. All species of marine turtles were exposed to named storms, with variation in exposure driven by the spatial distribution of each population&rsquo;s nesting ground, the temporal overlap between the storms and reproductive events, and nest placement on the beach. Loggerhead turtles were the most exposed species to named storms, with the northern management unit having significantly higher exposure levels than all other loggerhead management units. Kemp&rsquo;s ridley turtles, in contrast, were found to be the least exposed species to named storms. This study establishes a valuable current baseline against which to measure and compare future impacts that result as climate change progresses and storms become more frequent and intense. Importantly, cumulative and synergetic effects from other climatic processes and anthropogenic stressors should be considered in future analysis