Fishery-Independent Data Reveal Negative Effect of Human Population Density on Caribbean Predatory Fish Communities

BACKGROUND: Understanding the current status of predatory fish communities, and the effects fishing has on them, is vitally important information for management. However, data are often insufficient at region-wide scales to assess the effects of extraction in coral reef ecosystems of developing nations. METHODOLOGY/PRINCIPAL FINDINGS: Here, I overcome this difficulty by using a publicly accessible, fisheries-independent database to provide a broad scale, comprehensive analysis of human impacts on predatory reef fish communities across the greater Caribbean region. Specifically, this study analyzed presence and diversity of predatory reef fishes over a gradient of human population density. Across the region, as human population density increases, presence of large-bodied fishes declines, and fish communities become dominated by a few smaller-bodied species. CONCLUSIONS/SIGNIFICANCE: Complete disappearance of several large-bodied fishes indicates ecological and local extinctions have occurred in some densely populated areas. These findings fill a fundamentally important gap in our knowledge of the ecosystem effects of artisanal fisheries in developing nations, and provide support for multiple approaches to data collection where they are commonly unavailable

Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects

Estimates from genome-wide association studies (GWAS) of unrelated individuals capture effects of inherited variation (direct effects), demography (population stratification, assortative mating) and relatives (indirect genetic effects). Family-based GWAS designs can control for demographic and indirect genetic effects, but large-scale family datasets have been lacking. We combined data from 178,086 siblings from 19 cohorts to generate population (between-family) and within-sibship (within-family) GWAS estimates for 25 phenotypes. Within-sibship GWAS estimates were smaller than population estimates for height, educational attainment, age at first birth, number of children, cognitive ability, depressive symptoms and smoking. Some differences were observed in downstream SNP heritability, genetic correlations and Mendelian randomization analyses. For example, the within-sibship genetic correlation between educational attainment and body mass index attenuated towards zero. In contrast, analyses of most molecular phenotypes (for example, low-density lipoprotein-cholesterol) were generally consistent. We also found within-sibship evidence of polygenic adaptation on taller height. Here, we illustrate the importance of family-based GWAS data for phenotypes influenced by demographic and indirect genetic effects

Shared genetic risk between eating disorder- and substance-use-related phenotypes:Evidence from genome-wide association studies

First published: 16 February 202

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

A New Compact Rotating Video System for Rapid Survey of Reef Fish Populations

A new, compact, inexpensive, remote submersible rotating video system (SRV) is described in detail for use in fish and habitat surveys. The SRV was designed to remotely simulate the widely used Bohnsack-Bannerot fish-survey method. The positive attributes of SRV include: (1) elimination of potential diver effects on fish behavior; (2) efficiency (multiple simultaneous deployments); (3) less ship time; (4) cost effectiveness; (5) depth limits far exceed scuba; (6) non-destructive to habitat; (7) non-extractive; (8) useful in situations dangerous for divers; (9) provides a permanent high-resolution record of the survey and habitat condition; and (10) fish behaviors unlikely to be observed by divers may be recorded with SRV. However, the SRV may underrepresent small cryptic species and laboratory time would be necessary to evaluate the videos

Faunal Communities and Habitat Characteristics of the Big Bend Seagrass Meadows, 2009–2010.

Seagrass meadows are important habitats that serve as nursery, feeding, and sheltering grounds for many marine species. In addition to the ecosystem functions and services they provide, seagrass habitats and associated fauna are commonly observed to have naturally high levels of heterogeneity, making them ideal for the study of ecological patterns and processes across multiple spatial scales. However, seagrass systems worldwide have undergone sharp declines in coverage and increased levels of fragmentation at both local and regional spatial scales, thus compromising their ecological functions and services and reducing their value as unaltered marine systems in which to conduct ecological studies. Covering nearly 3000 km2, the seagrass meadows of the Big Bend region in the eastern Gulf of Mexico represents one of the largest in the world, and given its separation from human population centers and coastal development, is also considered to be one of the most intact and least disturbed. The objective of our study was to provide the first region-wide characterization of the habitats and faunal communities in seagrass meadows of the Big Bend. This two-year study occurred in 2009 and 2010 during the summers when peak productivity in seagrass systems is highest. Sites were selected using a spatially balanced approach and sampling was conducted with beam trawls. A total of 170 sites were sampled, and all animals were identified to lowest taxonomic level possible, counted, and their sizes measured. Habitat characteristics were concurrently measured at both local (e.g., seagrass areal coverage and composition, volume of drift algae) and regional scales (e.g., latitude, type of adjacent coastal habitat)

Non-lethal Approach Identifies Variability of δ\u3csup\u3e15\u3c/sup\u3eN Values in the Fin Rays of Atlantic Goliath Grouper, \u3cem\u3eEpinephelus itajara\u3c/em\u3e

The Atlantic Goliath Grouper, Epinephelus itajara, is critically endangered throughout its range but has begun to show initial signs of recovery in Florida state waters. As the population continues to rebound, researchers face a pressing need to fill the knowledge gaps about this iconic species. Here, we examined the δ15N isotopic records in fin rays collected from Atlantic Goliath Grouper, and related changes of isotopic ratios over time to life history characteristics. Fin-ray analysis was used as a non-lethal technique to sample individuals from two locations at similar latitudes from the west and east coasts of Florida, USA. δ15N data were acquired by mechanically separating the annuli of each fin ray and then analyzing the material in an Irradiance Elemental Analyzer Mass Spectrometer. The δ15N values were consistent among individuals within populations from each coast of Florida, and mirrored the expected changes over the lives of the fish. Overall, differences were found between δ15N values at juvenile life history phases versus adult phases, but the patterns associated with these differences were unique to each coastal group. We demonstrated, for the first time, that δ15N values from fin rays can be used to assess the life histories of Atlantic Goliath Grouper. The non-lethal strategies outlined here can be used to acquire information essential to the management of species of concern, such as those that are threatened or endangered

Non-lethal approach identifies variability of δ15N values in the fin rays of Atlantic Goliath Grouper, Epinephelus itajara

The Atlantic Goliath Grouper, Epinephelus itajara, is critically endangered throughout its range but has begun to show initial signs of recovery in Florida state waters. As the population continues to rebound, researchers face a pressing need to fill the knowledge gaps about this iconic species. Here, we examined the δ15N isotopic records in fin rays collected from Atlantic Goliath Grouper, and related changes of isotopic ratios over time to life history characteristics. Fin-ray analysis was used as a non-lethal technique to sample individuals from two locations at similar latitudes from the west and east coasts of Florida, USA. δ15N data were acquired by mechanically separating the annuli of each fin ray and then analyzing the material in an Irradiance Elemental Analyzer Mass Spectrometer. The δ15N values were consistent among individuals within populations from each coast of Florida, and mirrored the expected changes over the lives of the fish. Overall, differences were found between δ15N values at juvenile life history phases versus adult phases, but the patterns associated with these differences were unique to each coastal group. We demonstrated, for the first time, that δ15N values from fin rays can be used to assess the life histories of Atlantic Goliath Grouper. The non-lethal strategies outlined here can be used to acquire information essential to the management of species of concern, such as those that are threatened or endangered

The Effects of Spatial Scale on Assigning Nursery Habitats in Atlantic Goliath Groupers (\u3cem\u3eEpinephelus Itajara\u3c/em\u3e) Using Non-lethal Analyses of Fin Rays

We evaluated Atlantic Goliath Groupers, Epinephelus itajara, in their nursery habitats via microchemical analyses of fin rays. Juveniles were sampled from known nursery habitats off southwest Florida, and adults were primarily sampled from a spawning aggregation off southeast, Florida. We collected fin rays using a non-lethal technique that is minimally invasive with no known negative effects on growth or survival. Trace metal constituents in the fin rays were quantified with an inductively coupled plasma mass spectrometer via laser ablation (LA-ICP-MS). Two spatial scales were quantified to test the limitations of grouping individuals based on elemental compositions. On a small spatial scale (i.e., 100s of m), individuals were correctly classified within individual watersheds 64% of the time. On a larger spatial scale (i.e., 10s–100s of km), juveniles were classified with 100% accuracy. Trace metals in adults were analyzed by back-tracking across fin ray annuli to a year in which our previous studies have shown these adults occupied their juvenile habitats (i.e., 2006). These fish were grouped using a measure of dissimilarity and then analyzed to test whether we could reclassify them into these same groupings based solely on the chemical components in their fin rays, which was done with over 84% accuracy. Although juvenile habitats of the adults could not be determined due to the lack of baseline data, classifications were driven by similar elements to those that drove the classification of juveniles, suggesting similar physiological mechanisms. The results highlight the importance of spatial scale for interpreting microchemical analyses on calcified structures in fishes

Environmental Gradients Shape the Combined Effects of Multiple Parasites on Oyster Hosts in the Northern Gulf of Mexico

Parasites can shape population, community, and ecosystem dynamics, especially if their hosts play a key role in the ecosystem. Multiple parasites frequently co-infect hosts that alter disease dynamics via a variety of mechanisms. Further, abiotic and biotic factors often differentially affect hosts and their associated parasites, with direct and/or indirect effects on disease prevalence and intensity. We conducted a field survey of eastern oyster Crassostrea virginica populations in the northern Gulf of Mexico to examine spatial patterns in parasite species richness of this foundation species. We assessed whether environmental factors and/or host characteristics best predicted prevalence and intensity of the most common micro- (Perkinsus marinus; Dermo) and macro-parasites (boring sponges Cliona spp., mud blister worms Polydora websteri) in the region. The number of parasite species infecting each host (i.e. species richness) was spatially homogeneous due to variation in the predominant factors underlying the prevalence and intensity of each species. These factors were host density, tidal elevation, and temperature for Dermo; tidal elevation and host size for boring sponges; and salinity for mud blister worms. Host condition depended on abiotic and biotic factors, including tidal elevation (intertidal \u3e subtidal) and prevalence of both Dermo (positive relationship) and boring sponges (negative relationship). Abiotic influences on oysters and parasites, and multiple parasite effects, produced an unexpected positive correlation between host condition and Dermo prevalence. Thus, predicting the likelihood of disease outbreaks and assessing the long-term health of host populations requires consideration of the combined effects of multiple parasites, abiotic conditions, and biotic factors