Estimates Of Relative Abundance Research Articles

Accurate genome relative abundance estimation for closely related species in a metagenomic sample.

BackgroundMetagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree.ResultsWe developed a new homology-based approach called Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods designed for estimating taxonomic composition at a relatively low taxonomic rank, TAEC demonstrates greater accuracy in quantification of genomes in a given microbial sample. We also applied TAEC on two real metagenomic datasets, oral cavity dataset and Crohn’s disease dataset. Our results, while agreeing with previous findings at higher ranks of the taxonomy tree, provide accurate estimation of taxonomic compositions at the species/strain level, narrowing down which species/strains need more attention in the study of oral cavity and the Crohn’s disease.ConclusionsBy taking account of the similarity in the genomic sequence TAEC outperforms other available tools in estimating taxonomic composition at a very low rank, especially when closely related species/strains exist in a metagenomic sample.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-242) contains supplementary material, which is available to authorized users.

Calibration of pelagic stereo‐BRUVs and scientific longline surveys for sampling sharks

SummaryOur understanding of the ecology of sharks and other highly mobile marine species often relies on fishery‐dependent data or extractive fishery‐independent techniques that can result in catchability and size‐selectivity biases. Pelagic Baited Remote Underwater stereo‐Video Systems (pelagic stereo‐BRUVs) provide a standardized, non‐destructive and fishery‐independent approach to estimate biodiversity measures of fish assemblages in the water column. However, the performance of this novel method has not yet been assessed relative to other standard sampling techniques.We compared the catch composition, relative abundance and length distribution of fish assemblages sampled using pelagic stereo‐BRUVs and conventional scientific longline surveys. In particular, we focused on sharks of the family Carcharhinidae (requiem sharks) to assess the sampling effectiveness of this novel technique along a latitudinal gradient off the coast of Western Australia. We calibrated the sampling effort required for each technique to obtain equivalent samples of the target species and discuss the advantages, limitations and potential use of these methods to study highly mobile species.The proportion of sharks sampled by pelagic stereo‐BRUVs and scientific longline surveys was comparable across the latitudinal gradient.Carcharhinus plumbeuswas the most abundant species sampled by both the techniques. Longline surveys selected larger individuals of the family Carcharhinidae in comparison with the length distribution data obtained from pelagic stereo‐BRUVs. However, the relative abundance estimates (catch per unit of effort) from the pelagic stereo‐BRUVs were comparable to those from 5 to 30 longline hooks.Pelagic stereo‐BRUVs can be calibrated to standard techniques in order to study the species composition, behaviour, relative abundance and size distribution of highly mobile fish assemblages at broad spatial and temporal scales. This technique offers a non‐destructive fishery‐independent approach that can be implemented in areas that may be closed to fishing and is suitable for studies on rare or threatened species.

Chasing fish and catching data: recreational spearfishing videos as a tool for assessing the structure of fish assemblages on shallow rocky reefs

Several citizen science initiatives, taking advantage of growing numbers of re - creational SCUBA divers, have produced information for conserving marine biodiversity. In contrast, the potential benefits of involving recreational spearfishers in research activities has been utterly overlooked. A noteworthy aspect of modern breath-holding spearfishing is the use of full HD microcameras for recording the fishing action. When using the sit and wait fishing tech- nique, the spearfisher remains still on the bottom, waiting for the prey to approach. These videos may provide information on fish species richness and relative abundances. We explored the potential of recreational spearfishing footage for assessing the structure of fish assemblages on shallow rocky reefs. We assessed how estimates of fish species richness, composition and relative abundance from spearfishing videos compare to those from underwater visual censuses (UVC), at 2 sites in the NW Mediterranean. Species accumulation curves show that the 2 sampling methods provided comparable estimates of species richness for any sample size. Although the structure of fish assemblages differed between UVC and videos, the relative abundance of only a few species, mostly characterized by a sedentary habit, was greater in UVC than videos. In addition, in order to show the potential use of information from spearfishing videos, we modelled the occupancy of a species (the wrasse Symphodus rostratus) at increasing distances from a commercial port, explicitly incorporating imperfect detectability as a function of video length and habitat character- istics. While the occupancy of this species did not vary with distance from the port, its detectability depended on video length. Our study suggests that videos recorded by re creational spearfishers may be useful for monitoring fish assemblages and for testing hypotheses at large spatial and tem- poral scales.

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

BackgroundCulture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between species.ResultsBased on 2,900 sequenced reference genomes, we show that 16S rRNA gene copy number (GCN) is strongly linked to microbial phylogenetic taxonomy, potentially under-representing Archaea in amplicon microbial profiles. Using this relationship, we inferred the GCN of all bacterial and archaeal lineages in the Greengenes database within a phylogenetic framework. We created CopyRighter, new software which uses these estimates to correct 16S rRNA amplicon microbial profiles and associated quantitative (q)PCR total abundance. CopyRighter parses microbial profiles and, because GCN estimates are pre-computed for all taxa in the reference taxonomy, rapidly corrects GCN bias. Software validation with in silico and in vitro mock communities indicated that GCN correction results in more accurate estimates of microbial relative abundance and improves the agreement between metagenomic and amplicon profiles. Analyses of human-associated and anaerobic digester microbiomes illustrate that correction makes tangible changes to estimates of qPCR total abundance, α and β diversity, and can significantly change biological interpretation. For example, human gut microbiomes from twins were reclassified into three rather than two enterotypes after GCN correction.ConclusionsThe CopyRighter bioinformatic tools permits rapid correction of GCN in microbial surveys, resulting in improved estimates of microbial abundance, α and β diversity.

Quantitative video analysis of flatfish herding behavior and impact on effective area swept of a survey trawl

Uncertainty in fish behavior can introduce bias into density calculations from fishery-independent bottom trawl surveys that provide relative abundance estimates and population trends for stock assessments. In situ video was used to quantify flatfish behavioral responses to a bottom trawl sweep to improve the understanding of survey and assessment results. The behavior of 632 flatfishes was recorded during four tows. More than 90% of fish were observed in a perpendicular orientation away from the sweeps indicating a herding response. There was no significant effect of fish length on fish orientation or whether it reacted or remained stationary during the observation. Only 1.3% of fish were observed escaping the sweeps. A generalized linear model was used to estimate that at a distance of 73.8cm (±3.4 SE) 50% of observed fish reacted to the sweep. The mean distance that stationary fish were first observed reacting to the sweep was 36.6cm (±2.0 SE). Quantitative analysis indicates that flatfish herding occurs along trawl sweeps and the effective area swept is greater than the wing spread. Thus, the use of wing spread to calculate relative abundance estimates explains bias in stock assessment estimates of survey catchability that are greater than expected.

Relative abundance estimations of chengal tree in a tropical rainforest by using modified Canopy Fractional Cover (mCFC)

Tree species composition estimations are important to sustain forest management. This study challenged estimates of relative abundance of useful timber tree species (chengal) using Hyperion EO-1 satellite data. For the estimation, modified Canopy Fractional Cover (mCFC) was developed using Canopy Fractional Cover (CFC). mCFC was more sensitive to estimate relative abundance of chengal trees rather than Mixture Tuned Matched Filtering (MTMF). Meanwhile, MTMF was more sensitive to estimate the relative abundance of undisturbed forest. Accuracy suggests that the mCFC model is better to explain relative abundance of chengal trees than MTMF. Therefore, it can be concluded that relative abundance of trees species extracted from Hyperion EO-1 satellite data using modified Canopy Fractional Cover is an obtrusive approach used for identifying trees species composition.

Monitoring abundance and phenology in (multivoltine) butterfly species: a novel mixture model

Summary Data from ‘citizen science’ surveys are increasingly valuable in identifying declines in widespread species, but require special attention in the case of invertebrates, with considerable variation in number, seasonal flight patterns and, potentially, voltinism. There is a need for reliable and more informative methods of inference in such cases. We focus on data consisting of sample counts of individuals that are not uniquely identifiable, collected at one or more sites. Arrival or emergence and departure or death of individuals take place during the study. We introduce a new modelling approach, which borrows ideas from the ‘stopover’ capture–recapture literature, that permits the estimation of parameters of interest, such as mean arrival times and relative abundance, or in some cases, absolute abundance, and the comparison of these between sites. The model is evaluated using an extensive simulation study which demonstrates that the estimates for the parameters of interest obtained by the model are reliable, even when the data sets are sparse, as is often the case in reality. When applied to data for the common blue butterfly Polyommatus icarus at a large number of sites, the results suggest that mean emergence times, as well as the relative sizes of the broods, are linked to site northing, and confirm field experience that the species is bivoltine in the south of the UK but practically univoltine in the north. Synthesis and applications. Our proposed ‘stopover’ model is parameterized with biologically informative constituents: times of emergence, survival rate and relative brood sizes. Estimates of absolute or relative abundance that can be obtained alongside these underlying variables are robust to the presence of missing observations and can be compared in a statistically rigorous framework. These estimates are direct indices of abundance, rather than ‘sightings’, implicitly adjusted for the possible presence of repeat sightings during a season. At the same time, they provide indices of change in demographic and phenological parameters that may be of use in identifying the factors underlying population change. The model is widely applicable and this will increase the utility of already valuable and influential long‐standing surveys in monitoring the effects of environmental change on phenology or abundance.

Engineering and catch implications of variable wing-end spread on a penaeid trawl

The importance of wing-end spread on the performance of a generic penaeid trawl was assessed to investigate the potential for confounding effects when comparing modified anterior sections designed to improve selectivity and fuel efficiencies. Two identical beam-and-sled assemblies were configured to allow two identical trawls (7.35m headlines and footropes) to be adjusted to spread ratios (defined as wing-end spread÷headline length) of 0.5, 0.6, 0.7 and 0.8 and deployed (n=30 each) in a double rig across the same depth, current, towing speed and duration. Increasing spread ratio significantly increased drag (by up to 16%), without affecting absolute catch weights. However, when standardised to per ha trawled, significantly fewer targeted school prawns (Metapenaeus macleayi) and total bycatch by weight were retained in the wider-spread trawls. The significant reductions in standardised catch with increasing spread ratio were hypothesised to reflect either: (i) slightly reduced ground gear contact and headline heights offsetting the greater swept areas; or perhaps more likely (ii) steeper wing angles which increased the probability of mesh encounters and escape for school prawns and were less efficient for herding fish. Future research comparing modified trawl bodies should focus on maintaining similar spread ratios to minimise confounding effects. Similar logic applies to surveys using penaeid trawls to obtain relative abundance estimates.

A hierarchical model combining distance sampling and time removal to estimate detection probability during avian point counts

Imperfect detection during animal surveys biases estimates of abundance and can lead to improper conclusions regarding distribution and population trends. Farnsworth et al. (2005) developed a combined distance-sampling and time-removal model for point-transect surveys that addresses both availability (the probability that an animal is available for detection; e.g., that a bird sings) and perceptibility (the probability that an observer detects an animal, given that it is available for detection). We developed a hierarchical extension of the combined model that provides an integrated analysis framework for a collection of survey points at which both distance from the observer and time of initial detection are recorded. Implemented in a Bayesian framework, this extension facilitates evaluating covariates on abundance and detection probability, incorporating excess zero counts (i.e. zero-inflation), accounting for spatial autocorrelation, and estimating population density. Species-specific characteristics, such as behavioral displays and territorial dispersion, may lead to different patterns of availability and perceptibility, which may, in turn, influence the performance of such hierarchical models. Therefore, we first test our proposed model using simulated data under different scenarios of availability and perceptibility. We then illustrate its performance with empirical point-transect data for a songbird that consistently produces loud, frequent, primarily auditory signals, the Golden-crowned Sparrow (Zonotrichia atricapilla); and for 2 ptarmigan species (Lagopus spp.) that produce more intermittent, subtle, and primarily visual cues. Data were collected by multiple observers along point transects across a broad landscape in southwest Alaska, so we evaluated point-level covariates on perceptibility (observer and habitat), availability (date within season and time of day), and abundance (habitat, elevation, and slope), and included a nested point-within-transect and park-level effect. Our results suggest that this model can provide insight into the detection process during avian surveys and reduce bias in estimates of relative abundance but is best applied to surveys of species with greater availability (e.g., breeding songbirds).

Effects of low-level culling of feral cats in open populations: a case study from the forests of southern Tasmania

Context Feral cats (Felis catus) threaten biodiversity in many parts of the world, including Australia. Low-level culling is often used to reduce their impact, but in open cat populations the effectiveness of culling is uncertain. This is partly because options for assessing this management action have been restricted to estimating cat activity rather than abundance. Aims We measured the response, including relative abundance, of feral cats to a 13-month pulse of low-level culling in two open sites in southern Tasmania. Methods To do this we used remote cameras and our analysis included identification of individual feral cats. We compared estimates of relative abundance obtained via capture–mark–recapture and minimum numbers known to be alive, and estimates of activity obtained using probability of detection and general index methods, pre- and post-culling. We also compared trends in cat activity and abundance over the same time period at two further sites where culling was not conducted. Key results Contrary to expectation, the relative abundance and activity of feral cats increased in the cull-sites, even though the numbers of cats captured per unit effort during the culling period declined. Increases in minimum numbers of cats known to be alive ranged from 75% to 211% during the culling period, compared with pre- and post-cull estimates, and probably occurred due to influxes of new individuals after dominant resident cats were removed. Conclusions Our results showed that low-level ad hoc culling of feral cats can have unwanted and unexpected outcomes, and confirmed the importance of monitoring if such management actions are implemented. Implications If culling is used to reduce cat impacts in open populations, it should be as part of a multi-faceted approach and may need to be strategic, systematic and ongoing if it is to be effective.

The Relative Abundance of the Juvenile Phase of the Eastern Red-Spotted Newt at Harvard Forest Prior to the Arrival of the Hemlock Woolly Adelgid

The invasive insect pest Adelges tsugae (Hemlock Woolly Adelgid) threatens the ecologically unique Tsuga canadensis (Eastern Hemlock)-dominated forest type throughout its range. Relatively little is known about how the loss of this forest type will affect the relative abundance of amphibians. This study assessed the relative abundance of the juvenile phase of Notophthalmus viridescens viridescens (Eastern Red-spotted Newt, Red Eft) in Eastern Hemlock-dominated stands (n = 5) and mixed deciduous stands (n = 5) at Harvard Forest in Petersham, MA, using both transect surveys of the forest floor surface (n = 368 Red Eft observations over four seasons), and intensive searches of quadrats (n = 27 Red Eft observations over two seasons). Using data from transect surveys, the average relative abundance of Red Efts was more than two times greater in Eastern Hemlock-dominated stands than in mixed deciduous stands, however the differences were not statistically significant (P = 0.146). Quadrat surveys yielded relative abundance estimates for Red Efts that were more than 5 times greater in Eastern Hemlock-dominated stands than in mixed deciduous stands, but again the differences were not statistically significant (P = 0.213).

Predictions from harbor porpoise habitat association models are confirmed by long-term passive acoustic monitoring

Survey based habitat association models provide good spatial coverage, but only a snapshot in time of a species' occurrence in a particular area. A habitat association model for harbor porpoises was created using data from five visual surveys of the Moray Firth, Scotland. Its predictions were tested over broader temporal scales using data from static passive acoustic loggers, deployed in two consecutive years. Predictions of relative abundance (individuals per kilometer of survey transect) were obtained for each 4 km × 4 km grid cell, and compared with the median number of hours per day that porpoises were acoustically detected in those cells. There was a significant, but weak, correlation between predicted relative abundance and acoustic estimates of occurrence, but this was stronger when predictions with high standard errors were omitted. When grid cells were grouped into those with low, medium, and high predicted relative abundance, there were similarly significant differences in acoustic detections, indicating that porpoises were acoustically detected more often in cells where the habitat model predicted higher numbers. The integration of acoustic and visual data added value to the interpretation of results from each, allowing validation of patterns in relative abundance recorded during snapshot visual surveys over longer time scales.

Distribución, abundancia y hábitos alimentarios de la nutria (Lontra longicaudis annectens Major, 1897) en el Río Grande, Reserva de la Biosfera Tehuacán-Cuicatlán Oaxaca, México

We report information on the distribution, abundance and food habits of the Neotropical river otter Lontra longicaudis annectens, based on 386 collected scats (281 in the dry season, and 105 in the rainy season). The distribution along a 39.5 km transect was similar in both rainy and dry seasons. The estimates of relative abundance using two models varied according to rates: Gallo-Reynoso (0.508 scats/ km), and Eberhardt-Van Etten, modified for this study (0.016 scats/ km). We obtained a record of L. longicaudis with a collecting effort of 18 nights / camera confirming the presence of the species. Food habits analyzing 161 scats revealed presence of seven species of fish (89.62%) of the families Cichlidae, Heptapteridae and Poeciliidae, four reptiles (4.32%) of the families Corythophanidae, Iguanidae and Phrynosomatidae, an unidentified bird (1.77 %), insects of the family Megaloptera (4.13%), and unidentifiable organic matter (0.17%). We recommend continuing studying the natural history of this species for conservation purposes. Key words: Abundance, distribution, feeding habits, Lontra longicaudis annectens, Neotropical otter, Oaxaca.

Biases for detecting arbuscular mycorrhizal fungal mixture by terminal restriction fragment length polymorphism (T-RFLP)

Terminal restriction fragment length polymorphism (T-RFLP) analysis of amplified ribosomal RNA genes is used for profiling microbial communities and sometimes for species richness and relative abundance estimation in environmental samples. However, the T-RFLP fingerprint may be subject to biases during the procedure, influencing the detection of real community structures in the environment. To investigate possible sources of T-RFLP bias, 18S rRNA gene clones derived from two arbuscular mycorrhizal fungal sequences were combined in simple pairwise mixes to assess the effects of polymerase chain reaction cycle number, plant genomic DNA purification method and varying template ratio on the template-to-product ratio as measured by relative T-RF peak area. Varying cycle numbers indicated that amplification was still in the exponential phase at the cycle numbers lower than 18, so these small cycle numbers were used for the comparison of template-to-product quantities. Relative abundance estimated from T-RF peak ratios varied with different purification procedures, but the best results, closest to input ratios, were obtained by using phenol-chloroform purification. The presence of an excess of unpurified non-target plant genomic DNA generated a bias towards lower or overestimation of relative abundance. We conclude that a low number of amplification cycles and stringent DNA purification are necessary for accurate mixed sample analysis by T-RFLP.

Novel, Universal Approach for the Measurement of Natural products in a Variety of Botanicals and Supplements

Botanicals contain a great diversity of compounds that exhibit wide variation in their physicochemical properties. Although no single analytical method is available to measure all potentially active components, HPLC with charged aerosol detection is a nearly universal approach that nonselectively measures any nonvolatile and many semivolatile compounds; that is, charged aerosol detection does not require that analytes be ionizable (as required for MS) or contain a chromophore (as required for UV). Furthermore, all non-volatile analytes produce similar response independent of chemical structure, enabling estimation of relative abundance when external standards are lacking.

Effects of Forest Treatments on Abundance and Spatial Characteristics of Cerulean Warbler Territories

We examined effects of forest treatments on Cerulean Warbler relative abundance and spatial attributes of territories between pretreatment (2007–2008) and post treatment (2009–2010) years in Yellowwood and Morgan-Monroe state forests in southern Indiana. Three management units received uneven aged harvests (patch cuts), three units received even aged harvests (shelterwood and clearcut), and three units received no treatment (control). Cerulean Warblers occurred in greater abundance at study sites that received even aged harvests than in uneven aged harvested stands based on point - count surveys. Cerulean Warblers were attracted to areas with large canopy gaps resulting from even-aged harvests. Territory sizes were not significantly smaller after harvest treatments. Cerulean Warbler territories on harvested and control sites were clustered, closer to roads and streams, and on steeper slopes with an eastern aspect compared to random sites. Our relative abundance estimates suggested that Cerulean Warblers responded positively to some types of forest treatments during the 2 y post harvest period.

Influence of Survey Design on Fish Assemblages: Implications from a Study in Chesapeake Bay Tributaries

AbstractAquatic resource surveys that span multiple decades provide valuable information about fish population responses to environmental and human‐induced changes. Often, surveys are altered as scientific objectives change or in response to management needs. These modifications usually result in inconsistencies in the time series, which must be addressed for proper analysis of fish community data. Since 1997, juvenile fishes in Virginia tributaries of Chesapeake Bay have been captured monthly using a bottom trawl at both fixed and random sites. Previous surveys in these tributaries (1955–1996) were conducted at fixed sites only; thus, an understanding of the effect of this design change would allow us to infer fish community status through multiple decades. We compared samples from the fixed site design with those from the stratified random design in the James, York, and Rappahannock rivers and examined species composition, biodiversity, relative abundance estimates, and size distributions to understand the effects of survey design on these metrics. Catches from random sites were characterized by consistently higher species richness than those from fixed sites; biodiversity metrics varied by sampling site type (fixed versus random) and river. For most select species, we observed similar trends in relative abundance regardless of site type; however, for some species we noted differences in magnitude among years and between sampling site types. Community metrics, such as taxonomic diversity and distinctness, revealed subtle differences about fish species assemblages compared with traditional diversity metrics demonstrating that community metrics can characterize biodiversity of fishes at higher taxonomic levels. Thus, species‐specific and community metrics derived from assemblage data from fixed‐site surveys may not fully represent the magnitude of change in demersal fish assemblages, but can provide reliable indicators of patterns of change in abundance through time.

Distribution, Abundance and Roosts of the Fruit BatArtibeus fraterculus(Chiroptera: Phyllostomidae)

Where does a species live? How common is it? Where does it spend its inactive periods? These are basic questions about the biology of a species, which bring key information for application in conservation and management. Unfortunately, this information is available for only a minimum fraction of all animal species. Using 1) ecological niche modeling with maximum entropy (Maxent), 2) relative abundance estimates using museum records, and 3) field surveys of roosting sites, we report the fraternal fruit-eating bat, Artibeus fraterculus, as having a distribution limited to the Tumbesian ecoregion in Ecuador and west central Peru, being the relatively most abundant bat species throughout its range, with healthy populations which are primarily sustained by cultivated and introduced plants, and using human-made constructions as roost sites. Additionally, we described a large congregation of individuals of this species in a single roost, representing the largest colony reported for the genus Artibeus. These results may indicate resilience of A. fraterculus to human disturbance.

Characterization of the microbial acid mine drainage microbial community using culturing and direct sequencing techniques

We characterized the bacterial community from an AMD tailings pond using both classical culturing and modern direct sequencing techniques and compared the two methods. Acid mine drainage (AMD) is produced by the environmental and microbial oxidation of minerals dissolved from mining waste. Surprisingly, we know little about the microbial communities associated with AMD, despite the fundamental ecological roles of these organisms and large-scale economic impact of these waste sites. AMD microbial communities have classically been characterized by laboratory culturing-based techniques and more recently by direct sequencing of marker gene sequences, primarily the 16S rRNA gene. In our comparison of the techniques, we find that their results are complementary, overall indicating very similar community structure with similar dominant species, but with each method identifying some species that were missed by the other. We were able to culture the majority of species that our direct sequencing results indicated were present, primarily species within the Acidithiobacillus and Acidiphilium genera, although estimates of relative species abundance were only obtained from direct sequencing. Interestingly, our culture-based methods recovered four species that had been overlooked from our sequencing results because of the rarity of the marker gene sequences, likely members of the rare biosphere. Further, direct sequencing indicated that a single genus, completely missed in our culture-based study, Legionella, was a dominant member of the microbial community. Our results suggest that while either method does a reasonable job of identifying the dominant members of the AMD microbial community, together the methods combine to give a more complete picture of the true diversity of this environment.

Modeling the spatial distribution of commercially important reef fishes on the West Florida Shelf

Understanding the spatial distribution of a species is an important precondition to successfully managing marine populations. For reef fishes, this is of particular importance due to the patchy nature of reef communities. This study estimated the spatial distribution of five reef fish species on the West Florida Shelf: gag grouper (Mycteroperca microlepis), mutton snapper (Lutjanus analis), red grouper (Epinephelus morio), red snapper (Lutjanus campechanus), and vermilion snapper (Rhomboplites aurorubens). Estimation was done by combining large-scale fishery-dependent catch per unit of fishing effort with small scale fishery-independent video survey observation. Catch per unit of fishing effort was obtained from vessel logbook data while video observations of reef fish presence–absence and relative abundance were made by stratified random sampling on known reef and hard-bottom habitat in the Gulf of Mexico. Relative abundance estimates showed different abundance patterns for the five species depending on depth and geographical area. Variogram modeling suggested that gag grouper, mutton snapper, and red grouper were spatially autocorrelated on reef or hard-bottom habitats at short ranges of between 0.87 and 0.95km, while red and vermilion snapper were found to be randomly distributed. Range estimates for gag grouper, mutton snapper and red grouper were supported by variograms of depth soundings in the Gulf which produced range estimates of between 1.56 and 6.34km. Combining the relative estimates of abundance from catch per unit of effort with the spatial autocorrelation parameters from video surveys allowed us to provide stochastic fish abundance estimates at scales of about 2km2.