Re-Constructing Historical Adélie Penguin Abundance Estimates by Retrospectively Accounting for Detection Bias

Seabirds and other land-breeding marine predators are considered to be useful and practical indicators of the state of marine ecosystems because of their dependence on marine prey and the accessibility of their populations at breeding colonies. Historical counts of breeding populations of these higher-order marine predators are one of few data sources available for inferring past change in marine ecosystems. However, historical abundance estimates derived from these population counts may be subject to unrecognised bias and uncertainty because of variable attendance of birds at breeding colonies and variable timing of past population surveys. We retrospectively accounted for detection bias in historical abundance estimates of the colonial, land-breeding Adélie penguin through an analysis of 222 historical abundance estimates from 81 breeding sites in east Antarctica. The published abundance estimates were de-constructed to retrieve the raw count data and then re-constructed by applying contemporary adjustment factors obtained from remotely operating time-lapse cameras. The re-construction process incorporated spatial and temporal variation in phenology and attendance by using data from cameras deployed at multiple sites over multiple years and propagating this uncertainty through to the final revised abundance estimates. Our re-constructed abundance estimates were consistently higher and more uncertain than published estimates. The re-constructed estimates alter the conclusions reached for some sites in east Antarctica in recent assessments of long-term Adélie penguin population change. Our approach is applicable to abundance data for a wide range of colonial, land-breeding marine species including other penguin species, flying seabirds and marine mammals.     

Counts of coral reef fishes by an experienced observer are not biased by the number of target species

Fishes are commercially, recreationally and functionally important inhabitants of coral reefs. Accordingly, accurate assessments of fish abundance and diversity are necessary for effective reef management. While some reef fish monitoring programmes target all fishes, many survey a subset of common and visually obvious species. Changing to counts of all species, while desirable, risks new and unwelcome biases from altered observer swimming speeds and search patterns. Here we test whether substantially increasing the number of target species in an established fish monitoring programme biases counts of the original subset, so precluding ongoing comparisons with historical data. A subset of 141 fish species have been visually surveyed along 50 × 5 m transects over 27 years throughout Australia's Great Barrier Reef. We experimentally compared counts of the subset from standard subset-only surveys and from surveys of all species (excluding small site-attached fishes that are surveyed separately) at three diverse reefs. Subset species richness and abundance, in total and of major families, and assemblage structure did not differ due to survey method. The high-level experience of the one observer appeared to overcome new biases from counting more species and the extra 2 min/transect was not logistically excessive. Surveys of all fishes recorded almost 80% more species than subset-only surveys and >130% higher total abundance on average from >150% more genera that included abundant and functionally important taxa. Overall, fish counts by an experienced observer were not biased by the number of species surveyed and counts of all species markedly improved assessments of reef fish diversity and function.     

Elevational gradients in species abundance,assemblage structure and energy use of rainforest birds in the Australian Wet Tropics bioregion

Elevational patterns of species richness, local abundance and assemblage structure of rainforest birds of north‐eastern Australia were explored using data from extensive standardized surveys throughout the region. Eighty‐two species of birds were recorded with strong turnover in assemblage structure across the elevational gradient and high levels of regional endemism in the uplands. Both species richness and bird abundance exhibited a humped‐shaped pattern with elevation with the highest values being between 600 and 800 m elevation. While much of the variability in species richness could be explained by the species–area relationship, analyses of net primary productivity (NPP) and total daily energy consumption of the bird community (energy use) suggest that ecosystem energy flow or constraints may be a significant determinant of species richness. Species richness is positively correlated with local bird abundance which itself is closely related to total energy use of the bird community. We suggest the hypothesis that lower NPP limits bird abundance and energy use in the uplands (>500 m) and that low bird energy use and species richness in the lowlands is limited by a seasonal bottleneck in available primary productivity and/or a species pool previously truncated by an extinction filter imposed by the almost complete disappearance of rainforest in the lowlands during the glacial maxima. We suggest that some of the previously predicted impacts of global warming on biodiversity in the uplands may be partially ameliorated by increases in NPP because of increasing temperatures. However, these relationships are complex and require further data specifically in regard to direct estimates of primary productivity and detailed estimates of energy flow within the assemblage.     

A Comparison of Sampling Techniques for Quantifying Abundance of the Florida Apple Snail (Pomacea Paludosa Say)

Despite the long recognized importance of apple snails (Pomaceapaludosa Say) in Florida wetland food webs, surprisingly littleis known about their life history and ecology. The paucity ofinformation is due, in part, to the lack of a validated samplingtechnique. In this study, we compared the effectiveness of adip net, bar seine, and suction dredge in extracting apple snailsfrom 1-m² throw traps. We also evaluated the reliability ofegg cluster counts as an index of snail abundance. The bar seine was eliminated as a suitable extraction methodbased on poor performance in densely vegetated habitats. Thesuction dredge appeared slightly less sensitive than the dipnet to habitat differences with regards to both marked snailrecovery and higher yield of free-ranging (unmarked, not previouslyextracted) snails. Our results indicate that the probabilityof recovering snails from throw traps can be considerably lessthan 1.0, and that recovery probabilities vary among sites andhabitats. Therefore, without reliable estimates for the fraction ofanimals recovered, density estimates, especially comparisonsamong sites and habitats, are not reliable. We found no relationship between egg cluster counts and estimatesof snail density. The high degree of temporal and spatial variabilityin egg production precludes the use of egg clusters as a reliableindex of apple snail abundance. (Received 15 April 1998; accepted 30 June 1998)     

Using soundscape recordings to estimate bird species abundance, richness, and composition

ABSTRACT Point counts are the most frequently used technique for sampling bird populations and communities, but have well‐known limitations such as inter‐ and intraobserver errors and limited availability of expert field observers. The use of acoustic recordings to survey birds offers solutions to these limitations. We designed a Soundscape Recording System (SRS) that combines a four‐channel, discrete microphone system with a quadraphonic playback system for surveying bird communities. We compared the effectiveness of SRS and point counts for estimating species abundance, richness, and composition of riparian breeding birds in California by comparing data collected simultaneously using both methods. We used the temporal‐removal method to estimate individual bird detection probabilities and species abundances using the program MARK. Akaike's Information Criterion provided strong evidence that detection probabilities differed between the two survey methods and among the 10 most common species. The probability of detecting birds was higher when listening to SRS recordings in the laboratory than during the field survey. Additionally, SRS data demonstrated a better fit to the temporal‐removal model assumptions and yielded more reliable estimates of detection probability and abundance than point‐count data. Our results demonstrate how the perceptual constraints of observers can affect temporal detection patterns during point counts and thus influence abundance estimates derived from time‐of‐detection approaches. We used a closed‐population capture–recapture approach to calculate jackknife estimates of species richness and average species detection probabilities for SRS and point counts using the program CAPTURE. SRS and point counts had similar species richness and detection probabilities. However, the methods differed in the composition of species detected based on Jaccard's similarity index. Most individuals (83%) detected during point counts vocalized at least once during the survey period and were available for detection using a purely acoustic technique, such as SRS. SRS provides an effective method for surveying bird communities, particularly when most species are detected by sound. SRS can eliminate or minimize observer biases, produce permanent records of surveys, and resolve problems associated with the limited availability of expert field observers.     

Comparison of Methods for Estimating Bird Abundance and Trends From Historical Count Data

Abstract: The use of bird counts as indices has come under increasing scrutiny because assumptions concerning detection probabilities may not be met, but there also seems to be some resistance to use of model-based approaches to estimating abundance. We used data from the United States Forest Service, Southern Region bird monitoring program to compare several common approaches for estimating annual abundance or indices and population trends from point-count data. We compared indices of abundance estimated as annual means of counts and from a mixed-Poisson model to abundance estimates from a count-removal model with 3 time intervals and a distance model with 3 distance bands. We compared trend estimates calculated from an autoregressive, exponential model fit to annual abundance estimates from the above methods and also by estimating trend directly by treating year as a continuous covariate in the mixed-Poisson model. We produced estimates for 6 forest songbirds based on an average of 621 and 459 points in 2 physiographic areas from 1997 to 2004. There was strong evidence that detection probabilities varied among species and years. Nevertheless, there was good overall agreement across trend estimates from the 5 methods for 9 of 12 comparisons. In 3 of 12 comparisons, however, patterns in detection probabilities potentially confounded interpretation of uncorrected counts. Estimates of detection probabilities differed greatly between removal and distance models, likely because the methods estimated different components of detection probability and the data collection was not optimally designed for either method. Given that detection probabilities often vary among species, years, and observers investigators should address detection probability in their surveys, whether it be by estimation of probability of detection and abundance, estimation of effects of key covariates when modeling count as an index of abundance, or through design-based methods to standardize these effects.     

Improving multispecies rocky reef fish censuses by counting different groups of species using different procedures

Synopsis A number of factors can influence the accuracy and precision of underwater visual transect techniques. Among these are observer swimming speed and, during multispecies surveys, the effect of counting all fishes on estimates of particular species. This paper examines the effect of these factors on population estimates of inconspicuous fishes (defined as Type 1) in a temperate reef fish assemblage near Sydney, Australia. Counting Type 1 fishes with all others yielded significantly lower estimates of species richness and abundance than when counted alone. This suggests that multispecies surveys should be split into 2 or more counts, using a census procedure that is appropriate to the group of species cencused. Further, the effect of counting all other fishes on estimates of Type 1 fishes varied according to the relative abundance of the former: their effect was lowest when abundance of other fishes was lowest. There was a negative relationship between observer speed and estimated abundance for Type 1 fishes. Survey precision of Type 1 fishes was generally improved by surveying at slower observer speeds.     

Benthic invertebrates of Rutland Water

The colonisation of Rutland Water by benthic invertebrates has been monitored from 1976 when the reservoir was first filled. A modified Ekman grab was used to sample populations quantitatively while false substrates and dredge samples were used to obtain supplementary data. Hand net and hand-sorting were used to study the littoral zone.The dominant taxa in the reservoir are Asellus aquaticus, A. meridianus, Gammarus pulex, Crangonyx pseudogracilis, Helobdella stagnalis, Erpobdella octoculata, Polycelis tenuis, larval Chironomidae and Oligochaeta. Other species which appeared abundantly, such as Limnaea pereger and Planorbis albus, have now disappeared and it is suggested that the generally low levels of gastropods might account for the poor performance of species such as Dugesia lugubris and Glossiphonia complanata.Other aspects of abundance are discussed, as are the effects of maturation of the system.     

Aerial survey of waterbirds on wetlands as a measure of river and floodplain health

1. This study highlights the use of waterbird communities as potential measures of river and floodplain health at a landscape scale. 2. The abundance and diversity of a waterbird community (54 species) was measured over 15 trips with four aerial and three ground counts per trip on a 300-ha lake in arid Australia. 3. Aerial survey estimates of individual species were significantly less precise (SE/mean) than ground counts across two (11–100 and > 1000) out of four abundance classes of waterbirds: 0–10, 11–100, 101–1000 and > 1000. Standard error/mean as a percentage decreased with increasing abundance from about 60% for the lowest abundance class to 18% for the largest abundance class. 4. Aerial survey estimates were negatively biased for species in numbers of less than 10 and greater than 5000 but unbiased compared to ground counts for other abundance classes. Aerial surveys underestimated numbers of waterbirds by 50% when there were 40 000 waterbirds. Three ground counts found about seven more waterbird species than four aerial surveys. One ground count took about 150 times longer than two aerial surveys and cost 14 times more. 5. Regression models were derived, comparing aerial survey estimates to ground counts for 31 of 36 species for which there were sufficient data. Aerial survey estimates were unbiased for most of these species (67%), negatively biased for six species and positively biased for one species. Estimates were negatively biased in species that occurred in small numbers or that dived in response to the aircraft. 6. River system health encompasses the state of floodplain wetlands. Waterbirds on an entire wetland or floodplain may be estimated by aerial survey of waterbirds; this is a coarse but effective measure of waterbird abundance. Aerial survey is considerably less costly than ground survey and potentially provides a method for measuring river and floodplain health over long periods of time at the same scale as river management.     

Comparisons of abundance of coral-reef fish: Catch and effort surveys vs visual census

Abstract Catch per unit effort (CPUE) in fisheries science and visual counts in marine ecology are widely used to provide estimates of relative abundance. Concurrent use of these techniques therefore offers an opportunity for cross-validation. This study compares CPUE to underwater visual census (UVC) estimates of relative species abundance in a multispecies fishery: coral-reef fish in the Solomon Islands. Multivariate analyses showed large differences between CPUE and UVC estimates of abundance. The families Acanthuridae and Scandae tended to be the primary cause of differences between the techniques when the full assemblage offish was analysed. However, the relationship between CPUE and UVC did not improve when these families were excluded from the data set and the analyses repeated on families (Serranidae, Lutjamdae, Lethrinidae) caught by the predominant gear type, handlining. This result highlights the point that the choice and use of particular methods require careful consideration in conjunction with the nature of factors being investigated. Many problems of sampling are specific to particular methods and some investigations may benefit from a more pluralistic approach.     

On the use of Timed Species Counts to estimate avian abundance indices in species-rich communities

Timed Species Counts (TSCs) have been found to provide useful data for assessing the relative abundances of birds in conservation studies, particularly in species‐rich areas, such as many tropical habitats. An index is conventionally based upon the mean TSC from a number of counts. In this paper, we develop a new statistic, λ, which is based upon the assumption that the number of encounters with a species in unit time has a Poisson distribution. Using the same assumptions on detectability that underlie earlier analyses of TSC data, values of λ, unlike the simple mean TSC, are directly proportional to abundance. However, TSC data are affected by detectability, so that comparisons of relative abundance for the same species between similar sites have greater validity than those between different species. Explicit formulae for calculating an estimate of λ and its SE from sample data are described. Although λ can be estimated from either TSC data or the simple proportion of counts in which the species was encountered, for the commonest species a simulation study shows that only data in full TSC form provide accurate estimates. The difference becomes negligible for scarcer species. The use of λ in preference to mean TSC scores is recommended where it is important to compare values of relative abundance.     

Species richness and rarity of crane flies (Diptera, Tipuloidea) in a boreal mire

Species richness and abundance are central in biodiversity inventories and in measuring the structure of communities. Neglecting the assessment of sampling efficiency may lead to spurious estimates of species richness and conservation value. Our aim was to examine species richness, sampling effectiveness, species-abundance distribution (SAD) and rarity of a boreal, mire-dwelling crane fly (Diptera, Tipuloidea) assemblage in western Finland. 12 Malaise traps dispersed in 4 subplots and standardized sweep net samples were used to collect adult flies from the mire. A total of 23 species and 1,569 specimens were identified. In general all species richness estimators were highly correlated and indicated rather good sampling effort. Sample completeness, expressed as percentage of observed richness divided by estimated richness, was higher for mire-dwellers (mean 75 %) than for all species (mean 63 %). Crane fly assemblages of subplots and combined data fitted best with log-series SAD. Species spatial distribution was positively correlated with average abundance. In other words, the most abundant species occurred in the most of Malaise traps. Seven mire-dwelling species greatly outnumbered (94 % of the collected specimens) all other members in the assemblage, and only one observed species was rare by several definitions (local abundance, extent of occurrence in Finland and area of occupancy). Although the studied assemblage was characterized by commonness, five of the species have threatened status in Europe south of Finland. Separate species richness estimation of all species (vagrants and occasional species included) and focal species (here mire-dwellers) is supported if ecological information is available on the taxonomic group being studied.     

Species richness and structure of three Neotropical bat assemblages

We compared the assemblages of phyllostomid bats in three Neotropical rainforests with respect to species richness and assemblage structure and suggested a method to validate estimates of species richness for Neotropical bat assemblages based on mist-netting data. The fully inventoried bat assemblage at La Selva Biological Station (LS, 100 m elevation) in Costa Rica was used as a reference site to evaluate seven estimators of species richness. The Jackknife 2 method agreed best with the known bat species richness and thus was used to extrapolate species richness for an Amazonian bat assemblage (Tiputini Biodiversity Station; TBS, 200 m elevation) and an Andean premontane bat assemblage (Podocarpus National Park; BOM, 1000 m elevation) in Ecuador. Our results suggest that more than 100 bat species occur sympatrically at TBS and about 50 bat species coexist at BOM. TBS harbours one of the most species-rich bat assemblages known, including a highly diverse phyllostomid assemblage. Furthermore, we related assemblage structure to large-scale geographical patterns in floral diversity obtained from botanical literature. Assemblage structure of these three phyllostomid assemblages was influenced by differences in floral diversity at the three sites. At the Andean site, where understorey shrubs and epiphytes exhibit the highest diversity, the phyllostomid assemblage is mainly composed of understorey frugivores and nectarivorous species. By contrast, canopy frugivores are most abundant at the Amazonian site, coinciding with the high abundance of canopy fruiting trees. Assemblage patterns of other taxonomic groups also may reflect the geographical distribution patterns of floral elements in the Andean and Amazonian regions.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 617–629.     

Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in Sage Grouse Centrocercus urophasianus

The Sage Grouse Centrocercus urophasianus is a species of conservation concern throughout its range in western North America. Since the 1950s, the high count of males at leks has been used as an index for monitoring populations. However, the relationship between this lek-count index and population size is unclear, and its reliability for assessing population trends has been questioned. We used non-invasive genetic mark-recapture analysis of faecal and feather samples to estimate pre-breeding population size for the Parachute-Piceance-Roan, a small, geographically isolated population of Sage Grouse in western Colorado, during two consecutive winters from 2012 to 2014. We estimated total pre-breeding population size as 335 (95% confidence interval (CI): 287–382) in the first winter and 745 (95% CI: 627–864) in the second, an approximate doubling in abundance between years. Although we also observed a large increase in the spring lek-count index between those years, high male count data poorly represented mark-recapture estimates of male abundance in each year. Our data suggest that lek counts are useful for detecting the direction and magnitude of large changes in Sage Grouse abundance over time but they may not reliably reflect small changes in abundance that may be relevant to small populations of conservation concern.     

Intertidal estimates of sea urchin abundance reveal congruence in spatial structure for a guild of consumers

We hypothesized congruence in the spatial structure of abundance data sampled across multiple scales for an ecological guild of consumers that exploit similar nutritional and habitat resources. We tested this hypothesis on the spatial organization of abundance of an herbivorous guild of sea urchins. We also examined whether the amount of local along‐shore rocky habitat can explain the observed spatial patterns of abundance. Standardized estimates of abundance of four intertidal sea urchins—Diadema cf. savignyi, Echinometra mathaei, Parechinus angulosus, and Stomopneustes variolaris—were determined by six observers at 105 sites across 2,850 km of coast of South Africa. For each species and observer, wavelet analysis was used on abundance estimates, after controlling for potential biases, to examine their spatial structure. The relationship between local sea urchin abundance and the amount of upstream and downstream rocky habitat, as defined by the prevailing ocean current, was also investigated. All species exhibited robust structure at scales of 75–220 km, despite variability among observers. Less robust structure in the abundances of three species was detected at larger scales of 430–898 km. Abundance estimates of sympatric populations of two species (D. cf. savignyi and E. mathaei) were positively correlated with the amount of rocky habitat upstream of the site, suggesting that upstream populations act as larval sources across a wide range of scales. No relationship between abundance and habitat size was found for P. angulosus or S. variolaris. Within the range of scales examined, we found robust congruence in spatial structure in abundance at the lower, but not the larger, range of scales for all four species. The relationship between abundance and upstream habitat availability in two species suggests that larval supply from upstream populations was probably the mechanism linking habitat size and abundance.     

The Impact of the Species–Area Relationship on Estimates of Paleodiversity

Estimates of paleodiversity patterns through time have relied on datasets that lump taxonomic occurrences from geographic areas of varying size per interval of time. In essence, such estimates assume that the species–area effect, whereby more species are recorded from larger geographic areas, is negligible for fossil data. We tested this assumption by using the newly developed Miocene Mammal Mapping Project database of western North American fossil mammals and its associated analysis tools to empirically determine the geographic area that contributed to species diversity counts in successive temporal bins. The results indicate that a species–area effect markedly influences counts of fossil species, just as variable spatial sampling influences diversity counts on the modern landscape. Removing this bias suggests some traditionally recognized peaks in paleodiversity are just artifacts of the species–area effect while others stand out as meriting further attention. This discovery means that there is great potential for refining existing time-series estimates of paleodiversity, and for using species–area relationships to more reliably understand the magnitude and timing of such biotically important events as extinction, lineage diversification, and long-term trends in ecological structure.     

Rapid assessment in conservation research: a critique of avifaunal assessment techniques illustrated by Ecuadorian and Madagascan case study data

The urgency of conservation concerns in the tropics, linked with the limitations imposed on research efforts by the tropical environment has resulted in the development of methods for rapid assessment of biological communities. One such method, the MacKinnon list technique, has been increasingly applied in avifaunal surveys worldwide. Using paired tropical bird data sets from Ecuadorian cloud forest and Madagascan littoral forest, we compare the performance of the MacKinnon list with that of the more standard method of point counts in indicating when a site has been adequately surveyed, estimating the magnitude of species richness, quantifying relative species abundance, and providing an α‐index of diversity. In species‐rich Ecuadorian cloud forest, neither method produced data indicating adequate survey effort, despite extensive sampling, whereas in the relatively species‐poor Madagascan littoral forests, data collected by both methods indicated that the area had been sufficiently surveyed with comparable sampling effort. Species richness estimates generated from MacKinnon list data provided a more accurate estimate of the magnitude of the species richness for the Ecuadorian avifauna, whereas estimates for the Madagascan avifauna stabilised with relatively few samples using either method. Data collected by each method reflected different patterns of relative abundance among the five most abundant species, with MacKinnon list data showing a bias towards solitary and territorial species and against monospecific flocking species relative to the point count data. As a consequence of this bias, MacKinnon list data also fail to reflect accurately the structure of communities as quantified by an index of community evenness. Point counts, on the other hand, failed to capture the full species complement of the species‐rich Ecuadorian study area. As techniques for the rapid assessment of unsurveyed areas, both methods are subject to biases that limit their value, if used alone, in collecting data of scientific and management value. We propose a hybrid rapid assessment methodology that capitalises on the strengths of both techniques while compensating for their weaknesses.     

Temporal and spatial patterns in littoral-zone fish assemblages of a reservoir (Lake Texoma,Oklahoma-Texas,U.S.A.)

Synopsis We sampled the littoral-zone fish fauna of Lake Texoma reservoir by electrofishing from January through December 1986 to examine species abundance, species associations and assemblage structure. Although total fish abundance differed significantly across seasons, only one common species (Dorosoma cepedianum) exhibited significant seasonal movement into or out of the littoral zone. Overall littoral-zone assemblage structure (based on rank order of species abundance) was concordant across seasons and habitat types, (vegetation, wood, open). However, within individual seasons and habitat types, assemblage structure was likely influenced by temporal and spatial differences in habitat availability and physicochemical conditions. Associations characteristic of species in natural aquatic environments were not well developed among species in this partly artificial, evolutionarily short-lived reservoir assemblage. Conditions related to water-level fluctuation appeared to deter the formation of persistent species associations and assemblage structure, especially in vegetation and open littoral zone habitats of this multi-purpose reservoir.Senior author     

Ross Sea Mollusca from the Latitudinal Gradient Program: R/V Italica 2004 Rauschert dredge samples

Information regarding the molluscs in this dataset is based on the Rauschert dredge samples collected during the Latitudinal Gradient Program (LGP) on board the R/V “Italica” in the Ross Sea (Antarctica) in the austral summer 2004. A total of 18 epibenthic dredge deployments/samplings have been performed at four different locations at depths ranging from 84 to 515m by using a Rauschert dredge with a mesh size of 500μm. In total 8,359 specimens have been collected belonging to a total of 161 species. Considering this dataset in terms of occurrences, it corresponds to 505 discrete distributional records (incidence data). Of these, in order of abundance, 5,965 specimens were Gastropoda (accounting for 113 species), 1,323 were Bivalvia (accounting for 36 species), 949 were Aplacophora (accounting for 7 species), 74 specimens were Scaphopoda (3 species), 38 were Monoplacophora (1 species) and, finally, 10 specimens were Polyplacophora (1 species). This data set represents the first large-scale survey of benthic micro-molluscs for the area and provides important information about the distribution of several species, which have been seldom or never recorded before in the Ross Sea. All vouchers are permanently stored at the Italian National Antarctic Museum (MNA), Section of Genoa, enabling future comparison and crosschecking. This material is also currently under study, from a molecular point of view, by the barcoding project “BAMBi” (PNRA 2010/A1.10).