Testing methods to estimate abundance of Magellanic Penguins Spheniscus magellanicus

Capsule Using simulations in a geographical information system our results showed that systematic sampling with quadrats was the most accurate, precise and cost-effective method to survey Magellanic Penguin colonies.

Aims To determine which sampling method gives better estimations of penguin abundance.

Methods A virtual colony was generated deriving spatial parameters from a real survey and applying Kriging interpolation. Three sampling methods were then applied on this virtual colony: random sampling with quadrats; systematic sampling with quadrats; systematic sampling with fixed-width transects. The estimated abundance for each trial was compared to the abundance of the virtual colony to have a measure of accuracy and precision.

Results Systematic sampling with quadrats estimated penguin abundance better than random or systematic sampling with transects since it achieved 100% accuracy and great precision after sampling only 2.1% of the virtual colony.

Conclusion The use of a simulated colony allowed the comparison of several sampling methods traditionally used in Magellanic Penguin surveys. The results of this study are important in order to standardize sampling protocols for Magellanic Penguins and to have more comparable estimations to detect trends over time. Also, the methodological approach used here could be used to assess sampling methods for other colonial bird species.     

Improving the accuracy of population size estimates for burrow‐nesting seabirds

Seabird numbers can change rapidly as a result of environmental processes, both natural and anthropogenic. Informed management and conservation of seabirds requires accurate and precise monitoring of population size. However, for burrow‐nesting species this is rarely achieved due to spatial and temporal heterogeneity in burrow occupancy. Here, we describe a novel method for deriving more accurate population size estimates that employs mark‐recapture methods to correct for unknown variation in nest occupancy throughout a breeding season. We apply it to estimate breeding numbers of a colonial, burrowing seabird, the Little Penguin Eudyptula minor, on the Summerland Peninsula, Phillip Island, Australia. Estimates of active burrow numbers during the September 2008 to February 2009 breeding season were adjusted to numbers of breeding birds based on burrow occupation and modelled population demographics at six, fortnightly monitored reference sites. The population was estimated to be 26 100 (95% CI: 21 100–31 100) and 28 400 (23 800–33 000) breeding Penguins in two temporally separated surveys within one breeding season. We demonstrate using simulation that the method is robust to variation in burrow occupancy throughout the breeding season, providing consistent and more accurate estimates of population size. The advantage of using the corrected method is that confidence intervals will include the true population size. Confidence limits widened as burrow occupancy declined, reflecting the increased uncertainty as larger adjustments for low burrow occupancy were required. In contrast, the uncorrected method that uses burrow occupancy alone as a measure of breeding numbers was inconsistent and significantly underestimated population size across much of the breeding season. Although requiring considerably more survey effort, the corrected approach provides a more accurate means for monitoring population changes in colonially breeding animals while collecting demographic data that can help diagnose the drivers of population change.     

Simulations inform design of regional occupancy‐based monitoring for a sparsely distributed,territorial species

Sparsely distributed species attract conservation concern, but insufficient information on population trends challenges conservation and funding prioritization. Occupancy‐based monitoring is attractive for these species, but appropriate sampling design and inference depend on particulars of the study system. We employed spatially explicit simulations to identify minimum levels of sampling effort for a regional occupancy monitoring study design, using white‐headed woodpeckers (Picoides albolvartus), a sparsely distributed, territorial species threatened by habitat decline and degradation, as a case study. We compared the original design with commonly proposed alternatives with varying targets of inference (i.e., species range, space use, or abundance) and spatial extent of sampling. Sampling effort needed to achieve adequate power to observe a long‐term population trend (≥80% chance to observe a 2% yearly decline over 20 years) with the previously used study design consisted of annually monitoring ≥120 transects using a single‐survey approach or ≥90 transects surveyed twice per year using a repeat‐survey approach. Designs that shifted inference toward finer‐resolution trends in abundance and extended the spatial extent of sampling by shortening transects, employing a single‐survey approach to monitoring, and incorporating a panel design (33% of units surveyed per year) improved power and reduced error in estimating abundance trends. In contrast, efforts to monitor coarse‐scale trends in species range or space use with repeat surveys provided extremely limited statistical power. Synthesis and applications. Sampling resolutions that approximate home range size, spatially extensive sampling, and designs that target inference of abundance trends rather than range dynamics are probably best suited and most feasible for broad‐scale occupancy‐based monitoring of sparsely distributed territorial animal species.     

The depth of Sooty Shearwater Ardenna grisea burrows varies with habitat and increases with competition for space

The Sooty Shearwater Ardenna grisea, an abundant but declining petrel, is one of many seabird species that construct breeding burrows, presumably because these confer protection from predators and the elements. Little is known about the causes of variation in Sooty Shearwater burrow architecture, which can differ markedly both within and between breeding sites. We hypothesize that burrow architecture varies in response to habitat type and competition for space. To address these hypotheses, we recorded Sooty Shearwater burrow dimensions on Kidney Island, the largest Sooty Shearwater colony in the Falkland Islands, South Atlantic, and modelled these as functions of burrow density (a proxy for competition) and habitat indices. Our models suggest that Sooty Shearwaters burrow further underground in response to competition for breeding space, and that soil underlying dense tussac grass Poa flabellata is more easily excavated than other substrates, indicating how vegetation restoration could aid the conservation of this species.     

Characterizing termite assemblages in fragmented forests: A test case in the Argentinian Chaco

Abstract Termites are major decomposers in tropical ecosystems. To characterize their assemblages in terms of taxonomical and functional composition, Jones and Eggleton (2000, Journal of Applied Ecology 37, 191–203) recently proposed a standardized sampling protocol based on belt transects of 100 m × 2 m. We evaluated the representativeness of samples obtained by this protocol, and its suitability to calculate diversity statistics, by replicating it in an area of naturally fragmented subtropical forest. We sampled six 100 m transects in separate small forest islets, and one transect extended to 500 m in a large islet, recording presence/absence data (occurrences) of termite species in successive quadrats of 5 m × 2 m. In the large islet, strips of 100 m within the 500 m transect produced extremely variable species richness figures. This variability was primarily due to heterogeneity in the spatial distribution of soil‐dwelling termites. Combining non‐contiguous quadrats allowed us to span a broader diversity of microhabitats for an equal effort, providing less variable results and faster species accumulation. Individual transects of 100 m in small forest islets yielded too few samples to allow reliable estimations of total species richness, although these transects when pooled constituted a useful data set for comparison with other sites. In the focal habitat, a single 100 m transect appeared therefore inadequate to allow a reliable characterization of the termite assemblage, even at the level of a single forest islet. To improve the rate of species accumulation and to obtain diversity statistics allowing intersite comparisons, we suggest the use of smaller, non‐contiguous quadrats, and that sampling be continued until stable diversity estimates are obtained. In the habitat studied, such an alternative protocol could be adequately combined with a standardized protocol for collecting ground‐dwelling ants.     

Six years of submerged plant community dynamics in a freshwater tidal wetland

1. The dynamics of a submerged plant community were studied for 6 years in a freshwater tidal wetland. The degree and nature of change at several spatial scales (quadrat, transect and overall community) was determined, and the implications for community stability were assessed. 2. A high degree of change was recorded in 1 m² quadrats, and this was reflected in 10 m² transects as well. In quadrats, mean species richness changed every year. Species richness changed in >60% of quadrats each year. Stem number changed by as many as several 100 stems per quadrat from one year to the next. 3. Richness varied more among quadrats than among transects and varied less at the community level than among either quadrats or transects. Greater stability at the spatial scale of the whole community was reflected in high scores on the Jaccard and Morasita–Horn indices and Kendall's coefficient of concordance. 4. Although most of the submerged species were perennials, persistence at the local scale was low, and 4‐year persistence exceeded 50% for only one species. Change in abundance was largely independent among the species. 5. In the face of great small‐scale changes, species remain in the community (and the community persists) because of high recruitment rates.     

Sex identification in King Penguins Aptenodytes patagonicus through morphological and acoustic cues

In the context of sexual selection, animals have developed a variety of cues conveying information about the sex of an individual to conspecifics. In many colonial seabird species, where females and males are monomorphic and do not show obvious differences in external morphology, acoustic cues are an important signal for individual and sex recognition. Here, we study the vocal and morphological sex dimorphism in the King Penguin Aptenodytes patagonicus, a colonial, monomorphic seabird for which our knowledge about the role of vocalizations and morphology in mate choice is very limited. Data were collected at Possession Island, Crozet Archipelago, in a breeding colony consisting of about 16 000 breeding pairs. Using measurements of six morphological features and analysing acoustic parameters of call recordings of adult individuals, we show that King Penguins can be sexed based on a single morphological measurement of the beak with an accuracy of 79%. We found a sex‐specific syntax in adult King Penguin calls that provided a 100% accurate method to distinguish between the sexes in our study population. To confirm the method at the species level, we analysed calls recorded from King Penguin adults in Kerguelen Island, 1300 km away from our study population and found the same accuracy of the sex‐specific syntax. This sex‐specific syllable arrangement is rare in non‐passerines and is a first step in understanding the mate choice process in this species. Furthermore, it offers a cost‐effective, non‐invasive technique for researchers to sex King Penguins in the field.     

Estimating abundance of introduced Chinese muntjac Muntiacus reevesi and native roe deer Capreolus capreolus using portable thermal imaging equipment

• 1 Managing the conservation impacts of deer requires knowledge of their numbers. However, estimating densities in forested areas is problematic, with pellet‐group‐based methods subject to error and uncertainty in estimating defecation and decay rates in addition to sampling variance. Use of thermal imaging equipment allows direct census by distance sampling.
• 2 Densities of introduced Chinese muntjac Muntiacus reevesi and native roe deer Capreolus capreolus were estimated in 12.8 km² of conifer forest in eastern England by thermal imaging distance transects. Estimated density of introduced muntjac (±95% confidence intervals [CI]: 20 ± 8 km⁻²) exceeded that of native roe deer (16 ± 6 km⁻²); 95% CI of c. 40% were achieved in 10 days of fieldwork.
• 3 Density estimates were not sensitive to the number of width bands applied during analysis. Detectability functions differed, with narrower effective strip widths (ESW) for muntjac (74 m) than roe deer (123 m). Thus, it is important to discriminate between species when censusing mixed assemblages. Detectability and ESW also differed among plantation growth stages. Stratification by habitat may therefore improve accuracy of density estimates but would require additional survey effort.

     

Optimising sampling methods for small mammal communities in Neotropical rainforests

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Total Counts Versus Line Transects for Estimating Abundance of Small Gopher Tortoise Populations

Abstract: Status and trends of gopher tortoise (Gopherus polyphemus) populations are a critical information need for natural resource managers, researchers, and policy makers. Many tortoise populations are small and isolated, which can present challenges for deriving population estimates. Our objective was to compare abundance and density estimates for a small tortoise population derived using a total burrow count versus estimates obtained with line transect distance sampling (LTDS) using repeated surveys. We also compared results of the 2 survey methods using standard burrow-to-tortoise correction factors versus assessing occupancy of all burrows with a camera scope. In addition, we compared LTDS data obtained using a compass and measuring tape to define transects to those obtained using a Global Positioning System (GPS) and Personal Data Assistant (PDA) field computer to navigate transects. Line transect distance sampling with repeated surveys (both with a measuring tape and compass and with a GPS—PDA) yielded sufficient observations of tortoises to calculate population estimates. From 18% to 31% of burrows were occupied by tortoises as determined with the burrow camera. We found 25 burrows during the LTDS survey that we did not find in the total count survey, which demonstrated that the assumption of 100% detection for the total count was not met; hence, density or abundance measurements derived with this method were underestimates. We recommend using GPS—PDA technology, scoping all burrows detected, and using LTDS with repeated surveys to estimate abundance and density for small gopher tortoise populations.     

Corvids congregate to breeding colonies of a burrow‐nesting seabird

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Climate oscillation and the invasion of alien species influence the oceanic distribution of seabirds

Spatial and temporal distribution of seabird transiting and foraging at sea is an important consideration for marine conservation planning. Using at‐sea observations of seabirds (n = 317), collected during the breeding season from 2012 to 2016, we built boosted regression tree (BRT) models to identify relationships between numerically dominant seabird species (red‐footed booby, brown noddy, white tern, and wedge‐tailed shearwater), geomorphology, oceanographic variability, and climate oscillation in the Chagos Archipelago. We documented positive relationships between red‐footed booby and wedge‐tailed shearwater abundance with the strength in the Indian Ocean Dipole, as represented by the Dipole Mode Index (6.7% and 23.7% contribution, respectively). The abundance of red‐footed boobies, brown noddies, and white terns declined abruptly with greater distance to island (17.6%, 34.1%, and 41.1% contribution, respectively). We further quantified the effects of proximity to rat‐free and rat‐invaded islands on seabird distribution at sea and identified breaking point distribution thresholds. We detected areas of increased abundance at sea and habitat use‐age under a scenario where rats are eradicated from invaded nearby islands and recolonized by seabirds. Following rat eradication, abundance at sea of red‐footed booby, brown noddy, and white terns increased by 14%, 17%, and 3%, respectively, with no important increase detected for shearwaters. Our results have implication for seabird conservation and island restoration. Climate oscillations may cause shifts in seabird distribution, possibly through changes in regional productivity and prey distribution. Invasive species eradications and subsequent island recolonization can lead to greater access for seabirds to areas at sea, due to increased foraging or transiting through, potentially leading to distribution gains and increased competition. Our approach predicting distribution after successful eradications enables anticipatory threat mitigation in these areas, minimizing competition between colonies and thereby maximizing the risk of success and the conservation impact of eradication programs.     

On the importance of estimating detection probabilities from at‐sea surveys of flying seabirds

The primary and accepted method used to estimate seabird densities at sea from ships is the strip transect method, designed to correct for the effect of random directional bird movement relative to that of the ship. However, this method relies on the critical assumption that all of the birds within the survey strip are detected. We used the distance sampling method from line‐transects to estimate detection probability of a number of species of flying seabirds, and to test whether distance from the ship and bird body size affected detectability. Detection probability decreased from 0.987 (SE=0.029) to 0.269 (SE=0.035) with increasing strip half‐width from 100 to 1400 m. Detection probability also varied between size‐groups of species with strip half‐width. For all size‐groups, this probability was close to 1 for strip half‐width of 100 m, but was 0.869 (SE=0.115), 0.725 (SE=0.096) and 0.693 (SE=0.091) for strip half‐width of 300 m, a typical strip width used in seabird surveys, for respectively large, medium and small size flying seabirds. For larger strip half‐width, detection probability was higher for large sized species, intermediate for medium sized species and lower for smaller sized species. For strip half‐width larger than 100 m we suggest that more attention should be paid to testing the assumption of perfect detectability, because abundance estimates may be underestimated when this assumption is violated. Finally, the effect of the speed of travel of flying seabird on the detection probability was estimated in a simulation study, which suggests that detection probability was underestimated with increasing flying speed.     

Estimating the abundance of burrow‐nesting species through the statistical analysis of combined playback and visual surveys

The conservation of elusive species relies on our ability to obtain unbiased estimates of their abundance trends. Many species live or breed in cavities, making it easy to define the search units (the cavity) yet hard to ascertain their occupancy. One such example is that of certain colonial seabirds like petrels and shearwaters, which occupy burrows to breed. In order to increase the chances of detection for these types of species, their sampling can be done using two independent methods to check for cavity occupancy: visual inspection, and acoustic response to a playback call. This double‐detection process allows us to estimate the probability of burrow occupancy by accounting for the probability of detection associated with each method. Here we provide a statistical framework to estimate the occupancy and population size of burrow‐dwelling species. We show how to implement the method using both maximum likelihood and Bayesian approaches, and test its precision and bias using simulated datasets. We subsequently illustrate how to extend the method to situations where two different species may occupy the burrows, and apply it to a dataset on wedge‐tailed shearwaters Puffinus pacificus and tropical shearwaters P. bailloni on Aride Island, Seychelles. The simulations showed that the single‐species model performed well in terms of error and bias except when detection probabilities and occupancies were very low. The two‐species model applied to shearwaters showed that detection probabilities were highly heterogeneous. The population sizes of wedge‐tailed and tropical shearwaters were estimated at 13 716 (95% CI: 12 909–15 874) and 25 550 (23 667–28 777) pairs respectively. The advantages of formulating the call‐playback sampling method statistically is that it provides a framework to calculate uncertainty in the estimates and model assumptions. This method is applicable to a variety of cavity‐dwelling species where two methods can be used to detect cavity occupancy.     

Investigator disturbance reduces reproductive success in Short‐tailed Shearwaters Puffinus tenuirostris

Research procedures can have a detrimental effect on the reproductive success of the study species. In this study, the frequency of investigator disturbance on Short‐tailed Shearwaters Puffinus tenuirostris was examined experimentally throughout the incubation period to assess whether disturbance influences hatching success, pre‐fledging chick survival and chick body size. Handling of incubating birds every day, every 3 days and once a week reduced hatching success by 100, 61 and 39%, respectively, compared with pairs that were not disturbed. Most failures resulted from egg abandonment by the parents, particularly during the early stage of incubation. Chick survival did not differ between treatment groups, but control chicks were significantly heavier and had larger bill depths and longer wings. The difference in chick body mass and size observed between the control and disturbed chicks might be due to physiological or behavioural mechanisms in adults or carry‐over effects from the incubation stage to the next life‐history stage. Reduced offspring quality has the potential to affect post‐fledging survival and recruitment. These findings are significant in broader terms because any investigator disturbance that reduces reproductive success, survival and offspring fitness could interfere with the accurate assessment of demographic parameters and exacerbate population declines.     

Species-specific population trends detected for penguins,gulls and cormorants over 20 years in sub-Antarctic Fuegian Archipelago

Understanding the dynamics and causes of population trends are essential for seabird conservation. Long-term studies of seabirds at high-latitude (Antarctic, sub-Antarctic and Arctic) regions have shown contrasting species-specific trends in population size in response to climate change and anthropogenic pressures. We have studied for the last 20 years (1992–2012) the population trends of seven seabird species that breed in the Beagle Channel, south-eastern Tierra del Fuego and at Staten Island, a sub-Antarctic region in southern Argentina. The numbers of Magellanic and Gentoo Penguins increased significantly since 1992 (by >15 % year^?1). In comparison, the populations of Imperial Cormorants, Dolphin Gulls and Kelp Gulls increased at slower rates (<5 % year^?1), while the Rock Cormorant population even decreased by 1.3 % year^?1. At Staten Island, the numbers of Rockhopper Penguins decreased by 24 % between the censuses of 1998 and 2010, whereas the population of Magellanic Penguins increased by 227 % during the same period. Over the study period, air and sea-surface temperatures remained stable in our study area, suggesting that the detected population changes are not driven by the climate. This finding contrasts with the detected links between increasing temperature trends and seabird population changes reported from Antarctic and Arctic regions. The level of tourism and size of the permanent human population has increased in the Beagle Channel area during the last 20 years and could be responsible for the increase of gull populations. The seabird species that received the highest number of visitors (Imperial Cormorants and penguin species) seem to be adapted or at least indifferent to pressures exerted by tourism, as their populations increased during the study period. In addition, increasing numbers of seabirds in the area may generally be leading to higher abundances of scavenging species (e.g. gulls).     

Chick‐provisioning behaviour of two shearwaters breeding in south‐eastern Australia

The chick‐provisioning behaviour of the short‐tailed shearwater Puffinus tenuirostris and the wedge‐tailed shearwater Puffinus pacificus was investigated in a mixed colony on Montague Island, New South Wales, Australia, over two breeding seasons. This colony is located at opposite edges of the breeding distribution of the two species. Frequent weighing techniques were used to determine chick feeding frequency, feed timing, meal size, chick weight loss and indices of food conversion efficiency of the chicks. Short‐tailed shearwater parents fed their chicks larger more infrequent meals than wedge‐tailed shearwater parents. Short‐tailed shearwater chicks demonstrated higher food conversion efficiencies and lower weight loss than wedge‐tailed shearwater chicks, indicating either differences in diet or metabolic rates. The feeding frequency in wedge‐tailed shearwaters also fluctuated more widely than for short‐tailed shearwaters over the two breeding seasons. Despite the fact that the timing of the breeding cycle on Montague Island is almost identical for the two species, these differences in chick provisioning are probably a result of differences in prey type and location, so they may help explain variations in annual breeding success and limits to the distribution of the two species.     

Low frequency of extra-pair paternity in two colonies of the socially monogamous short-tailed shearwater Puffinus tenuirostris

The short-tailed shearwater is a colonially nesting, socially monogamous seabird. Little is known about mate fidelity and breeding behaviour in this species because breeding birds are nocturnal on land and spend much of their time within subterranean nesting burrows. Colonial breeding and extended sperm storage create opportunities for extra-pair copulations which may form a significant component of the mating strategy in this species. Multilocus DNA fingerprinting was used to examine the genetic relationship between nestlings and the male and female nest attendants in 83 burrows from two distinct breeding colonies. Genetic analyses identified nine nestlings, approximately equally distributed between the two colonies, that were not related to the attendant pair male in those burrows, implying extra-pair paternity through extra-pair copulations. These results are used retrospectively to discuss the characteristics of extra-pair copulations and extra-pair fertilizations and the implications for estimates of life-time reproductive success in the short-tailed shearwater.     

The ‘standardized search’: An improved way to conduct bird surveys

Abstract Bird surveys are among the most widely used biodiversity inventories and serve as the basis for an increasing proportion of pure and applied ecological research. It is rarely possible to conduct exhaustive censuses of all individuals present at a particular site, so stopping rules are routinely used to determine when sampling should finish. Most bird survey methods use (implicit) effort‐based stopping rules, either fixed times, fixed sampling areas (quadrats) or both, to standardize samples of different sites. If between‐site variation is high, however, a fixed sampling effort will generate samples of variable completeness with samples from smaller, less complex sites being more representative and complete than samples from larger, more complex sites. More importantly, quadrat‐based methods shift the scope of the overall study from bird occurrence in sites to bird occurrence in quadrats within sites, diminishing the impact of the research given that results cannot be extrapolated to relevant biological and management scales. Here I advocate an alternative means of conducting bird surveys, whereby the entire site is sampled and a results‐based stopping rule is used to ensure sample completeness is uniform across all sites. For example, a researcher may decide to continue sampling each site until two or fewer previously unencountered species are recorded in a 40‐min period. Samples of different sites will vary in both area and duration but will all be equivalently accurate estimates of species richness. This approach allows the avifauna of entire sites (whether territories, woodland remnants or catchments) to be sampled and compared directly, generating results and implications at the appropriate scale. In addition to yielding reliable measures of species richness, data collected this way can be used to calculate estimates of sample completeness and species incidence, two valuable metrics for ecological studies. This paper includes detailed worked examples of how to conduct a ‘standardized search’ and calculate sample completeness and species incidence estimates. I encourage further research on bird survey methods, and suggest that most current methods are insufficient, inconsistent and unreliable.