Massey Research Online - Browsing by Author "Smith ANH"

Browsing by Author "Smith ANH"

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A quantitative comparison of towed-camera and diver-camera transects for monitoring coral reefs
(PeerJ Inc., 2021) Cresswell AK; Ryan NM; Heyward AJ; Smith ANH; Colquhoun J; Case M; Birt MJ; Chinkin M; Wyatt M; Radford B; Costello P; Gilmour JP; Toonen R
Novel tools and methods for monitoring marine environments can improve efficiency but must not compromise long-term data records. Quantitative comparisons between new and existing methods are therefore required to assess their compatibility for monitoring. Monitoring of shallow water coral reefs is typically conducted using diver-based collection of benthic images along transects. Diverless systems for obtaining underwater images (e.g. towed-cameras, remotely operated vehicles, autonomous underwater vehicles) are increasingly used for mapping coral reefs. Of these imaging platforms, towed-cameras offer a practical, low cost and efficient method for surveys but their utility for repeated measures in monitoring studies has not been tested. We quantitatively compare a towed-camera approach to repeated surveys of shallow water coral reef benthic assemblages on fixed transects, relative to benchmark data from diver photo-transects. Differences in the percent cover detected by the two methods was partly explained by differences in the morphology of benthic groups. The reef habitat and physical descriptors of the site-slope, depth and structural complexity-also influenced the comparability of data, with differences between the tow-camera and the diver data increasing with structural complexity and slope. Differences between the methods decreased when a greater number of images were collected per tow-camera transect. We attribute lower image quality (variable perspective, exposure and focal distance) and lower spatial accuracy and precision of the towed-camera transects as the key reasons for differences in the data from the two methods and suggest changes to the sampling design to improve the application of tow-cameras to monitoring.
Benthic species patterns in and around the Cape Canyon: A large submarine canyon off the western passive margin of South Africa
(Frontiers Media S.A., 2022-11-18) Filander Z; Smith ANH; Cawthra HC; Lamont T; Davies JS
Although submarine canyons are internationally recognized as sensitive ecosystems and reported to be biological hotspots, regional studies are required to validate this consensus. To this end, hydrographic and benthic biodiversity data were collected during three cruises (2016-2017) to provide insights on the benthic patterns within South African canyon and non-canyon offshore areas. A total of 25 stations, sampled at 200-1000 m depth range, form the basis of the multivariate analysis. Diversity gradients were calculated and then differences were compared across substrate types and depth zones represented within 12 canyon and 13 non-canyon stations. Significant differences in both substrate and depth were evident, despite measures being highly variable. This observation of varying diversity in different substrates is in line with previous studies. No clear pattern was observed for species diversity (delta+). However, non-canyon stations overall showed a higher diversity in comparison to canyon stations. A notable peak in diversity is observed in canyon areas in the 401-500 m depth zone. Species richness followed an opposing pattern, as it decreased with depth and was consistently higher in canyon areas. These results align with the well-defined influence of depth-related variables on the distribution of taxonomic groups and the substrate available, at various scales. The eutrophic characteristic of the Benguela region may have attributed to the insignificant diversity differences between canyon and non-canyon stations. To assess the benthic species structure in canyon and non-canyon areas, we converted the 108 benthic species into a gamma+ matrix. We then modelled the biological response to predictor variables (substrate and depth). Although the canyon and non-canyon areas have an overlapping species composition, the main effects (canyon vs. non-canyon, depth, and substrate) showed significant differences. Thirteen species were characteristic of canyon areas, whilst only three distinguished non-canyon areas. The region has a long history of anthropogenic activities, so the observed benthic profiles may already be altered. The current study therefore provides the first detailed taxonomic description and analysis of benthic species profiles in the Cape Canyon, and advances important baseline information necessary for understanding the ecological importance of the Cape Canyon.
Cultural divergence and morphological variation of isolated remnant populations of the endangered Floreana mockingbird
(CSIRO Publishing, 2024-07-22) Reyes EMR; Roper MM; Sevilla C; Rueda D; Brunton DH; Smith ANH; Ortiz-Catedral L; Davis R
Context: Cultural divergence refers to changes over time in behavioural traits. These cultural changes could have important implications for conservation planning, and impact the success of conservation efforts such as translocations. Aims: Here, we investigate the extent, and potential impacts, of cultural divergence in two isolated populations of the Floreana mockingbird (Mimus trifasciatus) on the Galápagos Islands. Methods: Using contemporary recordings of vocalisations we test for spatial vocal differentiation between mockingbird populations. Furthermore, we explore the potential drivers of change using morphological measurements and historical recordings of the species. Key results: We found evidence of spatial and temporal differentiation in vocalisations between the two populations of the Floreana mockingbird. We accurately classified over 75% of the birds to the correct populations based on multivariate measures of audio recordings using canonical analysis of principal coordinates (CAP). We also found significant differences in morphometrics between populations specifically, beak depth was associated with frequency modulation, an acoustic measure that is significantly different between populations. Furthermore, we found evidence of change in the complexity of the vocalisations over a period of 57 years. Conclusions: Cultural divergence was found in the two remaining populations of this endangered species. Factors such as changes in morphology and cultural drift might have been influenced the change in vocalisation across time and populations. Implications: We highlight the importance of considering behavioural factors when planning reintroductions of endangered species where there is a need to minimise the risk of assortative mating so as to maximise genetic diversity.
Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns
(The Royal Society, 2022-09-14) Smith CE; Smith ANH; Cooper TF; Moore FB-G
Long-term evolution experiments have tested the importance of genetic and environmental factors in influencing evolutionary outcomes. Differences in phylogenetic history, recent adaptation to distinct environments and chance events, all influence the fitness of a population. However, the interplay of these factors on a population's evolutionary potential remains relatively unexplored. We tracked the outcome of 2000 generations of evolution of four natural isolates of Escherichia coli bacteria that were engineered to also create differences in shallow history by adding previously identified mutations selected in a separate long-term experiment. Replicate populations started from each progenitor evolved in four environments. We found that deep and shallow phylogenetic histories both contributed significantly to differences in evolved fitness, though by different amounts in different selection environments. With one exception, chance effects were not significant. Whereas the effect of deep history did not follow any detectable pattern, effects of shallow history followed a pattern of diminishing returns whereby fitter ancestors had smaller fitness increases. These results are consistent with adaptive evolution being contingent on the interaction of several evolutionary forces but demonstrate that the nature of these interactions is not fixed and may not be predictable even when the role of chance is small.
Lost in the Forest
(Cold Spring Harbor Laboratory, 2022) Smith HL; Biggs PJ; French NP; Smith ANH; Marshall JC
To date, there remains no satisfactory solution for absent levels in random forest models. Absent levels are levels of a predictor variable encountered during prediction for which no explicit rule exists. Imposing an order on nominal predictors allows absent levels to be integrated and used for prediction. The ordering of predictors has traditionally been via class probabilities with absent levels designated the lowest order. Using a combination of simulated data and pathogen source-attribution models using whole-genome sequencing data, we examine how the method of ordering predictors with absent levels can (i) systematically bias a model, and (ii) affect the out-of-bag error rate. We show that the traditional approach is systematically biased and underestimates out-of-bag error rates, and that this bias is resolved by ordering absent levels according to the a priori hypothesis of equal class probability. We present a novel method of ordering predictors via principal coordinates analysis (PCO) which capitalizes on the similarity between pairs of predictor levels. Absent levels are designated an order according to their similarity to each of the other levels in the training data. We show that the PCO method performs at least as well as the traditional approach of ordering and is not biased.
Lost in the Forest: Encoding categorical variables and the absent levels problem
(Springer Nature, 2024-04-10) Smith HL; Biggs PJ; French NP; Smith ANH; Marshall JC; Gama J
Levels of a predictor variable that are absent when a classification tree is grown can not be subject to an explicit splitting rule. This is an issue if these absent levels are present in a new observation for prediction. To date, there remains no satisfactory solution for absent levels in random forest models. Unlike missing data, absent levels are fully observed and known. Ordinal encoding of predictors allows absent levels to be integrated and used for prediction. Using a case study on source attribution of Campylobacter species using whole genome sequencing (WGS) data as predictors, we examine how target-agnostic versus target-based encoding of predictor variables with absent levels affects the accuracy of random forest models. We show that a target-based encoding approach using class probabilities, with absent levels designated the highest rank, is systematically biased, and that this bias is resolved by encoding absent levels according to the a priori hypothesis of equal class probability. We present a novel method of ordinal encoding predictors via principal coordinates analysis (PCO) which capitalizes on the similarity between pairs of predictor levels. Absent levels are encoded according to their similarity to each of the other levels in the training data. We show that the PCO-encoding method performs at least as well as the target-based approach and is not biased.
Marine reserves indirectly affect fine-scale habitat associations, but not overall densities, of small benthic fishes.
(2016-09) Smith ANH; Anderson MJ
Many large, fishery-targeted predatory species have attained very high relative densities as a direct result of protection by no-take marine reserves. Indirect effects, via interactions with targeted species, may also occur for species that are not themselves targeted by fishing. In some temperate rocky reef ecosystems, indirect effects have caused profound changes in community structure, notably the restoration of predator-urchin-macroalgae trophic cascades. Yet, indirect effects on small benthic reef fishes remain poorly understood, perhaps because of behavioral associations with complex, refuge-providing habitats. Few, if any, studies have evaluated any potential effects of marine reserves on habitat associations in small benthic fishes. We surveyed densities of small benthic fishes, including some endemic species of triplefin (Tripterygiidae), along with fine-scale habitat features in kelp forests on rocky reefs in and around multiple marine reserves in northern New Zealand over 3 years. Bayesian generalized linear mixed models were used to evaluate evidence for (1) main effects of marine reserve protection, (2) associations with habitat gradients, including complexity, and (3) differences in habitat associations inside versus outside reserves. No evidence of overall main effects of marine reserves on species richness or densities of fishes was found. Both richness and densities showed strong associations with gradients in habitat features, particularly habitat complexity. In addition, some species exhibited reserve-by-habitat interactions, having different associations with habitat gradients inside versus outside marine reserves. Two species (Ruanoho whero and Forsterygion flavonigrum) showed stronger positive associations with habitat complexity inside reserves. These results are consistent with the presence of a behavioral risk effect, whereby prey fishes are more strongly attracted to habitats that provide refuge from predation in areas where predators are more abundant. This work highlights the importance of habitat structure and the potential for fishing to affect behavioral interactions and the interspecific dynamic attributes of community structure beyond simple predator-prey consumption and archetypal trophic cascades.
Reproductive biology of female common dolphins (Delphinus delphis) in New Zealand waters
(Springer-Verlag GmbH, 2022-11-20) Palmer EI; Betty EL; Murphy S; Perrott MR; Smith ANH; Stockin KA; Crocker D
Reproductive biology was assessed in 106 female common dolphins (Delphinus delphis) examined post-mortem from stranding and bycatch events along the New Zealand coastline between 1997 and 2019. The average age (ASM) and length (LSM) at sexual maturity was estimated at 7.5 years and 183.5 cm, respectively. The total number of corpora in mature individuals increased with age and appeared to persist throughout life. Ovarian asymmetry was apparent, with the left ovary displaying higher rates of ovulation, and a maximum of 19 corpora recorded for a 24-year-old female. The estimated ovulation and annual pregnancy rates for mature females were 0.39 year-1 and 30%, respectively. Conception and calving occurred year-round, with a weak seasonal increase observed in late austral spring and early austral summer. As these data did not clearly show whether seasonality was present, the gestation, lactation, and resting periods were calculated as either 12.6 or 12.8 months based on the presence/absence of seasonality, respectively. Similarly, calving interval ranged from 3.15 to 3.2 years, depending upon whether seasonality was considered. The estimated LSM of the New Zealand population aligns with other populations globally, although the estimated ASM is younger by approximately 6 months. Other reproductive parameters align with Northern Hemisphere populations, although demonstrate variation, which may reflect adaptations to local conditions such as water temperature and prey availability. As the species is subject to anthropogenic impacts including pollution and bycatch, we suggest our findings be used as a baseline with which to monitor trends in population parameters.
Reproductive biology of male common dolphins (Delphinus delphis) in New Zealand waters.
(Springer Nature, 2023-10-06) Palmer EI; Betty EL; Murphy S; Perrott MR; Smith ANH; Stockin KA; Siebert U
Reproductive parameters were assessed in 64 male common dolphins (Delphinus delphis) examined post-mortem from strandings and bycatch in New Zealand between 1999 and 2020. The stages of male sexual maturation were assessed using morphological measurements and histological examination of testicular tissue. Age was determined via growth layer groups (GLGs) in teeth. The average age (ASM) and length (LSM) at attainment of sexual maturity were estimated to be 8.8 years and 198.3 cm, respectively. Individual variation in ASM (7.5–10 years) and LSM (190–220 cm) was observed in New Zealand common dolphins. However, on average, sexual maturity was attained at a similar length but at a marginally younger age (< 1 year) in New Zealand compared to populations in the Northern Hemisphere. All testicular variables proved better predictors of sexual maturity compared to demographic variables (age and total body length), with combined testes weight the best outright predictor of sexual maturity. Reproductive seasonality was observed in male common dolphins, with a significant increase in combined testes weight in austral summer. This aligns with most other studied populations, where seasonality in reproduction is typically observed. Given the known anthropogenic impacts on New Zealand common dolphins, we recommend that these findings be used as a baseline from which to monitor population-level changes as part of conservation management efforts.
Residency and movement patterns of an apex predatory shark (Galeocerdo cuvier) at the Galapagos Marine Reserve.
(2017) Acuña-Marrero D; Smith ANH; Hammerschlag N; Hearn A; Anderson MJ; Calich H; Pawley MDM; Fischer C; Salinas-de-León P
The potential effectiveness of marine protected areas (MPAs) as a conservation tool for large sharks has been questioned due to the limited spatial extent of most MPAs in contrast to the complex life history and high mobility of many sharks. Here we evaluated the movement dynamics of a highly migratory apex predatory shark (tiger shark Galeocerdo cuvier) at the Galapagos Marine Reserve (GMR). Using data from satellite tracking passive acoustic telemetry, and stereo baited remote underwater video, we estimated residency, activity spaces, site fidelity, distributional abundances and migration patterns from the GMR and in relation to nesting beaches of green sea turtles (Chelonia mydas), a seasonally abundant and predictable prey source for large tiger sharks. Tiger sharks exhibited a high degree of philopatry, with 93% of the total satellite-tracked time across all individuals occurring within the GMR. Large sharks (> 200 cm TL) concentrated their movements in front of the two most important green sea turtle-nesting beaches in the GMR, visiting them on a daily basis during nocturnal hours. In contrast, small sharks (< 200 cm TL) rarely visited turtle-nesting areas and displayed diurnal presence at a third location where only immature sharks were found. Small and some large individuals remained in the three study areas even outside of the turtle-nesting season. Only two sharks were satellite-tracked outside of the GMR, and following long-distance migrations, both individuals returned to turtle-nesting beaches at the subsequent turtle-nesting season. The spatial patterns of residency and site fidelity of tiger sharks suggest that the presence of a predictable source of prey and suitable habitats might reduce the spatial extent of this large shark that is highly migratory in other parts of its range. This highly philopatric behaviour enhances the potential effectiveness of the GMR for their protection.

Browsing by Author "Smith ANH"

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