A pilot study to estimate the population size of endangered Galápagos marine iguanas using drones.

BACKGROUND: Large-scale species monitoring remains a significant conservation challenge. Given the ongoing biodiversity crisis, the need for reliable and efficient methods has never been greater. Drone-based techniques have much to offer in this regard: they allow access to otherwise unreachable areas and enable the rapid collection of non-invasive field data. Herein, we describe the development of a drone-based method for the estimation of population size in Galápagos marine iguanas, Amblyrhynchus cristatus. As a large-bodied lizard that occurs in open coastal terrain, this endemic species is an ideal candidate for drone surveys. Almost all Amblyrhynchus subspecies are Endangered or Critically Endangered according to the IUCN yet since several colonies are inaccessible by foot, ground- based methods are unable to address the critical need for better census data. In order to establish a drone-based approach to estimate population size of marine iguanas, we surveyed in January 2021 four colonies on three focal islands (San Cristobal, Santa Fe and Espanola) using three techniques: simple counts (the standard method currently used by conservation managers), capture mark-resight (CMR), and drone-based counts. The surveys were performed within a 4-day window under similar ambient conditions. We then compared the approaches in terms of feasibility, outcome and effort. RESULTS: The highest population-size estimates were obtained using CMR, and drone-based counts were on average 14% closer to CMR estimates-and 17-35% higher-than those obtained by simple counts. In terms of field-time, drone-surveys can be faster than simple counts, but image analyses were highly time consuming. CONCLUSION: Though CMR likely produces superior estimates, it cannot be performed in most cases due to lack of access and knowledge regarding colonies. Drone-based surveys outperformed ground-based simple counts in terms of outcome and this approach is therefore suitable for use across the range of the species. Moreover, the aerial approach is currently the only credible solution for accessing and surveying marine iguanas at highly remote colonies. The application of citizen science and other aids such as machine learning will alleviate the issue regarding time needed to analyze the images.

Using bear rub data and spatial capture-recapture models to estimate trend in a brown bear population.

Trends in population abundance can be challenging to quantify during range expansion and contraction, when there is spatial variation in trend, or the conservation area is large. We used genetic detection data from natural bear rubbing sites and spatial capture-recapture (SCR) modeling to estimate local density and population growth rates in a grizzly bear population in northwestern Montana, USA. We visited bear rubs to collect hair in 2004, 2009-2012 (3,579-4,802 rubs) and detected 249-355 individual bears each year. We estimated the finite annual population rate of change 2004-2012 was 1.043 (95% CI = 1.017-1.069). Population density shifted from being concentrated in the north in 2004 to a more even distribution across the ecosystem by 2012. Our genetic detection sampling approach coupled with SCR modeling allowed us to estimate spatially variable growth rates of an expanding grizzly bear population and provided insight into how those patterns developed. The ability of SCR to utilize unstructured data and produce spatially explicit maps that indicate where population change is occurring promises to facilitate the monitoring of difficult-to-study species across large spatial areas.

Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards.

Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genome-wide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates.

Demographic mechanisms underpinning genetic assimilation of remnant groups of a large carnivore.

Current range expansions of large terrestrial carnivores are occurring following human-induced range contraction. Contractions are often incomplete, leaving small remnant groups in refugia throughout the former range. Little is known about the underlying ecological and evolutionary processes that influence how remnant groups are affected during range expansion. We used data from a spatially explicit, long-term genetic sampling effort of grizzly bears (Ursus arctos) in the Northern Continental Divide Ecosystem (NCDE), USA, to identify the demographic processes underlying spatial and temporal patterns of genetic diversity. We conducted parentage analysis to evaluate how reproductive success and dispersal contribute to spatio-temporal patterns of genetic diversity in remnant groups of grizzly bears existing in the southwestern (SW), southeastern (SE) and east-central (EC) regions of the NCDE. A few reproductively dominant individuals and local inbreeding caused low genetic diversity in peripheral regions that may have persisted for multiple generations before eroding rapidly (approx. one generation) during population expansion. Our results highlight that individual-level genetic and reproductive dynamics play critical roles during genetic assimilation, and show that spatial patterns of genetic diversity on the leading edge of an expansion may result from historical demographic patterns that are highly ephemeral.

The complete mitochondrial genomes of the Galápagos iguanas, Amblyrhynchus cristatus and Conolophus subcristatus.

The Galápagos iguanas are among the oldest vertebrate lineages on the Galápagos archipelago, and the evolutionary history of this clade is of great interest to biologists. We describe here the complete mitochondrial genomes of the marine iguana, Amblyrhynchus cristatus (Genbank accession number: KT277937) and the land iguana Conolophus subcristatus (Genbank accession number: KT277936). The genomes contain 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs genes, as well as a control region (CR). Both species have an identical gene order, which matches that of Iguana iguana. The CR of both Galápagos iguanas features similar tandem repeats units, which are absent in I. iguana. We present a phylogeny of the Iguanidae based on complete mitochondrial genomes, which confirms the sister-group relationship of Galápagos iguanas. These new mitochondrial genomes constitute an important data source for future exploration of the phylogenetic relationships and evolutionary history of the Galápagos iguanas.

Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana.

The effects of the direct interaction between hybridization and speciation-two major contrasting evolutionary processes--are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within--island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50,000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island--ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole.

Balancing precision and risk: should multiple detection methods be analyzed separately in N-mixture models?

Using multiple detection methods can increase the number, kind, and distribution of individuals sampled, which may increase accuracy and precision and reduce cost of population abundance estimates. However, when variables influencing abundance are of interest, if individuals detected via different methods are influenced by the landscape differently, separate analysis of multiple detection methods may be more appropriate. We evaluated the effects of combining two detection methods on the identification of variables important to local abundance using detections of grizzly bears with hair traps (systematic) and bear rubs (opportunistic). We used hierarchical abundance models (N-mixture models) with separate model components for each detection method. If both methods sample the same population, the use of either data set alone should (1) lead to the selection of the same variables as important and (2) provide similar estimates of relative local abundance. We hypothesized that the inclusion of 2 detection methods versus either method alone should (3) yield more support for variables identified in single method analyses (i.e. fewer variables and models with greater weight), and (4) improve precision of covariate estimates for variables selected in both separate and combined analyses because sample size is larger. As expected, joint analysis of both methods increased precision as well as certainty in variable and model selection. However, the single-method analyses identified different variables and the resulting predicted abundances had different spatial distributions. We recommend comparing single-method and jointly modeled results to identify the presence of individual heterogeneity between detection methods in N-mixture models, along with consideration of detection probabilities, correlations among variables, and tolerance to risk of failing to identify variables important to a subset of the population. The benefits of increased precision should be weighed against those risks. The analysis framework presented here will be useful for other species exhibiting heterogeneity by detection method.

Hearing threshold shifts and recovery in harbor seals (Phoca vitulina) after octave-band noise exposure at 4 kHz.

Safety criteria for underwater sounds from offshore pile driving are needed to protect marine mammals. As a first step toward understanding effects of impulsive sounds, two harbor seals were exposed to octave-band white noise centered at 4 kHz at three mean received sound pressure levels (SPLs; 124, 136, and 148 dB re 1 µPa) at up to six durations (7.5, 15, 30, 60, 120, and 240 min); mean received sound exposure level (SEL) range was 166-190 dB re 1 µPa(2) s. Hearing thresholds were determined before and after exposure. Temporary hearing threshold shifts (TTS) and subsequent recovery were quantified as changes in hearing thresholds at 1-4, 4-8, 8-12, 48, and 96 min after noise exposure in seal 01, and at 12-16, 16-20, 20-24, 60, and 108 min after exposure in seal 02. Maximum TTS (1-4 min after 120 min exposure to 148 dB re 1 µPa; 187 dB SEL) was 10 dB. Recovery occurred within ~60 min. Statistically significant TTSs (>2.5 dB) began to occur at SELs of ~170 (136 SPL, 60 min) and 178 dB re 1 µPa(2) s (148 SPL, 15 min). However, SEL is not an optimal predictor of TTS for long duration, low SPL continuous noise, as duration and SPL play unequal roles in determining induced TTS.