Acknowledging more biodiversity without more species

Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets ("genomic taxonomy"), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.

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.

Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands

BACKGROUND

Understanding the natural microbiome and resistome of wildlife from remote places is necessary to monitor the human footprint on the environment including antimicrobial use (AU). Marine iguanas are endemic species from the Galapagos Islands where they are highly affected by anthropogenic factors that can alter their microbiota as well as their abundance and diversity of antimicrobial-resistant genes (ARGs). Thus, this study aims to apply culture-independent approaches to characterize the marine iguana's gut metagenomic composition of samples collected from the uninhabited islands Rabida (n = 8) and Fernandina (Cabo Douglas, n = 30; Punta Espinoza, n = 30). Fresh feces from marine iguanas were analyzed through SmartChip RT-PCR, 16S rRNA, and metagenomic next-generation sequencing (mNGS) to identify their microbiome, microbial-metabolic pathways, resistome, mobilome, and virulome.

RESULTS

The marine iguana's gut microbiome composition was highly conserved despite differences in ecological niches, where 86% of taxa were shared in the three locations. However, site-specific differences were mainly identified in resistome, mobilome, virulorome, and metabolic pathway composition, highlighting the existence of factors that induce microbial adaptations in each location. Functional gut microbiome analyses revealed its role in the biosynthesis and degradation of vitamins, cofactors, proteinogenic amino acids, carbohydrates, nucleosides and nucleotides, fatty acids, lipids, and other compounds necessary for the marine iguanas. The overall bacterial ARG abundance was relatively low (0.006%); nevertheless, the presence of genes encoding resistance to 22 drug classes was identified in the iguana's gut metagenome. ARG-carrying contig and co-occurrence network analyses revealed that commensal bacteria are the main hosts of ARGs. Taxa of public health interest such as Salmonella, Vibrio, and Klebsiella also carried multidrug-resistance genes associated with MGEs which can influence the dissemination of ARGs through horizontal gene transfer.

CONCLUSION

Marine iguanas depend on the gut microbiome for the biosynthesis and degradation of several compounds through a symbiotic relationship. Niche-specific adaptations were evidenced in the pool of microbial accessory genes (i.e., ARGs, MGEs, and virulence) and metabolic pathways, but not in the microbiome composition. Culture-independent approaches outlined the presence of a diverse resistome composition in the Galapagos marine iguanas from remote islands. The presence of AR pathogens in marine iguanas raises concerns about the dispersion of microbial-resistant threats in pristine areas, highlighting wildlife as sentinel species to identify the impact of AU.

Microplastic distribution and composition on two Galápagos island beaches, Ecuador: Verifying the use of citizen science derived data in long-term monitoring

Monitoring beach plastic contamination across space and time is necessary for understanding its sources and ecological effects, and for guiding mitigation. This is logistically and financially challenging, especially for microplastics. Citizen science represents an option for sampling accessible sites to support long term monitoring, but challenges persist around data validation. Here we test a simple citizen science methodology to monitor visible microplastic contamination on sandy beaches using a standard quadrat unit (50 cm × 50 cm x 5 cm depth) sieved to 1 mm, to support the analysis of microplastic on two islands within the marine protected area of the Galápagos Archipelago, Ecuador (San Cristóbal and Santa Cruz islands). High school and university students undertook supervised sampling of two beaches in 2019-2020 collecting over 7000 particles. A sub-sample of the suspected microplastics collected (n = 2,213, ∼30% total) were analysed using FTIR spectrometry, confirming 93% of particles >1 mm visually identified by students were microplastics or rubber, validating this method as a crowd-sourced indicator for microplastic contamination. These data provide important insights into the plastic contamination of Galápagos, revealing plastic abundances of 0-2524 particles m^-2 over the two beaches (the highest reported in Galápagos). Strong accumulation gradients were measured parallel to the waterline at Punta Pitt (San Cristobal island) and perpendicular to the waterline at Tortuga Bay (Santa Cruz island), where four-fold higher concentrations were recorded at the sea turtle nesting habitat on the back-beach dune. No significant seasonal trends were measured during one year. These results demonstrate the value of citizen science in filling spatiotemporal knowledge gaps of beach contamination to support intervention design and conservation.

Phylogeography and Prevalence of Hemoparasites (Apicomplexa: Eucoccidiorida) in Galápagos Marine Iguanas, Amblyrhynchus cristatus (Reptilia: Iguanidae)

Parasitism is among the most common forms of coexistence of organisms of different species. Hemoparasites live in the bloodstream of the host where they complete different life-cycle stages. Members of the phylum Apicomplexa constitute a large portion of all hemoparasites infecting reptiles and their parasite transmitting vectors, including arthropods. In this study, we carried out a survey and molecular identification of hemoparasites in blood samples of the iconic Galápagos marine iguana (Amblyrhynchus cristatus). Major island populations of marine iguanas were sampled to examine large-scale biogeographic patterns of parasite diversity and prevalence. Nested PCRs were used to amplify segments of the 18S rRNA-gene of hemoparasites. Furthermore, ticks attached to marine iguanas were collected and analyzed in the same way to assess their potential use as a non-invasive method for the detection of hemoparasites in vertebrate host species. PCR products were sequenced and a phylogenetic analysis was carried out showing the presence of two genetically distinct clusters of hemoparasites, one more commonly distributed than the other one, belonging to the genera Hepatozoon and/or Hemolivia (Apicomplexa: Eucoccidiorida). Overall, 25% of marine iguanas were infected by hemoparasites. However, infection rates varied strongly among particular island populations (from 3.45% to 50%). Although marine iguanas are an extremely mobile species that has colonized all islands in the Galápagos archipelago, parasite occurrence was not related to geographical distance, suggesting that dispersal behavior has a minor role in parasite transmission. On most islands, females tended to have higher infection rates than males, but this relationship was only significant on one island. Overall, ticks and marine iguanas had similar prevalence and diversity of parasites. However, the infection profiles of ticks and their corresponding hosts (marine iguanas) did not mirror one another, indicating that this method cannot be used reliably to assess marine iguana infection status. Interestingly, we found that hemoparasite prevalence in marine iguanas and ticks tended to be positively correlated across islands. Our results indicate that certain populations of marine iguanas may have special mechanisms and adaptations to cope with parasite infection. In addition, other factors such as vector density, anthropogenic-related activities or the immunological state of marine iguanas could potentially affect the striking variation in hemoparasite prevalence across island populations.

Cranial anatomy of the Galápagos marine iguana Amblyrhynchus cristatus (Squamata: Iguanidae)

Amblyrhynchus cristatus, the marine iguana, is unique among the ~7,000 species of living limbed lizards as it has successfully evolved adaptations that allow it to live in both terrestrial and marine environments. This species is endemic to the Galápagos Archipelago and has evolved a specialized feeding behavior, consuming primarily the algae that grow on the rocky seafloor. The intriguing questions arising around the evolution of the marine iguana concerns the use of exaptations of terrestrial features for aquatic and specifically marine adaptations. However, the lack of fundamental information about its anatomy currently prevents us from understanding how it became adapted to such a peculiar lifestyle in comparison to all other iguanids. The goal of this study is to provide the first ever description of the skull, mandible, and hyoid of Amblyrhynchus. We examined several specimens of marine iguana, including skeletal, wet, and ct-scanned material, and individuals at different ontogenetic stages. We also analyzed specimens of all other modern iguanid genera (Conolophus, Iguana, Ctenosaura, Cyclura, Dipsosaurus, Brachylophus, Sauromalus) in order to make comparisons between Amblyrhynchus and its closest relatives. We were able to identify several autapomorphic features that distinguish the marine iguana from all other iguanids. These unique morphologies are mostly associated with the modified configuration of the snout (nasal chamber), increased muscle attachments in the temporal-postorbital region of the skull, and dentition. Since Amblyrhynchus is the only nonophidian squamate currently able to exploit the ocean at least for some vital functions (i.e., feeding), we used comparisons to fossil marine lizards (e.g., mosasaurids) to discuss some of these unique traits. The new cranial features described for Amblyrhynchus may represent a source of novel morphological characters for use in future phylogenetic analyses of iguanian (or squamate) relationships, which will then serve as the foundation for the exploration of evolutionary patterns and processes that led to the development of such unique adaptations.

Plastic contamination of a Galapagos Island (Ecuador) and the relative risks to native marine species

Ecuador's Galapagos Islands and their unique biodiversity are a global conservation priority. We explored the presence, composition and environmental drivers of plastic contamination across the marine ecosystem at an island scale, investigated uptake in marine invertebrates and designed a systematic priority scoring analysis to identify the most vulnerable vertebrate species. Beach contamination varied by site (macroplastic 0-0.66 items·m^-2, microplastics 0-448.8 particles·m^-2 or 0-74.6 particles·kg^-1), with high plastic accumulation on east-facing beaches that are influenced by the Humboldt Current. Local littering and waste management leakages accounted for just 2% of macroplastic. Microplastics (including anthropogenic cellulosics) were ubiquitous but in low concentrations in benthic sediments (6.7-86.7 particles·kg^-1) and surface seawater (0.04-0.89 particles·m^-3), with elevated concentrations in the harbour suggesting some local input. Microplastics were present in all seven marine invertebrate species examined, found in 52% of individuals (n = 123) confirming uptake of microplastics in the Galapagos marine food web. Priority scoring analysis combining species distribution information, IUCN Red List conservation status and literature evidence of harm from entanglement and ingestion of plastics in similar species identified 27 marine vertebrates in need of urgent, targeted monitoring and mitigation including pinnipeds, seabirds, turtles and sharks.

Morphological and performance modifications in the world’s only marine lizard, the Galápagos marine iguana, Amblyrhynchus cristatus

The Galápagos marine iguana (Amblyrhynchus cristatus), the world’s only extant marine lizard, may have had one of the most unique and challenging transitions to aquatic life. Curiously, previous studies have identified relatively few physiological adaptations in the marine iguana; however, little is known about the extent of morphological specialization and performance trade-offs associated with the marine environment. By examining the morphology and locomotory performance of the marine iguana in comparison to their closely related mainland ancestors, the black spiny-tailed iguana (Ctenosaura similis) and green iguana (Iguana iguana), we found variation reflected specialization to ecological niches. However, variation was more pronounced among subspecies of marine iguana, suggesting that little morphological or performance modification is required for iguanids to successfully invade aquatic environments, thus raising the question why there are so few extant aquatic reptilian lineages. Our findings indicate that specialization for the marine environment likely resulted in a trade-off in sprint speed in a terrestrial environment, which may explain why other lizards have not undergone transitions to the marine environment. Additionally, we found that the magnitude of morphological and performance variation was more pronounced between subspecies of marine iguana than between iguanid species. This illustrates that the form-function relationship is more complex than previously thought and sheds light on the ecomorphological mysteries of the marine iguana.

No impact of a short-term climatic "El Niño" fluctuation on gut microbial diversity in populations of the Galápagos marine iguana (Amblyrhynchus cristatus)

Gut microorganisms are crucial for many biological functions playing a pivotal role in the host's well-being. We studied gut bacterial community structure of marine iguana populations across the Galápagos archipelago. Marine iguanas depend heavily on their specialized gut microbiome for the digestion of dietary algae, a resource whose growth was strongly reduced by severe "El Niño"-related climatic fluctuations in 2015/2016. As a consequence, marine iguana populations showed signs of starvation as expressed by a poor body condition. Body condition indices (BCI) varied between island populations indicating that food resources (i.e., algae) are affected differently across the archipelago during 'El Niño' events. Though this event impacted food availability for marine iguanas, we found that reductions in body condition due to "El Niño"-related starvation did not result in differences in bacterial gut community structure. Species richness of gut microorganisms was instead correlated with levels of neutral genetic diversity in the distinct host populations. Our data suggest that marine iguana populations with a higher level of gene diversity and allelic richness may harbor a more diverse gut microbiome than those populations with lower genetic diversity. Since low values of these diversity parameters usually correlate with small census and effective population sizes, we use our results to propose a novel hypothesis according to which small and genetically less diverse host populations might be characterized by less diverse microbiomes. Whether such genetically depauperate populations may experience additional threats from reduced dietary flexibility due to a limited intestinal microbiome is currently unclear and calls for further investigation.

Galapagos Islands Endemic Vertebrates: A Population Genetics Perspective

The organisms of the Galapagos Islands played a central role in the development of the theory of evolution by Charles Darwin. Examination of the population genetics factors of many of these organisms with modern molecular methods has expanded our understanding of their evolution. Here, I provide a perspective on how selection, gene flow, genetic drift, mutation, and inbreeding have contributed to the evolution of 6 iconic Galapagos species: flightless cormorant, pink iguana, marine iguana, Galapagos hawk, giant tortoises, and Darwin's finches. Because of the inherent biological differences among these species that have colonized the Galapagos, different population genetic factors appear to be more or less important in these different species. For example, the Galapagos provided novel environments in which strong selection took place and the Darwin's finches diversified to produce new species and the cormorant adapted to the nutrient-rich western shores of the Galapagos by losing its ability to fly and genomic data have now identified candidate genes. In both the pink iguana, which exists in one small population, and the Galapagos hawk, which has small population sizes, genetic drift has been potentially quite important. There appears to be very limited interisland gene flow in the flightless cormorant and the Galapagos hawk. On the other hand, both the marine iguana and some of the Darwin's finches appear to have significant interisland gene flow. Hybridization between species and subspecies has also introduced new adaptive variation, and in some cases, hybridization might have resulted in despeciation. Overall, new population genetics and genomics research has provided additional insight into the evolution of vertebrate species in the Galapagos.

The spatial ecology of invasive feral cats Felis catus on San Cristóbal, Galápagos: first insights from GPS collars

The dangers posed by invasive species for endemic island wildlife are well recognised. Introduced domestic cats (Felis catus) represent a significant threat to several endemic species of the Galápagos archipelago—including hatchling marine iguanas (Amblyrhynchus cristatus) and potentially green turtles (Chelonia mydas)—yet little is known about their spatial ecology and habitat use on these islands. Here, we describe a pilot study using GPS collars to track the movements of three feral cats at a site of conservation interest on San Cristóbal Island. Based on 175 days of GPS data, we undertook spatial analyses to ascertain home ranges, and to investigate the overlap of ranges between the cats and potential prey species. Average home range was 1.27 km2 (1.12–1.46 km2), which—though small for feral cats—is in keeping with previous findings in Galápagos. We found the cats did use the habitat of a small marine iguana population but did not change their spatial habits before and after iguana hatchlings appeared. Changes over time in the daily movements of one cat indicated a possible response of the individual to the presence of hatchling green turtles (Chelonia mydas); though the data here are insufficient to show whether the cat was hunting these hatchlings. We recommend similar work be undertaken in areas with larger marine iguana populations, where hatchlings could represent a potentially important food source for invasive feral cats, as well as further work to determine the threat posed by cats to turtle hatchlings in Galápagos.

Painted black: Iguana melanoderma (Reptilia, Squamata, Iguanidae) a new melanistic endemic species from Saba and Montserrat islands (Lesser Antilles)

The Lesser Antilles, in the Eastern Caribbean, is inhabited by three Iguana species: the Lesser Antillean iguanaIguana delicatissima, which is endemic to the northernmost islands of the Lesser Antilles, the introduced common iguana from South America, Iguana iguana iguana, represented also by the two newly described endemic subspecies Iguana iguana sanctaluciae from Saint Lucia and Iguana iguana insularis from Saint Vincent and the Grenadines, and Grenada, and the introduced Iguana rhinolopha from Central America. Drawing on both morphological and genetic data, this paper describes the Iguana populations from Saba and Montserrat as a new species, Iguana melanoderma. This species is recognized on the basis of the following combination of characteristics: private microsatellite alleles, unique mitochondrial ND4 haplotypes, a distinctive black spot between the eye and tympanum, a dorsal carpet pattern on juveniles and young adults, a darkening of body coloration with aging (except for the anterior part of the snout), a black dewlap, pink on the jowl, the high number of large tubercular nape scales, fewer than ten medium sized-triangular dewlap spikes, high dorsal spikes, and lack of horns on the snout. This new melanistic taxon is threatened by unsustainable harvesting (including for the pet trade) and both competition and hybridization from escaped or released invasive alien iguanas (I. iguana iguana and I. rhinolopha) from South and Central America, respectively. The authors call for action to conserve Iguana melanoderma in Saba and Montserrat and for further research to investigate its relationship to other melanistic iguanas from the Virgin Islands and coastal islands of Venezuela.

Diversity of compounds in femoral secretions of Galápagos iguanas (genera: Amblyrhynchus and Conolophus), and their potential role in sexual communication in lek-mating marine iguanas (Amblyrhynchus cristatus)

Background

Chemical signals are widely used in the animal kingdom, enabling communication in various social contexts, including mate selection and the establishment of dominance. Femoral glands, which produce and release waxy secretions into the environment, are organs of central importance in lizard chemical communication. The Galápagos marine iguana (Amblyrhynchus cristatus) is a squamate reptile with a lek-mating system. Although the lekking behaviour of marine iguanas has been well-studied, their potential for sexual communication via chemical cues has not yet been investigated. Here we describe the diversity of the lipophilic fraction of males’ femoral gland secretions among 11 island populations of marine iguanas, and compare it with the composition of its sister species, the Galápagos land iguana (Conolophus subcristatus). We also conducted behavioural observations in marine iguana territorial males in order to explore the possible function of these substances in the context of male dominance in leks.

Methods

Femoral secretions were analysed by gas chromatography coupled to mass spectrometry (GC–MS), and chromatography with a flame ionisation detector (GC-FID) in order to characterise the lipophilic composition. To understand the potential role of femoral secretions in marine iguana intraspecific communication, territorial males were sampled for their femoral glands and monitored to record their head bob rate—a territorial display behaviour in males—as well as the number of females present in their leks.

Results

We found that the gland secretions were composed of ten saturated and unsaturated carboxylic acids ranging in chain length between C₁₆ and C₂₄, as well as three sterols. Cholesterol was the main compound found. Intriguingly, land iguanas have a higher diversity of lipophilic compounds, with structural group of lipids (i.e. aldehydes) entirely absent in marine iguanas; overall the chemical signals of both species were strongly differentiated. Lipid profiles also differed among populations of marine iguanas from different islands, with some islands demonstrating a high diversity of lipophilic compounds (i.e. full spectra of compounds), and others lacking one or more compounds. Among the compounds most frequently found missing were 11- and 13-eicosenoic acids. Gland secretions of males with a better body condition and with a higher dominance status (i.e. those accompanied by females and with higher head bob display) were proportionately richer in C₂₀-unsaturated fatty acids (11-eicosenoic acid).

Discussion

Land and marine iguanas strongly diverged in their chemical composition of the femoral glands likely due to ecological differences between both species. Despite that marine iguana populations varied in their femoral gland composition that was not related to their genetic structure. Our results indicated that 11-eicosenoic acid may play an important role in intraspecific chemical communication in marine iguanas.