Impacts of climate variability and human colonization on the vegetation of the Galápagos Islands

Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs

Similar to other insular birds around the world, the Galapagos rail (Laterallus spilonota Gould, 1841) exhibits reduced flight capacity following its colonization of the archipelago ~1.2 mya. Despite their short evolutionary history, rails have colonized seven different islands spanning the entire width of the archipelago. Galapagos rails were once common on islands with sufficiently high altitudes to support shrubs in humid habitats. After humans introduced goats, this habitat was severely reduced due to overgrazing. Habitat loss devastated some rail populations, with less than 50 individuals surviving, rendering the genetic diversity of Galapagos rail a pressing conservation concern. Additionally, one enigma is the reappearance of rails on the island of Pinta after they were considered extirpated. Our approach was to investigate the evolutionary history and geographic distribution of Galapagos rails as well as examine the genome-wide effects of historical population bottlenecks using 39 whole genomes across different island populations. We recovered an early divergence of rail ancestors leading to the isolated populations on Pinta and a second clade comprising the rest of the islands, historically forming a single landmass. Subsequently, the separation of the landmass ~900 kya may have led to the isolation of the Isabela population with more panmictic populations found on Santa Cruz and Santiago islands. We found that rails genomes contain long runs of homozygosity (>2 Mb) that could be related to the introduction of goats. Finally, our findings show that the modern eradication of goats was critical to avoiding episodes of inbreeding in most populations.

Temperature along an elevation gradient determines Galapagos tortoise sex ratios

Climate change threatens endemic island ectothermic reptiles that display small population sizes and temperature-dependent sex determination (TSD). Studies of captive Galapagos tortoises demonstrate type A TSD with warmer incubation temperatures producing females. However, there are few published data from free-living Galapagos tortoises on incubation temperature regimes, and none on hatchling sex ratios in the wild or the potential impacts of climate change on future sex ratios. We sought to address these deficits by quantifying incubation temperatures of nests and sex ratios of juvenile tortoises along an elevation gradient on Santa Cruz Island. We focused on three geographically separated nesting zones with mean elevations of 14 m (lower), 57 m (middle), and 107 m (upper) above sea level. Nest temperatures in 54 nests distributed across the three nesting zones were measured every 4 h throughout the incubation period using iButton thermochrons. We used coelioscopy to conduct visual exams of gonads to determine the sex of 40 juvenile tortoises from the three nesting zones. During the middle trimester of incubation, the period during which sex is determined in turtles, mean nest temperatures were 25.75°C (SD = 1.08) in the upper zone, and 27.02°C (SD = 1.09), and 27.09°C (SD = 0.85) in the middle and lower zones, respectively. The proportion of juveniles that was male increased from 11.1% in the lower zone and 9.5% in the middle zone, to 80% in the upper zone. A ca. 50 m increase in elevation induced a decrease of >1.25°C in mean nest temperature during the second trimester of incubation. Over the same elevation change, the proportion of males in the juvenile tortoise population increased by ca. 70%. Temperatures on Galapagos are predicted to increase by 1-4°C over the next 50 years, which is likely to increase the frequency of female tortoises across the archipelago.

Galápagos tortoise stable isotope ecology and the 1850s Floreana Island Chelonoidis niger niger extinction

A consequence of over 400 years of human exploitation of Galápagos tortoises (Chelonoidis niger ssp.) is the extinction of several subspecies and the decimation of others. As humans captured, killed, and/or removed tortoises for food, oil, museums, and zoos, they also colonized the archipelago resulting in the introduction of invasive plants, animals, and manipulated landscapes for farming, ranching, and infrastructure. Given current conservation and revitalization efforts for tortoises and their habitats, here we investigate nineteenth and twentieth century Galápagos tortoise dietary ecology using museum and archaeological specimens coupled with analysis of carbon (δ¹³C_collagen and δ¹³C_apatite), nitrogen (δ¹⁵N), hydrogen (δD) and oxygen (δ¹⁸O_apatite) stable isotopes and radiocarbon dating. We identify that Galápagos tortoise diets vary between and within islands over time, and that long-term anthropogenic impacts influenced change in tortoise stable isotope ecology by using 57 individual tortoises from 10 different subspecies collected between 1833 and 1967-a 134-year period. On lower elevation islands, which are often hotter and drier, tortoises tend to consume more C₄ vegetation (cacti and grasses). Our research suggests human exploitation of tortoises and anthropogenic impacts on vegetation contributed to the extinction of the Floreana Island tortoise (C. n. niger) in the 1850s.

Human-induced ecological cascades: Extinction, restoration, and rewilding in the Galápagos highlands

The Galápagos Islands are an iconic evolutionary and ecological setting, recognized to be both species-poor and ecologically sensitive. Here, we show an indirect ecological cascade initiated by whalers harvesting tortoises near the coast in the 1790s, which had lasting impacts on the highland interior of San Cristóbal Island. Our data also reveal how the replacement of endemic herbivores with exotic herbivores, namely, cattle, impacted the local vegetation. We advocate for the restoration of preimpact shrub species and tortoises to promote habitat rewilding, restoration, and especially the socioeconomic value of these highland ecosystems in providing tourist experiences.

Oceanic islands support unique biotas but often lack ecological redundancy, so that the removal of a species can have a large effect on the ecosystem. The larger islands of the Galápagos Archipelago once had one or two species of giant tortoise that were the dominant herbivore. Using paleoecological techniques, we investigate the ecological cascade on highland ecosystems that resulted from whalers removing many thousands of tortoises from the lowlands. We hypothesize that the seasonal migration of a now-extinct tortoise species to the highlands was curtailed by decreased intraspecific competition. We find the trajectory of plant community dynamics changed within a decade of the first whaling vessels visiting the islands. Novel communities established, with a previously uncommon shrub, Miconia, replacing other shrubs of the genera Alternanthera and Acalypha. It was, however, the introduction of cattle and horses that caused the local extirpation of plant species, with the most extreme impacts being evident after c. 1930. This modified ecology is considered the natural state of the islands and has shaped subsequent conservation policy and practice. Restoration of El Junco Crater should emphasize exclusion of livestock, rewilding with tortoises, and expanding the ongoing plantings of Miconia to also include Acalypha and Alternanthera.

Origin and dispersion pathways of guava in the Galapagos Islands inferred through genetics and historical records

Guava (Psidium guajava) is an aggressive invasive plant in the Galapagos Islands. Determining its provenance and genetic diversity could explain its adaptability and spread, and how this relates to past human activities. With this purpose, we analyzed 11 SSR markers in guava individuals from Isabela, Santa Cruz, San Cristobal, and Floreana islands in the Galapagos, as well as from mainland Ecuador. The mainland guava population appeared genetically differentiated from the Galapagos populations, with higher genetic diversity levels found in the former. We consistently found that the Central Highlands region of mainland Ecuador is one of the most likely origins of the Galapagos populations. Moreover, the guavas from Isabela and Floreana show a potential genetic input from southern mainland Ecuador, while the population from San Cristobal would be linked to the coastal mainland regions. Interestingly, the proposed origins for the Galapagos guava coincide with the first human settlings of the archipelago. Through approximate Bayesian computation, we propose a model where San Cristobal was the first island to be colonized by guava from the mainland, and then, it would have spread to Floreana and finally to Santa Cruz; Isabela would have been seeded from Floreana. An independent trajectory could also have contributed to the invasion of Floreana and Isabela. The pathway shown in our model agrees with the human colonization history of the different islands in the Galapagos. Our model, in conjunction with the clustering patterns of the individuals (based on genetic distances), suggests that guava introduction history in the Galapagos archipelago was driven by either a single event or a series of introduction events in rapid succession. We thus show that genetic analyses supported by historical sources can be used to track the arrival and spread of invasive species in novel habitats and the potential role of human activities in such processes.

Climate and sea surface trends in the Galapagos Islands

The Galapagos Islands are a global hotspot of environmental change. However, despite their potentially major repercussions, little is known about current and expected changes in regional terrestrial climate variables and sea surface temperatures (SST). Here, by analysing existing meteorological observations and secondary datasets, we find that the Islands have warmed by about 0.6 °C since the early 1980s, while at the same time becoming drier. In fact, the onset of the wet season is currently delayed 20 days. This drying trend may reverse, however, given that future climate projections for the region suggest mean annual precipitation may increase between 20 and 70%. This would also be accompanied by more extreme wet and hot conditions. Further, we find that regional SST has increased by 1.2 °C over the last two decades. These changes will, in turn, translate into deterioration of marine ecosystems and coral, proliferation of invasive species, and damages to human water, food, and infrastructure systems. Future projections, however, may be overestimated due to the poor capacity of climatic models to capture Eastern-Pacific ENSO dynamics. Our findings emphasize the need to design resilient climate adaptation policies that will remain robust in the face of a wide range of uncertain and changing climatic futures.

The human dimension of biodiversity changes on islands

Islands are among the last regions on Earth settled and transformed by human activities, and they provide replicated model systems for analysis of how people affect ecological functions. By analyzing 27 representative fossil pollen sequences encompassing the past 5000 years from islands globally, we quantified the rates of vegetation compositional change before and after human arrival. After human arrival, rates of turnover accelerate by a median factor of 11, with faster rates on islands colonized in the past 1500 years than for those colonized earlier. This global anthropogenic acceleration in turnover suggests that islands are on trajectories of continuing change. Strategies for biodiversity conservation and ecosystem restoration must acknowledge the long duration of human impacts and the degree to which ecological changes today differ from prehuman dynamics.

Baseline haematology, biochemistry, blood gas values and health status of the Galapagos swallow-tailed gull (Creagrus furcatus)

The swallow-tailed gull, Creagrus furcatus, is a seabird endemic to the Galápagos archipelago. In general health, blood chemistry and haematology, parameters have not been published for this species. Blood analyses were run on samples drawn from 58 clinically healthy swallow-tailed gulls captured at Islote Pitt on San Cristóbal Island in July 2016 (28) and South Plaza Island in June 2017 (30). A point of care blood analyzer (iSTAT) was used in the field to obtain results for HCO₃ ^-, pH, pCO₂, pO₂, TCO₂, anion gap, chloride, creatinine, glucose, haematocrit, haemoglobin, ionized calcium, potassium, sodium and urea nitrogen. A portable Lactate Plus™ analyzer was used to measure lactate. The baseline data reported is valuable for comparisons amongst different populations in the archipelago and to detect changes in health status of Galápagos swallow-tailed gulls.

Identifying drivers of forest resilience in long-term records from the Neotropics

Here, we use 30 long-term, high-resolution palaeoecological records from Mexico, Central and South America to address two hypotheses regarding possible drivers of resilience in tropical forests as measured in terms of recovery rates from previous disturbances. First, we hypothesize that faster recovery rates are associated with regions of higher biodiversity, as suggested by the insurance hypothesis. And second, that resilience is due to intrinsic abiotic factors that are location specific, thus regions presently displaying resilience in terms of persistence to current climatic disturbances should also show higher recovery rates in the past. To test these hypotheses, we applied a threshold approach to identify past disturbances to forests within each sequence. We then compared the recovery rates to these events with pollen richness before the event. We also compared recovery rates of each site with a measure of present resilience in the region as demonstrated by measuring global vegetation persistence to climatic perturbations using satellite imagery. Preliminary results indeed show a positive relationship between pre-disturbance taxonomic richness and faster recovery rates. However, there is less evidence to support the concept that resilience is intrinsic to a region; patterns of resilience apparent in ecosystems presently are not necessarily conservative through time.

Symbionts as Filters of Plant Colonization of Islands: Tests of Expected Patterns and Environmental Consequences in the Galapagos

The establishments of new organisms that arrive naturally or with anthropogenic assistance depend primarily on local conditions, including biotic interactions. We hypothesized that plants that rely on fungal symbionts are less likely to successfully colonize remote environments such as oceanic islands, and this can shape subsequent island ecology. We analyzed the mycorrhizal status of Santa Cruz Island, Galapagos flora compared with the mainland Ecuador flora of origin. We experimentally determined plant responsiveness and plant-soil feedback of the island flora and assessed mycorrhizal density and soil aggregate stability of island sites. We found that a greater proportion of the native island flora species belongs to families that typically do not associate with mycorrhizal fungi than expected based upon the mainland flora of origin and the naturalized flora of the island. Native plants benefited significantly less from soil fungi and had weaker negative soil feedbacks than introduced species. This is consistent with the observation that field sites dominated by native plant species had lower arbuscular mycorrhizal (AM) fungal density and lower soil aggregate stability than invaded field sites at the island. We found support for a mycorrhizal filter to the initial colonization of the Galapagos.

Effectiveness of water-saving technologies during early stages of restoration of endemic Opuntia cacti in the Galápagos Islands, Ecuador

Restoration of keystone species is a primary strategy used to combat biodiversity loss and recover ecological services. This is particularly true for oceanic islands, which despite their small land mass, host a large fraction of the planet’s imperiled species. The endemic Opuntia spp. cacti are one example and a major focus for restoration in the Galápagos archipelago, Ecuador. These cacti are keystone species that support much of the unique vertebrate animal community in arid zones, yet human activities have substantially reduced Opuntia populations. Extreme aridity poses an obstacle for quickly restoring Opuntia populations though water-saving technologies may provide a solution. The aim of this study was to evaluate current restoration efforts and the utility of two water-saving technologies as tools for the early stages of restoring Opuntia populations in the Galápagos archipelago. We planted 1,425 seedlings between 2013 and 2018, of which 66% had survived by the end of 2018. Compared with no-technology controls, seedlings planted with Groasis Waterboxx^® water-saving technology (polypropylene trays with water reservoir and protective refuge for germinants) had a greater rate of survival in their first two-years of growth on one island (Plaza Sur) and greater growth rate on four islands whereas the “Cocoon” water-saving technology (similar technology but made of biodegradable fiber) did not affect growth and actually reduced seedling survival. Survival and growth rate were also influenced by vegetation zone, elevation, and precipitation in ways largely contingent on island. Overall, our findings suggest that water-saving technologies are not always universally applicable but can substantially increase the survival and growth rate of seedlings in certain conditions, providing in some circumstances a useful tool for improving restoration outcomes for rare plants of arid ecosystems.

Psidium guajava in the Galapagos Islands: Population genetics and history of an invasive species

The threat of invasive plant species in island populations prompts the need to better understand their population genetics and dynamics. In the Galapagos islands, this is exemplified by the introduced guava (Psidium guajava), considered one of the greatest threats to the local biodiversity due to its effective spread in the archipelago and its ability to outcompete endemic species. To better understand its history and genetics, we analyzed individuals from three inhabited islands in the Galapagos archipelago with 11 SSR markers. Our results reveal similar genetic diversity between islands, and the populations appear to be distinct: the islands of San Cristobal and Isabela are genetically different while the population of Santa Cruz is a mixture from both. Additional evidence for genetic bottlenecks and the inference of introduction events suggests an original introduction of the species in San Cristobal, from where it was later introduced to Isabela, and finally into Santa Cruz. Alternatively, a second introduction in Isabela might have occurred. These results are contrasted with the historical record, providing a first overview of the history of P. guajava in the Galapagos islands and its current population dynamics.

The potential role of genetic assimilation during maize domestication

Domestication research has largely focused on identification of morphological and genetic differences between extant populations of crops and their wild relatives. Little attention has been paid to the potential effects of environment despite substantial known changes in climate from the time of domestication to modern day. In recent research, the exposure of teosinte (i.e., wild maize) to environments similar to the time of domestication, resulted in a plastic induction of domesticated phenotypes in teosinte. These results suggest that early agriculturalists may have selected for genetic mechanisms that cemented domestication phenotypes initially induced by a plastic response of teosinte to environment, a process known as genetic assimilation. To better understand this phenomenon and the potential role of environment in maize domestication, we examined differential gene expression in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) between past and present conditions. We identified a gene set of over 2000 loci showing a change in expression across environmental conditions in teosinte and invariance in maize. In fact, overall we observed both greater plasticity in gene expression and more substantial changes in co-expressionnal networks in teosinte across environments when compared to maize. While these results suggest genetic assimilation played at least some role in domestication, genes showing expression patterns consistent with assimilation are not significantly enriched for previously identified domestication candidates, indicating assimilation did not have a genome-wide effect.

Benefits of the destinations, not costs of the journeys, shape partial migration patterns

The reasons that lead some animals to seasonally migrate, and others to remain in the same area year-round, are poorly understood. Associations between traits, such as body size, and migration provide clues. For example, larger species and individuals are more likely to migrate. One explanation for this size bias in migration is that larger animals are capable of moving faster (movement hypothesis). However, body size is linked to many other biological processes. For instance, the energetic balances of larger animals are generally more sensitive to variation in food density because of body size effects on foraging and metabolism and this sensitivity could drive migratory decisions (forage hypothesis). Identifying the primary selective forces that drive migration ultimately requires quantifying fitness impacts over the full annual migratory cycle. Here, we develop a full annual migratory cycle model from metabolic and foraging theory to compare the importance of the forage and movement hypotheses. We parameterize the model for Galapagos tortoises, which were recently discovered to be size-dependent altitudinal migrants. The model predicts phenomena not included in model development including maximum body sizes, the body size at which individuals begin to migrate, and the seasonal timing of migration and these predictions generally agree with available data. Scenarios strongly support the forage hypothesis over the movement hypothesis. Furthermore, male Galapagos tortoises on Santa Cruz Island would be unable to grow to their enormous sizes without access to both highlands and lowlands. Whereas recent research has focused on links between traits and the migratory phases of the migratory cycle, we find that effects of body size on the non-migratory phases are far more important determinants of the propensity to migrate. Larger animals are more sensitive to changing forage conditions than smaller animals with implications for maintenance of migration and body size in the face of environmental change.

Population genomics of the endangered giant Galápagos tortoise

BACKGROUND

The giant Galápagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galápagos Islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological shift, we analyze the transcriptomic variability of five individuals of C. nigra, and compare it to similar data obtained from several continental species of turtles.

RESULTS

Having clarified the timing of divergence in the Chelonoidis genus, we report in C. nigra a very low level of genetic polymorphism, signatures of a weakened efficacy of purifying selection, and an elevated mutation load in coding and regulatory sequences. These results are consistent with the hypothesis of an extremely low long-term effective population size in this insular species. Functional evolutionary analyses reveal a reduced diversity of immunity genes in C. nigra, in line with the hypothesis of attenuated pathogen diversity in islands, and an increased selective pressure on genes involved in response to stress, potentially related to the climatic instability of its environment and its elongated lifespan. Finally, we detect no population structure or homozygosity excess in our five-individual sample.

CONCLUSIONS

These results enlighten the molecular evolution of an endangered taxon in a stressful environment and point to island endemic species as a promising model for the study of the deleterious effects on genome evolution of a reduced long-term population size.

Microrefugia and species persistence in the Galápagos highlands: a 26,000-year paleoecological perspective

The Galápagos Islands are known to have experienced significant drought during the Quaternary. The loss of mesophytic upland habitats has been suggested to underlie the relatively lower endemism of upland compared with lowland plant assemblages. A fossil pollen record spanning the last 26,000 years from an upland bog on Santa Cruz Island, revealed the persistent presence of highland pollen and spore types during the last glacial maximum and a millennial-scale series of droughts in the mid Holocene. The absence of lowland taxa and presence of mesic taxa led to the conclusion that the highland flora of the Galápagos persisted during both these periods. The resiliency of the highland flora of the Galápagos to long-term drought contradicts an earlier hypothesis that an extinction of highland taxa occurred during the last glacial maximum and that rapid Holocene speciation created the modern plant assemblage within the last 10,000 years. Based on the palynological data, we suggest that, even during the height of glacial and Holocene droughts, cool sea-surface temperatures and strong trade-wind activity would have promoted persistent ground level cloudiness that provided the necessary moisture inputs to maintain microrefugia for mesophytic plants. Although moist conditions were maintained, the lack of precipitation caused the loss of open water habitat during such events, and accounts for the known extinctions of species such as Azolla sp., and Elatine sp., while other moisture dependent taxa, i.e., Cyathea weatherbyana, persisted.

Seed dispersal networks in the Galápagos and the consequences of alien plant invasions

Alien plants are a growing threat to the Galápagos unique biota. We evaluated the impact of alien plants on eight seed dispersal networks from two islands of the archipelago. Nearly 10 000 intact seeds from 58 species were recovered from the droppings of 18 bird and reptile dispersers. The most dispersed invaders were Lantana camara, Rubus niveus and Psidium guajava, the latter two likely benefiting from an asynchronous fruit production with most native plants, which facilitate their consumption and spread. Lava lizards dispersed the seeds of 27 species, being the most important dispersers, followed by small ground finch, two mockingbirds, the giant tortoise and two insectivorous birds. Most animals dispersed alien seeds, but these formed a relatively small proportion of the interactions. Nevertheless, the integration of aliens was higher in the island that has been invaded for longest, suggesting a time-lag between alien plant introductions and their impacts on seed dispersal networks. Alien plants become more specialized with advancing invasion, favouring more simplified plant and disperser communities. However, only habitat type significantly affected the overall network structure. Alien plants were dispersed via two pathways: dry-fruited plants were preferentially dispersed by finches, while fleshy fruited species were mostly dispersed by other birds and reptiles.