Cryptic diversity in Black rats Rattus rattus of the Galápagos Islands,Ecuador

Human activity has facilitated the introduction of a number of alien mammal species to the Galápagos Archipelago. Understanding the phylogeographic history and population genetics of invasive species on the Archipelago is an important step in predicting future spread and designing effective management strategies. In this study, we describe the invasion pathway of Rattus rattus across the Galápagos using microsatellite data, coupled with historical knowledge. Microsatellite genotypes were generated for 581 R. rattus sampled from 15 islands in the archipelago. The genetic data suggest that there are at least three genetic lineages of R. rattus present on the Galápagos Islands. The spatial distributions of these lineages correspond to the main centers of human settlement in the archipelago. There was limited admixture among these three lineages, and these finding coupled with low rates of gene flow among island populations suggests that interisland movement of R. rattus is rare. The low migration among islands recorded for the species will have a positive impact on future eradication efforts.     

Introduction history and genetic diversity of the invasive ant <Emphasis Type="Italic">Solenopsis geminata</Emphasis> in the Galápagos Islands

The Galápagos Islands constitute one of the most pristine tropical systems on Earth. However, the complex and fragile equilibrium of native species is threatened by invasive species, among which is one of the most successful ants in the world, the tropical fire ant, Solenopsis geminata. We characterized the genetic structure and diversity of populations of S. geminata in the Galápagos Islands and unravelled the archipelago colonization by combining Bayesian clustering methods and coalescent-based scenario testing. Using 12 microsatellite markers and one mitochondrial DNA fragment (COI), we analysed individuals collected in all main invaded islands of the archipelago and from the native areas in Costa Rica and mainland Ecuador. We also used mitochondrial DNA to infer evolutionary relationships of samples collected in Galápagos Islands, Ecuador, Costa Rica and other Latin American countries. Our results showed that genetic diversity was significantly lower in Galápagos Islands and mainland Ecuador populations when compared to Costa Rican populations, and that samples from Galápagos Islands and mainland Ecuador (Guayaquil) clustered in a single group and all share a single mtDNA haplotype. Approximate Bayesian Computation favoured a scenario assuming that populations from Galápagos Islands diverged from mainland Ecuador. The city of Guyaquil, an obligatory hub for tourism and trade, could act as a bridgehead.     

Recent colonization of the Galápagos by the tree Geoffroea spinosa Jacq. (Leguminosae)

This study puts together genetic data and an approximate bayesian computation (ABC) approach to infer the time at which the tree Geoffroea spinosa colonized the Galápagos Islands. The genetic diversity and differentiation between Peru and Galápagos population samples, estimated using three chloroplast spacers and six microsatellite loci, reveal significant differences between two mainland regions separated by the Andes mountains (Inter Andean vs. Pacific Coast) as well as a significant genetic differentiation of island populations. Microsatellites identify two distinct geographical clusters, the Galápagos and the mainland, and chloroplast markers show a private haplotype in the Galápagos. The nuclear distinctiveness of the Inter Andean populations suggests current restricted pollen flow, but chloroplast points to cross‐Andean dispersals via seeds, indicating that the Andes might not be an effective biogeographical barrier. The ABC analyses clearly point to the colonization of the Galápagos within the last 160 000 years and possibly as recently as 4750 years ago (475 generations). Founder events associated with colonization of the two islands where the species occurs are detected, with Española having been colonized after Floreana. We discuss two nonmutually exclusive possibilities for the colonization of the Galápagos, recent natural dispersal vs. human introduction.     

<Emphasis Type="Italic">Anthidium vigintiduopunctatum</Emphasis> Friese (Hymenoptera: Megachilidae): the elusive “dwarf bee” of the Galápagos Archipelago?

The endemic large carpenter bee, Xylocopa darwini Cockerell, was the only known pollinator to the Galápagos Archipelago but as early as 1964 locals also spoke of the “dwarf bee of Floreana”. We report the presence of the wool carder bee, Anthidium vigintiduopunctatum Friese, on the island of Floreana and use a species distribution model to predict its distribution in the archipelago. We found that this species has the potential to invade almost one-third the surface area of the Galápagos Archipelago, primarily in low arid areas. Given that wool carder bees are uncommonly collected, we discuss whether this species is a previously undetected native bee or a recent adventive species to the Galápagos.     

Phylogeography of the Galápagos hawk (Buteo galapagoensis): a recent arrival to the Galápagos Islands

Galápagos hawks (Buteo galapagoensis) are one of the most inbred bird species in the world, living in small, isolated island populations. We used mitochondrial sequence and nuclear minisatellite data to describe relationships among Galápagos hawk populations and their colonization history. We sampled 10 populations (encompassing the entire current species range of nine islands and one extirpated population), as well as the Galápagos hawk's closest mainland relative, the Swainson's hawk (B. swainsoni). There was little sequence divergence between Galápagos and Swainson's hawks (only 0.42% over almost 3kb of data), indicating that the hawks colonized Galápagos very recently, likely less than 300,000 years ago, making them the most recent arrivals of the studied taxa. There were only seven, closely related Galápagos hawk haplotypes, with most populations being monomorphic. The mitochondrial and minisatellite data together indicated a general pattern of rapid population expansion followed by genetic isolation of hawk breeding populations. The recent arrival, genetic isolation, and phenotypic differentiation among populations suggest that the Galápagos hawk, a rather new species itself, is in the earliest stages of further divergence.     

Conservation status of landbirds on Floreana: the smallest inhabited Galápagos Island

On Floreana, the smallest inhabited island in the Galápagos, populations of several species of birds have either been extirpated or, based on anecdotal evidence and small‐scale surveys, are declining. Our objective, therefore, was to conduct a comprehensive survey of landbirds encompassing the entire island during three breeding seasons (2014–2016). We conducted surveys at 59 points in 2014, 257 in 2015, and 295 in 2016. Each survey point was sampled once. We detected 12 species during our surveys. Galápagos Flycatchers, Yellow Warblers, Small and Medium ground‐finches, and Small Tree‐Finches were widely distributed over the entire island. Common Cactus‐Finches and Medium Tree‐Finches had more restricted distributions in the lower or higher parts of the island. Few Dark‐billed Cuckoos (Coccyzus melacoryphus), Paint‐billed Crakes (Neocrex erythrops), Galápagos Doves (Zenaida galapagoensis), and Galápagos Short‐eared Owls (Asio flammeus galapagoensis) were recorded. Small Ground‐Finches and Small Tree‐Finches were found at densities comparable to those on other Galápagos Islands, whereas densities of Galápagos Flycatchers and Yellow Warblers were higher on Floreana than on other islands. Endemic Medium Tree‐Finches were confined to an area of 24 km², mainly in the highlands, but were still widespread and common in their restricted habitat, with the number of territories estimated to be between 3900 and 4700. Of 22 originally occurring landbirds on Floreana, no fewer than 10 species have either been extirpated or are likely to have been extirpated since the arrival of the first human inhabitants. The combined effects of introduced mammals, large‐scale habitat destruction, and direct human persecution were responsible for the extirpation of six species during the 19th century. Three additional species have been extirpated since 1960, likely due to the introduction of the parasitic fly Philornis downsi, and this fly remains a major threat for the remaining bird species. Developing strategies for reducing the impact of these flies on the birds of the Galapagos Islands must be a high priority. In addition, habitat management and restoration, including the control of invasive plants and promotion of native tree species, will be critically important in conserving landbird populations on Floreana.     

Eight polymorphic microsatellite markers isolated from the widespread avian louse Colpocephalum turbinatum (Phthiraptera: Amblycera: Menoponidae)

We report eight novel microsatellite loci for Colpocephalum turbinatum, a parasitic louse of the endangered Galápagos hawk (Buteo galapagoensis). Two island populations of C. turbinatum (N = 30) were genotyped for each locus. We found between two and 12 alleles per locus, polymorphic information content from 0.268 to 0.798, observed heterozygosity from 0.067 to 0.667 and no linkage disequilibrium was detected between loci. These markers will be useful in understanding contemporary gene flow of C. turbinatum among islands in the Galápagos and in understanding transmission dynamics between B. galapagoensis hosts, within and between social groups. Because this louse is unusually widespread among avian host taxa, parasitizing at least 53 bird species in the Falconiformes, Strigiformes and Columbiformes, these markers are likely to be useful outside the context of the Galápagos Islands.     

Low MHC variation in the endangered Galápagos penguin (<Emphasis Type="Italic">Spheniscus mendiculus</Emphasis>)

The major histocompatibility complex (MHC) is one of the most polymorphic regions of the genome, likely due to balancing selection acting to maintain alleles over time. Lack of MHC variability has been attributed to factors such as genetic drift in small populations and relaxed selection pressure. The Galápagos penguin (Spheniscus mendiculus), endemic to the Galápagos Islands, is the only penguin that occurs on the equator. It relies upon cold, nutrient-rich upwellings and experiences severe population declines when ocean temperatures rise during El Niño events. These bottlenecks, occurring in an already small population, have likely resulted in reduced genetic diversity in this species. In this study, we used MHC class II exon 2 sequence data from a DRB1-like gene to characterize the amount of genetic variation at the MHC in 30 Galápagos penguins, as well as one Magellanic penguin (S. magellanicus) and two king penguins (Aptenodytes patagonicus), and compared it to that in five other penguin species for which published data exist. We found that the Galápagos penguin had the lowest MHC diversity (as measured by number of polymorphic sites and average divergence among alleles) of the eight penguin species studied. A phylogenetic analysis showed that Galápagos penguin MHC sequences are most closely related to Humboldt penguin (Spheniscus humboldti) sequences, its putative sister species based on other loci. An excess of non-synonymous mutations and a pattern of trans-specific evolution in the neighbor-joining tree suggest that selection is acting on the penguin MHC.     

Tracing early stages of species differentiation: Ecological,morphological and genetic divergence of Galápagos sea lion populations

Background  

Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki) are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation.     

Ten novel dinucleotide microsatellite loci cloned from the Galápagos sea lion (Zalophus californianus wollebaeki) are polymorphic in other pinniped species

We isolated and characterized 10 novel dinucleotide microsatellite loci from the Galápagos sea lion (Zalophus californianus wollebaeki) and tested their amplification utility in four further otariid species (Zalophus californianus californianus, Arctocephalus gazella, Arctocephalus australis and Eumetopias jubatus) and three phocid species (Hydrurga leptonyx, Halichoerus grypus and Phoca vitulina). All of the loci amplified polymorphic polymerase chain reaction (PCR) products in at least three species other than the Galápagos sea lion. These markers will be useful for studies of pinniped mating systems, genetic structure and genetic diversity.     

Population Genetic Structure and Conservation of the Galápagos Petrel (Pterodroma phaeopygia)

The Galápagos petrel (Pterodroma phaeopygia) is endemic to the Galápagos archipelago, where it is known to breed only on five islands. The species has been listed as critically endangered due to habitat deterioration and predation by introduced mammals. Significant morphological and behavioural differences among petrels nesting on different islands suggest that island populations may differ genetically. Furthermore, nesting phenology suggests that genetically differentiated seasonal populations may exist within at least one island. We analysed variation in six microsatellite loci and part of the mitochondrial ATPase 6/8 gene in 206 Galápagos petrels sampled from all five islands. No evidence of genetic structuring within islands was found, although statistical power was low. In contrast, significant differences occurred among island populations. For the microsatellite loci, private alleles occurred at all islands, sometimes at high frequency; global and pairwise estimates of genetic differentiation were all statistically significant; Bayesian analysis of genotypes frequencies provided strong support for three genetic populations; and most estimates of migration between populations did not differ significantly from zero. Only two ATPase haplotypes were found, but the geographic distribution of haplotypes indicated significant differentiation among populations. For conservation purposes, populations from Floreana, Santa Cruz, San Cristóbal and Santiago should be regarded as separate genetic management units. Birds from Isabela appear to be derived recently from the Santiago population, and the population on San Cristóbal appears to be a mixture of birds from other populations. However, considering ecological and behavioural differences among birds from different islands, we recommend that all five populations be protected.     

The Galápagos Islands: biogeographic patterns and geology

In the traditional biogeographic model, the Galápagos Islands appeared a few million years ago in a sea where no other islands existed and were colonized from areas outside the region. However, recent work has shown that the Galápagos hotspot is 139 million years old (Early Cretaceous), and so groups are likely to have survived at the hotspot by dispersal of populations onto new islands from older ones. This process of metapopulation dynamics means that species can persist indefinitely in an oceanic region, as long as new islands are being produced. Metapopulations can also undergo vicariance into two metapopulations, for example at active island arcs that are rifted by transform faults. We reviewed the geographic relationships of Galápagos groups and found 10 biogeographic patterns that are shared by at least two groups. Each of the patterns coincides spatially with a major tectonic structure; these structures include: the East Pacific Rise; west Pacific and American subduction zones; large igneous plateaus in the Pacific; Alisitos terrane (Baja California), Guerrero terrane (western Mexico); rifting of North and South America; formation of the Caribbean Plateau by the Galápagos hotspot, and its eastward movement; accretion of Galápagos hotspot tracks; Andean uplift; and displacement on the Romeral fault system. All these geological features were active in the Cretaceous, suggesting that geological change at that time caused vicariance in widespread ancestors. The present distributions are explicable if ancestors survived as metapopulations occupying both the Galápagos hotspot and other regions before differentiating, more or less in situ.     

Isolation and characterization of microsatellite loci from Galápagos lava lizards (Microlophus spp.)

We describe the isolation of microsatellite loci from Galápagos lava lizards (Microlophus spp.) using an enriched genomic library. Twelve loci that are polymorphic among six populations from two species are described. Characterization of these loci in 20 individuals within one population (Isla Plaza Sur) showed seven to be polymorphic with 3–11 alleles. Heterozygosities within this population were high (0.32–0.90) and did not deviate from Hardy–Weinberg expectations. We suggest that these markers will be useful in studies of population differentiation within and among islands across the Galápagos archipelago.     

Effect of population size and selection on Toll-like receptor diversity in populations of Galápagos mockingbirds

The interactions of evolutionary forces are difficult to analyse in free-living populations. However, when properly understood, they provide valuable insights into evolutionary biology and conservation genetics. This is particularly important for the interplay of genetic drift and natural selection in immune genes that confer resistance to disease. The Galápagos Islands are inhabited by four closely related species of mockingbirds (Mimus spp.). We used 12 different-sized populations of Galápagos mockingbirds and one population of their continental relative northern mockingbird (Mimus polyglottos) to study the effects of genetic drift on the molecular evolution of immune genes, the Toll-like receptors (TLRs: TLR1B, TLR4 and TLR15). We found that neutral genetic diversity was positively correlated with island size, indicating an important effect of genetic drift. However, for TLR1B and TLR4, there was little correlation between functional (e.g., protein) diversity and island size, and protein structural properties were largely conserved, indicating only a limited effect of genetic drift on molecular phenotype. By contrast, TLR15 was less conserved and even its putative functional polymorphism correlated with island size. The patterns observed for the three genes suggest that genetic drift does not necessarily dominate selection even in relatively small populations, but that the final outcome depends on the degree of selection constraint that is specific for each TLR locus.     

DIATOMS (BACILLARIOPHYTA) OF ISOLATED ISLANDS: NEW TAXA IN THE GENUS NAVICULA SENSU STRICTO FROM THE GALáPAGOS ISLANDS1

The diatoms (Bacillariophyta) from a coastal lagoon from the Diablas wetlands (Isla Isabela, the Galápagos Islands) were studied in material from surface samples and a sediment core spanning the past 2,700 years in order to examine evidence of diatom evolution under geographic isolation. The total number of taxa found was ～100. Ultrastructural variation in valve morphology between members of Galápagos taxa was used to describe 10 species from the genus Navicula sensu stricto, which are new to science. Four taxa: N. isabelensis, N. isabelensoides, N. isabelensiformis, and N. isabelensiminor, shared several key characteristics that may be indicative of a common evolutionary heritage; these species therefore provide possible evidence for the in situ evolution of diatoms in the Galápagos coastal lagoons. Shared morphological characteristics include: (i) stria patterning in the central area, (ii) an elevated and thickened external raphe‐sternum, (iii) external central raphe endings that are slightly deflected toward the valve primary side, and (iv) an arched valve surface. To explain these findings, two models were proposed. The first suggested limited lateral diatomaceous transport of Navicula species between the Galápagos and continental South America. Alternatively, these new species may be ecological specialists arising from the unique environmental conditions of the Galápagos coastal lagoons, which restrict the colonization of common diatom taxa and enable the establishment of novel, rare species. The Diablas wetlands are an important site for diatom research, where local‐scale environmental changes have combined with global‐scale biogeographic processes resulting in unique diatom assemblages.     

The role of spines in anthropogenic seed dispersal on the Galápagos Islands

1. Dispersal has important ecological and evolutionary consequences for populations, but understanding the role of specific traits in dispersal can be difficult and requires careful experimentation. Moreover, understanding how humans alter dispersal is an important question, especially on oceanic islands where anthropogenic disturbance through species introductions can dramatically alter native ecosystems.
2. In this study, we investigated the functional role of spines in seed dispersal of the plant caltrop (Tribulus cistoides L., Zygophyllaceae) by anthropogenic dispersal agents. We also tested whether humans or wildlife are more important seed dispersers of T. cistoides on the Galápagos.
3. Tribulus cistoides is found on tropical mainland and oceanic island habitats. The dispersal structure of T. cistoides is called a mericarp, and they are typically protected by one pair of upper spines and a second pair of lower spines, but the presence and size of spines varies within and between populations. On the Galápagos, the upper and lower spines protect mericarps from seed predation by Darwin's finches. We tested whether spines play a dual role in dispersal by factorially manipulating the presence/absence of the upper and lower spines to simulate natural variation in mericarp morphology.
4. The upper spines greatly facilitated seed dispersal, whereas the lower spines had no discernible effect on dispersal. The presence of upper spines increased dispersal rate on shoes by pedestrians 23‐fold, on fabrics (e.g., towels) and cars by nearly twofold, and the presence of upper spines increased dispersal distance by cars sixfold. When comparing dispersal rates in habitats with high (roads and foot paths) versus low (arid forest) anthropogenic activity, dispersal rates were demonstrably higher in the habitats with more human activity.
5. These results have important implications for understanding the ecology and evolution of plant dispersal in the Anthropocene. Spines on the fruits of T. cistoides play important functional roles in anthropogenic dispersal, whereas native and introduced wildlife plays a minor role in dispersal on inhabited islands of the Galápagos. Our results imply that seed predators and humans are jointly shaping the ecology and evolution of contemporary populations of T. cistoides on the Galápagos.

     

A set of highly discriminating microsatellite loci for the Galápagos marine iguana Amblyrhynchus cristatus

We describe here the cloning of 12 (7 dinucleotide, 1 trinucleotide and 4 tetranucleotide) microsatellite loci for the Galápagos marine iguana Amblyrhynchus cristatus. When tested for individuals from five different island populations on the Galápagos archipelago, high genetic diversities (9–20 alleles per locus) and heterozygosities (0.200–0.944) were observed. All loci showed no obvious deviations from Hardy–Weinberg equilibrium. The new set of microsatellite loci was able to assign individuals reliably to their island of origin, thus being able to discriminate between residents and migrants between islands.     

The vector ecology of introduced Culex quinquefasciatus populations,and implications for future risk of West Nile virus emergence in the Galápagos archipelago

Culex quinquefasciatus Say (Diptera: Culicidae), an important vector of West Nile virus (WNV) in the U.S.A., was first detected on the Galápagos Islands (Ecuador) in the 1980s. However, little is known of its ecology, distribution or capacity for arbovirus transmission in the Galápagos. We characterize details of lifecycle (including gonotrophic period), temporal abundance, spatial distribution, vector competence and host‐feeding behaviour. Culex quinquefasciatus was detected on five islands of the Galápagos during 2006–2011. A period of 7–14 days was required for egg–adult emergence; water salinity above 5 ppt was demonstrated to hinder larval development. Blood‐meal analysis indicated feeding on reptiles, birds and mammals. Assessment of WNV vector competency of Galápagos C. quinquefasciatus showed a median infectious dose of 7.41 log₁₀ plaque‐forming units per millilitre and evidence of vertical transmission (minimal filial infection rate of 3.7 per 1000 progeny). The distribution of C. quinquefasciatus across the archipelago could be limited by salt intolerance, and its abundance constrained by high temperatures. Feeding behaviour indicates potential to act as a bridge vector for transmission of pathogens across multiple taxa. Vertical transmission is a potential persistence mechanism for WNV on Galápagos. Together, our results can be used for epidemiological assessments of WNV and target vector control, should this pathogen reach the Galápagos Islands.     

Radiation following long‐distance dispersal: the contributions of time,opportunity and diaspore morphology in Sicyos (Cucurbitaceae)

Aim  To infer the most plausible explanations for the presence of 14 species of the Neotropical cucurbit genus Sicyos on the Hawaiian Islands, two on the Galápagos Islands, two in Australia, and one in New Zealand. Location  Neotropics, the Hawaiian and Galápagos archipelagos, Australia and New Zealand. Methods  We tested long‐problematic generic boundaries in the tribe Sicyoeae and reconstructed the history of Sicyos using plastid and nuclear DNA sequences from 87 species (many with multiple accessions) representing the group’s generic and geographic diversity. Maximum likelihood and Bayesian approaches were used to infer relationships, divergence times, biogeographic history and ancestral traits. Results  Thirteen smaller genera, including Sechium, are embedded in Sicyos, which when re‐circumscribed as a monophyletic group comprises 75 species. The 14 Hawaiian species of Sicyos descended from a single ancestor that arrived c. 3 million years ago (Ma), Galápagos was reached twice at c. 4.5 and 1 Ma, the species in Australia descended from a Neotropical ancestor (c. 2 Ma), and New Zealand was reached from Australia. Time since arrival thus does not correlate with Sicyos species numbers on the two archipelagos. Main conclusions  A plausible mechanism for the four trans‐Pacific dispersal events is adherence to birds of the tiny hard fruit with retrorsely barbed spines found in those lineages that underwent long‐distance migrations. The Hawaiian clade has lost these spines, resulting in a lower dispersal ability compared with the Galápagos and Australian lineages, and perhaps favouring allopatric speciation.