Origin and population history of a recent colonizer, the yellow warbler in Galápagos and Cocos Islands

A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia)

The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.

What Darwin could not see: island formation and historical sea levels shape genetic divergence and island biogeography in a coastal marine species

Oceanic islands play a central role in the study of evolution and island biogeography. The Galapagos Islands are one of the most studied oceanic archipelagos but research has almost exclusively focused on terrestrial organisms compared to marine species. Here we used the Galapagos bullhead shark (Heterodontus quoyi) and single nucleotide polymorphisms (SNPs) to examine evolutionary processes and their consequences for genetic divergence and island biogeography in a shallow-water marine species without larval dispersal. The sequential separation of individual islands from a central island cluster gradually established different ocean depths between islands that pose barriers to dispersal in H. quoyi. Isolation by resistance analysis suggested that ocean bathymetry and historical sea level fluctuations modified genetic connectivity. These processes resulted in at least three genetic clusters that exhibit low genetic diversity and effective population sizes that scale with island size and the level of geographic isolation. Our results exemplify that island formation and climatic cycles shape genetic divergence and biogeography of coastal marine organisms with limited dispersal comparable to terrestrial taxa. Because similar scenarios exist in oceanic islands around the globe our research provides a new perspective on marine evolution and biogeography with implications for the conservation of island biodiversity.

Multi-character approach reveals a new mangrove population of the Yellow Warbler complex, Setophaga petechia, on Cozumel Island, Mexico

The Setophaga petechia complex includes 43 subspecies distributed within the new world, of which some are migratory and others are resident, with only two resident subspecies in the Mexican Caribbean: Setophaga petechia bryanti a mangrove subspecies belonging to the erithachorides group resident on the mainland of the Yucatan Peninsula and Setophaga petechia rufivertex endemic to Cozumel Island and belonging to the petechia group. Recently, a new population of individuals presenting intermediate phenotypic traits and living in mangrove ecosystems was discovered and reported for Cozumel Island. In this study, we used a multi-character approach including genetic (five ISSR genetic markers), morphometric (eight traits), phenotypic (four characteristics of males), and acoustic dataset (11 parameters) to understand the process of differentiation and the status of these new island individuals in relation to the two well-established subspecies using a total of 60 individuals (20 for each group). Through multivariate analyses based on different dataset used in our study, we show how the new population is related to the endemic island subspecies, S. p. rufivertex and to the mainland subspecies, S. p. bryanti while demonstrating finite differences. We conclude that the new population of S. petechia on Cozumel Island is a well-established population with high level of differentiation.

Avian disease surveillance on the island of San Cristóbal, Galápagos

Endemic island species face unprecedented threats, with many populations in decline or at risk of extinction. One important threat is the introduction of novel and potentially devastating diseases, made more pressing due to accelerating global connectivity, urban development, and climatic changes. In the Galápagos archipelago two important wildlife diseases: avian pox (Avipoxvirus spp.) and avian malaria (Plasmodium spp. and related Haemosporidia) challenge endemic species. San Cristóbal island has seen a paucity of disease surveillance in avian populations, despite the island's connectedness to the continent and the wider archipelago. To survey prevalence and better understand the dynamics of these two diseases on San Cristóbal, we captured 1205 birds of 11 species on the island between 2016 and 2020. Study sites included urban and rural lowland localities as well as rural highland sites in 2019. Of 995 blood samples screened for avian haemosporidia, none tested positive for infection. In contrast, evidence of past and active pox infection was observed in 97 birds and identified as strains Gal1 and Gal2. Active pox prevalence differed significantly with contemporary climatic conditions, being highest during El Niño events (~11% in 2016 and in 2019 versus <1% in the La Niña year of 2018). Pox prevalence was also higher at urban sites than rural (11% to 4%, in 2019) and prevalence varied between host species, ranging from 12% in medium ground finches (Geospiza fortis) to 4% in Yellow Warblers (Setophaga petechial aureola). In the most common infected species (Small Ground Finch: Geospiza fuliginosa), birds recovered from pox had significantly longer wings, which may suggest a selective cost to infection. These results illustrate the threat future climate changes and urbanization may present in influencing disease dynamics in the Galápagos, while also highlighting unknowns regarding species-specific susceptibilities to avian pox and the transmission dynamics facilitating outbreaks within these iconic species.

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.

Evolutionary History of the Galápagos Rail Revealed by Ancient Mitogenomes and Modern Samples

The biotas of the Galápagos Islands are one of the best studied island systems and have provided a broad model for insular species’ origins and evolution. Nevertheless, some locally endemic taxa, such as the Galápagos Rail Laterallus spilonota, remain poorly characterized. Owing to its elusive behavior, cryptic plumage, and restricted distribution, the Galápagos Rail is one of the least studied endemic vertebrates of the Galapagos Islands. To date, there is no genetic data for this species, leaving its origins, relationships to other taxa, and levels of genetic diversity uncharacterized. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here, we examine the genetics of Galápagos Rails using a combination of mitogenome de novo assembly with multilocus nuclear and mitochondrial sequencing from both modern and historical samples. We show that the Galápagos Rail is part of the “American black rail clade”, sister to the Black Rail L. jamaicensis, with a colonization of Galápagos dated to 1.2 million years ago. A separate analysis of one nuclear and two mitochondrial markers in the larger population samples demonstrates a shallow population structure across the islands, possibly due to elevated island connectivity. Additionally, birds from the island Pinta possessed the lowest levels of genetic diversity, possibly reflecting past population bottlenecks associated with overgrazing of their habitat by invasive goats. The modern and historical data presented here highlight the low genetic diversity in this endemic rail species and provide useful information to guide conservation efforts.

A simple dynamic model explains the diversity of island birds worldwide

Colonization, speciation and extinction are dynamic processes that influence global patterns of species richness^1-6. Island biogeography theory predicts that the contribution of these processes to the accumulation of species diversity depends on the area and isolation of the island^7,8. Notably, there has been no robust global test of this prediction for islands where speciation cannot be ignored⁹, because neither the appropriate data nor the analytical tools have been available. Here we address both deficiencies to reveal, for island birds, the empirical shape of the general relationships that determine how colonization, extinction and speciation rates co-vary with the area and isolation of islands. We compiled a global molecular phylogenetic dataset of birds on islands, based on the terrestrial avifaunas of 41 oceanic archipelagos worldwide (including 596 avian taxa), and applied a new analysis method to estimate the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation). Our model predicts-with high explanatory power-several global relationships. We found a decline in colonization with isolation, a decline in extinction with area and an increase in speciation with area and isolation. Combining the theoretical foundations of island biogeography^7,8 with the temporal information contained in molecular phylogenies¹⁰ proves a powerful approach to reveal the fundamental relationships that govern variation in biodiversity across the planet.

Strong phenotypic divergence in spite of low genetic structure in the endemic Mangrove Warbler subspecies (Setophaga petechia xanthotera) of Costa Rica

Despite the enormous advances in genetics, links between phenotypes and genotypes have been made for only a few nonmodel organisms. However, such links can be essential to understand mechanisms of ecological speciation. The Costa Rican endemic Mangrove Warbler subspecies provides an excellent subject to study differentiation with gene flow, as it is distributed along a strong precipitation gradient on the Pacific coast with no strong geographic barriers to isolate populations. Mangrove Warbler populations could be subject to divergent selection driven by precipitation, which influences soil salinity levels, which in turn influences forest structure and food resources. We used single nucleotide polymorphisms (SNPs) and morphological traits to examine the balance between neutral genetic and phenotypic divergence to determine whether selection has acted on traits and genes with functions related to specific environmental variables. We present evidence showing: (a) associations between environmental variables and SNPs, identifying candidate genes related to bill morphology (BMP) and osmoregulation, (b) absence of population genetic structure in neutrally evolving markers, (c) divergence in bill size across the precipitation gradient, and (d) strong phenotypic differentiation (P ST) which largely exceeds neutral genetic differentiation (F ST) in bill size. Our results indicate an important role for salinity, forest structure, and resource availability in maintaining phenotypic divergence of Mangrove Warblers through natural selection. Our findings add to the growing body of literature identifying the processes involved in phenotypic differentiation along environmental gradients in the face of gene flow.

Feeding innovations in a nested phylogeny of Neotropical passerines

Several studies on cognition, molecular phylogenetics and taxonomic diversity independently suggest that Darwin's finches are part of a larger clade of speciose, flexible birds, the family Thraupidae, a member of the New World nine-primaried oscine superfamily Emberizoidea. Here, we first present a new, previously unpublished, dataset of feeding innovations covering the Neotropical region and compare the stem clades of Darwin's finches to other neotropical clades at the levels of the subfamily, family and superfamily/order. Both in terms of raw frequency as well as rates corrected for research effort and phylogeny, the family Thraupidae and superfamily Emberizoidea show high levels of innovation, supporting the idea that adaptive radiations are favoured when the ancestral stem species were flexible. Second, we discuss examples of innovation and problem-solving in two opportunistic and tame Emberizoid species, the Barbados bullfinch Loxigilla barbadensis and the Carib grackle Quiscalus lugubris fortirostris in Barbados. We review studies on these two species and argue that a comparison of L. barbadensis with its closest, but very shy and conservative local relative, the black-faced grassquit Tiaris bicolor, might provide key insights into the evolutionary divergence of cognition.

Present diversity of Galápagos leaf-toed geckos (Phyllodactylidae: Phyllodactylus) stems from three independent colonization events

We re-examined the biogeography of the leaf-toed geckos (Phyllodactylus) endemic to the Galápagos Islands by analyzing for the first time samples of P. gilberti, a species endemic to Wolf island, in a phylogenetic framework. Our aim was to test the three-colonizations scenario previously proposed for these lizards and estimate the age of each colonization event. To achieve this we estimated simultaneously a species tree and divergence times with Bayesian methods. Our results supported the three-colonizations scenario. Similar to a previous hypothesis, the species tree obtained here showed that most species of Phyllodactylus are nested in a single clade with an age between 5.49 and 13.8Ma, whereas a second independent colonization corresponding to P. darwini from San Cristóbal island occurred 3.03Ma ago. The species from Wolf island, P. gilberti, stems from a more recent colonization event (0.69Ma). Thus, present diversity of Galápagos leaf-toed geckos stems from three independent, asynchronous colonization events. As with other Galápagos organisms, the Pacific coast of South America seems to be the source for the founders of P. gilberti.

Phylogeography of the Vermilion Flycatcher species complex: Multiple speciation events, shifts in migratory behavior, and an apparent extinction of a Galápagos-endemic bird species

The Vermilion Flycatcher (Pyrocephalus rubinus) is a widespread species found in North and South America and the Galápagos. Its 12 recognized subspecies vary in degree of geographic isolation, phenotypic distinctness, and migratory status. Some authors suggest that Galápagos subspecies nanus and dubius constitute one or more separate species. Observational reports of distinct differences in song also suggest separate species status for the austral migrant subspecies rubinus. To evaluate geographical patterns of diversification and taxonomic limits within this species complex, we carried out a molecular phylogenetic analysis encompassing 10 subspecies and three outgroup taxa using mitochondrial (ND2, Cyt b) and nuclear loci (ODC introns 6 through 7, FGB intron 5). We used samples of preserved tissues from museum collections as well as toe pad samples from museum skins. Galápagos and continental clades were recovered as sister groups, with initial divergence at ∼1mya. Within the continental clade, North and South American populations were sister groups. Three geographically distinct clades were recovered within South America. We detected no genetic differences between two broadly intergrading North American subspecies, mexicanus and flammeus, suggesting they should not be recognized as separate taxa. Four western South American subspecies were also indistinguishable on the basis of loci that we sampled, but occur in a region with patchy habitat, and may represent recently isolated populations. The austral migrant subspecies, rubinus, comprised a monophyletic mitochondrial clade and had many unique nuclear DNA alleles. In combination with its distinct song, exclusive song recognition behavior, different phenology, and an isolated breeding range, our data suggests that this taxon represents a separate species from other continental populations. Mitochondrial and nuclear genetic data, morphology, and behavior suggest that Galápagos forms should be elevated to two full species corresponding to the two currently recognized subspecies, nanus and dubius. The population of dubius is presumed to be extinct, and thus would represent the first documented extinction of a Galápagos-endemic bird species. Two strongly supported mitochondrial clades divide Galápagos subspecies nanus in a geographic pattern that conflicts with previous hypotheses that were based on plumage color. Several populations of nanus have recently become extinct or are in serious decline. Urgent conservation measures should seek to preserve the deep mitochondrial DNA diversity within nanus, and further work should explore whether additional forms should be recognized within nanus. Ancestral states analysis based on our phylogeny revealed that the most recent common ancestor of extant Vermilion Flycatcher populations was migratory, and that migratory behavior was lost more often than gained within Pyrocephalus and close relatives, as has been shown to be the case within Tyrannidae as a whole.

Historical isolation of the Galápagos carpenter bee (Xylocopa darwini) despite strong flight capability and ecological amplitude

Colonization across the Galápagos Islands by the carpenter bee (Xylocopa darwini) was reconstructed based on distribution of mitochondrial haplotypes (cytochrome oxidase II (COII) sequences) and haplotype lineages. A total of 12 haplotypes were found in 118 individuals of X. darwini. Distributional, phylogenetic and phylogeographic analyses suggest early colonization of most islands followed by historical isolation in two main groups: eastern and central-western islands. Evidence of recurrent inter-island colonization of haplotypes is largely lacking, despite strong flight capability and ecological amplitude of the species. Recent palaeogeographic data suggest that several of the current islands were connected in the past and thus the isolation pattern may have been even more pronounced. A contrast analysis was also carried out on 10 animal groups of the Galápagos Islands, and on haplotype colonization of seven animal and plant species from several oceanic archipelagos (the Galápagos, Azores, Canary Islands). New colonization metrics on the number of potential vs. inferred colonization events revealed that the Galápagos carpenter bee shows one of the most significant examples of geographic isolation.

Geographic distance affects dispersal of the patchy distributed greater long-tailed hamster (Tscherskia triton)

Dispersal is a fundamental process in ecology influencing the genetic structure and the viability of populations. Understanding how variable factors influence the dispersal of the population is becoming an important question in animal ecology. To date, geographic distance and geographic barriers are often considered as main factors impacting dispersal, but their effects are variable depending on different conditions. In general, geographic barriers affect more significantly than geographic distance on dispersal. In rapidly expanding populations, however, geographic barriers have less effect on dispersal than geographic distance. The effects of both geographic distance and geographic barriers in low-density populations with patchy distributions are poorly understood. By using a panel of 10 microsatellite loci we investigated the genetic structure of three patchy-distributed populations of the Greater long-tailed hamster (Tscherskia triton) from Raoyang, Guan and Shunyi counties of the North China Plain. The results showed that (i) high genetic diversity and differentiation exist in three geographic populations with patchy distributions; (ii) gene flow occurs among these three populations with physical barriers of Beijing city and Hutuo River, which potentially restricted the dispersal of the animal; (iii) the gene flow is negatively correlated with the geographic distance, while the genetic distance shows the positive correlation. Our results suggest that the effect of the physical barriers is conditional-dependent, including barrier capacity or individual potentially dispersal ability. Geographic distance also acts as an important factor affecting dispersal for the patchy distributed geographic populations. So, gene flow is effective, even at relatively long distances, in balancing the effect of geographic barrier in this study.

Genetic, morphological, and acoustic evidence reveals lack of diversification in the colonization process in an island bird

Songbirds with recently (i.e., early Holocene) founded populations are suitable models for studying incipient differentiation in oceanic islands. On such systems each colonization event represents a different evolutionary episode that can be studied by addressing sets of diverging phenotypic and genetic traits. We investigate the process of early differentiation in the spectacled warbler (Sylvia conspicillata) in 14 populations separated by sea barriers from three Atlantic archipelagos and from continental regions spanning from tropical to temperate latitudes. Our approach involved the study of sexual acoustic signals, morphology, and genetic data. Mitochondrial DNA did not provide clear population structure. However, microsatellites analyses consistently identified two genetic groups, albeit without correspondence to subspecies classification and little correspondence to geography. Coalescent analyses showed significant evidence for gene flow between the two genetic groups. Discriminant analyses could not correctly assign morphological or acoustic traits to source populations. Therefore, although theory predicting that in isolated populations genetic, morphological, or acoustic traits can lead to radiation, we have strikingly failed to document differentiation on these attributes in a resident passerine throughout three oceanic archipelagos.

Pronounced fixation, strong population differentiation and complex population history in the Canary Islands blue tit subspecies complex

Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible.

Multiple lineages of Avian malaria parasites (Plasmodium) in the Galapagos Islands and evidence for arrival via migratory birds

Haemosporidian parasites in the genus Plasmodium were recently detected through molecular screening in the Galapagos Penguin (Spheniscus mendiculus). We summarized results of an archipelago-wide screen of 3726 endemic birds representing 22 species for Plasmodium spp. through a combination of molecular and microscopy techniques. Three additional Plasmodium lineages were present in Galapagos. Lineage A-infected penguins, Yellow Warblers (Setophaga petechia aureola), and one Medium Ground Finch (Geospiza fortis) and was detected at multiple sites in multiple years [corrected]. The other 3 lineages were each detected at one site and at one time; apparently, they were transient infections of parasites not established on the archipelago. No gametocytes were found in blood smears of infected individuals; thus, endemic Galapagos birds may be dead-end hosts for these Plasmodium lineages. Determining when and how parasites and pathogens arrive in Galapagos is key to developing conservation strategies to prevent and mitigate the effects of introduced diseases. To assess the potential for Plasmodium parasites to arrive via migratory birds, we analyzed blood samples from 438 North American breeding Bobolinks (Dolichonyx oryzivorus), the only songbird that regularly migrates through Galapagos. Two of the ephemeral Plasmodium lineages (B and C) found in Galapagos birds matched parasite sequences from Bobolinks. Although this is not confirmation that Bobolinks are responsible for introducing these lineages, evidence points to higher potential arrival rates of avian pathogens than previously thought. Linajes Múltiples de Parásitos de Malaria Aviar (Plasmodium) en las Islas Galápagos y Evidencia de su Arribo por Medio de Aves Migratorias.

Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco)

The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis), and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands in driving divergence and speciation, but also their potential role as repositories of ancestral diversity.