A geometric morphometric appraisal of beak shape in Darwin's finches

Beak size and shape in Darwin's finches have traditionally been quantified using a few univariate measurements (length, depth, width). Here we show the improved inferential resolution of geometric morphometric methods, as applied to three hierarchical levels: (i) among seven species on Santa Cruz Island, (ii) among different sites on Santa Cruz for a single species (Geospiza fortis), and (iii) between large and small beak size morphs of G. fortis at one site (El Garrapatero). Our results support previous studies in finding an axis of shape variation (long/shallow/pointy vs. short/deep/blunt) that separates many of the species. We also detect additional differences among species in the relative sizes and positions of the upper and lower mandibles and in curvature of the mandibles. Small-scale, but potentially relevant, shape variation was also detected among G. fortis from different sites and between sympatric beak size morphs. These results suggest that adaptation to different resources might contribute to diversification on a single island.     

Reproductive isolation of sympatric morphs in a population of Darwin's finches

Recent research on speciation has identified a central role for ecological divergence, which can initiate speciation when (i) subsets of a species or population evolve to specialize on different ecological resources and (ii) the resulting phenotypic modes become reproductively isolated. Empirical evidence for these two processes working in conjunction, particularly during the early stages of divergence, has been limited. We recently described a population of the medium ground finch, Geospiza fortis, that features large and small beak morphs with relatively few intermediates. As in other Darwin's finches of the Galápagos Islands, these morphs presumably diverged in response to variation in local food availability and inter- or intraspecific competition. We here demonstrate that the two morphs show strong positive assortative pairing, a pattern that holds over three breeding seasons and during both dry and wet conditions. We also document restrictions on gene flow between the morphs, as revealed by genetic variation at 10 microsatellite loci. Our results provide strong support for the central role of ecology during the early stages of adaptive radiation.     

Sisyphean evolution in Darwin's finches

The trajectory of speciation involves geographic isolation of ancestral populations followed by divergence by natural selection, genetic drift or sexual selection. Once started, the process may experience fits and starts, as sometimes diverging populations intermittently reconnect. In theory populations might cycle between stages of differentiation and never attain species status, a process we refer to as Sisyphean evolution. We argue that the six putative ground finch species (genus Geospiza) of the Galápagos Islands represent a dramatic example of Sisyphean evolution that has been confused with the standard model of speciation. The dynamic environment of the Galápagos, closely spaced islands, and frequent dispersal and introgression have prevented the completion of the speciation process. We suggest that morphological clusters represent locally adapted ecomorphs, which might mimic, and have been confused with, species, but these ecomorphs do not form separate gene pools and are ephemeral in space and time. Thus the pattern of morphological, behavioural and genetic variation supports recognition of a single species of Geospiza, which we suggest should be recognized as Darwin's ground finch (Geospiza magnirostris). We argue that instead of providing an icon of insular speciation and adaptive radiation, which is featured in nearly every textbook on evolutionary biology, Darwin's ground finch represents a potentially more interesting phenomenon, one of transient morphs trapped in an unpredictable cycle of Sisyphean evolution. Instead of revealing details of the origin of species, the mechanisms underlying the transient occurrence of ecomorphs provide one of the best illustrations of the antagonistic effects of natural selection and introgression.     

Introgressive hybridization and natural selection in Darwin's finches

Introgressive hybridization, i.e. hybridization with backcrossing, can lead to the fusion of two species, but it can also lead to evolution of a new trajectory through an enhancement of genetic variation in a new or changed ecological environment. On Daphne Major Island in the Galápagos archipelago, ~1–2% of Geospiza fortis finches breed with the resident G. scandens and with the rare immigrant species G. fuliginosa in each breeding season. Previous research has demonstrated morphological convergence of G. fortis and G. scandens over a 30‐year period as a result of bidirectional introgression. Here we examine the role of hybridization with G. fuliginosa in the evolutionary trajectory of G. fortis. Geospiza fuliginosa (~12 g) is smaller and has a more pointed beak than G. fortis (~17 g). Genetic variation of the G. fortis population was increased by receiving genes more frequently from G. fuliginosa than from G. scandens (~21 g). A severe drought in 2003–2005 resulted in heavy and selective mortality of G. fortis with large beaks, and they became almost indistinguishable morphologically from G. fuliginosa. This was followed by continuing hybridization, a further decrease in beak size and a potential morphological fusion of the two species under entirely natural conditions.     

Darwin's finches and their diet niches: the sympatric coexistence of imperfect generalists

Adaptive radiation can be strongly influenced by interspecific competition for resources, which can lead to diverse outcomes ranging from competitive exclusion to character displacement. In each case, sympatric species are expected to evolve into distinct ecological niches, such as different food types, yet this expectation is not always met when such species are examined in nature. The most common hypotheses to account for the coexistence of species with substantial diet overlap rest on temporal variation in niches (often diets). Yet spatial variation in niche overlap might also be important, pointing to the need for spatiotemporal analyses of diet and diet overlap between closely related species persisting in sympatry. We here perform such an analysis by characterizing the diets of, and diet overlap among, four sympatric Darwin's ground finch species at three sites and over 5 years on a single Galápagos island (Santa Cruz). We find that the different species have broadly similar and overlapping diets – they are to some extent generalists and opportunists – yet we also find that each species retains some ‘private’ resources for which their morphologies are best suited. Importantly, use of these private resources increased considerably, and diet overlap decreased accordingly, when the availability of preferred shared foods, such as arthropods, was reduced during drought conditions. Spatial variation in food resources was also important. These results together suggest that the ground finches are ‘imperfect generalists’ that use overlapping resources under benign conditions (in space or time), but then retreat to resources for which they are best adapted during periods of food limitation. These conditions likely promote local and regional coexistence.     

Ecological and morphological determinants of evolutionary diversification in Darwin's finches and their relatives

Darwin''s finches are a classic example of adaptive radiation, a process by which multiple ecologically distinct species rapidly evolve from a single ancestor. Such evolutionary diversification is typically explained by adaptation to new ecological opportunities. However, the ecological diversification of Darwin''s finches following their dispersal to Galápagos was not matched on the same archipelago by other lineages of colonizing land birds, which diversified very little in terms of both species number and morphology. To better understand the causes underlying the extraordinary variation in Darwin''s finches, we analyze the evolutionary dynamics of speciation and trait diversification in Thraupidae, including Coerebinae (Darwin''s finches and relatives) and, their closely related clade, Sporophilinae. For all traits, we observe an early pulse of speciation and morphological diversification followed by prolonged periods of slower steady‐state rates of change. The primary exception is the apparent recent increase in diversification rate in Darwin''s finches coupled with highly variable beak morphology, a potential key factor explaining this adaptive radiation. Our observations illustrate how the exploitation of ecological opportunity by contrasting means can produce clades with similarly high diversification rate yet strikingly different degrees of ecological and morphological differentiation.     

Phylogenetic relationships and morphological diversity in Darwin's finches and their relatives

Despite the importance of Darwin's finches to the development of evolutionary theory, the origin of the group has only recently been examined using a rigorous, phylogenetic methodology that includes many potential outgroups. Knowing the evolutionary relationships of Darwin's finches to other birds is important for understanding the context from which this adaptive radiation arose. Here we show that analysis of mitochondrial DNA sequence data from the cytochrome b gene confirm that Darwin's finches are monophyletic. In addition, many taxa previously proposed as the sister taxon to Darwin's finches can be excluded as their closest living relative. Darwin's finches are part of a well-supported monophyletic group of species, all of which build a domed nest. All but two of the non-Darwin's finches included in this clade occur on Caribbean islands and most are Caribbean endemics. These close relatives of Darwin's finches show a diversity of bill types and feeding behaviors similar to that observed among Darwin's finches themselves. Recent studies have shown that adaptive evolution in Darwin's finches occurred relatively quickly. Our data show that among the relatives of Darwin's finches, the evolution of bill diversity was also rapid and extensive.     

Fission and fusion of Darwin's finches populations

This study addresses the causes and evolutionary consequences of introgressive hybridization in the sympatric species of Darwin's ground finches (Geospiza) on the small island of Daphne Major in the Galápagos archipelago. Hybridization occurs rarely (less than 2% of breeding pairs) but persistently across years, usually as a result of imprinting on the song of another species. Hybrids survive well under some ecological conditions, but not others. Hybrids mate according to song type. The resulting introgression increases phenotypic and genetic variation in the backcrossed populations. Effects of introgression on beak shape are determined by the underlying developmental genetic pathways. Introgressive hybridization has been widespread throughout the archipelago in the recent past, and may have been a persistent feature throughout the early history of the radiation, episodically affecting both the speed and direction of evolution. We discuss how fission through selection and fusion through introgression in contemporary Darwin's finch populations may be a reflection of processes occurring in other young radiations. We propose that introgression has the largest effect on the evolution of interbreeding species after they have diverged in morphology, but before the point is reached when genetic incompatibilities incur a severe fitness cost.     

The adaptive genomic landscape of beak morphology in Darwin's finches

Beak shape in Darwin's ground finches (Geospiza) is emblematic of natural selection and adaptive radiation, yet our understanding of the genetic basis of beak shape variation, and thus the genetic target of natural selection, is still evolving. Here we reveal the genomic architecture of beak shape variation using genomewide comparisons of four closely related and hybridizing species across 13 islands subject to parallel natural selection. Pairwise contrasts among species were used to identify a large number of genomic loci that are consistently related to species differences across a complex landscape. These loci are associated with hundreds of genes that have enriched GO categories significantly associated with development. One genomic region of particular interest is a section of Chromosome 1A with many candidate genes and increased linkage. The distinct, pointed beak shape of the cactus finch is linked to an excess of intermediate frequency alleles and increased heterozygosity in significant SNPs, but not across the rest of the genome. Alleles associated with pointier beaks among species were associated with pointier‐beaked populations within each species, thus establishing a common basis for natural selection, species divergence and adaptive radiation. The adaptive genomic landscape for Darwin's finches mirrors theoretical expectations based on morphological variation. The implication that a large number of genes are actively maintained to facilitate beak variation across parallel populations with documented interspecies admixture challenges our understanding of evolutionary processes in the wild.     

The West Indies as a laboratory of biogeography and evolution

Islands have long provided material and inspiration for the study of evolution and ecology. The West Indies are complex historically and geographically, providing a rich backdrop for the analysis of colonization, diversification and extinction of species. They are sufficiently isolated to sustain endemic forms and close enough to sources of colonists to develop a dynamic interaction with surrounding continental regions. The Greater Antilles comprise old fragments of continental crust, some very large; the Lesser Antilles are a more recent volcanic island arc, and the low-lying Bahama Islands are scattered on a shallow oceanic platform. Dating of island lineages using molecular methods indicates over-water dispersal of most inhabitants of the West Indies, although direct connections with what is now southern Mexico in the Early Tertiary, and subsequent land bridges or stepping stone islands linking to Central and South America might also have facilitated colonization. Species-area relationships within the West Indies suggest a strong role for endemic radiations and extinction in shaping patterns of diversity. Diversification is promoted by opportunities for allopatric divergence between islands, or within the large islands of the Greater Antilles, with a classic example provided by the Anolis lizards. The timing of colonization events using molecular clocks permits analysis of colonization-extinction dynamics by means of species accumulation curves. These indicate low rates of colonization and extinction for reptiles and amphibians in the Greater Antilles, with estimated average persistence times of lineages in the West Indies exceeding 30Myr. Even though individual island populations of birds might persist an average of 2Myr on larger islands in the Lesser Antilles, recolonization from within the archipelago appears to maintain avian lineages within the island chain indefinitely. Birds of the Lesser Antilles also provide evidence of a mass extinction event within the past million years, emphasizing the time-heterogeneity of historical processes. Geographical dynamics are matched by ecological changes in the distribution of species within islands over time resulting from adaptive radiation and shifts in habitat, often following repeatable patterns. Although extinction is relatively infrequent under natural conditions, changes in island environments as a result of human activities have exterminated many populations and others--especially old, endemic species--remain vulnerable. Conservation efforts are strengthened by recognition of aesthetic, cultural and scientific values of the unique flora and fauna of the West Indies.     

Genomic variation at the tips of the adaptive radiation of Darwin's finches

Adaptive radiation unfolds as selection acts on the genetic variation underlying functional traits. The nature of this variation can be revealed by studying the tips of an ongoing adaptive radiation. We studied genomic variation at the tips of the Darwin's finch radiation; specifically focusing on polymorphism within, and variation among, three sympatric species of the genus Geospiza. Using restriction site‐associated DNA (RAD‐seq), we characterized 32 569 single‐nucleotide polymorphisms (SNPs), from which 11 outlier SNPs for beak and body size were uncovered by a genomewide association study (GWAS). Principal component analysis revealed that these 11 SNPs formed four statistically linked groups. Stepwise regression then revealed that the first PC score, which included 6 of the 11 top SNPs, explained over 80% of the variation in beak size, suggesting that selection on these traits influences multiple correlated loci. The two SNPs most strongly associated with beak size were near genes associated with beak morphology across deeper branches of the radiation: delta‐like 1 homologue (DLK1) and high‐mobility group AT‐hook 2 (HMGA2). Our results suggest that (i) key adaptive traits are associated with a small fraction of the genome (11 of 32 569 SNPs), (ii) SNPs linked to the candidate genes are dispersed throughout the genome (on several chromosomes), and (iii) micro‐ and macro‐evolutionary variation (roots and tips of the radiation) involve some shared and some unique genomic regions.     

Colonization and diversification of Galápagos terrestrial fauna: a phylogenetic and biogeographical synthesis

Remote oceanic islands have long been recognized as natural models for the study of evolutionary processes involved in diversification. Their remoteness provides opportunities for isolation and divergence of populations, which make islands remarkable settings for the study of diversification. Groups of islands may share a relatively similar geological history and comparable climate, but their inhabitants experience subtly different environments and have distinct evolutionary histories, offering the potential for comparative studies. A range of organisms have colonized the Galápagos Islands, and various lineages have radiated throughout the archipelago to form unique assemblages. This review pays particular attention to molecular phylogenetic studies of Galápagos terrestrial fauna. We find that most of the Galápagos terrestrial fauna have diversified in parallel to the geological formation of the islands. Lineages have occasionally diversified within islands, and the clearest cases occur in taxa with very low vagility and on large islands with diverse habitats. Ecology and habitat specialization appear to be critical in speciation both within and between islands. Although the number of phylogenetic studies is continuously increasing, studies of natural history, ecology, evolution and behaviour are essential to completely reveal how diversification proceeded on these islands.     

Persistence of song types in Darwin's finches,Geospiza fortis,over four decades

Learned bird songs evolve via cultural evolution, with song patterns transmitted across generations by imitative learning. In Darwin''s finches of the Galápagos Islands, males learn songs from their fathers, and song types can be maintained across multiple generations. However, little is known about the time frame over which specific song types are preserved, in the face of copy errors and corresponding modifications to song structure. Here we investigate cultural evolution in songs of male Geospiza fortis, at Academy Bay, Santa Cruz Island, comparing songs recorded in 1961 by R. Bowman (20 individuals) to those recorded in 1999 by J. Podos (16 individuals). For each individual, we characterized four timing and six frequency parameters, and assessed inter-individual variation in song structure using multivariate analysis. Several 1961 song types persisted into 1999, some with remarkable fidelity. Variation among song types was extensive during both years, and we detected no changes in 10 vocal parameters across the sampling period. These results illustrate temporal continuity in a culturally acquired trait, and raise questions about mechanisms that promote stability in song structure.     

Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation

Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification.     

Rapid parallel evolution of aberrant traits in the diversification of the Gulf of Guinea white-eyes (Aves, Zosteropidae)

Archipelago-endemic bird radiations are familiar to evolutionary biologists as key illustrations of evolutionary patterns. However, such radiations are in fact rare events. White-eyes (Zosteropidae) are birds with an exceptionally high colonization and speciation potential; they have colonized more islands globally than any other passerine group and include the most species-rich bird genus. The multiplication of white-eye island endemics has been consistently attributed to independent colonizations from the mainland; the white-eyes of the Gulf of Guinea archipelago had been seen as a classic case, spanning as great a breadth of phenotypic diversity as the family worldwide. Contrary to this hypothesis, our molecular phylogenetic analysis places the Gulf of Guinea white-eyes in just two radiations, one grouping all five oceanic island taxa and the other grouping continental island and land-bridge taxa. Numerous 'aberrant' phenotypes (traditionally grouped in the genus Speirops) have evolved independently over a short space of time from nonaberrant (Zosterops) phenotypes; the most phenotypically divergent species have separated as recently as 0.22 Ma. These radiations rival those of Darwin's finches and the Hawaiian honeycreepers in terms of the extent of adaptive radiation per unit time, both in terms of species numbers and in terms of phenotypic diversity. Tempo and patterns of morphological divergence are strongly supportive of an adaptive radiation in the oceanic islands driven by ecological interactions between sympatric white-eyes. Here, very rapid phenotypic evolution mainly affected taxa derived from the youngest wave of colonization, in accordance with the model of asymmetric divergence owing to resource competition in sympatry.     

Density-dependent diversification in North American wood warblers

Evidence from both molecular phylogenies and the fossil record suggests that rates of species diversification often decline through time during evolutionary radiations. One proposed explanation for this pattern is ecological opportunity, whereby an initial abundance of resources and lack of potential competitors facilitate rapid diversification. This model predicts density-dependent declines in diversification rates, but has not been formally tested in any species-level radiation. Here we develop a new conceptual framework that distinguishes density dependence from alternative processes that also produce temporally declining diversification, and we demonstrate this approach using a new phylogeny of North American Dendroica wood warblers. We show that explosive lineage accumulation early in the history of this avian radiation is best explained by a density-dependent diversification process. Our results suggest that the tempo of wood warbler diversification was mediated by ecological interactions among species and that lineage and ecological diversification in this group are coupled, as predicted under the ecological opportunity model.     

Twenty years of body shape evolution in a threespine stickleback population adapting to a lake environment

Analysis of contemporary evolution can provide important insights into the pattern and rate of phenotypic evolution. The threespine stickleback population in Loberg Lake was exterminated in 1982, and a new population was founded between 1983 and 1989 by anadromous stickleback. The body shape of the Loberg Lake population resembled that of anadromous populations in 1990, although it had diverged markedly by 1992. Between 1992 and 2009, the population evolved more slowly to resemble typical lake populations in the region, diverging approximately 68% of the distance separating its putative ancestor and the original native population by 2009. Temporal evolution is the main source of variation, although spatial heterogeneity, armour phenotype, and allometry contribute significant variation. There was no significant effect of ancestral phenotypic shape covariance on the evolutionary trajectory of this population. Temporal variation in the Loberg Lake population provides a rare glimpse into the evolutionary response of a complex trait to natural selection after a major habitat shift. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 817–831.     

Specialization and generalization in the diversification of phytophagous insects: tests of the musical chairs and oscillation hypotheses

Evolutionary biologists have often assumed that ecological generalism comes at the expense of less intense exploitation of specific resources and that this trade-off will promote the evolution of ecologically specialized daughter species. Using a phylogenetic comparative approach with butterflies as a model system, we test hypotheses that incorporate changes in niche breadth and location into explanations of the taxonomic diversification of insect herbivores. Specifically, we compare the oscillation hypothesis, where speciation is driven by host-plant generalists giving rise to specialist daughter species, to the musical chairs hypothesis, where speciation is driven by host-plant switching, without changes in niche breadth. Contrary to the predictions of the oscillation hypothesis, we recover a negative relationship between host-plant breadth and diversification rate and find that changes in host breadth are seldom coupled to speciation events. By contrast, we present evidence for a positive relationship between rates of host switching and butterfly diversification, consonant with the musical chairs hypothesis. These results suggest that the costs of trophic generalism in plant-feeding insects may have been overvalued and that transitions from generalists to ecological specialists may not be an important driver of speciation in general.