Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions.

Biotic interactions are hypothesized to be one of the main processes shaping trait and biogeographic evolution during lineage diversification. Theoretical and empirical evidence suggests that species with similar ecological requirements either spatially exclude each other, by preventing the colonization of competitors or by driving coexisting populations to extinction, or show niche divergence when in sympatry. However, the extent and generality of the effect of interspecific competition in trait and biogeographic evolution has been limited by a dearth of appropriate process-generating models to directly test the effect of biotic interactions. Here, we formulate a phylogenetic parametric model that allows interdependence between trait and biogeographic evolution, thus enabling a direct test of central hypotheses on how biotic interactions shape these evolutionary processes. We adopt a Bayesian data augmentation approach to estimate the joint posterior distribution of trait histories, range histories, and coevolutionary process parameters under this analytically intractable model. Through simulations, we show that our model is capable of distinguishing alternative scenarios of biotic interactions. We apply our model to the radiation of Darwin's finches-a classic example of adaptive divergence-and find limited support for in situ trait divergence in beak size, but stronger evidence for convergence in traits such as beak shape and tarsus length and for competitive exclusion throughout their evolutionary history. These findings are more consistent with presympatric, rather than postsympatric, niche divergence. Our modeling framework opens new possibilities for testing more complex hypotheses about the processes underlying lineage diversification. More generally, it provides a robust probabilistic methodology to model correlated evolution of continuous and discrete characters. [Bayesian; biotic interactions; competition; data augmentation; historical biogeography; trait evolution.].

Evolution of Darwin's finches and their beaks revealed by genome sequencing.

Darwin's finches, inhabiting the Galápagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin's finch species and two close relatives. Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (Geospiza fortis), a species that has undergone rapid evolution of beak shape in response to environmental changes. The ALX1 haplotype has contributed to diversification of beak shapes among the Darwin's finches and, thereby, to an expanded utilization of food resources.

Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches.

Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.

Species Limits and Phylogenomic Relationships of Darwin's Finches Remain Unresolved: Potential Consequences of a Volatile Ecological Setting.

Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin's finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin's finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships. Expecting that idiosyncrasies of prior data and analytic methods explained different proposed classifications, we were surprised to observe that three new phylogenetic hypotheses derived mostly from the same genomics data were topologically inconsistent. We found that the differences between some of these genomics trees were as great as one would expect between two random trees with the same number of taxa. Thus, the phylogeny of Darwin's finches remains unresolved, as it has for more than a century. A component of phylogenetic uncertainty comes from unclear species limits, under any species concept, in the ground finches (Geospiza) and tree finches (Camarhynchus). We suggest that past authors should have tested the species limits of Lack, rather than uncritically accepting them. In fact, the impressive amount of genomics data do not provide unambiguous hypotheses of the number of species of Geospiza or Camarhynchus, although they imply greater species diversity than Lack's taxonomy. We suggest that insufficient sampling of species populations across islands (35.6% for morphometrics and 20.4% for genomics) prevents accurate diagnoses of species limits. However, it is unknown whether samples from a greater number of islands might result in bridging differences between species, or reveal many new ones. We conclude that attempts to interpret patterns of variation among the finches under standard evolutionary paradigms have obscured some major messages, most specifically the ongoing reciprocal interactions between geographic isolation and lineage divergence, and dispersal and gene flow caused by the volatile ecological conditions in the islands. Although the finches provide textbook examples of natural selection, better understanding of species limits and a robust phylogenetic hypothesis are required to corroborate past hypotheses of speciation and adaptive radiation in the finches of the Galapagos.

Cryptic Speciation of the Oriental Greenfinch Chloris sinica on Oceanic Islands.

The Oriental greenfinch, Chloris sinica, is a small seed-eating finch that breeds in the eastern Palearctic region, an area that spans from Russia in the east to China, Korea, and Japan in the south and southwest. Several subspecies have been described based on subtle morphological characteristics, although the taxonomy varies among different authors. Although many ecological studies have been performed, there has been no phylogenetic study that encompasses the species' entire geographical range. We used four regions of mitochondrial DNA to analyze the intraspecies genetic phylogeny and diversity of the Oriental greenfinch. In addition, we performed morphometric analyses using museum specimens. Genetic analysis identified two clades that diverged approximately 1.06 million years ago. These were a population from the Ogasawara Islands, Japan (subspecies kittlitzi, Clade B), and the other populations (Clade A, which could not be subdivided according to geographic context). Morphometric analyses showed that the population on the Kuril Islands (subspecies kawarahiba) had the longest mean wing length, whereas C. s. kittlitzi had the shortest wings. Chloris s. kittlitzi also had the longest mean bill length, probably because it has adapted to feeding on the Ogasawara Islands. Based on molecular phylogeny and morphology analyses, we recommend that C. s. kittlitzi should be treated as a completely distinct species, called the Ogasawara greenfinch, Chloris kittlitzi. It is critically endangered and needs to be specially protected.

Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins.

Genetic introgression among closely related species is a widespread phenomenon across the Tree of Life and could be an important source of adaptive variation during early stages of diversification. In particular, genomic studies have revealed that many rapidly radiating clades tend to have complex, reticulate evolutionary histories. Although rapid radiations appear to be susceptible to introgression, they present special challenges for its detection because formal tests require accurate phylogenies, and paradoxically, introgression itself may obscure evolutionary relationships. To address this methodological challenge, we assessed introgression in a recent, rapid avian radiation in the Andes, the South American siskins (Spinus). Using ~45,000 SNPs, we estimated the Spinus phylogeny using multiple analytical approaches and recovered four strongly conflicting topologies. We performed a series of complimentary introgression tests that included valid tests for each of the likely species trees. From the consilience of test results, we inferred multiple introgression events among Andean Spinus in a way that was robust to phylogenetic uncertainty in the species tree. Positive tests for introgression were corroborated by independent population structure and ancestral assignment analyses, as well as a striking geographic pattern of mitochondrial haplotype sharing among species. The methodological approach we describe could be applied using any genomewide data, including SNP data, for clades without fully resolvable species trees. Our discovery of multiple introgression events within the Andean radiation of Spinus siskins is consistent with an emerging paradigm, that introgression tends to accompany the early stages of diversification.

Estrogen levels influence medullary bone quantity and density in female house finches and pine siskins.

Medullary bone, a non-structural osseous tissue, serves as a temporary storage site for calcium that is needed for eggshell production in a number of avian species. Previous research focusing primarily on domesticated species belonging to the Anseriformes, Galliformes, and Columbiformes has indicated that rising estrogen levels are a key signal stimulating medullary bone formation; Passeriformes (which constitute over half of extant bird species and are generally small) have received little attention. In the current study, we examined the influence of estrogen on medullary bone and cortical bone in two species of Passeriformes: the Pine Siskin (Spinus pinus) and the House Finch (Haemorhous mexicanus). Females of these species received either an estradiol implant or were untreated as a control. After 4.5-5months, reproductive condition was assessed and leg (femora) and wing (humeri) bones were collected for analysis using high-resolution (10µm) micro-computed tomography scanning. We found that in both species estradiol-treated females had significantly greater medullary bone quantity in comparison to untreated females, but we found no differences in cortical bone quantity or microarchitecture. We were also able to examine medullary bone density in the pine siskins and found that estradiol treatment significantly increased medullary bone density. Furthermore, beyond the effect of the estradiol treatment, we observed a relationship between medullary bone quantity and ovarian condition that suggests that the timing of medullary bone formation may be related to the onset of yolk deposition in these species. Further research is needed to better understand the precise timing and endocrine regulation of medullary bone formation in Passerines and to determine the extent to which female Passerines rely on medullary bone calcium during the formation of calcified eggshells.

High major histocompatibility complex class I polymorphism despite bottlenecks in wild and domesticated populations of the zebra finch (Taeniopygia guttata).

BACKGROUND: Two subspecies of zebra finch, Taeniopygia guttata castanotis and T. g. guttata are native to Australia and the Lesser Sunda Islands, respectively. The Australian subspecies has been domesticated and is now an important model system for research. Both the Lesser Sundan subspecies and domesticated Australian zebra finches have undergone population bottlenecks in their history, and previous analyses using neutral markers have reported reduced neutral genetic diversity in these populations. Here we characterize patterns of variation in the third exon of the highly variable major histocompatibility complex (MHC) class I α chain. As a benchmark for neutral divergence, we also report the first mitochondrial NADH dehydrogenase 2 (ND2) sequences in this important model system. RESULTS: Despite natural and human-mediated population bottlenecks, we find that high MHC class I polymorphism persists across all populations. As expected, we find higher levels of nucleotide diversity in the MHC locus relative to neutral loci, and strong evidence of positive selection acting on important residues forming the peptide-binding region (PBR). Clear population differentiation of MHC allele frequencies is also evident, and this may be due to adaptation to new habitats and associated pathogens and/or genetic drift. Whereas the MHC Class I locus shows broad haplotype sharing across populations, ND2 is the first locus surveyed to date to show reciprocal monophyly of the two subspecies. CONCLUSIONS: Despite genetic bottlenecks and genetic drift, all surveyed zebra finch populations have maintained high MHC Class I diversity. The diversity at the MHC Class I locus in the Lesser Sundan subspecies contrasts sharply with the lack of diversity in previously examined neutral loci, and may thus be a result of selection acting to maintain polymorphism. Given uncertainty in historical population demography, however, it is difficult to rule out neutral processes in maintaining the observed diversity. The surveyed populations also differ in MHC Class I allele frequencies, and future studies are needed to assess whether these changes result in functional immune differences.

When taxonomy meets genomics: lessons from a common songbird.

Taxonomy is being increasingly informed by genomics. Traditionally, taxonomy has relied extensively on phenotypic traits for the identification and delimitation of species, though with a growing influence from molecular phylogenetics in recent decades. Now, genomics opens up new and more powerful tools for analysing the evolutionary history and relatedness among species, as well as understanding the genetic basis for phenotypic traits and their role in reproductive isolation. New insights gained from genomics will therefore have major effects on taxonomic classifications and species delimitation. How a genomics approach can inform a flawed taxonomy is nicely exemplified by Mason & Taylor () in this issue of Molecular Ecology. They studied redpolls, which comprise a genus (Acanthis) of fringillid finches with a wide distribution in the Holarctic region, and whose species taxonomy has been a matter of much controversy for decades (Fig. ). Current authoritative checklists classify them into one, two or three species, and five or six subspecies, based largely on geographical differences in phenotypic traits. Previous studies, including a recent one of the subspecies on Iceland (Amouret et al. ), have found no evidence of differentiation between these taxa in conventional molecular markers. The lack of genetic structure has been interpreted as incomplete lineage sorting among rapidly evolving lineages. Now Mason & Taylor (), using a large data set of genomewide SNPs, verify that they all belong to a single gene pool with a common evolutionary history, and with little or no geographical structuring. They also show that phenotypic traits used in taxonomic classifications (plumage and bill morphology) are closely associated with polygenic patterns of gene expression, presumably driven by ecological selection on a few regulatory genes. Several lessons can be learned from this study. Perhaps the most important one for taxonomy is the risk of taxonomic inflation resulting from overemphasizing phenotypic traits under local adaptation and ignoring a lack of phylogenetic signal in molecular markers.

Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird.

Understanding the patterns and processes that contribute to phenotypic diversity and speciation is a central goal of evolutionary biology. Recently, high-throughput sequencing has provided unprecedented phylogenetic resolution in many lineages that have experienced rapid diversification. The Holarctic redpoll finches (Genus: Acanthis) provide an intriguing example of a recent, phenotypically diverse lineage; traditional sequencing and genotyping methods have failed to detect any genetic differences between currently recognized species, despite marked variation in plumage and morphology within the genus. We examined variation among 20 712 anonymous single nucleotide polymorphisms (SNPs) distributed throughout the redpoll genome in combination with 215 825 SNPs within the redpoll transcriptome, gene expression data and ecological niche modelling to evaluate genetic and ecological differentiation among currently recognized species. Expanding upon previous findings, we present evidence of (i) largely undifferentiated genomes among currently recognized species; (ii) substantial niche overlap across the North American Acanthis range; and (iii) a strong relationship between polygenic patterns of gene expression and continuous phenotypic variation within a sample of redpolls from North America. The patterns we report may be caused by high levels of ongoing gene flow between polymorphic populations, incomplete lineage sorting accompanying very recent or ongoing divergence, variation in cis-regulatory elements, or phenotypic plasticity, but do not support a scenario of prolonged isolation and subsequent secondary contact. Together, these findings highlight ongoing theoretical and computational challenges presented by recent, rapid bouts of phenotypic diversification and provide new insight into the evolutionary dynamics of an intriguing, understudied non-model system.

Phylogeny and biogeography of the New World siskins and goldfinches: rapid, recent diversification in the Central Andes.

Time-calibrated molecular phylogenies can help us to understand the origins of the diverse and unique Andean avifauna. Previous studies have shown that the tempo of diversification differed between the Andes and adjacent lowland regions of South America. Andean taxa were found to have speciated more recently and to have avoided the decelerated diversification that is typical of Neotropical lowland clades. The South American siskins, a Pleistocene finch radiation, may typify this Andean pattern. We investigated the phylogenetic biogeography of all the New World siskins and goldfinches in new detail. To understand the specific role of the Andes in siskin diversification, we asked: (1) Was diversification faster in Andean siskin lineages relative to non-Andean ones? (2) Did siskin lineages move into and out of the Andes at different rates? We found that siskin lineages in the Andes had higher diversification rates and higher outward dispersal rates than siskin lineages outside the Andes. We conclude that páramo expansion and contraction in response to Pleistocene climatic cycles caused accelerated diversification and outward dispersal in Andean siskins. The younger average age of bird species in the Andes compared to lowland South America may be attributable to bursts of recent diversification in siskins and several other vagile, open-habitat clades.

Evidence from a house finch (Haemorhous mexicanus) spleen transcriptome for adaptive evolution and biased gene conversion in passerine birds.

Identifying genes influenced by natural selection can provide information about lineage-specific adaptations, and transcriptomes generated by next-generation sequencing are a useful resource for identifying such genes. Here, we utilize a spleen transcriptome for the house finch (Haemorhous mexicanus), an emerging model for sexual selection and disease ecology, together with previously sequenced avian genomes (chicken, turkey, and zebra finch), to investigate lineage-specific adaptations within birds. An analysis of 4,398 orthologous genes revealed a significantly higher ratio of nonsynonymous to synonymous substitutions and significantly higher GC content in passerines than in galliforms, an observation deviating from strictly neutral expectations but consistent with an effect of biased gene conversion on the evolutionary rate in passerines. These data also showed that genes exhibiting signs of positive selection and fast evolution in passerines have functional roles related to fat metabolism, neurodevelopment, and ion binding.

Inferring the geographic mode of speciation by contrasting autosomal and sex-linked genetic diversity.

When geographic isolation drives speciation, concurrent termination of gene flow among genomic regions will occur immediately after the formation of the barrier between diverging populations. Alternatively, if speciation is driven by ecologically divergent selection, gene flow of selectively neutral genomic regions may go on between diverging populations until the completion of reproductive isolation. It may also lead to an unsynchronized termination of gene flow between genomic regions with different roles in the speciation process. Here, we developed a novel Approximate Bayesian Computation pipeline to infer the geographic mode of speciation by testing for a lack of postdivergence gene flow and a concurrent termination of gene flow in autosomal and sex-linked markers jointly. We applied this approach to infer the geographic mode of speciation for two allopatric highland rosefinches, the vinaceous rosefinch Carpodacus vinaceus and the Taiwan rosefinch C. formosanus from DNA polymorphisms of both autosomal and Z-linked loci. Our results suggest that the two rosefinch species diverged allopatrically approximately 0.5 Ma. Our approach allowed us further to infer that female effective population sizes are about five times larger than those of males, an estimate potentially useful when comparing the intensity of sexual selection across species.

Refugia, colonization and diversification of an arid-adapted bird: coincident patterns between genetic data and ecological niche modelling.

Phylogeographical studies are common in boreal and temperate species from the Palaearctic, but scarce in arid-adapted species. We used nuclear and mitochondrial markers to investigate phylogeography and to estimate chronology of colonization events of the trumpeter finch Bucanetes githagineus, an arid-adapted bird. We used 271 samples from 16 populations, most of which were fresh samples but including some museum specimens. Microsatellite data showed no clear grouping according to the sampling locations. Microsatellite and mitochondrial data showed the clearest differentiation between Maghreb and Canary Islands and between Maghreb and Western Sahara. Mitochondrial data suggest differentiation between different Maghreb populations and among Maghreb and Near East populations, between Iberian Peninsula and Canary Islands, as well as between Western Sahara and Maghreb. Our coalescence analyses indicate that the trumpeter finch colonized North Africa during the humid Marine Isotope Stage 5 (MIS5) period of the Sahara region 125 000 years ago. We constructed an ecological niche model (ENM) to estimate the geographical distribution of climatically suitable habitats for the trumpeter finch. We tested whether changes in the species range in relation to glacial-interglacial cycles could be responsible for observed patterns of genetic diversity and structure. Modelling results matched with those from genetic data as the species' potential range increases in interglacial scenarios (in the present climatic scenario and during MIS5) and decreases in glacial climates (during the last glacial maximum, LGM, 21 000 years ago). Our results suggest that the trumpeter finch responded to Pleistocene climatic changes by expanding and contracting its range.

Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rosefinch (Carpodacus erythrinus).

A previously published phylogeographic analysis of mtDNA sequences from the widespread Palearctic common rosefinch (Carpodacus erythrinus) suggested the existence of three recently diverged groups, corresponding to the Caucasus, central-western Eurasia, and northeastern Eurasia. We re-evaluated the mtDNA data using coalescence methods and added sequence data from a sex-linked gene. The mtDNA gene tree and SAMOVA supported the distinctiveness of the Caucasian group but not the other two groups. However, UPGMA clustering of mtDNA Φ(ST)-values among populations recovered the three groups. The sex-linked gene tree recovered no phylogeographic signal, which was attributed to recent divergence and insufficient time for sorting of alleles. Overall, coalescence methods indicated a lack of gene flow among the three groups, and population expansion in the central-western and northeastern Eurasia groups. These three groups corresponded to named subspecies, further supporting their validity. A species distribution model revealed potential refugia at the Last Glacial Maximum. These three groups, which we hypothesized are in the early stages of speciation, provided an opportunity for testing tenets of ecological speciation. We showed that the early stages of speciation were not accompanied by ecological niche divergence, consistent with other avian studies.

The origin of finches on Tristan da Cunha and Gough Island, central South Atlantic ocean.

The Nesospiza finches of the Tristan da Cunha archipelago and Rowettia goughensis from Gough Island, 380 km distant, are both derived from tanager-finches (Thraupidae) that colonized the islands by crossing more than 3000 km of ocean from South America. Sequences from two mitochondrial and four nuclear genes indicate that the Patagonian bridled finches Melanodera are the closest relatives of the South Atlantic finches. Melanodera typically was sister to Rowettia, although some genes linked it more closely to Nesospiza. There was no evidence that Rowettia and Nesospiza are sister taxa, suggesting that the South Atlantic finches evolved from separate colonization events, as apparently was the case for moorhens Gallinula spp. at the two island groups. Genetic divergence between the two island finch genera thus provides an estimate of the maximum period of time they have been present at the islands, some 3-5 million years. A brief review of colonization histories suggests that island hopping by passerine birds is infrequent among islands more than 100-200 km apart.

Functional significance of a phylogenetically widespread sexual dimorphism in vasotocin/vasopressin production.

Male-biased production of arginine vasotocin/vasopressin (VT/VP) in the medial bed nucleus of the stria terminalis (BSTm) represents one of the largest and most phylogenetically widespread sexual dimorphisms in the vertebrate brain. Although this sex difference was identified 30 years ago, the function of the dimorphism has yet to be determined. Because 1) rapid transcriptional activation of BSTm VT/VP neurons is observed selectively in response to affiliation-related stimuli, 2) BSTm VT/VP content and release correlates negatively with aggression, and 3) BSTm VT/VP production is often limited to periods of reproduction, we hypothesized that the sexual dimorphism serves to promote male-specific reproductive behaviors and offset male aggression in the context of reproductive affiliation. We now show that antisense knockdown of BSTm VT production in colony-housed finches strongly increases aggression in a male-specific manner and concomitantly reduces courtship. Thus, the widespread dimorphism may serve to focus males on affiliation in appropriate reproductive contexts (e.g., when courting) while concomitantly offsetting males' tendency for greater aggression relative to females.

The phylogenetic relationships and generic limits of finches (Fringillidae).

Phylogenetic relationships among the true finches (Fringillidae) have been confounded by the recurrence of similar plumage patterns and use of similar feeding niches. Using a dense taxon sampling and a combination of nuclear and mitochondrial sequences we reconstructed a well resolved and strongly supported phylogenetic hypothesis for this family. We identified three well supported, subfamily level clades: the Holoarctic genus Fringilla (subfamly Fringillinae), the Neotropical Euphonia and Chlorophonia (subfamily Euphoniinae), and the more widespread subfamily Carduelinae for the remaining taxa. Although usually separated in a different family-group taxon (Drepanidinae), the Hawaiian honeycreepers are deeply nested within the Carduelinae and sister to a group of Asian Carpodacus. Other new relationships recovered by this analysis include the placement of the extinct Chaunoproctus ferreorostris as sister to some Asian Carpodacus, a clade combining greenfinches (Carduelis chloris and allies), Rhodospiza and Rhynchostruthus, and a well-supported clade with the aberrant Callacanthis and Pyrrhoplectes together with Carpodacus rubescens. Although part of the large Carduelis-Serinus complex, the poorly known Serinus estherae forms a distinct lineage without close relatives. The traditionally delimited genera Carduelis, Serinus, Carpodacus, Pinicola and Euphonia are polyphyletic or paraphyletic. Based on our results we propose a revised generic classification of finches and describe a new monotypic genus for Carpodacus rubescens.