Fission and fusion of Darwin's finches populations

Quantitative trait locus mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 single nucleotide polymorphism (SNP) markers and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favoured in the wild. QTL for a number of other ecophysiological, phenological and architectural traits colocalized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence.

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background

Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.

Results

Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.

Conclusions

Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.

Cross-species outlier detection reveals different evolutionary pressures between sister species

Lodgepole pine (Pinus contorta var. latifolia) and jack pine (Pinus banksiana) hybridize in western Canada, an area of recent mountain pine beetle range expansion. Given the heterogeneity of the environment, and indications of local adaptation, there are many unknowns regarding the response of these forests to future outbreaks. To better understand this we aim to identify genetic regions that have adaptive potential. We used data collected on 472 single nucleotide polymorphism (SNP) loci from 576 tree samples collected across 13 lodgepole pine-dominated sites and four jack pine-dominated sites. We looked at the relationship of genetic diversity with the environment, and we identified candidate loci using both frequency-based (arlequin and bayescan) and correlation-based (matsam and bayenv) methods. We found contrasting relationships between environmental variation and genetic diversity for the species. While we identified a number of candidate outliers (34 in lodgepole pine, 25 in jack pine, and 43 interspecific loci), we did not find any loci in common between lodgepole and jack pine. Many of the outlier loci identified were correlated with environmental variation. Using rigorous criteria we have been able to identify potential outlier SNPs. We have also found evidence of contrasting environmental adaptations between lodgepole and jack pine which could have implications for beetle spread risk.

Hybridization facilitates evolutionary rescue

The resilience of populations to rapid environmental degradation is a major concern for biodiversity conservation. When environments deteriorate to lethal levels, species must evolve to adapt to the new conditions to avoid extinction. Here, we test the hypothesis that evolutionary rescue may be enabled by hybridization, because hybridization increases genetic variability. Using experimental evolution, we show that interspecific hybrid populations of Saccharomyces yeast adapt to grow in more highly degraded environments than intraspecific and parental crosses, resulting in survival rates far exceeding those of their ancestors. We conclude that hybridization can increase evolutionary responsiveness and that taxa able to exchange genes with distant relatives may better survive rapid environmental change.

Does genetic distance between parental species influence outcomes of hybridization among coral reef butterflyfishes?

Christmas Island is located at the overlap of the Indian and Pacific Ocean marine provinces and is a hot spot for marine hybridization. Here, we evaluate the ecological framework and genetic consequences of hybridization between butterflyfishes Chaetodon guttatissimus and Chaetodon punctatofasciatus. Further, we compare our current findings to those from a previous study of hybridization between Chaetodon trifasciatus and Chaetodon lunulatus. For both species groups, habitat and dietary overlap between parental species facilitate frequent heterospecific encounters. Low abundance of potential mates promotes heterospecific pair formation and the breakdown of assortative mating. Despite similarities in ecological frameworks, the population genetic signatures of hybridization differ between the species groups. Mitochondrial and nuclear data from C. guttatissimus × C. punctatofasciatus (1% divergence at cyt b) show bidirectional maternal contributions and relatively high levels of introgression, both inside and outside the Christmas Island hybrid zone. In contrast, C. trifasciatus × C. lunulatus (5% cyt b divergence) exhibit unidirectional mitochondrial inheritance and almost no introgression. Back-crossing of hybrid C. guttatissimus × C. punctatofasciatus and parental genotypes may eventually confound species-specific signals within the hybrid zone. In contrast, hybrids of C. trifasciatus and C. lunulatus may coexist with and remain genetically distinct from the parents. Our results, and comparisons with hybridization studies in other reef fish families, indicate that genetic distance between hybridizing species may be a factor influencing outcomes of hybridization in reef fish, which is consistent with predictions from terrestrially derived hybridization theory.

Synergism of natural selection and introgression in the origin of a new species

This article explores how introgressive hybridization enhances the evolutionary effects of natural selection and how, reciprocally, natural selection can enhance the evolutionary effects of introgression. Both types of interaction were observed during a 40-year study of Darwin's finches (Geospiza) on the small Galápagos island of Daphne Major. Hybrids, produced rarely by Geospiza fortis (medium ground finch) breeding with Geospiza scandens (cactus finch) and Geospiza fuliginosa (small ground finch), survived and bred as well as the parental species in the past 3 decades. By backcrossing, they increased the standing genetic variation and thereby the evolutionary responsiveness of the populations to natural selection. Natural selection occurred in droughts and oscillated in direction as a result of climatically induced fluctuations in food composition. Introgressive hybridization has led to the formation of a new lineage. It was initiated by a large, introgressed, hybrid male with a unique song and genetic marker that immigrated from the nearby island of Santa Cruz and bred with local hybrids and with G. fortis. All members of the lineage died in the 2003-2005 drought except a brother and a sister, who then bred with each other. Subsequent increase in the lineage was facilitated by selective mortality of the largest G. fortis. Breeding endogamously, the lineage is behaving as a biological species.

Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data

Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000-80,000) and census sizes (5-50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species.

Introgressive hybridization in a trophically polymorphic cichlid

Trophically polymorphic species could represent lineages that are rapidly diverging along an ecological axis or could phenotypically mark the collapse of species through introgressive hybridization. We investigated patterns of introgression between the trophically polymorphic cichlid fish Herichthys minckleyi and its relative H. cyanoguttatus using a combination of population genetics and species tree analyses. We first examined the distribution of mitochondrial haplotypes within the alternative H. minckleyi pharyngeal jaw morphotypes that are endemic to the small desert valley of Cuatro Ciénegas. We recovered two clusters of mitochondrial haplotypes. The first contained a number of slightly differentiated cytochrome b (cytb) haplotypes that showed some phylogeographic signal and were present in both jaw morphotypes. The other haplotype was monomorphic, highly differentiated from the other cluster, present in equal frequencies in the morphotypes, and identical to H. cyanoguttatus haplotypes found outside Cuatro Ciénegas. Then, we investigated whether H. minckleyi individuals with the H. cyanoguttatus cytb were more evolutionarily similar to H. cyanoguttatus or other H. minckleyi using a species tree analysis of 84 nuclear loci. Both H. minckleyi pharyngeal morphotypes, regardless of their cytb haplotype, were quite distinct from H. cyanoguttatus. However, hybridization could be blurring subdivision within H. minckleyi as the alternative jaw morphotypes were not genetically distinct from one another. Accounting for introgression from H. cyanoguttatus will be essential to understand the evolution of the trophically polymorphic cichlid H. minckleyi.

Multilocus analysis of divergence and introgression in sympatric and allopatric sibling species of the Lutzomyia longipalpis complex in Brazil

BACKGROUND

Lutzomyia longipalpis, the main vector of visceral leishmaniasis in Latin America, is a complex of sibling species. In Brazil, a number of very closely related sibling species have been revealed by the analyses of copulation songs, sex pheromones and molecular markers. However, the level of divergence and gene flow between the sibling species remains unclear. Brazilian populations of this vector can be divided in two main groups: one producing Burst-type songs and the Cembrene-1 pheromone and a second more diverse group producing various Pulse song subtypes and different pheromones.

METHODOLOGY/PRINCIPAL FINDINGS

We analyzed 21 nuclear loci in two pairs of Brazilian populations: two sympatric populations from the Sobral locality (1S and 2S) in northeastern Brazil and two allopatric populations from the Lapinha and Pancas localities in southeastern Brazil. Pancas and Sobral 2S are populations of the Burst/Cembrene-1 species while Lapinha and Sobral 1S are two putative incipient species producing the same pheromone and similar Pulse song subtypes. The multilocus analysis strongly suggests the occurrence of gene flow during the divergence between the sibling species, with different levels of introgression between loci. Moreover, this differential introgression is asymmetrical, with estimated gene flow being higher in the direction of the Burst/Cembrene-1 species.

CONCLUSIONS/SIGNIFICANCE

The results indicate that introgressive hybridization has been a crucial phenomenon in shaping the genome of the L. longipalpis complex. This has possible epidemiological implications and is particularly interesting considering the potential for increased introgression caused by man-made environmental changes and the current trend of leishmaniasis urbanization in Brazil.

Hybrid ancestry of an island subspecies of Galápagos mockingbird explains discordant gene trees

Introgression of genes through hybridization has been proposed to be an important driver of speciation, but in animals this has been shown only in relatively few cases until recently. Additionally, introgressive hybridization among non-sister species leads to a change in the gene tree topology of the concerned loci and thus complicates phylogenetic reconstruction. However, such cases of ancient introgression have been very difficult to demonstrate in birds. Here, we present such an example in an island bird subspecies, the Genovesa mockingbird (Mimus parvulus bauri). We assessed phylogenetic relationships and population structure among mockingbirds of the Galápagos archipelago using mitochondrial and nuclear DNA sequences, autosomal microsatellites, and morphological measurements. Mitochondrial haplotypes of Genovesa mockingbirds clustered closely with the haplotypes from two different species, San Cristóbal (M. melanotis) and Española (M. macdonaldi) mockingbirds. The same pattern was found for some haplotypes of two nuclear gene introns, while the majority of nuclear haplotypes of Genovesa mockingbirds were shared with other populations of the same species (M. parvulus). At 26 autosomal microsatellites, Genovesa mockingbirds grouped with other M. parvulus populations. This pattern shows that Genovesa mockingbirds contain mitochondria and some autosomal alleles that have most likely introgressed from M. melanotis into a largely M. parvulus background, making Genovesa mockingbirds a lineage of mixed ancestry, possibly undergoing speciation. Consistent with this hypothesis, mockingbirds on Genovesa are more clearly differentiated morphologically from other M. parvulus populations than M. melanotis is from M. parvulus.

The causes and evolutionary consequences of mixed singing in two hybridizing songbird species (Luscinia spp.)

Bird song plays an important role in the establishment and maintenance of prezygotic reproductive barriers. When two closely related species come into secondary contact, song convergence caused by acquisition of heterospecific songs into the birds’ repertoires is often observed. The proximate mechanisms responsible for such mixed singing, and its effect on the speciation process, are poorly understood. We used a combination of genetic and bioacoustic analyses to test whether mixed singing observed in the secondary contact zone of two passerine birds, the Thrush Nightingale (Luscinia luscinia) and the Common Nightingale (L. megarhynchos), is caused by introgressive hybridization. We analysed song recordings of both species from allopatric and sympatric populations together with genotype data from one mitochondrial and seven nuclear loci. Semi-automated comparisons of our recordings with an extensive catalogue of Common Nightingale song types confirmed that most of the analysed sympatric Thrush Nightingale males were ‘mixed singers’ that use heterospecific song types in their repertoires. None of these ‘mixed singers’ possessed any alleles introgressed from the Common Nightingale, suggesting that they were not backcross hybrids. We also analysed songs of five individuals with intermediate phenotype, which were identified as F₁ hybrids between the Thrush Nightingale female and the Common Nightingale male by genetic analysis. Songs of three of these hybrids corresponded to the paternal species (Common Nightingale) but the remaining two sung a mixed song. Our results suggest that although hybridization might increase the tendency for learning songs from both parental species, interspecific cultural transmission is the major proximate mechanism explaining the occurrence of mixed singers among the sympatric Thrush Nightingales. We also provide evidence that mixed singing does not substantially increase the rate of interspecific hybridization and discuss the possible adaptive value of this phenomenon in nightingales.

Recent rapid speciation and ecomorph divergence in Indo-Australian sea snakes

The viviparous sea snakes (Hydrophiinae) are a young radiation of at least 62 species that display spectacular morphological diversity and high levels of local sympatry. To shed light on the mechanisms underlying sea snake diversification, we investigated recent speciation and eco-morphological differentiation in a clade of four nominal species with overlapping ranges in Southeast Asia and Australia. Analyses of morphology and stomach contents identified the presence of two distinct ecomorphs: a 'macrocephalic' ecomorph that reaches >2 m in length, has a large head and feeds on crevice-dwelling eels and gobies; and a 'microcephalic' ecomorph that rarely exceeds 1 m in length, has a small head and narrow fore-body and hunts snake eels in burrows. Mitochondrial sequences show a lack of reciprocal monophyly between ecomorphs and among putative species. However, individual assignment based on newly developed microsatellites separated co-distributed specimens into four significantly differentiated clusters corresponding to morphological species designations, indicating limited recent gene flow and progress towards speciation. A coalescent species tree (based on mitochondrial and nuclear sequences) and isolation-migration model (mitochondrial and microsatellite markers) suggest between one and three transitions between ecomorphs within the last approximately 1.2 million to approximately 840,000 years. In particular, the macrocephalic 'eastern' population of Hydrophis cyanocinctus and microcephalic H. melanocephalus appear to have diverged very recently and rapidly, resulting in major phenotypic differences and restriction of gene flow in sympatry. These results highlight the viviparous sea snakes as a promising system for speciation studies in the marine environment.

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

A high-resolution (2-9 year sampling interval) fossil pollen record from the Galápagos Islands, which spans the last 2690 years, reveals considerable ecosystem stability. Vegetation changes associated with independently derived histories of El Niño Southern Oscillation variability provided evidence of shifts in the relative abundance of individual species rather than immigration or extinction. Droughts associated with the Medieval Climate Anomaly induced rapid ecological change that was followed by a reversion to the previous state. The paleoecological data suggested nonneutral responses to climatic forcing in this ecosystem prior to the period of human influence. Human impacts on the islands are evident in the record. A marked decline in long-term codominants of the pollen record, Alternanthera and Acalypha, produced a flora without modern analogue before 1930. Intensified animal husbandry after ca. 1930 may have induced the local extinction of Acalypha and Alternanthera. Reductions in populations of grazing animals in the 1970s and 1980s did not result in the return of the native flora, but in invasions by exotic species. After ca. 1970 the trajectory of habitat change accelerated, continuously moving the ecosystem away from the observed range of variability in the previous 2690 years toward a novel ecosystem. The last 40 years of the record also suggest unprecedented transport of lowland pollen to the uplands, consistent with intensified convection and warmer wet seasons.

Adaptive introgression across species boundaries in Heliconius butterflies

It is widely documented that hybridisation occurs between many closely related species, but the importance of introgression in adaptive evolution remains unclear, especially in animals. Here, we have examined the role of introgressive hybridisation in transferring adaptations between mimetic Heliconius butterflies, taking advantage of the recent identification of a gene regulating red wing patterns in this genus. By sequencing regions both linked and unlinked to the red colour locus, we found a region that displays an almost perfect genotype by phenotype association across four species, H. melpomene, H. cydno, H. timareta, and H. heurippa. This particular segment is located 70 kb downstream of the red colour specification gene optix, and coalescent analysis indicates repeated introgression of adaptive alleles from H. melpomene into the H. cydno species clade. Our analytical methods complement recent genome scale data for the same region and suggest adaptive introgression has a crucial role in generating adaptive wing colour diversity in this group of butterflies.

Hybridisation occurs between many animal species, however its evolutionary relevance is still a matter of great debate. While some argue that hybridisation leads to maladaptive gene combinations, and therefore to an evolutionary dead end, others consider interspecific hybridisation as a process with great potential to fuel evolution. We examine this question by exploring the origins of red wing colouration, a trait under natural selection, in the adaptive radiation of closely related species of Heliconius butterflies. By sequencing genetic regions both linked and unlinked to the red wing pattern locus, we found experimental evidence supporting multiple hybridisation events that have mediated the acquisition of colour adaptations from H. melpomene to H. timareta. This introgression has allowed H. timareta to colonise new fitness peaks in the Müllerian mimicry landscape. In this way, our results support the idea that interspecific hybridisation in animals constitutes a source of genetic variation that promotes diversification.

Goldilocks Meets Santa Rosalia: An Ephemeral Speciation Model Explains Patterns of Diversification Across Time Scales

Understanding the rate at which new species form is a key question in studying the evolution of life on earth. Here we review our current understanding of speciation rates, focusing on studies based on the fossil record, phylogenies, and mathematical models. We find that speciation rates estimated from these different studies can be dramatically different: some studies find that new species form quickly and often, while others find that new species form much less frequently. We suggest that instead of being contradictory, differences in speciation rates across different scales can be reconciled by a common model. Under the "ephemeral speciation model", speciation is very common and very rapid but the new species produced almost never persist. Evolutionary studies should therefore focus on not only the formation but also the persistence of new species.

Development and evolution of character displacement

Character displacement occurs when competition for either resources or successful reproduction imposes divergent selection on interacting species, causing divergence in traits associated with resource use or reproduction. Here, we describe how character displacement can be mediated either by genetically canalized changes (i.e., changes that reflect allelic or genotype frequency changes) or by phenotypic plasticity. We also discuss how these two mechanisms influence the tempo of character displacement. Specifically, we suggest that, under some conditions, character displacement mediated by phenotypic plasticity might occur more rapidly than that mediated by genetically canalized changes. Finally, we describe how these two mechanisms may act together and determine character displacement's mode, such that it proceeds through an initial phase in which trait divergence is environmentally induced to a later phase in which divergence becomes genetically canalized. This plasticity-first hypothesis predicts that character displacement should be generally mediated by ancestral plasticity and that it will arise similarly in multiple, independently evolving populations. We conclude by highlighting future directions for research that would test these predictions.

The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. An essay on the close relationship between speciation, inbreeding and recessive mutations

Background

Speciation corresponds to the progressive establishment of reproductive barriers between groups of individuals derived from an ancestral stock. Since Darwin did not believe that reproductive barriers could be selected for, he proposed that most events of speciation would occur through a process of separation and divergence, and this point of view is still shared by most evolutionary biologists today.

Results

I do, however, contend that, if so much speciation occurs, the most likely explanation is that there must be conditions where reproductive barriers can be directly selected for. In other words, situations where it is advantageous for individuals to reproduce preferentially within a small group and reduce their breeding with the rest of the ancestral population. This leads me to propose a model whereby new species arise not by populations splitting into separate branches, but by small inbreeding groups "budding" from an ancestral stock. This would be driven by several advantages of inbreeding, and mainly by advantageous recessive phenotypes, which could only be retained in the context of inbreeding. Reproductive barriers would thus not arise as secondary consequences of divergent evolution in populations isolated from one another, but under the direct selective pressure of ancestral stocks. Many documented cases of speciation in natural populations appear to fit the model proposed, with more speciation occurring in populations with high inbreeding coefficients, and many recessive characters identified as central to the phenomenon of speciation, with these recessive mutations expected to be surrounded by patterns of limited genomic diversity.

Conclusions

Whilst adaptive evolution would correspond to gains of function that would, most of the time, be dominant, this type of speciation by budding would thus be driven by mutations resulting in the advantageous loss of certain functions since recessive mutations very often correspond to the inactivation of a gene. A very important further advantage of inbreeding is that it reduces the accumulation of recessive mutations in genomes. A consequence of the model proposed is that the existence of species would correspond to a metastable equilibrium between inbreeding and outbreeding, with excessive inbreeding promoting speciation, and excessive outbreeding resulting in irreversible accumulation of recessive mutations that could ultimately only lead to extinction.

Reviewer names

Eugene V. Koonin, Patrick Nosil (nominated by Dr Jerzy Jurka), Pierre Pontarotti

Community Genetics Reveal Elevated Levels of Sympatric Gene Flow among Morphologically Similar but Not among Morphologically Dissimilar Species of Lake Victoria Cichlid Fish

We examined genetic structure among five species of Lake Victoria haplochromine cichlids in four island communities, using a full factorial sampling design that compared genetic differentiation between pairs of species and populations of varying morphological similarity and geographical proximity. We found that allopatric conspecific populations were on average significantly more strongly differentiated than sympatric heterospecific populations of morphologically similar species. Allopatric heterospecific populations of morphologically dissimilar species were most differentiated. Our work demonstrates that phenotypic divergence can be maintained and perhaps even evolve in sympatry despite considerable gene flow between species. Conversely, phenotypic resemblance among conspecific populations can be maintained despite geographical isolation. Additionally we show that anthropogenically increased hybridization does not affect all sympatric species evenly but predominantly affects morphologically similar and closely related species. This has important implications for the evolution of reproductive isolation between species These findings are also consistent with the hypothesis of speciation reversal due to weakening of divergent selection and reproductive isolation as a consequence of habitat homogenization and offers an evolutionary mechanistic explanation for the observation that species poor assemblages in turbid areas of the lake are characterized by just one or two species in each of a few morphologically distinct genera.

Distribution and abundance of Darwin’s finches and other land birds on Santa Cruz Island, Galápagos: evidence for declining populations

Population monitoring is a vital tool for conservation management and for testing hypotheses about population trends in changing environments. Darwin’s finches on Santa Cruz Island in the Galápagos archipelago have experienced habitat alteration because of human activity, introduced predators, parasites and disease. We used point counts to conduct systematic quantitative surveys of Darwin’s finches and other land birds between 1997 and 2010. The temporal analysis revealed that six of the nine species investigated declined significantly and that this decline was most pronounced at higher elevations in humid native forest and agricultural areas; the highland areas have been most affected by introduced species or direct human impact. Five of the six declining species are insectivorous, which suggests that changes in insect abundance or insect availability are a critical factor in the declines. Further study is required to test this idea. Other factors including habitat alteration and introduced parasites or pathogens may be contributing to the observed declines.

Did hybridization save the Norfolk Island boobook owl Ninox novaeseelandiae undulata?

The population of the Norfolk Island boobook owl Ninox novaeseelandiae undulata, a nocturnal bird restricted to the Australian territory of Norfolk Island, was reduced to a single female in 1986. Deliberate introduction of two males of its nearest relative, the New Zealand boobook N. n. novaeseelandiae, as a conservation intervention has allowed the taxon to persist on Norfolk Island, albeit in hybrid form. Although declared Extinct in 2000, a re-examination of this unique situation has concluded there is a strong argument that the taxon should be categorized as Critically Endangered because, on average, approximately half the nuclear genome of the original taxon and all the mitochondrial DNA is conserved in all living owls on the island. This thus represents a special case in which the taxon can be considered to be extant, in hybrid form, even though no pure-bred individuals survive. More generally, we suggest that, in exceptional cases, hybridization may not be a threat to highly threatened species and that guidelines are needed to determine when to consider hybrid populations as extant forms of the original taxon, and when to declare extinction through hybridization.

Drivers of hybridization in a 66-generation record of Colias butterflies

Hybridization significantly affects the ecology and evolution of numerous plant and animal lineages. Most studies have focused on endogenous drivers of hybridization and neglected variation in exogenous factors, such as seasonal weather patterns. In this study, we take advantage of a unique dataset consisting of records of hybridization between the butterflies Colias eurytheme and C. eriphyle (Pieridae) for 66 generations (22 years) to investigate the importance of seasonal weather on the production and survival of hybrid offspring. Important seasonal weather variables for each parental species and hybrid offspring were determined using model averaging, and these weather variables, along with butterfly abundances, were analyzed using path analysis. The most important drivers of hybridization were the abundance of C. eriphyle, summer minimum temperature, and spring maximum temperature. In contrast, the abundance of C. eurytheme and weather variables prior to the current flight season were relatively unimportant for variation in hybrid abundance. Parental abundances were mostly driven by weather variables prior to the flight season possibly because these variables affect host plant quality. Our results suggest that exogenous, climatic factors can influence hybridization in natural systems, and that these factors can act both directly on hybrid abundance and indirectly through the population dynamics of parental species.

Hybrid fitness, adaptation and evolutionary diversification: lessons learned from Louisiana Irises

Estimates of hybrid fitness have been used as either a platform for testing the potential role of natural hybridization in the evolution of species and species complexes or, alternatively, as a rationale for dismissing hybridization events as being of any evolutionary significance. From the time of Darwin's publication of The Origin, through the neo-Darwinian synthesis, to the present day, the observation of variability in hybrid fitness has remained a challenge for some models of speciation. Yet, Darwin and others have reported the elevated fitness of hybrid genotypes under certain environmental conditions. In modern scientific terminology, this observation reflects the fact that hybrid genotypes can demonstrate genotype × environment interactions. In the current review, we illustrate the development of one plant species complex, namely the Louisiana Irises, into a 'model system' for investigating hybrid fitness and the role of genetic exchange in adaptive evolution and diversification. In particular, we will argue that a multitude of approaches, involving both experimental and natural environments, and incorporating both manipulative analyses and surveys of natural populations, are necessary to adequately test for the evolutionary significance of introgressive hybridization. An appreciation of the variability of hybrid fitness leads to the conclusion that certain genetic signatures reflect adaptive evolution. Furthermore, tests of the frequency of allopatric versus sympatric/parapatric divergence (that is, divergence with ongoing gene flow) support hybrid genotypes as a mechanism of evolutionary diversification in numerous species complexes.

Predictors for reproductive isolation in a ring species complex following genetic and ecological divergence

Background

Reproductive isolation (RI) is widely accepted as an important "check point" in the diversification process, since it defines irreversible evolutionary trajectories. Much less consensus exists about the processes that might drive RI. Here, we employ a formal quantitative analysis of genetic interactions at several stages of divergence within the ring species complex Ensatina eschscholtzii in order to assess the relative contribution of genetic and ecological divergence for the development of RI.

Results

By augmenting previous genetic datasets and adding new ecological data, we quantify levels of genetic and ecological divergence between populations and test how they correlate with a restriction of genetic admixture upon secondary contact. Our results indicate that the isolated effect of ecological divergence between parental populations does not result in reproductively isolated taxa, even when genetic transitions between parental taxa are narrow. Instead, processes associated with overall genetic divergence are the best predictors of reproductive isolation, and when parental taxa diverge in nuclear markers we observe a complete cessation of hybridization, even to sympatric occurrence of distinct evolutionary lineages. Although every parental population has diverged in mitochondrial DNA, its degree of divergence does not predict the extent of RI.

Conclusions

These results show that in Ensatina, the evolutionary outcomes of ecological divergence differ from those of genetic divergence. While evident properties of taxa may emerge via ecological divergence, such as adaptation to local environment, RI is likely to be a byproduct of processes that contribute to overall genetic divergence, such as time in geographic isolation, rather than being a direct outcome of local adaptation.

Ecological character displacement in the face of gene flow: evidence from two species of nightingales

Background

Ecological character displacement is a process of phenotypic differentiation of sympatric populations caused by interspecific competition. Such differentiation could facilitate speciation by enhancing reproductive isolation between incipient species, although empirical evidence for it at early stages of divergence when gene flow still occurs between the species is relatively scarce. Here we studied patterns of morphological variation in sympatric and allopatric populations of two hybridizing species of birds, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L. luscinia).

Results

We conducted principal component (PC) analysis of morphological traits and found that nightingale species converged in overall body size (PC1) and diverged in relative bill size (PC3) in sympatry. Closer analysis of morphological variation along geographical gradients revealed that the convergence in body size can be attributed largely to increasing body size with increasing latitude, a phenomenon known as Bergmann's rule. In contrast, interspecific interactions contributed significantly to the observed divergence in relative bill size, even after controlling for the effects of geographical gradients. We suggest that the divergence in bill size most likely reflects segregation of feeding niches between the species in sympatry.

Conclusions

Our results suggest that interspecific competition for food resources can drive species divergence even in the face of ongoing hybridization. Such divergence may enhance reproductive isolation between the species and thus contribute to speciation.

The Rules of Variation Expanded, Implications for the Research on Compatible Genomics

The main focus of this article is to present the practical aspect of the code rules of variation and the search for a second set of genomic rules, including comparison of sequences to understand how to preserve compatible organisms in danger of extinction and how to generate biodiversity. Three new rules of variation are introduced: 1) homologous recombination, 2) a healthy fertile offspring, and 3) comparison of compatible genomes. The novel search in the natural world for fully compatible genomes capable of homologous recombination is explored by using examples of human polymorphisms in the LDLRAP1 gene, and by the production of fertile offspring by crossbreeding. Examples of dogs, llamas and finches will be presented by a rational control of: natural crossbreeding of organisms with compatible genomes (something already happening in nature), the current work focuses on the generation of new varieties after a careful plan. This study is presented within the context of biosemiotics, which studies the processing of information, signaling and signs by living systems. I define a group of organisms having compatible genomes as a single theme: the genomic species or population, able to speak the same molecular language through different accents, with each variety within a theme being a different version of the same book. These studies have a molecular, compatible genetics context. Population and ecosystem biosemiotics will be exemplified by a possible genetic damage capable of causing mutations by breaking the rules of variation through the coordinated patterns of atoms present in the 9/11 World Trade Center contaminated dust (U, Ba, La, Ce, Sr, Rb, K, Mn, Mg, etc.), combination that may be able to overload the molecular quality control mechanisms of the human body. I introduce here the balance of codons in the circular genetic code: 2[1(1)+1(3)+1(4)+4(2)]=2[2(2)+3(4)].

Ice-cover effects on competitive interactions between two fish species

1. Variations in the strength of ecological interactions between seasons have received little attention, despite an increased focus on climate alterations on ecosystems. Particularly, the winter situation is often neglected when studying competitive interactions. In northern temperate freshwaters, winter implies low temperatures and reduced food availability, but also strong reduction in ambient light because of ice and snow cover. Here, we study how brown trout [Salmo trutta (L.)] respond to variations in ice-cover duration and competition with Arctic charr [Salvelinus alpinus (L.)], by linking laboratory-derived physiological performance and field data on variation in abundance among and within natural brown trout populations. 2. Both Arctic charr and brown trout reduced resting metabolic rate under simulated ice-cover (darkness) in the laboratory, compared to no ice (6-h daylight). However, in contrast to brown trout, Arctic charr was able to obtain positive growth rate in darkness and had higher food intake in tank experiments than brown trout. Arctic charr also performed better (lower energy loss) under simulated ice-cover in a semi-natural environment with natural food supply. 3. When comparing brown trout biomass across 190 Norwegian lakes along a climate gradient, longer ice-covered duration decreased the biomass only in lakes where brown trout lived together with Arctic charr. We were not able to detect any effect of ice-cover on brown trout biomass in lakes where brown trout was the only fish species. 4. Similarly, a 25-year time series from a lake with both brown trout and Arctic charr showed that brown trout population growth rate depended on the interaction between ice breakup date and Arctic charr abundance. High charr abundance was correlated with low trout population growth rate only in combination with long winters. 5. In conclusion, the two species differed in performance under ice, and the observed outcome of competition in natural populations was strongly dependent on duration of the ice-covered period. Our study shows that changes in ice phenology may alter species interactions in Northern aquatic systems. Increased knowledge of how adaptations to winter conditions differ among coexisting species is therefore vital for our understanding of ecological impacts of climate change.

Field studies reveal strong postmating isolation between ecologically divergent butterfly populations

A mismatch between hybrid butterflies and their ecological environment restricts gene flow between populations that feed on different host plants, highlighting the potential importance of a seldom-studied mechanism of reproductive isolation.

Gene flow between populations that are adapting to distinct environments may be restricted if hybrids inherit maladaptive, intermediate phenotypes. This phenomenon, called extrinsic postzygotic isolation (EPI), is thought to play a critical role in the early stages of speciation. However, despite its intuitive appeal, we know surprisingly little about the strength and prevalence of EPI in nature, and even less about the specific phenotypes that tend to cause problems for hybrids. In this study, we searched for EPI among allopatric populations of the butterfly Euphydryas editha that have specialized on alternative host plants. These populations recall a situation thought typical of the very early stages of speciation. They lack consistent host-associated genetic differentiation at random nuclear loci and show no signs of reproductive incompatibility in the laboratory. However, they do differ consistently in diverse host-related traits. For each of these traits, we first asked whether hybrids between populations that use different hosts (different-host hybrids) were intermediate to parental populations and to hybrids between populations that use the same host (same-host hybrids). We then conducted field experiments to estimate the effects of intermediacy on fitness in nature. Our results revealed strong EPI under field conditions. Different-host hybrids exhibited an array of intermediate traits that were significantly maladaptive, including four behaviors. Intermediate foraging height slowed the growth of larvae, while intermediate oviposition preference, oviposition site height, and clutch size severely reduced the growth and survival of the offspring of adult females. We used our empirical data to construct a fitness surface on which different-host hybrids can be seen to fall in an adaptive valley between two peaks occupied by same-host hybrids. These findings demonstrate how ecological selection against hybrids can create a strong barrier to gene flow at the early stages of adaptive divergence.

When two populations adapt to different ecological environments, they may become reproductively incompatible with each other and eventually form distinct species. One form of incompatibility thought to contribute to this process occurs when hybrids between diverging populations are ecologically maladapted. They suffer reduced survival and reproduction because they possess intermediate traits that are ill-suited to both parental environments. Although this phenomenon is potentially important at the early stages of speciation, it is difficult to study in the field and is often invisible in the laboratory—leaving us with few empirical examples. We use a series of behavioral assays and manipulative field experiments to examine hybrids between populations of a butterfly that have adapted to use distinct host plants. We show that the hybrids are perfectly healthy in the laboratory. However, when taken into the field, they interact with their host plants in intermediate and anomalous ways that lower the growth and survival of both themselves and their offspring. Our findings confirm that ecological selection against hybrids has great potential to block gene flow at the early stages of adaptive divergence.

Rapid parallel adaptive radiations from a single hybridogenic ancestral population

The Alpine lake whitefish (Coregonus lavaretus) species complex is a classic example of a recent radiation, associated with colonization of the Alpine lakes following the glacial retreat (less than 15 kyr BP). They have formed a unique array of endemic lake flocks, each with one to six described sympatric species differing in morphology, diet and reproductive ecology. Here, we present a genomic investigation of the relationships between and within the lake flocks. Comparing the signal between over 1000 AFLP loci and mitochondrial control region sequence data, we use phylogenetic tree-based and population genetic methods to reconstruct the phylogenetic history of the group and to delineate the principal centres of genetic diversity within the radiation. We find significant cytonuclear discordance showing that the genomically monophyletic Alpine whitefish clade arose from a hybrid swarm of at least two glacial refugial lineages. Within this radiation, we find seven extant genetic clusters centred on seven lake systems. Most interestingly, we find evidence of sympatric speciation within and parallel evolution of equivalent phenotypes among these lake systems. However, we also find the genetic signature of human-mediated gene flow and diversity loss within many lakes, highlighting the fragility of recent radiations.

Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus

*Adaptive trait introgression is increasingly recognized as common. However, it is unclear whether adaptive genetic exchanges typically affect only a single trait, or instead affect multiple aspects of the phenotype. Here, we examine introgression of abiotic tolerance traits between two hybridizing North American sunflower species, Helianthus annuus and Helianthus debilis. *In two common gardens in the hybrid range, we measured 10 ecophysiological, phenological, and architectural traits for parents and their natural and artificial hybrids, and examined how fitness covaried with trait values. *Eight of the 10 traits showed patterns consistent with introgression from H. debilis into H. annuus, and suggested that H. debilis-like traits allowing rapid growth and reproduction before summer heat and drought have been favored in the hybrid range. Natural selection currently favors BC(1) hybrids with H. debilis-like branching traits. *We demonstrate that introgression has altered multiple aspects of the H. annuus phenotype in an adaptive manner, has affected traits relevant to both biotic and abiotic environments, and may have aided expansion of the H. annuus range into central Texas, USA.

Acoustic discrimination of sympatric morphs in Darwin's finches: a behavioural mechanism for assortative mating?

Populations with multiple morphological or behavioural types provide unique opportunities for studying the causes and consequences of evolutionary diversification. A population of the medium ground finch (Geospiza fortis) at El Garrapatero on Santa Cruz Island, Galápagos, features two beak size morphs. These morphs produce acoustically distinctive songs, are subject to disruptive selection and mate assortatively by morph. The main goal of the present study was to assess whether finches from this population are able to use song as a cue for morph discrimination. A secondary goal of this study was to evaluate whether birds from this population discriminate songs of their own locality versus another St Cruz locality, Borrero Bay, approximately 24 km to the NW. I presented territorial males with playback of songs of their own morph, of the other morph, and of males from Borrero Bay. Males responded more strongly to same-morph than to other-morph playbacks, showing significantly shorter latencies to flight, higher flight rates and closer approaches to the playback speaker. By contrast, I found only minor effects of locality on responsiveness. Evidence for morph discrimination via acoustic cues supports the hypothesis that song can serve as a behavioural mechanism for assortative mating and sympatric evolutionary divergence.

Natural hybridization generates mammalian lineage with species characteristics

Most diploid species arise from single-species ancestors. Hybrid origins of new species are uncommon (except among polyploids) and are documented infrequently in animals. Examples of natural hybridization leading to speciation in mammals are exceedingly rare. Here, we show a Caribbean species of bat (Artibeus schwartzi) has a nuclear genome derived from two nonsister but congeneric species (A. jamaicensis and A. planirostris) and a mitochondrial genome that is from a third extinct or uncharacterized congener. Artibeus schwartzi is self-sustaining, morphologically distinct, and exists in near geographic isolation of its known parent species. Island effects (i.e., area, reduced habitat variability, and geographic isolation) likely have restricted gene flow from parental species into the Caribbean populations of this hybrid lineage, thus contributing to local adaptation and isolation of this newly produced taxon. We hypothesize differential rates of the development of reproductive isolation within the genus and estimate that 2.5 million years was an insufficient amount of time for the development of postzygotic isolation among the three species that hybridized to produce A. schwartzi. Reticulated evolution thus has resulted in a genomic combination from three evolutionary lineages and a transgressive phenotype that is distinct from all other known species of Artibeus. The data herein further demonstrate the phenomenon of speciation by hybridization in mammals is possible in nature.

Conspecific versus heterospecific gene exchange between populations of Darwin's finches

This study addresses the extent and consequences of gene exchange between populations of Darwin's finches. Four species of ground finches (Geospiza) inhabit the small island of Daphne Major in the centre of the Galápagos archipelago. We undertook a study of microsatellite DNA variation at 16 loci in order to quantify gene flow within species owing to immigration and between species owing to hybridization. A combination of pedigrees of observed breeders and assignments of individuals to populations by the program Structure enabled us to determine the frequency of gene exchange and the island of origin of immigrants in some cases. The relatively large populations of Geospiza fortis and G. scandens receive conspecific immigrants at a rate of less than one per generation. They exchange genes more frequently by rare but repeated hybridization. Effects of heterospecific gene flow from hybridization are not counteracted by lower fitness of the offspring. As a result, the standing genetic variation of the two main resident populations on Daphne Major is enhanced to a greater extent by introgressive hybridization than through breeding with conspecific immigrants. Immigrant G. fuliginosa also breeds with G. fortis. Conspecific immigration was highest in the fourth species, G. magnirostris. This species is much larger than the other three and perhaps for this reason it has not bred with any of them. The source island of most immigrants is probably the neighbouring island of Santa Cruz. Evolutionary change may be inhibited in G. magnirostris by continuing gene flow, but enhanced in G. fortis and G. scandens by introgressive hybridization.

Interspecific hybridization as a tool to understand vocal divergence: the example of crowing in quail (Genus Coturnix)

Understanding the mechanisms that lead organisms to be separated into distinct species remains a challenge in evolutionary biology. Interspecific hybridization, which results from incomplete reproductive isolation, is a useful tool to investigate such mechanisms. In birds, interspecific hybridization is relatively frequent, despite the fact that closed species exhibit morphological and behavioural differences. Evolution of behaviour is difficult to investigate on a large timescale since it does not ‘fossilize’. Here I propose that calls of hybrid non-songbirds that develop without the influence of learning may help in understanding the gradual process that leads to vocal divergence during speciation. I recorded crows produced by the European quail (Coturnix c. coturnix), the domestic Japanese quail (Coturnix c. japonica) and their hybrids (F1, F2 and backcrosses). Most crowing patterns were intermediate to those of the parental species; some were similar to one or the other parental species, or not present in either parental species. I also observed vocal changes in hybrid crows during the breeding season and from one year to the other. This vocal variability resembles those observed during the ontogeny of the crow in quails. It is likely that similar mechanisms involved in vocal changes during ontogeny might have driven vocal divergence in the species of Palearctic quails. I suggest that hybrid crows might have resembled those produced by intermediary forms of quails during speciation.

Integrating horizontal gene transfer and common descent to depict evolution and contrast it with "common design"

Horizontal gene transfer (HGT) and common descent interact in space and time. Because events of HGT co-occur with phylogenetic evolution, it is difficult to depict evolutionary patterns graphically. Tree-like representations of life's diversification are useful, but they ignore the significance of HGT in evolutionary history, particularly of unicellular organisms, ancestors of multicellular life. Here we integrate the reticulated-tree model, ring of life, symbiogenesis whole-organism model, and eliminative pattern pluralism to represent evolution. Using Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a bifunctional enzyme in the glycolytic pathway of amoeba, we illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. aldehyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), and subsequent functional integration of these enzymes into EhADH2, which is now inherited by amoeba via common descent. Natural selection has driven the evolution of EhADH2 active sites, which require specific amino acids (cysteine 252 in the ALDH domain; histidine 754 in the ADH domain), iron- and NAD(+) as cofactors, and the substrates acetyl-CoA for ALDH and acetaldehyde for ADH. Alternative views invoking "common design" (i.e. the non-naturalistic emergence of major taxa independent from ancestry) to explain the interaction between horizontal and vertical evolution are unfounded.

The secondary contact phase of allopatric speciation in Darwin's finches

Speciation, the process by which two species form from one, involves the development of reproductive isolation of two divergent lineages. Here, we report the establishment and persistence of a reproductively isolated population of Darwin's finches on the small Galápagos Island of Daphne Major in the secondary contact phase of speciation. In 1981, an immigrant medium ground finch (Geospiza fortis) arrived on the island. It was unusually large, especially in beak width, sang an unusual song, and carried some Geospiza scandens alleles. We followed the fate of this individual and its descendants for seven generations over a period of 28 years. In the fourth generation, after a severe drought, the lineage was reduced to a single brother and sister, who bred with each other. From then on this lineage, inheriting unusual song, morphology, and a uniquely homozygous marker allele, was reproductively isolated, because their own descendants bred with each other and with no other member of the resident G. fortis population. These observations agree with some expectations of an ecological theory of speciation in that a barrier to interbreeding arises as a correlated effect of adaptive divergence in morphology. However, the important, culturally transmitted, song component of the barrier appears to have arisen by chance through an initial imperfect copying of local song by the immigrant. The study reveals additional stochastic elements of speciation, in which divergence is initiated in allopatry; immigration to a new area of a single male hybrid and initial breeding with a rare hybrid female.

Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus

Prochlorococcus is a genus of marine cyanobacteria characterized by small cell and genome size, an evolutionary trend toward low GC content, the possession of chlorophyll b, and the absence of phycobilisomes. Whereas many shared derived characters define Prochlorococcus as a clade, many genome-based analyses recover them as paraphyletic, with some low-light adapted Prochlorococcus spp. grouping with marine Synechococcus. Here, we use 18 Prochlorococcus and marine Synechococcus genomes to analyze gene flow within and between these taxa. We introduce embedded quartet scatter plots as a tool to screen for genes whose phylogeny agrees or conflicts with the plurality phylogenetic signal, with accepted taxonomy and naming, with GC content, and with the ecological adaptation to high and low light intensities. We find that most gene families support high-light adapted Prochlorococcus spp. as a monophyletic clade and low-light adapted Prochlorococcus sp. as a paraphyletic group. But we also detect 16 gene families that were transferred between high-light adapted and low-light adapted Prochlorococcus sp. and 495 gene families, including 19 ribosomal proteins, that do not cluster designated Prochlorococcus and Synechococcus strains in the expected manner. To explain the observed data, we propose that frequent gene transfer between marine Synechococcus spp. and low-light adapted Prochlorococcus spp. has created a “highway of gene sharing” (Beiko RG, Harlow TJ, Ragan MA. 2005. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA. 102:14332–14337) that tends to erode genus boundaries without erasing the Prochlorococcus-specific ecological adaptations.

Molecular, morphological, and ecological niche differentiation of sympatric sister oak species, Quercus virginiana and Q. geminata (Fagaceae)

The genus Quercus (the oaks) is notorious for interspecific hybrization, generating questions about the mechanisms that permit coexistence of closely related species. Two sister oak species, Quercus virginiana and Q. geminata, occur in sympatry in Florida and throughout the southeastern United States. In 11 sites from northern and southeastern regions of Florida, we used a leaf-based morphological index to identify individuals to species. Eleven nuclear microsatellite markers significantly differentiated between the species with a high correspondence between molecular and morphological typing of specimens. Nevertheless, Bayesian clustering analysis indicates interspecific gene flow, and six of 109 individuals had mixed ancestry. The identity of several individuals also was mismatched using molecular markers and morphological characters. In a common environment, the two species performed differently in terms of photosynthetic performance and growth, corresponding to their divergent ecological niches with respect to soil moisture and other edaphic properties. Our data support earlier hypotheses that divergence in flowering time causes assortative mating, allowing these ecologically distinct sister species to occur in sympatry. Limited gene flow that permits ecological differentiation helps to explain the overdispersion of oak species in local communities.

The merging of community ecology and phylogenetic biology

The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.