Accounting for extinction dynamics unifies the geological and biological histories of Indo-Australian Archipelago.

Biogeographical reconstructions of the Indo-Australian Archipelago (IAA) have suggested a recent spread across the Sunda and Sahul shelves of lineages with diverse origins, which appears to be congruent with a geological history of recent tectonic uplift in the region. However, this scenario is challenged by new geological evidence suggesting that the Sunda shelf was never submerged prior to the Pliocene, casting doubt on the interpretation of recent uplift and the correspondence of evidence from biogeography and geology. A mismatch between geological and biogeographical data may occur if analyses ignore the dynamics of extinct lineages, because this may add uncertainty to the timing and origin of clades in biogeographical reconstructions. We revisit the historical biogeography of multiple IAA taxa and explicitly allow for the possibility of lineage extinction. In contrast to models assuming zero extinction, we find that all of these clades, including plants, invertebrates and vertebrates, have a common and widespread geographic origin, and each has spread and colonized the region much earlier than previously thought. The results for the eight clades re-examined in this article suggest that they diversified and spread during the early Eocene, which helps to unify the geological and biological histories of IAA.

Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders.

Phylosymbiosis is an association between host-associated microbiome composition and host phylogeny. This pattern can arise via the evolution of host traits, habitat preferences, diets, and the co-diversification of hosts and microbes. Understanding the drivers of phylosymbiosis is vital for modelling disease-microbiome interactions and manipulating microbiomes in multi-host systems. This study quantifies phylosymbiosis in Appalachian salamander skin in the context of infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd), while accounting for environmental microbiome exposure. We sampled ten salamander species representing >150M years of divergence, assessed their Bd infection status, and analysed their skin and environmental microbiomes. Our results reveal a significant signal of phylosymbiosis, whereas the local environmental pool of microbes, climate, geography, and Bd infection load had a smaller impact. Host-microbe co-speciation was not evident, indicating that the effect stems from the evolution of host traits influencing microbiome assembly. Bd infection is correlated with host phylogeny and the abundance of Bd-inhibitory bacterial strains, suggesting that the long-term evolutionary dynamics between salamander hosts and their skin microbiomes affect the present-day distribution of the pathogen, along with habitat-linked exposure risk. Five Bd-inhibitory bacterial strains showed unusual generalism: occurring in most host species and habitats. These generalist strains may enhance the likelihood of probiotic manipulations colonising and persisting on hosts. Our results underscore the substantial influence of host-microbiome eco-evolutionary dynamics on environmental health and disease outcomes.

Genetic assimilation of ancestral plasticity during parallel adaptation to zinc contamination in Silene uniflora.

Phenotypic plasticity in ancestral populations is hypothesized to facilitate adaptation, but evidence is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel adaptive changes has not been explored. The most general finding is that ancestral responses to a new environment are reversed following adaptation (known as reversion). We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared with zinc-sensitive plants. We show that ancestral plasticity that moves expression closer to the optimum value in the new environment influences the evolution of gene expression among genes that are likely to be involved in adaptation and increases the chance that genes are recruited repeatedly during adaptation. However, despite convergence in gene expression levels between independently adapted lineages, ancestral plasticity does not influence how similar expression values of adaptive genes become. Surprisingly, we also observed that ancestral plasticity that increases fitness often becomes genetically determined and fixed, that is, genetically assimilated. These results emphasize the important role of ancestral plasticity in parallel adaptation.

Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models.

Understanding the origins of diversity and the factors that drive some clades to be more diverse than others are important issues in evolutionary biology. Sophisticated SSE (state-dependent speciation and extinction) models provide insights into the association between diversification rates and the evolution of a trait. The empirical data used in SSE models and other methods is normally imperfect, yet little is known about how this can affect these models. Here, we evaluate the impact of common phylogenetic issues on inferences drawn from SSE models. Using simulated phylogenetic trees and trait information, we fitted SSE models to determine the effects of sampling fraction (phylogenetic tree completeness) and sampling fraction mis-specification on model selection and parameter estimation (speciation, extinction, and transition rates) under two sampling regimes (random and taxonomically biased). As expected, we found that both model selection and parameter estimate accuracies are reduced at lower sampling fractions (i.e., low tree completeness). Furthermore, when sampling of the tree is imbalanced across sub-clades and tree completeness is ≤ 60%, rates of false positives increase and parameter estimates are less accurate, compared to when sampling is random. Thus, when applying SSE methods to empirical datasets, there are increased risks of false inferences of trait dependent diversification when some sub-clades are heavily under-sampled. Mis-specifying the sampling fraction severely affected the accuracy of parameter estimates: parameter values were over-estimated when the sampling fraction was specified as lower than its true value, and under-estimated when the sampling fraction was specified as higher than its true value. Our results suggest that it is better to cautiously under-estimate sampling efforts, as false positives increased when the sampling fraction was over-estimated. We encourage SSE studies where the sampling fraction can be reasonably estimated and provide recommended best practices for SSE modeling. [Trait dependent diversification; SSE models; phylogenetic tree completeness; sampling fraction.].

Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing.

The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology.

Safeguarding Imperiled Biodiversity and Evolutionary Processes in the Wallacea Center of Endemism.

Wallacea-the meeting point between the Asian and Australian fauna-is one of the world's largest centers of endemism. Twenty-three million years of complex geological history have given rise to a living laboratory for the study of evolution and biodiversity, highly vulnerable to anthropogenic pressures. In the present article, we review the historic and contemporary processes shaping Wallacea's biodiversity and explore ways to conserve its unique ecosystems. Although remoteness has spared many Wallacean islands from the severe overexploitation that characterizes many tropical regions, industrial-scale expansion of agriculture, mining, aquaculture and fisheries is damaging terrestrial and aquatic ecosystems, denuding endemics from communities, and threatening a long-term legacy of impoverished human populations. An impending biodiversity catastrophe demands collaborative actions to improve community-based management, minimize environmental impacts, monitor threatened species, and reduce wildlife trade. Securing a positive future for Wallacea's imperiled ecosystems requires a fundamental shift away from managing marine and terrestrial realms independently.

Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects.

Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental and phenotypic data with Bayesian modelling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of Timema stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (that is, habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.

A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation.

Carotenoid-based polymorphisms are widespread in populations of birds, fish, and reptiles,1 but generally little is known about the factors affecting their maintenance in populations.2 We report a combined field and molecular-genetic investigation of a nestling beak color polymorphism in Darwin's finches. Beaks are pink or yellow, and yellow is recessive.3 Here we show that the polymorphism arose in the Galápagos half a million years ago through a mutation associated with regulatory change in the BCO2 gene and is shared by 14 descendant species. The polymorphism is probably a balanced polymorphism, maintained by ecological selection associated with survival and diet. In cactus finches, the frequency of the yellow genotype is correlated with cactus fruit abundance and greater hatching success and may be altered by introgressive hybridization. Polymorphisms that are hidden as adults, as here, may be far more common than is currently recognized, and contribute to diversification in ways that are yet to be discovered.

Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution.

The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, capacity of species to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonized isolated, disused mines with phytotoxic, zinc-contaminated soils. To test whether rapid, parallel adaptation to anthropogenic pollution has taken place, we used reduced representation sequencing (ddRAD) to reconstruct the evolutionary history of geographically proximate mine and coastal population pairs and found largely independent colonization of mines from different coastal sites. Furthermore, our results show that parallel evolution of zinc tolerance has occurred without gene flow spreading adaptive alleles between mine populations. In genomic regions where signatures of selection were detected across multiple mine-coast pairs, we identified genes with functions linked to physiological differences between the putative ecotypes, although genetic differentiation at specific loci is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities (and other environmental challenges) may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.

Sympatric speciation in mountain roses (Metrosideros) on an oceanic island.

Shifts in flowering time have the potential to act as strong prezygotic reproductive barriers in plants. We investigate the role of flowering time divergence in two species of mountain rose (Metrosideros) endemic to Lord Howe Island, Australia, a minute and isolated island in the Tasman Sea. Metrosideros nervulosa and M. sclerocarpa are sister species and have divergent ecological niches on the island but grow sympatrically for much of their range, and likely speciated in situ on the island. We used flowering time and population genomic analyses of population structure and selection, to investigate their evolution, with a particular focus on the role of flowering time in their speciation. Population structure analyses showed the species are highly differentiated and appear to be in the very late stages of speciation. We found flowering times of the species to be significantly displaced, with M. sclerocarpa flowering 53 days later than M. nervulosa. Furthermore, the analyses of selection showed that flowering time genes are under selection between the species. Thus, prezygotic reproductive isolation is mediated by flowering time shifts in the species, and likely evolved under selection, to drive the completion of speciation within a small geographical area. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna.

Recently diverged species present particularly informative systems for studying speciation and maintenance of genetic divergence in the face of gene flow. We investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations. We used a newly generated genome-wide single nucleotide polymorphism (SNP) dataset from 192 individuals collected over 18 localities along an elevational gradient to reconstruct the likely history of speciation, identify highly differentiated SNPs, and estimate the strength of divergent selection. We found that speciation in this system involved heterogeneous and bidirectional gene flow along the genome, and species experienced marked population size changes in the past. Furthermore, we identified highly-differentiated SNPs between the species, some of which are located in genes potentially involved in ecological differences between species (such as photosynthesis and UV response). We analysed the shape of these SNPs' allele frequency clines along the elevational gradient. These clines show significantly variable coincidence and concordance, indicative of the presence of multifarious selective forces. Selection against hybrids is estimated to be very strong (0.16-0.78) and one of the highest reported in literature. The combination of strong cumulative selection across the genome and previously identified intrinsic incompatibilities probably work together to maintain the genetic and phenotypic differentiation between these species - pointing to the importance of considering both intrinsic and extrinsic factors when studying divergence and speciation.

Adaptive Evolution Is Common in Rapid Evolutionary Radiations.

One of the most long-standing and important mysteries in evolutionary biology is why biological diversity is so unevenly distributed across space and taxonomic lineages. Nowhere is this disparity more evident than in the multitude of rapid evolutionary radiations found on oceanic islands and mountain ranges across the globe [1-5]. The evolutionary processes driving these rapid diversification events remain unclear [6-8]. Recent genome-wide studies suggest that natural selection may be frequent during rapid evolutionary radiations, as inferred from work in cichlid fish [9], white-eye birds [10], new world lupins [11], and wild tomatoes [12]. However, whether frequent adaptive evolution is a general feature of rapid evolutionary radiations remains untested. Here we show that adaptive evolution is significantly more frequent in rapid evolutionary radiations compared to background levels in more slowly diversifying lineages. This result is consistent across a wide range of angiosperm lineages analyzed: 12 evolutionary radiations, which together comprise 1,377 described species, originating from some of the most biologically diverse systems on Earth. In addition, we find a significant negative correlation between population size and frequency of adaptive evolution in rapid evolutionary radiations. A possible explanation for this pattern is that more frequent adaptive evolution is at least partly driven by positive selection for advantageous mutations that compensate for the fixation of slightly deleterious mutations in smaller populations.

How predictable is genome evolution?

Similar patterns of genomic divergence have been observed in the evolution of plant species separated by oceans.

Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea.

Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction site-associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, four of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.

Speciation in Howea Palms Occurred in Sympatry, Was Preceded by Ancestral Admixture, and Was Associated with Edaphic and Phenological Adaptation.

Howea palms are viewed as one of the most clear-cut cases of speciation in sympatry. The sister species Howea belmoreana and H. forsteriana are endemic to the oceanic Lord Howe Island, Australia, where they have overlapping distributions and are reproductively isolated mainly by flowering time differences. However, the potential role of introgression from Australian mainland relatives had not previously been investigated, a process that has recently put other examples of sympatric speciation into question. Furthermore, the drivers of flowering time-based reproductive isolation remain unclear. We sequenced an RNA-seq data set that comprehensively sampled Howea and their closest mainland relatives (Linospadix, Laccospadix), and collected detailed soil chemistry data on Lord Howe Island to evaluate whether secondary gene flow had taken place and to examine the role of soil preference in speciation. D-statistics analyses strongly support a scenario whereby ancestral Howea hybridized frequently with its mainland relatives, but this only occurred prior to speciation. Expression analysis, population genetic and phylogenetic tests of selection, identified several flowering time genes with evidence of adaptive divergence between the Howea species. We found expression plasticity in flowering time genes in response to soil chemistry as well as adaptive expression and sequence divergence in genes pleiotropically linked to soil adaptation and flowering time. Ancestral hybridization may have provided the genetic diversity that promoted their subsequent adaptive divergence and speciation, a process that may be common for rapid ecological speciation.

Phylotranscriptomic Insights into the Diversification of Endothermic Thunnus Tunas.

Birds, mammals, and certain fishes, including tunas, opahs and lamnid sharks, are endothermic, conserving internally generated, metabolic heat to maintain body or tissue temperatures above that of the environment. Bluefin tunas are commercially important fishes worldwide, and some populations are threatened. They are renowned for their endothermy, maintaining elevated temperatures of the oxidative locomotor muscle, viscera, brain and eyes, and occupying cold, productive high-latitude waters. Less cold-tolerant tunas, such as yellowfin tuna, by contrast, remain in warm-temperate to tropical waters year-round, reproducing more rapidly than most temperate bluefin tuna populations, providing resiliency in the face of large-scale industrial fisheries. Despite the importance of these traits to not only fisheries but also habitat utilization and responses to climate change, little is known of the genetic processes underlying the diversification of tunas. In collecting and analyzing sequence data across 29,556 genes, we found that parallel selection on standing genetic variation is associated with the evolution of endothermy in bluefin tunas. This includes two shared substitutions in genes encoding glycerol-3 phosphate dehydrogenase, an enzyme that contributes to thermogenesis in bumblebees and mammals, as well as four genes involved in the Krebs cycle, oxidative phosphorylation, ß-oxidation, and superoxide removal. Using phylogenetic techniques, we further illustrate that the eight Thunnus species are genetically distinct, but found evidence of mitochondrial genome introgression across two species. Phylogeny-based metrics highlight conservation needs for some of these species.

Arbuscular mycorrhizal fungi promote coexistence and niche divergence of sympatric palm species on a remote oceanic island.

Microbes can have profound effects on their hosts, driving natural selection, promoting speciation and determining species distributions. However, soil-dwelling microbes are rarely investigated as drivers of evolutionary change in plants. We used metabarcoding and experimental manipulation of soil microbiomes to investigate the impact of soil and root microbes in a well-known case of sympatric speciation, the Howea palms of Lord Howe Island (Australia). Whereas H. forsteriana can grow on both calcareous and volcanic soils, H. belmoreana is restricted to, but more successful on, volcanic soil, indicating a trade-off in adaptation to the two soil types. We suggest a novel explanation for this trade-off. Arbuscular mycorrhizal fungi (AMF) are significantly depleted in H. forsteriana on volcanic soil, relative to both H. belmoreana on volcanic soil and H. forsteriana on calcareous soil. This is mirrored by the results of survival experiments, where the sterilization of natural soil reduces Howea fitness in every soil-species combination except H. forsteriana on volcanic soil. Furthermore, AMF-associated genes exhibit evidence of divergent selection between Howea species. These results show a mechanism by which divergent adaptation can have knock-on effects on host-microbe interactions, thereby reducing interspecific competition and promoting the coexistence of plant sister species.

Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts.

The role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene-space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution.

Demographic history of speciation in a Senecio altitudinal hybrid zone on Mt. Etna.

Hybrid zones typically form as a result of species coming into secondary contact, but can also be established in situ as an ecotonal hybrid zone, a situation which has been reported far less frequently. An altitudinal hybrid zone on Mount Etna between two ragwort species (the low elevation Senecio chrysanthemifolius and high elevation S. aethnensis) could potentially represent either of these possibilities. However, a scenario of secondary contact vs. speciation with gene flow has not been explicitly tested. Here, we test these alternatives and demonstrate that the data do not support secondary contact. Furthermore, we report that the previous analyses of speciation history of these species were based on admixed populations, which has led to inflated estimates of ongoing, interspecific gene flow. Our new analyses, based on 'pure' S. aethnensis and S. chrysanthemifolius populations, reveal gene exchange of less than one effective migrant per generation, a level low enough to allow the species to accumulate neutral, genomewide differences. Overall, our results are consistent with a scenario of speciation with gene flow and a divergence time which coincides with the rise of Mt. Etna to altitudes above 2000 m (~150 KY). Further work to quantify the role of adaptation to contrasting environments of high and low altitudes will be needed to support the scenario of recent ecological speciation in this system.

Recent ecological selection on regulatory divergence is shaping clinal variation in senecio on Mount Etna.

The hybrid zone on Mount Etna (Sicily) between Senecio aethnensis and Senecio chrysanthemifolius (two morphologically and physiologically distinct species) is a classic example of an altitudinal cline. Hybridization at intermediate altitudes and gradients in phenotypic and life-history traits occur along altitudinal transects of the volcano. The cline is considered to be a good example of ecological selection with species differences arising by divergent selection opposing gene flow. However, the possibility that the cline formed from recent secondary contact following an allopatric phase is difficult to exclude. We demonstrate a recent split between S. aethnensis and S. chrysanthemifolius (as recent as ∼32,000 years ago) and sufficient gene flow (2Nm > 1) to have prevented divergence (implicating a role for diversifying selection in the maintenance of the cline). Differentially expressed genes between S. aethnensis and S. chrysanthemifolius exhibit significantly higher genetic divergence relative to "expression invariant" controls, suggesting that species differences may in part be mediated by divergent selection on differentially expressed genes involved with altitude-related adaptation. The recent split time and the absence of fixed differences between these two ecologically distinct species suggest the rapid evolution to an altitudinal cline involving selection on both sequence and expression variation.