Phylogenomics of the tetraploid Hawaiian lobeliads: Implications for their origin, dispersal history, and adaptive radiation

Molecular data provide several key insights into the origin and diversification of the Hawaiian lobeliads, which comprise one-ninth of the flora of the most isolated archipelago on earth. Soon after colonizing the Hawaiian chain from elsewhere in the Southern hemisphere, this group radiated into four major clades, adapted to bogs and other open, wet high-elevation habitats, to inland outcrops and rock walls, to sea cliffs and dry forest, and to rain- and cloud-forest edges and interiors. Woodiness and bird pollination arose long before the lobeliads arrived in Hawaii; fleshy fruits evolved autochthonously in moist to wet forests, and were lost on sea cliffs. Limited seed dispersal (associated with fleshy fruits in forest-interior plants) appears to have triggered substantial speciation in the genus Cyanea, and helped generate convergent radiations in flower length, elevational distribution, and plant height on each of the four major islands. Some of the processes that accelerated speciation in Cyanea —such as limited seed dispersal, narrow ranges, and highly specialized flowers — also appear to have increased the likelihood of extinction. The roles of adaptive radiation vis-a-vis limited dispersal and sexual selection in promoting speciation in other groups (African rift-lake cichlids, coral reef fish, lilies and their relatives) are also discussed, with special reference to the phenomena of convergent adaptive radiations and of visual selection. Natural enemies may exert stronger density-dependent mortality on their hosts under rainier, more humid, warmer, and less seasonal conditions, and help create strong ecological gradients in plant species diversity within the tropics. Adaptive radiation may thus have interacted synergistically with several processes to generate the taxonomic richness and ecological diversity of the largest clade in the Hawaiian flora.

The woodySonchus alliance consists of 19 species ofSonchus subg.Dendrosonchus, one species ofSonchus subg.Sonchus and species of five genera (i.e.Babcockia, Sventenia, Taeckholmia, Lactucosonchus, Prenanthes), and is restricted primarily to the archipelago of the Canaries in the Macaronesian phytogeographical region. An enzyme electrophoretic study, including 13 loci, was conducted to assess genetic diversity within and divergence among species of the alliance. Nei's genetic identities (distances) between genera and/or subgenera range from 0.490 (0.714) to 0.980 (0.013), and pairwise comparisons of all populations show relatively high genetic identities, with a mean of 0.804. The high identities further support the genetic cohesiveness of the alliance and its single origin on the Macaronesian islands. Species in the alliance also show about 50%; higher total genetic diversity (HT) than the mean for other oceanic endemics. There is greater divergence between endemics or species on older islands compared to those on younger islands, which suggests that time is a factor for divergence at allozyme loci. Furthermore, populations on older islands have higher total genetic diversities and lower identities than conspecific populations on younger islands. These results imply early colonization, radiation, and divergence of the woodySonchus alliance on older islands followed by subsequent colonization to younger islands. The taxonomic distribution of alleles in the alliance indicates lineage sorting also played a role in divergence among species. Lineage sorting may also produce nonconcordance with either taxonomic designation or the pattern of variation obtained from other molecular markers such as ITS sequences of nrDNA. Timing for the origin and radiation of the alliance agrees with the estimate based on ITS sequences, and suggests that the early divergence and rapid radiation took place during the Late Tertiary on either Gran Canaria or Tenerife.

Reappraising adaptive radiation

Adaptive radiation is an evolutionary process that has been promulgated in some clades as an explanation for species richness and disparity in morphological forms across ecological gradients. Studies designed to elucidate the mechanisms and causes of adaptive radiation have largely focused on animal systems, but plant clades have tremendous potential to answer elusive questions regarding adaptive radiations. The goals of this review are to (1) produce a synthetic understanding of adaptive radiations through studies that have investigated plants systems, (2) critically reflect on contemporary studies to highlight how approaches have been successful as well as limiting, and (3) outline gaps in our understanding of adaptive radiations while emphasizing that plants have ideal characteristics to answer future questions. Thirty-five adaptive radiation clades are highlighted, of which several are supported with multiple lines of evidence, such as the Hawaiian silverswords, Hawaiian lobeliads, and columbines. Plant adaptive radiation examples are commonly insular, diversified in the Miocene or Pliocene, are associated with dispersal-mediated ecological opportunities, are polyploids, and have experienced hybridization. From those studies, a general model of plant insular adaptive radiation is proposed. The limitations of the current reliance on phylogenetic comparative approaches to detect adaptive radiations are considered, and an integrative approach that includes phylogenetics, genomics, and evolutionary ecology is advocated. The review concludes with a call for additional studies that are needed before we are to fully understand adaptive radiations, and they include the following: (1) how do biological interactions influence adaptive radiations, (2) what role does environmental change play in generating ecological opportunity, (3) how does genetic evolution drive adaptive radiation, (4) do models adequately explain the adaptive radiation process, (5) what is the role of hybridization, and (6) why do some groups not undergo adaptive radiation after ecological opportunity?

Previous studies based on DNA restriction-site and sequence variation have shown that the Hawaiian lobeliads are monophyletic and that the two largest genera, Cyanea and Clermontia, diverged from each other ca. 9.7 Mya. Sequence divergence among species of Clermontia is quite limited, however, and extensive hybridization is suspected, which has interfered with production of a well-resolved molecular phylogeny for the genus. Clermontia is of considerable interest because several species posses petal-like sepals, raising the question of whether such a homeotic mutation has arisen once or several times. In addition, morphological and molecular studies have implied different patterns of inter-island dispersal within the genus. Here we use nuclear ISSRs (inter-simple sequence repeat polymorphisms) and five plastid non-coding sequences to derive biparental and maternal phylogenies for Clermontia. Our findings imply that (1) Clermontia is not monophyletic, with Cl. pyrularia nested within Cyanea and apparently an intergeneric hybrid; (2) the earliest divergent clades within Clermontia are native to Kauài, then Òahu, then Maui, supporting the progression rule of dispersal down the chain toward progressively younger islands, although that rule is violated in later-evolving taxa in the ISSR tree; (3) almost no sequence divergence among several Clermontia species in 4.5 kb of rapidly evolving plastid DNA; (4) several apparent cases of hybridization/introgression or incomplete lineage sorting (i.e., Cl. oblongifolia, peleana, persicifolia, pyrularia, samuelii, tuberculata), based on extensive conflict between the ISSR and plastid phylogenies; and (5) two origins and two losses of petaloid sepals, or—perhaps more plausibly—a single origin and two losses of this homeotic mutation, with its introgression into Cl. persicifolia. Our phylogenies are better resolved and geographically more informative than others based on ITS and 5S-NTS sequences and nuclear SNPs, but agree with them in supporting Clermontia's origin on Kauài or some older island and dispersal down the chain subsequently.

While the contribution of gene expression (GE) to adaptive evolution is widely accepted, the role of alternative splicing (AS) remains less understood. Here, we investigate AS and GE across three iconic adaptive radiations of African cichlid fishes that evolved within < 16,000 to 3.8 million years. We show that AS evolves faster than GE, with both sources of variation being ‘fine-tuned’ over evolutionary time to become species-specific and clade-specific, respectively. Ecologically divergent species from younger radiations exhibit greater differences in splicing than those from older radiations. Most of these differentially spliced isoforms arose from standing variation, which was also present at low levels in non-radiating species, and increased in frequency during the adaptive radiation process. We identified several novel isoforms of craniofacial remodelling genes that emerged within each lake radiation and were differentially incorporated in the jaws of herbivorous vs. carnivorous species. Our findings indicate that a complex temporal interplay of GE and AS underlies adaptive radiation, with ancestral splice variation enabling rapid ecological diversification at early stages of speciation.

The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($<$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just ILS, but also gene flow, under the multispecies network coalescent (MSNC) model, processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. We also show that it can accurately infer the true network more often than other similar SNP-based programs (PhyloNet and HyDe). Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic data set to date (RADseq data set of 679 individuals and $>$37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation. [Genomics; multispecies network coalescent; phylogenetic networks; phylogenomics; RADseq; SNPs.].

Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting in the rapidly radiated East Asian genus Nekemias (Vitaceae).

Mass extinction has often paved the way for rapid evolutionary radiation, resulting in the emergence of diverse taxa within specific lineages. The emergence and diversification of carnivorous nematode-trapping fungi (NTF) in Ascomycota have been linked to the Permian-Triassic (PT) extinction, but the processes underlying NTF radiation remain unclear. We conducted phylogenomic analyses using 23 genomes that represent three NTF lineages, each employing distinct nematode traps-mechanical traps (Drechslerella spp.), three-dimensional (3D) adhesive traps (Arthrobotrys spp.), and two-dimensional (2D) adhesive traps (Dactylellina spp.), and the genome of one non-NTF species as the outgroup. These analyses revealed multiple mechanisms that likely contributed to the tempo of the NTF evolution and rapid radiation. The species tree of NTFs based on 2,944 single-copy orthologous genes suggested that Drechslerella emerged earlier than Arthrobotrys and Dactylellina. Extensive genome-wide phylogenetic discordance was observed, mainly due to incomplete lineage sorting (ILS) between lineages. Two modes of non-vertical evolution (introgression and horizontal gene transfer) also contributed to phylogenetic discordance. The ILS genes that are associated with hyphal growth and trap morphogenesis (e.g., those associated with the cell membrane system and polarized cell division) exhibited signs of positive selection.IMPORTANCEBy conducting a comprehensive phylogenomic analysis of 23 genomes across three NTF lineages, the research reveals how diverse evolutionary mechanisms, including ILS and non-vertical evolution (introgression and horizontal gene transfer), contribute to the swift diversification of NTFs. These findings highlight the complex evolutionary dynamics that drive the rapid radiation of NTFs, providing valuable insights into the processes underlying their diversity and adaptation.

The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade. Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ILS), and identification and quantification of gene flow in the presence of ILS is challenging and requires knowledge about the true phylogenetic relationship among the species. We use whole nuclear, plastid, and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods. We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ILS following the rapid radiation of the genus rather than by postspeciation introgression. Our analyses support the idea of ancient introgression among the ancestral lineages followed by ILS, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group. Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ILS and introgression.

The endemic Hawaiian lobeliads are exceptionally species rich and exhibit striking diversity in habitat, growth form, pollination biology and seed dispersal, but their origins and pattern of diversification remain shrouded in mystery. Up to five independent colonizations have been proposed based on morphological differences among extant taxa. We present a molecular phylogeny showing that the Hawaiian lobeliads are the product of one immigration event; that they are the largest plant clade on any single oceanic island or archipelago; that their ancestor arrived roughly 13 Myr ago; and that this ancestor was most likely woody, wind-dispersed, bird-pollinated, and adapted to open habitats at mid-elevations. Invasion of closed tropical forests is associated with evolution of fleshy fruits. Limited dispersal of such fruits in wet-forest understoreys appears to have accelerated speciation and led to a series of parallel adaptive radiations in Cyanea, with most species restricted to single islands. Consistency of Cyanea diversity across all tall islands except Hawai ;i suggests that diversification of Cyanea saturates in less than 1.5 Myr. Lobeliad diversity appears to reflect a hierarchical adaptive radiation in habitat, then elevation and flower-tube length, and provides important insights into the pattern and tempo of diversification in a species-rich clade of tropical plants.

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].

Preface List of Contributors Part I. Introduction: 1. Adaptive radiation and molecular evolution: concepts and research issues Thomas J. Givnish 2. Homoplasy in molecular vs. morphological data: the likelihood of correct phylogenetic inference Thomas J. Givnish, and Kenneth J. Sytsma Part II. Integrative Studies: 3. Adaptive radiation of the Hawaiian silversword alliance: congruence and conflict of phylogenetic evidence from molecular and non-molecular investigations Bruce G. Baldwin 4. The chronicle of marsupial evolution Mark S. Springer, John A. W. Kirsch, and Judd A. Chase 5. Evolutionary origins of phenotypic diversity in Daphnia John K. Colbourne, Paul D. N. Hebert, and Derek J. Taylor 6. Evolutionary trends in the ecology of New World monkeys inferred from a combined phylogenetic analysis of nuclear, mitochondrial, and morphological data Ines Horovitz, and Axel Meye 7. Adaptive radiation in the aquatic plant family Pontederiaceae: insights from phylogenetic analysis Spencer C. H. Barrett, and Sean W. Graham 8. Molecular evolution and adaptive radiation in Brocchinia (Bromeliaceae: Pitcairnioideae) atop tepuis of the Guayana Shield Thomas J. Givnish, Kenneth J. Sytsma, James F. Smith, William J. Hahn, David H. Benzing, and Elizabeth M. Burkhardt Part III. Convergence: 9. You aren't always what you eat: evolution of nectar-feeding among Old World fruitbats (Megachiroptera: Pteropodidae) John A. W. Kirsch, and Francois-Joseph Lapointe 10. Chloroplast DNA restriction sites and floral versus non-floral characters in the obligate twig epiphytes in subtribe Oncidiinae (Orchidaceae) Mark W. Chase, and Jeffrey D. Palmer 11. Adaptation, cladogenesis, and the evolution of habitat association in North American tiger beetles: a phylogenetic perspective Alfried P. Vogler Part IV. Rapid Radiations: 12. Molecular phylogenetic tests of sympatric speciation models in Lake Malawi cichlid fishes Peter N. Reinthal, and Axel Mey 13. A rapid adaptive radiation due to a key innovation in Aquilegia Scott Hodges 14. Origin and evolution of Argyranthemum (Asteraceae: Anthemideae) in Macaronesia Javier Francisco-Ortega, Daniel J. Crawford, Arnoldo Santos-Guerra, and Robert K. Jansen Part V. Reproductive Strategies: 15. Floral diversification, pollination biology, and molecular evolution in Platanthera (Orchidaceae) Jeffrey R. Hapeman, and Kenneth Inoue 16. Phylogenetic perspectives on the evolution of dioecy: adaptive radiation in the endemic Hawaiian genera Schiedea and Alsinodendron (Caryophyllaceae: Alsinoideae) Ann K. Sakai, Stephen G. Weller, Warren L. Wagner, and Pamela S. Soltis 17. Ecological and reproductive shifts in the diversification of the endemic Hawaiian Drosophila Michael P. Kambysellis, and Elysse M. Craddock Part VI. Character Divergence and Community Assembly: 18. History of ecological selection in sticklebacks - uniting experimental and phylogenetic approaches Eric B. Taylor, James D. McPhail, and Dalph Schluter 19. Phylogenetic studies of convergent adaptive radiations in Caribbean Anolis lizards Todd Jackman, Jonathan B. Losos, Allan Larson, and Kevin de Queiros Part VII. Macroevolutionary Patterns: 20. Molecular and morphological evolution during the post-Palaeozoic diversification of echinoids Andrew B. Smith, and D. T. J. Littlewood 21. How fast is speciation: molecular, geological and phylogenetic evidences from adaptive radiations of fish Amy R. McCune Index.

Six endemic genera/sections of lobeliads (Campanulaceae) occupy nearly the full range of light regimes on moist sites in the Hawaiian Islands, from open alpine bogs and seacliffs to densely shaded rainforest interiors. To determine whether this clade has undergone a corresponding adaptive radiation in photosynthetic adaptations, we studied the natural light habitats and physiological characteristics of 11 species representing each sublineage. Across species in the field, average photon flux density (PFD) varies from 2.3 to 30.0 mol · m(-2) · d(-1), and maximum assimilation rate (A(max)) ranges from 0.17 to 0.35 μmol CO(2) · g(-1) · s(-1). Across species, A(max), dark respiration rate (R), Michaelis-Menten constant (k), light compensation point, specific leaf area (SLA), maximum carboxylation rate (V(cmax)), maximum rate of electron transport (J(max)), photosynthesis at saturating CO(2) (A(satCO(2))), and carboxylation efficiency (α) all increase significantly and in tightly coupled fashion with PFD, in accord with classical economic theory. Area-based rates have a higher degree of physiological integration with each other and tighter coupling to PFD than the corresponding mass-based rates, despite the energetic importance of the latter. Area-based rates frequently show adaptive cross-over: high-light species outperform low-light species at high PFD and vice versa at low PFD. A(max)-mass has little relationship to leaf mass per unit area (LMA), leaf N content, or leaf lifespan individually, but a multiple regression explains 96% of the variance in A(max)-mass across species in terms of SLA, leaf N content, and average PFD. Instantaneous leaf compensation points range from 0.1 to 1.2% full sunlight, far lower than the ecological (whole-plant) compensation points (ECPs) of 1.1 to 29.0% sunlight calculated based on photosynthetic parameters, leaf longevity, and allocation to leaf vs. nonleaf tissue. The ECPs are much closer to the lower limits of PFD actually experienced by lobeliads, suggesting they may play an important role in restricting species distributions. Taken together, these data provide evidence for an adaptive radiation in photosynthetic traits that is strongly correlated with-and indeed may help determine-the light regime that each species inhabits.

Cytonuclear discordance is commonly observed in phylogenetic studies, yet few studies have tested whether these patterns reflect incomplete lineage sorting or organellar introgression. Here, we used whole-chloroplast sequence data in combination with over 1000 nuclear single-nucleotide polymorphisms to clarify the extent of cytonuclear discordance in wild annual sunflowers (Helianthus), and to test alternative explanations for such discordance. Our phylogenetic analyses indicate that cytonuclear discordance is widespread within this group, both in terms of the relationships among species and among individuals within species. Simulations of chloroplast evolution show that incomplete lineage sorting cannot explain these patterns in most cases. Instead, most of the observed discordance is better explained by cytoplasmic introgression. Molecular tests of evolution further indicate that selection may have played a role in driving patterns of plastid variation - although additional experimental work is needed to fully evaluate the importance of selection on organellar variants in different parts of the geographic range. Overall, this study represents one of the most comprehensive tests of the drivers of cytonuclear discordance and highlights the potential for gene flow to lead to extensive organellar introgression in hybridizing taxa.