Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species

The biogeographic and evolutionary processes shaping population divergence in Laupala

Speciation generates biodiversity and the mechanisms involved are thought to vary across the tree of life and across environments. For example, well-studied adaptive radiations are thought to be fuelled by divergent ecological selection, but additionally are influenced heavily by biogeographic, genomic and demographic factors. Mechanisms of non-adaptive radiations, producing ecologically cryptic taxa, have been less well-studied but should likewise be influenced by these latter factors. Comparing among contexts can help pinpoint universal mechanisms and outcomes, especially if we integrate biogeographic, ecological and evolutionary processes. We investigate population divergence in the swordtail cricket Laupala cerasina, a wide-spread endemic on Hawai'i Island and one of 38 ecologically cryptic Laupala species. The nine sampled populations show striking population genetic structure at small spatio-temporal scales. The rapid differentiation among populations and species of Laupala shows that neither a specific geographical context nor ecological opportunity are pre-requisites for rapid divergence. Spatio-temporal patterns in population divergence, population size change, and gene flow are aligned with the chronosequence of the four volcanoes on which L. cerasina occurs and reveal the composite effects of geological dynamics and Quaternary climate change on population dynamics. Spatio-temporal patterns in genetic variation along the genome reveal the interplay of genetic and genomic architecture in shaping population divergence. In early phases of divergence, we find elevated differentiation in genomic regions harbouring mating song loci. In later stages of divergence, we find a signature of linked selection that interacts with recombination rate variation. Comparing our findings with recent work on complementary systems supports the conclusion that mostly universal factors influence the speciation process.

Allopolyploid origin and diversification of the Hawaiian endemic mints

Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin's thinking about the evolutionary process.

Foliar functional and genetic variation in a keystone Hawaiian tree species estimated through spectroscopy

Imaging spectroscopy has the potential to map closely related plant taxa at landscape scales. Although spectral investigations at the leaf and canopy levels have revealed relationships between phylogeny and reflectance, understanding how spectra differ across, and are inherited from, genotypes of a single species has received less attention. We used a common-garden population of four varieties of the keystone canopy tree, Metrosideros polymorpha, from Hawaii Island and four F1-hybrid genotypes derived from controlled crosses to determine if reflectance spectra discriminate sympatric, conspecific varieties of this species and their hybrids. With a single exception, pairwise comparisons of leaf reflectance patterns successfully distinguished varieties of M. polymorpha on Hawaii Island as well as populations of the same variety from different islands. Further, spectral variability within a single variety from Hawaii Island and the older island of Oahu was greater than that observed among the four varieties on Hawaii Island. F1 hybrids most frequently displayed leaf spectral patterns intermediate to those of their parent taxa. Spectral reflectance patterns distinguished each of two of the hybrid genotypes from one of their parent varieties, indicating that classifying hybrids may be possible, particularly if sample sizes are increased. This work quantifies a baseline in spectral variability for an endemic Hawaiian tree species and advances the use of imaging spectroscopy in biodiversity studies at the genetic level.

Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics

Although the monophyly of Phedimus has been strongly demonstrated, the species relationships among approximately 20 species of Phedimus have been difficult to determine because of the uniformity of their floral characteristics and extreme variation of their vegetative characters, often accompanied by high polyploid and aneuploid series and diverse habitats. In this study, we assembled 15 complete chloroplast genomes of Phedimus species from East Asia and generated a plastome-based backbone phylogeny of the subgenus Aizoon. As a proxy for nuclear phylogeny, we reconstructed the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) phylogeny independently. The 15 plastomes of subg. Aizoon were highly conserved in structure and organization; hence, the complete plastome phylogeny fully resolved the species relationships with strong support. We found that P. aizoon and P. kamtschaticus were polyphyletic and morphologically distinct or ambiguous species, and they most likely evolved from the two species complex. The crown age of subg. Aizoon was estimated to be 27 Ma, suggesting its origin to be in the late Oligocene; however, the major lineages were diversified during the Miocene. The two Korean endemics, P. takesimensis and P. zokuriensis, were inferred to have originated recently during the Pleistocene, whereas the other endemic, P. latiovalifolium, originated in the late Miocene. Several mutation hotspots and seven positively selected chloroplast genes were identified in the subg. Aizoon.

Evolutionary genomics of oceanic island radiations

A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.