Population genetics of Sida fallax Walp. (Malvaceae) in the Hawaiian Islands.

Introduction: Sida fallax (Malvaceae) is the most widespread and variable taxon of Malvaceae in the Hawaiian Islands, growing with a diversity of morphological forms in different habitats including Midway Atoll, Nihoa, and all the main islands. Morphological variation exists within and among populations. The study aimed to investigate the genetic variation within and among populations from various habitats and geographic locations throughout the Hawaiian range of S. fallax. Methods: A total of 124 samples, with up to five samples per population where possible, were collected from 26 populations across six of the main Hawaiian Islands (Kaua'i, O'ahu, Maui, Moloka'i, Lana'i, and Hawai'i) and Nihoa in the Northwestern Hawaiian Islands. The sampling strategy encompassed collecting populations from different habitats and geographic locations, including coastal and mountain ecotypes, with many intermediate morphological forms. Multiplexed ISSR genotyping by sequencing (MIG-seq) was used to detect single nucleotide polymorphisms (SNP) and genetic differences among individuals and populations were evaluated using PCO analyses. Results: The relationship of FST with the geographical distance between the populations was assessed using the Mantel test. The results showed that populations on a single island were more closely related to each other and to populations on islands within their respective groups than they were to populations on other islands. Discussion: The overall genetic relationships among islands were, to a large extent, predictive based on island position within the chain and, to a lesser extent, within island topography.

Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships.

The tribe Hydrangeeae displays a unique, distinctive disjunct distribution encompassing East Asia, North America and Hawaii. Despite its complex trait variations and polyphyletic nature, comprehensive phylogenomic and biogeographical studies on this tribe have been lacking. To address this gap, we sequenced and characterized 28 plastomes of Hydrangeeae. Our study highlights the highly conserved nature of Hydrangeaceae chloroplast (cp) genomes in terms of gene content and arrangement. Notably, synapomorphic characteristics of tandem repeats in the conserved domain of accD were observed in the Macrophyllae, Chinenses, and Dichroa sections within the Hydrangeeae tribe. Additionally, we found lower expression of accD in these sections using structure prediction and quantitative real-time PCR analysis. Phylogenomic analyses revealed the subdivision of the Hydrangeeae tribe into two clades with robust support values. Consistent with polyphyletic relationships, sect. Broussaisia was identified as the basal group in the tribe Hydrangeeae. Our study also provides insights into the phylogenetic relationships of Hydrangea petiolaris in the Jeju and Ulleung Island populations, suggesting the need for further studies with more samples and molecular data. Divergence time estimation and biogeographical analyses suggested that the common ancestors of the tribe Hydrangeeae likely originated from North America and East Asia during the Paleocene period via the Bering Land Bridge, potentially facilitating migration within the tribe between these regions. In conclusion, this study enhances our understanding of the evolutionary history and biogeography of the tribe Hydrangeeae, shedding light on the dispersal patterns and origins of this intriguing plant group with its unique disjunct distribution.

Duplication and expression patterns of CYCLOIDEA-like genes in Campanulaceae.

BACKGROUND: CYCLOIDEA (CYC)-like transcription factors pattern floral symmetry in most angiosperms. In core eudicots, two duplications led to three clades of CYC-like genes: CYC1, CYC2, and CYC3, with orthologs of the CYC2 clade restricting expression dorsally in bilaterally symmetrical flowers. Limited data from CYC3 suggest that they also play a role in flower symmetry in some asterids. We examine the evolution of these genes in Campanulaceae, a group that contains broad transitions between radial and bilateral floral symmetry and 180° resupination (turning upside-down by twisting pedicle). RESULTS: We identify here all three paralogous CYC-like clades across Campanulaceae. Similar to other core eudicots, we show that CamCYC2 duplicated near the time of the divergence of the bilaterally symmetrical and resupinate Lobelioideae. However, in non-resupinate, bilaterally symmetrical Cyphioideae, CamCYC2 appears to have been lost and CamCYC3 duplicated, suggesting a novel genetic basis for bilateral symmetry in Cyphioideae. We additionally, utilized qRT-PCR to examine the correlation between CYC-like gene expression and shifts in flower morphology in four species of Lobelioideae. As expected, CamCYC2 gene expression was dorsoventrally restricted in bilateral symmetrical flowers. However, because Lobelioideae have resupinate flowers, both CamCYC2A and CamCYC2B are highly expressed in the finally positioned ventral petal lobes, corresponding to the adaxial side of the flower relative to meristem orientation. CONCLUSIONS: Our sequences across Campanulaceae of all three of these paralogous groups suggests that radially symmetrical Campanuloideae duplicated CYC1, Lobelioideae duplicated CYC2 and lost CYC3 early in their divergence, and that Cyphioideae lost CYC2 and duplicated CYC3. This suggests a dynamic pattern of duplication and loss of major floral patterning genes in this group and highlights the first case of a loss of CYC2 in a bilaterally symmetrical group. We illustrate here that CYC expression is conserved along the dorsoventral axis of the flower even as it turns upside-down, suggesting that at least late CYC expression is not regulated by extrinsic factors such as gravity. We additionally show that while the pattern of dorsoventral expression of each paralog remains the same, CamCYC2A is more dominant in species with shorter relative finally positioned dorsal lobes, and CamCYC2B is more dominant in species with long dorsal lobes.

Repeated range expansion and niche shift in a volcanic hotspot archipelago: Radiation of C4 Hawaiian Euphorbia subgenus Chamaesyce (Euphorbiaceae).

Woody perennial plants on islands have repeatedly evolved from herbaceous mainland ancestors. Although the majority of species in Euphorbia subgenus Chamaesyce section Anisophyllum (Euphorbiaceae) are small and herbaceous, a clade of 16 woody species diversified on the Hawaiian Islands. They are found in a broad range of habitats, including the only known C4 plants adapted to wet forest understories. We investigate the history of island colonization and habitat shift in this group. We sampled 153 individuals in 15 of the 16 native species of Hawaiian Euphorbia on six major Hawaiian Islands, plus 11 New World close relatives, to elucidate the biogeographic movement of this lineage within the Hawaiian island chain. We used a concatenated chloroplast DNA data set of more than eight kilobases in aligned length and applied maximum likelihood and Bayesian inference for phylogenetic reconstruction. Age and phylogeographic patterns were co-estimated using BEAST. In addition, we used nuclear ribosomal ITS and the low-copy genes LEAFY and G3pdhC to investigate the reticulate relationships within this radiation. Hawaiian Euphorbia first arrived on Kaua`i or Ni`ihau ca. 5 million years ago and subsequently diverged into 16 named species with extensive reticulation. During this process Hawaiian Euphorbia dispersed from older to younger islands through open vegetation that is disturbance-prone. Species that occur under closed vegetation evolved in situ from open vegetation of the same island and are only found on the two oldest islands of Kaua`i and O`ahu. The biogeographic history of Hawaiian Euphorbia supports a progression rule with within-island shifts from open to closed vegetation.

Uncovering unseen fungal diversity from plant DNA banks.

Throughout the world DNA banks are used as storage repositories for genetic diversity of organisms ranging from plants to insects to mammals. Designed to preserve the genetic information for organisms of interest, these banks also indirectly preserve organisms' associated microbiomes, including fungi associated with plant tissues. Studies of fungal biodiversity lag far behind those of macroorganisms, such as plants, and estimates of global fungal richness are still widely debated. Utilizing previously collected specimens to study patterns of fungal diversity could significantly increase our understanding of overall patterns of biodiversity from snapshots in time. Here, we investigated the fungi inhabiting the phylloplane among species of the endemic Hawaiian plant genus, Clermontia (Campanulaceae). Utilizing next generation DNA amplicon sequencing, we uncovered approximately 1,780 fungal operational taxonomic units from just 20 DNA bank samples collected throughout the main Hawaiian Islands. Using these historical samples, we tested the macroecological pattern of decreasing community similarity with decreasing geographic proximity. We found a significant distance decay pattern among Clermontia associated fungal communities. This study provides the first insights into elucidating patterns of microbial diversity through the use of DNA bank repository samples.

Population Genetics of the Endemic Hawaiian Species Chrysodracon hawaiiensis and Chrysodracon auwahiensis (Asparagaceae): Insights from RAPD and ISSR Variation.

The genus Chrysodracon has six endemic species in the Hawaii Islands. Chrysodracon hawaiiensis is endemic to Hawaii Island and was described as a distinct species in 1980. It was listed as an endangered species on the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List in 1997. This woody plant species was, at one time, common in exposed dry forests, but it became very rare due to grazing pressure and human development. The tree species Chrysodracon auwahiensis (C. auwahiensis), endemic to Maui and Molokai, still has large adult populations in dry lands of the islands, but unfortunately no regeneration from seed has been reported in those areas for many years. The two endemic species were examined using the molecular technique of random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) to determine the genetic structure of the populations and the amount of variation. Both species possess similar genetic structure. Larger and smaller populations of both species contain similar levels of genetic diversity as determined by the number of polymorphic loci, estimated heterozygosity, and Shannon's index of genetic diversity. Although population diversity of Chrysodracon hawaiiensis (C. hawaiiensis) is thought to have remained near pre-disturbance levels, population size continues to decline as recruitment is either absent or does not keep pace with senescence of mature plants. Conservation recommendations for both species are suggested.

Global phylogeny and biogeography of grammitid ferns (Polypodiaceae).

We examined the global historical biogeography of grammitid ferns (Polypodiaceae) within a phylogenetic context. We inferred phylogenetic relationships of 190 species representing 31 of the 33 currently recognized genera of grammitid ferns by analyzing DNA sequence variation of five plastid DNA regions. We estimated the ages of cladogenetic events on an inferred phylogeny using secondary fossil calibration points. Historical biogeographical patterns were inferred via ancestral area reconstruction. Our results supported four large-scale phylogenetic and biogeographic patterns: (1) a monophyletic grammitid clade that arose among Neotropical polypod ancestors about 31.4 Ma; (2) a paraphyletic assemblage of clades distributed in the Neotropics and the Afro-Malagasy region; (3) a large clade distributed throughout the Asia-Malesia-Pacific region that originated about 23.4 Ma; and, (4) an Australian or New Zealand origin of the circumaustral genus Notogrammitis. Most genera were supported as monophyletic except for Grammitis, Oreogrammitis, Radiogrammitis, and Zygophlebia. Grammitid ferns are a well-supported monophyletic group with two biogeographically distinct lineages: a primarily Neotropical grade exhibiting several independent successful colonizations to the Afro-Malagasy region and a primarily Paleotropical clade exhibiting multiple independent dispersals to remote Pacific islands and temperate, austral regions.

Relatedness defies biogeography: the tale of two island endemics (Acacia heterophylla and A. koa).

Despite the normally strong link between geographic proximity and relatedness of recently diverged taxa, truly puzzling biogeographic anomalies to this expectation exist in nature. Using a dated phylogeny, population genetic structure and estimates of ecological niche overlap, we tested the hypothesis that two geographically very disjunct, but morphologically very similar, island endemics (Acacia heterophylla from Réunion Island and A. koa from the Hawaiian archipelago) are the result of dispersal between these two island groups, rather than independent colonization events from Australia followed by convergent evolution. Our genetic results indicated that A. heterophylla renders A. koa paraphyletic and that the former colonized the Mascarene archipelago directly from the Hawaiian Islands ≤ 1.4 million yr ago. This colonization sequence was corroborated by similar ecological niches between the two island taxa, but not between A. melanoxylon from Australia (a sister, and presumed ancestral, taxon to A. koa and A. heterophylla) and Hawaiian A. koa. It is widely accepted that the long-distance dispersal of plants occurs more frequently than previously thought. Here, however, we document one of the most exceptional examples of such dispersal. Despite c. 18 000 km separating A. heterophylla and A. koa, these two island endemics from two different oceans probably represent a single taxon as a result of recent extreme long-distance dispersal.

Investigating the pollination syndrome of the Hawaiian lobeliad genus Clermontia (Campanulaceae) using floral nectar traits.

PREMISE OF THE STUDY: Floral nectar sugar compositions have, for several decades, been used to predict a plant species' pollinator guild. Plants possessing a generalist ornithophilous pollination syndrome produce nectar that is dilute (8-12% w/v sugars) with a low sucrose to hexose (glucose and fructose) ratio. The Hawaiian lobeliad genus Clermontia contains 22 endemic species of shrubs and small trees that are believed to have evolved flowers adapted for pollination by now mostly extinct or endangered endemic passerines in the Drepanidinae and Mohoidae. METHODS: We analyzed the nectar sugar compositions, concentration, and nectar standing crop of 23 taxa to test the assumption that Clermontia taxa have evolved floral traits in response to selection pressures from these avian pollinators. KEY RESULTS: All Clermontia taxa produced nectar with sugar concentrations (mean: 9.2% w/v ± 1.8 SD) comparable to the nectar of other plant species with a generalized bird pollination system. Nectar sugars were overwhelmingly composed of hexoses in all taxa (mean sucrose/hexose ratio: 0.02 ± 0.02). Nectar standing crop volumes varied widely among taxa, ranging from 9.7 µL ± 7.1 to 430.5 µL ± 401.8 (mean volume: 177.8 ± 112.0). CONCLUSIONS: Collectively, the nectar traits indicate that Clermontia species possess a generalist passerine pollination syndrome.

Molecular phylogeny and dating of Asteliaceae (Asparagales): Astelia s.l. evolution provides insight into the Oligocene history of New Zealand.

Asteliaceae (4 genera, 36 species) are found on both continents and island archipelagos in the southern hemisphere and across the Pacific. The circumscription of Asteliaceae and intrageneric relationships are poorly understood. We generated a phylogeny including all genera and 99% of the species using DNA sequence data from chloroplast (trnL, psbA-trnH, rps16, and petL-psbE) and nuclear (NIA-i3) regions. Relaxed clock methods were applied to infer the age of the family and the timing of cladogenic events. Generic delimitations change as a result of this study. Collospermum is nested within Astelia and is recognized here only at the subgeneric level. Further, Astelia subgenera Astelia, Asteliopsis, and Tricella are paraphyletic and to achieve monophyly their recircumscriptions are proposed. Despite the presence of Asteliaceae taxa on multiple Gondwanan landmasses and proposed Cretaceous origins for the family, radiation of genera was during the Tertiary. The largest and oldest genus, Astelia s.l. (including Collospermum), radiated around the Eocene/Oligocene boundary (ca. 34.2 million years ago (Ma)). Astelia s.l. subgenera diverged from the Oligocene/Miocene boundary onwards (<24.0 Ma). These dates suggest that current distributions are most likely to be the result of long-distance dispersal. Alpine taxa in New Zealand and Australia radiated during the Late Miocene/Pliocene. These results are congruent with Astelia micro- and macro-fossil data and suggest that Astelia s.l. either persisted in New Zealand during the proposed Oligocene marine transgression or dispersed from Australia after the subsequent expansion of terrestrial habitat.

Molecular phylogeny and adaptive radiation of the endemic Hawaiian Plantago species (Plantaginaceae).

Insular oceanic islands provide excellent opportunities for the study of evolutionary processes and adaptive radiation. The Hawaiian Plantago radiation comprises six endemic taxa showing considerable inter- and intraspecific morphological and ecological diversity. The rDNA internal (ITS) and external (ETS) transcribed spacers and two recently described chloroplast spacers, ndhF-rpl32 and rpl32-trnL, were sequenced to study phylogenetic relationships within this morphologically complex group. Phylogenetic analysis provided strong evidence for the monophyly of Hawaiian Plantago, suggesting that the lineage arose from a single long-distance dispersal event. Inconsistencies between nuclear and chloroplast phylogenies suggest a history of hybridization. The basal, unresolved dichotomy of the combined phylogeny is consistent with rapid phenotypic diversification of the major lineages early in the history of this group. Speciation has largely occurred allopatrically, with divergence a result of intraisland ecological shifts between bog and woodland habitats and interisland dispersal events. Most interisland colonizations were from older to younger islands with initial colonization of Kaua'i. In our analysis, P. pachyphylla is paraphyletic and taxonomic separation of the distinct morphotypes of this species appears justified. Furthermore, the apparent hybrid ancestry and unique morphology and habitat of the endangered P. princeps var. longibracteata support its recognition at the specific rank.