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Hawaiian Plant DNA Library II: Endemic, Indigenous, and Introduced Species
Abstract and Figures
The Hawaiian Plant DNA Library of endemic and indigenous plant species preserves genetic material from all Hawaiian Islands. DNA accession numbers are reported here for 155 native species representing 92 genera and 48 families. Federal status of endangered species is indicated where applicable. Accessions for 71 species in 52 genera and 10 families of introduced species are also reported. Pest and invasive species are also indicated.
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... Thermo Scientific). Extra DNA materials were deposited into the Hawai'i Plant DNA library (Morden et al. 1996;Randell & Morden 1999). ...
... In the field, this plant was not recognized as a hybrid, so neither herbarium specimens nor DNA from putative parents were collected. Instead, DNA was obtained from a nearby collection of C. setaceus from the Hawai'i Plant DNA Library (HPDL# 120; Randell & Morden 1999) and destructive sampling of a C. clandestinus herbarium specimen collected nearby (W. Takeuchi 5746 BISH). ...
During grass surveys across the islands of Hawai‘i in 2022, two novel hybrids among non-native Poaceae were found growing on roadsides. Spontaneous hybridization was observed among Chloris barbata and C. divaricata on O‘ahu and among Cenchrus clandestinus and C. setaceus on Hawai‘i island. Morphological evidence initially suggested these plants may be hybrids and molecular analysis using the ITS and rpl32-trnL regions confirmed that the plants are hybrids and identified their parentage. These hybrids are named Chloris × pseudosagrana nothosp. nov. and Cenchrus × peregrinus nothosp. nov. No developed seeds could be found on either of these hybrids and they are suspected to be sterile F1 hybrids. The occurrence of hybridization events among other non-native species are also discussed.
... Ipomoea batatas DNA was obtained from various repositories: fresh plant tissues from gardens, markets, and collections across the Hawaiian Islands, germplasm originally sourced from the United States Department of Agriculture National Plant Germplasm System (USDA-NPGS), DNA sourced from a Hawaiian plant DNA library (Randell and Morden 1999), and herbarium voucher specimens. CHLOROPLAST LOCI SAMPLING: HAWAIFI ACCESSIONS DNA was obtained from 50 I. ...
... The differentiation of the Amy Greenwell Ethnobotanical Garden collection from other HawaiFi botanical gardens in the chloroplast analysis indicates garden-specific differences in Hawaiian sweet potato ex-situ conservation. We suggest that garden's location in fertile remnants of the Kona field system (Kelly 1983), explicit focus on Hawaiian ethnobotany/culturally-relevant plants, staff/ community commitment to Hawaiian crop plants, and stable leadership enabled continuity of its Hawaiian 'uala collection through the 1990s construction of the DNA library (Randell and Morden 1999). ...
Sweet potato (Ipomoea batatas [L.] Lam.) is one of the most important staple crops globally with particular cultural and economic significance in the Hawaiian Islands, yet the extent to which traditional cultivars persist remains unknown. The objective of this study was to elucidate the relationships between traditional Hawaiian sweet potato varieties and cultivars that originated elsewhere in the world. We sought to characterize genetic and phenotypic diversity of sweet potatoes represented in the Hawaiian Islands. To this end, a genetic assignment analysis was conducted on a sample of 77 individuals that consisted of traditional Hawaiian, USDA NPGS accessions, and recent herbarium samples. Additionally, voucher specimens of Hawaiian cultivars from the early twentieth century were assessed for variation in leaf morphology. We identified several inconsistencies within the Hawaiian-named varieties, as identically named varieties turned out to be genetically distinct, and similarly named voucher specimens varied in leaf morphology. Our findings call attention to the value of a set of Hawaiian sweet potatoes as “heirloom.” These genetically distinct traditional cultivars have unique value in local markets and present an opportunity to increase cultivar diversity in the markets and fields, support farmer income and diversified agriculture, all while contributing to reinvigoration of Hawaiian cultural heritage.
... Thermo Scientific). Extra DNA materials were deposited into the Hawai'i Plant DNA library (HPDL) (Morden et al. 1996;Randell & Morden 1999). ...
... DNA was extracted from all samples and purified following previously established laboratory protocols described in Morden et al. (1996). Each sample was assigned an accession number in the Hawaiian Plant DNA Library (HPDL; Morden et al. 1996;Randell and Morden 1999; http://www. botany.hawaii.edu/hawaiian-plant-dna-library; ...
—A new species endemic to Hawai‘i Island, Tetramolopium stemmermanniae, is described and illustrated. Molecular and morphological evidence support T. stemmermanniae as being distinct from T.arenarium var. arenarium, T.consanguineum ssp. leptophyllum, and T.humile ssp. humile, which occur at Pohakuloa Training Area, Hawai‘i Island. Tetramolopium stemmermanniae shares an upright and multibranched habit with T.arenarium var. arenarium and T.consanguineum ssp. leptophyllum but differs in the number and color of ray and disc flowers, and in having an open, paniculate inflorescence. We provide a description of the new taxon, include a key to the Tetramolopium species of Hawai‘i, and a brief description of the habitat where the newly described species occurs.
... Upon collection, samples were accessioned in the Joseph F. Rock Herbarium (Appendix 1). Fresh tissue for DNA extraction was field collected into a plastic bag and remained at 4°C until it was extracted via a modified cetyltrimethylammonium bromide (CTAB) protocol and cesium banded (Morden et al., 1996;Randell and Morden, 1999). Purified DNA was stored at −20°C until this analysis. ...
Premise:
The use of DNA from herbarium specimens is an increasingly important source for evolutionary studies in plant biology, particularly in cases where species are rare or difficult to obtain. Here we compare the utility of DNA from herbarium tissues to their freezer-stored DNA counterparts via the Hawaiian Plant DNA Library.
Methods:
Plants collected for the Hawaiian Plant DNA Library were simultaneously accessioned as herbarium specimens at the time of collection, from 1994-2019. Paired samples were sequenced using short-read sequencing and assessed for chloroplast assembly and nuclear gene recovery.
Results:
Herbarium specimen-derived DNA was statistically more fragmented than freezer-stored DNA derived from fresh tissue, leading to poorer chloroplast assembly and overall lower coverage. The number of nuclear targets recovered varied mostly by total sequencing reads per library and age of specimen, but not by storage method (herbarium or long-term freezer). Although there was evidence of DNA damage in the samples, there was no evidence that it was related to the length of time in storage, whether frozen or as herbarium specimens.
Discussion:
DNA extracted from herbarium tissues will continue to be invaluable, despite being highly fragmented and degraded. Rare floras would benefit from both traditional herbarium storage methods and extracted DNA freezer banks.
... Total genomic DNA was extracted using a modified CTAB method (cetyltrimethylammonium bromide) (Morden et al. 1996). DNA samples were accessioned into the Hawaiian Plant DNA Library (HPDL) at the University of Hawai'i at Manoa (UHM) (Morden et al. 1996, Randell andMorden 1999). ...
Sida fallax Walp. (‘ilima) (Malveae, Malvoideae, Malvaceae) is native to the Pacific area and is broadly distributed throughout this region. Sida fallax is the most widespread and variable taxon of Malvaceae in the Hawaiian Islands and it occurs with diverse morphological forms and in different habitats from Hawai‘i Island to Midway Atoll. The low elevation and mountain ecotypes are two
extreme ecological forms of S. fallax with many intermediate morphological types existing between these extreme ecotypes in the Hawaiian Islands. The range of morphological and ecological diversity in Sida fallax suggests that this species requires further biosystematics investigation. The purpose of this study was two-fold. First, explore the genetic diversity among S. fallax populations throughout its native range in the Pacific region to assess if it is a single species or potentially multiple cryptic species; second, investigate the biogeographic origin of S. fallax. To do this, Sida fallax was sampled throughout the Hawaiian Islands and in different parts of the Pacific region. Bayesian phylogenetic analyses based on nuclear (ITS and ETS) and chloroplast regions (psbA–trnH) were carried out. Results indicate that there is very little sequence-level variation in this species
throughout its distribution and phylogenetic analysis clearly demonstrated that Sida fallax is a single species throughout the Pacific region and the different forms of Hawaiian S. fallax are not genetically distinct at the sequence level. Although the pattern of dispersal of S. fallax is not clear, an American origin is most likely.
... Total genomic DNA was extracted from 1.0 g fresh leaves or 0.2 g from recently collected herbarium specimens (< 5 yr old) using the CTAB extraction protocol (Doyle and Doyle 1987) with some modifications (Morden et al. 1996). DNA specimens were accessioned into the Hawaiian Plant DNA Library (Randell and Morden 1999). Table 7. Taxonomic classification of Clermontia proposed by . ...
... The monophyly and placement of the following three classes of taxonomically problematic groups reviewed above are specifically investigated: (1) species assigned to the Caribbean Islands endemic genera Calyptrogenia, Hottea and Mitranthes, including those from Cuba; (2) Calycolpus and Pseudanamomis sensu Bisse (1983; and (3) Figure 1 shows the locations of field collections within the Greater Antilles included in this study. Additional material was included from cultivated plants, herbarium specimens and the Hawaiian Plant DNA Library (Morden & al., 1996;Randell & Morden, 1999). Field collections emphasized focal groups. ...
Myrtaceae are a large family of trees and shrubs, including ca. 2500 species within the predominantly Neotropical and taxonomically problematic tribe Myrteae. Nearly 500 species of Myrteae are endemic to the Caribbean Islands Biodiversity Hotspot, but few have been represented in phylogenetic systematic studies to date. The major goals of this survey are to identify the main lineages of Myrteae present in the Greater Antilles and potential clades for further investigation. Specific objectives are to evaluate the monophyly and placement of the following: (1) the three genera of Myrtaceae considered endemic to the Caribbean Islands (Calyptrogenia , Hottea , Mitranthes ); (2) Calycolpus and Pseudanamomis sensu Bisse; and (3) Greater Antillean species of Plinia . To accomplish these aims, species of Myrtaceae representing all genera native to the Greater Antilles were sampled from across the region for placement within previously established phylogenetic frameworks for Myrteae and the large genus Eugenia . In total, 160 terminal taxa of Myrtaceae (89 Caribbean Islands endemics) were analyzed for this study. Phylogenetic inference was conducted by maximum parsimony and Bayesian methods on alignments of DNA sequence data from one nuclear (ITS) and three chloroplast (psbA ‐trnH , ndhF‐rpl32 , trnL‐trnF ) regions. Results of both types of analysis were congruent with each other and with the major clades recovered in previous studies, but some conflict was observed between nuclear and chloroplast regions involving congeneric species. Calycorectes (= Hottea ) ekmanii from eastern Cuba was found to be closely related to Calycolpus within subtribe Myrtinae. Subtribes Myrciinae, Pliniinae, Pimentinae (Pimenta and Psidium groups) and Eugeniinae contained other Greater Antillean species. Sampled species of Plinia from Cuba emerged within Myrciaria , and Mitranthes was found to be non‐monophyletic. All sampled species of Eugenia endemic to the Caribbean fell within E. sect. Excelsae (including Calycolpus sensu Bisse), E. sect. Racemosae and E. sect. Umbellatae except for E. cycloidea , which was associated with the Old World species of E. sect. Jossinia . Within Eugenia sect. Umbellatae , Caribbean species formed two major clades, designated C1 and C2, containing species of Calyptrogenia and Hottea from southern Hispaniola, a polyphyletic Pseudanamomis sensu Bisse and the Lathberry Clade, a novel group of Eugenia species centered in Puerto Rico and the Virgin Islands. Calyptrogenia and Hottea species from southern Hispaniola are transferred to Eugenia along with Pseudanamomis nipensis , while Mitranthes species are transferred to Myrcia . Two additional combinations are made within Eugenia and Pimenta in accordance with the results, and lectotypes are designated as appropriate.
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.
Aim The taxon cycle hypothesis describes the cyclic movement of taxa during range expansion and contraction, accompanied by an evolutionary shift from open and often coastal vegetation to closed, and often inland forest vegetation in island systems. The Hawaiian Archipelago is an ideal system to test this hypothesis given the linear fashion of island formation and a relatively well-understood geological history.
Location Hawaiian Islands.
Methods We sampled 153 individuals in 15 of the 16 native species of Hawaiian Euphorbia section Anisophyllum on six major Hawaiian Islands, plus 11 New World close relatives, to elucidate the biogeographic movement of this lineage along 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. Connectivity among islands and habitat types was estimated using BayesTraits. 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.
Results We estimate that Hawaiian Euphorbia first arrived on Kauai or Niihau ca. 5 million years ago and subsequently diverged into 16 species on all major Hawaiian Islands. During this process Euphorbia dispersed from older to younger islands in a stepping-stone fashion through open, dispersal-prone habitats. Taxa that occupy closed vegetation on Kauai and Oahu evolved in situ from open vegetation taxa of the same island. Consequently, widespread species tend to occupy habitats with open vegetation, whereas single island endemic species predominantly occur in habitats with closed canopy and are only found on the two oldest islands of Kauai and Oahu.
Main conclusions The spatial and temporal patterns of dispersal and range shifts in Hawaiian Euphorbia support an intra-volcanic-archipelago version of the taxon cycle hypothesis.
Two species of Rubus occur naturally in the Hawaiian Islands, R. hawaiensis and R. macraei. It has been previously thought that R. spectabilis, a western North American species, and R. hawaiensis share a recent common ancestor based on morphological similarity, and that R. macraei was a later derivative of R. hawaiensis. DNA sequences of the chloroplast gene ndhF were used to reconstruct the phylogeny of these species with non-Hawaiian members of subgenus Idaeobatus. These findings strongly contradict the previous hypothesis for the origin of the Hawaiian Rubus. Although R. hawaiensis is closely related to R. spectabilis, R. macraei is distantly related to these species. Sequence identity, genetic distance, and phylogenetic analysis all suggest that R. macraei is distantly related to New World and Asian species of subg. Jdaeobatus. Consequently, R. macraei and R. hawaiensis may have arisen from two separate colonizations in the Hawaiian Islands rather than one as previously assumed. The ancestry of R. macraei may trace to other Pacific Rim islands.
Haplostachys haplostachya was at one time a prevalent species in the mid-elevation (1650–1800 m) xerophytic shrubland between Mauna Loa and Mauna Kea on Hawaii. Grazing pressure by feral ungulates, destruction of habitat from military activity, and conversion of forest to pastures have fragmented its range to small subpopulations restricted to several cinder cones and portions of the remaining shrubland. Some subpopulations are still extensive, while others are reduced to 20 or fewer individuals. Genetic analyses using random amplified polymorphic DNA (RAPD) markers demonstrate that plants in subpopulations with a large number of individuals maintain levels of genetic variation similar to the entire population, whereas plants in a small subpopulation at Pu‘u Leilani (14 individuals remaining) have reduced levels of variation. Of the 122 loci identified, 54 (44%) were polymorphic. Two large populations showed variation at 45 and 49 loci, but the Pu‘u Leilani plants showed variation at only 37 loci. The mean expected heterozygosity (H) in this subpopulation was also lower (0.137 vs. 0.163 and 0.154) and genetic differentiation (GST) was higher (0.167 vs. 0.018 and 0.052) than in other subpopulations. An examination of variation indicates that although plants of the three subpopulations are genetically similar, there is evidence of genetic restructuring among the subpopulations. The impact of these results towards conservation efforts of this and other endangered species is discussed.