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Seed germination. A, Sophora davidii (epigeal); B, S. chathamica (hypogeal); C, S. tomentosa (hypogeal).
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Sophora tomentosa, the type species of the genus Sophora, is shown by phylogenetic analyses of rbcL and ITS sequence data to be sister to Sophora sect. Edwardsia. S. tomentosa and most of the species from sect. Edwardsia share hypogeal germination, exstipulate leaves, and terete filaments. These species have buoyant seeds, and are distributed by oc...
Contexts in source publication
Context 1
... Mitchell & Heenan, 2002). The clade comprising S. microphylla and S. macrocarpa of sect. Edwardsia and S. tomentosa is supported by the rbcL and ITS sequence data as well as some morphological characters, including a large hypanthium in which the calyx veins are not obvious as they are obscured by prominent nectary glands, hypogeal germination (Fig. 4), and yellow petals. S. tomentosa also has exstipulate leaves and terete fil- aments like most species of sect. Edwardsia. Other species of Sophora have a small hypanthium with obvious calyx veins, small nectary glands, epigeal ger- mination (Polhill, 1981; Fig. 4), winged filaments, mainly blue or purple flowers, although some species ...
Context 2
... not obvious as they are obscured by prominent nectary glands, hypogeal germination (Fig. 4), and yellow petals. S. tomentosa also has exstipulate leaves and terete fil- aments like most species of sect. Edwardsia. Other species of Sophora have a small hypanthium with obvious calyx veins, small nectary glands, epigeal ger- mination (Polhill, 1981; Fig. 4), winged filaments, mainly blue or purple flowers, although some species have pale yellow flowers, and leaves with stipules. The relationship between S. tomentosa and the species of sect. Edwardsia appears to have been masked by its frutescent growth habit, an elongate terminal inflores- cence, legumes with a smooth and unwinged outer ...
Context 3
... smaller, oblong and yellow, and the standard petal is usually extended and parallel to the wing and keel petals. However, an exception in sect. Edwardsia is provided by the flow- ers of S. chrysophylla (Hawai'ian Islands) and S. denudata (Réunion Island) as these are like S. tomentosa in having the standard petal upright (Chock, 1956;Cadet, 1986: fig. 47), and this probably represents specialization for particular ...
Context 4
... occurrence of hypogeal germination (Fig. 4) and buoyant seeds in S. tomentosa and sect. Edwardsia (Guppy, 1906;Sykes & Godley, 1968;Ramírez & Romero, 1978;Molloy, 2002) appear to be innovations that have enhanced their dispersal in the tropics and dispersal and radiation around the southern oceans, respectively. S. tomentosa is a pantropical colonizer of beaches and sand dunes ...
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Vigna marina (Burm.) Merrill is a pan-tropical legume found in littoral zone vegetation in northeastern Australia and nearby islands. Its seeds are buoyant and ocean currents are the presumed main mechanism for its dispersal. In 1985, we immersed seeds in salt water to see how long they would remain buoyant and viable. In 2010, we germinated and gr...
Citations
... However, the morphological features are greatly affected by the environmental conditions. The complexity of these morphological characters has made it challenging to understand Sophora taxonomy and evolution (Hurr et al., 1999;Mitchell and Heenan, 2002;Heenan et al., 2004;Heenan, 2017, 2021;Duan et al., 2019). Recently, researchers focused on species located in New Zealand, where chloroplast and nuclear evidence do not conflict, but low bootstrapping support was observed for various nodes. ...
... Sophora, three morphologically similar species, S. prazeri, S. wilsonii, and S. franchetiana, clustered into one clade and S. tomentosa, S. macrocarpa, S. toromiro, and S. flavescens clustered into another clade. Also, S. tomentosa is sister to the S. macrocarpa and S. toromiro clade, an observation which is consistent with the results based on ITS and rbcL evidence (Mitchell and Heenan, 2002;Heenan et al., 2004). Therefore, we propose to include more material and evidence in future studies to establish a clearer phylogeny of sect. ...
The taxonomy and evolutionary history of Sophora L., a genus with high economic and medicinal value, remain uncertain due to the absence of genetic resource (especially in China) and low polymorphism of molecular markers. Our aim was to elucidate the molecular evolution and phylogenetic relationships in chloroplast genomes of Sophora species in the early-diverging legume subfamily Papilionoideae (Fabaceae). We reported nine Sophora chloroplast genome from China using Illumina sequencing. We performed a series of analyses with previously published genomes of Sophora species to investigate their genomic characteristics, identified simple sequence repeats, large repeat sequences, tandem repeats, and highly polymorphic loci. The genomes were 152,953–158,087 bp in length, and contained 111–113 unique genes, including 76–78 protein coding, 31 tRNA, and 4 rRNA. The expansion of inverted repeat boundary of Sophora resulted in rps12 entering into the LSC region and loss of trnT-CGU gene in some species. Also, we found an approximately 23 kb inversion between trnC-GCA and trnF-GAA within the genus. In addition, we identified seven highly polymorphic loci (pi (π) > 0.035) suitable for inferring the phylogeny of Sophora species. Among these, three regions also co-occurred with large repeat sequences and support use of repeats as a proxy for the identification of polymorphic loci. Based on whole chloroplast genome and protein-coding sequences data-set, a well-supported phylogenetic tree of Sophora and related taxa showed that this genus is monophyletic, but sect. Disamaea and sect. Sophora, are incongruent with traditional taxonomic classifications based on fruit morphology. Our finding provides significant genetic resources to support further investigation into the phylogenetic relationship and evolution of the genus Sophora.
... The failure of the earlier phylogenetic studies (e.g. Hurr et al. 1999;Mitchell and Heenan 2002;Heenan et al. 2004) to resolve species relationships in Sophora sect. Edwardsia prompted the development of microsatellite markers (Van Etten et al. 2014) which were used to characterise the New Zealand species (Heenan et al. 2018). ...
... Edwardsia reflects that shown in DNA sequence studies where it is sister to species of sect. Edwardsia (Hurr et al. 1999;Heenan et al. 2004). Morphological characters also distinguish S. tomentosa from sect. ...
... On the other hand, the relationship of S. tomentosa with most species of sect. Edwardsia is reflected in them sharing hypogeal germination, and usually exstipulate leaves and terete filaments; the exception, S. macrocarpa has leaves with caducous stipules and winged filaments (Heenan et al. 2004). Sophora tomentosa and sect. ...
We analysed nine microsatellite markers for 260 individuals representing Sophora tomentosa and 15 species from across the geographic range of Sophora sect. Edwardsia. The purpose of the study was to characterise the Sophora species from Pacific Ocean islands and South America and determine their relationships to the eight New Zealand species, with relationships of the extinct Rapa Nui/Easter Island S. toromiro a particular focus. Structure, PCoA and NeighborNet analyses showed S. tomentosa was distinct from species of sect. Edwardsia. Among the species of sect. Edwardsia, S. cassioides, S. howinsula, S. longicarinata, S. prostrata and S. toromiro were genetically distinct as each comprised a high proportion of membership of individuals assigned to them. The remaining species were assigned to four genetic groups, each of which had one species with a high proportion of membership and other species with lower proportions of membership. The S. chrysophylla group also included high proportions of S. macrocarpa, S. denudata and S. raivavaeensis. The S. fulvida, S. godleyi and S. molloyi genetic groups mostly included low proportions of other New Zealand species. In the PCoA, S. toromiro specimens clustered together and were placed at the margin of a large sect. Edwardsia group. Sophora toromiro comprised four specimens representing the Melbourne Botanic Gardens (Australia) genotype and two specimens in the Allan Herbarium (CHR) obtained from cultivated specimens in Valparaíso (Chile) during the early 1970s. One specimen from Valparaíso was originally identified as S. toromiro, while the other was misidentified as Sophora macnabiana (now S. cassioides). The lack of genetic variation in S. toromiro suggests they were perhaps derived from the last surviving tree on Rapa Nui / Easter Island. A cultivated plant from New Zealand known as the ‘Victoria Park toromiro’ had its identity confirmed as S. godleyi, which is consistent with its morphological identification.
... New Zealand has been geographically isolated for around 80 million years and has a unique native flora which evolved during the late Cenozoic [1,2]. There are four genera of indigenous nodulating legumes (family Fabaceae) in New Zealand, Carmichaelia, Clianthus, Montigena and Sophora [3][4][5][6]. Carmichaelia and Montigena both belong to the Carmichaelineae clade in the polyphyletic tribe Galegae. A taxonomic revision of New Zealand Carmichaelia recognized 23 endemic species that are characterized by leafless adult plants, the leaves being replaced by scales formed by the fusion of the stipules [7]. ...
Five strains of Gram-stain-negative, rod-shaped bacteria were isolated from Carmichaelia and Montigena root nodules. Based on 16S rRNA gene phylogeny, they were shown to belong to the genus Mesorhizobium, and to be most closely related to Mesorhizobium jarvisii ATCC 33669T (100-99.6 % sequence similarity), Mesorhizobium huakuii IAM 14158T (99.9-99.6 %), Mesorhizobium japonicum MAFF303099T (99.8-99.6 %) and Mesorhizobium erdmanii USDA 3471T (99.8-99.5 %). Additionally, the strains formed distinct groups based on housekeeping gene analysis and were most closely related to M. jarvisii ATCC 33669T (89.6-89.5 and 97.6-97.3 % sequence similarity for glnII and recA, respectively), M. erdmanii USDA 3471T (94.3-94.0 and 94.9-94.1 %), M. japonicum MAFF303099T (90.0-89.9 and 96.7-96.2 %) and M. huakuii IAM 14158T (89.9-90.0 and 95.4-94.9 %). Chemotaxonomic data supported the assignment of the strains to the genus Mesorhizobium and DNA-DNA hybridizations, average nucleotide identity analysis, matrix-assisted laser desorption ionization time-of-flight MS analysis, physiological and biochemical tests differentiated them genotypically and phenotypically from their nearest neighbouring species. Therefore, these strains are considered to represent a novel species, for which the name Mesorhizobium carmichaelinearum sp. nov. is proposed. The type strain is ICMP 18942T (=MonP1N1T=LMG 28414T).
... The subtropical beach strand Sophora tomentosa is the type species for the genus Sophora and is sister to all species of sect. Edwardsia [3]. ...
... Elucidating species relationships has proven difficult, with traditional phylogenetic markers (e.g., chloroplast DNA (cpDNA) atpB-rbcL spacer and rbcL, nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS)) offering little sequence variation among the 19 species of Sophora sect. Edwardsia [1,3,7]. Other attempts to establish species relationships have unsuccessfully used enzyme electrophoresis [8] and amplified fragment length polymorphism (AFLP) markers [9]. ...
... The failure of the earlier genetic studies-e.g., [1,3,[7][8][9]11]-to elucidate species relationships, and setting aside the more informative recent analyses [2,10,12], prompted the development of 12 microsatellite markers [13]. These microsatellite markers discriminated 14 individuals of Sophora chathamica and four populations of S. microphylla and have provided tools that will enable genetic variation among individual plants to be studied. ...
We
analysed nine microsatellite markers for 626 individuals representing the geographic range of eight closely related endemic New Zealand species ofSophora. Structure analysis identified the optimalKvalue as seven, with samples identified asSophorachathamica,Sophorafulvida,Sophoralongicarinata, andSophoraprostrataretrieved as well-defined groups. The remaining samples formed less resolved groups referable toSophoratetrapteraandSophoragodleyi, withSophoramicrophyllaandSophoramolloyiforming the seventh group. Our data suggest that considerable admixture occurs and this is most likely the result of hybridisation or introgression.S.fulvidashows admixture with the sympatricS.chathamica, and the widespreadS.microphyllaexhibits admixture with the sympatricS.godleyi,S.molloyi, andS.tetraptera.
... The other species of Thermopsis, including T. chinensis, T. rhombifolia, T. villosa, and T. montana, were mixed with Vuralia turcica, Baptisia tinctoria, and B. australis. The results regarding "core Thermopsidae" members (i.e., Piptanthus, Anagyris L., Thermopsis, and Baptisia Vent.) were consistent with the findings of Crisp et al. (2000), Heenan et al. (2004), and Wang et al. (2006). The Sophora clade, which included three species (S. davidii, S. flavescens, and S. tomentosa), was found to be embedded within Thermopsidae and to be sister to Ammopiptanthus. ...
Ammopiptanthus S. H. Cheng, a genus of Fabaceae with a unique evergreen broad-leaved habit found in arid northwest China, has been found either to contain two species-A. mongolicus (Maxim. ex Kom.) S. H. Cheng and A. nanus (Popov) S. H. Cheng-or only one species-A. mongolicus. Thus, the taxonomic status of this genus, and the species within it, is unclear. In this paper, we clarify the taxonomic relationship in Ammopiptanthus by analyzing morphological evidence (leaf characters, plant height, and canopy coverage), karyotypes (new indices), and new molecular data (ITS 1-4 gDNA markers as well as trnH-psbA, trnL-trnF, and trnS-trnG cpDNA markers), together with datasets from earlier papers, which described many other traits of Ammopiptanthus species, including genetic diversity, geographic differentiation, spatial distribution patterns, and mating systems. Our findings support the conclusion that the genus Ammopiptanthus contains two independent species, and we offer a corresponding revision of the position of Ammopiptanthus in the Flora of China.
... ex DC., Ammothamnus Bunge, Echinosophora Nakai and Euchresta Benn. Sophora is a widely distributed genus, and has been revised by various taxonomists (Bao & Vincent, 2010;Heenan, Dawson & Wagstaff, 2004;Ma, 1990;Ma, 1994;Tsoong & Ma, 1981a;Tsoong & Ma, 1981b;Vasil'chenko, 1945;Yakovlev, Sytin & Roskov 1996). The phylogeny and circumscription of the genus are long-standing puzzles that require considerable effort to solve. ...
Previous works resolved diverse phylogenetic positions for genera of the Fabaceae tribe Thermopsideae, without a thoroughly biogeography study. Based on sequence data from nuclear ITS and four cpDNA regions ( matK , rbcL , trnH-psbA , trnL-trnF ) mainly sourced from GenBank, the phylogeny of tribe Thermopsideae was inferred. Our analyses support the genera of Thermopsideae, with the exclusion of Pickeringia , being merged into a monophyletic Sophoreae. Genera of Sophoreae were assigned into the Thermopsoid clade and Sophoroid clade. Monophyly of Anagyris , Baptisia and Piptanthus were supported in the Thermopsoid clade. However, the genera Thermopsis and Sophora were resolved to be polyphyly, which require comprehensive taxonomic revisions. Interestingly, Ammopiptanthus , consisting of A. mongolicus and A. nanus , nested within the Sophoroid clade, with Salweenia as its sister. Ammopiptanthus and Salweenia have a disjunct distribution in the deserts of northwestern China and the Hengduan Mountains, respectively. Divergence age was estimated based on the ITS phylogenetic analysis. Emergence of the common ancestor of Ammopiptanthus and Salweenia , divergence between these two genera and the split of Ammopiptanthus species occurred at approximately 26.96 Ma, 4.74 Ma and 2.04 Ma, respectively, which may be in response to the second, third and fourth main uplifts of the Qinghai-Tibetan Plateau, respectively.
... Edwardsia from outside New Zealand plus an outgroup, S. tomentosa L., the type species of the genus Sophora and shown to be sister to sect. Edwardsia (Heenan et al. 2004). ...
... In contrast to previous phylogenies, our ncpGS phylogeny found strong support that S. macrocarpa is sister to the other species in the section. Sophora macrocarpa shares a number of morphological characters with other sections of Sophora (Heenan et al. 2004) which, combined with palynological characters and phytochemicals, led to the suggestion of a South American origin of the section (Peña & Cassels 1996;Peña et al. 2000). Flavonoid patterns (Ruiz et al. 1999) and chromosome symmetry (Espejo et al. 2016) have also indicated the isolation of S. macrocarpa within the section. ...
We examined the phylogenetic relationships within Sophora sect. Edwardsia using DNA sequences from the chloroplast trnQ-5′rps16 and trnHGUG-psbA intergenic spacers and the nuclear-encoded chloroplast-expressed glutamine synthetase gene. Sequences were analysed with median-joining networks and phylogenetic approaches. Low sequence diversity was detected, which is consistent with past genetic studies of the section. Chloroplast and nuclear sequences are shared across large geographic distances. The New Zealand species did not form a monophyletic group, nor did the species from Chile. However, species on some Pacific Islands (Lord Howe Island, Easter Island, Hawaii and French Polynesia) and Réunion Island in the Indian Ocean appear to have unique chloroplast haplotypes, indicating isolation. The S. chrysophylla chloroplast haplotype derives from the French Polynesian haplotype rather than S. denudata from Réunion Island, with which it shares morphological characters. In the nuclear phylogeny Sophora macrocarpa was sister to the remaining species that were sequenced in the section, a relationship that has been previously suggested from morphological analysis.
... Sister to sect. Edwardsia, and the type species for the genus Sophora (Heenan et al. 2004), is S. tomentosa in sect. Sophora L., a pantropical coloniser of beaches and sand dunes in Africa, Asia and central America. ...
We examined the origins of Sophora seeds collected from the beaches of the Kermadec and Chatham Islands using chloroplast DNA sequencing and comparison with published sequences of known provenance. Sophora does not grow on the Kermadec Islands but two species grow on the Chatham Islands, both in low numbers. All seeds sequenced were confirmed to be from Sophora sect. Edwardsia. Several seeds exhibited novel DNA sequences that had not been found in past sampling. The remaining haplotypes have all been previously detected in the North and/or South Islands and some have also been recorded from Chile, Gough Island or the Juan Fernandez Islands. The two haplotypes that had been sequenced in the resident Chatham Islands S. chathamica population were both found in the beach-cast seeds from the islands. However, an additional four haplotypes were also detected in the Chatham Islands beach-cast seeds, indicating dispersal from elsewhere.
... The number of samples collected per species ranged from 13 to 198, and two individuals identified from morphology as hybrids (S. chathamica 9 S. microphylla) were also included. The Chilean species S. macrocarpa was selected as outgroup for the AFLP analyses because morphological characters (Heenan et al., 2004b), flavonoid patterns (Ruiz et al., 1999) and nuclear sequences (Shepherd & Heenan, unpublished data) indicate it is distinct from the rest of sect. Edwardsia. ...
... Instead, we used S. tomentosa as the outgroup for our chloroplast analyses because it has been shown to be sister to sect. Edwardsia (Heenan et al., 2004b). For the majority of specimens, fresh Sophora leaf tissue was collected into silica gel, either from field-sampled plants or from cultivated specimens of known provenance grown at Landcare Research (Lincoln). ...
Aim
To date, there have been few studies investigating the phylogeography of forest trees that are widely distributed in New Zealand. Our main objective was to examine the phylogeographic distribution of chloroplast DNA from New Zealand Sophora trees with respect to known biogeographical regions, proposed refugia and species boundaries. A second objective was to investigate the origins of the southern and Chatham Island populations of Sophora chathamica , which have been proposed to derive from Māori translocation.
Location
The New Zealand archipelago coastal and lowland forests.
Methods
We sequenced the chloroplast trnQ5′‐rps16 intergenic spacer from 416 samples of Sophora , representing all of the New Zealand species. A median‐joining network was used to analyse haplotype relationships. Phylogeographic structuring was assessed with G ST and N ST calculations and spatial analysis of molecular variance ( SAMOVA ). Analyses of molecular variance were used to test partitioning schemes including species divisions and proposed biogeographical boundaries.
Results
A total of 22 haplotypes were recovered. Moderate genetic differentiation was detected and it had a phylogeographic component but no higher level groupings were found with a SAMOVA . Very little of the chloroplast variation was partitioned by species boundaries or geography. Haplotype diversity decreased from north to south but was not higher in proposed major lowland forest glacial refugia. Populations of Sophora chathamica suggested to derive from Māori translocations contained a haplotype not detected from the proposed natural range of the species.
Main conclusions
Sophora survived the Last Glacial Maximum in widespread populations throughout much of the country, although our data did not provide evidence for survival in the southern South Island. Chloroplast sharing among New Zealand Sophora species likely results from hybridization and introgression. Our results indicate that the occurrence of S. chathamica in the southern North Island, northern South Island and Chatham Islands is likely to be natural, although the planting by Māori of some of the individuals in the southern North Island and Chatham Islands cannot be excluded.
... belong to the genus Sophora and, in turn, are grouped in the section Edwardsia. (Mackinder & Staniforth 1997;Hurr et al. 1999;Peña et al. 2000;Mitchell & Heenan, 2002;Heenan et al. 2004). ...
... Results from flow cytometry show that the values are very close between the studied species and it confirms the similarity of the genomes in these species already reported in the literature. Molecular studies using DNA sequences from atpB-rbcL, nrDNA and ITS (Hurr et al. 1999;Mitchell & Heenan 2002;Heenan et al. 2004), suggest a close affinity and evidence of recent speciation. Finally, because there is little information on comparative genome size studies of the genus Sophora, this work provides valuable new information to enable further studies related to speciation phenomena in the Edwardsia section. ...
The genome of Sophora toromiro (Phil.) Skottsb. (Papilionaceae) is characterised by means of chromosome counts of accessions called Viña del Mar Botanical Garden (JBV), Göteborg (Got) and Titze. Karyotypes were obtained and genome size quantified using flow cytometry and compared to the closely related species Sophora macrocarpa J.E.Sm. and Sophora cassioides (Phil.) Sparre. No differences were detected in chromosome number of Sophora at intra-specific or inter-specific levels with 2n = 2x = 18. Analyses on the symmetry coefficients CVcl and Mca shows affinity between the analysed material of the Titze line. The graph clearly indicates differences between S. toromiro lines if compared with S. cassioides and S. macrocarpa. Genome size range from 788 Mbp for S. cassioides, 795 Mbp for S. macrocarpa and a range of 796–808 Mbp in S. toromiro. This is the first report of chromosome number and genome size for S. toromiro, S. macrocarpa and S. cassioides. This is of particular importance in S. toromiro, as it is has been considered extinct in its natural habitat for the past 50 years.
