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Comparison of phylogenies derived from parsimony and neighbor-joining analyses. (Left) Strict consensus of the 12 most parsimonious trees based on trnK/matK sequence data (length 4175; CI 0.56; RI 0.75), bootstrap values for internal nodes are shown. (Right) Topology obtained from neighbor-joining analysis. Bootstrap values were obtained from 1000 replicates. Current Millettieae taxa are shown in boldface. Figure Abbreviations: Ca. Callerya; Wi. Wisteria; Mi. Millettia; Ph. Philenoptera.
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Phylogenetic relationships in the tribe Millettieae and allies in the subfamily Papilionoideae (Leguminosae) were reconstructed from chloroplast trnK/matK sequences. Sixty-two accessions representing 57 traditionally recognized genera of Papilionoideae were sampled, including 27 samples from Millettieae. Phylogenies were constructed using maximum p...
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... major clade contains most of the sampled Millet- tieae, as well as taxa of Phaseoleae, Psoraleeae, and Abreae. Its sister group is Indigofereae (Fig. 1). Within this clade, a well-supported clade (100% bootstrap sup- port) is recognized, here denoted as ''core Millettieae'' (Figs. 1, 2), which includes Millettia, Philenoptera, Lon- chocarpus, Piscidia, Fordia, Neodunnia, Derris, Parad- erris, Brachypterum, Tephrosia, and Mundulea. Sister to the core-Millettieae clade is Galactia, from Phaseoleae subtribe Diocleinae, and Abrus from tribe Abreae. This pattern of relationships is in agreement with the rbcL phylogeny ( Doyle et al., 1997), where the tribe Desmo- dieae (not sampled here) is also placed in this major clade. These three taxa together formed a well-supported clade with 95% bootstrap support for parsimony and 97% for NJ analysis (Fig. 2). Within core Millettieae, a ''clade A'' is recognized, including Tephrosia, Derris, Loncho- carpus, and two sampled Millettia species. Tephrosia and Mundulea are the sister taxa to the rest of the clade A species ( Fig. 1) with bootstrap support of 80% (Fig. ...
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... major clade contains most of the sampled Millet- tieae, as well as taxa of Phaseoleae, Psoraleeae, and Abreae. Its sister group is Indigofereae (Fig. 1). Within this clade, a well-supported clade (100% bootstrap sup- port) is recognized, here denoted as ''core Millettieae'' (Figs. 1, 2), which includes Millettia, Philenoptera, Lon- chocarpus, Piscidia, Fordia, Neodunnia, Derris, Parad- erris, Brachypterum, Tephrosia, and Mundulea. Sister to the core-Millettieae clade is Galactia, from Phaseoleae subtribe Diocleinae, and Abrus from tribe Abreae. This pattern of relationships is in agreement with the rbcL phylogeny ( Doyle et al., 1997), where the tribe Desmo- dieae (not sampled here) is also placed in this major clade. These three taxa together formed a well-supported clade with 95% bootstrap support for parsimony and 97% for NJ analysis (Fig. 2). Within core Millettieae, a ''clade A'' is recognized, including Tephrosia, Derris, Loncho- carpus, and two sampled Millettia species. Tephrosia and Mundulea are the sister taxa to the rest of the clade A species ( Fig. 1) with bootstrap support of 80% (Fig. ...
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... sister clade of clade A comprises five taxa: three Philenoptera species (including Capassa), Millettia gran- dis from Millettia Section Compressogemmatae, and Mil- lettia leptobotrya (Fordia leptobotrys (Dunn) Schot; see Discussion for details). Our results suggest that the three sampled Philenoptera (including Capassa) species form a clade (100% bootstrap support; Fig. 1), and Mil- lettia grandis and Millettia leptobotrya are the sister groups. Within clade A, Pongamiopsis amygdalina/Mil- lettia thonningii/Neodunnia richardiana formed a distinct group with 96% bootstrap support (parsimony). Three other pairs of taxa also show relatively high bootstrap support, Lonchocarpus lanceolatus/Millettia dura (100%), Paraderris elliptica/Derris laxiflora (100%), and Brachypterum robusta/Fordia splendidissima (94%; bootstrap values refer to parsimony analysis; Fig. 2). The rest of the clade shows less bootstrap support (lower than 80%), and is ...
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... genera, Poecilanthe and Cyclolobium, which have been variously included in Millettieae or other groups, are distantly related to the core Millettieae clade (Fig. 1). Both taxa belong to a clade consisting of taxa from Brongniartieae, and Sophoreae, i.e., Bolusanthus, Ormo- sia, and Acosmium. Support for the monophyly of Poe- cilanthe, Cyclolobium, and Brongniartieae is very high (100% from both parsimony and NJ criteria), even though there are differences in the positions of Poecilan- the and Harpalyce in the two methods (Fig. ...
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... and Brachypterum, which are sister groups with fairly high support (94% from parsimony, 81% from NJ; Fig. 2), share few morphological similarities, and, again, this raises more questions about relationship in the Mil- lettia/Derris complex, where support among groups is low and more sampling of taxa and characters is neces- ...
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... monophyly of the IR-lacking group is well sup- ported in our trnK/matK phylogeny (100% bootstrap val- ue; Figs. 1, 2), and the loss of IR is indeed a distinct feature in Papilionoideae phylogeny. Callerya, Wisteria, and Glycyrrhiza (tribe Galegeae) are the sister groups to the rest of the IR-lacking clade (IRLC) (Fig. 1). However, the relationships between these three genera and the rest of the IRLC remain unresolved (Fig. 1). The phylogeny derived by NJ analysis shows weak support for the Cal- lerya/Wisteria clade (Fig. 2), but this is less resolved in the parsimony analysis (Fig. 2). Callerya atropurpurea causes the ambiguity in the phylogeny of IRLC, since the phylogeny is more resolved when it is removed from the data matrix (Hu, unpublished ...
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... monophyly of the IR-lacking group is well sup- ported in our trnK/matK phylogeny (100% bootstrap val- ue; Figs. 1, 2), and the loss of IR is indeed a distinct feature in Papilionoideae phylogeny. Callerya, Wisteria, and Glycyrrhiza (tribe Galegeae) are the sister groups to the rest of the IR-lacking clade (IRLC) (Fig. 1). However, the relationships between these three genera and the rest of the IRLC remain unresolved (Fig. 1). The phylogeny derived by NJ analysis shows weak support for the Cal- lerya/Wisteria clade (Fig. 2), but this is less resolved in the parsimony analysis (Fig. 2). Callerya atropurpurea causes the ambiguity in the phylogeny of IRLC, since the phylogeny is more resolved when it is removed from the data matrix (Hu, unpublished ...
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... circumscription of the genera Derris and Millettia is very complicated, and their classification at the species level has troubled taxonomists. Many specimens have Figs. 3-4. Character distribution of Millettieae and its allies plotted on the strict consensus tree used in Fig. 1. Outgroups are only represented by tribe names. 3. Distribution of canavanine, data were collected from the surveys by Bell, Lackey, and Polhill (1978) and Evans, Fellows, and Bell (1985). The first possible appearance of nonprotein amino acids in Papilionoideae is marked by an arrow. 4. Distribution of inflorescence types, mainly based on Geesink (1984) and Polhill and Raven (1981). The pseudoraceme/pseudopanicle clade is marked by an arrow. For taxon abbreviations see Fig. 2; current Millettieae taxa (following Geesink, 1984 (Figs. 1, 2). In contrast, the four Millettia species sampled here are not closely related (Fig. 1). In Dunn's (1912) classification, Millettia grandis (sect. Compressogemma- tae) and Millettia leptobotrya (sect. Albiflorae) are dis- tantly related to Millettia dura and Millettia thonningii (sect. Sericanthae). Millettia grandis and Millettia lep- tobotrya are distinguished from other Millettia species by a combination of pseudopaniculate inflorescences and the presence of canavanine in seeds (see discussion below). However, the pseudopanicle is not restricted to sections Compressogemmatae and Albiflorae, it can occasionally occur in some other species of Millettia, e.g., M. psilo- petula (section Truncaticalyces) (Gillett, 1971), and M. urophylloides (section Efulgentes) (Dunn, 1912), and not all species in section Compressogemmatae have pseu- dopanicles (e.g., Millettia micans has pseudoracemes). In addition, canavanine is present in at least 15 other Mil- lettia species (excluding the species transferred to Cal- lerya) (Evans, Fellows, and Bell, 1985). Until more in- tensive sampling is undertaken, any conclusion as to the classification of Millettia would be premature. Geesink (1984) raised Millettia section Albiflorae (in- cluding Millettia leptobotrya) to a new genus, Imbralyx, but no nomenclatural combination was made for the taxa other than the type species. Imbralyx was treated under Fordia based on cladistic analysis of morphological and anatomical characters using Millettia pulchra as the out-group ( Dasuki and Schot, 1991;. However, the rooting position of the tree is problematic. The anal- ysis did not include other outgroup taxa to eliminate the possibility that the tree does in fact have Imbralyx as the outgroup taxon, and Fordia species and Millettia pulchra forming a clade. If this is the case, then Imbralyx should not be judged as part of Fordia ( Dasuki and Schot, 1991;, therefore the name of Imbralyx should re- main at this point. The trnK/matK phylogenies show strong support for distinguishing Millettia leptobotrya and Fordia splendidissima (Figs. 1, 2), and thus we leave the name of Millettia leptobotrya unchanged. Re-estab- lishing the genus Imbralyx seems ...
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... trnK/matK phylogeny places Austrosteenisia blackii in an isolated position from core Millettieae (Fig. 1), but has a higher support as the sister group of the core Millettieae/Phaseoleae clade in NJ analysis (Fig. 2). It is clear that this species is distinct from Millettia and Lon- chocarpus, in which it was formerly placed. We did not include Kunstleria, a genus closely related to Austros- teenisia (Dixon, 1997), in our analyses. Kunstleria, de- spite its similar appearance and geographical distribution to Austrosteenisia, has the vexillary stamen free but con- nate to the claw of the standard (Ridder-Numan and Kornet, 1994;Ridder-Numan, 1995). It remains to be deter-[Vol. 87 AMERICAN JOURNAL OF BOTANY mined whether Kunstleria also belongs to the core Mil- ...
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... analysis produced 12 equally most parsi- monious trees of 3892 steps with a consistency index (CI) 0.56 (excluding autapomorphies) and a retention index (RI) 0.75. Figure 1 shows the strict consensus tree and the internal support from the bootstrap analysis. Figure 2 shows the comparison of the bootstrap trees using par- simony (Fig. 2, left) and the neighbor-joining (Fig. 2, right) methods, and bootstrap support for internal nodes from both methods is indicated. The two methods give very similar topologies, but with slightly different sup- port on the internal nodes. Three taxa also show incon-gruence on the trees, i.e., Poecilanthe, Harpalyce, and Austrosteenisia (see below for ...
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... analysis produced 12 equally most parsi- monious trees of 3892 steps with a consistency index (CI) 0.56 (excluding autapomorphies) and a retention index (RI) 0.75. Figure 1 shows the strict consensus tree and the internal support from the bootstrap analysis. Figure 2 shows the comparison of the bootstrap trees using par- simony (Fig. 2, left) and the neighbor-joining (Fig. 2, right) methods, and bootstrap support for internal nodes from both methods is indicated. The two methods give very similar topologies, but with slightly different sup- port on the internal nodes. Three taxa also show incon-gruence on the trees, i.e., Poecilanthe, Harpalyce, and Austrosteenisia (see below for ...
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... analysis produced 12 equally most parsi- monious trees of 3892 steps with a consistency index (CI) 0.56 (excluding autapomorphies) and a retention index (RI) 0.75. Figure 1 shows the strict consensus tree and the internal support from the bootstrap analysis. Figure 2 shows the comparison of the bootstrap trees using par- simony (Fig. 2, left) and the neighbor-joining (Fig. 2, right) methods, and bootstrap support for internal nodes from both methods is indicated. The two methods give very similar topologies, but with slightly different sup- port on the internal nodes. Three taxa also show incon-gruence on the trees, i.e., Poecilanthe, Harpalyce, and Austrosteenisia (see below for ...
Citations
... In the past two decades, molecular phylogenetic studies at various scales have made progress in clarifying the phylogenetic relationships of the Millettioid/Phaseoloid clade (Hu et al., 2000;Kajita et al., 2001;Pennington et al., 2001;Hu et al., 2002;Wojciechowski et al., 2004;Lavin et al., 2005;Egan & Crandall, 2008b;Cardoso et al., 2013;de Queiroz et al., 2015;Legume Phylogeny Working Group, 2017;Jabbour et al., 2018;Jin et al., 2019;Oyebanji et al., 2020;Zhang et al., 2020). These studies support the monophyly of the Millettioid/Phaseoloid clade and three of the six traditionally recognized tribal lineages (Desmodieae, Indigofereae, and Psoraleeae); two tribal lineages millettioids and phaseoloids have been recovered as polyphyletic, while the status of the lineage Abreae remains uncertain. ...
... This study presents a well-resolved phylogeny of the Millettioid/ Phaseoloid clade. Our results support the monophyly of the Millettioid/Phaseoloid clade and four of its tribes (Abreae, Desmodieae, Indigofereae, and Psoraleeae), and the nonmonophyly of the millettioids and phaseoloids, which is consistent with previous studies (Hu et al., 2000;Kajita et al., 2001;Wojciechowski et al., 2004;Lavin et al., 2005;de Queiroz et al., 2015;Legume Phylogeny Working Group, 2017;Oyebanji et al., 2020;Zhao et al., 2021). Also consistent with previous studies, our analyses placed tribe Indigofereae (L1) sister to all other members of the Millettioid/Phaseoloid clade (Kajita et al., 2001;Lavin et al., 2005;Legume Phylogeny Working Group, 2013;de Queiroz et al., 2015;Oyebanji et al., 2020). ...
... Lineage L2 contains four genera of the millettioids (M1; Aganope Miq., Craibia Harms & Dunn, Dewevrea Micheli, and Ostryocarpus Hook.f.), and the intergeneric relationships were well resolved in our phylogeny (BS = 100%; Fig. S2). In previous phylogenetic studies, only limited representative genera of L2 were sampled (Lavin et al., 2005;de Queiroz et al., 2015;Oyebanji et al., 2020) or intergeneric relationships were poorly resolved (Hu et al., 2000;Kajita et al., 2001;Legume Phylogeny Working Group, 2013 (100) Cell color indicates the range of inferred number of dispersal events: blue = ≤ 10; green = 10-30, and yellow = ≥ 30; rA = North America, rB = South America, rC = Africa (including Madagascar), rD = Europe, rE = Asia, and rF = Australia (including all Oceanian regions). ...
The Millettioid/Phaseoloid (or the Millettioid) clade is a major lineage of the subfamily Papilionoideae (Fabaceae) that is poorly understood in terms of its diversification and biogeographic history. To fill this gap, we generated a time‐calibrated phylogeny for 749 species representing c . 80% of the genera of this clade using nrDNA ITS, plastid matK , and plastome sequence (including 38 newly sequenced plastomes). Using this phylogenetic framework, we explored the clade's temporal diversification and reconstructed its ancestral areas and dispersal events. Our phylogenetic analyses support the monophyly of the Millettioid/Phaseoloid clade and four of its tribal lineages (Abreae, Desmodieae, Indigofereae, and Psoraleeae), while two tribal lineages sensu lato millettioids and phaseoloids are polyphyletic. The fossil‐calibrated dating analysis showed a nearly simultaneous divergence between the stem node ( c . 62 Ma) and the crown node ( c . 61 Ma) of the Millettioid/Phaseoloid clade in the Paleocene. The biogeographic analysis suggested that the clade originated in Africa and dispersed to Asia, Europe, Australia, and the Americas at different periods in the Cenozoic. We found evidence for shifts in diversification rates across the phylogeny of the Millettioid/Phaseoloid clade throughout the Cenozoic, with a rapid increase in net diversification rates since c . 10 Ma. Possible explanations for the present‐day species richness and distribution of the Millettioid/Phaseoloid clade include boreotropical migration, frequent intra‐ and intercontinental long‐distance dispersals throughout the Cenozoic, and elevated speciation rates following the Mid‐Miocene Climatic Optimum. Together, these results provide novel insights into major diversification patterns of the Millettioid/Phaseoloid clade, setting the stage for future evolutionary research on this important legume clade.
... For matK, we sequenced the entire matK gene and partial matK-trnK 3′ intron using four primers: trnK685F, KC6, matK4La and trnK2Rdet (Hu & al., 2000;Lavin & al., 2000;Wojciechowski & al., 2004;Bruneau & al., 2008). An initial amplification used the trnK685F/trnK2Rdet pair of primers, and a semi-nested amplification was then done using two pairs of primers, trnK685F/KC6 and matK4La/ trnK2Rdet, on 0.1 μl of the initial PCR products. ...
... For matK, we sequenced the entire matK gene and partial matK-trnK 3′ intron using four primers: trnK685F, KC6, matK4La and trnK2Rdet (Hu & al., 2000;Lavin & al., 2000;Wojciechowski & al., 2004;Bruneau & al., 2008). An initial amplification used the trnK685F/trnK2Rdet pair of primers, and a semi-nested amplification was then done using two pairs of primers, trnK685F/KC6 and matK4La/ trnK2Rdet, on 0.1 μl of the initial PCR products. ...
Highlight: Chamaecrista has shrunk from trees to shrubs as it has radiated from the rainforest into drier habitats; this has been accompanied by the adoption of more intimately efficient nodulating symbioses. Abstract All non-mimosoid nodulated genera in the legume subfamily Caesalpinioideae confine their rhizobial symbionts within cell wall-bound "fixation threads" (FTs). The exception is the large genus Chamaecrista in which shrubs and subshrubs house their rhizobial bacteroids more intimately within symbiosomes, whereas large trees have FTs. This study aimed to unravel the evolutionary relationships between Chamaecrista growth habit, habitat, nodule bacteroid type, and rhizobial genotype. The growth habit, bacteroid anatomy, and rhizobial symbionts of 30 nodulated Chamaecrista species native to different biomes in the Brazilian state of Bahia, a major centre of diversity for the genus, was plotted onto an ITS-TrnL-F-derived phylogeny of Chamaecrista. The bacteroids from most of the Chamaecrista species examined were enclosed in symbiosomes (SYM-type nodules), but those in arborescent species in the section Apoucouita, at the base of the genus, were enclosed in cell wall material containing homogalacturonan (HG) and cellulose (FT-type nodules). Most symbionts were Bradyrhizobium genotypes grouped according to the growth habits of their hosts, but the tree, C. eitenorum, was nodulated by Paraburkholderia. Chamaecrista has a range of growth habits that allow it to occupy several different biomes and to co-evolve with a wide range of (mainly) bradyrhizobial symbionts. FTs represent a less intimate symbiosis linked with nodulation losses, so the evolution of SYM-type nodules by most Chamaecrista species may have (a) aided the genus-wide retention of nodulation, and (b) assisted in its rapid speciation and radiation out of the rainforest into more diverse and challenging habitats.
... The American genera Cyclolobium Benth. and Poecilanthe Benth., which had once been variably associated with tribes Dalbergieae (Bentham, 1865), Millettieae (as Tephrosieae; Geesink, 1981), or Robinieae (Geesink, 1984), were then unequivocally demonstrated as phylogenetically closer to Brongniartieae by Hu et al. (2000Hu et al. ( , 2002. This placement was later confirmed by more comprehensively sampled phylogenetic analyses of the Papilionoideae Cardoso et al., 2012aCardoso et al., , 2013a. ...
... While single to few locus-based phylogenies (Cardoso et al., 2013a(Cardoso et al., , 2017Queiroz et al., 2017a,b) and recent plastome-based phylogenomic analyses (Choi et al., 2022) have settled the sister group relationship of Harpalyce to the clade comprised of Tabaroa and Amphiodon, the monophyly and species inter-relationships of Harpalyce deserve a closer examination. Previous phylogenetic studies (Crisp et al., 2000;Hu et al., 2000Hu et al., , 2002Thompson et al., 2001;Wojciechowski et al., 2004;Queiroz et al., 2010Queiroz et al., , 2017Cardoso et al., 2012aCardoso et al., , 2017Meireles et al., 2014) included only a minor fraction of the whole morphological, ecological, and geographical diversity of the genus, and no study has thus far incorporated representatives of the three recognized sections. ...
... For amplification of the ETS we used the primers ETS-B (5′-ATA GAG CGC GTG AGT GGT G-3′) (Beardsley and Olmstead, 2002) and 18S-IGS (5′-GAG ACA AGC ATA TGA CTA CTG GCA GGA TCA ACC AG-3′) (Baldwin and Markos, 1998) with initial denaturation at 94 • C for 3 min, 30 cycles of 94 • C denaturation for 1 min, 55 • C annealing for 1 min, 72 • C initial extension for 1:30 min and 72 • C final extension for 7 min. For amplification of the matK gene we used three different pairs of primers: trnK685F (5′-GTA TCG CAC TAT GTA TCA TTT GA-3′) and matK4R (5′-CAT CTT TCA CCC AGT ATC GAA G-3′); matK4La (5′-CCT TCG ATA CTG GGT GAA AGA T-3′) and matK1932R (5′-CAG ACC GGC TTA CTA ATG GG-3′) and; matK1100L (5′-TTC AGT GGT ACG GAG TCA AAT G-3′) and trnK2R* (5′-CCC GGA ACT AGT CGG ATG G-3′) (Hu et al., 2000;Wojciechowski et al., 2004). Regardless of the matK primers used, initial denaturation was at 94 • C for 4 min, with 35-40 cycles of 94 • C denaturation for 1 min, 50-55 • C annealing for 30 sec, 72 • C initial extension and for 1 min and 72 • C final extension for 7 min. ...
... PCR reagents were carried out in a 25 µL reaction mixture which contained 1 µL (10 µM) of each forward and reverse primer, 12.5 µL GoTag Green Master Mix (Promega), 2 µL (< 250 ng) of total DNA and Nuclease-free water to 25 µL. PCR conditions for trnL-F IGS and trnK-matK followed a modified protocol of Hu et al. (2000). The ITS/5.8S region was amplified following Wojciechowski et al. (1993Wojciechowski et al. ( , 1999. ...
Derris rubricosta Boonprajan & Sirich., sp. nov. , a new species of the genus Derris Lour. (Fabaceae) was discovered in Peninsular Thailand. The overall morphology demonstrates that the species most resembles D. pubipetala . Nevertheless, the species has several autapomorphies differentiating it from other Derris species, e.g., the presence of reddish midribs of the mature leaflets, sparsely hairy stamen filaments, prominent hairs at the base of the anthers, and presence of glandular trichomes along the leaflet midrib. Additionally, HPLC fingerprints of this species showed a distinction from D. pubipetala by the absence of phytochemical compound peaks after 13 min. Retention Time (RT). Results from molecular phylogenetic analyses also strongly supported the taxonomic status as a new species.
... Phylogenetic trees were rooted using Canavalia rosea (Sw.) DC., on the basis of Hu et al. (2000Hu et al. ( , 2002 and Sirichamorn et al. (2012a). ...
... The American genera Cyclolobium Benth. and Poecilanthe Benth., which had once been variably associated with tribes Dalbergieae (Bentham, 1865), Millettieae (as Tephrosieae; Geesink, 1981), or Robinieae (Geesink, 1984), were then unequivocally demonstrated as phylogenetically closer to Brongniartieae by Hu et al. (2000Hu et al. ( , 2002. This placement was later confirmed by more comprehensively sampled phylogenetic analyses of the Papilionoideae Cardoso et al., 2012aCardoso et al., , 2013a. ...
... While single to few locus-based phylogenies (Cardoso et al., 2013a(Cardoso et al., , 2017Queiroz et al., 2017a,b) and recent plastome-based phylogenomic analyses (Choi et al., 2022) have settled the sister group relationship of Harpalyce to the clade comprised of Tabaroa and Amphiodon, the monophyly and species inter-relationships of Harpalyce deserve a closer examination. Previous phylogenetic studies (Crisp et al., 2000;Hu et al., 2000Hu et al., , 2002Thompson et al., 2001;Wojciechowski et al., 2004;Queiroz et al., 2010Queiroz et al., , 2017Cardoso et al., 2012aCardoso et al., , 2017Meireles et al., 2014) included only a minor fraction of the whole morphological, ecological, and geographical diversity of the genus, and no study has thus far incorporated representatives of the three recognized sections. ...
... For amplification of the ETS we used the primers ETS-B (5′-ATA GAG CGC GTG AGT GGT G-3′) (Beardsley and Olmstead, 2002) and 18S-IGS (5′-GAG ACA AGC ATA TGA CTA CTG GCA GGA TCA ACC AG-3′) (Baldwin and Markos, 1998) with initial denaturation at 94 • C for 3 min, 30 cycles of 94 • C denaturation for 1 min, 55 • C annealing for 1 min, 72 • C initial extension for 1:30 min and 72 • C final extension for 7 min. For amplification of the matK gene we used three different pairs of primers: trnK685F (5′-GTA TCG CAC TAT GTA TCA TTT GA-3′) and matK4R (5′-CAT CTT TCA CCC AGT ATC GAA G-3′); matK4La (5′-CCT TCG ATA CTG GGT GAA AGA T-3′) and matK1932R (5′-CAG ACC GGC TTA CTA ATG GG-3′) and; matK1100L (5′-TTC AGT GGT ACG GAG TCA AAT G-3′) and trnK2R* (5′-CCC GGA ACT AGT CGG ATG G-3′) (Hu et al., 2000;Wojciechowski et al., 2004). Regardless of the matK primers used, initial denaturation was at 94 • C for 4 min, with 35-40 cycles of 94 • C denaturation for 1 min, 50-55 • C annealing for 30 sec, 72 • C initial extension and for 1 min and 72 • C final extension for 7 min. ...
... All genes chosen for our phylogenetic analyses have been successfully used in resolving relationships at different taxonomic levels in papilionoid legumes (e.g. Hu et al. 2000, McMahon and Hufford 2004, Wojciechowski et al. 2004, Pennington et al. 2010, Delgado-Salinas et al. 2011, Cardoso et al. 2012a, 2012b, 2013b, 2015a, Ramos et al. 2016, Choi et al. 2022. Clathrotropis rosea M.Yu.Gontsch. ...
Molecular phylogenetic studies focused on the early-branching papilionoid legumes have revealed many new clades and supported several generic realignments, yet the monophyly of some of the constituent genera has remained unassessed. This is the case for the Amazonian genus Clathrotropis of the tribe Ormosieae. The genus, as traditionally circumscribed, comprises seven species of trees, including some of the most ecologically hyper dominant taxa across the Amazonian terra firme and seasonally flooded forests. Here we employed a Bayesian analysis of densely sampled nuclear ribosomal ITS/5.8S and plastid matK and trnL intron DNA sequences to evaluate the monophyly of Clathrotropis. All individual and concatenated analyses concurred in showing the non-monophyletic nature of Clathrotropis, whose species fall into three distantly related lineages: one, comprised of C. brachypetala, C. brunnea, C. glaucophylla and the ecologically dominant C. macrocarpa, is circumscribed here as the new genus Cabari; the two others, comprising C. paradoxa and the widespread C. nitida, are more closely related to Spirotropis of the tribe Ormosieae. Such phylogeny-based dismemberment of Clathrotropis is further supported by vegetative, floral, fruit, and seed characters. Although the genes analysed in this study have provided phylogenetically informative data supporting the need for a new circumscription of Clathrotropis, we suggest that future phylogenomic studies should seek to better resolve the relationships of the newly described genus Cabari across the phylogenetically recalcitrant early-branching nodes of the Genistoid clade.
... Se actualizó la nomenclatura según la literatura taxonómica disponible, revisada para este género (Maxwell, 1980;Lackey, 1981;Wiersema et al., 1990;Burkill, 1995;Lewis & Polhill, 1998;Hu et al., 2000;Kajita et al. 2001;Chappill, 2001). ...
L. Hernández: Sinopsis preliminar de los géneros Herpyza C. Wright y Dioclea K. Kunth (Leguminosae-Papilionoideae) en Cuba. Rev. Acad. Colomb. Cienc. 28 (108): 313-322, 2004. ISSN: 0370-3908. Se presenta una sinopsis preliminar de los géneros Herpyza C. Wright y Dioclea K. Kunth para Cuba. Se incluyen claves dicotómicas, descripciones taxonómicas, ilustraciones y datos químicos, cromosómicos, palinológicos, etnobotánicos, así como de distribución y ecología de los 4 taxones que se registran en el país dentro de dichos géneros. Aunque los resultados definen los caracteres de cada género se requiere de un posterior análisis molecular y biogeográfico de Herpyza junto con otros taxones de Phaseoleae para poder dilucidar las relaciones filogenéticas de dicho género con otros de Leguminosas.
... Although genome organization and gene content of plastome are believed to be highly conserved in most angiosperms (Jansen et al. 2007), the current study demonstrated a high degree of diversity in the structure of Caragana plastome. These genomic rearrangements combined with variations at the gene structural levels provided valuable information to resolve relationships among several deep nodes of legumes (Doyle et al. 1996;Hu et al. 2000;Wojciechowski et al. 2004;Magee et al. 2010). ...
In this study, we assembled the complete plastome and mitogenome of Caragana spinosa and explored the multiple configurations of the organelle genomes.
Caragana spinosa belongs to the Papilionoidea subfamily and has significant pharmaceutical value. To explore the possible interaction between the organelle genomes, we assembled and analyzed the plastome and mitogenome of C. spinosa using the Illumina and Nanopore DNA sequencing data. The plastome of C. spinosa was 129,995 bp belonging to the inverted repeat lacking clade (IRLC), which contained 77 protein-coding genes, 29 tRNA genes, and four rRNA genes. The mitogenome was 378,373 bp long and encoded 54 unique genes, including 33 protein-coding, three ribosomal RNA (rRNA), and 18 transfer RNA (tRNA) genes. In addition to the single circular conformation, alternative conformations mediated by one and four repetitive sequences in the plastome and mitogenome were identified and validated, respectively. The inverted repeat (PDR12, the 12th dispersed repeat sequence in C. spinosa plastome) of plastome mediating recombinant was conserved in the genus Caragana. Furthermore, we identified 14 homologous fragments by comparing the sequences of mitogenome and plastome, including eight complete tRNA genes. A phylogenetic analysis of protein-coding genes extracted from the plastid and mitochondrial genomes revealed congruent topologies. Analyses of sequence divergence found one intergenic region, trnN-GUU-ycf1, exhibiting a high degree of variation, which can be used to develop novel molecular markers to distinguish the nine Caragana species accurately. This plastome and mitogenome of C. spinosa could provide critical information for the molecular breeding of C. spinosa and be used as a reference genome for other species of Caragana. In this study, we assembled the complete plastome and mitogenome of Caragana spinosa and explored the multiple configurations of the organelle genomes.
... This large clade is subdivided into three subclades, the first being represented by the tribes Phaseoleae, Psoraleeae, Desmodieae, Abreae, Millettieae and Indigofereae, with moderately supported relationships (BS = 87%). Our phylogenetic analysis also suggests the paraphyly of the Millettieae and Phaseoleae tribes, supported by previous studies (Egan et al. 2016;Hu et al. 2000b;Queiroz et al. 2015;Oyebanji et al. 2020;Vatanparast et al. 2018;Wojciechowski et al. 2004, Zhao et al. 2021. It was also observed that tribes Psoraleeae and Desmodieae nested within tribe Phaseoleae. ...
... We also highlight the Desmodieae and Psoraleeae tribes nested within Phaseoleae, as previously reported in analysis with plastid DNA markers (Kajita et al. 2001;LPWG 2017;Hu et al. 2000b;Queiroz et al. 2015;Oyebanji et al. 2020;Stefanovic et al. 2009;Vatanparast et al. 2018;Wojciechowski et al. 2004). This fact may possibly be related to the presence of nodules of determined growth and export of ureids, characteristic of the species of these tribes (Sprent 2008). ...
The Papilionoideae subfamily comprises more than 14,000 species, 501 genera and 32 tribes, representing two-thirds of all genera and species in the Fabaceae family. Papillonoids are recognized for their food and forage importance, wide distribution in different biomes and variation in floral architecture as well as plastome structure. Due to the high-level conservation of chloroplast genomes, when compared to nuclear and mitochondrial genomes, phylogenetic analysis based on chloroplast DNA (cpDNA) have been elucidating the relationships among the main Papilionoideae’s taxon. However, the phylogeny of some clades of the subfamily remains unresolved. Aiming at the phylogenetic reconstruction of the deep branching species of Papilionoideae, concatenated sequences of six loci (matK, psaA, psbA, psbD, rbcL and rpoC2) of cpDNA from 117 species of Papilionoideae were analyzed using the maximum likelihood methodology. The plastomes of Papilionoideae showed low conservation and similarity. Phylogenetic analysis resulted in a monophyletic tree, confirming the division of the subfamily into four main clades (NPAAA, ADA, Genistoids and Dalbergioids). The sibling group relationship of the ADA clade with the Genistoids clade was demonstrated, with high support. The paraphyly of the Phaseoleae and Millettiae tribes was evidenced within the NPAAA clade with unresolved phylogeny of the Genistoids clade. As well, was observed that only species of the ADA clade have no rhizobium nodules, which may be a possible synapomorphy to support the relationships of this group. The analysis also suggest that the main Papilionoideae clades diverged from the Paleocene onwards.
