Phylogenetic Analyses of Polemoniaceae Using Nucleotide Sequences of the Plastid Gene matK
Abstract and Figures
Nucleotide sequences of the plastid encoded gene matK were examined for their potential utility in phylogenetic analyses within angiosperm families. Sequences 661 bases in length were obtained from twenty species of Polemoniaceae. Phylogenetic analyses resulted in four equally parsimonious trees with a consistency index of 0.70. Several well supported groups allowed us to test hypotheses of relationship within Polemoniaceae. The segregation of Ipomopsis and Allophyllum from Gilia was supported by the placement of each in distinct groups separate from a group of four species of Gilia. Several strongly supported groups include genera now placed in different tribes. There was no support for the current separation of temperate Polemoniaceae into two tribes. The tropical genera were resolved as basal and paraphyletic within the family. The family as a whole was monophyletic with no support for the segregate family Cobaeaceae. Sequences of matK, a gene that had not been used previously for phylogenetic analyses, provided a sufficient number of reliable characters for phylogenetic analysis within Polemoniaceae. Pairwise comparisons of matK and rbcL sequences of the same taxa were performed. Sequences of matK varied at an overall rate twice that of rbcL sequences. Substitutions at the third codon position predominated in rbcL sequences, while in matK substitutions were more evenly distributed across codon positions.
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... Total genomic DNA was extracted from 0.5 g dried leaf tissue using the Invisorb â Spin Plant Mini Kit (Stratec Molecular GmbH, Berlin, Germany). The internal transcribed spacer was amplified using ITS 4 and ITS 5 (White et al., 1990) and chloroplast matK region trnK1F (Manos & Steele, 1997) and trnK2R (Steele & Vilgalys, 1994) primers following the conditions described in Z avesk a et al. (2012). PCR fragments were precipitated with sodium acetate and sequenced with PCR primers and the Zingiberaceaespecific internal matK primers mIF, m5R and mIR (Kress et al., 2002). ...
Plant species with large genomes tend to be excluded from climatically more extreme environments with a shorter growing season. Species that occupy such environments are assumed to be under natural selection for more rapid growth and smaller genome size (GS). However, evidence for this is available only for temperate organisms. Here, we study the evolution of GS in two subfamilies of the tropical family Zingiberaceae to find out whether species with larger genomes are confined to environments where the vegetative season is longer. We tested our hypothesis on 337 ginger species from regions with contrasting climates by correlating their GS with an array of plant traits and environmental variables. We revealed 16‐fold variation in GS which was tightly related to shoot seasonality. Negative correlations of GS with latitude, temperature and precipitation emerged in the subfamily Zingiberoidae, demonstrating that species with larger GS are excluded from areas with a shorter growing season. In the subfamily Alpinioideae, GS turned out to be correlated with the type of stem and light requirements and its members cope with seasonality mainly by adaptation to shady and moist habitats. The Ornstein–Uhlenbeck models suggested that evolution in regions with humid climates favoured larger GS than in drier regions. Our results indicate that climate seasonality exerts an upper constraint on GS not only in temperate regions but also in the tropics, unless species with large genomes find alternative ways to escape from that constraint.
... For diagnoses translated from Latin, the Latin text is included in parentheses. 1 Smith's (1972) groups distinguished by numbers are based on morphological characteristics and groups distinguished by letters are based on protein serology data. B4F and RETS-B3F (Alonso et al., 2014) and 18S-R (Starr, Harris & Simpson, 2003) at 95 C for 2 min, 29 cycles of 95 C for 45 s, 58 C for 45 s, 72 C for 2 min and a final extension step of 72 C for 5 min; matK-primers matK-AF and matK-BF (Ooi et al., 1995) and trnK-2R (Steele & Vilgalys, 1994) at 95 C for 1 min, 35 cycles of 95 C for 30 s, 55 C for 40 s, 72 C for 1 min and a final extension step of 72 C for 10 min. Amplification reactions were performed in 20 mL volumes containing 8 mL deionized water, 10 mL of Taq DNA Polymerase 2x Master Mix RED (Ampliqon, Denmark, Copenhagen), 0.5 mL of each primer (10 pmol/mL), and 1 mL of template DNA (ca. ...
To investigate phylogenetic relationships among and within major lineages of Bromus , with focus on Bromus sect. Bromus , we analyzed DNA sequences from two nuclear ribosomal (ITS, ETS) and two plastid ( rpl32-trnL UAG , matK ) regions. We sampled 103 ingroup accessions representing 26 taxa of B . section Bromus and 15 species of other Bromus sections. Our analyses confirm the monophyly of Bromus s.l. and identify incongruence between nuclear ribosomal and plastid data partitions for relationships within and among major Bromus lineages. Results support classification of B. pumilio and B. gracillimus within B . sect. Boissiera and B . sect. Nevskiella , respectively. These species are sister groups and are closely related to B. densus ( B . sect. Mexibromus ) in nrDNA trees and Bromus sect. Ceratochloa in plastid trees. Bromus sect. Bromopsis is paraphyletic. In nrDNA trees, species of Bromus sects. Bromopsis , Ceratochloa , Neobromus , and Genea plus B. rechingeri of B . sect. Bromus form a clade, in which B. tomentellus is sister to a B . sect. Genea – B. rechingeri clade. In the plastid trees, by contrast, B . sect. Bromopsis species except B. tomentosus form a clade, and B. tomentosus is sister to a clade comprising B . sect. Bromus and B . sect. Genea species. Affinities of B. gedrosianus , B. pulchellus , and B. rechingeri (members of the B. pectinatus complex), as well as B. oxyodon and B. sewerzowii , are discordant between nrDNA and plastid trees. We infer these species may have obtained their plastomes via chloroplast capture from species of B . sect. Bromus and B . sect. Genea . Within B . sect. Bromus , B. alopecuros subsp. caroli-henrici , a clade comprising B. hordeaceus and B. interruptus , and B. scoparius are successive sister groups to the rest of the section in the nrDNA phylogeny. Most relationships among the remaining species of B . sect. Bromus are unresolved in the nrDNA and plastid trees. Given these results, we infer that most B . sect. Bromus species likely diversified relatively recently. None of the subdivisional taxa proposed for Bromus sect. Bromus over the last century correspond to natural groups identified in our phylogenetic analyses except for a group including B. hordeaceus and B. interruptus .
... Referring to Wanke et al. (2006); Wanke et al. (2007), we used the chloroplast trnK-matK-psbA region for phylogenetic reconstructions (i.e., trnK intron, matK gene, and trnK-psbA spacer). Amplification was done in a single fragment employing the primers trnK-F (Wicke & Quandt, 2009) and psbA-R (Steele & Vilgalys, 1994). If this was not successful the region was divided in multiple smaller and overlapping fragments employing following primers: ...
The taxonomy of the Mediterranean Aristolochia pallida complex has been under debate since several decades with the following species currently recognized: A. pallida, A. lutea, A. nardiana, A. microstoma, A. merxmuelleri, A. croatica, and A. castellana. These taxa are distributed from Iberia to Turkey. To reconstruct phylogenetic and biogeographic patterns, we employed cpDNA sequence variation using both noncoding (intron and spacer) and protein-coding regions (i.e., trnK intron, matK gene, and trnK-psbA spacer). Our results show that the morphology-based traditional taxonomy was not corroborated by our phylogenetic analyses. Aristolochia pallida, A. lutea, A. nardiana, and A. microstoma were not monophyletic. Instead, strong geographic signals were detected. Two major clades, one exclusively occurring in Greece and a second one of pan-Mediterranean distribution, were found. Several subclades distributed in Greece, NW Turkey, Italy, as well as amphi-Adriatic subclades, and a subgroup of southern France and Spain, were revealed. The distribution areas of these groups are in close vicinity to hypothesized glacial refugia areas in the Mediterranean. According to molecular clock analyses the diversification of this complex started around 3-3.3 my, before the onset of glaciation cycles, and the further evolution of and within major lineages falls into the Pleistocene. Based on these data, we conclude that the Aristolochia pallida alliance survived in different Mediterranean refugia rarely with low, but often with a high potential for range extension, and a high degree of morphological diversity.
... Total genomic DNA was extracted from silica-gel dried leaves using both the CTAB method (Bhadra and Bandyopadhyay, 2015) and DNeasy Plant Mini Kit method (QIAGEN, Germany). We amplified one nuclear (ITS) and three chloroplast regions (trnK/matK, rps16, trnL) using polymerase chain reaction (PCR, primers listed in Table S2; White et al., 1990;Taberlet et al., 1991;Steele and Vilgalys, 1994;Oxelman et al., 1997;Prince, 2015). PCR were performed in a 10 μL volume containing MyTaq™ DNA polymerase buffer (Bioline Inc., USA) with preoptimized concentrations of dNTPs, MgCl 2 stabilizers and enhancers, 0.5 μM of each forward and reverse primer, 1 U of MyTaq™ DNA polymerase and 1 μL of genomic DNA (20-100 ng). ...
The Indo-Malayan Realm is a biogeographic realm that extends from the Indian Subcontinent to the islands of Southeast Asia (Malay Archipelago). Despite being megadiverse, evolutionary hypotheses explaining taxonomic diversity in this region have been rare. Here, we investigate the role of geoclimatic events such as Himalayan orogeny and monsoon intensification in the diversification of the ginger lilies (Hedychium J.Koenig: Zingiberaceae). We first built a comprehensive, time-calibrated phylogeny of Hedychium with 75% taxonomic and geographic sampling. We found that Hedychium is a very young lineage that originated in Northern Indo-Burma, in the Late Miocene (c. 10.6 Ma). This was followed by a late Neogene and early Quaternary diversification, with multiple dispersal events to Southern Indo-Burma, Himalayas, Peninsular India, and the Malay Archipelago. The most speciose clade IV i.e., the predominantly Indo-Burmese clade also showed a higher diversification rate, suggesting its recent rapid radiation. Our divergence dating and GeoHiSSE results demonstrate that the diversification of Hedychium was shaped by both the intensifications in the Himalayan uplift as well as the Asian monsoon. Ancestral state reconstructions identified the occurrence of vegetative dormancy in both clades I and II, whereas the strictly epiphytic growth behavior, island dwarfism, lack of dormancy, and a distinct environmental niche was observed only in the predominantly island clade i.e., clade III. Finally, we show that the occurrence of epiphytism in clade III corresponds with submergence due to sea-level changes, suggesting it to be an adaptive trait. Our study highlights the role of recent geoclimatic events and environmental factors in the diversification of plants within the Indo-Malayan Realm and the need for collaborative work to understand biogeographic patterns within this understudied region. This study opens new perspectives for future biogeographic studies in this region and provides a framework to explain the taxonomic hyperdiversity of the Indo-Malayan Realm.
... The plastid trnK region was amplified in two parts, the first using either 1F (Manos & Steele 1997) and mIR (Kress et al. 2002) or 1F (Manos & Steele 1997) and 1235R (Mood et al. 2018). The second half was amplified using mIF (Kress et al. 2002) and 2R (Steele & Vilgalys 1994). Data were sequenced on an ABI Genetic Analyzer and sequences were verified and edited in Sequencher v. 4.9 (Gene Codes Corporation, Ann Arbor, Michigan, USA). ...
The classification of Boesenbergia ( Zingiberaceae ) has long been a challenge, and recent insights from molecular phylogenetic studies have both raised and resolved a number of questions. Combined morphological and molecular revisions resulted in the description of new species as well as merging of Haplochorema and Jirawongsea into Boesenbergia . This study uses the most complete set of Boesenbergia accessions and sister genera to investigate the evolutionary relationships of the genus in a phylogenetic framework. This framework confirms the previously identified clades and the placement of the included accessions within those clades. These clades share being single-flowered and having a basipetalous flowering sequence, characters uniting all taxa in Boesenbergia , but also have unique or mostly unique characters that are clade specific. In addition, the phylogeny identifies two species, B. purpureorubra and B. siamensis , that are hard to place within these clades based on both molecular and morphological data, while the morphological data points to a stronger affiliation with the clade including the type of the genus.
DNA barcoding is a technique, used for the identification of living
organisms without involving any morphological characteristics. It
discriminates the species by using an automated system, so that unexplored
living organism can be named easily and quickly identified. The aim of the
barcoding is to identify the species, adulterants and it stores all the information
about the species, develops a simple diagnostic tool based on strong
taxonomic data that is collected in the DNA barcode reference library. The
reference library becomes useful by enabling the rapid identification of low
taxonomic level taxa with specific short DNA sequence. The key process in
DNA barcoding is identifying novel candidate gene universally. DNA barcode
proved to be a promising tool to identify the species across all forms of life
including animals, plants and microbes in a rapid and reliable manner.
Keywords: DNA barcoding, species, adulterants, Reference library
DNA barcoding is a technique, used for the identification of living
organisms without involving any morphological characteristics. It
discriminates the species by using an automated system, so that unexplored
living organism can be named easily and quickly identified. The aim of the
barcoding is to identify the species, adulterants and it stores all the information
about the species, develops a simple diagnostic tool based on strong
taxonomic data that is collected in the DNA barcode reference library. The
reference library becomes useful by enabling the rapid identification of low
taxonomic level taxa with specific short DNA sequence. The key process in
DNA barcoding is identifying novel candidate gene universally. DNA barcode
proved to be a promising tool to identify the species across all forms of life
including animals, plants and microbes in a rapid and reliable manner.
Keywords: DNA barcoding, species, adulterants, Reference library
Caryophyllaceae with a cushion-like life form occur with a large number of species at the higher altitudes of the Andes (3500–5000 m) and have evolved convergently in several different lineages. Based on molecular phylogenetic analysis it is shown that members of the former genera Plettkea and Pycnophyllopsis, but also certain species previously classified as Arenaria constitute a subclade nested within the monophyletic genus Stellaria. Both plastid (trnK-matK-psbA + trnL-F) and nuclear (nrITS) trees converged on such a highly supported ‘Plettkea’ clade. Morphologically, the members of the ‘Plettkea’ subclade of Stellaria are further characterized by reduced to completely absent petals and seeds with a more or less conspicuous tuberculate testa. This clade is described as S. sect. Plettkea (Mattf.) Montesinos & Borsch. Species-level relationships within S. sect. Plettkea are also congruently inferred by plastid and nuclear genomic compartments, with three further sublineages recognized: Altogether, our detailed taxonomic revision showed that the ‘Plettkea’ clade in fact constitutes an Andean radiation of 21 species within Stellaria, four of which are described as new to science. Earlier treatments indicated just a few species with a putative placement. The results of this investigation underscore the importance of fieldwork and integrated molecular-morphological approaches to assess the species diversity in Andean plant groups. In addition to the phylogenetic analysis, we provide a taxonomic backbone including all names and types, descriptions and information on distribution and ecology and a key for identification. Regarding the next relatives of the S. sect. Plettkea clade, our plastid trees depict the ‘Nitentes’ clade of Stellaria as sister, whereas nrITS instead suggests a sister group relationship of the ‘Nitentes’ with the speciose ‘Larbreae’ clade. Our inferred relationships of major clades further deviate from published molecular trees by indicating an early branching position of the ‘Petiolares’ clade.
A molecular systematic study of Globba section Nudae (Zingiberaceae) using ITS and matK sequences identifies three major clades, Globba subsection Nudae, G. subsection Mediocalcaratae and a new subsection, Globba subsection Pelecantherae, which is described here. The two species belonging in this subsection, Globba pelecanthera and Globba securifer, which are both new, are described. Rectangular anther appendages are reported in Globba for the first time. Evidence of hybridisation is given. The morphological characters of the flowers, which are likely to be important in pollination, are discussed.
The Rheum species are important medicinal plants that are facing extinction due to their unplanned development and overexploitation by pharmaceutical industries. DNA polymorphisms are not prone to environmental modifications, thus they are widely used for the identification and characterization of plants. The use of different molecular markers has enabled the researchers for the valuation of genetic variability and diversity in its natural zone of distribution. The conventional approach may take several years to yield this information. For the estimation of molecular and genetic variations in geographical zone of distribution, various molecular markers technique are available like RAPD (Randomly Amplified Polymorphic DNA), RFLP (Restriction fragment length polymorphism), ISSR (Inter-Simple Sequence Repeats), SSR and AFLP. The uses of different molecular markers for the study of genetic diversity have been discussed in the review.
The taxonomic composition of three principal and distantly related groups of the former tribe Millettieae, which were first identified from nuclear phytochrome and chloroplast trnK/matK sequences, was more extensively investigated with a phylogenetic analysis of nuclear ribosomal DNA ITS/5.8S sequences. The first of these groups includes the neotropical genera Poecilanthe and Cyclolobium, which are resolved as basal lineages in a clade that otherwise includes the neotropical genera Brongniartia and Harpalyce and the Australian Templetonia and Hovea. The second group includes the large millettioid genera, Millettia, Lonchocarpus, Derris, and Tephrosia, which are referred to as the “core Millettieae” group. Phylogenetic analysis of nuclear ribosomal DNA ITS/5.8S sequences reveals that Millettia is polyphyletic, and that subclades of the core Millettieae group, such as the New World Lonchocarpus or the pantropical Tephrosia and segregate genera (e.g., Chadsia and Mundulea), each form well supported monophyletic subgroups. The third lineage includes the genera Afgekia, Callerya, and Wisteria. These genera are resolved as a basal subclade in the inverted-repeat-lacking clade, which is a large legume group that includes the many well known temperate and herbaceous legumes, such as Astragalus, Medicago and Pisum, but not any other Millettieae. Communicating Editor: Jerrold I. Davis
Astragalus, the largest genus of flowering plants, contains upwards of 2500 species. Explanations for this exceptional species diversity have pointed to unusual population structure or modes of speciation. Surprisingly, however, three different statistical analyses indicate that diversification rates in Astragalus are not exceptionally high compared to its closest relatives. Instead, rates are high throughout the “Astragalean clade,” a much broader radiation distributed throughout the temperate zone. The increase in diversification rate is associated with the origin and divergence of this clade from common ancestors of it and several much less diverse and more narrowly distributed Asian genera. This suggests that causal factors in the shift toward higher rates of diversification must be due not to factors unique to Astragalus, but to characteristics common to the entire Astragalean clade. However, this larger clade has never been circumscribed in classifications based on morphological data. This raises the possibility that the causes of increased diversification may not be due to morphological innovation, but may instead be related to ecological factors or cryptic physiological or biochemical features.
The pollen brush commonly is referred to as a “bearded” or “pubescent” style in taxonomic literature and traditionally is taken to be an aggregation of trichomes on the distal end of the style, and occasionally including the stigma. We present data that support the taxonomic utility of the pollen brush but define it more specifically as a dense aggregation of erect trichomes emanating from the style (not stigma or ovary) and functioning in secondary pollen presentation. We recommend avoiding such vague terminology as bearded or pubescent styles as these refer not only to the pollen brush but also to ciliate and penicillate stigmas and ciliate styles. The latter three conditions have some taxonomic use, and since their occurrence is not necessarily correlated with the presence of a pollen brush, they should be distinguished from it. We estimate that the pollen brush has arisen independently in the following eight taxa: 1) Crotalaria and Bolusia (Crotalaraieae), 2) subtribe Coluteinae (Galegeae), 3) Tephrosia subgenus Barbistyla (Millettieae), 4) Adenodolichos (Phaseoleae subtribe Cajaninae), 5) Clitoria (Phaseoleae subtribe Clitoriinae), 6) the subtribe Phaseolinae (Phaseoleae), 7) the Robinia group (Robinieae), and 8) the tribe Vicieae. Its hypothesized homology within each of these groups is supported by a cooccurrence with other taxonomic characters, both morphological and molecular.