rbcL Sequence Analysis Research Articles

Molecular systematics of the Gelidiales: inferences from separate and combined analyses of plastid rbcL and nuclear SSU gene sequences

Nucleotide gene sequences for both the nuclear-encoded small-subunit RNA (SSU) and plastid-encoded large subunit of RuBisCO (rbcL) were determined for 16 species classified in the red algal order Gelidiales. Sequence comparisons indicate that rbcL is evolving at a faster rate than SSU in these species and that there is a more even distribution of changes across the length of the rbcL gene compared with that observed for the SSU gene. The rbcL sequences also showed a marked anti-GC bias at synonymous third-codon base positions. Parsimony and maximum-likelihood analyses were used to generate phylogenetic trees from both separate and combined analyses of the two sequence data sets. Relationships among most taxa are resolved robustly; however, the relative order of branching for the Capreolia and Ptilophora clades remains uncertain. The molecular data provide unambiguous, independent support for recognition of the newly established genus Pterocladiella. Although the position of Pterocladiella within the Gelidiales was not resolved clearly by the rbcL data alone, analyses of both the SSU and combined data matrices indicate that this genus is one of the three earliest-diverging lineages within the order. These data also suggest that Gelidium as currently circumscribed is not monophyletic. Molecular and morphological evidence suggests that the origin and, perhaps, diversification of the major lineages of gelidialean algae is correlated with distinct, independently evolved nutritional strategies for the developing carposporophyte.

Molecular systematics of the Gelidiales: inferences from separate and combined analyses of plastid rbcL and nuclear SSU gene sequences

Nucleotide gene sequences for both the nuclear-encoded small-subunit RNA (SSU) and plastid-encoded large subunit of RuBisCO (rbcL) were determined for 16 species classified in the red algal order Gelidiales. Sequence comparisons indicate that rbcL is evolving at a faster rate than SSU in these species and that there is a more even distribution of changes across the length of the rbcL gene compared with that observed for the SSU gene. The rbcL sequences also showed a marked anti-GC bias at synonymous third-codon base positions. Parsimony and maximum-likelihood analyses were used to generate phylogenetic trees from both separate and combined analyses of the two sequence data sets. Relationships among most taxa are resolved robustly; however, the relative order of branching for the Capreolia and Ptilophora clades remains uncertain. The molecular data provide unambiguous, independent support for recognition of the newly established genus Pterocladiella. Although the position of Pterocladiella within the Gelidiales was not resolved clearly by the rbcL data alone, analyses of both the SSU and combined data matrices indicate that this genus is one of the three earliest-diverging lineages within the order. These data also suggest that Gelidium as currently circumscribed is not monophyletic. Molecular and morphological evidence suggests that the origin and, perhaps, diversification of the major lineages of gelidialean algae is correlated with distinct, independently evolved nutritional strategies for the developing carposporophyte.

Phylogenetic relationships in Saxifragaceae sensu lato: a comparison of topologies based on 18S rDNA and rbcL sequences

Relationships among the morphologically diverse members of Saxifragaceae sensu lato were inferred using 130 18S rDNA sequences. Phylogenetic analyses were conducted using representatives of all 17 subfamilies of Saxifragaceae sensu lato, as well as numerous additional taxa traditionally assigned to subclasses Magnoliidae, Caryophyllidae, Hamamelidae, Dilleniidae, Rosidae, and Asteridae. This analysis indicates that Saxifragaceae should be narrowly defined (Saxifragaceae sensu stricto) to consist of ~30 herbaceous genera. Furthermore, Saxifragaceae s. s. are part of a well-supported clade (referred to herein as Saxifragales) that also comprises lteoideae, Pterostemonoideae, Ribesioideae, Penthoroideae, and Tetracarpaeoideae, all traditional subfamilies of Saxifragaceae sensu lato, as well as Crassulaceae and Haloragaceae (both of subclass Rosidae). Paeoniaceae (Dilleniideae), and Hamamelidaceae, Cercidiphyllaceae, and Daphniphyllaceae (all of Hamamelidae). The remaining subfamilies of Saxifragaceae sensu lato fall outside this clade. Francoa (Francooideae) and Bauera (Baueroideae) are allied, respectively, with the rosid families Greyiaceae and Cunoniaceae. Brexia (Brexioideae), Parnassia (Parnassioideae), and Lepuropetolon (Lepuropetaloideae) appear in a clade with Celastraceae. Representatives of Phyllonomoideae, Eremosynoideae, Hydrangeoideae, Escallonioideae, Montinioideae, and Vahlioideae are related to taxa belonging to an expanded asterid clade (Asteridae sensu lato). The relationships suggested by analysis of 18S rDNA sequences are highly concordant with those suggested by analysis of rbcL sequences. Furthermore, these relationships are also supported in large part by other lines of evidence, including embryology. serology, and iridoid chemistry.

Phylogeny of Labiatae and Verbenaceae Inferred from rbcL Sequences

Parsimony analysis of rbcL sequences supports monophyly of the Labiatae s.l., which includes the Labiatae, subfamilies Caryopteridoideae, Chloanthoideae, and Viticoideae of the Verbenaceae, and Symphoremataceae. Representatives of subfamily Verbenoideae (Verbenaceae s. str.) do not form a monophy- letic group with the Labiatae s.l. Avicennia (Avicenniaceae), Cyclocheilon (Nesogenaceae), and Euthystachys and Retzia (Stilbaceae), included in the Verbenaceae by many authors, are distinct from the Labiatae s.l. and Verbenaceae s. str. The inferred phylogeny also provides a framework to interpret character evolution. Results suggest that uniovulate locules have evolved in at least two lineages of Lamiales s.l. and that a gynoecium with four locules by the development of false partitions apparently has evolved independently in the Labiatae s.l. and th,e Verbenaceae s. str. Whereas a dry fruit is plesiomorphic in the Lamiales s.l., a fleshy fruit is plesiomorphic in the Labiatae s.l. with possible reversal in four lineages.

Phylogenetic analysis ofEremosyne pectinata (Saxifragaceae s. l.) based onrbcL sequence data

Earlier analyses ofrbcL sequences clarified phylogenetic relationships of 16 of 17 subfamilies ofSaxifragaceae s. l. This study investigates the affinities of the monotypicEremosynoideae, the only subfamily ofSaxifragaceae s. l. not examined previously forrbcL sequence variation. Our analyses suggest thatEremosyne is only distantly related to core members ofSaxifragaceae s. l. (i.e.Saxifragoideae = Saxifragaceae s. str.); it is allied instead with members ofAsteridae. A particularly close relationship is indicated betweenEremosyne andEscallonia, another traditional member ofSaxifragaceae s. l. that also appears as part ofAsteridae. Inclusion ofEremosyne withinAsteridae is in agreement with embryology, as well as with 18S rDNA sequence data.

The molecular systematics of some agar- and carrageenan-containing marine red algae based on rbcL sequence analysis

The molecular systematics of some agar- and carrageenan-containing marine red algae based on rbcL sequence analysis

Phylogenetic Implications of rbcL and ITS Sequence Variation in the Berberidaceae

In spite of the use of chromosome number, floral anatomy, pollen morphology, and serology, substantial disagreement remains regarding the systematics of the Berberidaceae. To test competing hypoth- eses about intergeneric relationships in the family, sequences of the chloroplast encoded rbcL gene and ITS regions of the nuclear ribosomal repeat were examined. Analysis of rbcL sequences does not support fragmentation of the Berberidaceae into smaller families, especially the separation of Nandina as a distinct family. The large woody genera, Berberis and Mahonia, are related to the monotypic herbaceous genus Ranzania. Bongardia is nested within a clade characterized by a basic chromosome number of x = 6, and has a remote relationship to the Leontice group with which the genus has been placed in most previous classifica- tions. The x = 6 group, the largest in the Berberidaceae, comprises two distinct lineages: Jeffersonia and the rest of the core genera (Diphylleia, Bongardia, Achlys, and Epimedium). Among the core genera, Diphylleia is sister to Epimedium/Achlys and their sister genus Bongardia. ITS sequence data provided additional support for the phylogenetic relationships of the x = 6 group observed in the rbcL gene tree. Berberidaceae (s.l.) is a heterogeneous assem-

The molecular systematics of some agar- and carrageenan-containing marine red algae based on rbcL sequence analysis

A hypothesis of phylogenetic relationships inferred by parsimony analysis of plastid-encoded rbcL sequences is presented for red algae containing agar- and carrageenan-like phycocolloids; rbcL encodes the large subunit of ribulose 1,5 bisphosphate carboxylase/oxygenase. Previous studies have shown that Floridean families that contain sulfated galactans as cell wall components are resolved as a monophyletic clade sister to the agarophyte order Ahnfeltiales. Families that have been identified as containing kappa-type carrageenans, often in addition to lambda-type carrageenans, are resolved in three clades: (1) a complex containing the families Solieriaceae, Cystocloniaceae, Hypneaceae, Caulacanthaceae, Tichocarpaceae, Furcellariaceae, and the genera Turnerella and Opuntiella; (2) the Gigartinaceae and Phyllophoraceae, and (3) the genus Endocladia. Except for Tichocarpus and Endocladia, these are all members of the Gigartinales sensu Kylin (1956). Most of the families previously placed in the Cryptonemiales by Kylin appear to contain only lambda-type carrageenans. These fall into two groups, one that clusters with typical carrageenophyte- and the other with typical agarophyte-taxa. The first of these includes the families Polyideaceae, Kallymeniaceae, Dumontiaceae, and Rhizophyllidaceae. The second includes the type family of the Cryptonemiales, the Halymeniaceae, which is divisible into two well-supported clades, one of which possesses special lambda-like carrageenans, the aeodans, and the Schizymeniaceae, a recently created family containing two former gigartinalean genera. The agarophyte orders Gelidiales, Gracilariales and Ceramiales are well resolved as monophyletic clades, but their topological positions are poorly resolved. The Gelidiales and Ceramiales are associated, but the Gracilariales is included in a clade that contains families belonging to the Rhodymeniales, a possible agarophyte order. Finally, two groups that may contain lambda-like carrageenans, the Plocamiales and the Sarcodiaceae, are resolved as separate clades.

Systematic studies of the antarctic species of the phyllophoraceae (Gigartinales, Rhodophyta) based on rbcL sequence analysis

Systematic studies of the antarctic species of the phyllophoraceae (Gigartinales, Rhodophyta) based on rbcL sequence analysis

Molecular evolution of the leguminosae: Phylogeny of the three subfamilies based on rbcL-sequences

The rbcL gene of 49 species (37 genera, 24 tribes of the Leguminosae and two species of the Polygalaceae) was amplified by polymerase chain reaction (PCR) and sequenced directly. rbcL sequences were evaluated with character state (Maximum Parsimony) and distance methods (Neighbour-Joining). The traditional classification of Leguminosae, especially in case of the basal groups, was assumed to be based on apparently ancestral or derived features. Analyses of molecular data show that such seemingly ‘old’ taxa, i.e. Cercideae, Gleditsia, Gymnocladus and Ceratonia, form distinct evolutionary lines, but not necessarily basal groups of the Leguminosae. Using Polygalaceae as an outgroup, the analysis of rbcL sequences showed that the tribes Detarieae/Amherstieae and Cercideae appear to have diverged earlier than the remaining tribes of Caesalpinioideae and might deserve a subfamily rank. The next groups to separate were the sister groups of Caesalpinieae/Cassieae and Papilionoideae. The closely interconnected Caesalpinieae/Cassieae complex forms the base of the Mimosoideae. Papilionoideae and Mimosoideae are monophyletic. Caesalpinioideae is paraphyletic to the other subfamilies, and the classical division of Leguminosae into three subfamilies is not supported. Within Papilionoideae, molecular data indicate that the tribe Sophoreae (and even the genus Sophora) is a heterogeneous collection of species that needs a comprehensive revision.

Higher level relationships of Apiales (Apiaceae and Araliaceae) based on phylogenetic analysis of rbcL sequences

The two families of the order Apiales (Apiaceae and Araliaceae) represent a classic example of the difficulty in understanding evolutionary relationships between tropical‐temperate family pairs. In Apiales, this problem is further compounded by phylogenetic confusion at almost every taxonomic level, including ordinal, interfamilial, and infrafamilial, due largely to difficulties in understanding trends in morphological evolution. Phylogenetic analyses of rbcL sequences were employed to resolve relationships at the ordinal and familial levels. The results of the ordinal analysis confirm the placement of Apiales in an expanded subclass Asteridae as the sister group to Pittosporaceae, and refute the traditional alliance of Apiales with Cornales and Rosidae. This study has also resolved relationships of a number of enigmatic genera, suggesting, for example, that Melanophylla, Aralidium, Griselinia, and Toricellia are close relatives of Apiales. Clarification of phylogenetic relationships has concomitantly provided insights into trends of morphological evolution, and suggests that the ancestral apialean taxon was probably bicarpellate, simple‐leaved, woody, and paleotropical. Phylogenetic analysis at the family level suggests that apiaceous subfamily Hydrocotyloideae, often envisioned as an intermediate group between Apiaceae and Araliaceae, is polyphyletic, with some hydrocotyloids closely allied with Araliaceae rather than Apiaceae. With the exception of some hydrocotyloids, Apiaceae appear to be monophyletic. The relationship between Apiaceae and Araliaceae remains problematic. Although the shortest rbcL trees suggest that Apiaceae are derived from within a paraphyletic Araliaceae, this result is only weakly supported.

Relationships and evolution of Hydrangeaceae based on RBCl sequence data

Phylogenetic analyses of rbcL sequences were used to address both systematic and evolutionary questions posed by the angiosperm family Hydrangeaceae. Our analyses suggest the presence of a monophyletic Hydrangeaceae most closely allied with Loasaceae, a finding in agreement with other molecular as well as morphological analyses. Molecular data indicate that Hydrangeaceae comprise Decumaria, Pileostegia, Schizophragma, Hydrangea, Dichroa, Broussaisia, Platycrater, Cardiandra, Deinanthe, Carpenteria, Philadelphus, Deutzia, Fendlerella, Whipplea, Fendlera, Jamesia, and the enigmatic Kirengeshoma. A particularly close relationship of Kirengeshoma and Deutzia is indicated. Analysis of rbcL sequences suggests that Fendlera and Jamesia are sister to the remainder of the family, lending support to the hypothesis that at least some Carpenterieae are basal in the family and that Hydrangeaceae may have originated in xeric habitats. If this phylogenetic placement of Jamesia and Fendlera is correct, the rbcL trees also suggest that the level of epigyny has decreased in these genera, as well as in the Fendlerella‐ Whipplea clade and Carpenteria when compared to the outgroup taxa, which are wholly epigynous. Furthermore, the rbcL trees support proposed evolutionary trends in wood anatomy, suggesting, for example, that upland tropical taxa have evolved longer vessel elements with more numerous bars on scalariform perforation plates. The xerophytic basal members of Hydrangeaceae, like the closely related Loasaceae, have short, narrow vessel elements with scalariform perforation plates bearing few bars. Following Jamesia and Fendlera, the remaining hydrangeoids are divided into two large subclades that closely parallel the traditional division of the family into Philadelpheae and Hydrangeae. Both rbcL sequences and morphological data suggest close relationships between: 1) Fendlerella and Whipplea; 2) Decumaria, Pileostegia, and Schizophragma; 3) Carpenteria and Philadelphus; 4) Deinanthe and Cardiandra; 5) Dichroa, Broussaisia, and Hydrangea macrophylla. Molecular and morphological data also concur in demonstrating that the large genus Hydrangea is not a monophyletic assemblage.

Higher‐level systematics of Acanthaceae determined by chloroplast DNA sequences

Parsimony analyses of ndhF chloroplast gene sequences were undertaken for 15 species of Acanthaceae and nine representative outgroup species. In addition, parsimony analyses of rbcL sequences were undertaken for 12 species of Acanthaceae and the same nine outgroup species as for ndhF. The results indicate that ndhF provides more informative characters and greater systematic resolution at this hierarchical level than rbcL. The ndhF analyses demonstrate that Elytraria and Thunbergia are successive sister taxa to all Acanthaceae taxa that have retinacula and explosive fruits. These data also demonstrate that taxa with both retinacula and explosive fruits can be subdivided further into two monophyletic groups that correspond to taxa with and without cystoliths. Within the group with cystoliths three putatively monophyletic groups correspond to taxa possessing quincuncial, left contort, and ascending‐cochlear corolla aestivation patterns. The results of the rbcL analysis provide less systematic resolution than ndhF but do contain several congruent arrangements of taxa within Acanthaceae.

Higher-Level Systematics of Acanthaceae Determined by Chloroplast DNA Sequences

Parsimony analyses of ndhF chloroplast gene sequences were undertaken for 15 species of Acanthaceae and nine representative outgroup species. In addition, parsimony analyses of rbcL sequences were undertaken for 12 species of Acanthaceae and the same nine outgroup species as for ndhF. The results indicate that ndhF provides more informative characters and greater systematic resolution at this hierarchical level than rbcL. The ndhF analyses demonstrate that Elytraria and Thunbergia are successive sister taxa to all Acanthaceae taxa that have retinacula and explosive fruits. These data also demonstrate that taxa with both retinacula and explosive fruits can be subdivided further into two monophyletic groups that correspond to taxa with and without cystoliths. Within the group with cystoliths three putatively monophyletic groups correspond to taxa possessing quincuncial, left contort, and ascending-cochlear corolla aestivation patterns. The results of the rbcL analysis provide less systematic resolution than ndhF but do contain several congruent arrangements of taxa within Acanthaceae.

Subfamilial and Tribal Relationships in the Rubiaceae Based on rbcL Sequence Data

A parsimony analysis of rbcL sequences from 49 Rubiaceae genera (representing 23 tribes) and 7 outgroup taxa was performed. Species representing 48 genera of Rubiaceae were sequenced: Anthospermum, ...

A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL.

A phylogeny for the Rhodophyta has been inferred by parsimony analysis of plastid rbcL sequences representing 81 species, 68 genera, 38 families, and 17 orders of red algae; rbcL encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Levels of sequence divergence among species, genera, and families are high in red algae, typically much greater than those reported for flowering plants. The Rhodophyta traditionally consists of one class, Rhodophyceae, and two subclasses, Bangiophycidae and Florideophycidae. The Bangiophycidae with three orders (Porphyridiales, Compsopogonales, and Bangiales) appears to be polyphyletic, and the Florideophycidae with 17 orders is monophyletic in this study. The current classification of the Florideophycidae based on ultrastructure of pit connections is supported. With the exception of the Rhodogorgonales, which appears to be misplaced, orders with one or two pit-plug cap layers (Hildenbrandiales, Corallinales, Acrochaetiales, Palmanales, Batrachospermales, and Nemaliales) terminate long branches of basal position within Florideophycidae in the most parsimonious rbcL tree. Orders that lack typical cap layers but possess a cap membrane are resolved as a monophyletic clade sister to the Ahnfeltiales. The large order Gigartinales, which is distributed among five rbcL clades, is polyphyletic. Families that possess typical carrageenan in their cell walls are resolved as a terminal clade containing two family complexes centered around the Solieriaceae and Gigartinaceae.

Systematic and Evolutionary Implications of rbcL Sequence Variation in Rosaceae

The angiosperm family Rosaceae poses a number of noteworthy systematic problems as well as many questions concerning morphological and chromosomal evolution. Phylogenetic analysis of rbcL gene sequences was performed to address systematic and evolutionary problems of Rosaceae. Both rbcL sequence variation and the presence of duplicated sequences near the 3' end of rbcL were useful in determining phylogenetic relationships in this family. Analyses of rbcL sequences indicate that there are groups of genera within Rosaceae comparable to the subfamilies Maloideae, Amygdaloideae, and Rosoideae, although the composition of each group differs from traditional circumscriptions. According to analysis of rbcL data, Maloideae and Amygdaloideae each include additional taxa not normally associated with them. All members of Rosoideae with x = 9 are phylogenetically well separated from the x = 8 and 7 members of the subfamily. In addition, Spiraeoideae are not monophyletic but appear to consist of several distinct evolutionary lineages. The rbcL-based phylogenies suggest that chromosome numbers are more reliable indicators of some generic alliances than the more commonly used fruit types. Sequence data are also useful in determining the alliances of several problematic genera, suggesting that the capsular and follicular-fruited genera Vauquelinia, Lindleya, and Kageneckia (usually placed in Spiraeoideae) should be included in the pome-fruited subfamily Maloideae, and that Quillaja is not a member of Rosaceae. Molecular data are consistent with several suggestions for the ancestral chromosome numbers and fruit types of Rosaceae, but do not support any one hypothesis for either. This study also suggests that the subfamily Maloideae may have descended from spiraeoid ancestors and that the pome is derived from follicular or capsular fruit types.

Systematic and evolutionary implications ofrbcL sequence variation in Rosaceae

The angiosperm family Rosaceae poses a number of noteworthy systematic problems as well as many questions concerning morphological and chromosomal evolution. Phylogenetic analysis ofrbcL gene sequences was performed to address systematic and evolutionary problems of Rosaceae. BothrbcL sequence variation and the presence of duplicated sequences near the 3' end ofrbcL were useful in determining phylogenetic relationships in this family. Analyses ofrbcL sequences indicate that there are groups of genera within Rosaceae comparable to the subfamilies Maloideae, Amygdaloideae, and Rosoideae, although the composition of each group differs from traditional circumscriptions. According to analysis ofrbcL data, Maloideae and Amygdaloideae each include additional taxa not normally associated with them. All members of Rosoideae withx= 9 are phylogenetically well separated from thex= 8 and 7 members of the subfamily. In addition, Spiraeoideae are not monophyletic but appear to consist of several distinct evolutionary lineages. TherbcL‐based phylogenies suggest that chromosome numbers are more reliable indicators of some generic alliances than the more commonly used fruit types. Sequence data are also useful in determining the alliances of several problematic genera, suggesting that the capsular and follicular‐fruited generaVauquelinia, Lindleya, andKageneckia(usually placed in Spiraeoideae) should be included in the pome‐fruited subfamily Maloideae, and thatQuillajais not a member of Rosaceae. Molecular data are consistent with several suggestions for the ancestral chromosome numbers and fruit types of Rosaceae, but do not support any one hypothesis for either. This study also suggests that the subfamily Maloideae may have descended from spiraeoid ancestors and that the pome is derived from follicular or capsular fruit types.

An Analysis of Relationships Within the Cupressaceae Sensu Stricto Based on rbcL Sequences

The analysis of rbcL sequences of representative species of 13 of the 20 genera of the Cupressaceae sens. str. has produced a cladogram that agrees with data derived from other sources. The monophyly of the family is well supported. The cladogram provides support for the recognition of a basically northern subfamily (Cupressoideae) and a southern subfamily (Callitroideae), but the boundary between the subfamilies needs to be realigned by moving Tetraclinis from the Callitroideae to the Cupressoideae. The tribal arrangement of Li is largely artificial: the Libocedreae, Cupresseae, and Thujopsideae are clearly paraphyletic

Gene phylogenies and the endosymbiotic origin of plastids

The endosymbiotic origin of chloroplasts from cyanobacteria has long been suspected and has been confirmed in recent years by many lines of evidence. Debate now is centered on whether plastids are derived from a single endosymbiotic event or from multiple events involving several photosynthetic prokaryotes and/or eukaryotes. Phylogenetic analysis was undertaken using the inferred amino acid sequences from the genes psbA, rbcL, rbcS, tufA and atpB and a published analysis (Douglas and Turner, 1991) of nucleotide sequences of small subunit (SSU) rRNA to examine the relationships among purple bacteria, cyanobacteria and the plastids of non-green algae (including rhodophytes, chromophytes, a cryptophyte and a glaucophyte), green algae, euglenoids and land plants. Relationships within and among groups are generally consistent among all the trees; for example, prochlorophytes cluster with cyanobacteria (and not with green plastids) in each of the trees and rhodophytes are ancestral to or the sister group of the chromophyte algae. One notable exception is that Euglenophytes are associated with the green plastid lineage in psbA, rbcL, rbcS and tufA trees and with the non-green plastid lineage in SSU rRNA trees. Analysis of psbA, tufA, atpB and SSU rRNA sequences suggests that only a single bacterial endosympbiotic event occurred leading to plastics in the various algal and plant lineages. In contrast, analysis of rbcL and rbcS sequences strongly suggests that plastids are polyphyletic in origin, with plastids being derived independently from both purple bacteria and cyanobacteria. A hypothesis consistent with these discordant trees is that a single bacterial endosymbiotic event occurred leading to all plastids, followed by the lateral transfer of the rbcLS operon from a purple bacterium to a rhodophyte.