Phylogenetic analyses of plastid DNA sequences of ndhF, trnL-F intron and spacer regions, and rpl... more Phylogenetic analyses of plastid DNA sequences of ndhF, trnL-F intron and spacer regions, and rpl16 are presented separately and combined for 41 taxa from all 12 genera of the Themidaceae and for 20 taxa from nine related families in the higher Asparagales. The results from the combined analysis are the most resolved and provide a high level of support for the monophyly of Themidaceae. Within Themidaceae, the Milla complex of Mexico is supported as monophyletic within a paraphyletic Brodiaea complex of western North America. Four major clades are identified in each of the individual and combined analyses: (1) the Milla complex; (2) Brodiaea, Dichelostemma, and Triteleiopsis; (3) Triteleia, Bloomeria, and Muilla clevelandii; and (4) Androstephium and the other species of Muilla. These well-defined clades suggest that morphological characters (e.g., an extended perianth tube) that have been traditionally used to circumscribe the genera within the Brodiaea complex have evolved independently at least twice. In addition, common bio-geographic distribution patterns (e.g., Brodiaea and Triteleia having centers of diversity in northern California and the Pacific Northwest) appear to be the result of separate evolutionary radiations.
We present a well-resolved, highly inclusive phylogeny for monocots, based on ndhF sequence varia... more We present a well-resolved, highly inclusive phylogeny for monocots, based on ndhF sequence variation, and use it to test a priori hypotheses that net venation and vertebrate-dispersed fleshy fruits should undergo concerted convergence, representing independent but often concurrent adaptations to shaded conditions. Our data demonstrate that net venation arose at least 26 times and was lost eight times over the past 90 million years; fleshy fruits arose at least 21 times and disappeared 11 times. Both traits show a highly significant pattern of concerted convergence (p!10 K9), arising 16 times and disappearing four times in tandem. This phenomenon appears driven by even stronger tendencies for both traits to evolve in shade and be lost in open habitats (p!10 K13 –10 K29). These patterns are among the strongest ever demonstrated for evolutionary convergence in individual traits and the predictability of evolution, and the strongest evidence yet uncovered for concerted convergence. The rate of adaptive shifts per taxon has declined exponentially over the past 90 million years, as expected when large-scale radiations fill adaptive zones.
We present an analysis of supra-familial relationships of monocots based on a combined matrix of ... more We present an analysis of supra-familial relationships of monocots based on a combined matrix of nuclear 18S and partial 26S rDNA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atp1 DNA sequences. Results are highly congruent with previous analyses and provide higher bootstrap support for nearly all relationships than in previously published analyses. Important changes to the results of previous work are a well-supported position of Petrosaviaceae as sister to all monocots above Acorales and Alismatales and much higher support for the commelinid clade. For the first time, the spine of the monocot tree has some bootstrap support, although support for paraphyly of liliids is still only low to moderate (79–82%). Dioscoreales and Pandanales are sister taxa (moderately supported, 87– 92%), and Asparagales are weakly supported (79%) as sister to the commelinids. Analysis of just the four plastid genes reveals that addition of data from the other two genomes contributes to generally better support for most clades, particularly along the spine. A new collection reveals that previous material of Petermannia was misidentified, and now Petermanniaceae should no longer be considered a synonym of Colchicaceae. Arachnitis (Corsiaceae) falls into Liliales, but its exact position is not well supported. Sciaphila (Triuridaceae) falls with Pandanales. Trithuria (Hydatellaceae) falls in Poales near Eriocaulaceae, Mayacaceae, and Xyridaceae, but until a complete set of genes are produced for this taxon, its placement will remain problematic. Within the commelinid clade, Dasypogonaceae are sister to Poales and Arecales sister to the rest of the commelinids, but these relationships are only weakly supported.
We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 mono... more We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 mono-cot families and all 12 orders. The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales–Pandanales in the strict consensus; Pandanales are sister to Dioscoreales in the bootstrap majority-rule tree, just above Petrosaviales. Acorales are sister to all other monocots, with Alismatales sister to all but Acorales. Relationships among the four major clades of commelinids remain unresolved. Relationships within orders are consistent with those based on rbcL, alone or in combination with atpB and 18S nrDNA, and generally better supported: ndhF contributes more than twice as many informative characters as rbcL, and nearly as many as rbcL, atpB, and 18S nrDNA combined. Based on functional arguments, we hypothesized that net venation and fleshy fruits should both evolve—and thus undergo concerted convergence—in shaded habitats, and revert to parallel venation and dry, passively dispersed fruits in open, sunny habitats. Our data show that net venation arose at least 26 times and disappeared 9 times, whereas fleshy fruits arose 22 times and disappeared 11 times. Both traits arose together at least 15 times and disappeared together 5 times. They thus show a highly significant pattern of concerted convergence (P 10 9) and are each even more strongly associated with shaded habitats (P 10 10 to 10 23); net venation is also associated, as predicted, with broad-leaved aquatic plants. Exceptions to this pattern illustrate the importance of other selective constraints and phylogenetic inertia.
Asparagales are a diverse monophyletic order that has numerous species (ca. 50% of monocots) incl... more Asparagales are a diverse monophyletic order that has numerous species (ca. 50% of monocots) including important crop plants such as Allium, Asparagus, and Vanilla, and a host of ornamentals such as irises, hyacinths, and orchids. Historically, Asparagales have been of interest partly because of their fascinating chromosomal evolution. We examine the evolutionary dynamics of Asparagales genomes in an updated phylogenetic framework that combines analyses of seven gene regions (atp1, atpB, matK, ndhF, rbcL, trnL intron, and trnL–F intergenic spacer) for 79 taxa of Asparagales and outgroups. Asparagales genomes are evolutionarily labile for many characters, including chromosome number and genome size. The history and causes of variation in chromosome number and genome size remain unclear, primarily because of the lack of data in small clades in the phylogenetic tree and the lack of comparative genetic maps, apart from Allium and Asparagus. Genomic tools such as bacterial artificial chromosome (BAC) libraries should be developed, as both molecular cytogenetic markers and a source of nuclear genes that can be widely used by evolutionary biologists and plant breeders alike to decipher mechanisms of chromosomal evolution.
Cladistic analysis of ndhF sequences identifies eight major bromeliad clades arranged in ladderli... more Cladistic analysis of ndhF sequences identifies eight major bromeliad clades arranged in ladderlike fashion. The traditional subfamilies Tillandsioideae and Bromelioideae are monophyletic, but Pitcairnioideae are paraphyletic, requiring the description of four new subfamilies, recircumscription of Pitcairnioideae and Navioideae, the sinking of Ayensua, and description of the new genus Sequencia. Brocchinioideae are basalmost, followed by Lindmanioideae, both restricted to the Guayana Shield. Next is an unresolved trichotomy involving Hechtioideae from Central America, Tillandsioideae, and the remaining bromeliads in subfamilies Navioideae, Pitcairnioideae, Puyoideae, and Bromelioideae. Bromeliads arose as C 3 terrestrial plants on moist infertile sites in the Guayana Shield roughly 70 Mya, spread centripetally in the New World, and reached tropical West Africa (Pitcairnia feliciana) via long-distance dispersal about 10 Mya. Modern lineages began to diverge from each other 19 Mya and invaded drier areas in Central and South America beginning 15 Mya, coincident with a major adaptive radiation involving the repeated evolution of epiphytism, CAM photosynthesis, impounding leaves, several features of leaf/trichome anatomy, and accelerated diversification at the generic level. This ''bromeliad revolution'' occurred after the uplift of the northern Andes and shift of the Amazon to its present course. Epiphytism may have accelerated speciation by increasing ability to colonize along the length of the Andes, while favoring the occupation of a cloud-forest landscape frequently dissected by drier valleys. Avian pollination (mainly by hummingbirds) evolved at least twice ca. 13 Mya; entomophily was ancestral. Hechtia, Abromeitiella-Deuterocohnia-Dyckia-Encholirium, and Puya exhibit a remarkable pattern of concerted convergence in six anatomical and physiological leaf traits adapted to drought.
Molecular phylogenetics and evolution, Jan 14, 2015
We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of i... more We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unresolved; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Six loci (rbcL, ndhF, matK, matR, 18S, and 26S) were amplified and sequenced for 102 taxa across Myrtales for phylogenetic reconstruction and ten fossil priors were utilized to produce a chronogram in BEAST. Combretaceae is identified as the sister clade to all remaining families with moderate support, and within the latter clade, two strongly supported groups are seen: (1) Onagraceae+Lythraceae, and (2) Melastomataceae+the Crypteroniaceae, Alzateaceae, Penaeaceae clade along with Myrtaceae+Vochysiaceae....
Proceedings of the National Academy of Sciences of the United States of America, 1986
Restriction-site variation in chloroplast DNA was examined in the morphologically distinct and mo... more Restriction-site variation in chloroplast DNA was examined in the morphologically distinct and monotypic genus Heterogaura and the related speciose genus Clarkia (Onagraceae), both native to California. Of the 605 restriction sites surveyed, a total of 119 mutations were identified. Of these, 55 were shared by at least two species and were used to construct a most parsimonious phylogenetic tree. This analysis, as well as one based on a distance metric, provided evidence that Heterogaura and Clarkia dudleyana, a member of a phylogenetically advanced section, share a more recent common ancestor than either does with any other species. The two species are more closely related than nearly all paris of Clarkia tested. The origin of Heterogaura from within another genus raises important questions about the adequacy of morphological data and suggests that the relationships of other well-known monotypic plant genera should be reinvestigated.
Phylogenetic analyses of plastid DNA sequences of ndhF, trnL-F intron and spacer regions, and rpl... more Phylogenetic analyses of plastid DNA sequences of ndhF, trnL-F intron and spacer regions, and rpl16 are presented separately and combined for 41 taxa from all 12 genera of the Themidaceae and for 20 taxa from nine related families in the higher Asparagales. The results from the combined analysis are the most resolved and provide a high level of support for the monophyly of Themidaceae. Within Themidaceae, the Milla complex of Mexico is supported as monophyletic within a paraphyletic Brodiaea complex of western North America. Four major clades are identified in each of the individual and combined analyses: (1) the Milla complex; (2) Brodiaea, Dichelostemma, and Triteleiopsis; (3) Triteleia, Bloomeria, and Muilla clevelandii; and (4) Androstephium and the other species of Muilla. These well-defined clades suggest that morphological characters (e.g., an extended perianth tube) that have been traditionally used to circumscribe the genera within the Brodiaea complex have evolved independently at least twice. In addition, common bio-geographic distribution patterns (e.g., Brodiaea and Triteleia having centers of diversity in northern California and the Pacific Northwest) appear to be the result of separate evolutionary radiations.
We present a well-resolved, highly inclusive phylogeny for monocots, based on ndhF sequence varia... more We present a well-resolved, highly inclusive phylogeny for monocots, based on ndhF sequence variation, and use it to test a priori hypotheses that net venation and vertebrate-dispersed fleshy fruits should undergo concerted convergence, representing independent but often concurrent adaptations to shaded conditions. Our data demonstrate that net venation arose at least 26 times and was lost eight times over the past 90 million years; fleshy fruits arose at least 21 times and disappeared 11 times. Both traits show a highly significant pattern of concerted convergence (p!10 K9), arising 16 times and disappearing four times in tandem. This phenomenon appears driven by even stronger tendencies for both traits to evolve in shade and be lost in open habitats (p!10 K13 –10 K29). These patterns are among the strongest ever demonstrated for evolutionary convergence in individual traits and the predictability of evolution, and the strongest evidence yet uncovered for concerted convergence. The rate of adaptive shifts per taxon has declined exponentially over the past 90 million years, as expected when large-scale radiations fill adaptive zones.
We present an analysis of supra-familial relationships of monocots based on a combined matrix of ... more We present an analysis of supra-familial relationships of monocots based on a combined matrix of nuclear 18S and partial 26S rDNA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atp1 DNA sequences. Results are highly congruent with previous analyses and provide higher bootstrap support for nearly all relationships than in previously published analyses. Important changes to the results of previous work are a well-supported position of Petrosaviaceae as sister to all monocots above Acorales and Alismatales and much higher support for the commelinid clade. For the first time, the spine of the monocot tree has some bootstrap support, although support for paraphyly of liliids is still only low to moderate (79–82%). Dioscoreales and Pandanales are sister taxa (moderately supported, 87– 92%), and Asparagales are weakly supported (79%) as sister to the commelinids. Analysis of just the four plastid genes reveals that addition of data from the other two genomes contributes to generally better support for most clades, particularly along the spine. A new collection reveals that previous material of Petermannia was misidentified, and now Petermanniaceae should no longer be considered a synonym of Colchicaceae. Arachnitis (Corsiaceae) falls into Liliales, but its exact position is not well supported. Sciaphila (Triuridaceae) falls with Pandanales. Trithuria (Hydatellaceae) falls in Poales near Eriocaulaceae, Mayacaceae, and Xyridaceae, but until a complete set of genes are produced for this taxon, its placement will remain problematic. Within the commelinid clade, Dasypogonaceae are sister to Poales and Arecales sister to the rest of the commelinids, but these relationships are only weakly supported.
We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 mono... more We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 mono-cot families and all 12 orders. The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales–Pandanales in the strict consensus; Pandanales are sister to Dioscoreales in the bootstrap majority-rule tree, just above Petrosaviales. Acorales are sister to all other monocots, with Alismatales sister to all but Acorales. Relationships among the four major clades of commelinids remain unresolved. Relationships within orders are consistent with those based on rbcL, alone or in combination with atpB and 18S nrDNA, and generally better supported: ndhF contributes more than twice as many informative characters as rbcL, and nearly as many as rbcL, atpB, and 18S nrDNA combined. Based on functional arguments, we hypothesized that net venation and fleshy fruits should both evolve—and thus undergo concerted convergence—in shaded habitats, and revert to parallel venation and dry, passively dispersed fruits in open, sunny habitats. Our data show that net venation arose at least 26 times and disappeared 9 times, whereas fleshy fruits arose 22 times and disappeared 11 times. Both traits arose together at least 15 times and disappeared together 5 times. They thus show a highly significant pattern of concerted convergence (P 10 9) and are each even more strongly associated with shaded habitats (P 10 10 to 10 23); net venation is also associated, as predicted, with broad-leaved aquatic plants. Exceptions to this pattern illustrate the importance of other selective constraints and phylogenetic inertia.
Asparagales are a diverse monophyletic order that has numerous species (ca. 50% of monocots) incl... more Asparagales are a diverse monophyletic order that has numerous species (ca. 50% of monocots) including important crop plants such as Allium, Asparagus, and Vanilla, and a host of ornamentals such as irises, hyacinths, and orchids. Historically, Asparagales have been of interest partly because of their fascinating chromosomal evolution. We examine the evolutionary dynamics of Asparagales genomes in an updated phylogenetic framework that combines analyses of seven gene regions (atp1, atpB, matK, ndhF, rbcL, trnL intron, and trnL–F intergenic spacer) for 79 taxa of Asparagales and outgroups. Asparagales genomes are evolutionarily labile for many characters, including chromosome number and genome size. The history and causes of variation in chromosome number and genome size remain unclear, primarily because of the lack of data in small clades in the phylogenetic tree and the lack of comparative genetic maps, apart from Allium and Asparagus. Genomic tools such as bacterial artificial chromosome (BAC) libraries should be developed, as both molecular cytogenetic markers and a source of nuclear genes that can be widely used by evolutionary biologists and plant breeders alike to decipher mechanisms of chromosomal evolution.
Cladistic analysis of ndhF sequences identifies eight major bromeliad clades arranged in ladderli... more Cladistic analysis of ndhF sequences identifies eight major bromeliad clades arranged in ladderlike fashion. The traditional subfamilies Tillandsioideae and Bromelioideae are monophyletic, but Pitcairnioideae are paraphyletic, requiring the description of four new subfamilies, recircumscription of Pitcairnioideae and Navioideae, the sinking of Ayensua, and description of the new genus Sequencia. Brocchinioideae are basalmost, followed by Lindmanioideae, both restricted to the Guayana Shield. Next is an unresolved trichotomy involving Hechtioideae from Central America, Tillandsioideae, and the remaining bromeliads in subfamilies Navioideae, Pitcairnioideae, Puyoideae, and Bromelioideae. Bromeliads arose as C 3 terrestrial plants on moist infertile sites in the Guayana Shield roughly 70 Mya, spread centripetally in the New World, and reached tropical West Africa (Pitcairnia feliciana) via long-distance dispersal about 10 Mya. Modern lineages began to diverge from each other 19 Mya and invaded drier areas in Central and South America beginning 15 Mya, coincident with a major adaptive radiation involving the repeated evolution of epiphytism, CAM photosynthesis, impounding leaves, several features of leaf/trichome anatomy, and accelerated diversification at the generic level. This ''bromeliad revolution'' occurred after the uplift of the northern Andes and shift of the Amazon to its present course. Epiphytism may have accelerated speciation by increasing ability to colonize along the length of the Andes, while favoring the occupation of a cloud-forest landscape frequently dissected by drier valleys. Avian pollination (mainly by hummingbirds) evolved at least twice ca. 13 Mya; entomophily was ancestral. Hechtia, Abromeitiella-Deuterocohnia-Dyckia-Encholirium, and Puya exhibit a remarkable pattern of concerted convergence in six anatomical and physiological leaf traits adapted to drought.
Molecular phylogenetics and evolution, Jan 14, 2015
We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of i... more We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unresolved; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Six loci (rbcL, ndhF, matK, matR, 18S, and 26S) were amplified and sequenced for 102 taxa across Myrtales for phylogenetic reconstruction and ten fossil priors were utilized to produce a chronogram in BEAST. Combretaceae is identified as the sister clade to all remaining families with moderate support, and within the latter clade, two strongly supported groups are seen: (1) Onagraceae+Lythraceae, and (2) Melastomataceae+the Crypteroniaceae, Alzateaceae, Penaeaceae clade along with Myrtaceae+Vochysiaceae....
Proceedings of the National Academy of Sciences of the United States of America, 1986
Restriction-site variation in chloroplast DNA was examined in the morphologically distinct and mo... more Restriction-site variation in chloroplast DNA was examined in the morphologically distinct and monotypic genus Heterogaura and the related speciose genus Clarkia (Onagraceae), both native to California. Of the 605 restriction sites surveyed, a total of 119 mutations were identified. Of these, 55 were shared by at least two species and were used to construct a most parsimonious phylogenetic tree. This analysis, as well as one based on a distance metric, provided evidence that Heterogaura and Clarkia dudleyana, a member of a phylogenetically advanced section, share a more recent common ancestor than either does with any other species. The two species are more closely related than nearly all paris of Clarkia tested. The origin of Heterogaura from within another genus raises important questions about the adequacy of morphological data and suggests that the relationships of other well-known monotypic plant genera should be reinvestigated.
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