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1.
Front Plant Sci ; 12: 767478, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34899789

RESUMO

Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.

2.
Evolution ; 75(6): 1431-1449, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33818785

RESUMO

Natural selection by pollinators is an important factor in the morphological diversity and adaptive radiation of flowering plants. Selection by similar pollinators in unrelated plants leads to convergence in floral morphology, or "floral syndromes." Previous investigations into floral syndromes have mostly studied relatively small and/or simple systems, emphasizing vertebrate pollination. Despite the importance of multiple floral traits in plant-pollinator interactions, these studies have examined few quantitative traits, so their co-variation and phenotypic integration have been underexplored. To gain better insights into pollinator-trait dynamics, we investigate the model system of the phlox family (Polemoniaceae), a clade of ∼400 species pollinated by a diversity of vectors. Using a comprehensive phylogeny and large dataset of traits and observations of pollinators, we reconstruct ancestral pollination system, accounting for the temporal history of pollinators. We conduct phylogenetically controlled analyses of trait co-variation and association with pollinators, integrating many analyses over phylogenetic uncertainty. Pollinator shifts are more heterogeneous than previously hypothesized. The evolution of floral traits is partially constrained by phylogenetic history and trait co-variation, but traits are convergent and differences are associated with different pollinators. Trait shifts are usually gradual, rather than rapid, suggesting complex genetic and ecological interactions of flowers at macroevolutionary scales.


Assuntos
Evolução Biológica , Ericales/anatomia & histologia , Flores/anatomia & histologia , Polinização , Seleção Genética , Animais , Ericales/genética , Fenótipo , Filogenia
3.
Syst Biol ; 70(1): 162-180, 2021 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-32617587

RESUMO

Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both ILS and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by ILS, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that the plastid genome does not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought. [Cyto-nuclear discordance, genomic discordance, phylogenetic networks, plastid capture, Polemoniaceae, Polemonium, reticulations.].


Assuntos
Genomas de Plastídeos , Magnoliopsida , Fluxo Gênico , Genomas de Plastídeos/genética , Filogenia , Plastídeos/genética
4.
Am J Bot ; 107(12): 1677-1692, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33315246

RESUMO

PREMISE: We tested 25 classic and novel hypotheses regarding trait-origin, trait-trait, and trait-environment relationships to account for flora-wide variation in life history, habit, and especially reproductive traits using a plastid DNA phylogeny of most native (96.6%, or 1494/1547 species) and introduced (87.5%, or 690/789 species) angiosperms in Wisconsin, USA. METHODS: We assembled data on life history, habit, flowering, dispersal, mating system, and occurrence across open/closed/mixed habitats across species in the state phylogeny. We used phylogenetically structured analyses to assess the strength and statistical significance of associations predicted by our models. RESULTS: Introduced species are more likely to be annual herbs, occupy open habitats, have large, visually conspicuous, hermaphroditic flowers, and bear passively dispersed seeds. Among native species, hermaphroditism is associated with larger, more conspicuous flowers; monoecy is associated with small, inconspicuous flowers and passive seed dispersal; and dioecy is associated with small, inconspicuous flowers and fleshy fruits. Larger flowers with more conspicuous colors are more common in open habitats, and in understory species flowering under open (spring) canopies; fleshy fruits are more common in closed habitats. Wind pollination may help favor dioecy in open habitats. CONCLUSIONS: These findings support predictions regarding how breeding systems depend on flower size, flower color, and fruit type, and how those traits depend on habitat. This study is the first to combine flora-wide phylogenies with complete trait databases and phylogenetically structured analyses to provide powerful tests of evolutionary hypotheses about reproductive traits and their variation with geographic source, each other, and environmental conditions.


Assuntos
Magnoliopsida , Flores , Magnoliopsida/genética , Melhoramento Vegetal , Polinização , História Reprodutiva , Wisconsin
5.
Evolution ; 74(7): 1335-1355, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32484910

RESUMO

Switches in pollinators have been argued to be key drivers of floral evolution in angiosperms. However, few studies have tested the relationship between floral shape evolution and switches in pollination in large clades. In concert with a dated phylogeny, we present a morphometric analysis of corolla, anther connective, and style shape across 44% of nearly 1000 species of Salvia (Lamiaceae) and test four hypotheses of floral evolution. We demonstrate that floral morphospace of New World (NW) Salvia is largely distinct from that of Old World (OW) Salvia and that these differences are pollinator driven; shifts in floral morphology sometimes mirror shifts in pollinators; anther connectives (key constituents of the Salvia staminal lever) and styles co-evolved from curved to linear shapes following shifts from bee to bird pollination; and morphological differences between NW and OW bee flowers are partly the legacy of constraints imposed by an earlier shift to bird pollination in the NW. The distinctive staminal lever in Salvia is a morphologically diverse structure that has evolved in concert with both the corolla and style, under different pollinator pressures, and in contingent fashion.


Assuntos
Evolução Biológica , Flores/anatomia & histologia , Polinização , Salvia/genética , Animais , Abelhas , Aves , Salvia/anatomia & histologia
6.
Am J Bot ; 106(4): 573-597, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30986330

RESUMO

PREMISE OF THE STUDY: A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia. METHODS: A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared. KEY RESULTS: A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade. CONCLUSIONS: Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.


Assuntos
Ecossistema , Especiação Genética , Filogenia , Polinização , Salvia , Animais , Abelhas , Aves , Filogeografia
7.
Mol Ecol ; 28(8): 2046-2061, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30614129

RESUMO

A proactive approach to conservation must be predictive, anticipating how habitats will change and which species are likely to decline or prosper. We use composite species distribution modelling to identify suitable habitats for 18 members of the North American Atlantic Coastal Plain Flora (ACPF) since the Last Glacial Maximum and project these into the future. We then use Scirpus longii (Cyperaceae), a globally imperiled ACPF sedge with many of the characteristics of extinction vulnerability, as a case study. We integrate phylogeographical and population genetic analyses and species distribution modelling to develop a broad view of its current condition and prognosis for conservation. We use genotyping-by-sequencing to characterize the genomes of 142 S. longii individuals from 20 populations distributed throughout its range (New Jersey to Nova Scotia). We measure the distribution of genetic diversity in the species and reconstruct its phylogeographical history using the snapp and rase models. Extant populations of S. longii originated from a single refugium south of the Laurentide ice sheet around 25 ka. The genetic diversity of S. longii is exceedingly low, populations exhibit little genetic structure and the species is slightly inbred. Projected climate scenarios indicate that nearly half of extant populations of S. longii will be exposed to unsuitable climate by 2070. Similar changes in suitable habitat will occur for many other northern ACPF species-centres of diversity will shift northward and Nova Scotia may become the last refuges for those species not extinguished.


Assuntos
Mudança Climática , Cyperaceae/genética , Genética Populacional , Filogeografia , Cyperaceae/crescimento & desenvolvimento , Ecossistema , Variação Genética/genética , Genótipo , Haplótipos/genética , Repetições de Microssatélites/genética , Análise de Sequência de DNA
8.
Am J Bot ; 105(11): 1938-1950, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30408151

RESUMO

PREMISE OF THE STUDY: We used spatial phylogenetics to analyze the assembly of the Wisconsin flora, linking processes of dispersal and niche evolution to spatial patterns of floristic and phylogenetic diversity and testing whether phylogenetic niche conservatism can account for these patterns. METHODS: We used digitized records and a new molecular phylogeny for 93% of vascular plants in Wisconsin to estimate spatial variation in species richness and phylogenetic α and ß diversity in a native flora shaped mainly by postglacial dispersal and response to environmental gradients. We developed distribution models for all species and used these to infer fine-scale variation in potential diversity, phylogenetic distance, and interspecific range overlaps. We identified 11 bioregions based on floristic composition, mapped areas of neo- and paleo-endemism to establish new conservation priorities and predict how community-assembly patterns should shift with climatic change. KEY RESULTS: Spatial phylogenetic turnover most strongly reflects differences in temperature and spatial distance. For all vascular plants, assemblages shift from phylogenetically clustered to overdispersed northward, contrary to most other studies. This pattern is lost for angiosperms alone, illustrating the importance of phylogenetic scale. CONCLUSIONS: Species ranges and assemblage composition appear driven primarily by phylogenetic niche conservatism. Closely related species are ecologically similar and occupy similar territories. The average level and geographic structure of plant phylogenetic diversity within Wisconsin are expected to greatly decline over the next half century, while potential species richness will increase throughout the state. Our methods can be applied to allochthonous communities throughout the world.


Assuntos
Evolução Biológica , Ecossistema , Traqueófitas/genética , Mudança Climática , Previsões , Filogeografia , Wisconsin
9.
Am J Bot ; 105(3): 463-469, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29574686

RESUMO

PREMISE OF THE STUDY: Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family-level phylogeny estimated using the plastid genome. METHODS: We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS: Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At-α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At-ß event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS: We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole-genome sequencing projects.


Assuntos
Evolução Biológica , Resistência à Doença/genética , Genes de Plantas , Genomas de Plastídeos , Magnoliopsida/genética , Filogenia , Poliploidia , Brassicaceae/química , Brassicaceae/genética , Núcleo Celular , Evolução Molecular , Magnoliopsida/química , Plastídeos , Especificidade da Espécie
10.
Mol Phylogenet Evol ; 122: 59-79, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29410353

RESUMO

Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one-third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points. Our results corroborate previous studies and also suggest several new but poorly supported relationships. Newly suggested relationships are: (1) holoparasitic Mitrastemonaceae is sister to Lecythidaceae, (2) the clade formed by Mitrastemonaceae + Lecythidaceae is sister to Ericales excluding balsaminoids, (3) Theaceae is sister to the styracoids + sarracenioids + ericoids, and (4) subfamilial relationships with Ericaceae suggest that Arbutoideae is sister to Monotropoideae and Pyroloideae is sister to all subfamilies excluding Arbutoideae, Enkianthoideae, and Monotropoideae. Our results indicate Ericales began to diversify 110 Mya, within Indo-Malaysia and the Neotropics, with exchange between the two areas and expansion out of Indo-Malaysia becoming an important area in shaping the extant diversity of many families. Rapid cladogenesis occurred along the backbone of the order between 104 and 106 Mya. Jump dispersal is important within the order in the last 30 My, but vicariance is the most important cladogenetic driver of disjunctions at deeper levels of the phylogeny. We detect between 69 and 81 shifts in speciation rate throughout the order, the vast majority of which occurred within the last 30 My. We propose that range shifting may be responsible for older shifts in speciation rate, but more recent shifts may be better explained by morphological innovation.


Assuntos
Biodiversidade , Magnoliopsida/classificação , Filogenia , Animais , Cloroplastos/genética , Extremo Oriente , Fósseis/história , Especiação Genética , História Antiga , Magnoliopsida/genética , Mitocôndrias/genética , Filogeografia/história , Ribossomos/genética
11.
PLoS One ; 12(12): e0187228, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29211730

RESUMO

The study of pollen morphology has historically allowed evolutionary biologists to assess phylogenetic relationships among Angiosperms, as well as to better understand the fossil record. During this process, pollen has mainly been studied by discretizing some of its main characteristics such as size, shape, and exine ornamentation. One large plant clade in which pollen has been used this way for phylogenetic inference and character mapping is the order Myrtales, composed by the small families Alzateaceae, Crypteroniaceae, and Penaeaceae (collectively the "CAP clade"), as well as the large families Combretaceae, Lythraceae, Melastomataceae, Myrtaceae, Onagraceae and Vochysiaceae. In this study, we present a novel way to study pollen evolution by using quantitative size and shape variables. We use morphometric and morphospace methods to evaluate pollen change in the order Myrtales using a time-calibrated, supermatrix phylogeny. We then test for conservatism, divergence, and morphological convergence of pollen and for correlation between the latitudinal gradient and pollen size and shape. To obtain an estimate of shape, Myrtales pollen images were extracted from the literature, and their outlines analyzed using elliptic Fourier methods. Shape and size variables were then analyzed in a phylogenetic framework under an Ornstein-Uhlenbeck process to test for shifts in size and shape during the evolutionary history of Myrtales. Few shifts in Myrtales pollen morphology were found which indicates morphological conservatism. Heterocolpate, small pollen is ancestral with largest pollen in Onagraceae. Convergent shifts in shape but not size occurred in Myrtaceae and Onagraceae and are correlated to shifts in latitude and biogeography. A quantitative approach was applied for the first time to examine pollen evolution across a large time scale. Using phylogenetic based morphometrics and an OU process, hypotheses of pollen size and shape were tested across Myrtales. Convergent pollen shifts and position in the latitudinal gradient support the selective role of harmomegathy, the mechanism by which pollen grains accommodate their volume in response to water loss.


Assuntos
Myrtaceae/fisiologia , Filogenia , Pólen , Myrtaceae/classificação , Myrtaceae/genética
12.
Am J Bot ; 104(11): 1695-1707, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-29158343

RESUMO

PREMISE OF THE STUDY: The subtribe Menthinae (Lamiaceae), with 35 genera and 750 species, is among the largest and most economically important subtribes within the mint family. Most genera of Menthinae are found exclusively in the New World, where the group has a virtually continuous distribution ranging from temperate North America to southern South America. In this study, we explored the presence, timing, and origin of amphitropical disjuncts within Menthinae. METHODS: Our analyses were based on a data set consisting of 89 taxa and the nuclear ribosomal DNA markers ITS and ETS. Phylogenetic relationships were determined under maximum likelihood and Bayesian criteria, divergence times were estimated with the program BEAST, and ancestral range estimated with BioGeoBEARS. KEY RESULTS: A North Atlantic Land Bridge migration event at about 10.6 Ma is inferred from western Eurasia to North America. New World Menthinae spread rapidly across North America, and then into Central and South America. Several of the large speciose genera are not monophyletic with nuclear rDNA, a finding mirrored with previous chloroplast DNA results. Three amphitropical disjunctions involving North and southern South America clades, one including a southeastern South American clade with several genera, were inferred to have occurred within the past 5 Myr. CONCLUSIONS: Although three New World Menthinae genera occur in both North and South America, none exhibit an amphitropical disjunction. However, three clades exhibit amphitropical disjunctions, all dating to the early Pliocene, and all involve jump dispersals to either southeastern or southwestern South America from southeastern North America.


Assuntos
Lamiaceae/fisiologia , Dispersão Vegetal , Teorema de Bayes , DNA de Plantas/química , DNA de Plantas/genética , Lamiaceae/genética , América do Norte , Filogeografia , Análise de Sequência de DNA , América do Sul
13.
Mol Phylogenet Evol ; 99: 204-224, 2016 06.
Artigo em Inglês | MEDLINE | ID: mdl-26993763

RESUMO

Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana. This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000bp) across 151 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis, based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5Mya (HPD=75.6-62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4Mya (HPD=46.6-40.3) and Arabidopsis separated from close congeners circa 10.4Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38Mya at the crown of Resedaceae+Stixis clade, and (3) 21Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae.


Assuntos
Brassicaceae/classificação , Fósseis , África , América , Arabidopsis/classificação , Arabidopsis/genética , Ásia , Austrália , Teorema de Bayes , Biodiversidade , Brassicaceae/genética , DNA Mitocondrial/isolamento & purificação , DNA Mitocondrial/metabolismo , DNA de Plantas/isolamento & purificação , DNA de Plantas/metabolismo , Europa (Continente) , Mitocôndrias/genética , Filogenia , Filogeografia , Plastídeos/genética
14.
Am J Bot ; 103(4): 652-62, 2016 04.
Artigo em Inglês | MEDLINE | ID: mdl-26944353

RESUMO

PREMISE OF THE STUDY: The alternation of generations life cycle represents a key feature of land-plant evolution and has resulted in a diverse array of sporophyte forms and modifications in all groups of land plants. We test the hypothesis that evolution of sporangium (capsule) shape of the mosses-the second most diverse land-plant lineage-has been driven by differing physiological demands of life in diverse habitats. This study provides an important conceptual framework for analyzing the evolution of a single, homologous character in a continuous framework across a deep expanse of time, across all branches of the tree of life. METHODS: We reconstruct ancestral sporangium shape and ancestral habitat on the largest phylogeny of mosses to date, and use phylogenetic generalized least squares regression to test the association between habitat and sporangium shape. In addition, we examine the association between shifts in sporangium shape and species diversification. RESULTS: We demonstrate that sporangium shape is convergent, under natural selection, and associated with habitat type, and that many shifts in speciation rate are associated with shifts in sporangium shape. CONCLUSIONS: Our results suggest that natural selection in different microhabitats results in the diversity of sporangium shape found in mosses, and that many increasing shifts in speciation rate result in changes in sporangium shape across their 480 million year history. Our framework provides a way to examine if diversification shifts in other land plants are also associated with massive changes in sporophyte form, among other morphological traits.


Assuntos
Evolução Biológica , Briófitas/anatomia & histologia , Embriófitas/fisiologia , Teorema de Bayes , Biodiversidade , Filogenia , Análise de Componente Principal , Especificidade da Espécie
15.
Mol Phylogenet Evol ; 95: 116-36, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26585030

RESUMO

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. Divergence time estimates suggest Myrtales diverged from Geraniales ∼124Mya during the Aptian of the Early Cretaceous. The crown date for Myrtales is estimated at ∼116Mya (Albian-Aptian). BioGeoBEARS showed significant improvement in the likelihood score when the "jump dispersal" parameter was added. South America and/or Africa are implicated as important ancestral areas in all deeper nodes. BAMM analyses indicate that the best configuration included three significant shifts in diversification rates within Myrtales: near the crown of Melastomataceae (∼67-64Mya), along the stem of subfamily Myrtoideae (Myrtaceae; ∼75Mya), and along the stem of tribe Combreteae (Combretaceae; ∼50-45Mya). Issues with conducting diversification analyses more generally are examined in the context of scale, taxon sampling, and larger sets of phylogenetic trees.


Assuntos
Evolução Molecular , Especiação Genética , Magnoliopsida/classificação , África , Sequência de Bases , Fósseis , Lythraceae/classificação , Lythraceae/genética , Magnoliopsida/genética , Melastomataceae/classificação , Melastomataceae/genética , Myrtaceae/classificação , Myrtaceae/genética , Onagraceae/classificação , Onagraceae/genética , Filogenia , Filogeografia , América do Sul
16.
Mol Phylogenet Evol ; 95: 183-95, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26702956

RESUMO

The role of geography and ecology in speciation are often discussed in the context of phylogenetic niche conservatism (PNC), the propensity of lineages to retain ancestral niche related traits. However, a recent paradigm shift focuses instead on measuring divergence of these traits in conjunction with patterns of speciation. Under this framework, we analyzed the diversification of North America's third most diverse family, Cyperaceae ("sedges"), using a modified Parsimony Analysis of Endemicity approach to identify floristic regions and ordination statistics to quantify species distribution in a continuous manner. Utilizing over 200,000 georeferenced specimens, we characterized the geographical distribution and climatic and edaphic niche space occupied by each species. We constructed a supermatrix phylogeny of the North American sedge flora, aided in part by the sequencing of all sedges of Wisconsin, and employed a multifaceted approach to assess the role of geographical and ecological divergence on lineage diversification. In addition to measuring phylogenetic signal for these traits, we also measured pairwise phylogenetic distance of species within floristic regions, calculated rates of speciation, and tested for correlations of speciation rate to tempo of geographical and ecological evolution. Our analyses consistently show that evolutionarily related species tend to be geographically unrelated. Rates of geographical and ecological diversification are closely linked to tempo of speciation, and exploration of geographical place coincides with divergence in ecological niche space. We highlight the benefits of treating geography in a continuous manner, and stress the importance of employing a diverse suite of analytical approaches in testing hypotheses regarding the evolution of range and niche.


Assuntos
Carex (Planta)/classificação , Carex (Planta)/genética , Evolução Molecular , Especiação Genética , Cyperaceae/classificação , Cyperaceae/genética , Ecossistema , Geografia , América do Norte , Fenótipo , Filogenia , Filogeografia , Estados Unidos
17.
Mol Phylogenet Evol ; 71: 55-78, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24513576

RESUMO

We present an integrative model predicting associations among epiphytism, the tank habit, entangling seeds, C3 vs. CAM photosynthesis, avian pollinators, life in fertile, moist montane habitats, and net rates of species diversification in the monocot family Bromeliaceae. We test these predictions by relating evolutionary shifts in form, physiology, and ecology to time and ancestral distributions, quantifying patterns of correlated and contingent evolution among pairs of traits and analyzing the apparent impact of individual traits on rates of net species diversification and geographic expansion beyond the ancestral Guayana Shield. All predicted patterns of correlated evolution were significant, and the temporal and spatial associations of phenotypic shifts with orogenies generally accorded with predictions. Net rates of species diversification were most closely coupled to life in fertile, moist, geographically extensive cordilleras, with additional significant ties to epiphytism, avian pollination, and the tank habit. The highest rates of net diversification were seen in the bromelioid tank-epiphytic clade (D(crown) = 1.05 My⁻¹), associated primarily with the Serra do Mar and nearby ranges of coastal Brazil, and in the core tillandsioids (D(crown) = 0.67 My⁻¹), associated primarily with the Andes and Central America. Six large-scale adaptive radiations and accompanying pulses of speciation account for 86% of total species richness in the family. This study is among the first to test a priori hypotheses about the relationships among phylogeny, phenotypic evolution, geographic spread, and net species diversification, and to argue for causality to flow from functional diversity to spatial expansion to species diversity.


Assuntos
Adaptação Biológica , Bromeliaceae/genética , Filogenia , Biodiversidade , América Latina , Sudoeste dos Estados Unidos
18.
Am J Bot ; 100(10): 2023-39, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-24091784

RESUMO

PREMISE OF THE STUDY: Sparganium (Typhaceae) is a genus of aquatic monocots containing ±14 species, with flowers aggregated in unisexual, spherical heads, and habit ranging from floating to emergent. Sparganium presents an opportunity to investigate diversification, character evolution, and biogeographical relationships in a widespread temperate genus of aquatic monocots. We present a fossil-calibrated, molecular phylogeny of Sparganium based on analysis of two chloroplast and two nuclear markers. Within this framework, we examine character evolution in both habit and stigma number and infer the ancestral area and biogeographic history of the genus. • METHODS: Sequence data from two cpDNA and two nDNA markers were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. We used the program BEAST to simultaneously estimate phylogeny and divergence times, S-DIVA and Lagrange for biogeographical reconstruction, and BayesTraits to examine locule number and habit evolution. • KEY RESULTS: Two major clades were recovered with strong support: one composed of S. erectum and S. eurycarpum; and the other containing all remaining Sparganium. We realigned the subgenera to conform to these clades. Divergence time analysis suggests a Miocene crown origin but Pliocene diversification. Importantly, the floating-leaved habit has arisen multiple times in the genus, from emergent ancestors-contrary to past hypotheses. • CONCLUSIONS: Cooling trends during the Tertiary are correlated with the isolation of temperate Eurasian and North American taxa. Vicariance, long-distance dispersal, and habitat specialization are proposed as mechanisms for Sparganium diversification.


Assuntos
Organismos Aquáticos/classificação , Biodiversidade , Evolução Biológica , Filogenia , Filogeografia , Typhaceae/classificação , Organismos Aquáticos/fisiologia , Núcleo Celular/genética , DNA de Cloroplastos/genética , Flores/fisiologia , Funções Verossimilhança , Reprodução , Análise de Sequência de DNA , Fatores de Tempo , Typhaceae/fisiologia
19.
Am J Bot ; 100(10): 2102-11, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-24107582

RESUMO

PREMISE OF STUDY: A monophyletic group composed of five genera of the Cleomaceae represents an intriguing lineage with outstanding taxonomic and evolutionary questions. Generic boundaries are poorly defined, and historical hypotheses regarding the evolution of fruit type and phylogenetic relationships provide testable questions. This is the first detailed phylogenetic investigation of all 22 species in this group. We use this phylogenetic framework to assess generic monophyly and test Iltis's evolutionary "reduction series" hypothesis regarding phylogeny and fruit type/seed number. • METHODS: Maximum likelihood and Bayesian analyses of four plastid intergenic spacer region sequences (rpl32-trnL, trnQ-rps16, ycf1-rps15, and psbA-trnH) and one nuclear (ITS) region were used to reconstruct phylogenetic relationships among the NA cleomoid species. Stochastic mapping and ancestral-state reconstruction were used to study the evolution of fruit type. • KEY RESULTS: Both analyses recovered nearly identical phylogenies. Three of the currently recognized genera (Wislizenia, Carsonia, and Oxystylis) are monophyletic while two (Cleomella and Peritoma) are para- or polyphyletic. There was a single origin of the two-seeded schizocarp in the ancestor of the Oxystylis-Wislizenia clade and a secondary derivation of elongated capsule-type fruits in Peritoma from a truncated capsule state in Cleomella. • CONCLUSIONS: Our well-resolved phylogeny supports most of the current species circumscriptions but not current generic circumscriptions. Additionally, our results are inconsistent with Iltis's hypothesis of species with elongated many-seed fruits giving rise to species with truncated few-seeded fruits. Instead, we find support for the reversion to elongated multiseeded fruits from a truncate few-seeded ancestor in Peritoma.


Assuntos
Magnoliopsida/classificação , Modelos Biológicos , Filogenia , Cromossomos de Plantas/genética , Funções Verossimilhança , América do Norte , Probabilidade
20.
PLoS One ; 8(5): e62566, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23658747

RESUMO

Previous studies based on DNA restriction-site and sequence variation have shown that the Hawaiian lobeliads are monophyletic and that the two largest genera, Cyanea and Clermontia, diverged from each other ca. 9.7 Mya. Sequence divergence among species of Clermontia is quite limited, however, and extensive hybridization is suspected, which has interfered with production of a well-resolved molecular phylogeny for the genus. Clermontia is of considerable interest because several species posses petal-like sepals, raising the question of whether such a homeotic mutation has arisen once or several times. In addition, morphological and molecular studies have implied different patterns of inter-island dispersal within the genus. Here we use nuclear ISSRs (inter-simple sequence repeat polymorphisms) and five plastid non-coding sequences to derive biparental and maternal phylogenies for Clermontia. Our findings imply that (1) Clermontia is not monophyletic, with Cl. pyrularia nested within Cyanea and apparently an intergeneric hybrid; (2) the earliest divergent clades within Clermontia are native to Kauài, then Òahu, then Maui, supporting the progression rule of dispersal down the chain toward progressively younger islands, although that rule is violated in later-evolving taxa in the ISSR tree; (3) almost no sequence divergence among several Clermontia species in 4.5 kb of rapidly evolving plastid DNA; (4) several apparent cases of hybridization/introgression or incomplete lineage sorting (i.e., Cl. oblongifolia, peleana, persicifolia, pyrularia, samuelii, tuberculata), based on extensive conflict between the ISSR and plastid phylogenies; and (5) two origins and two losses of petaloid sepals, or--perhaps more plausibly--a single origin and two losses of this homeotic mutation, with its introgression into Cl. persicifolia. Our phylogenies are better resolved and geographically more informative than others based on ITS and 5S-NTS sequences and nuclear SNPs, but agree with them in supporting Clermontia's origin on Kauài or some older island and dispersal down the chain subsequently.


Assuntos
Campanulaceae/fisiologia , Evolução Molecular , Repetições de Microssatélites/genética , Filogenia , Dispersão Vegetal , Plastídeos/genética , Polimorfismo Genético , Sequência de Bases , Campanulaceae/citologia , Campanulaceae/genética , Núcleo Celular/genética , DNA Intergênico/genética , DNA de Plantas/genética , Flores/genética , Ilhas , Mutação , Filogeografia
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