Charles D. Bell

Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms

Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes (≈42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence of Ceratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae + magnoliids as sister to a well supported clade of monocots + (Ceratophyllum + eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 ± 4.8 and 140.3 ± 4.8 Mya.

Angiosperm phylogeny: 17 genes, 640 taxa

PREMISE OF THE STUDY Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. METHODS We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). KEY RESULTS Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. CONCLUSIONS Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

Although Pentapetalae (comprising all core eudicots except Gunnerales) include ≈70% of all angiosperms, the origin of and relationships among the major lineages of this clade have remained largely unresolved. Phylogenetic analyses of 83 protein-coding and rRNA genes from the plastid genome for 86 species of seed plants, including new sequences from 25 eudicots, indicate that soon after its origin, Pentapetalae diverged into three clades: (i) a “superrosid” clade consisting of Rosidae, Vitaceae, and Saxifragales; (ii) a “superasterid” clade consisting of Berberidopsidales, Santalales, Caryophyllales, and Asteridae; and (iii) Dilleniaceae. Maximum-likelihood analyses support the position of Dilleniaceae as sister to superrosids, but topology tests did not reject alternative positions of Dilleniaceae as sister to Asteridae or all remaining Pentapetalae. Molecular dating analyses suggest that the major lineages within both superrosids and superasterids arose in as little as 5 million years. This phylogenetic hypothesis provides a crucial historical framework for future studies aimed at elucidating the underlying causes of the morphological and species diversity in Pentapetalae.

Rosid radiation and the rapid rise of angiosperm-dominated forests

The rosid clade (70,000 species) contains more than one-fourth of all angiosperm species and includes most lineages of extant temperate and tropical forest trees. Despite progress in elucidating relationships within the angiosperms, rosids remain the largest poorly resolved major clade; deep relationships within the rosids are particularly enigmatic. Based on parsimony and maximum likelihood (ML) analyses of separate and combined 12-gene (10 plastid genes, 2 nuclear; >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening spacers; >25,000 bp) datasets for >100 rosid species, we provide a greatly improved understanding of rosid phylogeny. Vitaceae are sister to all other rosids, which in turn form 2 large clades, each with a ML bootstrap value of 100%: (i) eurosids I (Fabidae) include the nitrogen-fixing clade, Celastrales, Huaceae, Zygophyllales, Malpighiales, and Oxalidales; and (ii) eurosids II (Malvidae) include Tapisciaceae, Brassicales, Malvales, Sapindales, Geraniales, Myrtales, Crossosomatales, and Picramniaceae. The rosid clade diversified rapidly into these major lineages, possibly over a period of <15 million years, and perhaps in as little as 4 to 5 million years. The timing of the inferred rapid radiation of rosids [108 to 91 million years ago (Mya) and 107–83 Mya for Fabidae and Malvidae, respectively] corresponds with the rapid rise of angiosperm-dominated forests and the concomitant diversification of other clades that inhabit these forests, including amphibians, ants, placental mammals, and ferns.

Laurasian migration explains Gondwanan disjunctions: Evidence from Malpighiaceae

Explanations for biogeographic disjunctions involving South America and Africa typically invoke vicariance of western Gondwanan biotas or long distance dispersal. These hypotheses are problematical because many groups originated and diversified well after the last known connection between Africa and South America (≈105 million years ago), and it is unlikely that “sweepstakes” dispersal accounts for many of these disjunctions. Phylogenetic analyses of the angiosperm clade Malpighiaceae, combined with fossil evidence and molecular divergence-time estimates, suggest an alternative hypothesis to account for such distributions. We propose that Malpighiaceae originated in northern South America, and that members of several clades repeatedly migrated into North America and subsequently moved via North Atlantic land connections into the Old World during episodes starting in the Eocene, when climates supported tropical forests. This Laurasian migration route may explain many other extant lineages that exhibit western Gondwanan distributions.

Origin and Early Evolution of Angiosperms

Contributions from paleobotany, phylogenetics, genomics, developmental biology, and developmental genetics have yielded tremendous insight into Darwins “abominable mystery”—the origin and rapid diversification of the angiosperms. Analyses of morphological and molecular data reveal a revised “anthophyte clade” consisting of the fossils glossopterids, Pentoxylon, Bennettitales, and Caytonia as sister to angiosperms. Molecular estimates of the age of crown group angiosperms have converged on 140–180 million years ago (Ma), older than the oldest fossils (132 Ma), suggesting that older fossils remain to be discovered. Whether the first angiosperms were forest shrubs (dark‐and‐disturbed hypothesis) or aquatic herbs (wet‐and‐wild hypothesis) remains unclear. The near‐basal phylogenetic position of Nymphaeales (water lilies), which may include the well‐known fossil Archaefructus, certainly indicates that the aquatic habit arose early. After initial, early “experiments,” angiosperms radiated rapidly (≤5 million years [Myr]), yielding the five lineages of Mesangiospermae (magnoliids and Chloranthaceae as sisters to a clade of monocots and eudicots + Ceratophyllaceae). This radiation ultimately produced approximately 97% of all angiosperm species. Updated estimates of divergence times across the angiosperms conducted using nonparametric rate smoothing, with one or multiple fossils, were older than previous reports, whereas estimates using PATHd8 were typically younger. Virtually all angiosperm genomes show evidence of whole‐genome duplication, indicating that polyploidy may have been an important catalyst in angiosperm evolution. Although the flower is the central feature of the angiosperms, its origin and subsequent diversification remain major questions. Variation in spatial expression of floral regulators may control major differences in floral morphology between basal angiosperms and eudicot models.

Phylogenetic Patterns in Northern Hemisphere Plant Geography

Geological and climatological processes that have impacted the biota of the Northern Hemisphere during the Tertiary are expected to yield little resolution when area cladograms are compared without taking the timing of diversification into account. In an attempt to establish a set of appropriate phylogenetic comparisons, we distinguished between a Pacific track involving (minimally) China, Japan, and eastern North America but not Europe, and an Atlantic track involving China, Europe, and eastern North America but not Japan (or, in most cases, western North America). Within the two Atlantic‐track taxa considered here—Liquidambar and Cercis—European and North American species are more closely related to one another than they are to the Asian species. Within a set of five Pacific‐track taxa—Hamamelis, Weigela‐Diervilla, Triosteum, Buckleya, and Torreya—we see all possible relationships involving China, Japan, and eastern North America. Estimates of minimum divergence times between Old World and New World lineages, based on molecular and fossil evidence, differ markedly between the two Atlantic‐track clades. Among the Pacific‐track taxa, we find no correlation between pattern of area relationships and estimated divergence times of the Old World–New World disjuncts. Instead, we see a wide range in the timing of these splitting events among and within phylogenetic patterns. Despite the existence of a variety of patterns, inferred ancestral areas and divergence times can be explained by assuming initial diversification within Asia in a number of lineages, followed by iterative trans‐Beringian dispersion and vicariance.

TESTING THE MUSEUM VERSUS CRADLE TROPICAL BIOLOGICAL DIVERSITY HYPOTHESIS: PHYLOGENY, DIVERSIFICATION, AND ANCESTRAL BIOGEOGRAPHIC RANGE EVOLUTION OF THE ANTS

Ants are one of the most ecologically and numerically dominant group of terrestrial organisms with most species diversity currently found in tropical climates. Several explanations for the disparity of biological diversity in the tropics compared to temperate regions have been proposed including that the tropics may act as a “museum” where older lineages persist through evolutionary time or as a “cradle” where new species continue to be generated. We infer the molecular phylogenetic relationships of 295 ant specimens including members of all 21 extant subfamilies to explore the evolutionary diversification and biogeography of the ants. By constraining the topology and age of the root node while using 45 fossils as minimum constraints, we converge on an age of 139–158 Mya for the modern ants. Further diversification analyses identified 10 periods with a significant change in the tempo of diversification of the ants, although these shifts did not appear to correspond to ancestral biogeographic range shifts. Likelihood‐based historical biogeographic reconstructions suggest that the Neotropics were important in early ant diversification (e.g., Cretaceous). This finding coupled with the extremely high‐current species diversity suggests that the Neotropics have acted as both a museum and cradle for ant diversity.

Dating the Dipsacales: comparing models, genes, and evolutionary implications.

Dipsacales is an asterid angiosperm clade of ca. 1100 species, with most of its lineages occupying temperate regions of the Northern Hemisphere. A recent phylogenetic analysis based on 7593 nucleotides of chloroplast DNA recovered a well-resolved and strongly supported phylogenetic hypothesis, which we use here to estimate divergence times within the group. A molecular clock is strongly rejected, regardless of data partition. We used recently proposed methods that relax the assumption of rate constancy among lineages (local clocks, nonparametric rate smoothing, penalized likelihood, and Bayesian relaxed clock) to estimate the ages of major lineages. Age estimates for Dipsacales varied widely among markers and codon positions, and depended on the fossils used for calibration and method of analysis. Some methods yielded dates for the Dipsacales diversification that appear to be too old (prior to the presumed 125 my [million years] age of eudicots), and others suggested ages that are too young based on well-documented Dipsacales fossils. Concordant penalized likelihood and Bayesian studies imply that Dipsacales originated in the Cretaceous, as did its two major lineages, Adoxaceae and Caprifoliaceae. However, diversification of crown Adoxaceae and Caprifoliaceae mainly occurred in the Tertiary, with the origin of major lineages within these clades mainly occurring during the Eocene. Another round of diversification appears to have occurred in the Miocene. Several radiations, such as Valerianaceae in South America and Dipsacaceae around the Mediterranean, are even more recent. This study demonstrates the wide range of divergence times that can be obtained using different methods and data sets, and cautions against reliance on age estimates based on only a single gene or methodology. Despite this variance, significant conclusions can be made about the timing of Dipsacales evolution.

Phylogeny of Acridocarpus brachylophon (Malpighiaceae) : implications for tertiary tropical floras and Afroasian biogeography

Abstract.— A major tenet of African Tertiary biogeography posits that lowland rainforest dominated much of Africa in the late Cretaceous and was replaced by xeric vegetation as a response to continental uplift and consequent widespread aridification beginning in the late Paleogene. The aridification of Africa is thought to have been a major factor in the extinction of many African humid‐tropical lineages, and in the present‐day disparity of species diversity between Africa and other tropical regions. This primarily geologically based model can be tested with independent phylogenetic evidence from widespread African plant groups containing both humid‐ and xeric‐adapted species. We estimated the phylogeny and lineage divergence times within one such angiosperm group, the acridocarpoid clade (Malpighiaceae), with combined ITS, ndhF, and trnL‐F data from 15 species that encompass the range of morphological and geographic variation within the group. Dispersal‐vicariance analysis and divergence‐time estimates suggest that the basal acridocarpoid divergence occurred between African and Southeast Asian lineages approximately 50 million years ago (mya), perhaps after a southward ancestral retreat from high‐latitude tropical forests in response to intermittent Eocene cooling. Dispersion of Acridocarpus from Africa to Madagascar is inferred between approximately 50 and 35 mya, when lowland humid tropical forest was nearly continuous between these landmasses. A single dispersal event within Acridocarpus is inferred from western Africa to eastern Africa between approximately 23 and 17 mya, coincident with the widespread replacement of humid forests by savannas in eastern Africa. Although the spread of xeric environments resulted in the extinction of many African plant groups, our data suggest that for others it provided an opportunity for further diversification.