Stefanie M. Ickert-Bond

Transcriptome Sequences Resolve Deep Relationships of the Grape Family

Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.

Phylogenetic Relationships in Ephedra (Gnetales): Evidence from Nuclear and Chloroplast DNA Sequence Data

Abstract Sequences from the nuclear ribosomal internal transcribed spacer region 1 (nrDNA ITS1) and the plastid rps4 gene from the genus Ephedra (Ephedraceae, Gnetales) were obtained in order to infer phylogenetic relationships, character evolution, and historical biogeography in the genus. Within Ephedra the length of the nrDNA ITS1 varied from 1,081 to 1,143 basepairs (bp), in contrast to dramatically shorter lengths in the outgroups (Gnetum, Welwitschia, and Pinus). The rps4 locus varied in length from 645 to 661 bp in the same set of taxa. Both parsimony and maximum likelihood analyses of these sequences resulted in a well-resolved phylogeny that supports the monophyly of Ephedra, but not its subdivision into the traditional sections Ephedra, Asarca, and Alatae. The resulting phylogeny also indicates a derivation of the New World clade from among the Old World taxa. Among the Old World species three highly-supported monophyletic groups are recognized that are highly concordant with morphological evidence. The New World clade includes two main subclades of North and South American species that are strongly supported, while the position of two, mostly Mexican species E. pedunculata and E. compacta remains unresolved. Character reconstruction of ovulate strobilus types in Ephedra indicates that fleshy bracts are ancestral, with shifts to dry, winged bracts having occurred multiple times. Low levels of sequence divergence within the North American clade suggest either recent and rapid ecological radiation or highly conservative ribosomal DNA evolution within the clade.

A fossil-calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America

Abstract  Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions (amphitropical range). Great heterogeneity in the substitution rates of Gnetales (Ephedra, Gnetum, and Welwitschia) has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species (and 7736 aligned nucleotides) to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil‐based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long‐distance dispersal, but finer‐scale studies are needed to test this hypothesis.

Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae)

Eastern North American plant biogeography has traditionally focused on two primary issues: (i) the location of temperate Pleistocene refugia and their proximity to the southern margin of the ice sheet during the last glacial maximum, and (ii) the origin of the temperate element of northern Latin America. While numerous population genetic and phylogeographical studies have focused on the first issue, few (if any) have considered the second. We addressed these issues by surveying 117 individuals from 24 populations of Liquidambar styraciflua (American sweetgum; Altingiaceae) across the southeastern USA, eastern Mexico, and Guatemala, using more than 2200 bp of chloroplast DNA sequence data. To specifically address the issue of timing, we estimated intraspecific divergence times on the basis of multiple fossil‐based calibration points, using taxa from Altingiaceae (Liquidambar and Altingia) and Hammamelidaceae (Hamamelis) as outgroups. More than half of the sampled localities exhibited multiple haplotypes. Remarkably, the greatest variation was observed within the USA, with Mexico and Guatemala sharing widespread haplotypes with Texas, Mississippi, Kentucky, Ohio, and northern Virginia. This lack of differentiation suggests shared ancestral polymorphisms, and that the genetic signal we observed is older than the disjunction itself. Our data provide support for previously proposed hypotheses of Pleistocene refugia in peninsular Florida and along the eastern Atlantic, but also for deeper divergences (~8 million years ago) within the USA. These patterns reflect a dynamic biogeographical history for eastern North American trees, and emphasize the importance of the inclusion of a temporal component in any phylogeographical study.

Intercontinental disjunctions between eastern Asia and western North America in vascular plants highlight the biogeographic importance of the Bering land bridge from late Cretaceous to Neogene

This review shows a close biogeographic connection between eastern Asia and western North America from the late Cretaceous to the late Neogene in major lineages of vascular plants (flowering plants, gymnosperms, ferns and lycophytes). Of the eastern Asian–North American disjuncts, conifers exhibit a high proportion of disjuncts between eastern Asia and western North America. Several lineages of ferns also show a recent disjunct pattern in the two areas. In flowering plants, the pattern is commonly shown in temperate elements between northeastern Asia and northwestern North America, as well as elements of the relict boreotropical and Neogene mesophytic and coniferous floras. The many cases of intercontinental biogeographic disjunctions between eastern Asia and western North America in plants supported by recent phylogenetic analyses highlight the importance of the Bering land bridge and/or the plant migrations across the Beringian region from the late Cretaceous to the late Neogene, especially during the Miocene. The Beringian region has permitted the filtering and migration of certain plant taxa since the Pliocene after the opening of the Bering Strait, as many conspecific taxa or closely related species occur on both sides of Beringia.

Molecular phylogeny of Cissus L. of Vitaceae (the grape family) and evolution of its pantropical intercontinental disjunctions

Pantropical intercontinental disjunct distribution is a major biogeographic pattern in plants, and has been explained mainly by boreotropical migration via the North Atlantic land bridges (NALB) and transoceanic long-distance dispersal (LDD), and sometimes by vicariance. However, well-resolved phylogenies of pantropical clades are still relatively few. Cissus is the largest genus of the grape family Vitaceae and shows a pantropical intercontinental disjunction with its 300 species distributed in all major tropical regions. This study constructed the phylogenetic relationships and biogeographic diversification history of Cissus, employing five plastid markers (rps16, trnL-F, atpB-rbcL, trnH-psbA and trnC-petN). The results confirmed that Cissus polyphyletic, consisting of three main clades: the core Cissus, the Cissus striata complex, and the Australian-Neotropical disjunct Cissus antarctica -C. trianae clade. The latter two clades need to be removed from Cissus to maintain the monophyly of the genus. The core Cissus is inferred to have originated in Africa and is estimated to have diverged from its relatives in Vitaceae in the late Cretaceous. It diversified in Africa into several main lineages in the late Paleocene to the early Eocene, colonized Asia at least three times in the Miocene, and the Neotropics in the middle Eocene. The NALB seems the most plausible route for the core Cissus migration from Africa to the Neotropics in the middle Eocene. Three African-Asian and two Neotropical-Australian disjunctions in Cissus s.l. are estimated to have originated in the Miocene and may be best explained by LDD.

Anatomically preserved Liquidambar (Altingiaceae) from the middle Miocene of Yakima Canyon, Washington state, USA, and its biogeographic implications

Liquidambar changii Pigg, Ickert-Bond & Wen sp. nov. (Altingiaceae) is established for anatomically preserved, middle Miocene infructescences from Yakima Canyon, Washington, USA. Specimens are spherical, ∼2.5 cm in diameter, and have ∼25-30 tightly packed, bilocular fruits per head. Fruits are 3.4-4.7 mm wide × 2.6-3.5 mm long and wedge shaped, fused at the base, and free distally. Each locule contains 1-2 mature, elongate seeds proximally and 5-9 aborted seeds of more irregular shape distally. Mature seeds are 1.5 mm long × 1.2 mm wide, elongate, and triangular transversely, with a slight flange. Seeds have a seed coat for which three zones can be well defined, a uniseriate outer palisade layer, a middle region of isodiametric cells comprising most of the integument, and a uniseriate inner layer of tangentially elongate cells lining the embryo cavity. Liquidambar changii is most similar to the eastern Asian L. acalycina H.-T. Chang on features of infructescence, fruit, and seed morphology and quite unlike the North American L. styraciflua L. and other species. Such a close relationship between these two species supports a Beringian biogeographic track between eastern Asia and western North America during the Miocene. Previous phylogenetic and allozyme analysis of modern Liquidambar demonstrates a close relationship between North American-western Asian taxa and suggests a North Atlantic biogeographic track in the middle Miocene. Together, these biogeographic tracks underscore the complexity of the biogeographic history of the Altingiaceae in the Northern Hemisphere throughout the Neogene.

Collections-based systematics: Opportunities and outlook for 2050

Systematic biology is a discipline rooted in collections. These collections play important roles in research and conservation and are integral to our efforts to educate society about biodiversity and conservation. Collections provide an invaluable record of the distribution of organisms throughout the world and through recent and geological time, and they are the only direct documentation of the biological, physical, and cultural diversity of the planet: past, present, and future. Recent developments in bioinformatics and cyberinfrastructure are transforming systematics by opening up new opportunities and as a result major digitization efforts have increasingly made available large amounts of biodiversity data. The collections‐based systematics community needs to train the next‐generation of systematists with integrative skills, address grand questions about biodiversity at different scales, develop a community‐wide cyberinfrastructure, effectively disseminate systematic data to biologists and the public, and proactively educate the public and policy makers on the importance of systematics and collections in the biodiversity crisis of the Anthropocene. Specifically, we call for a new global Biodiversity CyberBank, comparable to GenBank for genetic data, to be the repository of all biodiversity data, as well as a World Organization of Systematic Biology to lead major initiatives of the field. We also outline a new workflow for taxonomic monographs, which utilizes both the traditional strengths of synthesizing diverse collections‐based taxonomic data and the capacity of online resources and bioinformatics tools.

Biogeography: Where do we go from here?

Biogeography is a multidisciplinary science concerned with how and why organisms are distributed as they are on Earth. It links fields such as systematics, ecology, paleontology, and climatology, and occupies a central position in evolutionary biology, being fundamental to the study of processes such as speciation and adaptive radiation. Here we provide a brief overview of some particularly dynamic areas of inquiry and offer some perspectives on future directions for the field. We hope that some historical debates, such as those over the importance of dispersal, or the validity of molecular dating, are finally being put to rest. Over the last decade, biogeography has become increasingly integrative, and has benefited from advances in statistical methods for inferring geographic range dynamics in a phylogenetic context, molecular estimation of lineage divergence times, and modeling lineage birth and death. These are enabling greater insights into patterns of organismal diversification in time and space. In the next decade, analytical challenges are emerging on several fronts. For example, phylogenies are increasing in size and taxonomic breadth and new sequencing technologies enabling phylogenetic and phylogeographic datasets are increasingly genomic in depth. In addition, geographic occurrence data are accumulating in online repositories, yet tools for data mining and synthetic analysis are lacking for comparative multi-lineage studies. Biogeography is thus entering an era characterized by phylogenomic datasets, increasingly comprehensive sampling of clades, and interdisciplinary synthesis. We anticipate continued progress in our understanding of biodiversity patterns at regional and global scales, but this will likely require greater collaboration with specialists in bioinformatics and computational science. Finally, it is clear that biogeography has an increasingly important role to play in the discovery and conservation of biodiversity. Lessons learned from biogeographic studies of islands are being applied to better understand extinction dynamics as continental ecosystems become more fragmented, and phylogeography and ecological niche modeling offer innovative paths toward the discovery of previously unknown species distributions and priority areas for conservation. The future of biogeography is bright and filled with exciting challenges and opportunities.

Diversification in North American arid lands: Niche conservatism, divergence and expansion of habitat explain speciation in the genus Ephedra

A lineage of 12 arid land shrubby species in the gymnosperm genus Ephedra (Gnetales) from North America is used to evaluate the influence of climate on speciation. With a long evolutionary history, and a well documented fossil record this lineage is an ideal model for understanding the process of speciation under a niche conservatism scenario. Using seven DNA molecular markers, Bayesian inference is carried out to uncover sister species and to estimate time of divergence of the lineages. Ecological niche models are generated for four parapatric and sympatric sister species and two analyses of niche evolution are performed, one based on ecological niche models and another using raw data and multivariate analysis. As previous analyses suggest, the diversification of North America Ephedra species may be the result of a recent secondary radiation. Both parapatric and sympatric species diverged mostly in a scenario of climatic niche conservatism. However, we also found strong evidence for niche divergence for one of the sister species pairs (E. californica-E. trifurca). Moreover, the multivariate analysis found environmental differences for some variables between sister species. The estimated divergence time of three pairs of sister species distributed in southwestern North America (E. cutleri-E. aspera, E. californica-E. trifurca and E. torreyana-E. viridis) is inferred to have occurred in the Late Miocene to Pliocene and for the sister species pair E. antisyphilitica-E. coryi distributed in the southern United States and northeastern Mexico, it was inferred from the Pliocene to Pleistocene. The orogenetic and climatic changes documented for these regions related to expansion of arid lands, may have contributed to the diversification in North American Ephedra, rather than adaptations to new climatic conditions.