Vicki A. Funk

Advances in cladistics

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The value of sampling anomalous taxa in phylogenetic studies: Major clades of the Asteraceae revealed

The largest family of flowering plants Asteraceae (Compositae) is found to contain 12 major lineages rather than five as previously suggested. Five of these lineages heretofore had been circumscribed in tribe Mutisieae (Cichorioideae), a taxon shown by earlier molecular studies to be paraphyletic and to include some of the deepest divergences of the family. Combined analyses of 10 chloroplast DNA loci by different phylogenetic methods yielded highly congruent well-resolved trees with 95% of the branches receiving moderate to strong statistical support. Our strategy of sampling genera identified by morphological studies as anomalous, supported by broader character sampling than previous studies, resulted in identification of several novel clades. The generic compositions of subfamilies Carduoideae, Gochnatioideae, Hecastocleidoideae, Mutisioideae, Pertyoideae, Stifftioideae, and Wunderlichioideae are novel in Asteraceae systematics and the taxonomy of the family has been revised to reflect only monophyletic groups. Our results contradict earlier hypotheses that early divergences in the family took place on and spread from the Guayana Highlands (Pantepui Province of northern South America) and raise new hypotheses about how Asteraceae dispersed out of the continent of their origin. Several nodes of this new phylogeny illustrate the vast differential in success of sister lineages suggesting focal points for future study of species diversification. Our results also provide a backbone exemplar of Asteraceae for supertree construction.

Systematic data in biodiversity studies: Use it or lose it

Systematic data in the form of collections data are useful in biodiversity studies in many ways, most importantly because they serve as the only direct evidence of species distributions. However, collecting bias has been demonstrated for most areas of the world and has led some to propose methods that circumvent the need for collections data. New methods that model collections data in combination with abiotic data and predict potential total species distribution are examined using 25,111 records representing 5,123 species of plants and animals from Guyana; some methods use the reduced number of 320 species. These modeled species distributions are evaluated and potential high-priority biodiversity sites are selected based on the concept of irreplaceability, a measure of uniqueness. The major impediments to using collections data are the lack of data that are available in a useful format and the reluctance of most systematists to become involved in biodiversity and conservation research.

Mapping More of Terrestrial Biodiversity for Global Conservation Assessment

Abstract Global conservation assessments require information on the distribution of biodiversity across the planet. Yet this information is often mapped at a very coarse spatial resolution relative to the scale of most land-use and management decisions. Furthermore, such mapping tends to focus selectively on better-known elements of biodiversity (e.g., vertebrates). We introduce a new approach to describing and mapping the global distribution of terrestrial biodiversity that may help to alleviate these problems. This approach focuses on estimating spatial pattern in emergent properties of biodiversity (richness and compositional turnover) rather than distributions of individual species, making it well suited to lesser-known, yet highly diverse, biological groups. We have developed a global biodiversity model linking these properties to mapped ecoregions and fine-scale environmental surfaces. The model is being calibrated progressively using extensive biological data sets for a wide variety of taxa. We also describe an analytical approach to applying our model in global conservation assessments, illustrated with a preliminary analysis of the representativeness of the worlds protected-area system. Our approach is intended to complement, not compete with, assessments based on individual species of particular conservation concern.

Testing the use of specimen collection data and GIS in biodiversity exploration and conservation decision making in Guyana

This paper presents the results of a study conducted at the request of the Government of Guyana by the Centre for the Study of Biological Diversity at the University of Guyana, and the Smithsonian Institution. The purpose of the study was to evaluate the utility of using systematic collections in identifying areas with a high priority for conservation. A biodiversity database and a gazetteer were assembled and interpreted primarily through the use of maps generated in ARC/INFO and ArcView. The data were examined to determine coverage and completeness, and while in general the results support a continued use of the methodology for making informed decisions in conservation related issues, several recommendations are offered in order to enhance the data. The primary use of the results of this study is in the identification of areas of interest for conservation and in the location of eleven areas covering most ecoregions in Guyana that are in need of additional study. The eleven areas have been chosen to avoid areas that are already allocated to logging and mining concessions or Amerindian lands. While it is true that this study would benefit from additional data and further analysis of those data, it is also true that decisions concerning areas for conservation in Guyana are being made in the near future, and if any data are to be used in this process, it will be those data presented in this paper.

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae

Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.

Outcomes of the 2011 Botanical Nomenclature Section at the XVIII International Botanical Congress

Abstract The Nomenclature Section held just before the 18th International Botanical Congress in Melbourne, Australia in July 2011 saw sweeping changes to the way scientists name new plants, algae, and fungi. The changes begin on the cover: the title was broadened to make explicit that the Code applies not only to plants, but also to algae and fungi. The new title will now be the International Code of Nomenclature of algae, fungi, and plants. For the first time in history the Code will allow for the electronic publication of names of new taxa. In an effort to make the publication of new names more accurate and efficient, the requirement for a Latin validating diagnosis or description was changed to allow either English or Latin for these essential components of the publication of a new name. Both of these latter changes will take effect on 1 January 2012. The nomenclatural rules for fungi will see several important changes, the most important of which is probably the adoption of the principle of “one fungus, one name.” Paleobotanists will also see changes with the elimination of the concept of “morphotaxa” from the Code.

Insights into the evolution of the tribe Arctoteae (Compositae: subfamily Cichorioideae s.s.) using trnL-F, ndhF, and ITS

Compositae (Asteraceae) are the largest flowering plant family (23,000 to 30,000 species) and its members are found throughout the world in both temperate and tropical habitats. The subfamilies and tribes of Compositae remained relatively constant for many years; recent molecular studies, however, have identified new subfamilial groups and identified previously unknown relationships. Currently there are 35 tribes and 10 subfamilies (Baldwin & al., 2002; Panero & Funk, 2002). Some of the tribes and subfamilies have not been tested for monophyly and without a clear understanding of the major genera that form each tribe and subfamily, an accurate phylogeny for the family cannot be reconstructed. The tribe Arctoteae (African daisies) is a diverse and interesting group with a primarily southern African distribution (ca. 17 genera, 220 species). They are especially important in that most of the species are found in the Cape Floral Kingdom, the smallest floral kingdom and the subject of intense conservation interest. Arctoteae are part of the monophyletic subfamily Cichorioideae s.s. Other tribes in the subfamily include Eremothamneae, Gundelieae, Lactuceae, Liabeae, Moquineae, and Vernonieae, and these were all evaluated as potential outgroups. Ultimately 29 ingroup taxa and 16 outgroup taxa with a total of 130 sequences (125 newly reported), from three genetic regions, two from chloroplast DNA (trnL-F and ndhF) and one from the nuclear genome (ITS), were used to evaluate the tribe and its proposed outgroups. Each molecular region is examined separately, the chloroplast markers are examined together, and the data are combined. The data were analyzed with and without outgroups and problem taxa using parsimony and maximum likelihood methods. The analyses showed robust support for two outgroup clades, Liabeae-Vernonieae and Gundelieae-Lactuceae and two main subtribes within Arctoteae: Arctotineae and Gorteriinae. Support for monophyly of Arctoteae is weak. Within Arctoteae, some taxa of interest are easily placed: Didelta, Cuspidia and Heterorhachis are consistently part of subtribe Gorteriinae, Cymbonotus, the Australian genus, is nested within subtribe Arctotineae, and Haplocarpha is at the base of Arctotineae. Berkheya, Haplocarpha, and Hirpicium are probably paraphyletic. Furthermore, Platycarpha most likely does not belong in Arctoteae, and Heterolepis and the tribe Eremothamneae are within Arctoteae but not within either of the two main subtribes. After some rearrangements, the two main subtribes, Arctotineae and Gorteriinae, are monophyletic and the latter has three clades. The study shows that the unusual taxa are of critical importance, and they should be included in any molecular analysis. Adequate representation of the ingroup is also important as all previous studies of Arctoteae had involved only a few taxa from the core subtribes, and so did not reveal the problems. Multiple outgroups evaluated in an iterative manner had pronounced effects on the relationships within the ingroup, not only on the position of the root. Finally, unrooted consensus trees and unrooted phylograms were found to be very useful in analyzing the data, allowing for examination of placement of taxa without the bias of a rooted tree.

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.