[Show abstract][Hide abstract] ABSTRACT: Extensive radiation in oncidioid orchids (subtribe Oncidiinae) has resulted in over 1,700 species in tropical America in some 70 genera. They exhibit a wide range of habitats, occurring terrestrially or, more commonly, epiphytically and can be found from sea level to the Andean paramós and from deserts to rainforests.
[Show abstract][Hide abstract] ABSTRACT: Subtribe Pleurothallidinae (Epidendreae: Orchida- ceae) comprises an estimated 4000 Neotropical species in about 30 genera (Luer 1986), accounting for 15-20% of the species in the entire family.
[Show abstract][Hide abstract] ABSTRACT: Advances in recent years have revolutionized our understanding of both the context and occurrence of polyploidy in plants. Molecular phylogenetics has vastly improved our understanding of plant relationships, enabling us to better understand trait and character evolution, including chromosome number changes. This, in turn, has allowed us to appreciate better the frequent occurrence and extent of polyploidy throughout the history of angiosperms, despite the occurrence of low chromosome numbers in some groups, such as in Arabidopsis (A.thaliana was the first plant genome to be sequenced and assembled). In tandem with an enhanced appreciation of phylogenetic relationships, the accumulation of genomic data has led to the conclusion that all angiosperms are palaeopolyploids, together with better estimates of the frequency and type of polyploidy in different angiosperm lineages. The focus therefore becomes when a lineage last underwent polyploidization, rather than simply whether a plant is 'diploid' or 'polyploid'. This legacy of past polyploidization in plants is masked by large-scale genome reorganization involving repetitive DNA loss, chromosome rearrangements (including fusions and fissions) and complex patterns of gene loss, a set of processes that are collectively termed 'diploidization'. We argue here that it is the diploidization process that is responsible for the 'lag phase' between polyploidization events and lineage diversification. If so, diploidization is important in determining chromosome structure and gene content, and has therefore made a significant contribution to the evolutionary success of flowering plants.
Full-text · Article · Dec 2015 · Botanical Journal of the Linnean Society
[Show abstract][Hide abstract] ABSTRACT: Due to its special geological history, the New Caledonian Archipelago is a mosaic of soil types, and in combination with climatic conditions this results in a heterogeneous environment across relatively small distances. A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly and recently radiated on the archipelago after a single long-distance dispersal event. Most of the Diospyros species in the radiating group are morphologically and ecologically well differentiated, but they exhibit low levels of DNA variability. To investigate the processes that shaped the diversification of this group we employed restriction site associated DNA sequencing (RADseq). Over 8,400 filtered SNPs generally confirm species delimitations and produce a well-supported phylogenetic tree. Our analyses document local introgression, but only a limited potential for gene flow over longer distances. The phylogenetic relationships point to an early regional clustering among populations and species, indicating that allopatric speciation with respect to macrohabitat (i.e., climatic conditions) may have had a role in the initial differentiation within the group. A later, more rapid radiation involved divergence with respect to microhabitat (i.e., soil preference). Several sister species in the group show a parallel divergence in edaphic preference. Searches for genomic regions that are systematically differentiated in this replicated phenotypic divergence pointed to loci potentially involved in ion binding and cellular transport. These loci appear meaningful in the context of adaptations to soil types that differ in heavy-metal and mineral content. Identical nucleotide changes affected only two of these loci, indicating that introgression may have played a limited role in their evolution. Our results suggest that both allopatric diversification and (parapatric) ecological divergence shaped successive rounds of speciation in the Diospyros radiation on New Caledonia.
Full-text · Article · Oct 2015 · Systematic Biology
[Show abstract][Hide abstract] ABSTRACT: It is argued that a broad and expanded circumscription of Maxillaria is to be preferred over a narrower one that
necessitates the recognition of many segregate genera. These more narrowly circumscribed genera are often difficult to diagnose, increasing the risk of misidentifications, especially when material is only identified to genus level. The genera of the Maxillaria alliance as recognised in Genera orchidacearum are treated as sections of an expanded genus Maxillaria. Cryptocentrum, Cyrtidiorchis, Mormolyca, Pityphyllum, and Trigonidium are here included in Maxillaria. Criteria for generic delimitation are discussed, the necessary combinations are made, and a key to the sections as well as a provisional checklist of the 634 species of Maxillaria arranged according to section are provided. Maxillaria prolifera is shown to be the correct name for M. pendens. Maxillaria humilis is a new combination for M. gracilis.
[Show abstract][Hide abstract] ABSTRACT: High-throughput sequencing data have transformed molecular phylogenetics and a plethora of phylogenomic approaches are now readily available. Shotgun sequencing at low genome coverage is a common approach for isolating high-copy DNA, such as the plastid or mitochondrial genomes, and ribosomal DNA. These sequence data, however, are also rich in repetitive elements that are often discarded. Such data include a variety of repeats present throughout the nuclear genome in high copy number. It has recently been shown that the abundance of repetitive elements has phylogenetic signal and can be used as a continuous character to infer tree topologies. In the present study, we evaluate repetitive DNA data in tomatoes (Solanum section Lycopersicon) to explore how they perform at the inter- and intraspecific levels, utilizing the available data from the 100 Tomato Genome Sequencing Consortium. The results add to previous examples from angiosperms where genomic repeats have been used to resolve phylogenetic relationships at varying taxonomic levels. Future prospects now include the use of genomic repeats for population-level analyses and phylogeography, as well as potentially for DNA barcoding.
Full-text · Article · Jul 2015 · Biological Journal of the Linnean Society
[Show abstract][Hide abstract] ABSTRACT: Hybridization is a fundamental process in biology and can lead to new evolutionary lineages. However, if the parental taxa involved are rare, difficult decisi- ons may have to be made regarding the conservation of the biological process versus the conservation of the parental taxa. The genus Orchis in Europe is a good example of a group of species in which these types of questions arise as several of the species hybridize where they co-occur. The example used here relates to O. militaris, O. purpurea and O. simia in the anthropomorphic group (so called because the labellum has lobes thought to resemble arms and legs). All three species are widespread in Europe, al- though they are rare in large parts of their ranges, and they have substantial areas of overlap in distribution. All three are rare in Britain, occurring predominantly in south east England. Orchis militaris and O. simia and are only known from two and three natural sites in England, respectively. Orchis purpurea is less rare, but is still geographically localized.
[Show abstract][Hide abstract] ABSTRACT: Recently, DNA barcoding has emerged as an effec- tive tool for species identification. This has the poten- tial for many useful applications in conservation, such as biodiversity inventories, forensics and trade sur- veillance. It is being developed as an inexpensive and rapid molecular technique using short and standard- ized DNA sequences for species identification.
[Show abstract][Hide abstract] ABSTRACT: Conservation biologists have only finite resources, and so must prioritise some species over others. The EDGE-listing approach ranks species according to their combined evolutionary distinctiveness and degree of threat, but ignores the uncertainty surrounding both threat and evolutionary distinctiveness. We develop a new family of measures for species, which we name EDAM, that incorporates evolutionary distinctiveness, the magnitude of decline, and the accuracy with which decline can be predicted. Further, we show how the method can be extended to explore phyogenetic uncertainty. Using the vascular plants of Britain as a case study, we find that the various EDAM measures emphasise different species and parts of Britain, and that phylogenetic uncertainty can strongly affect the prioritisation scores of some species.
[Show abstract][Hide abstract] ABSTRACT: This study examines phylogenetic relationships among the 12 genera of Urticeae (Urticaceae) and investigates the pattern of morphological evolution based on analysis of nuclear ribosomal internal transcribed spacer (nrITS) and two plastid DNA regions (rbcL exon, trnL-F spacer). Sequence data were analyzed using maximum parsimony and Bayesian inference, and selected morphological traits were mapped onto the molecular tree. The molecular results strongly supported monophyly of Urticeae, excluding Gyrotaenia, which is related to Elatostemateae. All genera were monophyletic except for Urtica, Laportea, and Urera. Two Hesperocnide species are nested within Urtica. Laportea and Urera are divided into three groups with a strong geographical signal. The inferred phylogeny indicates five well-supported clades in Urticeae: clade A including Urtica (with
Hesperocnide), Zhengyia, Laportea I, and Nanocnide; clade B comprising Dendrocnide and Discocnide; clade C including only Girardinia; clade D including Laportea II; and clade E including Obetia, Urera I, II, III, and Poikilospermum. Although it is difficult to identify morphological synapomorphies for these well-defined clades within Urticeae, character analysis shows that the herbaceous habit and alternate leaves are the ancestral states in the tribe. The presence of stinging hairs is the derived status in Urticeae, and it might have been a key innovation triggering species diversification in the tribe.
[Show abstract][Hide abstract] ABSTRACT: Since its launch in 2009 Phytotaxa has grown to be the leading journal in taxonomic botany, publishing the greatest number of articles, pages, and new names. It has replaced Taxon as the top journal by volume and total citation to current papers but not impact factor. More than just a journal, Phytotaxa has made it easier for authors to publish in botanical taxonomy and has improved access to publication for disadvantaged authors. This is reflected in it gaining ‘market share’ from biodiversity-rich BRIC countries, which have invested in their taxonomic capacity. It could also reflect a shift away from Europe & US as main descriptors of plant diversity. We believe that Phytotaxa has been well accepted by the taxonomic community because it is free at point of publication (barrier-free to authors of all income brackets), flexible (unlimited issues and pages) and rapidly indexed with an impact factor that is relatively high for a taxonomic journal. Phytotaxa thus meets the needs of the broadest group of taxonomists who survive based on publication number and impact factor, and who do not have access to funds to support open-access publication. We suggest that it is eminently feasible to fully describe and typify all plant diversity using the Linnean system, but that do so in a timely manner and so meet Society’s needs in the face of the mass-extinction of biodiversity and climate change. Phytotaxa will work with all taxonomists to continue to promote taxonomy as a scientific discipline.
[Show abstract][Hide abstract] ABSTRACT: A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using
next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing
comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes
of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated
as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority
of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported
relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of
commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic
differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method
additionally yields a wealth of data for comparative studies of genome evolution.