Classification: More than Just Branching Patterns of Evolution

The past 35 years in biological systematics have been a time of remarkable philosophical and methodological developments. For nearly a century after Darwin\u27s Origin of Species, systematists worked to understand the diversity of nature based on evolutionary relationships. Numerous concepts were presented and elaborated upon, such as homology, parallelism, divergence, primitiveness and advancedness, cladogenesis and anagenesis. Classifications were based solidly on phylogenetic concepts; they were avowedly monophyletic. Phenetics emphasized the immense challenges represented by phylogeny reconstruction and advised against basing classifications upon it. Pheneticists forced reevaluation of all previous classificatory efforts, and objectivity and repeatability in both grouping and ranking were stressed. The concept of character state was developed, and numerous debates focused on other concepts, such as unit character, homology, similarity, and distance. The simultaneous availability of computers allowed phenetics to explore new limits. Despite numerous positive aspects of phenetics, the near absence of evolutionary insights led eventually to cladistics. Drawing directly from phenetics and from the Hennigian philosophical school, cladistics evolved as an explicit means of deriving branching patterns of phylogeny and upon which classifications might be based. Two decades of cladistics have given us: refined arguments on homology and the evolutionary content of characters and states, views of classifications as testable hypotheses, and computer algorithms for constructing branching patterns of evolution. In contrast to the phenetic movement, which was noteworthy for seeking newer concepts and methods, even including determining evolutionary relationships (which led eventually to numerical cladistics), many cladists have solidified their approaches based on parsimony, outgroups, and holophyly. Instead of looking for newer ways to represent phylogeny, some cladists have attempted to use branching patterns: (1) as a strict basis for biological classification and nomenclature and (2) to explain the origin of biological diversity even down to the populational level. This paper argues that cladistics is inappropriate to both these goals due to: (1) inability of branching patterns to reveal all significant dimensions of phylogeny; (2) acknowledged patterns of reticulate evolution, especially in flowering plants; (3) documented nonparsimonious pathways of evolution: and (4) nondichotomous distribution of genetic variation within populations. New concepts and methods of reconstructing phylogeny and developing classifications must be sought. Most important is incorporation of genetic-based evolutionary divergence within lineages for purposes of grouping and ranking

Plant Species Disjunctions

The use of molecular data in the study of plant species disjunctions is reviewed and evaluated. The major reason for employing molecular information is to estimate genetic divergence between morphologically similar disjunct species. Flavonoid chemistry offers few advantages over morphology because it is difficult, if not impossible, to infer genetic divergence from the arrays of flavonoid compounds sequestered by two species. Also, flavonoids can, like morphological characters, undergo stasis. Rather direct evidence for this comes from the fact that extant and fossil species may have identical or nearly identical flavonoids. Enzyme electrophoresis is useful for estimating divergence between disjunct species at gene loci encoding soluble enzymes. Disjunct species pairs in several genera are highly divergent at isozyme loci despite their morphological similarity. Restriction site analysis of chloroplast DNA (cpDNA) has proven useful for measuring divergence between disjunct species. The conservative rate of nucleotide substitutions in cpDNA allows one to estimate (albeit with several assumptions) sequence divergence between the DNAs. Whether isozyme and cpDNA data can be used to estimate divergence times with reasonable confidence remains an open question. In two studies employing both methods, similar divergence times were calculated with each. As two species become more divergent at isozyme loci, the variance in estimates of divergence times becomes larger, and the calculated times become less certain. Despite limitations, enzyme electrophoresis and cpDNA restriction site data are valuable for estimating genetic divergence between disjunct species. Future studies of plant species disjunctions will likely include nucleic acid sequence data. The molecular information should always be part of a broader study of species disjunctions, including detailed investigations of morphological features, chromosome numbers, ecology, and the geological histories of the species

Factors driving adaptive radiation in plants of oceanic islands: A case study from the Juan Fernández Archipelago

This work is licensed under a Creative Commons Attribution 4.0 International License.Adaptive radiation is a common evolutionary phenomenon in oceanic islands. From one successful immigrant population, dispersal into different island environments and directional selection can rapidly yield a series of morphologically distinct species, each adapted to its own particular environment. Not all island immigrants, however, follow this evolutionary pathway. Others successfully arrive and establish viable populations, but they remain in the same ecological zone and only slowly diverge over millions of years. This transformational speciation, or anagenesis, is also common in oceanic archipelagos. The critical question is why do some groups radiate adaptively and others not? The Juan Fernández Islands contain 105 endemic taxa of angiosperms, 49% of which have originated by adaptive radiation (cladogenesis) and 51% by anagenesis, hence providing an opportunity to examine characteristics of taxa that have undergone both types of speciation in the same general island environment. Life form, dispersal mode, and total number of species in progenitors (genera) of endemic angiosperms in the archipelago were investigated from literature sources and compared with modes of speciation (cladogenesis vs. anagenesis). It is suggested that immigrants tending to undergo adaptive radiation are herbaceous perennial herbs, with leaky self-incompatible breeding systems, good intra-island dispersal capabilities, and flexible structural and physiological systems. Perhaps more importantly, the progenitors of adaptively radiated groups in islands are those that have already been successful in adaptations to different environments in source areas, and which have also undergone eco-geographic speciation. Evolutionary success via adaptive radiation in oceanic islands, therefore, is less a novel feature of island lineages but rather a continuation of tendency for successful adaptive speciation in lineages of continental source regions.Austrian Science Fund Grant number P21723-B16National Fund for Scientific and Technological Development Grant number 1160794Japan Society for the Promotion of Science under Open Partnership Joint Projec

Plant Conservation in the Juan Fernandez Archipelago, Chile

Oceanic archipelagos often hold very specialized floras with high degrees of endemism. These floras are frequently highly vulnerable to disturbance by natural causes and human intervention. The Juan Fernandez Islands (Chile) in the Pacific Ocean are a small archipelago of only three islands. Since discovery in 1574 by Juan Fernandez, human activities have altered floristic composition and survival circumstances of the endemic species. In this paper we document past and present means of disturbance, both anthropogenic and natural, which have influenced the native vegetation. The most destructive past activities have been logging and .introduction of animals and plants, both deliberately and inadvertently. At the present time, exotic organisms are still introduced as pets, ornaments, or for soil conservation. All pose serious threats to the natural vegetation as shown by altered floristic composition, populational decline of endemic taxa, and even extinction. Weeds that form impenetrable thickets are Aristotelia chilensis, Rubus ulmifolius, and Ugni molinae. Recent introductions include the aggressive Lantana camara and Lonicera japonica. Examples of endemic taxa in need of conservation are Dendroseris, Lactoris, and Robinsonia. Previous studies reveal that island taxa frequently have low levels of genetic variation, a pattern also seen in many endemic taxa of the Juan Fernandez Islands. Conservation programs are urgently needed that emphasize physical and biological measures for controlling alien weeds and animals

Evidence for progenitor-derivative speciation in sexually deceptive orchids

Background and Aims Sexually deceptive orchids of the genus Ophrys use mimicry of pollinator females to attract specific pollinators. Pollinator shifts may drive speciation in Ophrys, since novel pollinators may in principle act as isolating factors immediately. It is thus possible that evolution of novel species occurs rapidly and with a progenitor-derivative pattern. The aims of this study are to compare genetic structure and diversity among widespread and geographically restricted Ophrys taxa, to test whether genetic structure is associated with specific pollinators, and to investigate whether any widespread species may have acted as a progenitor for the evolution of more restricted taxa. Methods Genetic differentiation and diversity were investigated in O. leucadica and O. cinereophila, the two taxa of the Ophrys fusca sensu lato complex widespread in the Aegean, and three geographically restricted taxa from Rhodes, O. attaviria, O. parvula and O. persephonae, all differing in their specific pollinators. This was done using amplified fragment length polymorphism (AFLP) DNA fingerprinting, and sequencing of the low-copy nuclear gene LEAFY (LFY). Key Results All taxa were found to be separate genetic entities, with O. leucadica forming two geographic groups from the west and east of the Aegean. Genetic structure was significantly shaped by pollinators and geography, and comparison of sequence and AFLP data revealed ancestral polymorphisms shared among several taxa. Among the sampled taxa, O. leucadica harbours the greatest genetic differentiation and geographic structure, and the highest genetic diversity. Part of the genome of O. parvula, endemic to Rhodes, may be derived from O. leucadica. Conclusions Pollinators probably influence the genetic structure of the investigated Ophrys species. The genetic pattern identified is consistent with O. leucadica being the oldest of the sampled taxa, making O. leucadica a candidate progenitor species from which more restricted taxa such as O. parvula may have evolve

Endemism in the Vascular Flora of the Juan Fernandez Islands

The Juan Fernandez archipelago contains 361 vascular plant species including 53 ferns, 65 monocots, and 243 dicots. Represented are 73 families and 219 genera. There is one endemic family (Lactoridaceae), 12 endemic genera, and 126 endemic species. The native vascular flora has II% endemism at the generic level and 60% at the specific level. Among the endemic species, 23 are ferns, 15 are monocots, and 88 are dicots. Of the endemic dicots, 29 species are Compositae, making up 33% of the endemic dicot flora. Most (97%) of the endemic angiosperms are perennials, and 64% of the dicots are woody (shrubs, rosette-trees, and trees). The endemic angiosperms are found in all of the major ecological zones in the islands: fern forest; dry forest; alpine zone; open ridges and cliffs; dry, open slopes; canyons (quebradas); and the shore. They are most abundant in the dry forest (38%) and open ridges and cliffs (22%). There is no evidence of change in chromosome number during evolution of the endemic dicots, and genetic differences between congeneric endemic species at isozyme loci are minimal. The endemic angiosperms are definitely in a fragile state with 75% of the species being regarded as either extinct, threatened, rare, or occasional. Santalum fernandezianum (Santalaceae) is definitely extinct, and Dendroseris macrantha (Compositae) presumed so

Chromosome numbers and karyotypes of South American species and populations of Hypochaeris (Asteraceae)

One hundred and thirty-seven new chromosome counts are reported from 104 populations of 26 native South American taxa of Hypochaeris (Asteraceae, Lactuceae), together with two invasive Mediterranean species: H. glabra and H. radicata. First reports are provided for seven taxa (H. alba, H. cf. eremophila, H. caespitosa, H. hookeri, H. parodii, H. patagonica and H. pinnatifida) and one new ploidy level is reported (diploid for H. incana, so far known only as a tetraploid). Including the results of this study, the chromosomes of 39 of the c. 50 Hypochaeris species known from the New World have now been counted. Most species are diploid with 2n = 2x = 8 and have bimodal, asymmetrical karyotypes. Tetraploidy (2n = 4x = 16) is reported here for the first time in H. caespitosa. Infra-specific polyploidy (probably autopolyploidy) is reported in H. incana and H. taraxacoides, both cases including infra-populational cytotype mixtures (2x and 4x). Polyploidy is now known from eight South American Hypochaeris species (c. 16%). Basic karyotype analyses allow the placement of the newly counted taxa into previously proposed but slightly modified groupings and provide the framework for further molecular cytogenetic analyses. The reported findings suggest that chromosomal change in South American Hypochaeris, in contrast to Old World species, has not involved aneuploidy, but polyploidy and/or more subtle changes in chromosome length, perhaps via satellite DNA amplification/deletion or activity of retroelements, and rDNA reorganization.Facultad de Ciencias Naturales y Muse

Molecular phylogeny of Nassauvia (Asteraceae, Mutisieae) based on nrDNA ITS sequences

The phylogeny of the genus Nassauvia and closely related genera was reconstructed using sequences from the internal transcribed spacer regions (ITS) of nuclear ribosomal DNA. The genus Triptilion is nested within Nassauvia, making the latter genus paraphyletic. Neither of the two subgenera Nassauvia and Strongyloma is resolved as monophyletic, and none of the sections of subgenus Nassauvia is recovered as monophyletic. The evolution of the compound secondary inflorescences has been complex in Nassauvia, with the highly aggregated forms representing the original condition in the genus. However, the ancestral condition is equivocal in several clades, and there are alternative reconstructions for the gains?losses of the variously aggregated conditions. There has been at least one gain of solitary capitula in Nassauvia. The evolution of flavonoid chemistry has been complex in Nassauvia, and flavonoids are of limited phylogenetictaxonomic utility in the genus. Gains?losses of flavonols occur only on terminals whereas changes in flavones and C-glycosyl flavones occur at various levels in the tree. Gains?losses of methylation of flavones and flavonols occur only on terminals.Nassauvia and closely related genera was reconstructed using sequences from the internal transcribed spacer regions (ITS) of nuclear ribosomal DNA. The genus Triptilion is nested within Nassauvia, making the latter genus paraphyletic. Neither of the two subgenera Nassauvia and Strongyloma is resolved as monophyletic, and none of the sections of subgenus Nassauvia is recovered as monophyletic. The evolution of the compound secondary inflorescences has been complex in Nassauvia, with the highly aggregated forms representing the original condition in the genus. However, the ancestral condition is equivocal in several clades, and there are alternative reconstructions for the gains?losses of the variously aggregated conditions. There has been at least one gain of solitary capitula in Nassauvia. The evolution of flavonoid chemistry has been complex in Nassauvia, and flavonoids are of limited phylogenetictaxonomic utility in the genus. Gains?losses of flavonols occur only on terminals whereas changes in flavones and C-glycosyl flavones occur at various levels in the tree. Gains?losses of methylation of flavones and flavonols occur only on terminals.Fil: Maraner, Fabrizio. Universidad de Viena; AustriaFil: Samuel, Rosabelle. Universidad de Viena; AustriaFil: Stuessy, Tod F.. Universidad de Viena; AustriaFil: Crawford, Daniel J.. University of Kansas; Estados UnidosFil: Crisci, Jorge Victor. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División de Plantas Vasculares; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Pandey, A.. University Of Delhi; IndiaFil: Mort, Mark E.. University of Kansas; Estados Unido

Plastid Phylogenomics of Dendroseris (Cichorieae; Asteraceae): Insights Into Structural Organization and Molecular Evolution of an Endemic Lineage From the Juan Fernández Islands

This work is licensed under a Creative Commons Attribution 4.0 International License.Dendroseris D. Don comprises 11 species endemic to the Juan Fernández islands in Chile. They demonstrate spectacular and unusual growth forms of rosette trees with extremely variable morphology and occupy wide ecological ranges on the islands. These unique plants are now highly threatened with extinction with very small population sizes, typically consisting of 10 or fewer individuals in wild. Despite morphological and ecological divergence among species of Dendroseris, their monophyly has been supported in previous studies, but with little resolution among subgeneric groups. We assembled seven complete plastome sequences from seven species of Dendroseris, including representatives from three subgenera, and carried out comparative phylogenomic analyses. The plastomes are highly conserved in gene content and order, with size ranging from 152,199 to 152,619 bp and containing 130 genes (87 coding genes, 6 rRNA genes, and 37 tRNA genes). Plastid phylogenomic analyses based on both the complete plastome sequences and 81 concatenated coding genes only show Dendroseris nested within Sonchus sensu lato, and also that inter-subgeneric relationships are fully resolved. Subg. Phoenicoseris is resolved as sister to the remaining species of the genus and a sister relationship between the two subgenera Dendroseris and Rea. Ten mutation hotspots from LSC and SSC regions and variable SSRs are identified as potential chloroplast markers for future phylogenetic and phylogeographic studies of Sonchus and related groups.Basic Science Research Program through the National Research Foundation of Korea (NRF) (NRF-2019R1A2C2009841