Eric J. Tepe

Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies

One of the longstanding questions in phylogenetic systematics is how to address incongruence among phylogenies obtained from multiple markers and how to determine the causes. This study presents a detailed analysis of incongruent patterns between plastid and ITS/ETS phylogenies of Tribe Senecioneae (Asteraceae). This approach revealed widespread and strongly supported incongruence, which complicates conclusions about evolutionary relationships at all taxonomic levels. The patterns of incongruence that were resolved suggest that incomplete lineage sorting (ILS) and/or ancient hybridization are the most likely explanations. These phenomena are, however, extremely difficult to distinguish because they may result in similar phylogenetic patterns. We present a novel approach to evaluate whether ILS can be excluded as an explanation for incongruent patterns. This coalescence-based method uses molecular dating estimates of the duration of the putative ILS events to determine if invoking ILS as an explanation for incongruence would require unrealistically high effective population sizes. For four of the incongruent patterns identified within the Senecioneae, this approach indicates that ILS cannot be invoked to explain the observed incongruence. Alternatively, these patterns are more realistically explained by ancient hybridization events.

Allozyme diversity in endemic flowering plant species of the Juan Fernandez Archipelago, Chile: Ecological and historical factors with implications for conservation

The level and apportionment of allozyme diversity were determined for 29 endemic (and 1 native) species from the Juan Fernández Islands, Chile. Mean diversities at the species level (H(es) = 0.065) are low but comparable to those measured for other insular endemics in the Pacific. A high mean proportion (0.338) of species-level diversity resides among populations. Diversity statistics were compared for species in different ecological-life history trait categories and abundance classes. Species occurring in large populations and those present in scattered small populations have higher diversities than species occurring in one or two populations. Although not significant with the conservative statistical test employed, lower diversity was found in highly selfing species as compared to animal- or wind-pollinated species. The apportionment of genetic diversity within and among populations (G(ST) values) is not significantly different for any of the species categories. Of particular interest is the lack of difference between animal- and wind-pollinated species because previous analyses of large data sets showed higher differentiation between populations of animal- than wind-pollinated species. Historical factors, both ecological and phylogenetic in nature, can influence the level and apportionment of diversity within insular endemics, and thus ecological correlates of diversity seen in many continental species may not apply to endemics. The results have several conservation implications. The preservation of large populations or several small populations is important for conserving diversity within species because when species are reduced to one or two populations, allozyme diversity is sharply reduced. High mean G(ST) values for the species examined illustrate the need for conserving as many populations as possible, either in the wild or in the garden, to preserve maximal diversity within species. Effective conservation strategies require empirical knowledge of each species.

A Phylogeny of the Tropical Genus Piper Using Its and the Chloroplast Intron psbJ–petA

Abstract Piper is one of the largest genera of flowering plants. The uniformity of its small flowers and the vast number of species in the genus has hindered the development of a stable infrageneric classification. We sampled 575 accessions corresponding to 332 species of Piper for the ITS region and 181 accessions for the psbJ–petA chloroplast intron to further test previous hypotheses about the major clades within Piper. Phylogenetic analyses were performed for each marker separately and in combination. The ITS region alone resolves eleven major clades within Piper, whereas the psbJ–petA intron fails to recover four of these major groupings and provides no resolution at the base of the phylogeny. The combined analysis provides support for ten monophyletic groups and offers the best hypothesis for relationships in Piper. Our massive ITS dataset allows us to assign confidently a large number of species in this “giant” genus to a major clade. Piper is here divided into ten major clades for which we provide a morphological description. Various clades and subclades are newly identified here: Peltobryon, Schilleria, Isophyllon, P. cinereum/P. sanctum. The clades described here provide a solid framework for future, and more focused, evolutionary studies. New names and combinations proposed herein include Piper bullulatum, P. hooglandii, and P. melchior.

Placing the Origin of Two Species-Rich Genera in the Late Cretaceous with Later Species Divergence in the Tertiary: a Phylogenetic, Biogeographic and Molecular Dating Analysis of Piper and Peperomia (Piperaceae)

Nearly all of the species diversity in Piperaceae is encompassed within Piper and Peperomia. Both genera are pan-tropical with areas of diversification in the Neotropics and Southeast Asia. Piperaceae are less diverse in Africa with only two native species of Piper. This study examines the distribution of both Piper and Peperomia with representative samples from the Neotropics, Asia, Pacific Islands, and Africa. Molecular dating is used to place an age for the crown clades of Piper and Peperomia as well as ages for diversification within the clades. Both genera have origins in the late Cretaceous, but species level diversification occurred much later in the Tertiary. Biogeography of both genera are correlated with paleoclimate evidence to better explain the distribution and diversification of these large genera.

Host conservatism, host shifts and diversification across three trophic levels in two Neotropical forests

Host–parasite systems have been models for understanding the connection between shifts in resource use and diversification. Despite theoretical expectations, ambiguity remains regarding the frequency and importance of host switches as drivers of speciation in herbivorous insects and their parasitoids. We examine phylogenetic patterns with multiple genetic markers across three trophic levels using a diverse lineage of geometrid moths (Eois), specialist braconid parasitoids (Parapanteles) and plants in the genus Piper. Host–parasite associations are mapped onto phylogenies, and levels of cospeciation are assessed. We find nonrandom patterns of host use within both the moth and wasp phylogenies. The moth–plant associations in particular are characterized by small radiations of moths associated with unique host plants in the same geographic area (i.e. closely related moths using the same host plant species). We suggest a model of diversification that emphasizes an interplay of factors including host shifts, vicariance and adaptation to intraspecific variation within hosts.

Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons

BackgroundThe most frequent case of horizontal transfer in plants involves a group I intron in the mitochondrial gene cox1, which has been acquired via some 80 separate plant-to-plant transfer events among 833 diverse angiosperms examined. This homing intron encodes an endonuclease thought to promote the introns promiscuous behavior. A promising experimental approach to study endonuclease activity and intron transmission involves somatic cell hybridization, which in plants leads to mitochondrial fusion and genome recombination. However, the cox1 intron has not yet been found in the ideal group for plant somatic genetics - the Solanaceae. We therefore undertook an extensive survey of this family to find members with the intron and to learn more about the evolutionary history of this exceptionally mobile genetic element.ResultsAlthough 409 of the 426 species of Solanaceae examined lack the cox1 intron, it is uniformly present in three phylogenetically disjunct clades. Despite strong overall incongruence of cox1 intron phylogeny with angiosperm phylogeny, two of these clades possess nearly identical intron sequences and are monophyletic in intron phylogeny. These two clades, and possibly the third also, contain a co-conversion tract (CCT) downstream of the intron that is extended relative to all previously recognized CCTs in angiosperm cox1. Re-examination of all published cox1 genes uncovered additional cases of extended co-conversion and identified a rare case of putative intron loss, accompanied by full retention of the CCT.ConclusionsWe infer that the cox1 intron was separately and recently acquired by at least three different lineages of Solanaceae. The striking identity of the intron and CCT from two of these lineages suggests that one of these three intron captures may have occurred by a within-family transfer event. This is consistent with previous evidence that horizontal transfer in plants is biased towards phylogenetically local events. The discovery of extended co-conversion suggests that other cox1 conversions may be longer than realized but obscured by the exceptional conservation of plant mitochondrial sequences. Our findings provide further support for the rampant-transfer model of cox1 intron evolution and recommend the Solanaceae as a model system for the experimental analysis of cox1 intron transfer in plants.

Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars

Summary Chemically mediated plant–herbivore interactions contribute to the diversity of terrestrial communities and the diversification of plants and insects. While our understanding of the processes affecting community structure and evolutionary diversification has grown, few studies have investigated how trait variation shapes genetic and species diversity simultaneously in a tropical ecosystem. We investigated secondary metabolite variation among subpopulations of a single plant species, Piper kelleyi (Piperaceae), using high‐performance liquid chromatography (HPLC), to understand associations between plant phytochemistry and host‐specialized caterpillars in the genus Eois (Geometridae: Larentiinae) and associated parasitoid wasps and flies. In addition, we used a genotyping‐by‐sequencing approach to examine the genetic structure of one abundant caterpillar species, Eois encina, in relation to host phytochemical variation. We found substantive concentration differences among three major secondary metabolites, and these differences in chemistry predicted caterpillar and parasitoid community structure among host plant populations. Furthermore, E. encina populations located at high elevations were genetically different from other populations. They fed on plants containing high concentrations of prenylated benzoic acid. Thus, phytochemistry potentially shapes caterpillar and wasp community composition and geographic variation in species interactions, both of which can contribute to diversification of plants and insects.

A 10-gene phylogeny of Solanum section Herpystichum (Solanaceae) and a comparison of phylogenetic methods

PREMISE OF THE STUDY Solanum section Herpystichum is a lineage that comprises both widespread and very narrowly distributed species. This study investigates the phylogenetic relationships of sect. Herpystichum and evaluates several phylogenetic methods for analysis of multiple sequences. METHODS Sequence data from seven nuclear (ITS, GBSSI, and five COSII) and three plastid (psbA-trnH, trnT-trnF, and trnS-trnG) regions were concatenated and analyzed under maximum parsimony and Bayesian criteria. In addition, we used two analytical methods that take into account differences in topologies resulting from the analyses of the individual markers: Bayesian Estimation of Species Trees (BEST) and supertree analysis. KEY RESULTS The monophyletic Solanum sect. Herpystichum was resolved with moderate support in the concatenated maximum parsimony and Bayesian analyses and the supertree analysis, and relationships within the section were well-resolved and strongly supported. The BEST topology, however, was poorly resolved. Also, because of how BEST deals with missing sequences, >25% of our accessions, including two species, had to be excluded from the analyses. Our results indicate a progenitor-descendent relationship with two species nested within the widespread S. evolvulifolium. CONCLUSIONS Analytical methods that consider individual topologies are important for studies based on multiple molecular markers. On the basis of analyses in this study, BEST had the serious shortcoming that taxa with missing sequences must be removed from the analysis or they can produce spurious topologies. Supertree analysis provided a good alternative for our data by allowing the inclusion of all 10 species of sect. Herpystichum.

Stem diversity, cauline domatia, and the evolution of ant–plant associations in Piper sect. Macrostachys (Piperaceae)

Plants possess a variety of structures that harbor ant nests, and the morphology of these domatia determines the nature of ant-plant mutualisms in a given plant species. In this study, we report on the differences in anatomy between myrmecophytes of Piper, which are regularly excavated by an obligate ant mutualist (Pheidole bicornis) and nonmyrmecophytes of Piper, which consistently have solid stems. Stems of excavated plant species lacked outward evidence of modification; however, striking anatomical differences were apparent between hollow-stemmed species before excavation and the remainder of the solid-stemmed species studied. Prior to excavation by ants, stems of myrmecophytes were characterized by strongly heterogeneous piths in which a large, central area had relatively large cells lacking intracellular crystals with a periphery of smaller cells containing numerous crystals. The domatium excavated by the ants was restricted to the large-celled region. This is the first report of the absence of crystals in ant-excavated portions of stems of myrmecophytes. Cauline domatia became lined with 3-8 cell layers of suberized wound tissue, which may have an impact on nutrient absorption by Piper myrmecophytes.

Allozyme variation and the taxonomy of Wolffiella

Abstract Allozyme electrophoresis was carried out to estimate genetic diversity within and assess divergence between the 10 recognized species in three sections of the aquatic angiosperm genus Wolffiella . Eleven presumptive loci were used in the calculations. Highest variation was found in W. lingulata and W. oblonga , two common species with widespread distributions in North and South America. Four of the species showing low allozyme variation include W. caudata, W. denticulata, W. neotropica , and W. rotunda , all of which have restricted distributions. W. hyalina exhibits low allozyme diversity despite being widely distributed in Africa. Three species with intermediate levels of diversity include: W. welwitschii , which is widely distributed on two continents; W. gladiata , which occurs widely in North America; and W. repanda , which has a restricted distribution in Africa. Genetic identities between species of Wolffiella vary from 0.00 (no alleles in common) to over 0.94. W. lingulata and W. oblonga share the highest identity of any two species. These two species are viewed as most closely related and are difficult to distinguish in some instances. Species within the large sect. Wolffiella (incl. W. caudata, W. denticulata, W. gladiata, W. lingulata, W. neotropica and W. welwitschii ) have identities ranging from 0.00 to 0.940, whereas identities with species in this section and the two species of sect. Stipitatae (incl. W. hyalina and W. repanda ) are mostly 0.000, and the same applies for W. rotunda , the only species in sect. Rotundae . The two species of sect. Stipitatae, W. hyalina and W. repanda , have an identity of 0.800, which is higher than they share with any other species. Species of sect. Stipitatae have higher identities with W. rotunda (0.538, 0.504) than they do with any species of sect. Wolffiella , and W. rotunda is more closely related to sect. Stipitatae than to sect. Wolffiella . Allozyme data support the recognition of sect. Stipitatae as now constituted and provide evidence for the circumscription of sect. Wolffiella as presently recognized. However, W. denticulata is rather isolated within this section.