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.

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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.

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.

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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.

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 intron's 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.

Understanding civilizations of the past and how they emerge and eventually falter is a primary research focus of archaeological investigations because these provocative data sets offer critical insights into long-term human behavior patterns, especially in regard to land use practices and sustainable environmental interactions. the ancient Maya serve as an intriguing example of this research focus, yet the details of their spectacular emergence in a tropical forest environment followed by their eventual demise have remained enigmatic. tikal, one of the foremost of the ancient Maya cities, plays a central role in this discussion because of its sharp population decline followed by abandonment during the late 9 th century ce. our results, based on geochemical and molecular genetic assays on sediments from four of the main reservoirs, reveal that two of the largest reservoirs at tikal, essential for the survival of the city during the dry seasons, were contaminated with high levels of mercury, phosphate and cyanobacteria known to produce deadly toxins. our observations demonstrate severe pollution problems at a time when episodes of climatic aridity were prevalent. this combination of catastrophic events clearly threatened the sustainability of the city and likely contributed to its abandonment. The ancient Maya abandoned the major center of Tikal in the mid-ninth century CE and although scholars have studied this site intensively for the past 60 years, exactly how and why the city met its ill-fated ending have remained unanswered questions. Our investigations, combining novel aDNA and soil geochemistry assays, however, shed significant new light on the abandonment of this once-powerful political, ceremonial and commercial hub. Recent explanations for the downfall of Tikal have centered on population expansion 1,2 coupled with extensive landscape degradation 3,4 and a period of multidecadal droughts from 820 to 870 CE 5-11. Extended episodes of climatic aridity made the city especially vulnerable because it lacked access to permanent bodies of water such as lakes or rivers, and the groundwater table, approximately 200 m below the surface, was inaccessible using existing technology 12. Inhabitants relied on reservoirs that ringed the city and filled during the rainy season to provide water during the dry season 13-15. To enhance this water collection process, numerous large paved plazas in the site core of Tikal, e.g., the Great Plaza, the Plaza of the Seven Temples and the West Plaza 14-16 were canted to drain water into the reservoirs, particularly the Temple and Palace Reservoirs, during the rainy season for storage 14. In this study, we seek to bring about a greater understanding of the reservoir system at Tikal and how it played a crucial role in sustaining the inhabitants. In particular, we were interested in how the reservoirs were used and how they were maintained as sources of potable drinking water and water for irrigation. Towards this end, we collected sediment samples during excavations in 2009 and 2010 f...