Ancestral character reconstruction

Next generation sequencing techniques currently represent a practical and efficient way to infer robust evolutionary hypotheses. Palyadini is a small Neotropical tribe of geometrid moths composed of six genera that feature strikingly colourful wings. Here, we investigated patterns of evolution and amount of phylogenetic signal contained in various colour characters featured in the wings of members of this tribe by (i) inferring a robust phylogenetic hypothesis using ultraconserved elements (UCEs), and afterwards, (ii) mapping the morphological characters onto the molecular topology under a parsimonious ancestral character optimization...

Ancestral reconstruction is a widely-used technique that has been applied to understand the evolutionary history of gain and loss of gene families. Ancestral gene content can be reconstructed via different phylogenetic methods, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character cannot be regained...

The living fossil metaphor is tightly linked with the cycads. This group of gymnosperms is supposed to be characterised by long-term morphological stasis, particularly after their peak of diversity and disparity in the Jurassic. However, no formal test of this hypothesis exists. Here, we use a recent phylogenetic framework and an improved character matrix to reconstruct the Disparity Through Time for cycad leaves using a Principal Coordinate Analysis and employing Pre-Ordination Ancestral State Reconstruction to test the impact of sampling on the results...

Ardisia S.W. (Primulaceae), naturally distributed in tropical and subtropical areas, has edible and medicinal values and is prevalent in clinical and daily use in China. More genetic information for distinct species delineation is needed to support the development and utilization of the genus Ardisia. We sequenced, annotated, and compared the chloroplast genomes of five Ardisia species: A. brunnescens, A. pusilla, A. squamulosa, A. crenata, and A. brevicaulis in this study. We found a typical quadripartite structure in all five chloroplast genomes, with lengths ranging from 155,045 to 156,943 bp...

BACKGROUND: One of the most peculiar groups of the mostly colonial phylum Bryozoa is the taxon Monobryozoon, whose name already implies non-colonial members of the phylum. Its peculiarity and highly unusual lifestyle as a meiobenthic clade living on sand grains has fascinated many biologists. In particular its systematic relationship to other bryozoans remains a mystery. Despite numerous searches for M. ambulans in its type locality Helgoland, a locality with a long-lasting marine station and tradition of numerous courses and workshops, it has never been reencountered until today...

Convergent morphological evolution is widespread in flowering plants, and understanding this phenomenon relies on well-resolved phylogenies. Nuclear phylogenetic reconstruction using transcriptome datasets has been successful in various angiosperm groups, but it is limited to taxa with available fresh materials. Asteraceae are one of the two largest angiosperm families and important for both ecosystems and human livelihood, having multiple examples of convergent evolution. Nuclear Asteraceae phylogenies have resolved relationships among most subfamilies and many tribes, but many phylogenetic and evolutionary questions regarding subtribes and genera remain due to limited sampling...

Fern-spore-feeding (FSF) is rare and found in only four families of Lepidoptera. Stathmopodidae is the most speciose family that contains FSF species, and its subfamily Cuprininae exclusively specializes on FSF. However, three species of Stathmopodinae also specialize on FSF. To better understand the evolutionary history of FSF and, more generally, the significance of specialization on a peculiar host, a phylogenetic and taxonomic revision for this group is necessary. We reconstructed the most comprehensive molecular phylogeny, including one mitochondrial and four nuclear genes, of Stathmopodidae to date, including 137 samples representing 62 species, with a particular focus on the FSF subfamily, Cuprininae, including 33 species (41% of named species) from 6 of the 7 Cuprininae genera...

C4 photosynthesis is a key innovation in land plant evolution, but its immediate effects on population demography are unclear. We explore the early impact of the C4 trait on the trajectories of C4 and non-C4 populations of the grass Alloteropsis semialata. We combine niche models projected into paleoclimate layers for the last 5 million years with demographic models based on genomic data. The initial split between C4 and non-C4 populations was followed by a larger expansion of the ancestral C4 population, and further diversification led to the unparalleled expansion of descendant C4 populations...

Our knowledge of the systematics of the papilionoid legume tribe Brongniartieae has greatly benefitted from recent advances in molecular phylogenetics. The tribe was initially described to include species marked by a strongly bilabiate calyx and an embryo with a straight radicle, but recent research has placed taxa from the distantly related core Sophoreae and Millettieae within it. Despite these advances, the most species-rich genera within the Brongniartieae are still not well studied, and their morphological and biogeographical evolution remains poorly understood...

Body size is a fundamental characteristic of animals that impacts every aspect of their biology from anatomical complexity to ecology. In Mollusca, Solenogastres has been considered important to understanding the group's early evolution as most morphology-based phylogenetic reconstructions placed it as an early branching molluscan lineage. Under this scenario, molluscs were thought to have evolved from a small, turbellarian-like ancestor and small (i.e., macrofaunal) body size was inferred to be plesiomorphic for Solenogastres...

BACKGROUND: Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and species trees. However, it is well-known that sequences have difficulty identifying ancient transfers since mutations have enough time to erase all evidence of such events. In this work, we ask whether character-based methods can predict gene transfers...

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny...

Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants).1 , 2 , 3 , 4 Next to embryophytes are however a range of freshwater and terrestrial algae that bear important information on the emergence of key traits of land plants. Among these, the Klebsormidiophyceae stand out. Thriving in diverse environments-from mundane (ubiquitous occurrence on tree barks and rocks) to extreme (from the Atacama Desert to the Antarctic)-Klebsormidiophyceae can exhibit filamentous body plans and display remarkable resilience as colonizers of terrestrial habitats...

Nidulariaceae, also known as bird's nest fungi, is an understudied group of mushroom-forming fungi. The common name is derived from their nest-like morphology. Bird's nest fungi are ubiquitous wood decomposers or saprobes on dung. Recent studies showed that species in the Nidulariaceae form a monophyletic group with five sub-clades. However, phylogenetic relationships among genera and placement of Nidulariaceae are still unclear. We present phylogenomic analyses of bird's nest fungi and related Agaricales fungi to gain insight into the evolution of Nidulariaceae...

Asian warty treefrogs, genus Theloderma , are morphologically variable arboreal frogs endemic to Southeast Asia and Southern China. However, integrated systematic studies are lacking, and knowledge of the genus in terms of diversity, origin, and historical diversification remains limited. To address these knowledge gaps, we used three mitochondrial and five nuclear gene fragments to reconstruct the Theloderma phylogeny, estimate divergence times, and examine the biogeography of the genus. Phylogenetic and species delimitation analyses suggest that the genus Theloderma comprises three major clades corresponding to two subgenera and seven species groups, and mPTP identified at least 12 putative cryptic species, suggesting that species diversity has been underestimated...

Capitate hydrozoans are a morphologically and ecologically diverse hydrozoan suborder, currently including about 200 species. Being grouped in two clades, Corynida and Zancleida, these hydrozoans still show a number of taxonomic uncertainties at the species, genus and family levels. Many Capitata species established symbiotic relationships with other benthic organisms, including bryozoans, other cnidarians, molluscs and poriferans, as well as with planktonic dinoflagellates for mixotrophic relationships and with bacteria for thiotrophic ectosymbioses...

Suckermouth armoured catfish (Loricariidae) are a highly speciose and diverse freshwater fish family, which bear upper and lower lips forming an oral disc. Its hierarchical organisation allows the attachment to various natural surfaces. The discs can possess papillae of different shapes, which are supplemented, in many taxa, by small horny projections, i.e. unculi. Although these attachment structures and their working mechanisms, which include adhesion and interlocking, are rather well investigated in some selected species, the loricariid oral disc is unfortunately understudied in the majority of species, especially with regard to comparative aspects of the diverse oral structures and their relationship to the ecology of different species...

PREMISE: The representatives of the ANA-grade of angiosperms demonstrate a diverse pattern of morphological characters, but their apocarpous gynoecium (except in Nymphaeaceae), composed of at least partly ascidiate carpels, the four-nucleate and four-celled female gametophyte, and the diploid endosperm (except in Amborella) are inferred to be plesiomorphies. Since the structure of fruits in Austrobaileyales is under-investigated, this research aims to fill this gap in these data, describing the carpological characters of ANA-grade taxa, and potentially illuminating the ancestral fruit and seed types of angiosperms...

Flowers are the complex and highly diverse reproductive structures of angiosperms. Because of their role in sexual reproduction, the evolution of flowers is tightly linked to angiosperm speciation and diversification. Accordingly, the quantification of floral morphological diversity (disparity) among angiosperm subgroups and through time may give important insights into the evolutionary history of angiosperms as a whole. Based on a comprehensive dataset focusing on 30 characters describing floral structure across angiosperms, we used 1201 extant and 121 fossil flowers to measure floral disparity and explore patterns of floral evolution through time and across lineages...

This paper discusses methods to take into account interactions between characters, in the context of parsimony analysis. These interactions can be in the form of some characters becoming inapplicable given certain states of other, primary characters; in the form of only certain states being allowed in some characters when a given state or set of states occurs for other characters; or in the form of transformation costs in some character being higher or lower when other characters have certain states or transformations between states...