An Extraordinary Rosette and Resurrection New Spikemoss, Selaginella iridescens (Selaginellaceae) from Hainan Island, China

Selaginella iridescens (Selaginellaceae), a new species of spikemoss from Hainan Island, China, is described based on morphological and molecular evidence. The new species morphologically resembles S. pseudotamariscina from Vietnam which was recently recognized and segregated from S. tamariscina and S. pulvinata. Some characters of S. iridescens, including the iridescent leaves and long arista (0.35–1.20 mm long), the widely membranaceous margin of axillary leaves (ca. 2/3), dorsal leaves sulcate extending to the top, and slender main stem, dorsoventrally prostrate, distinguish it from S. pseudotamariscina. Phylogenetic results based on rbcL of 28 Selaginella species indicate that S. iridescens is sister to S. pseudotamariscina, and distant from the S. tamariscina-S.pulvinata clade. The ancestral character reconstruction result reveals that the rosette is apomorphic and has evolved independently at least six times in Selaginella.

Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics

The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. [Adaptive radiation; bowerbirds; mating system, sexual selection; whole genome sequencing.]

Coping with the extremes: comparative osteology of the tepui-associated toad Oreophrynella and its bearing on the evolution of osteological novelties in the genus

The only study of the osteology of the toad genus Oreophrynella dates back to 1971 and was based on a single species. Here, we use high-resolution X-ray microcomputed tomography to analyse the osteology of all nine described Oreophrynella species, which are compared with representatives of other bufonid lineages. Oreophrynella is unique among bufonids in having opposable digits. Osteological synapomorphies confirmed for the genus are as follows: presence of parietal fontanelles and exposed frontoparietal fontanelle, absence of quadratojugal, five presacral vertebrae, distally enlarged terminal phalanges and urostyle greatly expanded into flanges. Ancestral character reconstruction indicates that arboreal habits in some Oreophrynella species are likely to have evolved after the evolution of opposable digits. Opposable digits, in combination with an extension of the interdigital integument and the relative length/orientation of the digits, are likely to be adaptations to facilitate life on rocky tepui summits and an exaptation to arboreality. Cranial simplification in Oreophrynella, in the form of cranial fontanelles and absence of the quadratojugal, is possibly driven by a reduction of developmental costs, increase in flexibility and reduction of body weight. Cranial simplification combined with the shortening of the vertebral column and the shift towards a partly firmisternal girdle might be adaptations to the peculiar tumbling behaviour displayed by Oreophrynella.

The role of floral oils in the evolution of apid bees (Hymenoptera: Apidae)

Most bees collect pollen and nectar for their larvae, while some also collect other resources. We investigated the evolution of floral oil-collecting behaviour in the Apidae and the evolutionary effects of floral oils on host brood cells for cuckoo bees. Focusing on apid bee phylogeny, we reconstructed the evolution of floral oil collection by females, use of floral oils in cell construction and the inclusion of oils in provisioning immatures. Ancestral character reconstruction demonstrates that floral oil-collecting behaviour arose four times independently. We also found that in cuckoo bees, parasitization of oil-collecting bees arose three times (including one secondary return) in Apidae. Except for Ctenoplectrina, oil cuckoo bees are all closely related to each other, forming an independent clade within the Nomadinae. Analysis of evolutionary transition rates indicates that there is a greater tendency for switching from an oil-collecting host to a non-oil-collecting host than the reverse. In apid bees, evolutionary transition rates are higher for switching to cuckoo behaviour from an ancestral lineage in which females collect floral oils than from other pollen-collecting lineages. We conclude that adaptation to oil collection is advantageous for pollen-collecting bees, and that the origin of oil cuckoo bees from non-oil cuckoo bees is constrained.

Studying 3D genome evolution using genomic sequence

The 3D genome is essential to numerous key processes such as the regulation of gene expression and the replication-timing program. In vertebrates, chromatin looping is often mediated by CTCF, and marked by CTCF motif pairs in convergent orientation. Comparative Hi-C recently revealed that chromatin looping evolves across species. However, Hi-C experiments are complex and costly, which currently limits their use for evolutionary studies over a large number of species. Here, we propose a novel approach to study the 3D genome evolution in vertebrates using the genomic sequence only, e.g. without the need for Hi-C data. The approach is simple and relies on comparing the distances between convergent and divergent CTCF motifs (ratio R). We show that R is a powerful statistic to detect CTCF looping encoded in the human genome sequence, thus reflecting strong evolutionary constraints encoded in DNA and associated with the 3D genome. When comparing vertebrate genomes, our results reveal that R which underlies CTCF looping and TAD organization evolves over time and suggest that ancestral character reconstruction can be used to infer R in ancestral genomes.

Phylogenetic position of Echeveria heterosepala (Crassulaceae): a rare species with diagnostic characters of Pachyphytum

<p><strong>Background: </strong><em>Echeveria</em> and <em>Pachyphytum</em> are two closely related Neotropical genera in the Crassulaceae. Several species in <em>Echeveria</em> possess characters cited as diagnostic for <em>Pachyphytum</em> such as a clearly defined stem, a nectary scale on the inner face of petals and as inflorescence a scorpioid cyme or cincinnus. <em>Pachyphytum</em> has been identified as monophyletic while <em>Echeveria</em> as polyphyletic in previous molecular phylogenetic analysess.</p><p><strong>Hypothesis: </strong>The objective of this paper is to identify the phylogenetic position of a rare species with restricted distribution in <em>Echeveria</em>, <em>E. heterosepala</em> that possesses the diagnostic characters of <em>Pachyphytum</em> to better understand the generic limits between these two genera. We expect this species to be closely related to <em>Pachyphytum</em>.</p><p><strong>Methods</strong>: Bayesian inference and Maximum Likelihood analyses were carried out using 47 taxa, including as ingroup, species of <em>Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Sedum</em>, <em>Thompsonella</em> and <em>Villadia</em> and as outgroup, species in<em> Dudleya</em>. Analyses were conducted based on plastid (<em>rpl16, trnL-F</em>) and nuclear (ETS, ITS) markers. Ancestral character reconstruction was carried out under a parsimony criterion based on the molecular trees retrieved by the phylogenetic analyses. Four morphological characters were considered: defined stem, type of inflorescence, nectary scale in petals and position of sepals.</p><strong>Results</strong>: Accessions of <em>E</em>. <em>heterosepala</em> were retrieved in a well-supported clade group comprising exclusively <em>Echeveria</em> species. Therefore this species belongs to <em>Echeveria</em> although possessing characters similar to <em>Pachyphytum</em> and moreover it was not identified closely related to this genus. None of the traits considered have taxonomic importance. The node at the <em>Pachyphytum</em> clade identified unambiguous character states such as stem present, straight sepals, nectary scale on petals, however these character states were identified in the rest of the clades as well. Remarkably, the monophyly of <em>Pachyphytum</em> was corroborated, while <em>Echeveria</em> remains poorly understood.

Towards uncovering evolution of lineage-specific calcium oxalate crystal patterns in Piperales

Piperales is among the largest and most diverse angiosperm orders (>4000 species), occurring broadly in tropical and temperate habitats. Twenty-four of the species from 12 genera, representing all lineages of Piperales, except the holoparasitic Hydnoraceae, display a mixture of leaf calcium oxalate crystal types found in previous studies of the two genera of Piperaceae subfamily Piperoideae (Peperomia Ruiz & Pav. and Piper L.). Crystal macropatterns, a result of varying leaf anatomies and diverse habitats, are investigated in a comparative way by using clearings and recent molecular phylogenetic hypotheses to trace crystal types and macropattern evolution. Ancestral character reconstruction reveals that the most recent common ancestor of Piperales had either crystal sand or druses or both and that prisms, raphides, and styloids are derived from the ancestral crystal type(s). These results are also recovered for both the ancestors of the perianth-less and the perianth-bearing Piperales. Raphides or druses are found in the two other subfamilies of Piperaceae (Verhuellioideae and Zippelioideae). Asaraceae and Lactoridaceae display crystal sand, whereas Aristolochia L. (Aristolochiaceae) species display mainly druses. Our crystal investigation, combined with ancestral character reconstruction, suggests that styloids, raphides, and prisms are derived within Piperales from crystal sand or druses.