Evolution of exceptional species richness among lineages of fleshy-fruited Myrtaceae

MethodsBayesian phylogenetic analyses of plastid and nuclear DNA sequences were used to estimate intertribal relationships and lineage divergence times in Myrtaceae. Focusing on the fleshy-fruited tribes, a variety of statistical approaches were used to assess diversification rates and diversification rate shifts across the family.ConclusionsFleshy fruits have evolved independently in Syzygieae and Myrteae, and this is accompanied by exceptional diversification rate shifts in both instances, suggesting that the evolution of fleshy fruits is a key innovation for rainforest Myrtaceae. Noting the scale dependency of this hypothesis, more complex explanations may be required to explain diversification rate shifts occurring within the fleshy-fruited tribes, and the suggested phylogenetic hypothesis provides an appropriate framework for this undertaking.     

Investigating the evolution of floras: problems and progress — An introduction

The Cape flora of southern Africa is a remarkable hotspot for plant species diversity and endemism. At a meeting in Zurich in 2004 progress in understanding the evolution of this diversity was reviewed. In this symposium, four papers presenting several of the methods used in this investigation were reported. These papers deal with molecular dating methods, the reconstruction of ancestral habitats, with possible speciation scenarios for the Cape flora, and the importance of the correct sampling strategies.     

Tree-ring dating of Russian Pomor settlements in Svalbard

Results of the tree-ring dating of samples from the three Russian settlements of the 18th century (Bjornbeinflyene, Palffyodden, and Schonningholmane) at Svalbard are presented. The present study is a development of a previous work (Chochorowski and Krapiec, 2017). These stations were discovered during excavations conducted by the Polish archaeological expedition of Jagiellonian University in the Sorkappland and Hornsund fjord regions of the Svalbard Archipelago. In total, 5 non-dated samples of the previous work were reanalyzed for these sites: Bjornbeinflyene (2 samples), Palffyodden (1 sample), Schonningholmane (1 sample) and relics from the landing site on the Torrflya coast (1 sample). All samples from these settlements are constructional elements of dwellings, appearing to be prefabricates brought from the continent, and only one of them is a driftwood timber. These floating chronologies were cross-dated against more than 200 master tree-ring chronologies from the Arctic coast, including as well our own data. Cross-dating was performed by CORINA software which includes t-values calculated with different detrending options. As a result, it was possible to successfully date and determine the place of origin of these samples. Results obtained do not contradict the data of radiocarbon and archaeological dating and indicate the possible use of wood from the territories of the White and Kara Sea basins as a building material for the Russian Pomor settlements in Svalbard.     

Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals

Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and nonvisual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time, and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems.     

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra‐ and interspecies samples (mixed samples). As a result, the phylogenetic trees contain interspecies, interpopulation and within‐population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter‐ and intraspecies branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior on Bayesian divergence time estimates by analysing computer‐simulated data sets. We also examined the effect of the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non‐Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyse data sets containing both populations and species variation when its computational efficiency is needed.     

Dendrochronological analysis of an English chest: Contributing to knowledge about wood supply and chest production in 16th century England

Historic furniture has a great ethnographic and historical value, as styles and designs responded to specific uses, fashion trends and the social status of the buyer or the commissioner. Placing it in an exact chronological and geographical production context increases our knowledge about preferences for materials, designs, and woodworking practices for household commodities. Here we present the results of dendrochronological research carried out on an English chest from a private collection. The chest is of a hybrid construction, with boarded sides and back, and a joined front with four carved linenfold panels. It had been described as made of Baltic oak and dating to the mid-16th century, a crucial transition period for which only a few early chests have been analysed. Our results demonstrate, however, that the wood from the lid, side boards and back originates from the south of England. Heartwood/sapwood border in the left side board has allowed an estimated felling date for the tree of between 1520 and 1552. Terminus post quem dates of the rest of the elements pre-dating this interval indicate that the chest was likely made in the second quarter of the 16th century, as initially described. Three linenfold panels show typical features of Baltic wood, whereas the fourth one has different characteristics and could have been made with English oak, but the lack of access to the tree-ring patterns hampers verifying this hypothesis. Mixture of provenances suggests a production workshop in London, although other town in the south with a major timber market cannot be discarded. The construction features are described, and two distinct marks found in the chest are discussed in the regional context of its production. To allow the compilation and inventory of such marks, the ‘Marks on Wood’ community has been created in Zenodo and is presented here.     

Cryptic species,taxonomic inflation,or a bit of both? New species phenomenon in Sri Lanka as suggested by a phylogeny of dwarf geckos (Reptilia,Squamata, Gekkonidae,Cnemaspis)

We evaluated the status of 16 of 22 recognized Sri Lankan Cnemaspis Strauch species, and flagged overlooked diversity with two mitochondrial (cyt b & ND2) and two nuclear markers (RAG1 & PDC) totalling 2829 base pairs. A fossil-calibrated timetree and sampling of other South Asian Cnemaspis provide insights into the diversification of the genus in peninsular India and Sri Lanka. Phylogenetic analyses consistently inferred two broad clades within South Asian Cnemaspis, with Sri Lankan species in two clades, which we call the podihuna and kandiana clades. Each Sri Lankan clade as a whole is sister to Indian taxa and nested within Indian lineages. Cnemaspis modigliani Das from Indonesia is a member of the kandiana clade. This suggests a minimum of two dispersal events between India and Sri Lanka and one between Sri Lanka/India and South-east Asia. South Asian Cnemaspis date back to at least the Eocene, in Sri Lanka to the early Miocene, with late Miocene diversification in the kandiana clade. All but one of the named species we sampled is likely to be valid, and 10 divergent unnamed lineages may warrant specific recognition. A resolution of Sri Lankan Cnemaspis taxonomy will require thorough sampling and the use of both morphological and molecular data.     

Dating the Lower to Middle Paleolithic transition in the Levant: A view from Misliya Cave,Mount Carmel,Israel

The transition from the Lower to the Middle Paleolithic in the Levant is a crucial event in human evolution, since it may involve the arrival of a new human population. In the current study, we present thermoluminescence (TL) dates obtained from 32 burnt flints retrieved from the late Lower Paleolithic (Acheulo-Yabrudian) and Early Middle Paleolithic (Mousterian) layers of Misliya Cave, Mount Carmel, Israel. Early Middle Paleolithic industries rich in Levallois and laminar products were assigned mean ages ranging from ∼250 to ∼160 ka (thousands of years ago), suggesting a production of this industry during MIS 7 and the early part of MIS 6. The mean ages obtained for the samples associated with the Acheulo-Yabrudian (strengthened by an isochron analysis) indicate a production of this cultural complex ∼250 ka ago, at the end of MIS 8. According to the Misliya TL dates, the transition from the Lower to the Middle Paleolithic in the site took place at the limit MIS 8/7 or during the early part of MIS 7. The dates, together with the pronounced differences in lithic technology strongly suggest the arrival of a new population during this period.     

Intraracial harassment on campus: explaining between- and within-group differences

Using the National Longitudinal Survey of Freshmen (NLSF), we examine both between- and within-group differences in the odds of feeling intraracially harassed. Specifically, we investigate the effects of colleges’ and universities’ racial composition as well as the nature of students’ associations with non-group members, including involvement in racially homogeneous campus organizations, ethnoracial diversity of friendship networks, and interracial dating. Our findings suggest that although college racial composition appears to have little effect on experiencing intraracial harassment, the nature of students’ involvement with other-race students matters a great deal. For all groups, interracial dating increased odds of harassment. Among black and white students, more diverse friendship networks did as well. And among Asian and Latino students, involvement in any racially homogeneous campus organization was associated with increases in reports of intraracial harassment. Thus, we propose a baseline theoretical model of intraracial harassment that highlights the nature of students’ associations with outgroups.