A protocol for temporal calibration of general area cladograms

Aim To describe a protocol for incorporating a temporal dimension into historical biogeographical analysis, while maintaining the essential independence of all datasets, involving the generation of general area cladograms. Location Global. Methods General area cladograms (GACs) are a reconstruction of the evolutionary history of a set of areas and unrelated clades within those areas. Nodes on a GAC correspond to speciation events in a group of taxa; general nodes are those at which multiple unrelated clades speciate. We undertake temporal calibration of GACs using molecular clock estimates of splitting events between extant taxa as well as first appearance data from the fossil record. We present two examples based on re‐analysis of previously published data: first, a temporally calibrated GAC generated from secondary Brooks parsimony analysis (BPA) of six extant bird clades from the south‐west of North America using molecular clock estimates of divergence times; and second, an analysis of African Neogene mammals based on a phylogenetic analysis for comparing trees (PACT) analysis. Results A hypothetical example demonstrates how temporal calibration reveals potentially critical information about the timing of both unique and general events, while also illustrating instances of incongruence between dates generated from molecular clock estimates and fossils. For the African Neogene mammal dataset, our analysis reveals that most mammal clades underwent geodispersal associated with the Neogene climatic optimum (c. 16 Ma) and vicariant speciation in central Africa correlated with increased aridity and cooler temperatures around 2.5 Ma. Main conclusions Temporally calibrated GACs are valuable tools for assessing whether coordinated patterns of speciation are associated with large‐scale climatic or tectonic phenomena.     

The Effect of Leaf Age on Gas Exchange and Malate Accumulation in C3-CAM Plant Marrubium Frivaldszkyanum (Lamiaceae)

For the first time the expression of C₃ and CAM in the leaves of different age of Marrubium frivaldszkyanum Boiss, is reported. With increasing leaf age a typical C₃ photosynthesis pattern and high transpiration rate were found. In older leaves a shift to CAM occurred and the 24-h transpiration water loss decreased. A correlation was established between leaf area and accumulation of malate. Water loss at early stages of leaf expansion may be connected with the shift to CAM and the water economy of the whole plant.     

The Amount of BCL6 in B Cells Shortly after Antigen Engagement Determines Their Representation in Subsequent Germinal Centers

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The fifteenth- and twentieth-century colonization of the Basin of Mexico by the Great-tailed Grackle (Quiscalus mexicanus)

Historical evidence indicates that Great‐tailed Grackles colonized the Basin of Mexico from the Gulf Coast lowlands in the fifteenth century. They were probably assisted by an intentional introduction, but colonization succeeded because of anthropogenic habitat alterations over the previous two centuries. During the Colonial period, grackles withdrew from the Basin, only to recolonize it in recent decades. This withdrawal was also due probably to changes in land use, including drainage of much of the water from the Basin's lakes.     

Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation

Accounting for historical demographic features, such as the strength and timing of gene flow and divergence times between closely related lineages, is vital for many inferences in evolutionary biology. Approximate Bayesian computation (ABC) is one method commonly used to estimate demographic parameters. However, the DNA sequences used as input for this method, often microsatellites or RADseq loci, usually represent a small fraction of the genome. Whole genome sequencing (WGS) data, on the other hand, have been used less often with ABC, and questions remain about the potential benefit of, and how to best implement, this type of data; we used pseudo‐observed data sets to explore such questions. Specifically, we addressed the potential improvements in parameter estimation accuracy that could be associated with WGS data in multiple contexts; namely, we quantified the effects of (a) more data, (b) haplotype‐based summary statistics, and (c) locus length. Compared with a hypothetical RADseq data set with 2.5 Mbp of data, using a 1 Gbp data set consisting of 100 Kbp sequences led to substantial gains in the accuracy of parameter estimates, which was mostly due to haplotype statistics and increased data. We also quantified the effects of including (a) locus‐specific recombination rates, and (b) background selection information in ABC analyses. Importantly, assuming uniform recombination or ignoring background selection had a negative effect on accuracy in many cases. Software and results from this method validation study should be useful for future demographic history analyses.     

Links between global taxonomic diversity,ecological diversity and the expansion of vertebrates on land

Tetrapod biodiversity today is great; over the past 400 Myr since vertebrates moved onto land, global tetrapod diversity has risen exponentially, punctuated by losses during major extinctions. There are links between the total global diversity of tetrapods and the diversity of their ecological roles, yet no one fully understands the interplay of these two aspects of biodiversity and a numerical analysis of this relationship has not so far been undertaken. Here we show that the global taxonomic and ecological diversity of tetrapods are closely linked. Throughout geological time, patterns of global diversity of tetrapod families show 97 per cent correlation with ecological modes. Global taxonomic and ecological diversity of this group correlates closely with the dominant classes of tetrapods (amphibians in the Palaeozoic, reptiles in the Mesozoic, birds and mammals in the Cenozoic). These groups have driven ecological diversity by expansion and contraction of occupied ecospace, rather than by direct competition within existing ecospace and each group has used ecospace at a greater rate than their predecessors.     

Bayesian Estimation of the Distribution Function of the Poisson Model

This paper presents the Bayes estimators of the Poisson distribution function based on complete and truncated data under a natural conjugate prior. Laplace transform of the incomplete gamma function and the Gauss hypergeometric function have been employed in order to overcome the intractability of the integrals. Numerical examples from biosciences are given to illustrate the results. A Monte Carlo study has been carried out to compare Bayes estimators under complete data with the corresponding maximum liklihood estimators.     

Potential novel hosts for the lily leaf beetle Lilioceris lilii Scopoli (Coleoptera: Chrysomelidae) in eastern North America

Abstract.  1. Introduced insects often incorporate native plants into their diets and might be expected to show a predilection for novel hosts that are phylogenetically related to their normal hosts. The lily leaf beetle, Lilioceris lilii (Coleoptera: Chrysomelidae), is an introduced pest of cultivated lilies. Oviposition behaviour, larval behaviour, and development of L. lilii was examined on a range of potential host plants, as well as on the normal host, Asiatic hybrid lilies Lilium sp.
2. Neonate larval feeding behaviour was quantified on 15 food plant species: 10 from the Liliales, three from the Asparagales and two eudicots. Larvae fed plants closely related to the genus Lilium were more likely to initiate feeding, less likely to abandon their food leaf, and consumed more leaf area.
3. In no-choice tests, females oviposited on the novel hosts Lilium philadelphicum , Medeola virginiana , Clintonia borealis , Streptopus amplexifolius , and Polygonatum biflorum ; however, all but L. philadelphicum received very few eggs. Non- Lilium novel hosts were not used for oviposition when presented along with Asiatic lilies in choice tests.
4. A single individual was reared to the adult stage on the novel host S. amplexifolius . Several larvae survived to the pupal stage on M. virginiana , although no adults emerged from those pupae. Larvae reared on the native wood lily L. philadelphicum performed equally well or better than on the Asiatic cultivar.
5. Our results indicate that the lily leaf beetle poses a threat to native Liliaceae. Several native Lilium species, including L. philadelphicum , are threatened or endangered in certain jurisdictions throughout their range; these species should be monitored closely for colonisation by the beetle.     

Effect of volume expansion on hemodynamic variables in nephrectomized dogs

We have previously demonstrated that blood pressure elevation by acute blood volume expansion is volume-dependent during the infusion period and resistance-dependent in the post-infusion period in normal anesthetized dogs, and that such an increase in blood pressure is associated with a potentiation of the pressor response to norepinephrine. To evaluate the possible renal contribution to these hemodynamic changes, blood volume expansion was performed for 1 h with dextran dissolved in lactated Ringer's solution (20 ml/kg) in 15 nephrectomized dogs. The mean blood pressure, cardiac output and total peripheral resistance at the end of infusion were 126%, 225% and 60%, respectively; 3 h after volume expansion they were 126%, 151%, and 92% respectively. However, in 4 dogs, there was an increase in mean blood pressure (138%) 3 h after volume expansion. This was thought to result from an increase in the total peripheral resistance (133%) associated with the recovery of cardiac output (106%). The pressor response to norepinephrine (0.5 microgram/kg) was potentiated after volume expansion. These results indicate that the handling of volume by the kidney contributed to the maintenance of an elevated level of cardiac output. However, nephrectomy did not seem to interfere with the hemodynamic switching of the causative factor for blood pressure elevation from increased cardiac output to increased total peripheral resistance. Neither was the potentiation of pressor response to norepinephrine affected.