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.     

Assessment of mass transfer and mixing in rigid lab‐scale disposable bioreactors at low power input levels

Mass transfer, mixing times and power consumption were measured in rigid disposable stirred tank bioreactors and compared to those of a traditional glass bioreactor. The volumetric mass transfer coefficient and mixing times are usually determined at high agitation speeds in combination with sparged aeration as used for single cell suspension and most bacterial cultures. In contrast, here low agitation speeds combined with headspace aeration were applied. These settings are generally used for cultivation of mammalian cells growing adherent to microcarriers. The rigid disposable vessels showed similar engineering characteristics compared to a traditional glass bioreactor. On the basis of the presented results appropriate settings for adherent cell culture, normally operated at a maximum power input level of 5 W m^?3, can be selected. Depending on the disposable bioreactor used, a stirrer speed ranging from 38 to 147 rpm will result in such a power input of 5 W m^?3. This power input will mix the fluid to a degree of 95% in 22 ± 1 s and produce a volumetric mass transfer coefficient of 0.46 ± 0.07 h^?1. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1269–1276, 2014     

Formation of zeatin allylic phosphate by the microsomal fractions of bulb disks of Iris × hollandica Tub. and tubers of Helianthus tuberosus L.

It is shown that in bulbous Iris zeatin originates from a nucleotide. This nucleotide is probably zeatin-allylic-phosphate, in which a phosphate group is attached to the isoprenoid side-chain of zeatin. The formation of zeatin-allylic-phosphate from t-zeatin and 8-[¹⁴C]-zeatin by the microsomal fractions of Iris bulb disks and Helianthus tubers was demonstrated. The responsible enzyme was partially purified. 5-AMP was found to be a phosphate group delivering substrate. Adenosine and adenine inhibited the enzyme reaction. The significance of the results is discussed in relation to cytokinin biosynthesis and the occurrence of bud blast in Iris.     

Solar irradiance as the proximate cue for flowering in a tropical moist forest

We compared flowering times predicted by six possible proximate cues involving seasonal changes in rainfall and irradiance and flowering times observed over 30 years of weekly censuses for 19 tree and liana species from Barro Colorado Island (BCI), Panama. Hypotheses concerning variation in the timing and intensity of rainfall failed to predict flowering times in any species. In contrast, 10 to 12 weeks of consistent high levels of irradiance predicted flowering times well for eight species, and six or seven weeks of rapidly increasing levels of irradiance predicted flowering times well for two species. None of the six possible proximate cues predicted flowering times adequately for the nine remaining species. We conclude that high and increasing levels of irradiance are the proximate cues for flowering in many BCI species. The seasonal movements of the Intertropical Convergence Zone cause strong seasonal changes in cloud cover, atmospheric transmissivity, and irradiance reaching the BCI forest. Inter‐annual variation in the timing of movements of the Intertropical Convergence Zone is the most likely cause of inter‐annual variation in the timing of flowering in these species. Much work remains to be done as the physiological mechanisms linking flowering and irradiance are unknown and the proximate cues for flowering remain to be identified for many other BCI species.     

Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages

Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substantial karyotypic shuffling. Neotropical primates (NP) represent an ideal case for assessing the performance of MSC methods in such scenarios because chromosome diploid number varies significantly in this lineage. To this end, we investigated the effect of sequence length on the theoretical expectations of MSC model, as well as the results of coalescent‐based tree inference methods. This was carried out by comparing NP with hominids, a lineage in which chromosome macrostructure has been stable for at least 15 million years. We found that departure from the MSC model in Neotropical primates decreased with smaller sequence fragments, where sites sharing the same evolutionary history were more frequently found than in longer fragments. This scenario probably resulted from extensive karyotypic rearrangement occurring during the radiation of NP, contrary to the comparatively stable chromosome evolution in hominids.     

中华绒螯蟹蜕壳生长及其与相关基因表达的关联分析

蜕壳是甲壳动物常见的生长发育现象,但对调控蜕壳与生长的内在机制尚缺乏足够了解。本研究在室内条件下,对中华绒螯蟹(Eriocheir sinensis)一个蜕壳周期内的个体蜕壳与生长现象进行了连续观察,分析了2个蜕壳相关基因,即蜕皮激素受体基因(Ec R)和维甲类X受体基因(RXR),以及1个生长相关基因肌肉生长抑制素基因(MSTN)的表达及其与生长性状的相关性。结果发现,中华绒螯蟹在蜕壳后会出现一个跳跃式生长期,之后进入了一个缓慢持续上升过程,当营养物质积累到一定程度(肥满度达60%左右时)时启动下一次蜕壳;MSTN基因的表达与壳长(r=﹣0.450,P0.05)、壳宽(r=﹣0.410,P0.05)增长率呈显著负相关,而与肥满度呈显著正相关(r=0.450,P0.05),Ec R和RXR基因的表达与体重、壳长和壳宽的增长率均没有显著相关性;相对来说,MSTN在蜕壳后的表达量越高,则增重率越小;而Ec R和RXR在蜕壳后表达量越高,其增重率越大。本研究结果表明,中华绒螯蟹在蜕壳后其生长具有一定的规律性,肥满度可以作为衡量中华绒螯蟹体内营养积累启动蜕壳的指标,Ec R、RXR及MSTN基因表达与生长表型具有一定的相关性。     

Seasonal abundance of nonbreeding Piping Plovers on a Georgia barrier island

ABSTRACT.   Although breeding populations of Piping Plovers are well studied, their winter distribution is less clear. We studied the seasonal abundance of nonbreeding Piping Plovers ( Charadrius melodus ) during the winters of 2003–2004 and 2004–2005 on Little St. Simons Island (LSSI), Georgia. Our objectives were to determine the relative abundance of individuals from three breeding populations at LSSI, and identify possible differences among populations in arrival time, winter movements, or departure time. We observed up to 100 Piping Plovers during peak migration, and approximately 40 plovers wintered at LSSI. From July 2004 to May 2005, approximately 20% of the Great Lakes breeding population used LSSI. Plovers were not present at LSSI during June. All breeding populations of Piping Plovers had similar patterns of temporal occurrence on LSSI, suggesting no need for population-specific management plans at this site. Our results suggest that LSSI is among the most important wintering sites on the Atlantic coast for Piping Plovers, especially for individuals from the endangered Great Lakes population.     

Small hosts infrequently disrupt laying by Brown-headed Cowbirds and Bronzed Cowbirds

ABSTRACT Brood parasites often must overcome host defenses that may include behaviors that serve other functions, such as deterrence of predators and nest attendance during laying and incubation. Host use by brood parasites may also be influenced by competitors in areas where more than one parasitic species occurs. We identified the degree to which behavior of potential hosts and potential competitors affected laying by Brown‐headed Cowbirds (Molothrus ater) and Bronzed Cowbirds (M. aeneus) at a site in south Texas where they co‐occur. We watched potential host nests during the presunrise period to record cowbird laying and document nest visitation, laying, cowbird‐host encounters, and nest attentiveness by hosts. Hosts were frequently at their nests when cowbirds laid eggs (83% of 121 watches among nests of five host species) and cowbirds regularly encountered hosts (43–74% and 40–77% of watches per species of host for Brown‐headed and Bronzed cowbirds, respectively). Host nest defense infrequently interfered with cowbird laying and cowbirds rarely interacted with one another during laying. Overall, 12% of the 42 cowbird laying attempts that elicited host nest defense failed, resulting in cowbird eggs either laid atop hosts as they sat in nests or laid outside the nest cup. We clearly documented that relatively small hosts can thwart parasitism by cowbirds. Thus, the potential for successful defense of nests should be considered when assessing the evolution of behaviors to deter the removal of host eggs by cowbirds and mechanisms leading to nest abandonment. Regarding the latter, the presence of a cowbird at a nest would be a poor indicator for parasitism as some laying attempts were thwarted and unparasitized broods were reared at those nests. Despite the potential for nest defense to affect host use by cowbirds, we did not detect an effect of nest defense. Because most host defense was ineffective, we examined hypotheses for the timing of cowbird laying and host nest attendance. Our analysis of time of day of laying by Brown‐headed Cowbirds at our site and data compiled from the literature suggests that laying time is best predicted by the time of civil twilight (first light) rather than sunrise.     

Anciently duplicated <Emphasis Type="Italic">Broad Complex</Emphasis> exons have distinct temporal functions during tissue morphogenesis

Broad Complex (BRC) is an essential ecdysone-pathway gene required for entry into and progression through metamorphosis in Drosophila melanogaster. Mutations of three BRC complementation groups cause numerous phenotypes, including a common suite of morphogenesis defects involving central nervous system (CNS), adult salivary glands (aSG), and male genitalia. These defects are phenocopied by the juvenile hormone mimic methoprene. Four BRC isoforms are produced by alternative splicing of a protein-binding BTB/POZ-encoding exon (BTB _BRC ) to one of four tandemly duplicated, DNA-binding zinc-finger-encoding exons (Z1 _BRC , Z2 _BRC , Z3 _BRC , Z4 _BRC ). Highly conserved orthologs of BTB _BRC and all four Z _BRC were found among published cDNA sequences or genome databases from Diptera, Lepidoptera, Hymenoptera, and Coleoptera, indicating that BRC arose and underwent internal exon duplication before the split of holometabolous orders. Tramtrack subfamily members, abrupt, tramtrack, fruitless, longitudinals lacking (lola), and CG31666 were characterized throughout Holometabola and used to root phylogenetic analyses of Z _BRC exons, which revealed that the Z _BRC clade includes Z _abrupt . All four Z _BRC domains, including Z4 _BRC , which has no known essential function, are evolving in a manner consistent with selective constraint. We used transgenic rescue to explore how different BRC isoforms contribute to shared tissue-morphogenesis functions. As predicted from earlier studies, the common CNS and aSG phenotypes were rescued by BRC-Z1 in rbp mutants, BRC-Z2 in br mutants, and BRC-Z3 in 2Bc mutants. However, the isoforms are required at two different developmental stages, with BRC-Z2 and -Z3 required earlier than BRC-Z1. The sequential action of BRC isoforms indicates subfunctionalization of duplicated Z _BRC exons even when they contribute to common developmental processes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Isolation, identification and quantitation of hydroxycinnamic acid conjugates, potential platform chemicals, in the leaves and stems of Miscanthus × giganteus using LC-ESI-MSn

Miscanthus × giganteus is a source of platform chemicals and bioethanol through fermentation. Cinnamates in leaves and stems were analysed by LC–ESI-MSⁿ. Free phenols were extracted and separated chromatographically. More than 20 hydroxycinnamates were identified by UV and LC–ESI-MSⁿ. Comparative LC–MS studies on the leaf extract showed isomers of O-caffeoylquinic acid (3-CQA, 4-CQA and 5-CQA), O-feruloylquinic acid (3-FQA, 4-FQA and 5-FQA) and para-coumaroylquinic acid (3-pCoQA and 5-pCoQA). Excepting 3-pCoQA, all were also detected in stem. 5-CQA dominated in leaf; a mandelonitrile–caffeoylquinic acid dominated in stem. Three minor leaf components were distinguished by fragmentation patterns in a targetted MS² experiment as dicaffeoylquinic acid isomers. Others (M_r 516) were tentatively identified as hexosylcaffeoyl-quinates. Three positional isomers of O-caffeoylshikimic acid were minor components. p-Hydroxybenzaldehyde was also a major component in stem. This is the first report of the hydroxycinnamic acid profile of leaves and stems of M. × giganteus.