Exchange of genetic information between therian X and Y chromosome gametologs in old evolutionary strata

Therian X and Y sex chromosomes arose from a pair of autosomes. Y chromosomes consist of a pseudoautosomal region that crosses over with the X chromosome and a male‐specific Y‐chromosomal region that does not. The X chromosome can be structured into “evolutionary strata”. Divergence of X‐chromosomal genes from their gametologs is similar within a stratum, but differs among strata, likely caused by a different onset of suppression of crossing over between gametologs. After stratum formation, exchange of information between gametologs has long been believed absent; however, recent studies have shown limited exchange, likely through gene conversion. Herein we investigate exchange of genetic information between gametologs in old strata that formed before the split of Laurasiatheria (cattle) from Euarchontoglires (primates and rodents) with a new phylogenetic approach. A prerequisite for our test is an overall preradiative topology, that is, all X‐chromosomal gametologs are more similar among themselves than to Y‐chromosomal sequences. Screening multiple sequence alignments of the coding sequences of genes from cattle, mice, and humans identified four genes, DDX3X/Y, RBMX/Y, USP9X/Y, and UTX/Y, exhibiting a preradiation topology. Applying our test, we detected exchange of genetic information between all four X and Y gametologs after stratum formation.     

Tempo of Degeneration Across Independently Evolved Nonrecombining Regions

Recombination is beneficial over the long term, allowing more effective selection. Despite long-term advantages of recombination, local recombination suppression can evolve and lead to genomic degeneration, in particular on sex chromosomes. Here, we investigated the tempo of degeneration in nonrecombining regions, that is, the function curve for the accumulation of deleterious mutations over time, leveraging on 22 independent events of recombination suppression identified on mating-type chromosomes of anther-smut fungi, including newly identified ones. Using previously available and newly generated high-quality genome assemblies of alternative mating types of 13 Microbotryum species, we estimated degeneration levels in terms of accumulation of nonoptimal codons and nonsynonymous substitutions in nonrecombining regions. We found a reduced frequency of optimal codons in the nonrecombining regions compared with autosomes, that was not due to less frequent GC-biased gene conversion or lower ancestral expression levels compared with recombining regions. The frequency of optimal codons rapidly decreased following recombination suppression and reached an asymptote after ca. 3 Ma. The strength of purifying selection remained virtually constant at d_N/d_S = 0.55, that is, at an intermediate level between purifying selection and neutral evolution. Accordingly, nonsynonymous differences between mating-type chromosomes increased linearly with stratum age, at a rate of 0.015 per My. We thus develop a method for disentangling effects of reduced selection efficacy from GC-biased gene conversion in the evolution of codon usage and we quantify the tempo of degeneration in nonrecombining regions, which is important for our knowledge on genomic evolution and on the maintenance of regions without recombination.     

Phylogenetic Diversity of Aerobic Saprotrophic Bacteria Isolated from the Daqing Oil Field

A diverse and active microbial community in the stratal waters of the Daqing oil field (China), which is exploited with the use of water-flooding, was found to contain aerobic chemoheterotrophic bacteria (including hydrocarbon-oxidizing ones) and anaerobic fermentative, sulfate-reducing, and methanogenic bacteria. The aerobic bacteria were most abundant in the near-bottom zones of injection wells. Twenty pure cultures of aerobic saprotrophic bacteria were isolated from the stratal waters. Under laboratory conditions, they grew at temperatures, pH, and salinity values typical of the stratal water from which they were isolated. These isolates were found to be able to utilize crude oil and a wide range of hydrocarbons, fatty acids, and alcohols. Phylogenetic analysis carried out with the use of complete 16S rRNA sequences showed that the isolates could be divided into three major groups: gram-positive bacteria with a high and a low G+C content of DNA and gram-negative bacteria of the -subclass of the Proteobacteria. Gram-positive isolates belonged to the genera Bacillus, Brevibacillus, Rhodococcus, Dietzia, Kocuria, Gordonia, Cellulomonas, and Clavibacter. Gram-negative isolates belonged to the genera Pseudomonas and Acinetobacter. In their 16S rRNA sequences, many isolates were similar to the known microbial species and some probably represented new species.     

川东北及陕南三叠纪有孔虫

四川宣汉、万源、旺苍及陕西镇巴三叠纪有孔虫产于中统雷口坡组,下统嘉陵江组及飞仙关组上部.根据有孔虫的分布,划分下统为两个带,5个亚带,中统1个带,并讨论了其对比问题.     

英国北海盆地北部侏罗系微体浮游藻类组合带

研究基于英国北海盆地北部两个钻孔剖面的侏罗纪地层,发现大量的多样化的沟鞭藻及其它有机质藻类（统称为微体浮游藻类）,描述了各组的微体浮游藻类组合,建立了１０个沟鞭藻组合带,并与其它地区同时代地层中的沟鞭藻组合带进行了对比。     

Reconstruction of sedimentary environments in Holocene coastal deposits of the southwest Netherlands; the Poortvliet boring,a case study of palaeoenvironmental diatom research

Diatoms are valuable indicators of palaeosedimentary environments in coastal wetlands. In this paper, the utilization of diatoms in coastal reconstructions will be demonstrated in a case study, the Poortvliet boring (southwest Netherlands). Diatoms supply valuable information about palaeosalinity gradients and palaeotide levels in addition to the existing geological data set, obtained from sediment cores.The ecological data of taxa are usually gathered from diatom studies in recent coastal environments. The study of the Poortvliet boring shows that information can also be obtained from the past (the past as key to the past) by comparing the trends of the relative abundances of species of which the ecology is well-known to those of which the ecology is unknown. It is argued both on recent and fossil data that Cymatosira belgica and Rhaphoneis minutissima have a tychoplanktonic life form.     

Paleocene and Lower Eocene shallow-water limestones of Tibet: Microfacies analysis and correlation of the eastern Neo-Tethyan Ocean

Microfacial investigations of the Lower Paleogene sediments were based on four sections of the passive Indian (Ladakh, Tingri County, Gamba County and Yadong County) and one of the active Asian continental margin (Zhongba County). Eleven microfacies from the Tethyan Himalaya (prefixed with P for passive continental margin) and four from the Xigaze forearc basin (prefixed with A for active continental margin) were observed. The distribution of fossil assemblages in the environment ranges from the tidal flat and restricted lagoonal part of the inner carbonate ramp to the outer carbonate ramp: (P1) green algae pack-/grainstone with small miliolids, (P2) bioclast grainstone, (P3) Rotaliidae packstone, (P4) Miscellaneidae-Rotaliidae-Nummulitidae pack-/grainstone, (P5) laminated and bioturbated mud- and grainstone, (P6) Alveolina wacke-/packstone with Soritidae, (P7) Nummulites-Alveolina-Orbitolites pack-/floatstone, (P8) Discocyclinidae-Nummulitidae pack-/floatstone, (P9) Rhodolith wacke-/packstone, (P10) mudstone with anhydrite nodules, (P11) planktonic foraminiferal wackestone, (A1) molluskan float-/rudstone, (A2) Nummulitidae wacke-/packstone, (A3) rhodolith wacke-/packstone, (A4) Discocyclinidae-Nummulitidae float-/rudstone. The correlation of our observations provides a detailed overview of the paleoenvironmental development and the sedimentary history of the eastern Neo-Tethyan Ocean, showing a deepening trend in two stages from Lower Paleocene to Lower Eocene.     

隆安县荔枝适生地层研究

本文研究隆安县不同地层的土壤元素含量对荔枝生产的影响。通过分析地层的岩石、土壤、荔枝叶矿物元素含量及其与产量的相关性,确定隆安县荔枝适生地层。提出可能促进隆安县荔枝高产的有ＳｉＯ２和Ｍｇ元素;隆安荔枝生产中,土壤的Ｚｎ、Ｂ及Ｎ、Ｐ、Ｋ均感不足;引起荔枝中毒造成地层劣势可能是因为Ａｌ、Ｃｕ、Ａｓ和Ｍｎ含量过高;荔枝含硫量很低,可能为低硫植物。在上述基础上,进行隆安县荔枝生产布局和管理建议。     

Inflorescence Height Affects Visitation Behavior of Bees–A Case Study of an Aquatic Plant Community in Bolivia1

We studied the bee fauna visiting a plant community of 10 species of flowering aquatic plants in an inundated savanna region in Bolivia. In total we observed 36 bee species in 17 genera at the flowers. Cluster analysis of the similarities among the plant species in terms of their visitor spectra showed a division into two groups: plants with inflorescence heights shorter than the grass height and plants with inflorescences projecting out of the surrounding vegetation. Larger bees of the genera Apis, Melipona, Bombus, and Xylocopa were observed only at flowers above the surrounding vegetation. Smaller, mainly solitary bees (e.g., Augochlorella, Ancyloscelis) visited flowers in the dense vegetation near the water surface. Analyses of the pollen loads revealed that most individuals were highly flower constant. When bees carried different pollen types, it was generally pollen from flowers within a single stratum. We discuss specialization, flower constancy, competition, and different foraging strategies as possible reasons for stratum fidelity.     

浅议峡东陡山沱组的“瓶状微化石”

通过对峡东晚震旦世陡山沱组岩石样品的化学浸解处理、连续切片研究及大量薄片观察,作者认为先前报道的陡山沱组“瓶状微化石”,即所谓最古老的原生动物的外壳遗骸,实际上并非什么瓶状微化石,而是一种有蓝藻（可能还有细菌）参与的沉积构造。