贵州台江下-中寒武统凯里组遗迹化石群落与环境关系的探讨

通过贵州台江凯里组中丰富的、分异度较高的、以原地埋藏为特征的遗迹化石的研究,探讨凯里组遗迹化石群落的沉积环境和埋藏环境。凯里组遗迹化石群落以节肢动物和软体动物的停息迹、爬行迹和游泳迹占优势,浅层内生爬行觅食潜穴和系统觅食潜穴占有一定的地位,也见有浅的居住滤食性潜穴,属Seilacher的Cruziana遗迹相,为正常浪基面和风暴浪基面之间的浅海软质基底陆棚低能环境,那里盐度正常、光照充足、含氧量充分、水体平静、沉积速率较快。在此环境中,浮游、游泳以及底栖爬行和固着生物类型大量地生长、繁殖和活动,表生遗迹和浅层内生遗迹十分丰富。生物死亡后的腐烂和分解,使得食泥生物大量繁盛。随着沉积物的覆盖和被埋藏生物遗体的分解、腐烂,沉积物内部还原能力逐渐增强,导致分解和腐烂过程终止。     

Palaeoenvironmental research on diatoms in early and middle Holocene deposits in central North Holland (The Netherlands)

In the geological research of the Holocene coastal deposits of The Netherlands, diatoms are used to reconstruct the sedimentary facies, palaeo-tide levels and salinity gradients during the deposition of the sediments. In this paper, the results of diatom research from 4 borings, taken from the early and middle Holocene deposits of central North Holland are presented. The oldest marine influenced sediments in the area are the deposits of the ‘Velsen layer’, a clay layer rich in organic matter and deposited about 8000–7000¹⁴C years before present (BP) at a depth of 20–12 m below present mean sea-level. This clay layer was formed in a shallow, permanently submerged environment with a limited tidal influence (lagoonal or pond-like conditions). The salinity changed from brackish/freshwater to marine/brackish. The younger sandy and clayey sediments, formed about 7000–4500 BP at a depth of 16–3 m below present mean sea-level, are classified as ‘tidal channel’ and ‘interchannel’ deposits. It is argued, on the base of both diatom and non-diatom criteria, that the lower and middle parts of the interchannel deposits in the central area of the palaeo-tidal basin of North Holland were formed in a subtidal environment. The upper part of the interchannel deposits and the deposits at the fringe of the North Holland tidal basin were formed in the intertidal zone or, at the fringe of the basin, even in the supratidal zone. The salinity in the North Holland tidal basin during the sedimentation of the tidal channel and interchannel deposits was marine/brackish to marine. This study indicates that diatoms, besides their palaeoecological applications, have chronostratigraphical significance (on a regional scale). The diatomsCymatosira belgica andActinoptychus splendens appear to be a useful (eco)stratigraphical marker in the Holocene coastal deposits of The Netherlands and Belgium.     

A review of the sub-species carpatica and tortuosa within the species betula pubescens Ehrh.

Summary

The classifications employed during the last decade for defining sub-specific variation within the species B. pubescens Ehrh. have produced a situation in which the terms carpatica and tortuosa, originally and usually applied to separate taxa, could be regarded as synonymous. This has been caused by the association of both terms, at different times, with B. odorata Bechst. Recent research at Merlewood supports the use of the term ssp. tortuosa and its distinction from ssp. carpatica whose presence in the British flora requires further verification.     

Sequence stratigraphic analysis and sea-level history of the Upper Jurassic deposits (Mozduran Formation), south of Aghdarband,NE Iran

Abstract

The Kopet-Dagh Basin is a large sedimentary basin in northeastern Iran that host the giant Khangiran and Gonbadli gas fields. The Mozduran Formation with its various sedimentary facies is an important reservoir widely distributed in the basin. A sedimentological analysis of Upper Jurassic Mozduran Formation resulted in an accurate reconstruction of the sedimentary environments and the sequence stratigraphic framework south of Aghdarband. The strata consist of six different facies associations including 12 carbonate, one evaporate and two siliciclastic subfacies. On the basis of their various components, structural and textural characteristics, these facies were deposited on a homoclinal ramp in tidal flat to open marine environments ranging from supratidal to subtidal settings. Facies A1 and A2 represent open marine, B1-B4 Shoal, C1-C4 lagoonal and D1, D2, E, T1 and T2 tidal flat and Salina environments. In addition, based on detailed field and laboratory studies on the facies architecture, several large-scale (long-term) depositional sequences could be distinguished in the stratigraphic sections of the study area. These sequences are composed of LST, TST and HST that are separated by a SB1 and SB2 sequence boundaries. The paleogeography of the study area during the Late Jurassic time is reconstructed in five block diagrams.     

A model for the paleoenvironmental distribution of larger foraminifera of Oligocene–Miocene carbonate rocks at Khaviz Anticline,Zagros Basin,SW Iran

Platform carbonate sediments of Oligocene–Miocene age (Asmari Formation) in the Zagros Basin (SW Iran) have been investigated in order to determine their paleoecology and depositional environment. The Zagros Basin is the result of the opening and closure of the Neo-Tethys Ocean along the northeastern border of the Arabian Plate. The thick sedimentary sequences of the Zagros Basin contain rocks ranging in age from Cambrian to recent. The geological evidence suggests that the region was part of a passive continental margin, which subsequently underwent rifting in the Permo-Trias and collision in the Late Tertiary. The Asmari carbonate system was dominated by foraminifera and corallinacean assemblage. Based on the distribution of the larger foraminifera, four assemblage zones have been recognised. Facies analysis allowed the recognition of nine microfacies types that are grouped into three depositional environments that correspond to the inner, middle and outer shelf. The biota assemblage of the Asmari Formation suggests that carbonate sedimentation took place in tropical waters and oligotrophic to slightly mesotrophic conditions. Our detailed analysis of microfacies and paleoecology shows that the Asmari Formation deposited on a carbonate open shelf dominated by heterozoan and, subordinately, photozoan skeletal assemblage.     

Holocene chloroplast genetic variation of shrubs (Alnus alnobetula,Betula nana,Salix sp.) at the siberian tundra‐taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses

Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest‐tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species‐specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.     

Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex

Sex chromosomes often carry large nonrecombining regions that can extend progressively over time, generating evolutionary strata of sequence divergence. However, some sex chromosomes display an incomplete suppression of recombination. Large genomic regions without recombination and evolutionary strata have also been documented around fungal mating-type loci, but have been studied in only a few fungal systems. In the model fungus Podospora anserina (Ascomycota, Sordariomycetes), the reference S strain lacks recombination across a 0.8-Mb region around the mating-type locus. The lack of recombination in this region ensures that nuclei of opposite mating types are packaged into a single ascospore (pseudohomothallic lifecycle). We found evidence for a lack of recombination around the mating-type locus in the genomes of ten P. anserina strains and six closely related pseudohomothallic Podospora species. Importantly, the size of the nonrecombining region differed between strains and species, as indicated by the heterozygosity levels around the mating-type locus and experimental selfing. The nonrecombining region is probably labile and polymorphic, differing in size and precise location within and between species, resulting in occasional, but infrequent, recombination at a given base pair. This view is also supported by the low divergence between mating types, and the lack of strong linkage disequilibrium, chromosomal rearrangements, transspecific polymorphism and genomic degeneration. We found a pattern suggestive of evolutionary strata in P. pseudocomata. The observed heterozygosity levels indicate low but nonnull outcrossing rates in nature in these pseudohomothallic fungi. This study adds to our understanding of mating-type chromosome evolution and its relationship to mating systems.     

Habitat use by a primate community in a lowland dipterocarp forest in Danum Valley,Borneo

Knowledge of niche partitioning with respect to habitat is indispensable to understand the mechanism of coexistence of multiple species. Among primates, however, data are still deficient because repeated survey for a sufficiently long time, covering seasonal changes over a large area, is the only way to clarify habitat segregation within a seasonally fluctuating environment. Southeast Asia is particularly interesting because of the supra-annual, highly unpredictable seasonality in fruiting known as mast fruiting. We conducted repeated route census, habitat monitoring, and group tracking for 25 months in two study sites (ca. 10 km apart) in the largely primary lowland dipterocarp forest of the Danum Valley Conservation Area, eastern Sabah, northern Borneo, Malaysia. The five species of diurnal primates (Bornean orangutan Pongo pygmaeus, Müeller's gibbon Hylobates muelleri, red leaf monkey Presbytis rubicunda, long-tailed macaque Macaca fascicularis, and southern pig-tailed macaque M. nemestrina) did not show horizontal spatial segregation. Red leaf monkeys showed preferences for places with short tree height, but their distribution was not confined to such places. In response to the fruiting peak observed once during the study period, orangutans increased their numbers simultaneously in the two study sites. The average tree height used by the five species was different, but their range overlapped substantially. Compared with other primate communities, the lack of horizontal spatial segregation and the suggested long-distance movement of orangutans seem to be unique characteristics in Borneo, although the use of different forest strata is a widespread phenomenon among primate communities throughout the world.     

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.