570 Biowissenschaften; Biologie
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The anatomically modern human Homo sapiens sapiens is distinguished by a high adaptability in physiology, physique and behaviour in short term changing environmental conditions. Since our environmental factors are constantly changing because of anthropogenic influences, the question arises as to how far we have an impact on the human phenotype in the very sensitive growth phase in children and adolescents. Growth and development of all children and adolescents follow a universal and typical pattern. This pattern has evolved as the result of trade-offs in the 6-7 million years of human evolution. This typically human growth pattern differs from that of other long-living social primate species. It can be divided into different biological age stages, with specific biological, cognitive and socio-cultural signs. Phenotypic plasticity is the ability of an organism to react to an internal or external environmental input with a change in the form, state, and movement rate of activity (West-Eberhard 2003). The plasticity becomes visible and measurable particularly when, in addition to the normal variability of the phenotypic characteristics within a population, the manifestation of this plasticity changes within a relatively short time. The focus of the present work is the comparison of age-specific dimensional changes. The basic of the presented studies are more than 75,000 anthropometric data-sets of children and adolescence from 1980 up today and historical data of height available in scientific literature. Due to reduced daily physical activity, today's 6-18 year-olds have lower values of pelvic and elbow breadths. The observed increase in body height can be explained by hierarchies in social networks of human societies, contrary to earlier explanations (influence of nutrition, good living conditions and genetics). A shift towards a more feminine fat distribution pattern in boys and girls is parallel to the increase in chemicals in our environment that can affect the hormone system. Changing environmental conditions can have selective effects over generations so that that genotype becomes increasingly prevalent whose individuals have a higher progeny rate than other individuals in this population. Those then form the phenotype which allows optimum adaptation to the changes of the environmental conditions. Due to the slow patterns of succession and the low progeny rate (Hawkes et al. 1998), fast visible in the phenotype due to changes in the genotype of a population are unlikely to occur in the case of Homo sapiens sapiens within short time. In the data sets on which the presented investigations are based, such changes appear virtually impossible. The study periods cover 5-30 to max.100 years (based on data from the body height from historical data sets).
High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present ‘TAPAS’, (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.
Background
The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely related species triggers embryogenesis of the apomictic oocytes, but typically does not contribute genetic material to the next generation. We compare for the first time the gonadal transcriptome of the Amazon molly to those of both ancestral species, P. mexicana and P. latipinna.
Results
We sequenced the gonadal transcriptomes of the P. formosa and its parental species P. mexicana and P. latipinna using Illumina RNA-sequencing techniques (paired-end, 100 bp). De novo assembly of about 50 million raw read pairs for each species was performed using Trinity, yielding 106,922 transcripts for P. formosa, 115,175 for P. latipinna, and 133,025 for P. mexicana after eliminating contaminations. On the basis of sequence similarity comparisons to other teleost species and the UniProt databases, functional annotation, and differential expression analysis, we demonstrate the similarity of the transcriptomes among the three species. More than 40% of the transcripts for each species were functionally annotated and about 70% were assigned to orthologous genes of a closely related species. Differential expression analysis between the sexual and unisexual species uncovered 2035 up-regulated and 564 down-regulated genes in P. formosa. This was exemplary validated for six genes by qRT-PCR.
Conclusions
We identified more than 130 genes related to meiosis and reproduction within the apomictically reproducing P. formosa. Overall expression of these genes seems to be down-regulated in the P. formosa transcriptome compared to both ancestral species (i.e., 106 genes down-regulated, 29 up-regulated). A further 35 meiosis and reproduction related genes were not found in the P. formosa transcriptome, but were only expressed in the sexual species. Our data support the hypothesis of general down-regulation of meiosis-related genes in the apomictic Amazon molly. Furthermore, the obtained dataset and identified gene catalog will serve as a resource for future research on the molecular mechanisms behind the reproductive mode of this unisexual species.