Search for evolutionary ancient, relict, regulatory peptides

Among numerous regulatory peptides (RP) it is possible to presumably indicate the relict, evolutionary ancient RP. They combine three features: formation from non-specialized peptides-precursors, a comparatively high resistance to action of proteases in the organism media, and maximal simplicity of their structure. The examples of them are glyprolines—a recently identified RP family, as well as tuftsin. Several other praline-containing RP in terminal sites also seem to belong to the evolutionary ancient RP. The proposed approach to studies on the RP evolution is additional to those used traditionally in this problem.     

Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: Implications for phylogeny,species delimitation and life history inference

Ribosomal RNA genes have long been a favoured locus in phylogenetic and metabarcoding studies. Within a genome, rRNA loci are organized as tandem repeated arrays and the copies are homogenized through the process of concerted evolution. However, some level of rRNA variation (intragenomic polymorphism) is known to persist and be maintained in the genomes of many species. In nematode worms, the extent of rRNA polymorphism (RP) across species and the evolutionary and life history factors that contribute to the maintenance of intragenomic RP is largely unknown. Here, we present an extensive analysis across 30 terrestrial nematode species representing a range of free‐living and parasitic taxa isolated worldwide. Our results indicate that RP is common and widespread, ribosome function appears to be maintained despite mutational changes, and intragenomic variants are stable in the genome and neutrally evolving. However, levels of variation were varied widely across rRNA locus and species, with some taxa observed to lack RP entirely. Higher levels of RP were significantly correlated with shorter generation time and high reproductive rates, and population‐level factors may play a role in the geographic and phylogenetic structuring of rRNA variants observed in genera such as Rotylenchulus and Pratylenchus. Although RP did not dramatically impact the clustering and recovery of taxa in mock metabarcoding analyses, the present study has significant implications for global biodiversity estimates of nematode species derived from environmental rRNA amplicon studies, as well as our understanding of the evolutionary and ecological factors shaping genetic diversity across the nematode Tree of Life.     

真菌化石研究进展

随着真菌化石被不断发现,利用化石中的真菌研究真菌类群的起源和进化历程逐渐成为真菌进化生物学研究的一个热点。真菌化石还是研究古生态中真菌与其他生物之间相互作用的重要材料,而这种相互作用既能用于研究古生物间的协同进化,也能成为判断古生态、古气候的重要依据。本文综述了国内外真菌化石的研究进展,旨在为更加系统准确地确定不同真菌类群的分化时间,重建真菌的系统发育树提供参考,同时也为研究生物间相互作用以及推断古生态环境提供帮助。     

Ancient hyaenas highlight the old problem of estimating evolutionary rates

Phylogenetic analyses of ancient DNA data can provide a timeline for evolutionary change even in the absence of fossils. The power to infer the evolutionary rate is, however, highly dependent on the number and age of samples, the information content of the sequence data and the demographic history of the sampled population. In this issue of Molecular Ecology, Sheng et al. ( 2014 ) analysed mitochondrial DNA sequences isolated from a combination of ancient and present‐day hyaenas, including three Pleistocene samples from China. Using an evolutionary rate inferred from the ages of the ancient sequences, they recalibrated the timing of hyaena diversification and suggest a much more recent evolutionary history than was believed previously. Their results highlight the importance of accurately estimating the evolutionary rate when inferring timescales of geographical and evolutionary diversification.     

Ancient DNA enables timing of the pleistocene origin and holocene expansion of two adélie penguin lineages in antarctica

The timing of divergent events in history is one of the central goals of contemporary evolutionary biology. Such studies are however dependent on accurate evolutionary rates. Recent developments in ancient DNA analysis enable the estimation of more accurate evolutionary rates and therefore more accurate timing of divergence events. Consequently, this leads to a better understanding of changes in populations through time. We use an evolutionary rate calculated from ancient DNA of Adélie penguins (Pygoscelis adeliae) to time divergent events in their history. We report the presence of two distinct and highly variable mitochondrial DNA lineages and track changes in these lineages through space and time. When the ancient DNA and the phylogenetic rates are used to estimate the time of origin of the lineages, two very different estimates resulted. In addition, these same rates provide very different estimates of the time of expansion of these lineages. We suggest that the rate calculated from ancient DNA is more consistent with the glacial history of Antarctica and requires fewer assumptions than does a narrative based on the phylogenetic rate. Finally, we suggest that our study indicates an important new role for ancient DNA studies in the timing of divergent events in history.     

Shorter food chain length in ancient lakes: evidence from a global synthesis

Food webs may be affected by evolutionary processes, and effective evolutionary time ultimately affects the probability of species evolving to fill the niche space. Thus, ecosystem history may set important evolutionary constraints on community composition and food web structure. Food chain length (FCL) has long been recognized as a fundamental ecosystem attribute. We examined historical effects on FCL in large lakes spanning >6 orders of magnitude in age. We found that food chains in the world's ancient lakes (n?=?8) were significantly shorter than in recently formed lakes (n?=?10) and reservoirs (n?=?3), despite the fact that ancient lakes harbored much higher species richness, including many endemic species. One potential factor leading to shorter FCL in ancient lakes is an increasing diversity of trophic omnivores and herbivores. Speciation could simply broaden the number of species within a trophic group, particularly at lower trophic levels and could also lead to a greater degree of trophic omnivory. Our results highlight a counter-intuitive and poorly-understood role of evolutionary history in shaping key food web properties such as FCL.     

古代DNA研究实验技术

现代分子生物技术的发展,使从古代样品中获取微量DNA成为现实。在过去的十多年里,古DNA研究取得了重大进展,但实验方案还需要加以改进,其结果的分析与推论也需要多方面的验证。本综述着重介绍了古DNA研究的实验技术及可靠性分析。 Experimental Techniques for Ancient DNA Research YANG Shu-juan1,LAI Xu-long1,2,TANG Xian-hua1,SHENG Gui-lian1,2 1.Faculty of Earth Sciences,China University of Geosciences,Wuhan,430074,China; 2.Institute of Life Sciences,China University of Geosciences,Wuhan,430074,China Abstract:The development of modern molecular biological techniques makes it possible to study minimum DNA from ancient materials.During past decade,a lot of significant achievements on ancient DNA research have been made in many fields especially in molecular evolutionary biology.The nature of degradation and contamination of ancient DNA from ancient biological materials pose a dominating problem in ancient DNA research.Therefore,the experiments should be modified based on the modern molecular techniques and more factors should be considered when the results are analyzed.In this paper,authors review the general experimental protocols on sampling,extraction and amplification as well as authenticity of ancient DNA. Key words：ancient DNA;authenticity;ancient DNA techniques     

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon‐date and calibration error into Bayesian phylogenetic analyses of ancient DNA

Studies of DNA from ancient samples provide a valuable opportunity to gain insight into past evolutionary and demographic processes. Bayesian phylogenetic methods can estimate evolutionary rates and timescales from ancient DNA sequences, with the ages of the samples acting as calibrations for the molecular clock. Sample ages are often estimated using radiocarbon dating, but the associated measurement error is rarely taken into account. In addition, the total uncertainty quantified by converting radiocarbon dates to calendar dates is typically ignored. Here, we present a tool for incorporating both of these sources of uncertainty into Bayesian phylogenetic analyses of ancient DNA. This empirical calibrated radiocarbon sampler (ECRS) integrates the age uncertainty for each ancient sequence over the calibrated probability density function estimated for its radiocarbon date and associated error. We use the ECRS to analyse three ancient DNA data sets. Accounting for radiocarbon‐dating and calibration error appeared to have little impact on estimates of evolutionary rates and related parameters for these data sets. However, analyses of other data sets, particularly those with few or only very old radiocarbon dates, might be more sensitive to using artificially precise sample ages and should benefit from use of the ECRS.     

Sequence of plasmid pBS228 and reconstruction of the IncP-1alpha phylogeny

The antibiotic resistance plasmid pBS228 has been completely sequenced, and revealed to be descended from a plasmid virtually identical to the Birmingham IncP-1alpha plasmid RK2/RP4/RP1. However, it has three additional transposon insertions, one of which is responsible for the extra antibiotic resistances conferred. Loss of kanamycin resistance, which is characteristic of most IncP-1alpha plasmids, is the result of this insertion. A second transposon causes inactivation of the mating pair formation apparatus, rendering the plasmid non-self-transmissible. Comparison with the published data for other IncP-1alpha plasmids gives insight into the recent evolutionary history of this group as well as the acquisition and transmission of one of the first ampicillin resistance transposons discovered.     

方兴未艾的古代DNA的研究

保留在古代生物遗骸中的遗传物质DNA是一种重要的遗传资源。古代DNA的研究对于了解包括人类在内的各种生物的起源、进化和迁徙有重要意义。古代DNA的研究有其自身的特点,并且已经取得一系列重要成就。本文综述古代DNA研究的历史、方法和进展。 Abstract：DNA present in ancient samples can be recovered,amplified and analysed.It opens a new window for genetic analysis in many different disciplines,such as anthropology,archaeology,human population genetics,animal and plant evolutionary taxonomy and forensic science.In general,ancient DNA is rare in quantity,damaged in quality.To ensure the reproducibility and reliability of the results,great cares should be taken,such as various measurements against contamination and phylogenetic analysis of ancient DNA sequences.In this paper we review recovery,amplification and analysis of ancient DNA,also discuss the guidelines to ensure the authenticity of ancient DNA and the recent advances in ancient DNA study.     

Testing two contrasting evolutionary patterns in ancient lakes: species flock versus species scatter in valvatid gastropods of Lake Ohrid

Ancient lakes have long been recognized as “hot spots of evolution” and “evolutionary theatres” and they have significantly contributed to a better understanding of speciation and radiation processes in space and time. Yet, phylogenetic relationships of many ancient lake taxa, particularly invertebrate groups, are still unresolved. Also, the lack of robust morphological, anatomical, and phylogeographical data has largely prevented a rigorous testing of evolutionary hypotheses. For the freshwater gastropod genus Valvata—a group with a high degree of endemism in several ancient lakes—different evolutionary scenarios are suggested for different ancient lakes. Lake Baikal, for example, is inhabited by several endemic Valvata taxa that presumably do not form a monophyletic group. For such an evolutionary pattern, the term ancient lake species scatter is introduced here. In contrast, for the Balkan Lake Ohrid, workers previously suggested the presence of a monophyletic group of endemic Valvata species, that is, an ancient lake species flock. Sequence data of the mitochondrial cytochrome oxidase c subunit I gene (COI) from worldwide taxa, with a strong emphasis on Balkan species, are here used to test whether the putative Ohrid Valvata endemics represent an ancient lake species flock and to study patterns of speciation both on the Ohrid and the Balkan scale. The study reveals three distinct clades of endemic Valvata in Lake Ohrid. Monophyly of these taxa, however, is rejected, and they therefore do not represent an ancient lake species flock, but rather an ancient lake species scatter. Also, in contrast to many other gastropod groups in Lake Ohrid, the valvatids apparently did not radiate. Many Valvata taxa in ancient lakes are characterized by enhanced levels of shell complexity. However, it remains unclear whether these patterns are associated with ancient lake environments per se. It is here suggested that similarities in shell structure between North American and Balkan taxa might simply be due to convergent evolution.     

Ancient DNA

In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.     

Rapid evolution of an ancient lake species flock: Freshwater limpets (Gastropoda: Ancylidae) in the Balkan Lake Ohrid

Ancient lakes have long been recognized as evolutionary theatres and hot spots of endemism; the evolution of their morphologically often highly diverse species flocks has received much attention. However, as each ancient lake has its own geological and evolutionary history, modes of speciation may differ from system to system. Ancient lakes can act as evolutionary reservoirs that assure the survival of relict species, but at the same time extant species may evolve through intralacustrine speciation. Other aspects of interest are the actual rates of immigration, diversification or extinction as well as the temporal framework of morphological change. Many of these questions have been addressed in the African (e.g. Lake Tanganyika) and Asian (e.g. Lake Baikal) ancient lakes. For an European ancient lakes (e.g. Lakes Ohrid and Prespa), such studies are largely missing. In the present paper, extraordinarily shaped endemic freshwater limpets of the genus Ancylus from the Balkan Lake Ohrid are used in a phylogeographic and phylogenetic context to test whether they represent an ancient lake species flock, to study the mode of speciation, and to assess the timing of morphological change. Based on DNA data from two mitochondrial genes (COI, LSU rDNA), it has been found that the Lake Ohrid Ancylus species form an endemic monophyletic group. In addition, the lake's feeder springs are inhabited by another, undescribed Ancylus species. All other studied waterbodies within the watershed do not support their own Ancylus lineages but are inhabited by a widespread Mediterranean taxon. The split between the species endemic to the lake and its sister taxon is dated to 1.4±0.6 million years ago. The study presents the first genetic confirmation for the existence of a species flock in a European ancient lake. Contrary to the prevailing opinion it shows that, concerning Ancylus, Lake Ohrid represents a site of intralacustrine speciation rather than an evolutionary reservoir. Moreover, it provides the first evidence for rapid morphological change in an European ancient lake species flock. See also Electronic Supplement at: http://www.senckenberg.de/odes/06-12.htm.     

Dimetrodon Is Not a Dinosaur: Using Tree Thinking to Understand the Ancient Relatives of Mammals and their Evolution

The line of descent that includes all living mammals extends back in time over 300 million years. Many of the ancient relatives of mammals that fall along this line are very different in appearance from living mammals and are frequently mistaken for reptiles such as dinosaurs. This misconception is reinforced by the fact that these animals are often referred to as “mammal-like reptiles,” a term reflecting outdated methods for classifying organisms. In reality, these ancient mammal-relatives, known as synapsids, are more closely related to living mammals than they are to any reptiles. Evolutionary trees, which depict patterns of descent from common ancestors among organisms, are very useful for understanding why this is the case and for reconstructing the evolutionary histories of many of the unique characters found in mammals. Here, I provide an introduction to evolutionary trees and their implications for understanding the relationships between mammals, synapsids, and reptiles. This is followed by a review of synapsid diversity and a discussion of how evolutionary trees can be used to investigate when in synapsid history different mammalian characteristics first appeared.     

Comparative cytogenetics of human chromosome 3q21.3 reveals a hot spot for ectopic recombination in hominoid evolution

Fluorescence in situ hybridization mapping of fully integrated human BAC clones to primate chromosomes, combined with precise breakpoint localization by PCR analysis of flow-sorted chromosomes, was used to analyze the evolutionary rearrangements of the human 3q21.3-syntenic region in orangutan, siamang gibbon, and silvered-leaf monkey. Three independent evolutionary breakpoints were localized within a 230-kb segment contained in BACs RP11-93K22 and RP11-77P16. Approximately 200 kb of the human 3q21.3 sequence was not present on the homologous orangutan, siamang, and Old World monkey chromosomes, suggesting a genomic DNA insertion into the breakpoint region in the lineage leading to humans and African great apes. The breakpoints in the orangutan and siamang genomes were narrowed down to 12- and 20-kb DNA segments, respectively, which are enriched with endogenous retrovirus long terminal repeats and other repetitive elements. The inserted DNA segment represents part of an ancestral duplication. Paralogous sequence blocks were found at human 3q21, approximately 4 Mb proximal to the evolutionary breakpoint cluster region; at human 3p12.3, which contains an independent orangutan-specific breakpoint; and at the subtelomeric and pericentromeric regions of multiple human and orangutan chromosomes. The evolutionary breakpoint regions between human chromosome 3 and orangutan 2 as well their paralogous segments in the human genome coincide with breaks of chromosomal synteny in the mouse, rat, and/or chicken genomes. Collectively our data reveal reuse of the same short recombinogenic DNA segments in primate and vertebrate evolution, supporting a nonrandom breakage model of genome evolution.     

Ancient lakes revisited: from the ecology to the genetics of speciation

Explosive speciation in ancient lakes has fascinated biologists for centuries and has inspired classical work on the tempo and modes of speciation. Considerable attention has been directed towards the extrinsic forces of speciation—the geological, geographical and ecological peculiarities of ancient lakes. Recently, there has been a resurgence of interest in the intrinsic nature of these radiations, the biological characteristics conducive to speciation. While new species are thought to arise mainly by the gradual enhancement of reproductive isolation among geographically isolated populations, ancient lakes provide little evidence for a predominant role of geography in speciation. Recent phylogenetic work provides strong evidence that multiple colonization waves were followed by parallel intralacustrine radiations that proceeded at relatively rapid rates despite long‐term gene flow through hybridization and introgression. Several studies suggest that hybridization itself might act as a key evolutionary mechanism by triggering major genomic reorganization/revolution and enabling the colonization of new ecological niches in ancient lakes. These studies propose that hybridization is not only of little impediment to diversification but could act as an important force in facilitating habitat transitions, promoting postcolonization adaptations and accelerating diversification. Emerging ecological genomic approaches are beginning to shed light on the long‐standing evolutionary dilemma of speciation in the face of gene flow. We propose an integrative programme for future studies on speciation in ancient lakes.     

A way of functional classification of regulatory peptides. Parameters of divergent and convergent evolution of regulatory peptides

A mathematical method has been presented for systematization of functions of regulatory peptides (RP) and evaluation of directions of evolutionary development of RP systems. For this purpose, traditional methods of vector algebra and multi-dimensional space were used. Effects of various peptide regulators on anxiety, depression, and memory are considered by the example of the three-dimensional space. A way of the functional classification of peptides has been proposed.