mtDNA diversity in Chukchi and Siberian Eskimos: implications for the genetic history of Ancient Beringia and the peopling of the New World.

The mtDNAs of 145 individuals representing the aboriginal populations of Chukotka-the Chukchi and Siberian Eskimos-were subjected to RFLP analysis and control-region sequencing. This analysis showed that the core of the genetic makeup of the Chukchi and Siberian Eskimos consisted of three (A, C, and D) of the four primary mtDNA haplotype groups (haplogroups) (A-D) observed in Native Americans, with haplogroup A being the most prevalent in both Chukotkan populations. Two unique haplotypes belonging to haplogroup G (formerly called "other" mtDNAs) were also observed in a few Chukchi, and these have apparently been acquired through gene flow from adjacent Kamchatka, where haplogroup G is prevalent in the Koryak and Itel'men. In addition, a 16111C-->T transition appears to delineate an "American" enclave of haplogroup A mtDNAs in northeastern Siberia, whereas the 16192C-->T transition demarcates a "northern Pacific Rim" cluster within this haplogroup. Furthermore, the sequence-divergence estimates for haplogroups A, C, and D of Siberian and Native American populations indicate that the earliest inhabitants of Beringia possessed a limited number of founding mtDNA haplotypes and that the first humans expanded into the New World approximately 34,000 years before present (YBP). Subsequent migration 16,000-13,000 YBP apparently brought a restricted number of haplogroup B haplotypes to the Americas. For millennia, Beringia may have been the repository of the respective founding sequences that selectively penetrated into northern North America from western Alaska.     

Life history traits as predictors of plant rarity, with particular reference to hemiparasiticOrobanchaceae

We made a comparison between life history and reproductive characteristics of a group of Dutch rare (30) and common (105) plant species, all dicotyledonous and insect-visited forbs. The traits life span, clonality, breeding system, seed production, seed dispersal, and soil seed bank longevity are considered. All trait values have been ranked according to their possible effect on the vulnerability of a species for extinction, where low values indicate a low risk and high values a high risk for a species. Rare and common plants differed significantly in four traits: seed production, breeding system, seed bank longevity and clonality. The discriminant analysis showed that 79% of the 135 species was correctly classified in the group they presently belong to. Especially species that are rare now but were much more common 50–100 years ago were classified as being common species, pointing at the detrimental effect of habitat loss these species encountered at which they have not yet been able to adapted to. The data set include eight hemiparasitic plant species (familyOrobanchaceae), of which six are endangered in The Netherlands and two more common. Both rare and common hemiparasites scored high traits values, indicating that they are vulnerable for extinction. The hemiparasites had several characteristics in common: they are all annuals or biennials that have no means of clonal reproduction. They all have non-clustered, zygomorphic flowers that produce nectar and have a precise pollen presentation and are mainly visited by (bumble) bees. Mean life span was significantly shorter in the eight hemiparasiticOrobanchaceae than in the non-hemiparasiticScrophulariaceae used for comparison (4 species). Overall, we concluded that hemiparasitic plants have a special combination of life history traits which makes them vulnerable for local and regional extinction.     

Ascomycetes associated with ectomycorrhizas: molecular diversity and ecology with particular reference to the Helotiales

Mycorrhizosphere microbes enhance functioning of the plant–soil interface, but little is known of their ecology. This study aims to characterize the ascomycete communities associated with ectomycorrhizas in two Tasmanian wet sclerophyll forests. We hypothesize that both the phyto‐ and mycobiont, mantle type, soil microbiotope and geographical distance affect the diversity and occurrence of the associated ascomycetes. Using the culture‐independent rDNA sequence analysis, we demonstrate a high diversity of these fungi on different hosts and habitats. Plant host has the strongest effect on the occurrence of the dominant species and community composition of ectomycorrhiza‐associated fungi. Root endophytes, soil saprobes, myco‐, phyto‐ and entomopathogens contribute to the ectomycorrhiza‐associated ascomycete community. Taxonomically these Ascomycota mostly belong to the orders Helotiales, Hypocreales, Chaetothyriales and Sordariales. Members of Helotiales from both Tasmania and the Northern Hemisphere are phylogenetically closely related to root endophytes and ericoid mycorrhizal fungi, suggesting their strong ecological and evolutionary links. Ectomycorrhizal mycobionts from Australia and the Northern Hemisphere are taxonomically unrelated to each other and phylogenetically distant to other helotialean root‐associated fungi, indicating independent evolution. The ubiquity and diversity of the secondary root‐associated fungi should be considered in studies of mycorrhizal communities to avoid overestimating the richness of true symbionts.     

mtDNA polymorphism in East Asian Populations,with special reference to the peopling of Japan.

Nucleotide sequences of the major noncoding (D-loop) region of human mtDNA from five East Asian populations including mainland Japanese, Ainu, Ryukyuans, Koreans, and Chinese were analyzed. On the basis of a comparison of 482-bp sequences in 293 East Asians, 207 different sequence types were observed. Of these, 189 were unique to their respective populations, whereas 18 were shared between two or three populations. Among the shared types, eight were found in common between the mainland Japanese and Koreans, which is the largest number in the comparison. The intergenic COII/tRNA(Lys) 9-bp deletion was observed in every East Asian population with varying frequencies. The D-loop sequence variation suggests that the deletion event occurred only once in the ancestry of East Asians. Phylogenetic analysis revealed that East Asian lineages were classified into at least 18 monophyletic clusters, though lineages from the five populations were completely intermingled in the phylogenetic tree. However, we assigned 14 of the 18 clusters for their specificity on the basis of the population from which the maximum number of individuals in each cluster was derived. Of note is the finding that 50% of the mainland Japanese had continental specificity in which Chinese or Koreans were dominant, while < 20% of either Ryukyuans or Ainu possessed continental specificity. Phylogenetic analysis of the entire human population revealed the closest genetic affinity between the mainland Japanese and Koreans. Thus, the results of this study are compatible with the hybridization model on the origin of modern Japanese. It is suggested that approximately 65% of the gene pool in mainland Japanese was derived from the continental gene flow after the Yayoi Age.     

Stress in fishes: a diversity of responses with particular reference to changes in circulating corticosteroids

Physical, chemical and perceived stressors can all evoke non-specificresponses in fish, which are considered adaptive to enable thefish to cope with the disturbance and maintain its homeostaticstate. If the stressor is overly severe or long-lasting to thepoint that the fish is not capable of regaining homeostasis,then the responses themselves may become maladaptive and threatenthe fish's health and well-being. Physiological responses tostress are grouped as primary, which include endocrine changessuch as in measurable levels of circulating catecholamines andcorticosteroids, and secondary, which include changes in featuresrelated to metabolism, hydromineral balance, and cardiovascular,respiratory and immune functions. In some instances, the endocrineresponses are directly responsible for these secondary responsesresulting in changes in concentration of blood constituents,including metabolites and major ions, and, at the cellular level,the expression of heat-shock or stress proteins. Tertiary orwhole-animal changes in performance, such as in growth, diseaseresistance and behavior, can result from the primary and secondaryresponses and possibly affect survivorship. Fishes display a wide variation in their physiological responsesto stress, which is clearly evident in the plasma corticosteroidchanges, chiefly cortisol in actinopterygian fishes, that occurfollowing a stressful event. The characteristic elevation incirculating cortisol during the first hour after an acute disturbancecan vary by more than two orders of magnitude among speciesand genetic history appears to account for much of this interspecificvariation. An appreciation of the factors that affect the magnitude,duration and recovery of cortisol and other physiological changescaused by stress in fishes is important for proper interpretationof experimental data and design of effective biological monitoringprograms.     

中国黑斑蛙种群的线粒体DNA多样性和生物地理演化过程的初探

本文通过对黑斑蛙 8个地方种群 2 5 7个标本的线粒体基因组Cytb基因片段的序列分析 ,探讨了其种群遗传多样性的现代分布格局及其生物地理演化过程。对所检测出的 79个单倍型的分析表明 :黑斑蛙在我国分布区内中部地区的种群遗传多样性高于南北边缘种群。种群间基因流同地理隔离距离呈显著负相关 ,种群遗传分化符合距离隔离或脚踏石模型。线粒体单倍型以广西和四川种群的个体的遗传分化为最深 ,反映出西部山区的屏障隔离效应。单倍型歧点分布分析表明 ,约 10 3- 2 2 6万年前 ,即在末次间冰期 ,黑斑蛙在其分布范围内经历过一次大规模的种群扩张事件。单倍型的分布格局和共享情况显示黑斑蛙种群在冰期后的重新扩张过程主要表现为由南往北的递进式扩散形式。第四纪冰期气候的反复波动导致了黑斑蛙适宜生境在纬度方向上的平移 ,进而导致黑斑蛙种群随生境变化而进行扩张或收缩 ,使黑斑蛙种群的遗传多样性能始终保持在分布区中间高而南北两端低 ,并形成了现代的分布格局     

An evolutionary view of the mechanism for immune and genome diversity

An ortholog of activation-induced cytidine deaminase (AID) was, evolutionarily, the first enzyme to generate acquired immune diversity by catalyzing gene conversion and probably somatic hypermutation (SHM). AID began to mediate class switch recombination (CSR) only after the evolution of frogs. Recent studies revealed that the mechanisms for generating immune and genetic diversity share several critical features. Meiotic recombination, V(D)J recombination, CSR, and SHM all require H3K4 trimethyl histone modification to specify the target DNA. Genetic instability related to dinucleotide or triplet repeats depends on DNA cleavage by topoisomerase 1, which also initiates DNA cleavage in both SHM and CSR. These similarities suggest that AID hijacked the basic mechanism for genome instability when AID evolved in jawless fish. Thus, the risk of introducing genome instability into nonimmunoglobulin loci is unavoidable but tolerable compared with the advantage conferred on the host of being protected against pathogens by the enormous Ig diversification.     

The diversity of ectomycorrhizal fungi associated with introduced Pinus spp. in the Southern Hemisphere, with particular reference to Western Australia

Accepted: 15 June 1998     

Mitochondrial DNA variation and the evolutionary history of cryptic Gammarus fossarum types

The evolutionary history of the cryptic Gammarus fossarum species complex (Crustacea, Amphipoda) in Central Europe was approached by investigating the genetic variation in populations of a natural contact zone. Nucleotide sequence variation of a 395-bp segment of the mitochondrial 16S rRNA gene was compared to that of six nuclear allozyme loci. Three major mtDNA lineages were found, the eastern clade being consistent with the former allozyme type A. The two western clades (types B and C) were not distinguished previously. Strong sequence divergence and correlation with nuclear genetic isolation in syntopic populations, however, justifies the specific status of the three G. fossarum types. The common speciation event is believed to be very old (Miocene). The within-type mtDNA variation is probably molded by the ice ages, with type B populations being most affected. Moreover, the patch-like distribution of mtDNA type B lineages in an area near the contact zone corroborates the hypothesis of a recent colonization.     

Mitochondrial evidence for multiple radiations in the evolutionary history of small apes

Background  

Gibbons or small apes inhabit tropical and subtropical rain forests in Southeast Asia and adjacent regions, and are, next to great apes, our closest living relatives. With up to 16 species, gibbons form the most diverse group of living hominoids, but the number of taxa, their phylogenetic relationships and their phylogeography is controversial. To further the discussion of these issues we analyzed the complete mitochondrial cytochrome b gene from 85 individuals representing all gibbon species, including most subspecies.     

Biogeography of limno-terrestrial Tardigrada, with particular reference to the Antarctic fauna

The Tardigrada is a cosmopolitan phylum of pre-Pangaean origin, yet tardigrade families and genera show distinct biogeographic components isolated by two major geological events. Separate Laurasian and Gondwanan familial clusters correlate with the Triassic disintegration of Pangaea, while discrete Antarctic, Australian and New Zealand familial/generic clusters relate to the subsequent Jurassic/Cretaceous disintegration of Gondwana.     

Early evolutionary history and genomic features of gene duplicates in the human genome

Background

Human gene duplicates have been the focus of intense research since the development of array-based and targeted next-generation sequencing approaches in the last decade. These studies have primarily concentrated on determining the extant copy-number variation from a population-genomic perspective but lack a robust evolutionary framework to elucidate the early structural and genomic characteristics of gene duplicates at emergence and their subsequent evolution with increasing age.

Results

We analyzed 184 gene duplicate pairs comprising small gene families in the draft human genome with 10 % or less synonymous sequence divergence. Human gene duplicates primarily originate from DNA-mediated events, taking up genomic residence as intrachromosomal copies in direct or inverse orientation. The distribution of paralogs on autosomes follows random expectations in contrast to their significant enrichment on the sex chromosomes. Furthermore, human gene duplicates exhibit a skewed gradient of distribution along the chromosomal length with significant clustering in pericentromeric regions. Surprisingly, despite the large average length of human genes, the majority of extant duplicates (83 %) are complete duplicates, wherein the entire ORF of the ancestral copy was duplicated. The preponderance of complete duplicates is in accord with an extremely large median duplication span of 36 kb, which enhances the probability of capturing ancestral ORFs in their entirety. With increasing evolutionary age, human paralogs exhibit declines in (i) the frequency of intrachromosomal paralogs, and (ii) the proportion of complete duplicates. These changes may reflect lower survival rates of certain classes of duplicates and/or the role of purifying selection. Duplications arising from RNA-mediated events comprise a small fraction (11.4 %) of all human paralogs and are more numerous in older evolutionary cohorts of duplicates.

Conclusions

The degree of structural resemblance, genomic location and duplication span appear to influence the long-term maintenance of paralogs in the human genome. The median duplication span in the human genome far exceeds that in C. elegans and yeast and likely contributes to the high prevalence of complete duplicates relative to structurally heterogeneous duplicates (partial and chimeric). The relative roles of regulatory sequence versus exon-intron structure changes in the acquisition of novel function by human paralogs remains to be determined.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1827-3) contains supplementary material, which is available to authorized users.     

Evolutionary ecology of colonial reef-organisms, with particular reference to corals

Sedentary reef-organisms such as sponges, colonial coelenterates, bryozoans and compound ascidians produce repeated modules (aquiferous systems, polyps, zooids) as they grow. Modular construction alleviates constraints on biomass imposed by mechanical and energetic factors that are functions of the surface area to volume ratio. Colonies thus may grow large whilst preserving optimal modular dimensions. Among corals, optimal polyp size is smaller in the more autotrophic than in the more heterotrophic species. Modular construction allows flexibility of growth form, which can adapt to factors such as water currents, silting, light intensity and proximity of competitors. Modular colonies have great regenerative capacities, even separated fragments may survive and grow into new colonies. All fragments from a parental colony are genetically identical and large branching corals frequently undergo clonal propagation through fragmentation during storms. Soft corals can also fragment endogenously. By spreading the risk of mortality among independent units, the generation and dispersal of fragments lessens the likelihood of clonal extinction. In spite of their ability to propagate asexually, most benthic colonial animals also reproduce asexually. The selective advantages of the genetic diversity among sexually produced offspring seem not to be linked with dispersal, but probably lie in the biological interactions with competitors, predators and pathogens in the parental habitat. Age at first sexual maturity and the proportional investment of resources in sexual reproduction are related to colonial survivorship. Small branching corals on reef flats grow quickly, attain sexual maturity within 1–4 years, planulate extensively, but reach only small sizes before dying. Massive corals are longer lived and have the opposite characteristics of growth and reproduction. Most sessile reef organisms compete for space, food or light. Faster growers can potentially outcompete slower growers, but are often prevented from doing so by several forms of aggression from competitors and by the damage inflicted by storms. Competitive interactions among sedentary organisms on coral reefs are unlikely to be linear or deterministic, and so the co-existence of diverse species is possible.