The dauer hypothesis and the evolution of parasitism: 20 years on and still going strong

How any complex trait has evolved is a fascinating question, yet the evolution of parasitism among the nematodes is arguably one of the most arresting. How did free-living nematodes cross that seemingly insurmountable evolutionary chasm between soil dwelling and survival inside another organism? Which of the many finely honed responses to the varied and harsh environments of free-living nematodes provided the material upon which natural selection could act? Although several complementary theories explain this phenomenon, I will focus on the dauer hypothesis. The dauer hypothesis posits that the arrested third-stage dauer larvae of free-living nematodes such as Caenorhabditis elegans are, due to their many physiological similarities with infective third-stage larvae of parasitic nematodes, a pre-adaptation to parasitism. If so, then a logical extension of this hypothesis is that the molecular pathways which control entry into and recovery from dauer formation by free-living nematodes in response to environmental cues have been co-opted to control the processes of infective larval arrest and activation in parasitic nematodes. The molecular machinery that controls dauer entry and exit is present in a wide range of parasitic nematodes. However, the developmental outputs of the different pathways are both conserved and divergent, not only between populations of C. elegans or between C. elegans and parasitic nematodes but also between different species of parasitic nematodes. Thus the picture that emerges is more nuanced than originally predicted and may provide insights into the evolution of such an interesting and complex trait.     

Determinants of Life-history Evolution in Nematodes

What are the determinants of parasite life-history evolution? Does life-history evolution of parasitic species differ from their free-living relatives? How and why do host and parasite life-history traits covary? Here, Serge Morand and Gabriele Sorci use recent comparative studies to investigate life-history evolution in nematodes which present both parasitic and free-living groups. Application of life-history theory to nematodes suggests that the conventional wisdom concerning the high fecundity of parasitic species could simply be the result of the larger body size of the latter when compared with free-living forms. The authors also emphasize, with the use of examples, that in most cases parasite life-history evolution depends on host features.     

中国淡水蟹分类与分布名录(十足目: 拟地蟹科, 溪蟹科)

中国是世界上淡水蟹物种多样性最高的国家。然而, 迄今为止还没有一个系统的、涵盖全国范围的淡水蟹分类和分布名录。本文收集了涉及中国淡水蟹分类和分布的文献, 采用国际上更新的短尾下目淡水蟹类高级阶元分类系统, 通过系统梳理, 汇编成中国淡水蟹分类与分布名录。该名录共收录了截至2018年1月记述的所有中国淡水蟹类, 共计2科45属311种。其中, 拟地蟹科(Gecarcinucidae Rathbun, 1904) 1属28种; 溪蟹科(Potamidae Ortmann, 1896) 44属283种及亚种; 中国特有属共计38属, 占总数的84%; 特有种共计302种, 占97%。对各省淡水蟹的分布分析发现, 云南是中国淡水蟹物种多样性最丰富的省份, 已记述16属50种; 其次为台湾(4属41种)。本名录首次全面概括了中国淡水蟹类的分类和分布, 可为深入开展全国范围的淡水蟹类生物多样性保护提供科学依据。     

On the extent and origins of genic novelty in the phylum Nematoda

Background

The phylum Nematoda is biologically diverse, including parasites of plants and animals as well as free-living taxa. Underpinning this diversity will be commensurate diversity in expressed genes, including gene sets associated specifically with evolution of parasitism.

Methods and Findings

Here we have analyzed the extensive expressed sequence tag data (available for 37 nematode species, most of which are parasites) and define over 120,000 distinct putative genes from which we have derived robust protein translations. Combined with the complete proteomes of Caenorhabditis elegans and Caenorhabditis briggsae, these proteins have been grouped into 65,000 protein families that in turn contain 40,000 distinct protein domains. We have mapped the occurrence of domains and families across the Nematoda and compared the nematode data to that available for other phyla. Gene loss is common, and in particular we identify nearly 5,000 genes that may have been lost from the lineage leading to the model nematode C. elegans. We find a preponderance of novelty, including 56,000 nematode-restricted protein families and 26,000 nematode-restricted domains. Mapping of the latest time-of-origin of these new families and domains across the nematode phylogeny revealed ongoing evolution of novelty. A number of genes from parasitic species had signatures of horizontal transfer from their host organisms, and parasitic species had a greater proportion of novel, secreted proteins than did free-living ones.

Conclusions

These classes of genes may underpin parasitic phenotypes, and thus may be targets for development of effective control measures.     

Phylogeny of Trichostrongyloidea nematodes as seen through some of their vertebrate hosts]

Reconstruction of the phylogenetic history of a parasitic group is clearly difficult due to a lack of fossil forms. Among the nematodes parasites of vertebrates, the superfamily Trichostrongyloidea is one of the richest groups in terms of number of species (more than 1000 described) and genera (175) and they therefore offer excellent opportunities to reconstruct their phylogeny. Trichostrongyles occur in the gut and less commonly in the stomach and the lungs of all classes of terrestrial vertebrates except the Perissodactyls and the Proboscidian. They have a world wide distribution and direct life cycle. The criteria used in the classification of the Trichostrongyloidea are essentially morphological. Morphological characters are numerous and an attempt has been made to distinguish their relative value. Information concerning the synlophe, which is the apparatus of locomotion and attachment of the worms in the gut of the hosts, has been found essential in order to construct a classification of the superfamily and understand its evolution. This analysis was greatly facilitated by information from two sources: 1) the morphology of free-living rhaditids, which are the ancestors of the trichostrongyles; 2) the ontogeny of the synlophe. The classification established above takes into account the different morphological characters, but only concerns extant animals. Data provided by the hosts permit us to date the appearance of different lineages and to follow their evolution in time and space. These data come from extant hosts and from paleobiogeography. 1) The evidence from extant host species includes the host distribution of the trichostrongyles in relation to the geographic distribution of the hosts. 2) The evidence from extinct forms includes the date of appearance of the host in the geological record as well as mammalian migration in geologic time periods: a) The date of the appearance of the hosts in the geological records permits us to date the origin of the different families of parasites. b) The manner in which host migration interacts with the parasite is very complex and a few examples will be considered, mainly from the caviomorphs, the sciuromorphs and the myomorphs. The combination of evidence from the morphology of the worms and evidence from the paleobiogeography of the hosts allows us not only to explain the present day host and geographic distributions of the parasites but also to reconstruct their evolutionary history. The phylogenetic tree of the Trichostrongyloidea proposed with Chabaud consists of three main branches which are morphologically clearly defined.(ABSTRACT TRUNCATED AT 400 WORDS)     

The Fine Structure of the Integument of Free-Living and Parasitic Copepods. A Review

A perusal of the literature on copepod cuticles has been made, and results of the investigation of six species made by the author are included in this review. The integument of copepods is of the arthropod type. Pore canals and other structures traversing the cuticle, common in most arthropods, are not always present in free-living and some parasitic copepods. In parasitic forms, with advanced morphological changes, the cuticle is generally very thin and the epicuticle in many species forms external microvilli-like structures. In the copepods hitherto investigated the epicuticle is probably the sole layer present in the cuticle. Some copepods show specialized regions of the cuticular surface, the function of which still remains obscure. Integumental organs and integumental structures are numerous and variable. The association of bacteria with the cuticle has been observed in many species. The structure of the integument of parasitic species lacking an alimentary tube and in close contact with the host tissue or hemocoelic cavity supports the idea that the integument could be the obligatory site of nutrient uptake. In spite of the relatively few species of copepods that have been investigated, a remarkable variation of cuticular fine structure has been revealed.     

Macroevolutionary patterns of sexual size dimorphism in copepods

Major theories compete to explain the macroevolutionary trends observed in sexual size dimorphism (SSD) in animals. Quantitative genetic theory suggests that the sex under historically stronger directional selection will exhibit greater interspecific variance in size, with covariation between allometric slopes (male to female size) and the strength of SSD across clades. Rensch''s rule (RR) also suggests a correlation, but one in which males are always the more size variant sex. Examining free-living pelagic and parasitic Copepoda, we test these competing predictions. Females are commonly the larger sex in copepod species. Comparing clades that vary by four orders of magnitude in their degree of dimorphism, we show that isometry is widespread. As such we find no support for either RR or for covariation between allometry and SSD. Our results suggest that selection on both sexes has been equally important. We next test the prediction that variation in the degree of SSD is related to the adult sex ratio. As males become relatively less abundant, it has been hypothesized that this will lead to a reduction in both inter-male competition and male size. However, the lack of such a correlation across diverse free-living pelagic families of copepods provides no support for this hypothesis. By comparison, in sea lice of the family Caligidae, there is some qualitative support of the hypothesis, males may suffer elevated mortality when they leave the host and rove for sedentary females, and their female-biased SSD is greater than in many free-living families. However, other parasitic copepods which do not appear to have obvious differences in sex-based mate searching risks also show similar or even more extreme SSD, therefore suggesting other factors can drive the observed extremes.     

Cryptic diversity of free-living parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. g., n. sp., as inferred from small subunit rDNA sequences

Ultrastructural and molecular phylogenetic evidence indicate that the Parabasalia consists of seven main subgroups: the Trichomonadida, Honigbergiellida, Hypotrichomonadida, Tritrichomonadida, Cristamonadida, Spirotrichonymphida, and Trichonymphida. Only five species of free-living parabasalids are known: Monotrichomonas carabina, Ditrichomonas honigbergii, Honigbergiella sp., Tetratrichomonas undula, and Pseudotrichomonas keilini. Phylogenetic analyses show that free-living species do not form a clade and instead branch in several different positions within the context of their parasitic relatives. Because the diversity of free-living parabasalids is poorly understood, the systematics of these lineages is in a significant state of disarray. In order to better understand the phylogenetic distribution of free-living parabasalids, we sequenced the small subunit rDNA from three different strains reminiscent of P. keilini; the strains were isolated from different geographical locations: (1) mangrove sediments in Japan and (2) sediments in Cyprus. These data demonstrated that the free-living parabasalids P. keilini and Lacusteria cypriaca n. g., n. sp., form a paraphyletic assemblage near the origin of a clade consisting mostly of parasitic trichomonadids (e.g. Trichomonas vaginalis). This paraphyletic distribution of similar morphotypes indicates that free-living trichomonadids represent a compelling example of morphostasis that provides insight into the suite of features present in the most recent free-living ancestor of their parasitic relatives.     

Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.     

伞形科“东亚分支”系统学研究进展

伞形科作为被子植物中非常重要的类群,一直以来都是分类学研究的热点和难点。分类学家基于分子生物学的证据,正在努力构建一个相对合理,且能够反映各类群系统发育关系的分类系统。东亚分支(East-Asia Clade)正是近年来通过分子生物学手段在构建伞形科新的分类系统过程中命名的分支之一。该分支在地理空间上以东亚为主体,集中分布于中国喜马拉雅区域。在东亚地区复杂的地质演化历史背景下,目前该分支的范围并未准确界定,分支内部复杂的演化关系也尚未解决。东亚分支系统学问题的最终解决,将给芹亚科大系统框架的构建带来新的认识。该文结合最新的分子系统学研究结果,回顾了东亚分支提出的历史背景,东亚分支的建立及其在芹亚科中的系统位置,以及东亚分支各属的界定及其系统关系。目前已有的研究结果表明,东亚分支现有约16个属,在芹亚科系统树上与Komarovieae构成姐妹群关系;除了Heptaptera、Keraymonia和膜苞芹属外,其余各属均不构成单系,部分属(如滇芎属、茴芹属和瘤果芹属等)的模式种落入芹亚科别的分支。此外,该文还对研究东亚分支的意义以及该分支目前存在的问题进行了讨论,同时指明了其未来的研究方向。     

Scuticociliate endosymbionts of echinoids (phylum Echinodermata): phylogenetic relationships among species in the genera Entodiscus, Plagiopyliella, Thyrophylax, and Entorhipidium (phylum Ciliophora)

Morphological research on over 50 species of ciliates recorded as endosymbionts of echinoids suggests that invasion of the echinoid microhabitat occurred on at least 4 occasions. Gene sequence data confirm the phylogenetic distinctness of spirotrichean, armophorean, plagiopylean, and oligohymenophorean endosymbionts. It is also likely that oligohymenophoreans have repeatedly invaded the gut habitat. To test this hypothesis, we sequenced small subunit rRNA (SSrRNA) genes of 6 species representing the larger scuticociliate species found in the intestine of Strongylocentrotus pallidus from the northeast Pacific Ocean: Entodiscus borealis (Entodiscidae); Plagiopyliella pacifica and Thyrophylax vorax (Thyrophylacidae); and Entorhipidium pilatum, Entorhipidium tenue, and Entorhipidium sp. (Entorhipidiidae). SsrRNA genes were amplified by PCR, and sequences obtained in both directions. In all phylogenetic analyses, the scuticociliates are well supported as a clade. Entodiscus is distinct from these other echinoid taxa and is the sister taxon to the facultatively parasitic Uronema marinum. The other 5 echinoid species always form a clade whose basal species is the free-living Parauronema longum. The greatest genetic distance among these latter 5 species is less than 1.5%. This probably explains why the Thyrophylacidae and Entorhipidiidae are paraphyletic based on the SSrRNA gene sequences.     

Classification and ordination of cryptogamic communities in Wilkes Land,Continental Antarctica

The entirely cryptogamic vegetation of Bailey and Clark Peninsulas, Windmill Islands, Budd Coast, Wilkes Land, Antarctica, is described for the first time. The vegetation of this area is exceptionally well developed and diverse and represents one of the most important botanical sites on the continent. The macroflora comprises three species of moss, one liverwort, three fruticose lichens, four foliose and over 20 crustose lichens; several macroalgae also occur. Seventy stands of relatively homogeneous vegetation were analysed and the percentage cover afforded by every species within 20 quadrats per site was recorded. A subjective classification was developed by visual ordering of the data sets and a hierarchical system erected which incorporates one moss- and one lichen-dominated sub-formation; the former includes two associations and seven sociations, while the latter comprises one association which includes four sociations. The data were then arranged by centroid linkage analysis to produce and objective classification, and subsequently ordinated by principal components analysis to generate groups of stands, the inter-relations of which were interpreted in ecological and environmental terms. The objective classification and ordination strongly support the subjectively derived groupings or sociations. Examples of plant interactions are qualitatively described.     

Annotated checklist of the leech species diversity in the Maloe More Strait of Lake Baikal,Russia

In this paper, the very first checklist of the freshwater leeches of Maloe More Strait, a special part of Lake Baikal, is presented. It includes 14 free-living and parasitic species, of which four species belong to endemic Baikal genera – two species from Baicalobdella and one species each from Baicaloclepsis and Codonobdella. The checklist highlights six potentially new morphological species recorded for the first time in the area. The exact systematic position is stated for all leech species. Each species from the list is provided with information on taxonomic synonymy, data on its geographic distribution, and ecological characteristics. New species records are additionally provided with brief morphological characteristics and photos of their external morphology.     

基于无人机多源遥感数据的亚热带森林树种分类

树种多样性是生态学研究的重要内容,树木的种类和空间分布信息可有效服务于可持续森林管理。但在复杂林分条件下,获取高精度分类结果的难度大。而无人机遥感可获取局域超精细数据,为树种分类精度的提高提供了可能。基于可见光、高光谱、激光雷达等多源无人机遥感数据,探究其在亚热带林分条件下的树种分类潜力。研究发现:(1)随机森林分类器总体精度和各树种的F1分数最高,适合亚热带多树种的分类制图,其区分13种类别(8乔木,4草本)的总体精度为95.63%,Kappa系数为0.948;(2)多源数据的使用可以显著提高分类精度,全特征模型精度最高,且高光谱和激光雷达数据显著影响全特征模型分类精度,可见光纹理数据作用较小;(3)分类特征重要性从大到小排序为结构信息,植被指数,纹理信息,最小噪声变换分量。     

Exploiting the life cycle of Strongyloides ratii.

The nematode Strongyloides ratti has a remarkable life cycle, which has both a parasitic and a free-living phase. The free-living phase includes a choice between two developmental routes. Here, Mark Viney discusses recent advances in understanding the biology of this developmental switch and shows how the life cycle of this nematode can be used to explore the lifestyle transitions common to all parasitic nematodes, as well as to address other basic biological questions.     

Caenorhabditis elegans as a model for parasitic nematodes: a focus on the cuticle

The phylum Nematoda consists of over half a million species of worms that inhabit astoundingly diverse environments. Nematodes can live as obligatory parasites of plants and animals, or alternate a parasitic with a free-living life style. The fact that the vast majority of species are strictly free living often surprises parasitology students, for obviously the highest research priorities in this field have involved parasites of medical, veterinary and agricultural importance. Here Samuel Politz and Mario Philipp contend that some basic questions concerning the biology of the parasite cuticle can be investigated more easily and in greater depth in the free-living nematode Caenorhabditis elegans than in the parasites themselves.     

Application of flow cytometry to studies of pathogenic free-living amoebae

Species of small, free-living amoebae of the genera Naegleria and Acanthamoeba can cause fatal amoebic meningoencephalitis. Previous investigations have shown that pathogenic amoebae are associated with thermally altered water. Flow cytometric techniques for identifying species of pathogenic and nonpathogenic amoebae from such water have been developed, using immunofluorescence and fluorescein-bound concanavalin A. Flow cytometry is accomplished with a cytofluorograph, in which cells are dispersed in a suspended carrier liquid and passed in front of a focused argon ion laser beam. Cells are then distinguished by the degree of scattered light (size) or fluorescence. Flow cytometry techniques have proven efficient for environmental samples, as indicated by the identification of pathogenic Naegleria fowleri and nonpathogenic Naegleri gruberi and Acanthamoeba castellanii isolated from the Savannah River Plant in South Carolina. Cytofluorographic analysis of environmental samples has several advantages over the current methods of isolation and classification of free-living amoebae. With this system, it is possible to rapidly identify species and quantitate mixtures of pathogenic amoebae in environmental samples. Cytofluorographic analysis of amoebic isolates reduces the time presently required to screen environmental sites for pathogenic amoebae. The cytofluorograph permits detection and species identification of nonthermophilic Naegleria spp. and Acanthamoeba spp. that could not easily be isolated for species identification by conventional methods. Other advantages of flow cytometry over fluorescent microscopy include a high degree of statistical precision due to the large numbers measured, high immunofluorescent titers, and elimination of subjectivity and fluorescence fading.