Molecular Markers Reveal Cryptic Species Within Polytrichum commune (Common Hair-Cap Moss)

Abstract: Based on morphological characters only, the taxonomy of the moss genus Polytrichum has still not been fully resolved. Application of molecular techniques might clarify some of these problems. Within P. commune s.l., the taxonomic status of several varieties, e.g., P. commune var. commune and P. commune var. uliginosum, is still debated. This study uses allozyme electrophoresis to show that there are two distinct allozyme multi-locus genotypes within our P. commune samples. These two multi-locus genotypes coincide with both differences in morphology and differences in habitat association. This division is corroborated by observations from different Danish and Dutch populations. Based on these results, in connection with a genetic comparison of the two infraspecific taxa of P. commune s.l. with a related species P. formosum, we argue that P. commune var. commune and P. commune var. uliginosum are two genetically distinct entities with fixed morphological differences and a considerable niche differentiation. They should, therefore, be regarded as two distinct species: P. commune and P. uliginosum.     

球状绿藻的隐性生物多样性及其分类学进展

球状绿藻主要指绿藻门中多为单细胞, 形状为球形、近球形, 或由球形衍生出来的其他形状的藻类。球状绿藻分布广泛, 遍布全球, 生活于淡水、海水和亚气生等生境中, 其相似的简单形态下隐藏着复杂的物种多样性。球状绿藻分类学上主要位于绿藻门的两纲四目及其一些独立支系的类群。球状绿藻分类学正由传统的基于形态特征向基于分子信息的复合分类方法转变。球状绿藻隐性的物种多样性涉及约40属, 其中15属是依据新标本材料而建立的新属, 12个属是依据新证据建立的新组合。本文重点介绍了1998年以后在共球藻纲和绿藻纲中新发现和命名的单细胞球状绿藻, 介绍了它们的形态特征、分类学迁移及理由, 特别对常见的小球藻属和栅藻属的分类学概念变迁作了详细介绍, 对一些尚没有中文名的拉丁学名给出了中文命名。另外, 本文讨论了基于DNA的分类学方法在球状绿藻分类学中的应用, 目前系统发育位置的不同已经成为球状绿藻分类的主要依据。目前球状绿藻分类面临的问题是大多分类位置未用分子系统发育方法的验证。 未来, 球状绿藻分类学家应用系统发育研究结合形态学研究探索单细胞球状绿藻的生物多样性。     

Spatial phenotypic and genetic structure of threespine stickleback (Gasterosteus aculeatus) in a heterogeneous natural system,Lake Mývatn,Iceland

Eco‐evolutionary responses of natural populations to spatial environmental variation strongly depend on the relative strength of environmental differences/natural selection and dispersal/gene flow. In absence of geographic barriers, as often is the case in lake ecosystems, gene flow is expected to constrain adaptive divergence between environments – favoring phenotypic plasticity or high trait variability. However, if divergent natural selection is sufficiently strong, adaptive divergence can occur in face of gene flow. The extent of divergence is most often studied between two contrasting environments, whereas potential for multimodal divergence is little explored. We investigated phenotypic (body size, defensive structures, and feeding morphology) and genetic (microsatellites) structure in threespine stickleback (Gasterosteus aculeatus) across five habitat types and two basins (North and South) within the geologically young and highly heterogeneous Lake Mývatn, North East Iceland. We found that (1) North basin stickleback were, on average, larger and had relatively longer spines than South basin stickleback, whereas (2) feeding morphology (gill raker number and gill raker gap width) differed among three of five habitat types, and (3) there was only subtle genetic differentiation across the lake. Overall, our results indicate predator and prey mediated phenotypic divergence across multiple habitats in the lake, in face of gene flow.     

Environmental factors associated with genetic and phenotypic divergence among sympatric populations of Arctic charr (Salvelinus alpinus)

The mechanisms by which phenotypic and genetic divergence may occur among sympatric, conspecific populations have been widely discussed but are still not well understood. Possible mechanisms include assortative mating based on morphology or variation in the reproductive behaviour of phenotypes, and both have been suggested to be relevant to the differentiation of salmonid populations in post-glacial lakes. Here, we studied Arctic charr (Salvelinus alpinus) in Windermere, where putative populations are defined by spatial and temporal variation in spawning. Genetic differentiation was assessed based on nine microsatellite loci, and phenotypic variation was assessed from morphometric characters. We test hypotheses about the relative role of morphology, spawning season and spawning habitat in the evolution of genetic divergence among these populations. Distinct from other lake systems, we find that both morphological and genetic differentiation are restricted primarily to one of two interconnecting basins, that genetic and morphological differentiation are decoupled in this lake and that both phenotype and environment have changed over the last 20 years. The implication is that breeding habitat plays a primary role in isolating populations that differentiate by drift and that phenotypically plastic changes, potentially related to foraging specializations, have either become secondarily decoupled from the genetically defined populations or were never fundamental in driving the evolution of genetic diversity in the Windermere system.     

Cryptic species in the Andean hemiparasite Quinchamalium chilense (Schoepfiaceae: Santalales)

The integration of different characters (e.g. morphological, ecological, and molecular) is now recognized as important in species delimitation. In particular, genetic distances between homologous genes have been suggested as one of the main tools to identify species, especially in the case of cryptic species. Quinchamalium is morphologically variable and occupies a diverse set of biomes across its distribution in the Southern Andes. Recent work based on morphology has synonymized the entire genus as a single morphospecies, Quinchamalium chilense. This widely distributed taxon presents the opportunity to find potential cryptic species. The main objective of this study was to test the existence of cryptic species, based mainly on phylogenetic gene trees, genetic distances, and geographic patterns of haplotypes from molecular markers of the nuclear (ITS) and chloroplast (trnL-F) genomes, considering climatic and morphological characteristics. The ITS phylogeny and corresponding haplotype network resulted in three lineages with strong genetic differentiation and distinct geographic patterns. These lineages were informally named Desert, Matorral, and Mountain, based on their geographic distribution in different biomes. The trnL-F chloroplast phylogeny did not distinguish Desert from Matorral, and the haplotype network showed overlap between these last two lineages. Overall, we hypothesize the existence of two cryptic species within Quinchamalium chilense (Mountain and Matorral–Desert) that correspond to genetic, climatic, and morphological differences.     

甘蔗近缘种滇蔗茅(Erianthus rockii)表型性状遗传多样性研究

选用6个数量性状和23个质量性状对滇蔗茅野生资源的表型变异、多样性及聚类关系进行分析。结果表明,数量性状变异系数在12.72%~22.38%之间,最大的是田间锤度,为22.38%,其次是茎径,为22.27%,最小的是叶长,为12.72%;质量性状的曝光后节间颜色多样性丰富,茎形、芽形、生长裂缝、节间形状、花序形状等5个性状均表现一致;聚类分析表明51份滇蔗茅无性系材料可分为4大类群和5个亚类群。遗传多样性和聚类分析为资源杂交利用和优异基因挖掘提供参考。     

甘蔗近缘种滇蔗茅(Erianthus rockii)表型性状遗传多样性研究

为有效评价和利用蔗茅种质资源,挖掘其优良性状,以滇、黔、川考察收集的29份蔗茅为材料,选取5个数量性状为指标,对其多样性指数、变异系数、数量性状之间的相关性、数量性状与经纬度、海拔的相关性进行研究。分析结果表明：(1)共采集到25份高海拔种质资源,其中海拔超过2800米有4份,进一步丰富了甘蔗野生种质资源库;(2)蔗茅种质资源数量性状的Shannon-Wiener多样性指数均较高,株高多样性指数最高(1.441),锤度多样性指数最低(1.291);数量性状遗传变异较丰富,各性状变异系数范围为21%～38%,变异系数最大的为株高(38%),最小的为叶长(21%);(3)蔗茅种质资源性状差异显著,叶长、叶宽、株高、茎径存在较大相关性,而与锤度不相关;叶宽与经度呈正相关,与纬度、海拔呈负相关。(4)聚类分析结果表明,蔗茅种质资源可分为四大类群,其中Ⅱ类群(EF-27)具有良好的数量性状和锤度品质潜力,可推荐作为甘蔗育种杂交利用首选材料。     

Cryptic biodiversity and phylogeographical patterns in a snapping shrimp species complex

Recent investigations suggest that marine biodiversity may be much higher than earlier estimates, and an important hidden source of diversity in marine systems is the phenomenon of cryptic species complexes. Such complexes are informative models for research into the evolutionary processes that govern species compositions of marine fauna. The snapping shrimp genera Alpheus and Synalpheus are known to harbour large numbers of cryptic species; here, I characterize the genetic structure of the Alpheus armillatus species complex in the northern Caribbean, west Atlantic, and Gulf of Mexico using mitochondrial and nuclear sequence data. Over this geographical region, the complex harbours at least three lineages that are probable reproductively isolated species; all major lineages diverged subsequent to the close of the Isthmus of Panama. Only one lineage was present in the Gulf of Mexico, whereas outside the Gulf of Mexico there was no clear tendency for lineage dominance by geographical region, as most sites were populated by shrimp from at least two lineages. However, within each lineage, there was strong evidence of population genetic differentiation between geographical regions. All lineages showed strong signals of demographic expansion, and one lineage showed sharply reduced genetic diversity, suggestive of past population bottlenecks or recently founded populations with low gene flow from other sites. These results show that evolutionary processes leading to divergence and speciation have been common and recent in the snapping shrimp, and suggest that connectivity among shrimp populations may be limited.     

Evolutionary consequences of human disturbance in a rainforest bird species from Central Africa

Relatively little attention has been directed towards understanding the impacts of human disturbance on evolutionary processes that produce and maintain biodiversity. Here, we examine the influence of anthropogenic habitat changes on traits typically associated with natural and sexual selection in the little greenbul (Andropadus virens), an African rainforest bird species. Using satellite remote-sensing and field survey data, we classified habitats into nonhuman-altered mature and human-altered secondary forest. Mature rainforest consisted of pristine rainforest, with little or no human influence, and secondary forest was characterized by plantations of coffee and cacao and high human impacts. Andropadus virens abundance was higher in secondary forest, and populations inhabiting mature rainforest were significantly larger in wing and tarsus length and bill size; characters often correlated with fitness. To assess the extent to which characters important in sexual section and mate choice might be influenced by habitat change, we also examined differences in plumage colour and song. Plumage colour and the variance in plumage luminance were found to differ between forest types, and song duration was found to be significantly longer in mature forest. The possible adaptive significance of these differences in traits is discussed. Despite relatively high levels of gene flow across habitats, amplified fragment length polymorphism analysis revealed that a small proportion of high-F(ST) loci differentiated mature from secondary forest populations. These loci were significant outliers against neutral expectations in a simulation analysis, suggesting a role for divergent selection in differentiation across habitats. A distance-based redundancy analysis further showed that forest type as defined by remote-sensing variables was significantly associated with genetic dissimilarities between habitats, even when controlling for distance. The observed shifts in morphology, plumage and song were consistent with divergent selection on heritable variation, but a role for plasticity cannot be ruled out. Results suggest that anthropogenic habitat changes may have evolutionary consequences, with implications for conservation and restoration.     

Cryptic species as a window into the paradigm shift of the species concept

The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new “species” paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category—which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a “process” counterpart to the long‐studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance‐based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large‐scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.     

Vicariance in a Cryptic Species Pair of European Pseudoscorpions (Arachnida, Pseudoscorpiones, Chthoniidae)

Following the first records of Chthonius (Ephippiochthonius) boldorii Beier, 1934 in central Europe, a species which was previously assumed to occur exclusively in Mediterranean caves, 116 series (595 specimens) of the cryptic taxa C. (E.) boldorii and C. (E.) fuscimanus Simon, 1900 (Syn. C. (E.) austriacus Beier, 1931) were re-examined. Although multivariate analyses suggest specific separation, there is only one unequivocal character for discrimination: the presence or absence of a single isolated tooth on the moveable finger of the chelicerae. The distributions were found to be largely allopatric, therefore it is concluded that the species rank of the two morphospecies is justified. North of the Alps, an almost vicariant pattern emerged: east of 14° E fuscimanus occurs, west of this line boldorii occurs. The results provide a basis for discussing the relevance of minute morphological differences in pseudoscorpion taxonomy.     

Hidden Biodiversity in an Ecologically Important Freshwater Amphipod: Differences in Genetic Structure between Two Cryptic Species

Cryptic species, i.e. species that are morphologically hard to distinguish, have been detected repeatedly in various taxa and ecosystems. In order to evaluate the importance of this finding, we have to know in how far cryptic species differ in various aspects of their biology. The amphipod Gammarus fossarum is a key invertebrate in freshwater streams and contains several cryptic species. We examined the population genetic structure, genetic diversity and demographic history of two of them (type A and type B) using microsatellite markers and asked whether they show significant differences. We present results of population genetic analyses based on a total of 37 populations from the headwaters of two major European drainages, Rhine and Rhone. We found that, in both species, genetic diversity was geographically structured among and within drainages. For type A in the Rhine and type B in the Rhone, we detected significant patterns of isolation by distance. The increase of genetic differentiation with geographical distance, however, was much higher in type A than in type B. This result indicates substantial interspecific differences in population history and/or the extent of current gene flow between populations. In the Rhine, type B does not show evidence of isolation by distance, and population differentiation is relatively low across hundreds of kilometres. The majority of these populations also show signatures of recent bottlenecks. These patterns are consistent with a recent expansion of type B into the Rhine drainage. In summary, our results suggest considerable and previously unrecognized interspecific differences in the genetic structure of these cryptic keystone species.     

Variability and divergence in Pongamia pinnata (L.) Pierre germplasm – a candidate tree for biodiesel

Three explorations were undertaken in South East Coastal zone of India covering parts of Andhra Pradesh (AP) and Orissa states to collect Pongamia pinnata (L.) Pierre germplasm during March–June 2007. A total of 123 accessions were collected and seed data recorded were analyzed for morphometric traits viz., seed length, seed width, seed thickness, 100‐seed weight and oil content. Variation in the collected germplasm was analyzed using anova , simple measures of variation and D² statistics. Significant genetic variability between seed traits and oil content and association among the seed traits was recorded. Phenotypic variance was higher than genotypic variance for all the characters indicating dominant role of environment. High heritability (broad sense) for 100‐seed weight (97.6%) and oil content (86.7%) indicated the reliability of these characters as selection criteria for plus trees. Genetic gain was maximum for 100‐seed weight (62.6%) followed by oil content (30.5%). D² analysis grouped the accessions into 12 clusters. Cluster XII and cluster IX were the most diverse based on the intercluster distance. Based on the observed diversity, Chittoor, Srikakulam and Adilabad districts of AP are most suitable for collecting diverse germplasm lines and also for in situ conservation.     

Effects of Competition and Temporal Variation on the Evolutionary Potential of Two Native Bunchgrass Species

The capacity of restored plant populations to adapt to new environmental challenges depends on within‐population genetic variation. We examined how much genetic and environmentally based variation for fitness‐associated traits exists within populations of two native grasses commonly used for restoration in California. We were also interested in understanding how phenotypic expression of genetic variation for these traits varies with growth environment. Thirty maternal families of Elymus glaucus (Blue wild rye) and Nassella pulchra (Purple needlegrass) were sampled from both coastal and interior populations and reciprocally transplanted into three replicated common gardens with and without interspecific competition at each site. Reproductive output of families differed both among years and with competition treatments. Phenotypic expression of genetic variation in culm production differed among populations and was very low when families were grown with interspecific competition. Without interspecific competition, the degree of genetic determination peaked in year two in both species (8.4 and 15.1% in E. glaucus and N. pulchra, respectively). Significant genetic differences in reproduction and phenotypic plasticity were found among N. pulchra subpopulations sampled less than 3 km apart, further highlighting the importance of thoroughly sampling available genetic variation in populations used for restoration. The variable and generally low expression of genetic variation indicates that rates of adaptation in restored populations of these native grasses may vary temporally and may be especially slow within competitive environments.     

Quantitative criteria for species delimitation

Species are the fundamental units of biology, ecology and conservation, and progress in these fields is therefore hampered by widespread taxonomic bias and uncertainty. Numerous operational techniques based on molecular or phenotypic data have been designed to overcome this problem, yet existing procedures remain subjective or inconsistent, particularly when applying the biological species concept. We address this issue by developing quantitative methods for a classic technique in systematic zoology, namely the use of divergence between undisputed sympatric species as a yardstick for assessing the taxonomic status of allopatric forms. We calculated mean levels of differentiation in multiple phenotypic characters – including biometrics, plumage and voice – for 58 sympatric or parapatric species‐pairs from 29 avian families. We then used estimates of mean divergence to develop criteria for species delimitation based on data‐driven thresholds. Preliminary tests show that these criteria result in relatively few changes to avian taxonomy in Europe, yet are capable of extensive reassignment of species limits in poorly known tropical regions. While we recognize that species limits are in many cases inherently arbitrary, we argue that our system can be applied to the global avifauna to deliver taxonomic decisions with a high level of objectivity, consistency and transparency.     

中国华东地区孤雌生殖的滨棘虫兆属一新种记述及DNA条形码分析（弹尾纲：棘虫兆科）

记述中国华东地区上海市的滨棘虫兆属1新种:后滩滨棘虫兆Thalassaphorura houtanensis sp.nov.。该种与T.encarpata(Denis,1931)近似,二者均具有A型下唇和相同的假眼式,但可通过爪的形状、下唇毛序、下颚须和腹管加以区分;实验室内的繁殖实验证明该种为严格孤雌生殖种类;同时,对该新种的DNA条形码序列进行了测定分析,发现该新种的种内遗传变异平均为0.18%,介于0~0.46%之间。     

Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics

Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here, we compare genetic differentiation across the genomes of bumblebee species living in sympatry and allopatry to reveal the potential impact of gene flow during species divergence and uncover genetic barrier loci. We first compared the genomes of the alpine bumblebee Bombus sylvicola and a previously unidentified sister species living in sympatry in the Rocky Mountains, revealing prominent islands of elevated genetic divergence in the genome that colocalize with centromeres and regions of low recombination. This same pattern is observed between the genomes of another pair of closely related species living in allopatry (B. bifarius and B. vancouverensis). Strikingly however, the genomic islands exhibit significantly elevated absolute divergence (d_XY) in the sympatric, but not the allopatric, comparison indicating that they contain loci that have acted as barriers to historical gene flow in sympatry. Our results suggest that intrinsic barriers to gene flow between species may often accumulate in regions of low recombination and near centromeres through processes such as genetic hitchhiking, and that divergence in these regions is accentuated in the presence of gene flow.     

Evolutionary and plastic rescue in multitrophic model communities

Under changing environmental conditions, intraspecific variation can potentially rescue populations from extinction. There are two principal sources of variation that may ultimately lead to population rescue: genetic diversity and phenotypic plasticity. We compared the potential for evolutionary rescue (through genetic diversity) and plastic rescue (through phenotypic plasticity) by analysing their differential ability to produce dynamical stability and persistence in model food webs. We also evaluated how rescue is affected by the trophic location of variation. We tested the following hypotheses: (i) plastic communities are more likely to exhibit stability and persistence than communities in which genetic diversity provides the same range of traits. (ii) Variation at the lowest trophic level promotes stability and persistence more than variation at higher levels. (iii) Communities with variation at two levels have greater probabilities of stability and persistence than communities with variation at only one level. We found that (i) plasticity promotes stability and persistence more than genetic diversity; (ii) variation at the second highest trophic level promotes stability and persistence more than variation at the autotroph level; and (iii) more than variation at two trophic levels. Our study shows that proper evaluation of the rescue potential of intraspecific variation critically depends on its origin and trophic location.     

The probability of genetic parallelism and convergence in natural populations

Genomic and genetic methods allow investigation of how frequently the same genes are used by different populations during adaptive evolution, yielding insights into the predictability of evolution at the genetic level. We estimated the probability of gene reuse in parallel and convergent phenotypic evolution in nature using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies. The probability declines with increasing age of the common ancestor of compared taxa, from about 0.8 for young nodes to 0.1–0.4 for the oldest nodes in our study. Probability of gene reuse is higher when populations begin from the same ancestor (genetic parallelism) than when they begin from divergent ancestors (genetic convergence). Our estimates are broadly consistent with genomic estimates of gene reuse during repeated adaptation to similar environments, but most genomic studies lack data on phenotypic traits affected. Frequent reuse of the same genes during repeated phenotypic evolution suggests that strong biases and constraints affect adaptive evolution, resulting in changes at a relatively small subset of available genes. Declines in the probability of gene reuse with increasing age suggest that these biases diverge with time.