Morphological evolution and genetic differentiation in Daphnia species complexes

Despite many ecological and evolutionary studies, the history of several species complexes within the freshwater crustacean genus Daphnia (Branchiopoda, Anomopoda) is poorly understood. In particular, the Daphnia longispina group, comprising several large-lake species, is characterized by pronounced phenotypic plasticity, many hybridizing species and backcrossing. We studied clonal assemblages from lakes and ponds comprising daphnids from several species complexes. In order to reveal patterns of reticulate evolution and introgression among species, we analysed three data sets and compared nuclear, mtDNA and morphological divergence using animals from 158 newly established clonal cultures. By examining 15 nuclear and 11 mitochondrial (12S/16S rDNA) genetic characters (allozymes/restriction enzymes), and 48 morphological traits, we found high clonal diversity and discontinuities in genotypic and morphological space which allowed us to group clones by cytonuclear differentiation into seven units (outgroup D. pulex). In contrast to six groups emerging from nuclear divergence (related to three traditional species, D. cucullata, D. galeata, D. hyalina and three pairwise intermediate hybrids), a seventh group of clones was clearly resolved by morphological divergence: distinct mtDNA haplotypes within one nuclear defined cluster, ‘D. hyalina’, resembled traditional D. hyalina and D. rosea phenotypes, respectively. In other nuclear defined clusters, association between mtDNA haplotype and morphology was low, despite hybridization being bidirectional (reciprocal crosses). Morphological divergence was greatest between young sister species which are separated on the lake/pond level, suggesting a significant role for divergent selection during speciation along with habitat shifts. Phylogenetic analyses were restricted to four cytonuclear groups of clones related to species. mtDNA and nuclear phylogenies were consistent in low genetic divergence and monophyly of D. hyalina and D. rosea. Incongruent patterns of phylogenies and different levels of genetic differentiation between traditional species suggest reticulate evolutionary processes.     

Genetic diversity within and genetic differentiation between blooms of a microalgal species

The field of genetic diversity in protists, particularly phytoplankton, is under expansion. However, little is known regarding variation in genetic diversity within populations over time. The aim of our study was to investigate intrapopulation genetic diversity and genetic differentiation in the freshwater bloom-forming microalga Gonyostomum semen (Raphidophyceae). The study covered a 2-year period including all phases of the bloom. Amplified fragment length polymorphism (AFLP) was used to determine the genetic structure and diversity of the population. Our results showed a significant differentiation between samples collected during the two blooms from consecutive years. Also, an increase of gene diversity and a loss of differentiation among sampling dates were observed over time within a single bloom. The latter observations may reflect the continuous germination of cysts from the sediment. The life cycle characteristics of G.?semen, particularly reproduction and recruitment, most likely explain a high proportion of the observed variation. This study highlights the importance of the life cycle for the intraspecific genetic diversity of microbial species, which alternates between sexual and asexual reproduction.     

Morphological differentiation within the Daphnia longispina group

Although morphological evolution is assumed to be slow within Daphnia species complexes, discontinuities in morphological space can be detected. Here, morphological data derived from females of genetically-defined clones (cf. Gießler et al., 1999) are presented, in order to estimate the genetic component of phenotypic variance under standardised laboratory conditions. Animals originated from clonal assemblages of pre-alpine lakes and ponds, and a remote lake in western Germany, covering a wide range of morphotypes known from the traditional species D. cucullata, D. galeata, D. hyalina, D. rosea, and a variety of interspecific hybrids. Phenotypic analyses were based on quantitative and qualitative morphological characters of females in the first and fifth instars. Morphological divergence between clones was analysed using discriminant analysis or multidimensional scaling and the significance of the morphological groupings was estimated using neighbour-joining trees and bootstrapping. All analyses confirmed that (a) phenotypic similarities among taxa change with instar, (b) in contrast to low genetic divergence, pronounced morphological divergence exists between animals separated on the lake/pond level favouring speciation by the habitat shift hypothesis.     

Intraspecific spatial niche differentiation: Evidence from Phyllostachys edulis

Interspecific niche differentiation has attracted much more attention than intraspecific niche differentiation. If the intraspecific competition of invasive species is greater than the interspecific competition, it should reduce the invasive abilities of invasive species. Thus, it is important to understand how invasive species avoid or reduce the intraspecific competition. Phyllostachys edulis in southern China is more competitive than many trees. After it invades a community, it can displace other trees. In the current study, we tested whether the different aged bamboo plants (aged two to eight in two-yr increments) exhibited spatial segregation (spatial niche differentiation). The study was performed in the Ecological Station of Dagang Mountain (114°30′～114°45′E, 27°30′～27°50′N), about 200 km east from Nanchang City, Jiangxi province, China. We recorded the planar coordinates of all the plants with diameter at breast height (DBH) ?3 cm. We used the conditional probability (type-specific probability) surface to show the spatial niche differentiation. We also compared the DBH of four aged groups of bamboo plants. We used the Shapiro–Wilk test to test the normality of DBHs of each age group. If DBHs did not follow the Normal distribution, we used the Weibull function to fit these data. Then we used the Kolmogorov–Smirnov test to test whether any two aged groups of DBHs came from the same population. At the end, we used the generalized additive models (GAMs) and a local regression model (LOESS) to explore whether there is a correlation between DBHs and the corresponding planar coordinates. We found that there was significant spatial segregation in four aged groups based on the statistical test. Bamboo plants may reduce their intraspecific competition by spatial niche differentiation. We found that the DBHs approximated the Weibull distribution, and there were very weak relationships between the DBHs and the spatial locations. We concluded that different aged bamboo plants exhibited spatial segregation and may reduce their intraspecific competition by spatial niche differentiation.     

Evaluation of non-predatory mortality of two Daphnia species in a Siberian reservoir

A new method of estimating non-predatory mortality of zooplanktonbased on live/dead sorting and sediment trap measurement isdescribed. Preliminary results on Daphnia cucullata and Daphnialongispina are given. Estimations of average non-predatory mortalitydemonstrated a significant contribution of this kind of mortalityto total mortality.     

Unravelling plant diversification: Intraspecific genetic differentiation in hybridizing Anacyclus species in the western Mediterranean Basin

Premise

The interfertile species Anacyclus clavatus, A. homogamos, and A. valentinus represent a plant complex coexisting in large anthropic areas of the western Mediterranean Basin with phenotypically mixed populations exhibiting a great floral variation. The goal of this study was to estimate the genetic identity of each species, to infer the role of hybridization in the observed phenotypic diversity, and to explore the effect of climate on the geographic distribution of species and genetic clusters.

Methods

We used eight nuclear microsatellites to genotype 585 individuals from 31 populations of three Anacyclus species for population genetic analyses by using clustering algorithms based on Bayesian models and ordination methods. In addition, we used ecological niche models and niche overlap analyses for both the species and genetic clusters. We used an expanded data set, including 721 individuals from 129 populations for ecological niche models of the genetic clusters.

Results

We found a clear correspondence between species and genetic clusters, except for A. clavatus that included up to three genetic clusters. We detected individuals with admixed genetic ancestry in A. clavatus and in mixed populations. Ecological niche models predicted similar distributions for species and genetic clusters. For the two specific genetic clusters of A. clavatus, ecological niche models predicted remarkably different areas.

Conclusions

Gene flow between Anacyclus species likely explains phenotypic diversity in contact areas. In addition, we suggest that introgression could be involved in the origin of one of the two A. clavatus genetic clusters, which also showed ecological differentiation.     

珍稀濒危飘带兜兰叶绿体全基因组种内变异研究(附录)

飘带兜兰(Paphiopedilum parishii)分布范围狭窄,仅在中国、缅甸、泰国以及老挝有少量分布。近年来,因生境破坏和人为滥采而导致飘带兜兰野生种群极度缩减。为开发种内多态性的分子标记用于保护生物学研究,该研究对飘带兜兰4个野生个体经测序、组装、注释获得的叶绿体基因组序列,与已公布的飘带兜兰2个个体的叶绿体全基因组序列进行比对,分析飘带兜兰叶绿体基因组的种内差异。结果表明:(1)飘带兜兰叶绿体基因组具有典型被子植物叶绿体基因组环状四分体结构,基因组长度为154 403～154 809 bp,共编码129个基因,包括78个蛋白质编码基因、39个tRNA基因、8个rRNA基因,以及4个假基因。(2)在飘带兜兰6个个体叶绿体基因组中检测到103～107个SSRs(simple sequence repeats)位点,其中21个SSR位点具有多态性。此外,在6个个体叶绿体基因组中还检测到60个长序列重复,包括17～21个正向重复、18～29个反向重复、9～16个回文重复、4～9个互补重复。(3)通过比较6个个体叶绿体基因组序列的核苷酸多样性,共发现70处变异,包括10个SNPs(single nucleotide polymorphism)、60个插入缺失(InDels)。其中,有3个SNP位点发生了非同义替换,导致编码功能基因的氨基酸发生改变; 19个插入缺失多态性较高,具有开发为分子标记的潜力。(4)通过计算核苷酸多样性值(P_i)共发现8个有变异的区域,P_i值为0～0.006 32,其中变异度较大的是rps3-rpl22、trnL-UAC-rpl32、rpoB-trnC-GCA以及ycf4,这些高变区可开发为分子标记用于评估飘带兜兰遗传多样性。(5)系统发生分析结果表明,飘带兜兰6个个体叶绿体基因组序列聚在一起,与长瓣兜兰互为姐妹群。综上表明,飘带兜兰叶绿体基因组的SSRs、长序列重复、SNPs、InDels以及核苷酸序列呈现了足够的种内多样性,可开发成分子标记用于该种的系统演化及保护生物学研究。     

Effects of winter conditions on Daphnia dynamics and genetic diversity in a dimictic temperate reservoir

1. Winter conditions shape plankton dynamics and community composition in temperate regions, but their effect on dynamics and genetic composition of cyclical parthenogens like Daphnia is largely unclear. 2. For 5 years, we studied the dynamics, hatching from resting eggs and genetic structure of a D. galeata × longispina hybrid complex in a dimictic, temperate reservoir. Our main hypothesis was that higher spring densities and an earlier population peak will be observed after warmer winters, with a lower genetic diversity because of a lower contribution of resting eggs to population growth. 3. The study period could clearly be categorised into cold‐winter years (n = 3) and warm‐winter years (n = 2). Daphnia densities at the end of spring overturn were ～10‐fold lower after cold winters than after warm ones, but no pattern emerged concerning the timing and the height of the population peak in early summer. 4. Hatching intensity from resting eggs was higher and contributed up to 8.5% to Daphnia abundance in a cold‐winter year compared to a negligible contribution in a warm‐winter year. Consistent with this finding, new multilocus genotypes (MLGs) adding to the overwintering stock after the end of spring overturn and presumably originating from resting eggs increased genetic diversity and attained high frequencies within the population only after a cold winter. New MLGs were recorded also after warm winters, but they never gained dominance and no shift in genetic diversity was observed. However, genetic diversity was not generally reduced after warm winters. 5. Our results confirm earlier findings that winter conditions have only a limited effect on the main growth phase and the peak of Daphnia during late spring and early summer. However, winter conditions determine the contribution of resting eggs to the population development, which may profoundly alter the genetic composition of the population compared to the previous season.     

Genetic differentiation among Oregon lake populations of the Daphnia pulex species complex

Gene flow among invertebrate populations inhabiting bodies of nonflowing freshwater such as ponds or lakes must at some stage involve transport across habitat unsuitable for adult stages. Consequently the potential for interpopulational differentiation is high in these species, yet empirical studies of lake populations of Cladocerans such as Daphnia have failed to reveal high levels of genetic distinctiveness among populations and have led to much speculation about how these populations exchange genes and remain cohesive evolutionary units. In this study we surveyed 42 Oregon lake populations of Daphnia from the D. pulex species complex for genetic variation within the mitochondrial DNA control region. We have used this data to test the relative abilities of various ecological factors to explain the observed patterns in genetic differentiation among lakes. Despite limited genetic variation detected among our samples--11 very similar RFLP-defined mtDNA genotypes from 388 individuals--analyses of nucleotide variance using analogs to Wright's F statistics indicate that when multilake populations are defined in terms of the river drainage basin to which they belong, strong and significant amounts of among-population genetic variation can be detected at this locus (F(ST) estimates between 0.5 and 0.6). In contrast, we fail to detect consistent significant among-population variation when populations are defined on the basis of regional physical geography, bird migratory flyways, or lake trophic status. The manner in which the data are compiled, that is, whether RFLPs or nucleotide sequences are used, has little effect on the overall conclusions, yet it is clear that nucleotide sequence data would lower the standard errors of F(ST) estimates. We propose that periodic widescale flooding during the late Pleistocene may be an important mechanism to homogenize genetic differences among lake Daphnia continent-wide south of the southern-most extent of Pleistocene glaciation.     

Does local adaptation to resources explain genetic differentiation among Daphnia populations?

Substantial genetic differentiation is frequently observed among populations of cyclically parthenogenetic zooplankton despite their high dispersal capabilities and potential for gene flow. Local adaptation has been invoked to explain population genetic differentiation despite high dispersal, but several neutral models that account for basic life history features also predict high genetic differentiation. Here, we study genetic differentiation among four populations of Daphnia pulex in east central Illinois. As with other studies of Daphnia, we demonstrate substantial population genetic differentiation despite close geographic proximity (<50 km; mean θ = 0.22). However, we explicitly tested and failed to find evidence for, the hypothesis that local adaptation to food resources occurs in these populations. Recognizing that local adaptation can occur in traits unrelated to resources, we estimated contemporary migration rates (m) and tested for admixture to evaluate the hypothesis that observed genetic differentiation is consistent with local adaptation to other untested ecological factors. Using Bayesian assignment methods, we detected migrants in three of the four study populations including substantial evidence for successful reproduction by immigrants in one pond, allowing us to reject the hypothesis that local adaptation limits gene flow for at least this population. Thus, we suggest that local adaptation does not explain genetic differentiation among these Daphnia populations and that other factors related to extinction/colonization dynamics, a long approach to equilibrium F_ST or substantial genetic drift due to a low number of individuals hatching from the egg bank each season may explain genetic differentiation.     

Phenotypic differentiation within a foundation grass species correlates with species richness in a subalpine community

The effects of species loss on ecosystems depend on the community’s functional diversity (FD). However, how FD responds to environmental changes is poorly understood. This applies particularly to higher trophic levels, which regulate many ecosystem processes and are strongly affected by human-induced environmental changes. We analyzed how functional richness (FRic), evenness (FEve), and divergence (FDiv) of important generalist predators—epigeic spiders—are affected by changes in woody plant species richness, plant phylogenetic diversity, and stand age in highly diverse subtropical forests in China. FEve and FDiv of spiders increased with plant richness and stand age. FRic remained on a constant level despite decreasing spider species richness with increasing plant species richness. Plant phylogenetic diversity had no consistent effect on spider FD. The results contrast with the negative effect of diversity on spider species richness and suggest that functional redundancy among spiders decreased with increasing plant richness through non-random species loss. Moreover, increasing functional dissimilarity within spider assemblages with increasing plant richness indicates that the abundance distribution of predators in functional trait space affects ecological functions independent of predator species richness or the available trait space. While plant diversity is generally hypothesized to positively affect predators, our results only support this hypothesis for FD—and here particularly for trait distributions within the overall functional trait space—and not for patterns in species richness. Understanding the way predator assemblages affect ecosystem functions in such highly diverse, natural ecosystems thus requires explicit consideration of FD and its relationship with species richness.     

Allochronic differentiation among Daphnia species, hybrids and backcrosses: the importance of sexual reproduction for population dynamics and genetic architecture

Seasonal dynamics of the abundance, sexual reproduction and genetic architecture in a Daphnia hyalina-galeata hybrid complex were studied in the large and deep Lake Constance. We found evidence for the occurrence of first and second order hybridization. Our study revealed strong differences between the parental species not only regarding their seasonal dynamics, genetic architecture and diversity, but also their sexual reproductive behaviour. The overwintering D. hyalina showed low genetic diversity, no genetic differentiation during the season, and reproduced sexually in autumn, whereas D. galeata reached higher levels of genetic diversity, reproduced sexually in early summer, and exhibited changes in genetic structure during the season, but was only present from spring to autumn. However, in both species sexual reproduction was a rare event, and daphnids, including hybrids, reproduced predominantly asexually. This allows long-term persistence of hybrids as well without continuing hybridization events. Within all variables studied, F1 and F2 hybrids showed an intermediate pattern, whereas proposed backcross hybrids were more similar to their respective parentals. These differences in phenotype as well as significant differences in pairwise Fst values between parentals suggest that gene flow seems to be relatively low in the Lake Constance hybrid system. We found evidence for unidirectional introgression by backcrossing from D. galeata to D. hyalina and found a decrease in at least one of the proposed introgressed alleles in the hyalina-backcross while the season progressed. Our findings suggest allochronic differentiation within this hybrid population and different microevolutionary trajectories of the parental species, which will be discussed in the light of the ongoing reoligotrophication process of Lake Constance.     

Genetic diversity and genetic differentiation in Daphnia metapopulations with subpopulations of known age

If colonization of empty habitat patches causes genetic bottlenecks, freshly founded, young populations should be genetically less diverse than older ones that may have experienced successive rounds of immigration. This can be studied in metapopulations with subpopulations of known age. We studied allozyme variation in metapopulations of two species of water fleas (Daphnia) in the skerry archipelago of southern Finland. These populations have been monitored since 1982. Screening 49 populations of D. longispina and 77 populations of D. magna, separated by distances of 1.5-2180 m, we found that local genetic diversity increased with population age whereas pairwise differentiation among pools decreased with population age. These patterns persisted even after controlling for several potentially confounding ecological variables, indicating that extinction and recolonization dynamics decrease local genetic diversity and increase genetic differentiation in these metapopulations by causing genetic bottlenecks during colonization. We suggest that the effect of these bottlenecks may be twofold, namely decreasing genetic diversity by random sampling and leading to population-wide inbreeding. Subsequent immigration then may not only introduce new genetic material, but also lead to the production of noninbred hybrids, selection for which may cause immigrant alleles to increase in frequency, thus leading to increased genetic diversity in older populations.     

Patterns of Intraspecific DNA Variation in the Daphnia Nuclear Genome

Understanding nucleotide variation in natural populations has been a subject of great interest for decades. However, many taxonomic groups, especially those with atypical life history attributes remain unstudied, and Drosophila is the only arthropod genus for which DNA polymorphism data are presently abundant. As a result of the recent release of the complete genome sequence and a wide variety of new genomic resources, the Daphnia system is quickly becoming a promising new avenue for expanding our knowledge of nucleotide variation in natural populations. Here, we examine nucleotide variation in six protein-coding loci for Daphnia pulex and its congeners with particular emphasis on D. pulicaria, the closest extant relative of D. pulex. Levels of synonymous intraspecific variation, π_s, averaged 0.0136 for species in the Daphnia genus, and are slightly lower than most prior estimates in invertebrates. Tests of neutrality indicated that segregating variation conforms to neutral model expectations for the loci that we examined in most species, while K_a/K_s ratios revealed strong purifying selection. Using a full maximum-likelihood coalescent-based method, the ratio of the recombination rate to the mutation rate (c/u), averaged 0.5255 for species of the Daphnia genus. Lastly, a divergence population-genetics approach was used to investigate gene flow and divergence between D. pulex and D. pulicaria.     

Cryptic barriers to dispersal within a lake allow genetic differentiation of Eurasian perch

Gene flow between coexisting or nearby populations normally prevents genetic divergence and local adaptation. Despite this, there are an increasing number of reports of sympatric sister taxa, indicating potential divergence and speciation in the face of gene flow. A large number of such reported cases involve lake-dwelling fish, which are expected to run into few physical barriers to dispersal within their aquatic habitat. However, such cases may not necessarily reflect sympatric speciation if cryptic dispersal barriers are common in lakes and other aquatic systems. In this study, we examined genetic differentiation in perch (Perca fluviatilis L.) from nine locations in a single, small lake (24 km(2)), using microsatellites. We detected significant genetic differentiation in all but two pairwise comparisons. These patterns were not consistent with divergence by distance or the existence of kin groups. Instead, they suggest that cryptic barriers to dispersal exist within the lake, allowing small-scale genetic divergence. Such an observation suggests that allopatric (or parapatric) divergence may be possible, even in small, apparently homogenous environments such as lakes. This has important consequences for how we currently view evidence from nature for sympatric speciation.     

The importance of hatching from resting eggs for population dynamics and genetic composition of Daphnia in a deep reservoir

1. Cyclical parthenogens, organisms switching between sexual and asexual mode of reproduction, are common in aquatic habitats. In permanent waterbodies with year‐round persistence of populations, the relevance of sexually produced resting eggs for population dynamics and structure is still largely unexplored. 2. The aim of this study was to investigate the importance of recruitment from resting eggs to Daphnia spp. in a deep dimictic reservoir with overwintering populations (Saidenbach Reservoir, Germany). We linked field studies on Daphnia population dynamics, hatching rates and diapausing egg abundances in the sediment with allozyme analysis of the genetic variability of both the pelagic population and hatchlings from resting eggs. 3. We found higher hatching rates at intermediate depths (10–18 m), although highest diapausing egg abundances were found in the deeper parts of the reservoir. From the extensive field data, we calculated a population budget for the main basin of the reservoir, which showed that hatched daphnids accounted for <1% of the total abundance and explained only a tiny fraction of population growth. 4. The genetic composition (MultiLocus Genotypes, MLG) of the pelagic population was relatively stable throughout the stratified period with up to five among 39 detected MLGs attaining frequencies >5% per date. From 11 MLGs differentiated among hatched daphnids, three were recovered in the pelagic population in perceptible, albeit low frequencies (1–4%). 5. We conclude that the contribution of hatched animals to the spring population dynamics is negligible in situations with an overwintering population present and will only become relevant if densities are extremely low. In this type of system, the significance of the resting egg bank is presumably mainly related to the maintenance of genetic diversity.     

Low levels of genetic variation within and high levels of genetic differentiation among populations of species of Abies from southern Mexico and Guatemala

Populations of Abies in southern Mexico and Guatemala (A. flinckii, A. guatemalensis, A. hickeli, and A. religiosa) have a patchy distribution. This pattern is particularly clear in A. guatemalensis. Genetic diversity within populations, measured by average heterozygosity at 16 isozyme loci, is lower than the range reported for most conifers (mean H(o) ranging from 0.069 in A. guatemalensis to 0.113 in A. flinckii), while differentiation among populations is higher than that observed in most conifer species studied (θ = F(st) ranging from 0.073 in A. hickeli to 0.271 in A. flinckii). Estimated levels of gene flow are low (ranging from 0.672 in A. flinckii to 3.17 in A. hickeli). Populations in most cases had an excess of homozygosity over that expected under Hardy-Weinberg equilibrium, suggesting some inbreeding (F(is) ranging from 0.074 in A. flinckii to 0.235 in A. guatemalensis). A significant relationship between gene flow and geographic distance was observed in A. religiosa, but not in the other three taxa studied. The patterns of genetic variation appear to have been influenced by the distributions and histories of these species. Paleoclimatic evidence suggests that the ranges of these species retreated upwards during the Pleistocene glaciation and became fragmented during the warming period that followed. The populations could have passed through genetic bottlenecks that reduced genetic variation and led to interpopulation differentiation.     

Intraspecific adaptive radiation: Competition,ecological opportunity,and phenotypic diversification within species

Intraspecific variation in resource‐use traits can have profound ecological and evolutionary implications. Among the most striking examples are resource polymorphisms, where alternative morphs that utilize different resources evolve within a population. An underappreciated aspect of their evolution is that the same conditions that favor resource polymorphism—competition and ecological opportunity—might foster additional rounds of diversification within already existing morphs. We examined these issues in spadefoot toad tadpoles that develop into either a generalist "omnivore" or a specialist "carnivore" morph. Specifically, we assessed the morphological diversity of tadpoles from natural ponds and experimentally induced carnivores reared on alternative diets. We also surveyed natural ponds to determine if the strength of intramorph competition and the diversity and abundance of dietary resources (measures of ecological opportunity) influenced the diversity of within‐morph variation. We found that five omnivore and four carnivore types were present in natural ponds; alternative diets led to shape differences, some of which mirrored variation in the wild; and both competition and ecological opportunity were associated with enhanced morphological diversity in natural ponds. Such fine‐scale intraspecific variation might represent an underappreciated form of biodiversity and might constitute a crucible of evolutionary innovation and diversification.