Phylogeography and regional endemism of a passively dispersing zooplankter: mitochondrial DNA variation in rotifer resting egg banks.

We investigated the phylogeography of the salt water rotifer Brachionus plicatilis, a cyclical parthenogen with passive dispersal mechanisms, using resting eggs recovered from saline lake sediments. Individual resting eggs were obtained from a large selection of lakes which were representative of five endorheic basins and the chain of coastal ponds in the Iberian Peninsula. The novel use of resting eggs allows the integration of seasonal and annual variations as well as the impact of stochastic effects such as drift and local extinction. A 653 bp fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene was sequenced from 98 eggs. Our results revealed a deep phylogeographical structure in this species, with a division into two main lineages with distinct geographical distributions, which probably diverged at the beginning of the Pleistocene period. Most of the mitochondrial DNA haplotypes were restricted to single lakes. Nested clade analysis supported Early Pleistocene fragmentation of populations, low gene flow and some long-distance colonization. These conclusions contrast strongly with previous ideas on rotifer biogeography and this pattern is consistent with a recolonization of the Iberian Peninsula from two glacial refugia. The results provide new insights into the processes responsible for the genetic diversification of passive dispersers, a life-history trait typical of zooplanktonic biotas.     

Long-term coexistence of rotifer cryptic species

Despite their high morphological similarity, cryptic species often coexist in aquatic habitats presenting a challenge in the framework of niche differentiation theory and coexistence mechanisms. Here we use a rotifer species complex inhabiting highly unpredictable and fluctuating salt lakes to gain insights into the mechanisms involved in stable coexistence in cryptic species. We combined molecular barcoding surveys of planktonic populations and paleogenetic analysis of diapausing eggs to reconstruct the current and historical coexistence dynamics of two highly morphologically similar rotifer species, B. plicatilis and B. manjavacas. In addition, we carried out laboratory experiments using clones isolated from eight lakes where both species coexist to explore their clonal growth responses to salinity, a challenging, highly variable and unpredictable condition in Mediterranean salt lakes. We show that both species have co-occurred in a stable way in one lake, with population fluctuations in which no species was permanently excluded. The seasonal occurrence patterns of the plankton in two lakes agree with laboratory experiments showing that both species differ in their optimal salinity. These results suggest that stable species coexistence is mediated by differential responses to salinity and its fluctuating regime. We discuss the role of fluctuating salinity and a persistent diapausing egg banks as a mechanism for species coexistence in accordance with the 'storage effect'.     

Decoupling of molecular and morphological evolution in deep lineages of a meiobenthic harpacticoid copepod

Molecular and biochemical genetic analyses have revealed that many marine invertebrate taxa, including some well-studied and presumably cosmopolitan species, are actually complexes of sibling species. When morphological differences are slight and estimated divergence times are old, data suggest either unusually high rates of sequence evolution or long-term morphological stasis. Here, five gene regions (mitochondrial cytochrome oxidase subunit I and large-subunit ribosomal 16S rDNA and nuclear ITS1, 5.8S rDNA, and ITS2) were analyzed in four geographic samples of the meiobenthic harpacticoid copepod Cletocamptus deitersi. Molecular sequences revealed four extremely differentiated molecular lineages with unalignable nuclear intergenic spacers and mitochondrial uncorrected divergences reaching 25% (cytochrome oxidase) and 36% (16S rDNA). These levels of divergence are greater than those reported previously for congeneric species in diverse invertebrate taxa, including crustaceans. The nominally intraspecific divergence matches or exceeds the corresponding divergence from a known congener (Cletocamptus helobius). A molecular clock applied to the cytochrome oxidase subunit I data suggests that these lineages split in the Miocene, consistent with the fossil record of a North American Cletocamptus from the same period. Morphological differences among the major lineages are subtle but congruent with the patterns of genetic differentiation. Our conclusion, based on concordant patterns of variation in two mitochondrial and three nuclear gene regions, as well as morphological observations, is that C. deitersi in North America is composed of at least four separate species by the genealogical concordance, phylogenetic, and morphological-species criteria. Alternative explanations for the deep phylogenetic nodes and apparent morphological stasis, including high rates of sequence evolution, balancing selection, and genetic signatures of historical events, are considered unlikely.     

Population structuring in the monogonont rotifer Synchaeta pectinata: high genetic divergence on a small geographical scale

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Persistent genetic signatures of colonization in Brachionus manjavacas rotifers in the Iberian Peninsula

Recent phylogeographical assessments have consistently shown that continental zooplankton display high levels of population subdivision, despite the high dispersal capacity of their diapausing propagules. As such, there is an apparent paradox between observed cosmopolitanism in the zooplankton that is associated with long-distance dispersal, and strong phylogeographical structures at a regional scale. Such population dynamics, far from migration-drift equilibrium, have been shown in the rotifer species complex Brachionus plicatilis, a group of over a dozen species inhabiting salt lakes and coastal lagoons worldwide. Here we present the mitochondrial DNA phylogeography of one of these species, Brachionus manjavacas, in the Iberian Peninsula, where it often co-occurs with the morphologically similar species B. plicatilis sensu stricto. We obtained sequences from 233 individuals from diapausing eggs and clonal cultures from 16 lakes in the Iberian Peninsula, and a Tunisian lake. Two strongly supported deep mitochondrial DNA clades were found (A and B). Phylogenetic and nested clade analysis showed that clade A has a strong phylogeographical structure, with a strong similarity of phylogeographical patterns between B. manjavacas clade A and B. plicatilis s.s. These include (i) signatures of allopatric fragmentation between central and southern populations, and (ii) range expansions in the Iberian Peninsula, both likely to have occurred during the Pleistocene. We find evidence for a glacial refugium in the Guadiana basin. Clades A and B co-occurred in several of these lakes because of range expansion and secondary contact between both clades. The co-occurrence between B. plicatilis s.s. and B. manjavacas is not recent, and both species might have experienced similar environmental challenges during the Pleistocene. The strong correlation of genetic and geographical distance found suggests that historical events can lead to such correlation, mirroring the effects of 'isolation by distance' in equilibrium populations.     

Sex, parthenogenesis and genetic structure of rotifers: microsatellite analysis of contemporary and resting egg bank populations

Cyclically parthenogenetic rotifers are a valuable model for investigating the relationship between reproductive mode and population structure, although advances in this field have been hindered by low allozyme variability in these organisms. A high genotypic diversity is predicted after population establishment, which would be eroded by clonal selection during the parthenogenetic phase. The resting egg bank, produced sexually, is presumed to store high levels of genetic diversity, with subsequent effects on planktonic population structure. Here, we provide the first application of microsatellite markers to a rotifer planktonic population and its associated resting egg bank. Seven polymorphic microsatellite loci were screened in populations of the rotifer Brachionus plicatilis in a temporary pond to analyse: (i) the genetic structure of the resting egg bank; (ii) the changes in the genetic structure of rotifer populations during the parthenogenetic phase; and (iii) the population structure after its initiation from resting eggs. Microsatellites proved to be a useful tool for clone identification, revealing a surprisingly high clonal diversity in rotifer populations. The last sample in the parthenogenetic phase showed evidence of clonal selection, as indicated by a low observed clonal diversity and the appearance of linkage disequilibria. The resting egg bank, analysed comprehensively for the first time in any zooplankter, is in Hardy-Weinberg and linkage equilibrium, and contains a high genotypic diversity. Unexpectedly, the resting egg bank differed from the planktonic population in its allelic composition, suggesting that resting egg hatching is biased.     

褶皱臂尾轮虫同胞物种复合类群分类的研究进展

褶皱臂尾轮虫包含复杂的同胞物种,对其分类研究经过了一个长期发展的过程。综述了轮虫分类手段的发展进程,介绍和分析了轮虫特别是褶皱臂尾轮虫同胞物种复合类群分类的研究进展。褶皱臂尾轮虫的L-型和S-型属于B.plicatilis和B.rotundiformis两个物种。这个复合类群中还包括更多的种类,如B.plicatilis sensu stricto、B.ibericus和B.rotundiformis,其中B.plicatilis sensu stricto属于L型,B.ibericus属于SM-型,B.rotundiformis属于SS-型。此类研究丰富了轮虫系统分类学,提高了水域生态调查的准确性。     

Molecular Ecology of Rotifers: From Population Differentiation to Speciation

The development of cost-effective molecular tools allowing the amplification of minute amounts of DNA effectively opened the field of molecular ecology for rotifers. Here I review these techniques and the advances they have provided in the understanding of sibling species complexes, clonal structure, resting egg banks, population structure, phylogeographic patterns and phylogenetic relationships in rotifers. Most of the research to date has focused on the rotifer species complex Brachionus plicatilis. The use of DNA sequence and microsatellite variation, in the context of the background knowledge of life history, mating behaviour, and temporal population dynamics in these organisms have revolutionised our views into the processes shaping the genetic diversity in aquatic invertebrates. Rotifers have populations with a very high number of clones in genetic equilibrium. In temporary populations clonal selection is effective in eroding the number of clones. Rotifer populations are strongly differentiated genetically for neutral markers, even at small geographical scales, and exhibit deep phylogeographic structure which might reflect the impact of Pleistocene glaciations. Despite the high potential for dispersal afforded by resting eggs, rotifers display persistent historical colonisation effects, with gene flow effective only at a local scale and with marked isolation by distance. Instances of long-distance transcontinental migration resulting in successful colonisation have also been revealed. B. plicatilis is composed of a group of several ancient species and sympatry is common. Despite this, the presence of cosmopolitan species in this species complex cannot be discounted. I discuss future priorities and point out the main areas where our knowledge is still insufficient.     

Distribution of rotifers in North Island,New Zealand,and their potential use as bioindicators of lake trophic state

The distribution and ecology of planktonic rotifers was investigated in 33 lakes in the North Island, New Zealand, between 1997 and 1999. A total of 79 species of monogonont rotifer were identified, with an average of 21 species per lake, a diversity which is high in comparison with many previous New Zealand studies. Most species recorded were cosmopolitan taxa, and were widespread in their distribution over the North Island. Multivariate analyses (Multi-Dimensional Scaling and Canonical Correspondence Analysis) did not distinguish distinct lake groupings based on rotifer communities, but rather gradients in assemblages, which were most highly associated with lake trophic state. Based on these responses, the development of potential rotifer bioindicator schemes for lake trophic state is described and discussed.     

Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus

Established empirical cases of sympatric speciation are scarce, although there is an increasing consensus that sympatric speciation might be more common than previously thought. Midas cichlid fish are one of the few substantiated cases of sympatric speciation, and they formed repeated radiations in crater lakes. In contrast, in the same environment, such radiation patterns have not been observed in other species of cichlids and other families of fish. We analyze morphological and genetic variation in a cichlid species (Archocentrus centrarchus) that co‐inhabits several crater lakes with the Midas species complex. In particular, we analyze variation in body and pharyngeal jaw shape (two ecologically important traits in sympatrically divergent Midas cichlids) and relate that to genetic variation in mitochondrial control region and microsatellites. Using these four datasets, we analyze variation between and within two Nicaraguan lakes: a crater lake where multiple Midas cichlids have been described and a lake where the source population lives. We do not observe any within‐lake clustering consistent across morphological traits and genetic markers, suggesting the absence of sympatric divergence in A. centrarchus. Genetic differentiation between lakes was low and morphological divergence absent. Such morphological similarity between lakes is found not only in average morphology, but also when analyzing covariation between traits and degree of morphospace occupation. A combined analysis of the mitochondrial control region in A. centrarchus and Midas cichlids suggests that a difference between lineages in the timing of crater lake colonization cannot be invoked as an explanation for the difference in their levels of diversification. In light of our results, A. centrarchus represents the ideal candidate to study the genomic differences between these two lineages that might explain why some lineages are more likely to speciate and diverge in sympatry than others.     

On the taxonomy of three sympatric sibling species of the Brachionus plicatilis (Rotifera) complex from Spain, with the description of B. ibericus n. sp.

The accumulation of evidence during the last decade led to thesplitting of the Brachionus plicatilis complex (Rotifera) intotwo morphologically recognizable species: B. plicatilis Müllerand B. rotundiformis Tschugunoff, previously referred to asL- and S-type B. plicatilis (s.l.), respectively. However, recentpopulation genetics and molecular studies have revealed thateach of these taxa concern cryptic species complexes. In particular,in Torreblanca Marsh, a wetland on the Mediterranean coast ofSpain, three genetically distinct groups in this rotifer complexhave been shown to co-occur. Differences in genetic markers,ecological preferences, mixis responses, mating behaviour andno evidence of gene flow between them have led to the conclusionthat they must be considered as three different biological species.In this study we present a detailed comparative analysis usinglight and scanning electron microscopy of laboratory strainsenabling a morphological characterization of the three species.Fine morphology and morphometry revealed taxonomic charactersconstant enough to recognize three well-defined morphologies,which always correspond with the respective biological speciesidentified. Since no type material of both B. plicatilis andB. rotundiformis is available, we designed our Spanish clonesas neotypes, which would allow further comparative work. Furthermore,B. ibericus n. sp. is described. This study sets the first stepfor a complete characterization of the biological diversitycontained within this economically important species complex.     

长江口疏浚弃土悬沙对褶皱臂尾轮虫的影响

采用克隆培养法 (编制生命表 )和群体累积培养法 ,研究了长江口疏浚弃土悬沙对褶皱臂尾轮虫(Brachionusplicatilis)的影响 .实验设 0 (CK)、1、3、5、7、9mg·ml-16个悬沙梯度和 2 0、12× 10 6cells·ml-1两个饵料密度 .结果表明 ,克隆培养时 ,悬沙可使该轮虫种群的内禀增长率 (rm)下降 2 9.6 %～ 6 4 .1% ,最大降幅为 130 .0 % .悬沙对轮虫种群的存活率 (lx)有影响 ,而对种群的繁殖率 (mx)无显著影响 .群体累积培养时 ,悬沙对轮虫种群的雌体密度、雄体密度、孤雌生殖卵和休眠卵的密度以及种群的动态变化规律无显著影响 .可见 ,长江口疏浚工程会对轮虫动物有一定的负面影响     

An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis

Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.     

Predatory interactions between a cyclopoid copepod and three sibling rotifer species

SUMMARY 1. Cyclopoid copepod predation on rotifers affects the dynamics and structure of zooplankton communities. We address the differential vulnerability of three sympatric rotifer sibling species belonging to the Brachionus plicatilis species complex. These co-occur with their cyclopoid predator, Diacyclops bicuspidatus odessanus .
2. Using video recording and tracking, we analysed the steps in predation including attack distance, attack angle, and rotifer species swimming in the presence and absence of the predator. Our results show the greater vulnerability of B. rotundiformis (the smallest species) to D. b. odessanus predation, which is associated with a high percentage of attacks after contact. Brachionus plicatilis (the biggest species) is the less vulnerable prey, with low percentage of attacks after contact and captures after attacks. Branchionus ibericus , the intermediate sized species, had also intermediate vulnerability.
3. The differential vulnerability provides insight into the coexistence and seasonal succession of these competing rotifer species. Our results show that the competitive superiority of B. rotundiformis may be balanced by its greater vulnerability to copepod predation.     

Dynamics of lake herring (Coregonus artedi) reactive volume for different crustacean zooplankton

Lake Torrens, a large ( 6000 km²), episodic, saline playa lake in arid central Australia, filled for the first recorded time in March 1989. This unique event followed unprecedently heavy rain over its catchment. Water remained in the lake until early 1990. Salinities remained low (<40 g l^-1) until November 1989, then increased rapidly to >200 g l^-1 before the water evaporated completely. Na and Cl probably dominated the ions. Twenty-nine taxa of aquatic animals were recorded. Crustaceans dominated and of these Parartemia minuta (anostracan), Daphniopsis queenslandensis and Moina baylyi (cladocerans), and several species of ostracods were the most important. Other significant taxa included Tanytarsus barbitarsis (chironomid), Brachionus plicatilis (rotifer) and Craterocephalus eyresii (fish). The fauna was dominated by widespread forms that are either part of a distinct assemblage found widely in central Australian salt lakes (especially P. minuta, D. queenslandensis, M. baylyi and Trigonocypris subglobusus [ostracod]), or cosmopolitan forms (B. plicatilis), or forms found widely in Australian salt lakes (e.g. Diacypris compacta, Tanytarsus barbitarsis). However, possibly three new species also occurred: a new species of a new genus of mytilocypridinid, Branchinella nov.sp. and Heterocypris nov. sp. Their occurrence is anomolous. It is suggested that further work will show that they too are widely distributed. Both genera of the latter two taxa are typical of temporary waters and specimens may have been washed in from nearby water-bodies. Sixty-four species of bird were recorded when the lake contained water, many breeding. The breeding of the banded stilt (Cladorhynchus leucocephalus) was notable; breeding of this species had been unknown in South Australia since 1930. A large population built up until breeding was stopped by predation from the silver gull (Larus novaehollandiae). When dry, the lake has a depauperate but well-defined and regionally restricted terrestrial fauna (scorpions, spiders, beetles, ants).     

Not as Ubiquitous as We Thought: Taxonomic Crypsis,Hidden Diversity and Cryptic Speciation in the Cosmopolitan Fungus Thelonectria discophora (Nectriaceae,Hypocreales, Ascomycota)

The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan species or an assemblage of sibling species, we conducted various phylogenetic analyses, including standard gene concatenation, Bayesian concordance methods, and coalescent-based species tree reconstruction on isolates collected from a wide geographic range. Results show that diversity among isolates referred as T. discophora is greatly underestimated and that it represents a species complex. Within this complex, sixteen distinct highly supported lineages were recovered, each of which has a restricted geographic distribution and ecology. The taxonomic status of isolates regarded as T. discophora is reconsidered, and the assumed cosmopolitan distribution of this species is rejected. We discuss how assumptions about geographically widespread species have implications regarding their taxonomy, true diversity, biological diversity conservation, and ecological functions.     

The nucleotide sequences of 5S rRNAs from a rotifer, Brachionus plicatilis, and two nematodes, Rhabditis tokai and Caenorhabditis elegans.

The nucleotide sequences of 5S rRNAs from a rotifer, Brachionus plicatilis, and two nematodes, Rhabditis tokai and Caenorhabditis elegans have been determined. The rotifer has two 5S rRNA species that are composed of 120 and 121 nucleotides, respectively. The sequences of these two 5S rRNAs are the same except that the latter has an additional base at its 3'-terminus. The 5S rRNAs from the two nematode species are both 119 nucleotides long. The sequence similarity percents are 79% (Brachionus/Rhabditis), 80% (Brachionus/Caenorhabditis), and 95% (Rhabditis/Caenorhabditis) among these three species. Brachionus revealed the highest similarity to Lingula (89%), but not to the nematodes (79%).     

塔玛亚历山大藻和东海原甲藻对褶皱臂尾轮虫种群数量的影响

通过对2002年5月东海赤潮原因种一东海原甲藻和亚历山大藻的单一藻种和两种藻混合情况下对褶皱臂尾轮虫种群数量影响的实验研究,发现塔玛亚历山大藻(ATHK)对轮虫有致死作用,其48hLC50为1300cell·ml^-1．藻的各组分毒性比较研究表明,只有藻液和藻细胞具有这种毒害作用,藻在早期生长阶段的毒害作用较强,毒性大小与藻细胞活性相关．东海原甲藻在高密度(4×10^4、5×10^4、10×10^4cell·ml^-1)时对轮虫种群数量在第5d时开始有影响;东海原甲藻在低密度(1×10^4、2×10^4、3×10^4cell·ml^-1)时,轮虫能够以其为食并进行生长繁殖．两种藻混合情况下,东海原甲藻能够减轻塔玛亚历山大藻对轮虫的毒害作用．实验结果表明,此次赤潮对东海的微型浮游动物种群能够产生一定的影响．     

Molecular systematics of short-horned lizards: biogeography and taxonomy of a widespread species complex

We surveyed mitochondrial DNA (mtDNA) sequence variation in short-horned lizards (Phrynosoma douglasi) from throughout western North America and used these data to estimate an intraspecific phylogeny and to assess biogeographic scenarios underlying the geographic structure of lineages in this species. We sequenced 783 base pairs from 38 populations of P. douglasi and three putative outgroups (P. ditmarsi, P. orbiculare, P. platyrhinos). We detected high levels of nucleotide variation among populations and a spatial distribution of mtDNA lineages compatible with major geographic regions. The phylogenetic hypotheses best supported by the data suggest that P. douglasi, as currently described, is paraphyletic with respect to P. ditmarsi. Populations of P. douglasi from the Pacific Northwest (ID, CA, OR, WA) form a monophyletic group that is sister to the subsequent radiation of P. ditmarsi and other P. douglasi clades. These results suggest that divergences within this widespread species are fairly old. We focused on the genetic structure of populations of P. douglasi from a geographic perspective and interpreted the intraspecific phylogeny in light of geologic and climatic changes in western North America during the last 20 million years. The generally high levels of genetic variation found in these population comparisons are in accord with high levels of morphological variation in this species group; however, only in the Pacific Northwest region is there spatial congruence between these phylogenetic results and subspecific ranges based on previous morphological studies. We compared the evolutionary units delineated in this study with previously described subspecies of P. douglasi and evaluated the support (from morphology and mtDNA) for each population lineage in the phylogeny and the implications for the taxonomy of this group.     

Widespread secondary contact and new glacial refugia in the halophilic rotifer Brachionus plicatilis in the Iberian Peninsula

Small aquatic organisms harbour deep phylogeographic patterns and highly structured populations even at local scales. These patterns indicate restricted gene flow, despite these organisms' high dispersal abilities, and have been explained by a combination of (1) strong founder effects due to rapidly growing populations and very large population sizes, and (2) the development of diapausing egg banks and local adaptation, resulting in low effective gene flow, what is known as the Monopolization hypothesis. In this study, we build up on our understanding of the mitochondrial phylogeography of the halophilic rotifer Brachionus plicatilis in the Iberian Peninsula by both increasing the number of sampled ponds in areas where secondary contact is likely and doubling sample sizes. We analyzed partial mitochondrial sequences of 252 individuals. We found two deep mitochondrial DNA lineages differing in both their genetic diversity and the complexity of their phylogeographic structure. Our analyses suggest that several events of secondary contact between clades occurred after their expansion from glacial refugia. We found a pattern of isolation-by-distance, which we interpret as being the result of historical colonization events. We propose the existence of at least one glacial refugium in the SE of the Iberian Peninsula. Our findings challenge predictions of the Monopolization hypothesis, since coexistence (i.e., secondary contact) of divergent lineages in some ponds in the Iberian Peninsula is common. Our results indicate that phylogeographic structures in small organisms can be very complex and that gene flow between diverse lineages after population establishment can indeed occur.