Local adaptation in populations of a Brachionus group plicatilis cryptic species inhabiting three deep crater lakes in Central Mexico

1. Salinity is a strong selective force for many aquatic organisms, affecting both ecological and evolutionary processes. Most of our knowledge on the effects of salinity on rotifers in the Brachionus plicatilis species complex is based mainly on populations from waterbodies that experience broad environmental changes both seasonally and annually. We tested the hypothesis that, despite the supposedly high potential for gene flow among rotifers inhabiting neighbouring environments, constant salinity has promoted local adaptation, genetic population divergence and even cryptic speciation in B. plicatilis complex populations from three deep maar lakes of distinct salinities [1.1, 6.5 and 9.0 g L^?1 total dissolved solids (TDS)] in Central Mexico. 2. To look for local adaptation, we performed common garden experiments to test the effect of different salinities on population density and intrinsic growth rate (r). Then, we evaluated the genetic divergence by sequencing the cytochrome c oxidase subunit I (COI) gene and performed reproductive trials to assess the potential gene flow among the three populations and with other closely related B. plicatilis complex species. 3. We confirmed that the rotifer populations have phenotypic plasticity in tolerance of salinity, but only rotifers from the least saline lake are adapted to low salinity. Among the populations, sequence divergence at COI was very low (just a single haplotype was found), suggesting a persistent founder effect from a relatively recent single colonisation event and a subsequent dispersal from one lake to the others, and a very restricted immigration rate. In the phylogenetic analysis, rotifers from this area of Mexico clustered in the same clade with the middle‐sized species Brachionus ibericus and B. sp. ‘Almenara’. Mexican rotifers showed successful recognition, copulation and formation of hybrids among them, but interpopulation breeding with the Spanish B. ibericus and B. sp. ‘Almenara’ was unsuccessful. 4. We conclude that the B. plicatilis complex populations from these three lakes belong to a new biological species not yet described (presently named B. sp. ‘Mexico’). To our knowledge, this is the first report of local adaptation of a natural B. plicatilis complex population living in freshwater conditions (1.1 g L^?1 TDS).     

Molecular genetics of rotifers: preliminary restriction napping of the mitochondrial genome of Brachionus plicatilis

Methods are presented to extract and purify mitochondrial DNA from the rotifer Brachionus plicatilis. The mtDNA obtained is of sufficient purity for digestion with restriction endonucleases. EcoR I restriction patterns are presented for 4 geographically separated clones. A restriction map based on digestion with 5 different restriction enzymes is included for one of these clones. Finally, use of mtDNA analysis for studies on the population structure and biogeography of rotifers is discussed.     

Genetic variability and transgenerational regulation of investment in sex in the monogonont rotifer Brachionus plicatilis

In cyclical parthenogens such as aphids, cladocerans and rotifers, the coupling between sexual reproduction and the production of resting stages (diapausing eggs) imposes strong constraints on the timing of sex. Whereas induction of sex is generally triggered by environmental cues, the response to such cues may vary across individuals according to genetic and nongenetic factors. In this study, we explored genetic and epigenetic causes of variation for the propensity for sex using a collection of strains from a Spanish population of monogonont rotifers (Brachionus plicatilis) in which variation for the threshold population density at which sex is induced (mixis threshold) had been documented previously. Our results show significant variation for the mixis threshold among 20 clones maintained under controlled conditions for 15 asexual generations. The effect of the number of clonal generations since hatching of the diapausing egg on the mixis ratio (proportion of sexual offspring produced) was tested on 4 clones with contrasted mixis thresholds. The results show a negative correlation between the mixis threshold and mixis ratio, as well as a significant effect of the number of clonal generations since fertilization, sex being repressed during the first few generations after hatching of the diapausing egg.     

Behavioural Reproductive Isolation in a Rotifer Hybrid Zone

A hybrid zone between two Brachionus plicatilis rotifer mitochondrial DNA (mtDNA) lineages was recently described in the Iberian Peninsula between a pond (Santed 2) and a lake (Gallocanta). The patterns of mitochondrial and nuclear genetic variation observed suggested that gene flow is mainly male-mediated from the lake to the pond. Here we test two hypotheses: (a) that male-mediated gene flow occurs through assortative mating between individuals from these ponds, (b) that behavioural isolation occurs between the two mtDNA lineages. We isolated, reared and genotyped rotifer clones from resting eggs collected in the sediments of these and two other distant ponds. We devised a quick, inexpensive RFLP method to discriminate between B. plicatilis and its sibling species B. ‘Manjavaeas’ and between both mtDNA B. plicatilis lineages. Behavioural no-choice tests using new-born, virgin males and females were performed between five clones. B. ‘Manjavacas’ and B. plicatilis were reproductively isolated. B. plicatilis clones did not show evidence of reproductive isolation, regardless of their mtDNA lineage, except Santed 2 males, which discriminated strongly against Gallocanta females. These results could help to explain the discrepancies between mitochondrial and nuclear genetic variation reported in the two populations.     

Ecological genetics of a cyclical parthenogen in temporary habitats

Populations of the rotifer Brachionus plicatilis inhabiting three temporary ponds in Torreblanca Marsh (Castellón, Spain) were regularly screened for allozyme variation, sexual reproduction levels and population densities during an annual cycle. Relevant ecological parameters in the ponds were also recorded. The electrophoretic survey of the three ponds (Poza Sur, Poza Norte and Canal Central) revealed a high level of overall genetic polymorphism in four marker loci, but only 13 multilocus genotypes were found. We classified clones into three clonal groups (SS, SM, L) characterized by unique arrays of alleles in the four marker loci, and significant differences in body shape and size. Clonal group succession took place in Poza Sur; SM clones occurring in spring, SS clones from spring to fall, and L clones from fall to spring. Despite the partial overlapping of sexual periods, the absence of heterozygotes indicates that gene flow is strongly restricted between clonal groups. In the transition periods, the population was far from Hardy—Weinberg equilibrium due to hetereozygote deficiencies in all four markers. In clonal group L, the only polymorphic locus, Pgi, was in Hardy—Weinberg equilibrium. In clonal group SM, both polymorphic loci were in Hardy—Weinberg equilibrium in Poza Norte, but not in Poza Sur. Factor analysis on the limnological parameters recorded during field sampling indicates that genetically different clonal groups are also ecologically specialized. These findings suggest that the taxonomical species B. plicatilis is in fact a species complex. The complete genetic discontinuity model of rotifer population succession is supported by these data. Our results are similar to those found in cladocerans inhabiting temporary habitats.     

Low Phylogeographic Structure in a Wide Spread Endangered Australian Frog <Emphasis Type="Italic">Litoria aurea</Emphasis> (Anura: Hylidae)

The green and golden bell frog (Litoria aurea) has a widespread distribution along the south-east coast of Australia. The species range, however, is highly fragmented and remaining populations are predominately isolated and restricted to the coastline. Previously, the range extended further inland and the species was considered common. Here we report a study designed to identify the phylogeographic and conservation genetic parameters of L. aurea. Mitochondrial DNA sequences were examined from 263 individuals sampled from 26 locations using both phylogenetic and population analyses. Despite a general consensus that amphibians are highly structured we found no phylogeographic divisions within the species, however, there was significant structure amongst extant populations (F _ST=0.385). Patterns of haplotype relatedness, high haplotypic diversity (mean h=0.547) relative to low nucleotide diversity (mean π=0.003) and mismatch distribution analysis supported a Pleistocene expansion hypothesis with continued restricted dispersal and gene flow. We conclude that the genetic structure of the species may permit ‘well managed’ intervention to mediate gene flow amongst isolated populations and provide some guidelines for the implementation of such conservation strategies.     

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.     

Phylogeography of island canary (Serinus canaria) populations

Island canaries (Serinus canaria) are characterised as a species living exclusively on North Atlantic islands, mainly on the Azores, Madeira and Canary Islands. Although they are very common in their habitats, their behaviour and breeding system has only recently been studied systematically. To advance the understanding of their ecology and to see if the rather isolated archipelagos are already promoting a genetic differentiation, we investigated their phylogeographic relationship as revealed by mtDNA sequences of the cytochrome b gene and investigated whether this measure corresponds to morphological characteristics within the islands. Genetic distances were very low throughout the distribution range of the species. Although the variation of genetic distances within the population of Pico (Azores) was larger than that on Madeira and Canary Islands, the genetic distances between island populations were very low throughout which prevented a clear phylogeographic differentiation. Moreover, morphological measurements did not reveal a consistent pattern to reliably separate the populations, although the measures of beak length and body weight revealed a clear island-specific differentiation. These data lead to the assumption that the colonisation of the Atlantic islands by the canaries occurred very recently, while there is no persisting gene flow between the populations.     

Holarctic phylogeography of an asexual species complex – II. Allozymic variation and clonal structure in Arctic Daphnia

Previous mitochondrial (mt)DNA sequencing and restriction fragment length polymorphism (RFLP) studies have shown that the Holarctic Daphnia pulex complex is divisible into two major groups (pulicaria and tenebrosa) that exhibit distinct phylogeographic patterns. Here we examine allozymic variation at six polymorphic enzyme loci to ascertain clonal structure and clonal distribution patterns within each group. Specimens were collected from a total of 850 populations encompassing the Arctic. A significant negative relationship (Mantel test) between similarity of regional clonal arrays and geographical distance was observed. A small fraction of clones in each group was widespread (in the order of 1000s of kilometres). However, most clones were restricted to single regions, and were often found only in a single population. These data indicate that the population genetic structure is highly fragmented in this complex, but the potential for long-distance passive dispersal exists. Further, ‘hot spots’ of high clonal richness and diversity were found in each group, which is concordant with earlier work. In addition, ≈ 20% of pulicaria group clones possess nuclear genes from tenebrosa, while approximately 10% of tenebrosa group clones harbour pulicaria nuclear genes. These data indicate nuclear introgression between the two groups, which was found to be prominent in a broad zone of secondary contact encompassing parts of northwestern Russia, northern Fennoscandia, Svalbard, and extending into the high eastern Canadian Arctic.     

Mechanisms of population differentiation in seabirds

Despite recent advances in population genetic theory and empirical research, the extent of genetic differentiation among natural populations of animals remains difficult to predict. We reviewed studies of geographic variation in mitochondrial DNA in seabirds to test the importance of various factors in generating population genetic and phylogeographic structure. The extent of population genetic and phylogeographic structure varies extensively among species. Species fragmented by land or ice invariably exhibit population genetic structure and most also have phylogeographic structure. However, many populations (26 of 37) display genetic structure in the absence of land, suggesting that other barriers to gene flow exist. In these populations, the extent of genetic structure is best explained by nonbreeding distribution: almost all species with two or more population-specific nonbreeding areas (or seasons) have phylogeographic structure, and all species that are resident at or near breeding colonies year-round have population genetic structure. Geographic distance between colonies and foraging range appeared to have a weak influence on the extent of population genetic structure, but little evidence was found for an effect of colony dispersion or population bottlenecks. In two species (Galapagos petrel, Pterodroma phaeopygia, and Xantus's murrelet, Synthliboramphus hypoleucus), population genetic structure, and even phylogeographic structure, exist in the absence of any recognizable physical or nonphysical barrier, suggesting that other selective or behavioural processes such as philopatry may limit gene flow. Retained ancestral variation may be masking barriers to dispersal in some species, especially at high latitudes. Allopatric speciation undoubtedly occurs in this group, but reproductive isolation also appears to have evolved through founder-induced speciation, and there is strong evidence that parapatric and sympatric speciation occur. While many questions remain unanswered, results of the present review should aid conservation efforts by enabling managers to predict the extent of population differentiation in species that have not yet been studied using molecular markers, and, thus, enable the identification of management units and evolutionary significant units for conservation.     

Does genetic diversity reduce intraspecific competition in rotifer populations?

As a result of reduced intraspecific competition, genetically diverse populations may have higher relative fitness than genetically uniform populations. To test this hypothesis, we compared polyclonal (i.e., genetically diverse) versus monoclonal (i.e., composed of a single clonal genotype) experimental populations of the rotifer Brachionus plicatilis (Müller, 1786) growing separately and in competition. We estimated the following fitness components: intrinsic growth rate; carrying capacity; proportion of sexual females; diapausing egg production per sexual female and total egg production. Polyclonal populations showed similar dynamics to monoclonal populations and no statistical difference between their fitness components was detected. Therefore, results do not support the hypothesis that genetically diverse populations reduce competition through diversification in resource use. Instead, results suggest that B. plicatilis is a generalist consumer whose polyphagy does not depend on genetic differences, but on the broad diet of each genotype. However, clones showed significant differences in almost all fitness components demonstrating among-clone variation in life-history traits. We found a trade-off between sexual ratio and carrying capacity, highlighting the cost of sex in cyclical parthenogenetic rotifers. We discuss the mechanisms that could maintain the observed among-clone genetic variation in natural populations, and speculate on results implication for sex maintenance in rotifers.     

Phylogeographic histories of representative herpetofauna of the southwestern U.S.: mitochondrial DNA variation in the desert iguana (Dipsosaurus dorsalis) and the chuckwalla (Sauromalus obesus)

To determine whether genetic variation in representative reptiles of the southwestern U.S. may have been similarly molded by the geologic history of the lower Colorado River, we examined restriction site polymorphisms in the mitochondrial DNA (mtDNA) of desert iguanas (Dipsosaurus dorsalis) and chuckwallas (Sauromalus obesus). Observed phylogeographic structure in these lizards was compared to that reported for the desert tortoise (Xerobates agassizi), whose mtDNA phylogeny demonstrates a striking genetic break at the Colorado River. Both the desert iguana and chuckwalla exhibit extensive mtDNA polymorphism, with respective genotypic diversities G = 0.963 and 0.983, close to the maximum possible value of 1.0. Individual mtDNA clones, as well as clonal assemblages defined by specific levels of genetic divergence, showed pronounced geographic localization. Nonetheless, for each species the distributions of certain clones and most major clonal groupings encompass both sides of the Colorado River valley, and hence are clearly incongruent with the phylogeographic pattern of the desert tortoise. Overall, available molecular evidence provides no indication that the intraspecific phylogenies of the southwestern U.S. herpetofauna have been concordantly shaped by a singular vicariant factor of overriding significance.     

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

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Clonality in the Endangered <Emphasis Type="Italic">Ambrosia pumila</Emphasis> (Asteraceae) Inferred from RAPD Markers; Implications for Conservation and Management

Clonal plants have the ability to spread and survive over long periods of time by vegetative growth. For endangered species, the occurrence of clonality can have significant impacts on levels of genetic diversity, population structure, recruitment, and the implementation of appropriate conservation strategies. Here we␣examine clone structure in three populations of Ambrosia pumila (Nutt.) Gray (Asteraceae), a federally endangered clonal species from southern California. Ambrosia pumila is a perennial herbaceous species spreading from a rhizome, and is frequently found in dense patches of several hundred stems in a few square meters. The primary habitat for this species is upper terraces of rivers and drainages in areas that have been heavily impacted by anthropogenic disturbances and changing flood regimes. RAPD markers were employed to document the number and distribution of clones within multiple 0.25 m² plots from each of three populations. Thirty-one multi-locus genotypes were identified from the 201 stems sampled. The spatial distribution of clones was limited with no genotypes shared between plots or populations. Mean clone size was estimated at 9.10 ramets per genet. Genets in most plots were intermingled, conforming to a guerrilla growth form. The maximum genet spread was 0.59 m suggesting that genets can be larger than the sampled 0.25 m² plots. Spatial autocorrelation analysis found a lack of spatial genetic structure at short distances and significant structure at large distances within populations. Due to the occurrence of multiple genets within each population, the limited spread of genets, and a localized genetic structure, conservation activities should focus on the maintenance of multiple populations throughout the species range.     

Effects of population outcrossing on rotifer fitness

Background  

Outcrossing between populations can exert either positive or negative effects on offspring fitness. Cyclically parthenogenetic rotifers, like other continental zooplankters, show high genetic differentiation despite their high potential for passive dispersal. Within this context, the effects of outcrossing may be relevant in modulating gene flow between populations through selection for or against interpopulation hybrids. Nevertheless, these effects remain practically unexplored in rotifers. Here, the consequences of outcrossing on the rotifer Brachionus plicatilis were investigated. Cross-mating experiments were performed between a reference population and three alternative populations that differed in their genetic distance with regard to the former. Two offspring generations were obtained: F1 and BC ('backcross'). Fitness of the outcrossed offspring was compared with fitness of the offspring of the reference population for both generations and for three different between-population combinations. Four fitness components were measured throughout the rotifer life cycle: the diapausing egg-hatching proportion, clone viability (for the clones originating from diapausing eggs), initial net growth rate R for each viable clone, and the proportion of male-producing clones. Additionally, both the parental fertilisation proportion and a compound fitness measure, integrating the complete life cycle, were estimated.     

Phylogeography of <Emphasis Type="Italic">Ceriops tagal</Emphasis> (Rhizophoraceae) in Southeast Asia: the land barrier of the Malay Peninsula has caused population differentiation between the Indian Ocean and South China Sea

The genetic structure of mangrove species is greatly affected by their geographic history. Nine natural populations of Ceriops tagal were collected from Borneo, the Malay Peninsula, and India for this phylogeographic study. Completely different haplotype compositions on the east versus west coasts of the Malay Peninsula were revealed using the atpB-rbcL and trnL-trnF spacers of chloroplast DNA. The average haplotype diversity (Hd) of the total population was 0.549, nucleotide diversity (θ) was 0.030, and nucleotide difference (π) was 0.0074. The cladogram constructed by the index of population differentiation (G _ST) clearly separated the South China Sea populations from the Indian Ocean populations. In the analysis of the minimum spanning network, the Indian Ocean haplotypes were all derived from South China Sea haplotypes, suggesting a dispersal route of C. tagal from Southeast Asia to South Asia. The Sunda Land river system and surface currents might be accountable for the gene flow directions in the South China Sea and Bay of Bengal, respectively. The historical geography not only affected the present genotype distribution but also the evolution of C. tagal. These processes result in the genetic differentiation and the differentiated populations that should be considered as Management Units (MUs) for conservation measurements instead of random forestation, which might lead to gene mixing and reduction of genetic variability of mangrove species. According to this phylogeographic study, populations in Borneo, and east and west Malay Peninsula that have unique genotypes should be considered as distinct MUs, and any activities resulting in gene mixing with each other ought to be prevented.     

不同年龄巴山木竹种群克隆结构

很多竹类植物是典型的克隆植物,也是大熊猫的食物。研究典型竹子种群克隆结构的形成和发展对竹林的生产和抚育具有理论和实践意义,可为预测该竹林群落的演替趋势和大熊猫保护提供科学依据。利用SSR标记研究不同年龄A(7龄)、B(30龄)和C(60龄)巴山木竹种群的克隆结构和多样性,探讨小尺度范围内不同年龄巴山木竹种群的克隆结构及斑块的建立和发展。8对SSR引物共扩增出了118个位点,3个种群样地的256个样本共检测到了49个克隆(基因型),A、B和C种群分别检测出31、10个和8个克隆。随着种群年龄的增长,巴山木竹克隆面积增加,克隆数量减少;A和B样地各克隆分布格局为团块状,而C样地克隆既有团块状又有离散状。这一结果显示出在幼苗定居的初期,基株可能以短距离的克隆延伸为主从而呈现出团块状;而随着年龄的增长,克隆面积不断扩大,当复轴混生型的巴山木竹克隆受到强大的压迫时,基株可能会进行较多的单轴和长距离克隆延伸,呈现出离散状。Mantel检测和空间自相关分析都支持3个样地在小尺度范围内存在明显的克隆空间遗传结构。3个样地在10 m等级下显著的正相关空间遗传结构距离为3.1、28、48 m,X-轴截距为9.051、30.698和50.536,空间自相关系数的范围分别为0.1—0.167、0.008—0.703和0.006—0.735。由此可推断,随着年龄的增长,巴山木竹克隆斑块的规模在不断地扩大,同一克隆的分株数量增加,在均匀取样情况下,正相关空间遗传结构距离范围内取到具有相同基因型的可能性越大。A、B和C 3样地的基因型比率(G/N)为1、0.14和0.055,Simpson多样性指数(D)分别为1、0.876和0.744。这说明巴山木竹幼苗期基因型比例远远高于成年的竹林,随着年龄的增长巴山木竹克隆多样性虽有所降低,但由于有性繁殖的作用仍然保持了较高的多样性。聚类和主坐标分析均表明总体上各样地的克隆被聚为一类,但不同样地少数克隆的基因型有重叠和聚集,可推断出不同巴山木竹种群之间可能存在着基因流动和近似的克隆起源。     

The clonal and population structure of a rare endemic plant, Wyethia reticulata (Asteraceae): allozyme and RAPD analysis

Genetic structure arises when limited gene flow between populations favours the development of distinct arrays of genetic characters within each population. Determining the spatial scale at which this differentiation occurs is critical to our understanding of population biology and microevolution of species. The genetic structure and spatial pattern of genetic variation in an endemic, clonal perennial, Wyethia reticulata E. Greene, was investigated using random amplified polymorphic DNA (RAPD) markers and allozyme alleles. Large stands (250–360 m²) were found to contain few genetic individuals. Despite the small population sizes and endemism of the species, W. reticulata was highly diverse genetically, with most of the variation (75–81%) distributed within populations. A population structure in full agreement with spatially defined populations was achieved only by combining RAPD and allozyme markers. Analysis using both types of markers appeared to provide estimates of genetic similarity between individuals that were most consistent with empirical data on plant distributions. We postulated that large, long-lived clones dominated genetic relationships within populations but also provided opportunities for gene flow between populations on a longer time scale. The two marker types yielded different estimates of between-individual similarity and revealed disparate patterns of population structure. This result will arise because allozymes and random DNA segments have dissimilar evolutionary dynamics with respect to mutation and selection.     

Clonal and fine-scale genetic structure in populations of a restricted Korean endemic, Hosta jonesii (Liliaceae) and the implications for conservation

BACKGROUND AND AIMS: In plant populations the magnitude of spatial genetic structure of apparent individuals (including clonal ramets) can be different from that of sexual individuals (genets). Thus, distinguishing the effects of clonal versus sexual individuals in population genetic analyses could provide important insights for evolutionary biology and conservation. To investigate the effects of clonal spread on the fine-scale spatial genetic structure within plant populations, Hosta jonesii (Liliaceae), an endemic species to Korea, was chosen as a study species. METHODS: Using allozymes as genetic markers, spatial autocorrelation analysis of ramets and of genets was conducted to quantify the spatial scale of clonal spread and genotype distribution in two populations of H. jonesii. KEY RESULTS: Join-count statistics revealed that most clones are significantly aggregated at < 3-m interplant distance. Spatial autocorrelation analysis of all individuals resulted in significantly higher Moran's I values at 0-3-m interplant distance than analyses of population samples in which clones were excluded. However, significant fine-scale genetic structure was still observed when clones were excluded. CONCLUSIONS: These results suggest that clones enhance the magnitude of spatial autocorrelation due to localized clonal spread. The significant fine-scale genetic structure detected in samples excluding clones is consistent with the biological and ecological traits exhibited by H. jonesii including bee pollination and limited seed dispersal. For conservation purposes, genetic diversity would be maximized in local populations of H. jonesii by collecting or preserving individuals that are spaced at least 5 m apart.     

Diversity of the rotifer Brachionus plicatilis species complex (Rotifera: Monogononta) in Iran through integrative taxonomy

Faunistic survey using a DNA taxonomy approach may provide different results from morphological methods, especially for small and understudied animals. In this study, we report the results from morphometric analyses (linear measurements of the lorica) and DNA taxonomy (generalized mixed Yule coalescent model on the barcoding mtDNA locus cytochrome c oxidase subunit I) performed on 15 clonal lineages of the rotifer Brachionus plicatilis species complex from six Iranian inland saltwaters. The DNA taxonomy approach found more units of diversity (four) than the morphometric approach (two) in the studied rotifers. Three of the taxa identified in this study are already known as described valid species or as‐yet unnamed lineages, but a new, additional lineage is also identified from Iran. © 2014 The Linnean Society of London