Mitochondrial DNA diversity in an apomictic Daphnia complex from the Canadian High Arctic

Cyclic parthenogenesis is the ancestral mode of reproduction in the cladoceran crustacean, Daphnia pulex, but some populations have made the transition to obligate parthenogenesis and this is the only mode of reproduction known to occur in arctic populations. Melanism and polyploidy are also common in arctic populations of this species. Prior allozyme studies of arctic D. pulex revealed substantial levels of clonal diversity on a regional scale. Clonal groupings based on cluster analysis of allozyme genotypes do not conform to groupings based on the presence/absence of melanin or on ploidy level. In order to further elucidate genetic relationships among arctic D. pulex clones, mitochondrial DNA (mtDNA) variation was examined in 31 populations from two Canadian high-arctic sites. The data were also compared to a previous study of mtDNA variation in populations from a Canadian low-arctic site. Cladistic analysis of restriction site variation of the entire mitochondrial genome and nucleotide sequence variation of the mitochondrial control region was used to construct genetic relationships among mitochondrial genotypes. Three distinct mitochondrial lineages were detected. One lineage was associated with diploid, nonmelanic clones and is the same as the lineage that is found in temperate populations of D. pulex. The other two lineages (A & B) were associated with polyploid, melanic clones. Sequence divergence between the A and B lineages was 2.4%. Sequence divergence between D. pulex and either of these two lineages exceeded 3%. It is suggested that the melanic, polyploid clones are hybrids between males of D. pulex (and/or a closely related congener, D. pulicaria) and females of either of two ancestral melanic species that have mitochondrial lineages A and B. Geographic patterns of mitochondrial diversity in ‘melanic’ lineage B support the hypothesis of an high-arctic refuge for the ancestral species during the last glacial period.     

Molecular genetic identification and phylogeny of Daphnia species (Crustacea, Cladocera) from water bodies of the Lake Chany basin

The data on the molecular genetic identification of Daphnia species from the water bodies of the Lake Chany basin are presented. Phylogenetic relationships between these species have been established. The fragments of the mitochondrial DNA genes were used as genetic markers. According to the data obtained, the water bodies examined were inhabited by five Daphnia species, including Daphnia (Daphnia) galeata Sars, D. (D.) longispina O. F. Müller, D. (D.) curvirostris Eylmann, D. (D.) pulex Leydig, and D. (Ctenodaphnia) magna Straus. In addition, longispina a-like individuals that form a separate phylogenetic lineage was identified.     

Pleistocene glaciations and polyphyletic origins of polyploidy in an arctic cladoceran

RFLP analysis of the ND4-ND5 genes of the mtDNA genome in Daphnia middendorffiana and three closely allied species was used to investigate its origin and age. Populations of D. middendorffiana from arctic Canada were found to possess three distinct mtDNA lineages, only one of which appears unique to this species. The other two mtDNA lineages are either closely allied or identical to haplotypes in D. pulicaria, suggesting that it is the maternal parent of many clones of D. middendorffiana. Within D. pulicaria, mtDNA lineages have largely disjunct distributions, suggesting that populations of this species persisted in three glacial refugia (arctic, western, eastern) during the Pleistocene. Hybridizations between these refugial stocks and other species such as D. melanica and D. pulex likely generated many of the polyploid lineages of D. middendorffiana following the Wisconsinan glaciation. The presence of one unique mtDNA lineage in D. middendorffiana suggests that at least some of its clones are more ancient, but further studies are needed to rule out the possibility of their recent derivation from an as yet undetected sexual species. As a general result, this study suggests that polyploid cladocerans are unlikely to predate the Pleistocene.     

Global spread of wheat curl mite by its most polyphagous and pestiferous lineages

The wheat curl mite (WCM), Aceria tosichella, is an important pest of wheat and other cereal crops that transmits wheat streak mosaic virus and several other plant viruses. Wheat curl mite has long been considered a single polyphagous species, but recent studies in Poland revealed a complex of genetically distinct lineages with divergent host‐acceptance traits, ranging from highly polyphagous to host‐specific. This diversity of WCM genotypes and host‐acceptance phenotypes in Europe, the presumed native range of WCM, raises questions about the lineage identities of invasive WCM populations on other continents and their relationships to European lineages. The goals of this study were to examine the global presence of WCM and determine the relatedness of lineages established in different continents, on the basis of phylogenetic analyses of mitochondrial and nuclear DNA sequence data. Host‐range bioassays of a highly polyphagous WCM lineage were performed to supplement existing data on this lineage's ability to colonise graminaceous and non‐graminaceous hosts. Invasive WCM populations in North and South America and Australia assorted with the only three known polyphagous and pestiferous WCM lineages (‘MT‐1’, ‘MT‐7’ and ‘MT‐8’) from a total of eight currently described lineages. These results show that the most polyphagous lineages were more successful colonisers and reflect a need for extensive surveys for WCM on both crops and wild grass species in invaded continents. The most invasive lineage (‘MT‐1’) was shown to successfully colonise all 10 plant species tested in three families and has spread to North and South America and Australia from its presumed origins in Eurasia.     

Competitive abilities and distribution ranges of four asexual Daphnia pulex lineages and Daphnia mitsukuri in Eurasian continental islands

Daphnia pulex and D. mitsukuri are morphologically similar and distributed in small lowland Japanese lakes. Daphnia pulex in Japan reproduces by obligate parthenogenesis and is composed of four different lineages (JPN1–JPN4) with North American origins. Although this species is found throughout Japan, JPN1 has the largest distribution range, followed by JPN2. Daphnia mitsukuri is a putatively endemic species that is now rarely found in Japan. Since Daphnia share the same algal food, the difference in distribution ranges among the four asexual D. pulex lineages and D. mitsukuri may be caused by exploitative competition for algal food. To examine this possibility, we measured the threshold food concentration (TFC) at zero-net growth rate and the food concentration required for 50% of the individuals to survive (FC50). In addition, we examined the effects of temperature on the somatic growth rate (SGR) and the mortality rates of four asexual D. pulex lineages and D. mitsukuri. The experiments showed that TFC was lowest in D. pulex JPN1 and highest in D. mitsukuri, supporting the idea that the largest distribution range of JPN1 is due to its superiority in inter-lineage competition, and that the distribution area of D. mitsukuri is reduced through exploitative competition with D. pulex. However, although JPN2 was found in relatively large areas, it had higher TFC than JPN3 and JPN4, which appear in very limited areas. These results clearly showed that the difference in distribution ranges among D. pulex lineages are not necessarily determined by their competitive superiority alone.     

Diversity in the reproductive modes of European Daphnia pulicaria deviates from the geographical parthenogenesis

Background

Multiple transitions to obligate parthenogenesis have occurred in the Daphnia pulex complex in North America. These newly formed asexual lineages are differentially distributed being found predominantly at high latitudes. This conforms to the rule of geographical parthenogenesis postulating prevalence of asexuals at high latitudes and altitudes. While the reproductive mode of high-latitude populations is relatively well studied, little is known about the reproduction mode in high altitudes. This study aimed to assess the reproductive mode of Daphnia pulicaria, a species of the D. pulex complex, from high altitude lakes in Europe.

Methodology/Principal Findings

Variation at eight microsatellite loci revealed that D. pulicaria from the High Tatra Mountains (HTM) had low genotype richness and showed excess of heterozygotes and significant deviations from Hardy-Weinberg expectations, and was thus congruent with reproduction by obligate parthenogenesis. By contrast, populations from the Pyrenees (Pyr) were generally in Hardy-Weinberg equilibrium and had higher genotypic richness, suggesting that they are cyclic parthenogens. Four lakes from lowland areas (LLaP) had populations with an uncertain or mixed breeding mode. All D. pulicaria had mtDNA ND5 haplotypes of the European D. pulicaria lineage. Pyr were distinct from LLaP and HTM at the ND5 gene. By contrast, HTM shared two haplotypes with LLaP and one with Pyr. Principal Coordinate Analysis of the microsatellite data revealed clear genetic differentiation into three groups. HTM isolates were intermediate to Pyr and LLaP, congruent with a hybrid origin.

Conclusion/Significance

Inferred transitions to obligate parthenogenesis have occurred only in HTM, most likely as a result of hybridizations. In contrast to North American populations, these transitions do not appear to involve meiosis suppressor genes and have not been accompanied by polyploidy. The absence of obligate parthenogenesis in Pyr, an environment highly similar to the HTM, may be due to the lack of opportunities for hybridization.     

Evolutionary history of alpine and subalpine Daphnia in western North America

相似文献   

Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers

The study of species complexes is of particular interest to understand how evolutionary young species maintain genomic integrity. The Daphnia pulex complex has been intensively studied as it includes species that dominate freshwater environments in the Northern hemisphere and as it is the sole North American complex that shows transitions to obligate parthenogenesis. Past studies using mitochondrial markers have revealed the presence of 10 distinct lineages in the complex. This study is the first to examine genetic relationships among seven species of the complex at nuclear markers (nine microsatellite loci and one protein-coding gene). Clones belonging to the seven species of the Daphnia pulex complex were characterized at the mitochondrial NADH dehydrogenase (ND5) gene and at the Lactate dehydrogenase (LDH) locus. K-means, principal coordinate analyses and phylogenetic network analyses on the microsatellite data all separated European D. pulicaria, D. tenebrosa, North American D. pulex, D. pulicaria and their hybrids into distinct clusters. The hybrid cluster was composed of diploid and polyploid hybrids with D. pulex mitochondria and some clones with D. pulicaria mitochondria. By contrast, the phylogeny of the D. pulex complex using Rab4 was not well resolved but still showed clusters consisting mostly of D. pulex alleles and others of D. pulicaria alleles. Incomplete lineage sorting and hybridization may obscure genetic relationships at this locus. This study shows that hybridization and introgression have played an important role in the evolution of this complex.     

Phylogenetics and evolution of a circumarctic species complex (Gladocera: Daphnia pulex)

The evolutionary history of freshwater zooplankton is still relatively unknown. However, studies of the microcrustacean Daphnia have revealed interesting patterns; the daphniids that dominate ponds and lakes in the northern hemisphere may have recent origins, likely associated with the glacial advances and retreats during the Pleistocene. Moreover, they form species complexes that actively engage in hybridization and introgression. The present study examines the phylogenetic relationships among circumarctic members of the Daphnia pulex complex, through the analysis of sequence diversity in 498 nt of the ND5 mitochondrial gene. Our results suggest that the complex is composed of three major clades, two of which are subdivided into at least eight different lineages. Clearly, species in the complex show genetic discontinuity. Many lineages originated during the Pleistocene, but at least three lineages diverged during the Pliocene. Two taxa ( D. pulex, D. pulicaria ), thought to be broadly distributed in the northern hemisphere, are shown to be endemic to single continents. In general, the diversification of the pulex complex is characterized by rapidly dispersed lineages spanning enormous distances and also by endemism in temperate areas. Gene flow among lineages from the temperate region of different continents are restricted to rare intercontinental migrations across a polar bridge followed by convergent morphological evolution.     

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.     

Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri,Ranidae)

Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045–0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.     

Cryptic diversity within the invasive virile crayfish <Emphasis Type="Italic">Orconectes virilis</Emphasis> (Hagen, 1870) species complex: new lineages recorded in both native and introduced ranges

The virile crayfish (Orconectes virilis) represents a cryptic species complex with several lineages known in the USA, and a wide introduced range. In Europe, O. virilis is an emerging invader, established during the last decade in at least two areas—one in the United Kingdom and another in the Netherlands. We assessed the position of both known European populations within the species complex by sequencing part of the mitochondrial gene for cytochrome c oxidase subunit I. Tested UK and Dutch individuals did not belong to any mitochondrial lineage recorded in North America so far but formed a separate clade, the original distribution area of which is unknown. Additionally sequenced virile crayfish from Iowa (USA) also represented a new clade, suggesting that undiscovered lineage variation within O. virilis remains high. This exemplifies that genetic analyses of invading populations may provide new insights into diversity of a taxon in its original range.     

The genetic legacy of polyploid Bolivian Daphnia: the tropical Andes as a source for the North and South American D. pulicaria complex

We investigated genetic variation in asexual polyploid members of the water flea Daphnia pulex complex from a set of 12 Bolivian high-altitude lakes. We used nuclear microsatellite markers to study genetic relationships among all encountered multilocus genotypes, and combined this with a phylogenetic approach using DNA sequence data of three mitochondrial genes. Analyses of mitochondrial gene sequence divergence showed the presence of three very distinct clades that likely represent cryptic undescribed species. Our phylogenetic results suggest that the Daphnia pulicaria group, a complex of predominantly North American species that has diversified rapidly since the Pleistocene, has its origin in South America, as specific tests of topology indicated that all three South American lineages are ancestral to the North American members of this species group. A comparison between variation of nuclear and mitochondrial markers revealed that closely related polyploid nuclear genotypes sometimes belonged to very divergent mitochondrial lineages, while distantly related nuclear genotypes often belonged to the same mitochondrial lineage. This discrepancy suggests that these South American water fleas originated through reciprocal hybridization between different endemic, sexually reproducing parental lineages. It is also likely that polyploidy of the investigated lineages resulted from this hybridization. Nevertheless, no putative diploid parental lineages were found in the studied region.     

Proteomic Profile of Daphnia pulex using Data‐Independent Acquisition Mass Spectrometry and Ion Mobility Separation

Daphnia pulex is a keystone species for aquatic habitats and an ecological/evolution model organism. Although significant progress has been made on characterizing its genome, the D. pulex proteome remains largely uncharacterized partially due to abnormally high protein degradation during homogenization and emphasis on genomic analysis. In this study, various sample preparation and mass spectrometry acquisition methods are performed for the purpose of improving D. pulex proteome exploration. Benefits for employing both in‐gel and in‐solution methods of trypsin digestion are observed. Furthermore, acquisition methods employing ion mobility separation greatly increase peptide identification and more than doubled the proteome coverage. Bioinformatic analysis suggests that mitochondrial and hydrolytic activities are enriched in D. pulex compared to closely related invertebrates or Homo sapiens. Also, novel D. pulex proteins possessing putative genome modifying functional domains are identified. Data are available via ProteomeXchange with identifier PXD008455.     

Multiple cryptic species with divergent substrate affinities in the Serpula himantioides species complex

Serpula himantioides is a widespread saprotrophic morphospecies mainly colonising coniferous wood in nature, but it appears frequently in buildings as well. From an earlier study, it is known that at least three divergent lineages occur within the S. himantioides species complex. In this study, a broader sample of S. himantioides isolates has been analysed by multi-locus sequencing, including new isolates from Asia, North and South America. Altogether five phylogenetical species (PS1-5) were detected, all recognised across independent gene phylogenies. A new southern South American phylogenetic species (PS1) was found, representing an early diverging lineage within the S. himantioides species complex. The two closely related PS2 and PS3 lineages included isolates from North America only, and PS4 was also dominated by North American isolates. Most of the investigated isolates (76%) clustered into PS5, a lineage that has been found on most continents, including North America. Overall, little phylogeographical structure was found in PS5, indicating frequent and recent long-distance dispersal events within this widespread lineage. Our analyses indicate that South and North America are the centres of divergence for the S.?himantioides species complex. Some of the lineages seem adapted to various substrates, but PS5 is able to decay a wide array of angiosperms and gymnosperms, which may have facilitated the spread of this lineage throughout the world.     

Quaternary diversification in a sexual Holarctic zooplankter, Daphnia galeata

The effects of Quaternary glacial range partitioning on the diversification of Holarctic biota remain unclear. Glacial refugial lineages may form vicariant species, hybrid products, or merge after secondary contact. Here, we assess the effects of Quaternary glaciation on a Holarctic sexual zooplankter, Daphnia galeata, with apparently marked dispersal capacity and a widespread hybrid lineage in the New World. We collected samples of this species from 148 Holarctic lakes, analysed the nuclear and mitochondrial gene sequences, and tested predictions for hypotheses that account for the origin and spread of the New World D. galeata. We detected five nuclear phylogroups and four mitochondrial phylogroups, most of which were restricted to either the New World or the Old World. The oldest mitochondrial phylogroup was restricted to Japan. One major mitochondrial clade was distributed throughout the Holarctic, but only four haplotypes were shared among continents, and analysis of molecular variance indicated significant structure at the continental level. Haplotype sharing among continents could largely be attributed to anthropogenic introductions. Mismatch distributions, haplotype networks, phylogenetic trees, longitudinal haplotype diversity erosion and coalescence analyses are consistent with colonization from an Old World and a New World refugium. Our nuclear and mitochondrial DNA sequence evidence supports the hypothesis that the New World D. galeata underwent introgression with Daphnia dentifera, with dispersal being enhanced by glaciation. We conclude that Quaternary glaciation had a pronounced effect on the diversification of a Holarctic sexual zooplankter.     

Conservation Genetics of Kangaroo Mice, Genus Microdipodops

The two currently recognized species of kangaroo mice, Microdipodops megacephalus and M. pallidus, inhabit sandy soils of the Great Basin Desert in western North America. Given their habitat specificity and the fluctuating climate throughout the Pleistocene, kangaroo mice likely endured a turbulent biogeographic history that resulted in disjunct distributions and isolation of genetic lineages. Recent phylogenetic investigations using mitochondrial data have revealed several mitochondrial clades within this genus that may represent cryptic species. These mitochondrial clades are genetically unique, occupy relatively small distributions, and, as such, may be at an increased risk of extinction due to climate change and extensive recent habitat alteration. Herein, we apply haplotype network, population genetic, and historical demographic analyses to mitochondrial data of each Micropdipodops species and mitochondrial clade to assess conservation genetics within kangaroo mice. Results indicate that each mitochondrial clade is a distinct lineage with little to no gene flow occurring among clades. Additionally, historical demographic analyses support past population expansions and identify locations of past refugium for each distinct lineage. Although mitochondrial data indicate that the clades appear to be in approximate genetic equilibrium and have not suffered any extreme bottlenecks over time, there is still concern for the survival of smaller and more vulnerable Microdipodops subpopulations due to impending habitat threats in the Great Basin Desert.     

Predictors of invasion success by Daphnia species: influence of food, temperature and species identity

Non-indigenous North American Daphnia ‘pulex’ has recently invaded lakes and reservoirs in South Island, New Zealand, that formerly contained only native Daphnia carinata. New Zealand is characterised by a wide range of freshwater ecosystems and low species diversity of planktonic crustaceans, particularly Cladocera. The potential success of a species to invade and establish in a new community is likely to be predicted more accurately when reproductive response norms and fitness of key resident species, as well as the non-indigenous species, have been established under a range of relevant environmental conditions. Based on the results of experiments to test aspects of reproduction and fitness of the invader, D. ‘pulex’, and D. carinata when grown together at a range of relevant temperatures (8–23 °C) and related photoperiods, I predict the species-specific potential of D. ‘pulex’ to be dispersed and colonise New Zealand lentic habitats, and the potential of D. carinata to persist with the invader in these habitats. Larger population densities of D. ‘pulex’ compared to D. carinata at higher temperatures and food level, and larger densities of D. carinata at low temperatures, imply a potential for both species to coexist in New Zealand lakes, facilitated by seasonal succession; increased water temperature and nutrient input associated with climate and land use changes appear likely to promote the wider establishment of D. ‘pulex’, with both negative and positive implications for the conservation and management of New Zealand’s freshwater ecosystems.     

Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl's Pipistrelles (Chiroptera)

The Kuhl’s pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages occurring in Western Europe, and used both mitochondrial and nuclear markers to measure degrees of genetic isolation between bats carrying them. The sampling focused on an area of strict lineage sympatry in Switzerland but also included bats from further south, in North Africa. All individuals were barcoded for the COI gene to identify their mitochondrial lineages and five highly polymorphic microsatellite loci were used to cluster them according to their nuclear genotypes. Despite this low number of nuclear markers, all North African nuclear genotypes were grouped in a highly distinct subpopulation when compared with European samples sharing the same mitochondrial barcodes. The reverse situation prevailed in Switzerland where bats carrying distinct barcodes had similar nuclear genotypes. There was a weak east/west nuclear structure of populations, but this was independent of mitochondrial lineages as bats carrying either variant were completely admixed. Thus, the divergent mitochondrial barcodes present in Western Europe do not represent cryptic species, but are part of a single biological species. We argue that these distinct barcodes evolved in allopatry and came recently into secondary contact in an area of admixture north of the Alps. Historical records from this area and molecular dating support such a recent bipolar spatial expansion. These results also highlight the need for using appropriate markers before claiming the existence of cryptic species based on highly divergent barcodes.