Parsimony Network Research Articles

Did the parasitoid Pnigalio mediterraneus (Hymenoptera: Eulophidae) track the invasion of the horse chestnut leafminer?

How communities of natural enemies, such as parasitoids, adapt to the range expansion of their hosts or the arrival of a novel invasive host is an important question in invasion biology. Do parasitoids track the expansion of their hosts from their shared native range? Do they locally adapt both behaviorally and physiologically to the arrival of a novel species by shifting hosts? Few studies have addressed those questions, yet they are important to develop efficient methods to manage invasive species. Here we focus on Pnigalio mediterraneus Ferriere and Delucchi (Hymenoptera: Eulophidae), an important parasitoid of two major agricultural and ornamental pests, the olive fruit fly Bactrocera oleae Rossi (Diptera: Tephritidae) and the horse chestnut leafminer Cameraria ohridella Deschka & Dimic (Lepidoptera: Gracillariidae). C. ohridella recently invaded Europe starting from the Southern Balkans, whereas B. oleae has been associated since the Quaternary with wild olives in the Mediterranean, where it largely spread after the domestication of cultivated olives. We used two markers, the ribosomal spacer ITS2 and the mitochondrial gene COI. Although the ITS2 dataset provided little variation and no phylogeographic signal, analysis of mtDNA of 188 individuals of P. mediterraneus from 54 European localities allowed us to identify 53 haplotypes. Both nucleotide and haplotype diversity were higher for Mediterranean samples, and from samples reared from B. oleae. The statistical parsimony network identified one haplotype as the most frequent, ancestral and mainly associated with C. ohridella. Our findings suggest that P. mediterraneus locally host switched to C. ohridella from other hosts in the Balkans and later tracked the horse chestnut leafminer invasion over Europe. Therefore both host-tracking and ecological sorting could explain the current distribution of P. mediterraneus haplotypes.

Deconstructing an assemblage of “turtle” barnacles: species assignments and fickle fidelity in Chelonibia

Barnacles in the genus Chelonibia are commensal with a variety of motile marine animals including sea turtles, crustaceans, and sirenians. We conducted a worldwide molecular phylogenetic survey of Chelonibia collected from nearly all known hosts to assess species relationships, host-fidelity, and phylogeographic structure. Using DNA sequences from a protein-coding mitochondrial gene (COI), a mitochondrial rRNA gene (12S), and one nuclear rRNA gene (28S), we found that of four species, three (C. testudinaria, C. patula, and C. manati) are genetically indistinguishable. In addition, we show each utilizes a rare androdioecious mode of reproduction involving complemental males. In contrast, the fourth species (C. caretta), which is hermaphroditic and specializes on turtles, is genetically distinct—leading to the conclusion that the three former taxa are morphotypes of the same species and should be synonymized under C. testudinaria. Phylogenetic analysis resulted in three geographic clades (Atlantic, Indian Ocean/western Pacific, and eastern Pacific) with haplotype parsimony networks revealing no shared haplotypes among geographic regions. Analysis of molecular variance detected significant differences among sequences by region (p < 0.005); conversely, there were no significant differences among sequences when grouped by host or taxonomic designation. Average pairwise genetic distances were lower between the eastern Pacific and Atlantic clades (0.053 ± 0.006) than between the eastern Pacific and Indian Ocean/western Pacific clades (0.073 ± 0.008), suggesting Atlantic and eastern Pacific populations were connected more recently, perhaps until the rise of the Isthmus of Panama. Host use by Chelonibia morphotypes is discussed along with speculation on possible ancestral hosts and support for a “turtle-first” hypothesis.

Capturing the population structure of microparasites: using ITS‐sequence data and a pooled DNA approach

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a common marker not only for the molecular identification of different taxa and strains, but also for the analysis of population structure of wild microparasite communities. Importantly, the multicopy nature of this region allows the amplification of low-quantity samples of the target DNA, a common problem in studies on unicellular, unculturable microparasites. We analysed ITS sequences from the protozoan parasite Caullerya mesnili (class Ichthyosporea) infecting waterflea (Daphnia) hosts, across several host population samples. We showed that analysing representative ITS-types [as identified by statistical parsimony network analysis (SPN)] is a suitable method to address relevant polymorphism. The spatial patterns were consistent regardless of whether parasite DNA was extracted from individual hosts or pooled host samples. Remarkably, the efficiency in detecting different sequence types was even higher after sample pooling. As shown by simulations, aneasily manageable number of sequences from pooled DNA samples are sufficient to resolve the spatial population structure in this system. In summary, the ITS region analysed from pooled DNA samples can provide valuable insights into the spatial and temporal dynamics of microparasites. Moreover, the application of SPN analysis is a good alternative to the well-established neighbour-joining method (NJ) for the identification of representative ITS-types. SPN can even outperform NJ by joining most of the singleton sequences to representative sequence clusters.

Distinct population structure for co-occurring Anopheles goeldii and Anopheles triannulatus in Amazonian Brazil

To evaluate whether environmental heterogeneity contributes to the genetic heterogeneity in Anopheles triannulatus, larval habitat characteristics across the Brazilian states of Roraima and Pará and genetic sequences were examined. A comparison with Anopheles goeldii was utilised to determine whether high genetic diversity was unique to An. triannulatus. Student t test and analysis of variance found no differences in habitat characteristics between the species. Analysis of population structure of An. triannulatus and An. goeldii revealed distinct demographic histories in a largely overlapping geographic range. Cytochrome oxidase I sequence parsimony networks found geographic clustering for both species; however nuclear marker networks depicted An. triannulatus with a more complex history of fragmentation, secondary contact and recent divergence. Evidence of Pleistocene expansions suggests both species are more likely to be genetically structured by geographic and ecological barriers than demography. We hypothesise that niche partitioning is a driving force for diversity, particularly in An. triannulatus.

Origin and evolution of the Italian subterranean termiteReticulitermes lucifugus(Blattodea, Termitoidae, Rhinotermitidae)

The Holarctic genus Reticulitermes shows seven species within the Mediterranean Basin. While phylogeny and systematics at continental level has been deeply investigated, a few studies concentrated on local ranges. To gain a clearer picture of the diversity and evolution of the Italian species Reticulitermes lucifugus, we analyzed the mitochondrial cytochrome oxidase II (COII) gene marker in newly collected colonies across the Peninsula. Data were gathered with all R. lucifugus sequences available from previous studies; COII sequences of the closely related Iberian taxa were also added to the data set. Maximum-likelihood, median-joining and statistical parsimony network elaborations on the resulting 119 colonies all agreed in indicating that: (i) the Sardo-Corsican subspecies R. lucifugus corsicus, strictly related to Southern Italian populations (including the Sicilian ones), is phylogenetically closer to the Iberian Reticulitermes grassei; and (ii) R. lucifugus lucifugus peninsular populations are structured into three clusters. The phylogenetic relationships and the biogeography of extant taxa suggest a scenario in which R. lucifugus ancestors colonized the Italian region through the Sardo-Corsican microplate during its Oligocene-Miocene anticlockwise rotation. Moreover, well after the colonization took place, northward range expansion might have produced the presently observed genetic diversity, as inferred from haplotype and nucleotide diversity estimates. On the whole, this study highlights the evolution of Italian Reticulitermes taxa and supports the importance of a wide taxon sampling especially when dealing with organisms easily dispersed by human activities.

Phylogeography of two closely related species of Nolana from the coastal Atacama Desert of Chile: post‐glacial population expansions in response to climate fluctuations

AbstractAimTo investigate the impact of Quaternary climate cycles on the coastal Atacama Desert flora by assessing phylogeographical patterns of the desert shrub Nolana crassulifolia (Solanaceae) and its congener Nolana incana.LocationThe latitudinal aridity gradient from the southern margin of the coastal Atacama Desert to the mediterranean semi‐arid region of Chile (25–33° S).MethodsTwo cpDNA regions were sequenced for 130 individuals in 15 populations of these two closely related species, covering their entire distribution range (1000 km) along the arid to semi‐arid Chilean coast. We explored haplotype relationships in a statistical parsimony network, and assessed population genetic diversity, population differentiation and phylogeographical structure. In addition, we conducted demographic analyses and spatial analysis of genetic variation, identified barriers to gene flow with Monmonier's algorithm, and used Bayesian phylogenetic reconstruction to estimate divergence dates between lineages.ResultsWe found a total of 14 haplotypes – four of them shared by both species – and high levels of genetic differentiation among populations, but no past distribution breaks that could account for major vicariant events. Genetic diversity decreased continuously from north to south, with loss of haplotypes and a greater number of monomorphic populations in the southern range. Landscape analysis revealed greater genetic differentiation in the northernmost populations of both species.Main conclusionsThe documented north–south gradient of declining genetic diversity, the origin and location of ancestral haplotypes in northern sites, and the loss of haplotypes from southern populations all support the hypothesis of post‐glacial range expansion of Nolana southwards during arid/warmer cycles in the Atacama. The higher genetic diversity and greater differentiation of northern populations of both Nolana species support the hypothesis that populations survived in northern arid sites during wetter/colder episodes of the glacial cycles. We suggest that Quaternary arid phases in the Atacama promoted southward expansion of the coastal desert vegetation.

Mitochondrial DNA analyses reveal low genetic diversity in Culex quinquefasciatus from residential areas in Malaysia

The present study explored the intraspecific genetic diversity, dispersal patterns and phylogeographic relationships of Culex quinquefasciatus Say (Diptera: Culicidae) in Malaysia using reference data available in GenBank in order to reveal this species' phylogenetic relationships. A statistical parsimony network of 70 taxa aligned as 624 characters of the cytochrome c oxidase subunit I (COI) gene and 685 characters of the cytochrome c oxidase subunit II (COII) gene revealed three haplotypes (A1-A3) and four haplotypes (B1-B4), respectively. The concatenated sequences of both COI and COII genes with a total of 1309 characters revealed seven haplotypes (AB1-AB7). Analysis using tcs indicated that haplotype AB1 was the common ancestor and the most widespread haplotype in Malaysia. The genetic distance based on concatenated sequences of both COI and COII genes ranged from 0.00076 to 0.00229. Sequence alignment of Cx. quinquefasciatus from Malaysia and other countries revealed four haplotypes (AA1-AA4) by the COI gene and nine haplotypes (BB1-BB9) by the COII gene. Phylogenetic analyses demonstrated that Malaysian Cx. quinquefasciatus share the same genetic lineage as East African and Asian Cx. quinquefasciatus. This study has inferred the genetic lineages, dispersal patterns and hypothetical ancestral genotypes of Cx. quinquefasciatus.

Mitochondrial DNA analyses show that Zambia's South Luangwa Valley giraffe (Giraffa camelopardalis thornicrofti) are genetically isolated

AbstractThornicroft's giraffe, Giraffa camelopardalis thornicrofti, is a geographically isolated subspecies of giraffe found only in north‐east Zambia. The population only occurs in Zambia's South Luangwa Valley, an area which interestingly places it between the current distribution of Masai (G. c. tippelskirchi) giraffe to the north, and the Angolan (G. c. angolensis) and South African (G. c. giraffa) giraffe in the south‐west and south, respectively. Specific studies have been undertaken on the ecology of this subspecies, but their population genetics remains unknown. We studied 34 individuals from the South Luangwa National Park and adjacent Lupande Game Management Area and seven individuals from northern Botswana. The complete cytochrome b and control region sequences of the mitochondrial genome were sequenced and analysed together with database data by maximum likelihood tree reconstruction and maximum parsimony network analyses. The giraffe from Zambia's South Luangwa Valley are most closely related to the subspecies G. c. tippelskirchi and part of their radiation. However, they form a unique population that would benefit from increased research and conservation management.

Integrative analysis of DNA phylogeography and morphology of the European rose chafer (Cetonia aurata) to infer species taxonomy and patterns of postglacial colonisation in Europe

Integrative taxonomy has been proposed as a framework to unify new conceptual and methodological developments in quantitative assessment of trait variation used in species delimitation, but empirical studies in this young branch of systematics are rare. Here we use standard phylogenetic and parsimony network analyses on nuclear and mitochondrial DNA (Cox1, ITS1) of 230 individuals from 65 European sampling sites in order to deduce population structure of Cetonia beetles from geno- and haplotypes. Statistical measures of population differentiation are inferred on genealogical and geographical scales to test hypotheses about species limits and population history. By combining results of phylogenetic structure with features of morphology, including genital shape morphometrics and discrete external body characters, as well as with measures of population genetics, we attempt to integrate the results as a test of the validity of species limits, in particular of currently recognised subspecies. Despite high Cox1 divergence between some haplotype lineages, even some sympatric lineages (9%, e.g. N2 vs. N4), nDNA and morphology, as well as pattern of geographical and genealogical divergence measured by AMOVA analysis did not support the hypothesis of separate species. Highest divergence in nuclear markers was found among Italian populations of C. aurata pisana and C. a. sicula, and moderately high fixation indices along measurable morphological divergence suggest the correctness of their status as ‘subspecies’. Divergence time estimates of the lineages suggest a glacial divergence in different refugia between the major haplogroups, while population differentiation in mtDNA among these was primarily attributable to restricted gene flow caused by geographic isolation.

DNA barcoding at riverscape scales: assessing biodiversity among fishes of the genus Cottus (Teleostei) in northern Rocky Mountain streams

There is growing interest in broad-scale biodiversity assessments that can serve as benchmarks for identifying ecological change. Genetic tools have been used for such assessments for decades, but spatial sampling considerations have largely been ignored. Here, we demonstrate how intensive sampling efforts across a large geographical scale can influence identification of taxonomic units. We used sequences of mtDNA cytochrome c oxidase subunit 1 and cytochrome b, analysed with maximum parsimony networks, maximum-likelihood trees and genetic distance thresholds, as indicators of biodiversity and species identity among the taxonomically challenging fishes of the genus Cottus in the northern Rocky Mountains, USA. Analyses of concatenated sequences from fish collected in all major watersheds of this area revealed eight groups with species-level differences that were also geographically circumscribed. Only two of these groups, however, were assigned to recognized species, and these two assignments resulted in intraspecific genetic variation (>2.0%) regarded as atypical for individual species. An incomplete inventory of individuals from throughout the geographical ranges of many species represented in public databases, as well as sample misidentification and a poorly developed taxonomy, may have hampered species assignment and discovery. We suspect that genetic assessments based on spatially robust sampling designs will reveal previously unrecognized biodiversity in many other taxa.

Phylogeography of the neotropical Anopheles triannulatus complex (Diptera: Culicidae) supports deep structure and complex patterns.

BackgroundThe molecular phylogenetic relationships and population structure of the species of the Anopheles triannulatus complex: Anopheles triannulatus s.s., Anopheles halophylus and the putative species Anopheles triannulatus C were investigated.MethodsThe mitochondrial COI gene, the nuclear white gene and rDNA ITS2 of samples that include the known geographic distribution of these taxa were analyzed. Phylogenetic analyses were performed using Bayesian inference, Maximum parsimony and Maximum likelihood approaches.ResultsEach data set analyzed septely yielded a different topology but none provided evidence for the seption of An. halophylus and An. triannulatus C, consistent with the hypothesis that the two are undergoing incipient speciation. The phylogenetic analyses of the white gene found three main clades, whereas the statistical parsimony network detected only a single metapopulation of Anopheles triannulatus s.l. Seven COI lineages were detected by phylogenetic and network analysis. In contrast, the network, but not the phylogenetic analyses, strongly supported three ITS2 groups. Combined data analyses provided the best resolution of the trees, with two major clades, Amazonian (clade I) and trans-Andean + Amazon Delta (clade II). Clade I consists of multiple subclades: An. halophylus + An. triannulatus C; trans-Andean Venezuela; central Amazonia + central Bolivia; Atlantic coastal lowland; and Amazon delta. Clade II includes three subclades: Panama; cis-Andean Colombia; and cis-Venezuela. The Amazon delta specimens are in both clades, likely indicating local sympatry. Spatial and molecular variance analyses detected nine groups, corroborating some of subclades obtained in the combined data analysis.ConclusionCombination of the three molecular markers provided the best resolution for differentiation within An. triannulatus s.s. and An. halophylus and C. The latest two species seem to be very closely related and the analyses performed were not conclusive regarding species differentiation. Further studies including new molecular markers would be desirable to solve this species status question. Besides, results of the study indicate a trans-Andean origin for An. triannulatus s.l. The potential implications for malaria epidemiology remain to be investigated.

Mitochondrial Haplotypes Indicate Parapatric-like Phylogeographic Structure in Blue-Spotted Maskray (Neotrygon kuhlii) from the Coral Triangle Region

Phylogeographic structure was investigated in the blue-spotted maskray, Neotrygon kuhlii, focusing on the Coral Triangle region. We used as genetic marker a 519-bp fragment of the cytochrome c-oxidase subunit I (COI) gene, sequenced in a total of 147 individuals from 26 sampling locations. The parsimony network of COI haplotypes was split into seven distinct clades within the Coral Triangle region. Different clades had exclusive but contiguous geographic distributions, indicating parapatric-like phylogeographic structure. Strong genetic differences were also inferred between local populations within a clade, where reciprocal monophyly between geographically adjacent samples was observed on several instances. Nearly 25% of the total molecular variance could be ascribed to differences between geographic samples within a clade, whereas interclade variation accounted for >65% of the total variance. The strong phylogeographic structure observed within a clade can be explained by either sedentarity or female philopatry. We interpret the parapatric distribution of clades as the joint result of 1) expansion from refuge populations at times of low sea level, and 2) possible enhanced competition between individuals from different clades, or assortative mating, or hybrid zones, along lines of secondary contact. The parapatric-like structure uncovered in the present study parallels regional differences at nuclear marker loci, thus pointing to incipient speciation within Coral Triangle N. kuhlii.

Population differentiation of the European pond turtle (Emys orbicularis) in Poland inferred by the analysis of mitochondrial and microsatellite DNA: implications for conservation

We investigated the genetic diversity of Polish populations of the European pond turtle (Emys orbicularis) using complete sequences of the mitochondrial cytochrome b gene and allelic variation at thirteen microsatellite loci. We collected data from 146 turtles from 28 locations covering most of the species’ range in Poland. Our results showed a low haplotype diversity and high levels of microsatellite diversity in all populations. We applied two Bayesian approaches using the multilocus data and determined relationships of mtDNA haplotypes by constructing a parsimony network. We observed relatively consistent results of the two Bayesian clustering methods and largely concordant differentiation patterns between mitochondrial and microsatellite markers. All eastern Polish populations were assigned in a highly supported eastern group, while the majority of turtles from western Poland were joined in a distinct western group. The most probable number of population clusters corresponded to the number of native mtDNA lineages. Additionally, we detected a hierarchical structure within the eastern lineage splitting the populations into two subgroups. Polish populations generally constitute genetically homogenous groups, characterized by a low population admixture, with only negligible impact from allochthonous turtles.

Molecular Taxonomy of Anopheles (Nyssorhynchus) benarrochi (Diptera: Culicidae) and Malaria Epidemiology in Southern Amazonian Peru

Anopheline specimens were collected in 2011 by human landing catch, Shannon and CDC traps from the malaria endemic localities of Santa Rosa and San Pedro in Madre de Dios Department, Peru. Most specimens were either Anopheles (Nyssorhynchus) benarrochi B or An. (Nys.) rangeli, confirmed by polymerase chain reaction-restriction fragment length polymorphism-internal transcribed spacer 2 (PCR-RFLP-ITS2) and, for selected individuals, ITS2 sequences. A few specimens from Lupuna, Loreto Department, northern Amazonian Peru, were also identified as An. benarrochi B. A statistical parsimony network using ITS2 sequences confirmed that all Peruvian An. benarrochi B analyzed were identical to those in GenBank from Putumayo, southern Colombia. Sequences of the mtDNA COI BOLD region of specimens from all three Peruvian localities were connected using a statistical parsimony network, although there were multiple mutation steps between northern and southern Peruvian sequences. A Bayesian inference of concatenated Peruvian sequences of ITS2 + COI detected a single clade with very high support for all An. benarrochi B except one individual from Lupuna that was excluded. No samples were positive for Plasmodium by CytB-PCR.

Phylogeography and genetic diversity of East Asian Neolitsea sericea (Lauraceae) based on variations in chloroplast DNA sequences

Neolitsea sericea is an evergreen broad leaved tree in the warm-temperate regions of East Asia. This area is a hotspot for plant species richness and endemism caused by dynamic changes in land configuration during the Quaternary. However, the historical migration of such evergreen tree species is still poorly understood. In an attempt to reconstruct the phylogeographic history of N. sericea during the Quaternary, we identified the chloroplast DNA haplotypes of 287 individuals from 33 populations covering almost all of its geographic range. Analyses were based on sequence data from the trnL-F, psbC-trnS, and rps16 regions. Nine haplotypes were identified. The majority included ancestral types in the southwestern part of the main islands of Japan, with other region-specific haplotypes being found in populations on the Korean Peninsula, Taiwan (Isl. Lanyu), and elsewhere in Japan. A statistical parsimony network revealed two lineages derived from Japanese main islands. One was represented on the Korean Peninsula, the other on Isl. Lanyu. The current distribution of N. sericea has been shaped by colonization via land bridges. During the glacial periods, two primary, but separate migration routes were followed--from the southwestern part of the Japanese main islands to either the Korean Peninsula or Taiwan. In addition, we believe the Zhoushan populations were shaped by post-glacial processes through an ECS land bridge (East China Sea basin) from northern refugia that existed during the late Pleistocene.

Phylogenetic relationships among North Atlantic redfish (genusSebastes) as revealed by mitochondrial DNA sequence analyses

Summary Species structure and phylogenetic relationships among the four currently recognised North Atlantic redfish species, Sebastes mentella (‘deep-sea’ and ‘oceanic’ phenotype), S. marinus (including ‘giant’ phenotype), S. fasciatus and S. viviparus, were investigated by sequencing the complete mitochondrial NADH dehydrogenase subunit 3 (ND3) gene for 313 individuals (333 including outliers). Low levels of sequence divergence of 0.3–2.3% between the North Atlantic Sebastes haplotypes, low resolution in phylogenetic trees and a star-like statistical parsimony network indicate a population bottleneck and/or founder event with a subsequent population expansion and a rapid speciation in North Atlantic Sebastes. Diagnostic mutations within the ND3 gene were recognised for some of the species. The results lead to the hypothesis that the ancestral haplotype lineage is now very rare or has suffered extinction and that the most basal lineage is found in S. viviparus. The results further indicate direct descendants in the S. fasciatus and S. marinus lineages from the S. mentella lineage, whereas the S. viviparus lineage originates from an earlier division. The observation of two haplotype lineages in S. marinus with a relatively high level of intraspecific genetic divergence, points towards a possible cryptic speciation.

Intraspecific variation and emendation of Hannaella kunmingensis

In order to investigate the intraspecific variability in Hannaella kunmingensis, 11 isolates, including the type strain, were analyzed for their morphological and biochem- ical traits. The combined internal transcribed spacer region (ITS), D1/D2 domains of the large subunit rDNA (LSU), and cytochrome b gene were examined using phylogenetic and parsimony network analyses. Our investigations revealed differences in colony morphology as well as differences in 31 out of 64 phenotypic characteristics exam- ined, including growth in lactose, vitamin free medium, xylitol, L-arabinitol, and nitrite. Growth in the presence of 0.1 % cycloheximide was also highlighted in H. kunmin- gensis. All the 11 strains were conspecific in the LSU; however, variations of about 2.5 % were found in the ITS while isolate CBS 8356 exhibited a 27.3 % divergence from the other strains in the cytochrome b gene. Parsimony net- work analysis revealed the existence of three haplotypes among the H. kunmingensis strains studied but excluded CBS 8356 from the network connecting these haplotypes. This study contributes to the knowledge of the intraspecific diversity of H. kunmingensis. To accommodate such intra- specific variations, an emendation of the species diagnosis is proposed.

Evolutionary relationships in Oxytropis species, as estimated from the nuclear ribosomal internal transcribed spacer (ITS) sequences point to multiple expansions into the Arctic

Species of the genus Oxytropis are distributed in the northern hemisphere, especially in alpine and arctic areas. Although comprehensive taxonomic treatments exist for local floras, an understanding of the evolutionary relationships is lacking for the genus as a whole. To determine if different ancestral Oxytropis species colonized the North American Arctic separately, as suggested by taxonomy, we sequenced the nuclear ribosomal internal transcribed spacer (ITS) region from 16 Oxytropis specimens, including four species that were used in a previous transcriptome study. In addition, 81 other Oxytropis ITS sequences were retrieved from public sequence databases and included in the analysis. The whole data set was analyzed using phylogenetic trees and statistical parsimony networks. Results show that all Oxytropis ITS sequences are very similar. Furthermore, at least six lineages evolved from different temperate ancestors to colonize the North American Arctic. This pattern is believed to be typical of the arctic flora. Additionally, the sequence relationship analyses confirm that the subgenus Phacoxytropis may be ancestral in Oxytropis.

Genetically diverse but with surprisingly little geographical structure: the complex history of the widespread herb Carex nigra (Cyperaceae)

AbstractAim Based on extensive range‐wide sampling, we address the phylogeographical history of one of the most widespread and taxonomically complex sedges in Europe, Carex nigra s. lat. We compare the genetic structure of the recently colonized northern areas (front edge) and the long‐standing southern areas (rear edge), and assess the potential genetic basis of suggested taxonomic divisions at the rank of species and below.Location Amphi‐Atlantic, central and northern Europe, circum‐Mediterranean mountain ranges, central Siberia, Himalayas.Methods A total of 469 individuals sampled from 83 populations, covering most of the species’ range, were analysed with amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) markers. Bayesian clustering, principal coordinates analysis, and estimates of diversity and differentiation were used for the analysis of AFLP data. CpDNA data were analysed with statistical parsimony networks and maximum parsimony and Bayesian inference of phylogenetic trees.Results Overall genetic diversity was high, but differentiation among populations was limited. Major glacial refugia were inferred in the Mediterranean Basin and in western Russia; in addition, there may have been minor refugia in the North Atlantic region. In the southern part of the range, we found high levels, but geographically quite poorly structured genetic diversity, whereas the levels of genetic diversity varied among different areas in the north. North American populations were genetically very similar to the European populations.Main conclusions The data are consistent with extensive gene flow, which has obscured the recent history of the taxon. The limited differentiation in the south probably results from the mixing of lineages expanding from several local refugia. Northward post‐glacial colonization resulted in a leading‐edge pattern of low diversity in the Netherlands, Belgium, Scotland and Iceland, whereas the observed high diversity levels in Fennoscandia suggest broad‐fronted colonization from the south as well as from the east. The patterns found in the American populations are consistent with post‐glacial colonization, possibly even with anthropogenic introduction from Europe. Our data also suggest that the tussock‐forming populations of C. nigra, often referred to as a distinct species (Carex juncella), represent an ecotype that has originated repeatedly from different populations with creeping rhizomes.

Genetic Diversity of Bloom-Forming Microcystis (Cyanobacteria) Populations in a Hyper-Eutrophic Pond in Central China

Sequencing the environmental rRNA genes of Microcystis populations, such as by internal transcribed spacer (ITS), has been proven to provide a new insight into the genetic diversity of Microcystis in freshwater. In this study, a 19-month monitoring of Microcystis populations in a hyper-eutrophic pond in Wuhan city, China was conducted through molecular method by sequencing ITS fragments from the environmental DNA library. Three hundred twenty ITS genotypes of Microcystis in this pond were identified from a total of 563 sequences, thus exhibiting high genetic diversity of Microcystis in the pond. Dramatic changes and succession in ITS genotypes were also found during the survey period. Despite the absence of significant dominant ITS genotypes in the pond, several main genotypes were found to have been dominated for a short term. However, Microcystis ITS genotype patterns from 2007 to 2008 presented a complicated situation in this pond. The parsimony network (TCS) analysis showed that two groups were formed based on ITS genotypes.