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

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

Frequent chloroplast capture among Isodon (Lamiaceae) species in Japan revealed by phylogenies based on variation in chloroplast and nuclear DNA

A recent phylogenetic study based only on chloroplast DNA (cpDNA) variation revealed that populations of an Isodon species are frequently embedded paraphyletically among other Isodon species. This phylogenetic discrepancy between species taxonomy and molecular phylogeny was considered to have resulted from chloroplast DNA captures and/or incomplete lineage sorting. To elucidate which of these factors was mainly responsible for the observed phylogenetic pattern, we performed phylogenetic analyses of multiple populations of Isodon species in Japan using cpDNA variation, three single-copy nuclear genes, and double-digest restriction-site-associated DNA sequencing (ddRAD-seq). Although a species often shared chlorotypes with other species, our phylogenetical analyses based on variation in the three single-copy nuclear genes and the ddRAD-seq data showed that most populations belonging to the same species were monophyletic at the species level, suggesting that chloroplast capture may have frequently occurred between Isodon species. Some populations of an intraspecific taxon were embedded paraphyletically within the species, regardless of the large amount of phylogenetic information in nuclear DNA; this incongruity may have resulted from incomplete lineage sorting.     

Phylogenetic relationships among Acanthaceae: evidence from noncoding trnL-trnF chloroplast DNA sequences

We used sequence data from the intron and spacer of the trnL-trnF chloroplast region to study phylogenetic relationships among Acanthaceae. This region is more variable than other chloroplast loci that have been sequenced for members of Acanthaceae (rbcL and ndhF), is more prone to length mutations, and is less homoplasious than these genes. Our results indicate that this region is likely to be useful in addressing phylogenetic questions among but not within genera in these and related plants. In terms of phylogenetic relationships, Elytraria (representing Nelsonioideae) is more distantly related to Acanthaceae sensu stricto (s.s.) than Thunbergia and Mendoncia. These last two genera are strongly supported as sister taxa. Molecular evidence does not support monophyly of Acanthaceae s.s., although there is strong morphological evidence for this relationship. There is strong support for monophyly of four major lineages within Acanthaceae s.s.: the Acanthus, Barleria, Ruellia, and Justicia lineages as here defined. The last three of these comprise a strongly supported monophyletic group, and there is weaker evidence linking the Ruellia and Justicia lineages as closest relatives. Within the Acanthus lineage, our results confirm the existence of monophyletic lineages representing Aphelandreae and Acantheae. Lastly, within the Justicia lineage, we develop initial hypotheses regarding the definition of sublineages; some of these correspond to earlier ideas, whereas others do not. All of these hypotheses need to be tested against more data.     

Evolutionary history of endangered and relict tree species Dipteronia sinensis in response to geological and climatic events in the Qinling Mountains and adjacent areas

Geological and climatic events are considered to profoundly affect the evolution and lineage divergence of plant species. However, the evolutionary histories of tree species that have responded to past geological and climate oscillations in central China''s mountainous areas remain mostly unknown. In this study, we assessed the evolutionary history of the endangered and relict tree species Dipteronia sinensis in the Qinling Mountains (QM) and adjacent areas in East Asia based on variations in the complete chloroplast genomes (cpDNA) and reduced‐genomic scale single nucleotide polymorphisms (SNPs). Population structure and phylogenetic analysis based on the cpDNA variations suggested that D. sinensis could be divided into two intraspecific genetic lineages in the eastern and western sides of the QM (EQM and WQM, respectively) in East Asia. Molecular dating suggested that the intraspecific divergence of D. sinensis occurred approximately 39.2 million years ago during the later Paleogene. It was significantly correlated with the orogeny of the QM, where the formation of this significant geographic barrier in the region may have led to the divergence of independent lineages. Bayesian clustering and demographic analysis showed that intraspecific gene flow was restricted between the EQM and WQM lineages. Isolation‐with‐migration analysis indicated that the two genetic lineages experienced significant demographic expansions after the Pleistocene ice ages. However, the genetic admixture was determined in some populations between the two lineages by the large scale of SNP variations due to DNA incompatibility, the large significant population size, and rapid gene flow of nuclear DNA markers. Our results suggest that two different conservation and management units should be constructed for D. sinensis in the EQM and WQM areas. These findings provide novel insights into the unprecedented effects of tectonic changes and climatic oscillations on lineage divergence and plant population evolution in the QM and adjacent areas in East Asia.     

Genetic diversity enhanced by ancient introgression and secondary contact in East Pacific black mangroves

Regional distribution of genetic diversity in widespread species may be influenced by hybridization with locally restricted, closely related species. Previous studies have shown that Central American East Pacific populations of the wide-ranged Avicennia germinans , the black mangrove, harbour higher genetic diversity than the rest of its range. Genetic diversity in this region might be enhanced by introgression with the locally restricted Avicennia bicolor . We tested the hypotheses of ancient hybridization using phylogenetic analysis of the internal transcribed spacer region (ITS) of the nuclear ribosomal DNA and intergenic chloroplast DNA; we also tested for current hybridization by population level analysis of nuclear microsatellites. Our results unveiled ancient ITS introgression between a northern Pacific Central American A. germinans lineage and A. bicolor . However, microsatellite data revealed contemporary isolation between the two species. Polymorphic ITS sequences from Costa Rica and Panama are consistent with a zone of admixture between the introgressant ITS A. germinans lineage and a southern Central American lineage of A. germinans . Interspecific introgression influenced lineage diversity and divergence at the nuclear ribosomal DNA; intraspecific population differentiation and secondary contact are more likely to have enhanced regional genetic diversity in Pacific Central American populations of the widespread A. germinans .     

One Species, Three Pleistocene Evolutionary Histories: Phylogeography of the Italian Crested Newt, Triturus carnifex

Phylogeographic patterns of temperate species from the Mediterranean peninsulas have been investigated intensively. Nevertheless, as more phylogeographies become available, either unique patterns or new lines of concordance continue to emerge, providing new insights on the evolution of regional biotas. Here, we investigated the phylogeography and evolutionary history of the Italian crested newt, Triturus carnifex, through phylogenetic, molecular dating and population structure analyses of two mitochondrial gene fragments (ND2 and ND4; overall 1273 bp). We found three main mtDNA lineages having parapatric distribution and estimated divergence times between Late Pliocene and Early Pleistocene. One lineage (S) was widespread south of the northern Apennine chain and was further geographically structured into five sublineages, likely of Middle Pleistocene origin. The second lineage (C) was widespread throughout the Padano-Venetian plain and did not show a clear phylogeographic structure. The third lineage (N) was observed in only two populations located on western Croatia/Slovenia. Results of analysis of molecular variance suggested that partitioning populations according to the geographic distribution of these lineages and sublineages explains 76% of the observed genetic variation. The phylogeographic structure observed within T. carnifex and divergence time estimates among its lineages, suggest that responses to Pleistocene environmental changes in this single species have been as diverse as those found previously among several codistributed temperate species combined. Consistent with the landscape heterogeneity, physiographic features, and palaeogeographical evolution of its distribution range, these responses encompass multiple refugia along the Apennine chain, lowland refugia in large peri-coastal plains, and a 'cryptic' northern refugium.     

Boreotropical migration explains hybridization between geographically distant lineages in the pantropical clade Sideroxyleae (Sapotaceae)

To determine whether the fragmented pantropical distribution of present day Sideroxyleae primarily is the result of long-distance dispersals or represents the remnants of a once continuous distribution in the northern hemisphere, the boreotropical flora, we used phylogenetic analyses of chloroplast and nuclear ribosomal DNA data, Bayesian molecular dating, and Bayesian estimation of ancestral areas. Incongruence between the two data sets was examined with a nuclear low copy gene phylogeny to discover any occurrences of reticulate evolution. The Pacific clade Nesoluma was shown to have two distinct copies of the nuclear low copy gene AAT, one from an African and one from an American ancestral lineage, indicating that it is of allopolyploid origin. We conclude that Sideroxyleae, including the ancestral lineages of Nesoluma, were part of the boreotropical flora and entered the New World via the north Atlantic land bridge. We also suggest that the distribution of extant species resulted from the cooling climate at the end of the Eocene. Sideroxylon oxyacanthum is shown not to belong in the group, but in Chrysophylloideae. A classification reflecting phylogenetic relationships, as well as new combinations for the species in Nesoluma under Sideroxylon, is presented.     

Chloroplast DNA variation in a hyperdiverse tropical tree community

• We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequent in genetically diverse species, as expected in the presence of introgression.
• We sampled a total of 1,681 individual trees from 472 species corresponding to 198 genera and sequenced them at a noncoding chloroplast DNA fragment.
• Polymorphism was more frequent in species that have congeneric species in the study site than in those without congeners (30% vs. 12%). Moreover, more chloroplast haplotypes were shared with congeners in polymorphic species than in monomorphic ones (44% vs. 28%).
• Despite large heterogeneities caused by genus‐specific behaviors in patterns of hybridization, these results suggest that the higher polymorphism in the presence of congeners is caused by local introgression rather than by incomplete lineage sorting. Our findings suggest that introgression has the potential to drive intraspecific genetic diversity in species‐rich tropical forests.

     

GENE FLOW AND SPECIES DELIMITATION: A CASE STUDY OF TWO PINE SPECIES WITH OVERLAPPING DISTRIBUTIONS IN SOUTHEAST CHINA

Species delimitation detected by molecular markers is complicated by introgression and incomplete lineage sorting between species. Recent modeling suggests that fixed genetic differences between species are highly related to rates of intraspecific gene flow. However, it remains unclear whether such differences are due to high levels of intraspecific gene flow overriding the spread of introgressed alleles or favoring rapid lineage sorting between species. In pines, chloroplast (cp) and mitochondrial (mt) DNAs are normally paternally and maternally inherited, respectively, and thus their relative rates of intraspecific gene flow are expected to be high and low, respectively. In this study, we used two pine species with overlapping geographical distributions in southeast China, P. massoniana and P. hwangshanensis, as a model system to examine the association between organelle gene flow and variation within and between species. We found that cpDNA variation across these two pine species is more species specific than mtDNA variation and almost delimits taxonomic boundaries. The shared mt/cp DNA genetic variation between species shows no bias in regard to parapatric versus allopatric species’ distributions. Our results therefore support the hypothesis that high intraspecific gene flow has accelerated cpDNA lineage sorting between these two pine species.     

COMPARATIVE METHODS AT THE SPECIES LEVEL: GEOGRAPHIC VARIATION IN MORPHOLOGY AND GROUP SIZE IN GREY-CROWNED BABBLERS (POMATOSTOMUS TEMPORALIS)

We show that a new comparative method that sheds light on evolutionary trends among species may also illuminate trends within species. This finding comes from a phylogenetic autocorrelation analysis of morphological traits among individuals sampled from ten populations of a cooperatively breeding songbird, the Grey-crowned Babbler (Pomatostomus temporalis). Highly variable mitochondrial DNA (mtDNA) sequences from both the eastern (Pomatostomus temporalis temporalis) and western (Pomatostomus temporalis rubeculus) lineages were used to define genetic distances among 120 individuals and to estimate correlations among individuals in wing length, tarsus length, and body weight via an intraspecific weighting matrix. The autoregressive model effectively removed intraspecific correlations for all three morphological variables, and the proportion of the total phenotypic variance due to genealogical relationships varied from 0.68 (weight) to 0.23 (tarsus). The analysis revealed correlations among the specific components of traits, in which none were previously detected (type-I error) and diminished correlations that appeared strong when phylogeny was ignored. Group size was the only trait for which the autoregressive model failed to remove intraspecific correlations, a result likely due to the plasticity, convergence, and clinal variation in this trait in both the eastern and western lineages. The autocorrelation analysis weakened significant negative correlations between group size and total values for wing length and body weight, but the interpretation of this result depends on the adaptive significance ascribed to the “phylogenetic component” of trait values removed by the analysis. Comparative methods employing distance matrices are one useful way of summarizing the pattern of nonhierarchical relationships among conspecific individuals (“tokogenetic” relationships, sensu Hennig).     

A study of the phylogeny of Brassica rapa,B. nigra,Raphanus sativus,and their related genera using noncoding regions of chloroplast DNA

There are two evolutionary lineages in the genus Brassica: the rapa/oleracea lineage and the nigra lineage. Using nuclear DNA sequences such as the intergenic spacer between 5S rRNA genes and the internal transcribed spacer between 18S and 25S rRNA genes, we and others had previously demonstrated that Raphanus sativus is closely related to the nigra lineage. In the present study, we sequenced the chloroplast noncoding region between trnT and trnF and that between trnD and trnT in seven species and showed that R. sativus is more closely related to the rapa/oleracea lineage than to the nigra lineage. The conflicting results from nuclear DNA and chloroplast DNA support the hypothesis that Raphanus was derived from a hybridization between the rapa/oleracea and the nigra lineages. We estimated the date of this hybridization event to be 60% of the divergence time between the two Brassica lineages. In addition, the pattern and rate of nucleotide substitution were studied. There were more transversions than transitions in these noncoding regions, which have a high AT content. Furthermore, the proportion of transversions among the substitutions at a site increases with increasing A + T content of its two adjacent nucleotides. An influence of immediate 5(') pyrimidine on substitution pattern is also observed when both adjacent bases in the two DNA strands are A or T. The rate of nucleotide substitution in the trnL group I intron is only about one third of the rate in the nearby intergenic spacers in the trnT-trnF fragment. The rate of nucleotide substitution in the rapa/oleracea lineage is at least 1.5 times that in the nigra lineage.     

EVOLUTIONARY IMPLICATIONS OF INTRASPECIFIC CHLOROPLAST DNA VARIATION IN DWARF DANDELIONS (KRIGIA; ASTERACEAE)

Intraspecific chloroplast DNA polymorphisms were examined for 51 populations of seven species in the genus Krigia. A total of 1,100 restriction sites was surveyed and 46 of these were variable at the intraspecific level. Twenty-two of the variable sites were found within K. virginica, giving this species one of the highest levels of intraspecific chloroplast DNA divergence of any examined species. In contrast, no restriction site variation was detected within K. dandelion, K. wrightii, and K. occidentalis. Five polymorphisms were identified from the 16 populations of the K. cespitosa-gracilis complex, but no mutations distinguished the K. cespitosa and K. gracilis types. Krigia montana and K. biflora showed 11 and eight restriction site polymorphisms, respectively. The chloroplast genome of the hexaploid K. montana was derived from the diploid K. biflora rather than the tetraploid K. montana. High levels of polymorphism were found in species having different ploidy levels, such as K. virginica, K. biflora, and K. montana. Furthermore, most mutations found in these three species were recorded from the tetraploid lineages. As a result, evolutionary rates between different ploidy levels differ significantly. The chloroplast DNA restriction site data suggest that all surveyed populations of the autotetraploid K. virginica originated from a common ancestor. Our results also indicate that certain regions of the chloroplast genome have changed more rapidly than others and have the potential to resolve evolutionary questions at the population level.     

Molecular taxonomy of the suborder Bodonina (Order Kinetoplastida), including the important fish parasite,Ichthyobodo necator

Ichthyobodo necator is an important fish ectoparasite with a broad host and ecological range. A novel method, involving the use of an anesthetic, allowed the collection of large numbers of parasites from the skin and gills of hybrid striped bass (Morone saxatilis male x M. chrysops female). Genomic DNA from these samples was used to amplify and clone the 18S rRNA gene. The 18S rRNA gene was similarly cloned from Bodo caudatus, Bodo edax, Bodo saltans, an unidentified Bodo species, and Dimastigella trypaniformis. The resulting sequences were aligned with other representative kinetoplastid species using pileup and similarities in secondary structure. Phylogenetic relationships within the suborder Bodonina and representatives of the suborder Trypanosomatina were determined using maximum-likelihood statistics. The phylogenetic analyses strongly supported the order Kinetoplastida as a monophyletic assemblage consisting of at least two major lineages. One lineage consisted exclusively of L. necator, indicating that it may represent a new suborder. The second lineage consisted of all other kinetoplastid species. This second lineage appeared to contain at least 8 bodonine sublineages, none of which correlated with currently recognized families. For three sublineages, there was a close correspondence between the 18S phylogeny and the classical taxonomy of Dimastigella, Rhynchobodo, and Rhynchomonas. In contrast, Bodo and Cryptobia were polyphyletic, containing species in two or more sublineages that may represent separate genera.     

Differentiation within the genus Leptocarabus (excl. L. kurilensis) in the Japanese Islands as deduced from mitochondrial ND5 gene sequences (Coleoptera, Carabidae)

The phylogenetic trees have been constructed for the mitochondrial ND5 gene sequences from the Japanese Leptocarabus ground beetles, which contain 101 specimens collected from nearly the complete distribution ranges of them consisting of five morphological species, i.e., Leptocarabus procerulus, L. kumagaii, L. hiurai, L. kyushuensis and L. arboreus. On the trees, there are recognized two major lineages, each of which is further divided into two or more sublineages. The phylogenetic lines are geographically linked. Two or more species occur in a single lineage, and the same species appear in different lines. We suggest that transformation from one type of morphology to another took place in parallel in various periods of evolution of the Japanese Leptocarabus. From the phylogenetic tree and the dating from the nucleotide substitution rate and the geohistorical data it is inferred that the ancestry of all the Japanese Leptocarabus species was derived from a protoform of L. kyushuensis inhabited the ancient Japan area, followed by separation into two lineages after split of the Japanese Islands from the Eurasian Continent. They then propagated distribution to occupy their own habitat ranges, during which the morphological transformation took place in some lineages.     

Postembryonic nongonadal cell lineages of the nematode Panagrellus redivivus: Description and comparison with those of Caenorhabditis elegans

The postembryonic nongonadal cell lineages of the nematode Panagrellus redivivus are described and compared with those of Caenorhabditis elegans. The newly hatched larvae of P. redivivus females and males and C. elegans hermaphrodites and males are very similar. An almost identical set of blast cells divides postembryonically in P. redivivus and C. elegans to produce similar changes in the neuronal, muscular, hypodermal, and digestive systems. Most of these cell lineages are invariant; however, there is substantial variability in the number of cell divisions in the relatively extensive lineages of the lateral hypodermis of P. redivivus. Typically, in P. redivivus females, 55 blast cells generate 635 surviving progeny and 29 cell deaths; in P. redivivus males, 59 blast cells generate 758 surviving progeny and 35 cell deaths. The lineages generating the cells of the male tails of P. redivivus and C. elegans are almost identical; thus, the grossly different characteristics of these structures must reflect differences in the morphogenesis of cells equivalent in lineage history. Laser ablation experiments demonstrate that the gonad induces vulva development and that cell-cell interactions are important in specifying the fates of hypodermal precursor cells. The lateral hypodermal lineages provide striking examples of the apparent construction of complex lineages from modular sublineages; one simple pattern of cell divisions and cell fates occurs 70 times in the P. redivivus female. The differences in cell lineage between P. redivivus and C. elegans are relatively minor, and many appear to have involved two types of evolutionary change: the replacement of sublineages, and the modification of sublineages by the four classes of lineage transformations previously proposed based on a comparison of P. redivivus and C. elegans gonadal cell lineages (Sternberg and Horvitz, 1981). These types of differences suggest that the genetic programming of cell lineage includes instructions specifying where and when a particular sublineage is utilized, and other instructions specifying the nature of that sublineage.     

Multiple Pleistocene refugia and post‐glacial colonization in the European chub (Squalius cephalus) revealed by combined use of nuclear and mitochondrial markers

Aim To analyse patterns of nuclear and mitochondrial genetic variation in the European chub, Squalius cephalus (Linnaeus, 1758), in order to understand the evolutionary history of this species and to test biogeographical hypotheses for the existence of co‐distributed European freshwater fish species. Location Rivers in Europe (Finland, Poland, Czech Republic, France, Bulgaria, Spain, Italy). Methods We genotyped 12 polymorphic microsatellite markers derived from 310 individuals collected from across the distribution of S. cephalus in Europe (including a total of 15 populations) and sequenced mitochondrial DNA (mtDNA) from a subset of 75 individuals. Sequences of mtDNA cytochrome b were analysed using both phylogenetic (median‐joining networks) and population genetic methods (tests for demographic history, mismatch distributions, Bayesian coalescent analysis). Geographical structure in microsatellite loci was examined using a distance method (F_ST), factorial correspondence analysis (FCA) and a Bayesian clustering method (structure ). Results The mtDNA network showed a clear split into four different haplogroup lineages: Western (separated into Atlantic and Danubian sublineages), Eastern, Aegean (occurring in two distinct sublineages in the Balkans and in Spain) and Adriatic. Our results indicate recent population expansion in the Eastern and Western Atlantic lineages and the admixture of two previously separate sublineages (Atlantic and Danubian) in the Western lineage. Bayesian structure analysis as well as FCA results roughly corresponded to the mtDNA‐based structure, separating the sampled individuals into almost non‐overlapping groups. Main conclusions Our results support hypotheses suggesting origins of extant lineages of freshwater fishes in multiple refugia and the subsequent post‐glacial colonization of Europe via different routes. We confirmed the previously proposed two‐step expansion scenario from the Danube refuge, the existence of a secondary (Atlantic) refuge during the last glaciation (probably in the Rhone River) and population expansion of this lineage. Conspicuous divergences among Mediterranean populations reflect their different origin, as well as their low contribution to the recent genetic pool of chub in central Europe.     

A REASSESSMENT OF SPECIES BOUNDARIES IN CYSTOSEIRA AND HALIDRYS (PHAEOPHYCEAE,FUCALES) ALONG THE NORTH AMERICAN WEST COAST1

Application of phylogenetic species recognition to morphologically recognized species in the genera Cystoseira Agardh and Halidrys Lyngbye on North American west coasts revealed little genetic variation despite a remarkable degree of morphological variation currently used to recognize and delineate species. Whereas morphological characteristics allow recognition of two genera, four morphological species and three informal forms, maximum genetic variation among them was similar to that characteristic of the intraspecific level in European congeners and other Fucales. Among morphological species and forms, nucleotide variation in a combined 26S (large subunit (LSU)) and internal transcribed spacer (ITS) ribosomal DNA analysis was below 3% while it was 1% or less for the RUBISCO spacer of the chloroplast DNA. Comparison of the LSU data to available data for European congeners showed that the genera Cystoseira and Halidrys are not monophyletic and that the previously recognized Cystoseiraceae should be included within the family Sargassaceae. These observations suggest that the current taxonomy for the Sargassaceae fails to reflect evolutionary history because Atlantic and Pacific Cystoseira and Halidrys appear to have arrived at similar morphologies independently. Our results indicate a comparatively recent establishment on the west coast of North America of a sargassacean progenitor whose descendant taxa have experienced limited genetic divergence and are characterized by a high capacity for phenotypic variation despite their overall genetic similarity.     

Out of the Pan-Himalaya: Evolutionary history of the Paeoniaceae revealed by phylogenomics

Peonies (the Paeoniaceae, Paeonia L.) are famous garden flowers, medicinal plants, and edible oil crops, but their evolutionary history largely remains unknown. To probe into their phylogenetic relationships, evolutionary history, formation of present distribution pattern, and origins of tetraploids, we sequenced 25 fragments belonging to 20 single copy nuclear genes and 14 chloroplast regions of all species in the genus to reconstruct phylogenetic relationships, date the divergence times of lineages, infer the ancestral biogeographical regions, and document the parents of tetraploids. Our results show that Paeoniaceae separated from the other members in Saxifragales in the Campanian of the late Cretaceous and diverged into two clades, woody and herbaceous clades, in the late Oligocene or early Miocene. They survived and early diverged in the Pan-Himalaya where they migrated eastwards to East Asia and further to NW America, and northwards to Middle Asia, and further to Europe. The woody lineage differentiated into two sublineages with accelerated root or floral disk evolution, while the herbaceous lineage diverged into five sublineages. Multiple glacial and interglacial cycles in Europe in the late Pliocene and early Pleistocene created opportunities for the peony species to meet and hybridize in the Mediterranean refugia, giving rise to eight allotetraploid species and four infraspecific tetraploids. Paeonia daurica Andrews, P. obovata Maxim., and P. tenuifolia L. served as the most important parents. The phylogeny of Paeonia L. implies that a new taxonomic system with two subgenera and seven sections should be proposed.     

Extensive intraspecific chloroplast DNA (cpDNA) variation in the alpine Draba aizoides L. (Brassicaceae): haplotype relationships and population structure

Chloroplast DNA (cpDNA) sequence variation is currently the most widely used tool for the inference of phylogenetic relationships among plants at all taxonomic levels. Generally, noncoding regions tend to evolve faster than coding sequences and have recently been applied to the study of phylogenetic relationships among closely related taxa. An implicit assumption of many of these studies is that intraspecific cpDNA variation is either absent or low and therefore will not interfere with the reconstruction of interspecific relationships. A survey of cpDNA sequence variation in the common alpine plant species Draba aizoides L. was undertaken to assess levels of intraspecific cpDNA sequence variation. These levels were compared to levels of interspecific sequence divergence between D. aizoides and related alpine Draba species. Intraspecific cpDNA sequence divergence was extensive in D. aizoides, and intraspecific differences were often larger than interspecific differences. cpDNA haplotype relationships were explored using a maximum parsimony approach and minimum-spanning networks. Results from both methods were largely congruent but comparisons provided interesting insights into the presumed evolutionary history of cpDNA haplotypes. A combined effect of cpDNA introgression and complex lineage sorting was inferred to explain the pattern of cpDNA variation found in D. aizoides. Our results suggest that intraspecific cpDNA variation can be extensive and that intraspecific variation needs to be taken into account when inferring phylogenetic relationships among closely related taxa.     

Intra-specific and intra-sporocarp ITS variation of ectomycorrhizal fungi as assessed by rDNA sequencing of sporocarps and pooled ectomycorrhizal roots from a <Emphasis Type="Italic">Quercus</Emphasis> woodland

The Internal Transcribed Spacer (ITS) regions of ribosomal DNA are widely used as markers for phylogenetic analyses and environmental sampling from a variety of organisms including fungi, plants, and animals. In theory, concerted evolution homogenizes multicopy genes so that little or no variation exists within populations or individuals. However, contrary to theory, ITS variation has been confirmed in populations and individuals from a diverse range of eukaryotes. The presence of intraspecific and intra-individual variation in multicopy genes has important implications for ecological and phylogenetic studies, yet relatively little is known about natural variation of these genes, particularly at the community level. In this study, we examined intraspecific and intra-sporocarp ITS variation by DNA sequencing from sporocarps and pooled roots from 68 species of ectomycorrhizal fungi collected at a single site in a Quercus woodland. We detected ITS variation in 27 species, roughly 40% of the taxa examined. Although intraspecific ITS variation was generally low (0.16–2.85%, mean = 0.74%), it was widespread within this fungal community. We detected ITS variation in both sporocarps and ectomycorrhizal roots, and variation was present within species of Ascomycota and Basidiomycota, two distantly related lineages within the Fungi. We discuss the implications of such widespread ITS variability with special reference to DNA-based environmental sampling from diverse fungal communities. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.