Intra-specific phenotypic and genotypic variation in toxic cyanobacterial Microcystis strains

Aims:  We determined if the intra-specific genetic diversity of Microcystis aeruginosa correlates with phenotypic characteristics.
Methods and Results:  Microcystis aeruginosa isolates from various Japanese waters were characterized using genetic analyses based on the 16S–23S rDNA internal transcribed spacer (ITS) region and DNA-independent RNA polymerase ( rpoC1 ) gene sequences. In addition, morphological and biochemical properties, and the toxicity of M. aeruginosa strains were determined. We found a correlation in phylogenetic clusters of the ITS region and rpoC1 gene sequences. Using a polyphasic approach, genotypic and phenotypic variations in M. aeruginosa showed that the three genetic lineage groups are comprised of a particular phenotype or subgroup of closely related phenotypes. However, some strains had high phenotypic and genotypic diversity compared to the three lineage groups and did not show distinct lineages; therefore, these strains were designated as the 'complex group'.
Conclusions:  The 'complex group' consisted of genetically and phenotypically incoherent and high diverse populations in M. aeruginosa , although some genotypes or lineages displayed consistent phenotypes.
Significance and Impact of the Study:  The polyphasic approach combining phenotypic and genetic characterization was effective for comprehending distinct lineages and discriminating the potential complexity of M. aeruginosa populations at the intra-species level.     

Phylogeography and Domestication of Chinese Swamp Buffalo

To further probe into whether swamp buffaloes were domesticated once or multiple times in China, this survey examined the mitochondrial DNA (mtDNA) Control Region (D-loop) diversity of 471 individuals representing 22 populations of 455 Chinese swamp buffaloes and 16 river buffaloes. Phylogenetic analysis revealed that Chinese swamp buffaloes could be divided into two distinct lineages, A and B, which were defined previously. Of the two lineages, lineage A was predominant across all populations. For predominant lineage A, Southwestern buffalo populations possess the highest genetic diversity among the three hypothesized domestication centers (Southeastern, Central, and Southwestern China), suggesting Southwestern China as the most likely location for the domestication of lineage A. However, a complex pattern of diversity is detected for the lineage B, preventing the unambiguous pinpointing of the exact place of domestication center and suggesting the presence of a long-term, strong gene flow among swamp buffalo populations caused by extensive migrations of buffaloes and frequent human movements along the Yangtze River throughout history. Our current study suggests that Southwestern China is the most likely domestication center for lineage A, and may have been a primary center of swamp buffalo domestication. More archaeological and genetic evidence is needed to show the process of domestication.     

Mitochondrial diversity and phylogeographic structure of Chinese domestic goats

China has numerous native domestic goat breeds, but so far there has been no extensive study on genetic diversity, population demographic history, and origin of Chinese goats. Here, we examined the genetic diversity and phylogeographic structure of Chinese domestic goats by determining a 481-bp fragment of the first hypervariable region of mitochondrial DNA (mtDNA) control region from 368 individuals representing 18 indigenous breeds. Phylogenetic analyses revealed that there were four mtDNA lineages (A-D) identified in Chinese goats, in which lineage A was predominant, lineage B was moderate, and lineages C and D were at low frequency. These results further support the multiple maternal origins of domestic goats. The pattern of genetic variation in goat mtDNA sequences indicated that the two larger lineages A and B had undergone population expansion events. In a combined analysis of previously reported sequences and our sequences belonging to lineage B, we detected two subclades, in which one was unique to eastern Asia and another was shared between eastern and southern Asia. A larger genetic variation in eastern Asia than southern Asia and the pattern of phylogeographic variation in lineage B suggest that at least one subclade of lineage B originated from eastern Asia. There was no significant geographical structuring in Chinese goat populations, which suggested that there existed strong gene flow among goat populations caused by extensive transportation of goats in history.     

DIFFERING LEVELS OF AMONG-POPULATION DIVERGENCE IN THE MITOCHONDRIAL DNA OF PERIODICAL CICADAS RELATED TO HISTORICAL BIOGEOGRAPHY

Mitochondrial DNA (mtDNA) haplotypes were determined for 118 individuals of 13-and 17-year periodical cicadas (genus Magicicada) collected from 16 localities throughout the Midwest and eastern United States. Two distinct mtDNA lineages, identified as A and B, differ by 2.5% based on analysis of fragment patterns and restriction maps. Observed levels of mtDNA diversity within each lineage are low compared to estimates for other taxa. The two lineages are regionally segregated, with the boundary line occurring at a latitude of approximately 33° North. The levels of mtDNA diversity and population genetic structure differ within the two lineages. There is a remarkably low level of mean mtDNA divergence and no genetic structure in lineage A, whereas lineage B exhibits an order of magnitude higher level of mtDNA diversity and significant genetic structure among sampled populations. The low level of mtDNA diversity in cicadas may be attributed to (1) a population bottleneck that most likely occurred during the Pleistocene, (2) recent colonization following the retreat of the glaciers and the expansion of deciduous forests, and/or (3) high among-family reproductive variance (as a consequence of large population size, high fecundity, aggregative behavior of adults, and clumping of eggs). The difference in mtDNA diversity and population genetic structure between the lineages suggests that they experienced different biogeographic histories; we relate this to Pleistocene changes.     

Intraspecific phylogeography in the sedge frog Litoria fallax (Hylidae) indicates pre-Pleistocene vicariance of an open forest species from eastern Australia

The eastern sedge frog Litoria fallax (Anura: Hylidae) is common throughout the open forests and coastal wetlands along the eastern coast of Australia. Its range spans four biogeographical zones from northern Queensland to central New South Wales. Phylogenetic analysis of mitochondrial DNA (mtDNA) haplotypes of 87 L. fallax individuals from 22 populations identified two major mtDNA lineages, differing by 11-12% sequence divergence. The two clades of haplotypes were separated by the McPherson Range, indicating that this mesic upland area has acted as a major long-term barrier to gene flow for this open forest species. Slight isolation by distance was observed within both the northern and southern lineages but was insufficient to explain the large sequence divergence between lineages. Within the northern lineage, additional phylogeographical structure was observed across the relatively dry Burdekin Gap which separates Atherton populations from all populations in the central and eastern Queensland biogeographical zones. There was less phylogeographical structure in the southern lineage suggesting historical gene flow across the drier portions of the Great Dividing Range. These data, together with recent observations of deep phylogeographical divergences in rainforest-restricted Litoria suggest that the east coast hylids of Australia represent an old (Tertiary) radiation. Individual species of Litoria have been strongly affected by climatic and ecological barriers to gene flow during the Quaternary.     

Examining the Role of Effective Population Size on Mitochondrial and Multilocus Divergence Time Discordance in a Songbird

Estimates of speciation times are subject to a number of potential errors. One source of bias is that effective population size (N_e) has been shown to influence substitution rates. This issue is of particular interest for phylogeographic studies because population sizes can vary dramatically among genetically structured populations across species’ ranges. In this study, we used multilocus data to examine temporal phylogeographic patterns in a widespread North American songbird, the Northern Cardinal (Cardinalis cardinalis). Species tree estimation indicated that the phylogeographic structure of C. cardinalis was comprised of four well-supported mainland lineages with large population sizes (large N_e) and two island lineages comprised of much smaller populations (small N_e). We inferred speciation times from mtDNA and multilocus data and found there was discordance between events that represented island-mainland divergences, whereas both estimates were similar for divergences among mainland lineages. We performed coalescent simulations and found that the difference in speciation times could be attributed to stochasticity for a recently diverged island lineage. However, the magnitude of the change between speciation times estimated from mtDNA and multilocus data of an older island lineage was substantially greater than predicted by coalescent simulations. For this divergence, we found the discordance in time estimates was due to a substantial increase in the mtDNA substitution rate in the small island population. These findings indicate that in phylogeographic studies the relative tempo of evolution between mtDNA and nuclear DNA can become highly discordant in small populations.     

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.     

MITOCHONDRIAL DNA VARIATION IN THE FIELD VOLE (MICROTUS AGRESTIS): REGIONAL POPULATION STRUCTURE AND COLONIZATION HISTORY

Restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) was used to examine the genetic structure among field voles (Microtus agrestis) from southern and central Sweden. A total of 57 haplotypes was identified in 158 voles from 60 localities. Overall mtDNA diversity was high, but both haplotype and nucleotide diversity exhibited pronounced geographic heterogeneity. Phylogenetic analyses revealed a shallow tree with seven primary mtDNA lineages separated by sequence divergences ranging from 0.6% to 1.0%. The geographic structure of mtDNA diversity and lineage distribution was complex but strongly structured and deviated significantly from an equilibrium situation. The extensive mtDNA diversity observed and the recent biogeographic history of the region suggests that the shallow mtDNA structure in the field vole cannot be explained solely by stochastic lineage sorting in situ or isolation by distance. Instead, the data suggest that the genetic imprints of historical demographic conditions and vicariant geographic events have been preserved and to a large extent determine the contemporary geographic distribution of mtDNA variation. A plausible historical scenario involves differentiation of mtDNA lineages in local populations in glacial refugia, a moving postglacial population structure, and bottlenecks and expansions of mtDNA lineages during the postglacial recolonization of Sweden. By combining the mtDNA data with an analysis of Y-chromosome variation, a specific population unit was identified in southwestern Sweden. This population, defined by a unique mtDNA lineage and fixation of a Y-chromosome variant, probably originated in a population bottleneck in southern Sweden about 12,000 to 13,000 calendar years ago.     

Novel insights into the phylogenetic relationships of the endangered marsupial genus Potorous

The three extant potoroo species of the marsupial genus Potorous -Potorous tridactylus, P. longipes and P. gilbertii - are all of conservation concern due to introduced predators and habitat loss associated with the European settlement of Australia. Robust phylogenies can be useful to inform conservation management, but past phylogenetic studies on potoroos have been unable to fully resolve relationships within the genus. Here, a multi-locus approach was employed, using three mitochondrial DNA (mtDNA): NADH dehydrogenase subunit 2, cytochrome c oxidase subunit 1 and 12S rRNA and four nuclear DNA (nuDNA) gene regions: breast and ovarian cancer susceptibility gene, recombination activating gene-1, apolipoprotein B and omega globin. This was coupled with widespread geographic sampling of the broadly distributed P. tridactylus, to investigate the phylogenetic relationships within this genus. Analyses of the mtDNA identified five distinct and highly divergent lineages including, P. longipes, P. gilbertii and three distinct lineages within P. tridactylus (northern mainland, southern mainland and Tasmanian). P. tridactylus was paraphyletic with the P. gilbertii lineage, suggesting that cryptic taxa may exist within P. tridactylus. NuDNA sequences lacked the resolution of mtDNA. Although they resolved the three currently recognised species, they were unable to differentiate lineages within P. tridactylus. Current management of P. tridactylus as two sub-species (mainland and Tasmania) does not recognise the full scope of genetic diversity within this species, especially that of the mainland populations. Until data from more informative nuDNA markers are available, we recommend this species be managed as the following three subspecies: Potorous tridactylus tridactylus (southern Queensland and northern New South Wales); Potorous tridactylus trisulcatus (southern New South Wales and Victoria) Potorous tridactylus apicalis (Tasmania). Molecular dating estimated that divergences within Potorous occurred in the late Miocene through to the early Pliocene.     

Genetic Structure of Brown Trout (Salmo trutta) Populations from Turkey Based on Microsatellite Data

This present study investigated micro- and macro-geographic microsatellite DNA variations using five polymorphic microsatellite loci from 27 brown trout populations in Turkey. Average number of alleles and average observed heterozygosity were 7.4 and 0.254, respectively. Even populations from the same sea basin and river system (the so called micro-geographic regions) had unique alleles. Genetic variation among the populations from macro-geographic regions (different sea basins and river systems) was 45.78%. The mtDNA lineages of brown trout that have previously been identified by mtDNA analyses were supported by the analysis of the microsatellite DNA data in general. The Çatak population, which belongs to the Tigris lineage, was clustered together with the Euphrates populations within the Adriatic mtDNA lineage, based on microsatellite data. Both mitochondrial and microsatellite DNA analyses have made it possible to determine a secondary contact between Adriatic and Tigris lineages.     

Variability in triactinomyxon production from Tubifex tubifex populations from the same mitochondrial DNA lineage infected with Myxobolus cerebralis, the causative agent of whirling disease in salmonids

Myxobolus cerebralis, the causative agent of whirling disease, infects both salmonid fish and an aquatic oligochaete, Tubifex tubifex. Although M. cerebralis has been detected in river drainages throughout the United States, disease severity among wild fish populations has been highly variable. Tubifex tubifex populations have been genetically characterized using sequences from the 16S mitochondrial DNA (mtDNA) gene, the 18S ribosomal RNA gene, the internal transcribed spacer region 1 (ITS1), and randomly amplified polymorphic DNA (RAPD). Our earlier work indicated that large differences in compatibility between the parasite and populations of T. tubifex may play a substantial role in the distribution of whirling disease and resulting mortality in different watersheds. In the present study, we examined 4 laboratory populations of T. tubifex belonging to 16S mtDNA lineage III and 1 population belonging to 16S mtDNA lineage I for triactinomyxon (TAM) production after infection with M. cerebralis myxospores. All 4 16S mtDNA lineage III populations produced TAMs, but statistically significant differences in TAM production were observed. Most individuals in the 16S mtDNA lineage III-infected populations produced TAMs. The 16S mtDNA lineage I population produced few TAMs. Further genetic characterization of the 16S mtDNA lineage III populations with RAPD markers indicated that populations producing similar levels of TAMs had more genetic similarity.     

High molecular and phenotypic diversity in the Merodon avidus complex (Diptera,Syrphidae): cryptic speciation in a diverse insect taxon

This paper examines molecular and phenotypic variability in the widely spread European hoverfly species complex Merodon avidus. Herein, based on the mitochondrial DNA (mtDNA) sequences of the cytochrome c oxidase subunit I (COI) and morphometric wing parameters, M. avidus is shown to comprise a complex of cryptic species, and one variety is redefined as a valid species: M. bicolor Gil Collado, 1930 (as var. of spinipes). The species M. bicolor, M. avidus A, and M. avidus B were clearly delimited based on their wing size. A total of 29 M. avidus and M. bicolor individuals presented 20 mtDNA haplotypes, four of which were shared by M. avidus A and M. avidus B, three were confined to M. bicolor, seven to M. avidus A, and six to M. avidus B. Sequence divergences between lineages occurring in the Balkan and in Spain ranged from 4.93 to 6.0 (uncorrected p in %) whereas divergences between M. avidus A and M. avidus B were 0.26 to 1.56. Divergence among morphologically identified individuals of M. avidus A and M. avidus B species ranged from 0.13 to 1.58, and from 0.13 to 0.52, respectively. The phenotypic substructuring and observed genetic uniqueness of populations in spatially and temporally fragmented M. avidus taxa were used to identify genetic units. The early split of two allopatric lineages, Spanish M. bicolor and Balkan M. avidus, was followed by diversification in each lineage. Present‐day morphological uniformity masks much of the genetic complexity of lineages within the M. avidus complex. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 819–833.     

Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species)

A previous analysis of Pacific herring mitochondrial (mt) DNA with Bayesian skyline plots (BSPs) was interpreted to reflect population growth in the late Pleistocene that was preceded by population stability over several hundred thousand years. Here we use an independent set of mtDNA control region (CR) sequences and simulations to test these hypotheses. The CR haplotype genealogy shows three deeply divided lineages, A, B and C, with divergences ranging from d=1.6% to 1.9% and with similar genetic diversities (h=0.95, 0.96, 0.94; Θ(π)=0.011, 0.012, 0.014, respectively). Lineage A occurs almost exclusively in the NW Pacific and Bering Sea, but lineages B and C are co-distributed in the Northeastern Pacific. This distribution points to a historical allopatric separation between A and B-C across the North Pacific during Pleistocene glaciations. The origins of B and C are uncertain. One hypothesis invokes long-term isolation of lineage C in the Sea of Cortez, but the present-day lack of geographical segregation from lineage B argues for lineage sorting to explain the deep divergence between B and C. BSPs depict rapid population growth in each lineage, but the timing of this growth is uncertain, because of questions about an appropriate molecular clock calibration. We simulated historical demographies under a Pleistocene climate model using observed genetic parameters. BSPs for these sequences showed rapid population growth after the Last Glacial Maximum (LGM) 18-20kyears ago and a flat population history during previous climate fluctuations. Population declines during the LGM appear to have erased signals of previous population fluctuations.     

Origin, genetic diversity, and population structure of Chinese domestic sheep

To characterize the origin, genetic diversity, and phylogeographic structure of Chinese domestic sheep, we here analyzed a 531-bp fragment of mtDNA control region of 449 Chinese autochthonous sheep from 19 breeds/populations from 13 geographic regions, together with previously reported 44 sequences from Chinese indigenous sheep. Phylogenetic analysis showed that all three previously defined lineages A, B, and C were found in all sampled Chinese sheep populations, except for the absence of lineage C in four populations. Network profiles revealed that the lineages B and C displayed a star-like phylogeny with the founder haplotype in the centre, and that two star-like subclades with two founder haplotypes were identified in lineage A. The pattern of genetic variation in lineage A, together with the divergence time between the two central founder haplotypes suggested that two independent domestication events have occurred in sheep lineage A. Considerable mitochondrial diversity was observed in Chinese sheep. Weak structuring was observed either among Chinese indigenous sheep populations or between Asian and European sheep and this can be attributable to long-term strong gene flow induced by historical human movements. The high levels of intra-population diversity in Chinese sheep and the weak phylogeographic structuring indicated three geographically independent domestication events have occurred and the domestication place was not only confined to the Near East, but also occurred in other regions.     

Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: comparison with other Asian,European, and North American populations

To illustrate phylogeography of red deer (Cervus elaphus) populations of Xinjiang, we determined their mitochondrial DNA (mtDNA) control region sequences, and then investigated geographic variations and phylogenetic relationships between Xinjiang populations and other populations from Asia, Europe, and North America. The C. elaphus mtDNA control region shared different copy numbers of tandem repeats of 38 to 43-bp motifs which clearly distinguished the Western lineage from the Eastern lineage of this species in Eurasia. The western lineage comprised the Tarim populations from southern Xinjiang and the European populations, all of which had four copies of the motifs. By contrast, the Eastern lineage consisted of populations from northern Xinjiang (Tianshan and Altai Mountains), other Asian areas (Alashan, Gansu, Tibet, Mongolia, and northeastern China), and North America, all of which shared six copies of the motifs. MtDNA phylogenetic trees showed that there are two major clusters of haplotypes which referred to the Western and Eastern lineages, and that subgroupings of haplotypes in each cluster were congruent with their geographic distributions. The present study revealed that a boundary separating the Western lineage from the Eastern lineage occurs between Tarim Basin and Tianshan Mountains in Xinjiang. Meanwhile, North American populations were genetically closer to those of northern Xinjiang, northeastern China, and Mongolia, supporting that C. elaphus immigrated from northeastern Eurasia to North America through the glacier-induced land-bridge (Beringia) which had formed between the two continents after Late Pleistocene.     

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.     

Behavioural Reproductive Isolation in a Rotifer Hybrid Zone

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

Two mitochondrial lineages occur in the Asian corn borer, Ostrinia furnacalis (Lepidoptera: Crambidae), in Japan

The genealogy and diversity of the mitochondrial cytochrome oxidase subunit II (COII) gene were investigated for Ostrinia furnacalis in Japan. A preliminary examination of mitochondrial lineages in China and the Philippines was also made. Two lineages (A and B) were found in the COII gene. Lineage A was frequent throughout the Japanese main islands (Hokkaido, Honshu, Shikoku and Kyushu), while the frequency of lineage B varied among these islands. No clear patterns of geographical population structure were found. Population genetic features suggested that the O. furnacalis population harboring the lineage A mitochondria expanded in the recent past, while lineage B showed weak signals of a population expansion. It is not clear whether the two lineages of mtDNA evolved in separate or identical geographical regions. We discuss two hypotheses regarding the two lineages of mtDNA: a cryptic race/species hypothesis and a selective sweep hypothesis.     

Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex

Species whose geographical distribution encompasses both mainland and island populations provide an ideal system for examining isolation and genetic divergence. In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and phylogeography of Pinus luchuensis, a species found in eastern China (ssp. hwangshanensis), Taiwan (ssp. taiwanensis), and the Ryukyu Archipelago (ssp. luchuensis). Gene genealogies of both mtDNA and cpDNA reveal two major lineages. Molecular dating indicates that these lineages diverged before the colonization of P. luchuensis subspecies in Taiwan and the Ryukyu Archipelago. Both mtDNA and cpDNA show a lack of correspondence between molecular phylogeny and subspecies designation. Phylogeographical analysis suggests that paraphyly of the subspecies is the result of recent divergence rather than secondary contacts. In spite of the short divergence history of P. luchuensis on islands, the island populations show the same degree of genetic divergence as mainland populations. Low levels of genetic diversity in the mainland ssp. hwangshanensis suggest demographic bottlenecks. In contrast, the high heterogeneity of genetic composition for island populations is likely to be associated with a history of multiple colonization from the mainland. The spatial apportionment of organelle DNA polymorphisms is consistent with a pattern of stepwise colonization on island populations.     

Reticulate evolution and the origins of ribosomal internal transcribed spacer diversity in apomictic Meloidogyne

Among root knot nematodes of the genus Meloidogyne, the polyploid obligate mitotic parthenogens M. arenaria, M. javanica, and M. incognita are widespread and common agricultural pests. Although these named forms are distinguishable by closely related mitochondrial DNA (mtDNA) haplotypes, detailed sequence analyses of internal transcribed spacers (ITSs) of nuclear ribosomal genes reveal extremely high diversity, even within individual nematodes. This ITS diversity is broadly structured into two very different groups that are 12%-18% divergent: one with low diversity (< 1.0%) and one with high diversity (6%-7%). In both of these groups, identical sequences can be found within individual nematodes of different mtDNA haplotypes (i.e., among species). Analysis of genetic variance indicates that more than 90% of ITS diversity can be found within an individual nematode, with small but statistically significant (5%-10%; P < 0.05) variance distributed among mtDNA lineages. The evolutionarily distinct parthenogen M. hapla shows a similar pattern of ITS diversity, with two divergent groups of ITSs within each individual. In contrast, two diploid amphimictic species have only one lineage of ITSs with low diversity (< 0.2%). The presence of divergent lineages of rDNA in the apomictic taxa is unlikely to be due to differences among pseudogenes. Instead, we suggest that the diversity of ITSs in M. arenaria, M. javanica, and M. incognita is due to hybrid origins from closely related females (as inferred from mtDNA) and combinations of more diverse paternal lineages.