SYNTHESIS OF MOLECULAR RESEARCH ON BATRACHOSPERMUM HELMINTHOSUM (RHODOPHYTA) FROM STREAM REACHES IN EASTERN NORTH AMERICA

Vis, M. L., Hall, M. M., Machesky, N. J. & Miller, E. J. Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701 USA The freshwater red alga Batrachospermum helminthosum was collected from eleven streams throughout the species range in eastern North America as follows: three stream reaches from Ohio, and one each from Michigan, Indiana, Tennessee, Louisiana, North Carolina, Connecticut, Rhode Island and Massachusetts. The molecular marker technique of inter-simple sequence repeats (ISSR) and sequence data from the plastid encoded rubisco large subunit gene (rbcL), the mitochondrial COX2-COX3 gene spacer region, and the nuclear region of ITS1-5.8S rDNA-ITS2 were employed to examine biogeographic trends in this alga. Analysis of the rbcL sequence revealed 5 genotypes with one genotype representing individuals from seven stream reaches. Data from the ISSR molecular markers gave a distinct banding pattern for each of 165 individuals examined. ISSR results showed all individuals within a reach clustered together but did not provide well-defined groupings based on stream reach. The sequence data for the COX2-COX3 gene spacer was invariant among individuals from a stream reach. The individuals from Connecticut, Rhode Island and 2 Ohio stream reaches were identical and similarly the individuals from the North Carolina and another Ohio location did not vary in sequence so that seven genotypes were recorded among the individuals from the eleven stream reaches. Analysis of the ITS1-5.8S rDNA-ITS2 region showed sequence variation not only among individuals from different streams but also among individuals from the same reach. The utility and congruency of these data sets to answer biogeographic questions will be discussed.     

Genetic variation in Batrachospermum helminthosum (Batrachospermales, Rhodophyta) among and within stream reaches using intersimple sequence repeat molecular markers

Intersimple sequence repeat molecular markers were utilized to investigate the genetic relationship among individual gametophyte thalli of the freshwater red alga Batrachospermum helminthosum among distant stream reaches and within a stream reach. Fifteen thalli per stream reach were sampled from 11 streams throughout the known distribution in eastern North America from three locations in Ohio, and one location in Indiana, Michigan, North Carolina, Tennessee, Louisiana, Rhode Island, Massachusetts and Connecticut. The pairwise φ_ST analysis showed significant genetic differences (P<0.05) among all streams. The partitioning of genetic variation was almost equal within and among streams (45% and 55%, respectively). Genetic variation among populations did not reflect geographic distance, suggesting that long distance dispersal may be important in the distribution of this alga. Fifty‐eight individuals from Five Mile Creek, Ohio, were investigated from three distinct segments of the stream (upstream, middle and downstream) to examine small‐scale genetic variation within a stream reach. A much higher proportion of genetic variation was observed within a stream segment (79%) than among the three segments (21%). Among these stream segments within Five Mile Creek, the individuals were variously related, with genetic similarity and spatial distance uncorrelated. A similar result was obtained among individuals within other stream reaches, suggesting that genetic structure within a stream reach may be more complex than just reproduction among closely located individuals.     

Potential oversummering and overwintering regions for the wheat stripe rust pathogen in the contiguous United States

Epidemics of wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), are more frequent in the regions where Pst can oversummer and overwinter. Regions for potential oversummering and overwintering of Pst were determined in the contiguous United States using a survival index (SI) ranging from 0 (most unfavorable) to 10 (most favorable) developed based on long-term weather data. The pathogen can survive in cool summer in the most regions north of latitude 40°N, particularly Washington, Idaho, Montana, Oregon and California. Due to limiting high temperatures, it survives marginally during summer in Arkansas, Delaware, Georgia, Iowa, Illinois, Indiana, Kansas, Kentucky, Massachusetts, Missouri, Ohio, Oklahoma, Rhode Island and Texas. Similarly, unfavorable hot summer restricts summer survival of the pathogen in the most regions south of 40°N except for highlands in the Rocky or Appalachian Mountains. Warm winters favor fungal survival in most regions south of 40°N and the Pacific Coast, including Alabama, Arkansas, Arizona, California, Florida, Georgia, Idaho, Louisiana, Mississippi, New Mexico, Nevada, Oregon, South Carolina, Texas and Washington. Severe winters do not allow survival in most regions north of 40°N and east of the Rocky Mountains, whereas less severe winter in Delaware, Illinois, Indiana, Kansas, Kentucky, Massachusetts, Maryland, Michigan, Missouri, North Carolina, New Jersey, New York, Ohio, Oklahoma, Pennsylvania, Rhode Island, Tennessee, Utah and Virginia permits marginal survival of Pst. Most wheat-growing regions have climatic suitability for either oversummering or overwintering. Both oversummering and overwintering can occur in the Pacific Northwest (Idaho, Oregon and Washington), Arizona, California, North Carolina, New Mexico, Pennsylvania, Virginia and West Virginia. These regions may provide primary inoculum for stripe rust epidemics in their own and surrounding regions.     

Phylogeography of postglacial range expansion in Nigronia serricornis Say (Megaloptera: Corydalidae)

We have examined the effects of post-Wisconsinan glacial range expansion on the phylogeography of the saw-combed fishfly, Nigronia serricornis Say (Megaloptera: Corydalidae) because aquatic insects are under-represented in postglacial studies (and in phylogeography in general), and because the effects of ecological degradation on the population genetics of environmental indicator species like N. serricornis cannot be measured unless the underlying phylogeography is understood. Sequence data from a 630-base fragment of the mitochondrial cytochrome oxidase I (COI) gene were subjected to amova and nested clade analysis for 30 populations (n = 344) of N. serricornis. Both the amova and nested clade analysis revealed substantial population structure; 44.4% of the variance occured among populations. Three northward migrations are apparent: one from Tennessee into Illinois, Indiana, Wisconsin, Michigan and Ontario, a second that radiated eastward from Pennsylvania, and a third that moved along the coast from North Carolina into Connecticut, Massachusetts, Maine and then into New York. The latter two of these migrations were the result of contiguous range expansions, while the former expansion, out of Tennessee, appears to have been rapid with little gene flow from the source population. Additional clades included a group of haplotypes in central Kentucky that appear to have expanded along preglacial drainages, and clades in North Carolina and Georgia that have remained centrally located. Haplotype diversity decreased from south to north, a pattern that has been widely reported for animal and plant populations that expanded with the retreat of the Wisconsinan glaciation.     

The relative roles of contemporary and ancient processes in shaping genetic variation of a generalist fish in a catchment dominated by agriculture

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Population genetic effects of urban habitat fragmentation in the perennial herb Viola pubescens (Violaceae) using ISSR markers

BACKGROUND AND AIMS: Fragmentation of natural habitats can negatively impact plant populations by leading to reduced genetic variation and increased genetic distance as populations become geographically and genetically isolated from one another. To test whether such detrimental effects occur within an urban landscape, the genetic structure of six populations of the perennial herb Viola pubescens was characterized in the metropolitan area of Greater Cincinnati in southwestern Ohio, USA. METHODS: Using three inter-simple sequence repeat (ISSR) markers, 51 loci amplified across all urban populations. For reference, four previously examined agricultural populations in central/northern Ohio and a geographically distant population in Michigan were also included in the analysis. KEY RESULTS: Urban populations retained high levels of genetic variation (percentage of polymorphic loci, P(p) = 80.7 %) with similar genetic distances among populations and an absence of unique alleles. Geographic and genetic distances were correlated with one another, and all populations grouped according to region. Individuals from urban populations clustered together and away from individuals from agricultural populations and from the Michigan population in a principle coordinates analysis. Hierarchical analysis of molecular variance (AMOVA) revealed that most of the genetic variability was partitioned within populations (69.1 %) and among groups (22.2 %) of southwestern Ohio, central/northern Ohio and Michigan groups. Mean F(st) was 0.308, indicating substantial population differentiation. CONCLUSIONS: It is concluded that urban fragmentation does not appear to impede gene flow in V. pubescens in southwestern Ohio. These results are consistent with life history traits of this species and the possibility of high insect abundance in urban habitats due to diverse floral resources and nesting sites. Combined with the cleistogamous breeding system of this species, pollinator availability in the urban matrix may buffer populations against detrimental effects of habitat fragmentation, at least in larger forest fragments. Consequently, it may be inappropriate to generalize about genetic effects of fragmentation across landscapes or even across plant species with different pollination systems.     

Gene flow, dispersal, and nested clade analysis among populations of the stonefly Peltoperla tarteri in the southern Appalachians

We examined the genetic structure and phylogeography of populations of the stonefly Peltoperla tarteri in the Southern Appalachians to determine the extent and likely mechanism for dispersal of this stream insect. A 454-base-pair (bp) portion of the mitochondrial control region was sequenced from a minimum of 20 individuals from eight populations. Pairwise FST and exact tests showed high levels of differentiation among almost all populations except those on the same stream. amova analysis detected significant genetic differentiation between streams within drainages (phi(SD) = 0.14, P < 0.001), and there was a slight positive correlation between aquatic distance and genetic distance (r = 0.295, P = 0.03). According to nested clade analysis, the present day pattern of genetic variation in P. tarteri is the result of a historical range expansion coupled with restricted gene flow with isolation by distance. Together, these analyses suggest that adult dispersal is limited and that movement by larvae is the primary dispersal mechanism for P. tarteri.     

Genetic differentiation of the Thorn‐tailed Rayadito Aphrastura spinicauda (Furnariidae: Passeriformes) revealed by ISSR profiles suggests multiple palaeorefugia and high recurrent gene flow

Nucleotide sequence data (cytochrome b) and ISSR genomic fingerprints were used to analyse the genetic variation and population differentiation in Thorn‐tailed Rayadito, a widespread Patagonian forest bird. We included samples from eight populations of Thorn‐tailed Rayadito covering most of the distribution range of the species: from fragmented patches of Olivillo forest in northern Chile to Isla Navarino forests in the extreme south of South America. Low levels of genetic diversity were found among populations, with a large within‐population molecular variance indicating high levels of gene flow. The multivariate and cluster analyses based on ISSR markers show that the subspecies bullocki (from Mocha Island) differs significantly from all other populations. The subspecies fulva (Chiloé Island) shows less differentiation than bullocki, sharing several alleles with continental populations. Bayesian analyses suggest that the Mocha Island population contributes most to the total genetic diversity observed in the species. Mantel tests revealed no significant correlation between geographical distance and pairwise genetic distance and cytochrome b sequence analyses failed to detect differentiation among subspecies. Mocha Island might have been a palaeorefuge and this population may have diversified by genetic drift after the last glacial maximum. There is also the possibility of a postglacial colonization of the Thorn‐tailed Rayadito from an austral palaeorefugium, supporting a multiple refugia hypothesis. This study illustrates the usefulness of the rarely used ISSR genomic fingerprint method in avian phylogeography.     

GENETIC VARIABILITY AND POTENTIAL SOURCES OF GRATELOUPIA DORYPHORA (HALYMENIACEAE,RHODOPHYTA), AN INVASIVE SPECIES IN RHODE ISLAND WATERS (USA)1

Grateloupia doryphora (Montagne) M.Howe is an invasive foliose alga that was reported for the first time in Rhode Island, USA in 1997. The population has since increased in size and expanded in range. In this study, the genetic variation and potential sources of the Rhode Island G. doryphora population were examined using three types of molecular markers: randomly amplified polymorphic DNA (RAPD), nuclear internal transcribed spacer (ITS) sequences, and mitochondrial cox2–cox3 intergenic spacer (COX) sequences. No variation was detected in ITS or COX sequences among Rhode Island G. doryphora individuals. RAPDs, however, did reveal genetic variation, although banding patterns were similar, with RAPD genetic distances between individuals ranging from 0.00 to 0.17. The low level of genetic diversity observed within the Rhode Island population may be due to a small founder population or a founder population derived from a genetically uniform source. To identify possible sources of the Rhode Island invasion, individuals from nine geographically diverse populations of foliose Grateloupia were compared. Phylogenetic trees inferred from RAPD distances and ITS and COX sequences had similar topologies; thus there was phylogenetic congruence among these independent loci. The Rhode Island G. doryphora specimens were genetically similar to specimens from G. doryphora populations located in Portsmouth, England; Tholen Island, The Netherlands; and Brittany and Hérault, France. Interestingly, the G. doryphora population in each of these locations is itself due to an introduction event within the past 40 years.     

Population genetic structure and history of fragmented remnant populations of the New England cottontail (<Emphasis Type="Italic">Sylvilagus transitionalis</Emphasis>)

The New England cottontail (Sylvilagus transitionalis) has suffered from extensive loss and fragmentation of its habitat and is now a species of conservation priority in the northeastern United States. Remnant New England cottontail populations currently occur in five geographically disjunct locations: southern Maine and southeastern New Hampshire (MENH); the Merrimack Valley in central New Hampshire (NH-MV); Cape Cod, Massachusetts (CC); parts of eastern Connecticut and Rhode Island (CTRI); and western Connecticut, southeastern New York and southwestern Massachusetts (CTNY). We used microsatellite genotyping to discern patterns of population structure, genetic variability, and demographic history across the species’ range and to assess whether the observed patterns are a consequence of recent habitat loss and fragmentation. Our findings show that the geographic populations are highly differentiated (overall F _ST = 0.145; P < 0.001). Using Bayesian clustering analyses, we identified five genetic clusters, which corresponded closely to the geographic populations, but grouped MENH & NH-MV together (ME/NH) and identified an isolated population in eastern Connecticut (Bluff Point). The genetic clusters showed little evidence of recent gene flow and are highly influenced by genetic drift. The CC and Bluff Point populations show signs they experienced a genetic bottleneck, whereas the ME/NH population shows evidence of ongoing decline. Populations in Bluff Point, CC, and ME/NH also show significantly reduced genetic variation relative to the other clusters (CTNY and CTRI without Bluff Point). Without immediate human intervention, the short-term persistence of New England cottontail populations in Maine, New Hampshire and Cape Cod is at great risk. Conservation efforts at this time should focus on within-population sustainability and eventually restoring connectivity among these isolated populations.     

Population Genetics of the Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis) across Multiple Spatial Scales

Conservation genetics is a powerful tool to assess the population structure of species and provides a framework for informing management of freshwater ecosystems. As lotic habitats become fragmented, the need to assess gene flow for species of conservation management becomes a priority. The eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a large, fully aquatic paedamorphic salamander. Many populations are experiencing declines throughout their geographic range, yet the genetic ramifications of these declines are currently unknown. To this end, we examined levels of genetic variation and genetic structure at both range-wide and drainage (hierarchical) scales. We collected 1,203 individuals from 77 rivers throughout nine states from June 2007 to August 2011. Levels of genetic diversity were relatively high among all sampling locations. We detected significant genetic structure across populations (F_st values ranged from 0.001 between rivers within a single watershed to 0.218 between states). We identified two genetically differentiated groups at the range-wide scale: 1) the Ohio River drainage and 2) the Tennessee River drainage. An analysis of molecular variance (AMOVA) based on landscape-scale sampling of basins within the Tennessee River drainage revealed the majority of genetic variation (∼94–98%) occurs within rivers. Eastern hellbenders show a strong pattern of isolation by stream distance (IBSD) at the drainage level. Understanding levels of genetic variation and differentiation at multiple spatial and biological scales will enable natural resource managers to make more informed decisions and plan effective conservation strategies for cryptic, lotic species.     

中国杯萼海桑遗传多样性的ISSR研究

杯萼海桑(Sonneratia alba J.Smith.)是海桑科红树植物,在我国分布于海南岛的东海岸.本文采用简单序列霞复区间扩增(ISSR)分子标记技术对分布于海南岛的杯萼海桑的4个天然居群和东寨港红树林自然保护区引种的一人工居群共100个个体进行了遗传变异分析.11个引物共扩增出133条带,其中103条具多态性,多态位点百分率为77.44%.在居群水平上相对较低,多态位点百分率为51.88%～65.41%,平均为57.74%.期望杂合度、香农信息指数在物种水平上分别为0.227 1和0.348 9;在居群水平上分别为0.1 83 7和0.227 5.依据Gst值,杯萼海桑绝大多数遗传变异发生在居群内的个体间(81.02%),18.98%的遗传变异发生在居群间.AMOVA分析也表明了类似的遗传结构.居群间平均遗传一致度为0.934 2.依据Nei(1972)的遗传距离对不同居群进行UPGMA聚类,将居群分为两组,来自三亚(SY)和陵水(LS)的居群聚为一类;东寨港引种栽培的人工居群(DZ)和琼海(QH)、文昌(WC)的居群聚为另一类.Mantel检验表明,遗传距离与地理距离呈极显著相关.     

Phylogenetic and taxonomic assessment of the endangered Cumberland bean, <Emphasis Type="Italic">Villosa trabalis</Emphasis> and purple bean, <Emphasis Type="Italic">Villosa perpurpurea</Emphasis> (Bivalvia: Unionidae)

Inadequate understanding of the phylogeography, taxonomy, and historical distribution of two critically imperiled freshwater mussels, Cumberland bean, Villosa trabalis, and purple bean, Villosa perpurpurea, has hindered management and recovery actions related to population restoration within their extant ranges. For more than 100 years, the purple-to-pink nacre of V. perpurpurea and white nacre of V. trabalis have been the only defining phenotypic characteristics used to distinguish each species. Genetic samples were analyzed from 140 individuals collected from 10 streams located in Virginia, Tennessee, and Kentucky, representing all known extant populations of each species. A 784-bp section of the mitochondrial DNA ND1 region was sequenced to assess the phylogeography and taxonomic validity of these taxa. Results of our phylogenetic analyses showed 100 % Bayesian posterior support for two distinct clades, one occurring in the Cumberland River basin and the other in the Tennessee River basin, separated by a mean genetic distance of 4 %. Mean genetic distances between haplotypes within each clade was <1 %. Among individuals from the Cumberland River basin, the nacre of shells was white to bluish-white, but in the Tennessee River basin, nacre graded from white to pink to dark purple; thus, nacre color is a variable and inconsistent character in nominal V. trabalis and V. perpurpurea occurring in the Tennessee River basin. Our data suggest that these morphologically similar species do not co-occur, as was previously believed. Instead, we conclude that the two species most likely share a common ancestor, but became isolated within each basin and experienced allopatric speciation. Updates to nomenclature, taxonomic placement, and recovery plans for the investigated species are needed.     

Sibship reconstruction for inferring mating systems,dispersal and effective population size in headwater brook trout (<Emphasis Type="Italic">Salvelinus fontinalis</Emphasis>) populations

Brook trout Salvelinus fontinalis populations have declined in much of the native range in eastern North America and populations are typically relegated to small headwater streams in Connecticut, USA. We used sibship reconstruction to infer mating systems, dispersal and effective population size of resident (non-anadromous) brook trout in two headwater stream channel networks in Connecticut. Brook trout were captured via backpack electrofishing using spatially continuous sampling in the two headwaters (channel network lengths of 4.4 and 7.7 km). Eight microsatellite loci were genotyped in a total of 740 individuals (80–140 mm) subsampled in a stratified random design from all 50 m-reaches in which trout were captured. Sibship reconstruction indicated that males and females were both mostly polygamous although single pair matings were also inferred. Breeder sex ratio was inferred to be nearly 1:1. Few large-sized fullsib families (>3 individuals) were inferred and the majority of individuals were inferred to have no fullsibs among those fish genotyped (family size = 1). The median stream channel distance between pairs of individuals belonging to the same large-sized fullsib families (>3 individuals) was 100 m (range: 0–1,850 m) and 250 m (range: 0–2,350 m) in the two study sites, indicating limited dispersal at least for the size class of individuals analyzed. Using a sibship assignment method, the effective population size for the two streams was estimated at 91 (95%CI: 67–123) and 210 (95%CI: 172–259), corresponding to the ratio of effective-to-census population size of 0.06 and 0.12, respectively. Both-sex polygamy, low variation in reproductive success, and a balanced sex ratio may help maintain genetic diversity of brook trout populations with small breeder sizes persisting in headwater channel networks.     

Scale‐dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks

The network architecture of streams and rivers constrains evolutionary, demographic and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho giant salamander, Dicamptodon aterrimus, in stream networks of Idaho and Montana, USA. We used microsatellite data to test population structure models by (i) examining hierarchical partitioning of genetic variation in stream networks; and (ii) testing for genetic isolation by distance along stream corridors vs. overland pathways. Replicated sampling of streams within catchments within three river basins revealed that hierarchical scale had strong effects on genetic structure and gene flow. amova identified significant structure at all hierarchical scales (among streams, among catchments, among basins), but divergence among catchments had the greatest structural influence. Isolation by distance was detected within catchments, and in‐stream distance was a strong predictor of genetic divergence. Patterns of genetic divergence suggest that differentiation among streams within catchments was driven by limited migration, consistent with a stream hierarchy model of population structure. However, there was no evidence of migration among catchments within basins, or among basins, indicating that gene flow only counters the effects of genetic drift at smaller scales (within rather than among catchments). These results show the strong influence of stream networks on population structure and genetic divergence of a salamander, with contrasting effects at different hierarchical scales.     

Response of zooplankton to the reduction and elimination of submerged vegetation by grass carp and herbicide in four Florida lakes

Thirteen physical and chemical characteristics of five softwater streams in Rhode Island, U.S.A. were examined biweekly to monthly for seventeen months. One first-order, two second-order and two third-order streams were included in the study. The mean annual temperature ranged from 9.4 °C in the spring-fed headwater stream to 14 °C in an open, third-order stream, with seasonal fluctuations of 14.5 ° to 28.0 °C. The heavily shaded first-order stream generally received less than 30% incident light at its surface throughout the year. By contrast, the other streams either were unshaded or were associated with distinct periodicity of incident light quantity due to seasonality of the tree canopy. The mean annual current velocity ranged from 22 to 100 cm s^–1 among the streams, pH ranged from 3.7 to 6.4, and specific conductance was generally less than 50 µS cm^–1. The first-order stream was associated with lowest mean annual temperature, current velocity, light penetration and nitrate, as well as relatively high and constant silica concentrations. Temperature was negatively correlated with current speed in second- and third-order streams, and temperature was also negatively correlated with light in shaded streams. There was a general pattern in all streams for decreasing pH following precipitation events. Concentrations of total phophorus, nitrate-nitrogen, ammonium-nitrogen and silica were among the lowest reported for lotic systems.     

DNA restriction polymorphism in wild isolates of Spodoptera frugiperda nuclear polyhedrosis virus.

Restriction endonuclease analysis was used to examine variation in DNA of 22 wild isolates of Spodoptera frugiperda nuclear polyhedrosis virus (SfNPV). Eleven of the 15 isolated from Louisiana were distinguishable based on restriction fragment profiles from the enzymes BamHI, HindIII, and EcoRI. There was significant genetic variation in SfNPV isolates within single agricultural fields. Nucleotide sequence divergence values, based on restriction fragment profiles, indicated that genetic variation among isolates foreign to Louisiana (Ohio, Ecuador, Mexico, Georgia, Colombia, and Venezuela) was greater than that among the Louisiana isolates. However, certain foreign isolates were similar to or identical with Louisiana isolates. Genetic variation of the viral DNA was not influenced by the insect's host plan species.     

The genetic structure of populations of the vulnerable aquatic macrophyte <Emphasis Type="Italic">Ranunculus nipponicus</Emphasis> (Ranunculaceae)

Ranunculus nipponicus (Makino) Nakai is a vulnerable aquatic macrophyte in the Kinki district, which is the southernmost distribution of this species in Japan. The genetic diversity and structure within and among eleven extant populations were assessed using the inter-simple sequence repeats (ISSR) polymerase chain reaction in association with combinations of propagation pattern (clonal and/or seeds) and genotypic geographical structure. In total, 53 bands were amplified, of which 18 (34%) were polymorphic. Analysis of the ISSR bands identified 46 genotypes among 81 individuals from one stream population and 72 distinct genotypes among 147 individuals in the Kinki district. An unweighted pair group method with arithmetic mean (UPGMA) dendrogram showed some unity among upstream and downstream subpopulations within one stream and eleven populations. The Shannon index of genetic diversity was 0.109 for one stream population and 0.313 for total genetic diversity, suggesting relatively high genetic diversity. Analysis of molecular variance (AMOVA) revealed that 84.1% of the total genetic diversity occurred among populations and the remaining diversity (15.9%) occurred within populations. Significant genetic differentiation occurred among populations in the Kinki district. These results suggest that conservation of each population is important for maintaining genetic diversity of R. nipponicus in this district. An erratum to this article can be found at     

Drawbacks with the use of microsatellites in phylogeography: the song sparrow Melospiza melodia as a case study

Microsatellites are commonly used molecular markers in phylogeography, and many view them as superior to mitochondrial DNA (mtDNA) gene trees. Being based on frequencies of alleles, and not gene trees, microsatellites exhibit the same analytical drawbacks that resulted in the abandonment of allozymes in genetic studies of population history. I illustrate some these familiar drawbacks by reanalyzing microsatellite data on the song sparrow. Subspecies were previously evaluated with hierarchical analyses of molecular variance, suggesting that subspecies explain 8% of the total variance in microsatellite frequencies. However, this useful heuristic technique only evaluates a priori groupings, and the objective of the study ought to be to discover such groupings, not assume them. In fact, other arbitrary groupings of samples explained the same or greater amounts of variance, and I suggest that for testing subspecies limits, a gene tree is preferable. Grouping population samples by subspecies in the San Francisco Bay area accounts for 1.2% of the microsatellite variation, and despite claims that this informs conservation planning, the data do not support any particular population or subspecies as being genetically or evolutionarily significant. A distance phenogram was used to infer a sequential colonization of the Aleutian Islands, but because individuals were pooled into a priori groups and the phenogram was arbitrarily rooted, this conclusion is tenuous. A plot of heterozygosity vs number of alleles per sample showed that an equally parsimonious interpretation is that current genetic diversity tracks effective population size. Microsatellites should be replaced in nuclear-gene phylogeography by analyses of sequences, which will benefit the study of phylogeography, comparison of nuclear and mtDNA results, and aid in interpreting the results in a conservation context.     

Intersimple sequence repeat (ISSR) variation in Lactoris fernandeziana (Lactoridaceae), a rare endemic of the Juan Fernández Archipelago, Chile

Sixteen populations and 89 individuals of Lactoris fernandeziana were examined for variation in intersimple sequence repeat (ISSR) banding patterns. The species is a rare endemic of Masatierra Island in the Juan Fernández Archipelago, and is the only member of the endemic family Lactoridaceae. Five populations showed a single genotype whereas the other 11 populations had from two to 16 multilocus genotypes. Over 73% of the ISSR diversity occurred across populations, with only about 27% within populations. Diversity among populations results from the presence of different subsets of loci within each population rather than unique loci within populations; only two populations displayed novel loci, with one and three in each. Levels of differentiation at ISSR loci among populations are not correlated with geographic distance on Masatierra; rather, the pattern of variation is mosaic. The presence of differentiated local populations is concordant with the geitonogamous breeding system of the species and suggests low levels of long distance pollen or seed dispersal. The mosaic pattern of ISSR variation on Masatierra may result, in part, from drift and inbreeding in small populations following fragmentation of a once more continuous distribution of Lactoris with the formation of canyons by erosion. Also, the generation of new ISSR loci by mutation could occur with rare, sporadic gene flow among populations accounting for the mosaic pattern of variation and the paucity of unique alleles within populations. The ISSR results for Lactoris suggest that studies of morphological, ecological and physiological features may elucidate differentiation among populations of L. fernandeziana . Field studies have demonstrated that plants occur both in the dense forest understory and in the full sunlight in forest openings.