Data from: The pitcher plant flesh fly exhibits a mixture of patchy and metapopulation attributes

We investigated the pattern of spatial genetic structure and the extent of gene flow in the pitcher plant flesh fly Fletcherimyia fletcheri, the largest member of the inquiline community of the purple pitcher plant Sarracenia purpurea. Using microsatellite loci, we tested the theoretical predictions of different hypothesized population models (patchy population, metapopulation or isolated populations) among 11 bogs in Algonquin Provincial Park (Canada). Our results revealed that the pitcher plant flesh fly exhibits a mixture of patchy and metapopulation characteristics. There is significant differentiation among bogs and limited gene flow at larger spatial scales, but local populations do not experience frequent local extinctions/recolonizations. Our findings suggest a strong dispersal ability and stable population sizes in F. fletcheri, providing novel insights into the ecology of this member of a unique ecological microcosm

Data from: The relative influence of habitat amount and configuration on genetic structure across multiple spatial scales

Despite strong interest in understanding how habitat spatial structure shapes the genetics of populations, the relative importance of habitat amount and configuration for patterns of genetic differentiation remains largely unexplored in empirical systems. In this study, we evaluate the relative influence of, and interactions among, the amount of habitat and aspects of its spatial configuration on genetic differentiation in the pitcher plant midge, Metriocnemus knabi. Larvae of this species are found exclusively within the water-filled leaves of pitcher plants (Sarracenia purpurea) in a system that is naturally patchy at multiple spatial scales (i.e., leaf, plant, cluster, peatland). Using generalized linear mixed models and multimodel inference, we estimated effects of the amount of habitat, patch size, interpatch distance, and patch isolation, measured at different spatial scales, on genetic differentiation (FST) among larval samples from leaves within plants, plants within clusters, and clusters within peatlands. Among leaves and plants, genetic differentiation appears to be driven by female oviposition behaviors and is influenced by habitat isolation at a broad (peatland) scale. Among clusters, gene flow is spatially restricted and aspects of both the amount of habitat and configuration at the focal scale are important, as is their interaction. Our results suggest that both habitat amount and configuration can be important determinants of genetic structure and that their relative influence is scale dependent

Rasic&Keyghobadi_Supl_Tables

Supplemental Tables 1-

F. fletcheri microsatellite genotyping data

Individuals (e.g. ff2009-DL-10A) genotyped at 10 microsatellite loci (e.g. FF72), with one allele per column for each locus. The year of collection is designated after ff (e.g. ff2009 for the collection year 2009), followed by the bog code (e.g. DL), followed by an unique plant number (e.g. 10), followed by a leaf number where multiple individuals from the same plant are collected (e.g. A). The list of bog codes is found in Table 2 of the main text

Metriocnemus knabi microsatellite data

10 loci, GenalEx forma

Data from: A call for more transparent reporting of error rates: the quality of AFLP data in ecological and evolutionary research

Despite much discussion of the importance of quantifying and reporting genotyping error in molecular studies, it is still not standard practice in the literature. This is particularly a concern for amplified fragment length polymorphism (AFLP) studies, where differences in laboratory, peak-calling and locus-selection protocols can generate data sets varying widely in genotyping error rate, the number of loci used and potentially estimates of genetic diversity or differentiation. In our experience, papers rarely provide adequate information on AFLP reproducibility, making meaningful comparisons among studies difficult. To quantify the extent of this problem, we reviewed the current molecular ecology literature (470 recent AFLP articles) to determine the proportion of studies that report an error rate and follow established guidelines for assessing error. Fifty-four per cent of recent articles do not report any assessment of data set reproducibility. Of those studies that do claim to have assessed reproducibility, the majority (~90%) either do not report a specific error rate or do not provide sufficient details to allow the reader to judge whether error was assessed correctly. Even of the papers that do report an error rate and provide details, many (≥23%) do not follow recommended standards for quantifying error. These issues also exist for other marker types such as microsatellites, and next-generation sequencing techniques, particularly those which use restriction enzymes for fragment generation. Therefore, we urge all researchers conducting genotyping studies to estimate and more transparently report genotyping error using existing guidelines and encourage journals to enforce stricter standards for the publication of genotyping studies

Data from: Population genetic structure of the western cherry fruit fly Rhagoletis indifferens (Diptera: Tephritidae) in British Columbia, Canada

1. Population connectivity and movement are key ecological parameters influencing the impact of pests, and are important considerations in control strategies. For many insects, these parameters are difficult to assess directly, although they may be assessed indirectly using population genetic data. 2. We used microsatellite markers to examine population genetic structure of the western cherry fruit fly, the main pest of cherry crops in western North America, in British Columbia, Canada, and make inferences about connectivity and potential for movement among populations. 3. Comparing populations from four geographical regions (separated by up to approximately 400 km), we found significant genetic differentiation both among and within regions. Using populations as the units of analysis, we observed significant isolation by distance (IBD) at larger spatial scales but not below approximately 20 km. By contrast, using individual flies as the units of analysis, we found significant IBD at scales as small as < 100 m. We saw no evidence of genetic differentiation among populations sampled from different species/varieties of plants. 4. Our results suggest that the movement of individual flies is limited, although high levels of gene flow are maintained at scales of up to 20 km, possibly through combined effects of stepping-stone gene flow and large population sizes

Population genetic structure and assessment of allochronic divergence in the Macoun’s arctic butterfly (Oeneis macounii)

Patterns in the genetic variation of species can be used to infer their specific demographic and evolutionary history and provide insight into the general mechanisms underlying population divergence and speciation. The Macounâ s arctic butterfly (MA; Oeneis macounii [W. H. Edwards, 1885]) occurs across Canada and parts of the northern US in association with jack (Pinus banksiana Lamb.) and lodgepole (Pinus contorta Doug. ex Loud.) pine. MAâ s current distribution is highly fragmented, and the extent of reproductive isolation among allopatric populations is unknown. Furthermore, although MA is biennial, adults emerge every year in some populations. These populations presumably consist of two alternate-year cohorts, providing the opportunity for sympatric divergence via allochronic isolation. Using mitochondrial (mt) DNA and amplified fragment length polymorphism (AFLP) markers, we analyzed MAâ s genetic structure to determine the current and historical role of allopatric and allochronic isolation in MA population divergence. Both markers revealed high diversity and a low, but significant, degree of spatial structure and pattern of isolation by distance. Phylogeographic structure was generally absent, with low divergence among mtDNA haplotypes. MA likely exhibits low dispersal and gene flow among most allopatric populations; however, there was no evidence of differentiation resulting from allochronic isolation for sympatric cohorts.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Data Paper. Data Paper

<h2>File List</h2><div> <p><a href="PopulationAbunMark-Recap.csv">PopulationAbunMark-Recap.csv</a> (MD5: 70a47c25ad7f7dc317474c883bf9dc18)</p> <p><a href="PopulationAbunTransect.csv">PopulationAbunTransect.csv</a> (MD5: e07c022497c4e70e2d4e86abf79b8083)</p> <p><a href="Dispersal.csv">Dispersal.csv</a> (MD5: d425332598dd2cc8e3adb9f6513c9b47)</p> <p><a href="Landscape.csv">Landscape.csv</a> (MD5: b3712322e4d1c5347171cd1c2a36198f)</p> </div><h2>Description</h2><div> <p> Spatial population networks (metapopulations sensu lato) have distinct properties from isolated populations. Within a population network, the abundance, persistence, and dynamics of local populations are affected by other populations within the network. Similarly, the abundance of local populations within the network has a strong effect on the dynamics and persistence of the entire network. In this data paper, we present 10 years (1995–2004) of local population abundance and seven years of dispersal data within a spatial population network consisting of 21 local populations of the Rocky Mountain Apollo butterfly, Parnassius smintheus. Populations were located within alpine meadows above treeline (≈2100 m) along Lusk (51.01°N, 114.97°W) and Jumpingpound Ridges (50.95°N, 114.91°W) in the front ranges of the Rocky Mountains in Alberta, Canada. Mark–recapture methods were used to monitor all populations in 1995 and 1996, and most populations in 1997 and from 2001–2004. For these years, abundance was estimated using Craig’s method. In other years, population size was estimated via Pollard transects and converted to a common estimate of abundance based on a statistical relationship between transect counts and Craig’s estimate. We present multiple estimates of abundance for most populations over the adult flight season each year, and the observed number of emigrants and immigrants over the flight season for populations in years where mark–recapture was conducted. These data should be useful in synthetic studies of factors affecting local population abundance within spatial population networks, landscape genetics, spatial population dynamics, and the persistence of spatial population networks. </p> <p> <i>Key words</i>: <i>colonization; density; dispersal; extinction; fragmentation; landscape; Lepidoptera; metapopulation; migration; patch; population dynamics; recolonization.</i> </p> </div