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21.
JOHN J. WIENS CAITLIN A. KUCZYNSKI PATRICK R. STEPHENS 《Biological journal of the Linnean Society. Linnean Society of London》2010,99(2):445-461
Do phylogenies and branch lengths based on mitochondrial DNA (mtDNA) provide a reasonable approximation to those based on multiple nuclear loci? In the present study, we show widespread discordance between phylogenies based on mtDNA (two genes) and nuclear DNA (nucDNA; six loci) in a phylogenetic analysis of the turtle family Emydidae. We also find an unusual type of discordance involving the unexpected homogeneity of mtDNA sequences across species within genera. Of the 36 clades in the combined nucDNA phylogeny, 24 are contradicted by the mtDNA phylogeny, and six are strongly contested by each data set. Two genera (Graptemys, Pseudemys) show remarkably low mtDNA divergence among species, whereas the combined nuclear data show deep divergences and (for Pseudemys) strongly supported clades. These latter results suggest that the mitochondrial data alone are highly misleading about the rate of speciation in these genera and also about the species status of endangered Graptemys and Pseudemys species. In addition, despite a strongly supported phylogeny from the combined nuclear genes, we find extensive discordance between this tree and individual nuclear gene trees. Overall, the results obtained illustrate the potential dangers of making inferences about phylogeny, speciation, divergence times, and conservation from mtDNA data alone (or even from single nuclear genes), and suggest the benefits of using large numbers of unlinked nuclear loci. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 445–461. 相似文献
22.
MELODY J. BERNOT DANIEL J. SOBOTA ROBERT O. HALL JR PATRICK J. MULHOLLAND WALTER K. DODDS JACKSON R. WEBSTER JENNIFER L. TANK LINDA R. ASHKENAS LEE W. COOPER CLIFFORD N. DAHM STANLEY V. GREGORY NANCY B. GRIMM STEPHEN K. HAMILTON SHERRI L. JOHNSON WILLIAM H. MCDOWELL JUDITH L. MEYER BRUCE PETERSON GEOFFREY C. POOLE H. MAURICE VALETT CLAY ARANGO JAKE J. BEAULIEU AMY J. BURGIN CHELSEA CRENSHAW ASHLEY M. HELTON LAURA JOHNSON JEFF MERRIAM B. R. NIEDERLEHNER JONATHAN M. O’BRIEN JODY D. POTTER RICHARD W. SHEIBLEY SUZANNE M. THOMAS KYM WILSON 《Freshwater Biology》2010,55(9):1874-1890
1. Rates of whole‐system metabolism (production and respiration) are fundamental indicators of ecosystem structure and function. Although first‐order, proximal controls are well understood, assessments of the interactions between proximal controls and distal controls, such as land use and geographic region, are lacking. Thus, the influence of land use on stream metabolism across geographic regions is unknown. Further, there is limited understanding of how land use may alter variability in ecosystem metabolism across regions. 2. Stream metabolism was measured in nine streams in each of eight regions (n = 72) across the United States and Puerto Rico. In each region, three streams were selected from a range of three land uses: agriculturally influenced, urban‐influenced, and reference streams. Stream metabolism was estimated from diel changes in dissolved oxygen concentrations in each stream reach with correction for reaeration and groundwater input. 3. Gross primary production (GPP) was highest in regions with little riparian vegetation (sagebrush steppe in Wyoming, desert shrub in Arizona/New Mexico) and lowest in forested regions (North Carolina, Oregon). In contrast, ecosystem respiration (ER) varied both within and among regions. Reference streams had significantly lower rates of GPP than urban or agriculturally influenced streams. 4. GPP was positively correlated with photosynthetically active radiation and autotrophic biomass. Multiple regression models compared using Akaike’s information criterion (AIC) indicated GPP increased with water column ammonium and the fraction of the catchment in urban and reference land‐use categories. Multiple regression models also identified velocity, temperature, nitrate, ammonium, dissolved organic carbon, GPP, coarse benthic organic matter, fine benthic organic matter and the fraction of all land‐use categories in the catchment as regulators of ER. 5. Structural equation modelling indicated significant distal as well as proximal control pathways including a direct effect of land‐use on GPP as well as SRP, DIN, and PAR effects on GPP; GPP effects on autotrophic biomass, organic matter, and ER; and organic matter effects on ER. 6. Overall, consideration of the data separated by land‐use categories showed reduced inter‐regional variability in rates of metabolism, indicating that the influence of agricultural and urban land use can obscure regional differences in stream metabolism. 相似文献
23.
AUDREY J. MAGOUN JUSTINA C. RAY DEVIN S. JOHNSON PATRICK VALKENBURG F. NEIL DAWSON JEFF BOWMAN 《The Journal of wildlife management》2007,71(7):2221-2229
ABSTRACT We designed a novel approach to determining extent of distribution and area of occupancy for wolverines (Gulo gulo) by using aerial surveys of tracks in snow and hierarchical spatial modeling. In 2005 we used a small, fixed-wing aircraft with pilot and one observer to search 575 of 588 survey units for wolverine tracks in approximately 60,000 km2 of boreal forest in northwestern Ontario, Canada. We used sinuous flight paths to scan open areas in the forest in the 100-km2 survey units. We detected tracks in 138 (24%) of the 575 sampled units. There was strong evidence of occurrence (probability of occurrence >0.80) in 30% of the 588 survey units, weak evidence of occurrence (0.50–0.80) in 12%, weak evidence of absence (0.20–0.50) in 15%, and strong evidence of absence (< 0.20) in 43%. Wolverine range comprised 59% of the study area and area of occupancy was 33,400 km2. With information on probability of occurrence and core areas of occupation for wolverines in our study area, resource managers and others can examine factors that influence wolverine distribution patterns and use this information to formulate best management practices that will maintain wolverines on the landscape in the face of increasing resource development. Comparing future survey results with those of our 2005 survey will provide an objective way to assess the efficacy of management practices. 相似文献
24.
Climate change effects on walnut pests in California 总被引:1,自引:0,他引:1
EIKE LUEDELING KIMBERLY P. STEINMANN MINGHUA ZHANG PATRICK H. BROWN JOSEPH GRANT EVAN H. GIRVETZ 《Global Change Biology》2011,17(1):228-238
Increasing temperatures are likely to impact ectothermic pests of fruits and nuts. This paper aims to assess changes to pest pressure in California's US$0.7 billion walnut industry due to recent historic and projected future temperature changes. For two past (1950 and 2000) and 18 future climate scenarios (2041–2060 and 2080–2099; each for three General Circulation Models and three greenhouse gas emissions scenarios), 100 years of hourly temperature were generated for 205 locations. Degree‐day models were used to project mean generation numbers for codling moth (Cydia pomonella L.), navel orangeworm (Amyelois transitella Walker), two‐spotted spider mite (Tetranychus urticae Koch), and European red mite (Panonychus ulmi Koch). In the Central Valley, the number of codling moth generations predicted for degree days accumulated between April 1 and October 1 rose from 2–4 in 1950 to 3–5 among all future scenarios. Generation numbers increased from 10–18 to 14–24 for two‐spotted spider mite, from 9–14 to 14–20 for European red mite, and from 2–4 to up to 5 for navel orangeworm. Overall pest pressure can thus be expected to increase substantially. Our study did not include the possibility of higher winter survival rates, leading to higher initial pest counts in spring, or of extended pest development times in the summer, factors that are likely to exacerbate future pest pressure. On the other hand, initiation of diapause may prevent an extension of the season length for arthropods, and higher incidence of heat death in summer may constrain pest population sizes. More information on the impact of climate change on complex agroecological food webs and on the response of pests to high temperatures is needed for improving the reliability of projections. 相似文献
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29.
GWYNNE SHIMIN LIM WEI SONG HWANG SUJATHA NARAYANAN KUTTY RUDOLF MEIER PATRICK GROOTAERT 《Systematic Entomology》2010,35(1):59-70
Abstract. The Dolichopodidae is a species‐rich dipteran group with almost 7000 described species. The monophyly of the subfamilies and their relationships remain largely unknown because the polarities of key morphological characters are unclear and molecular data are available only for 9 of the 19 proposed subfamilies. Here we test whether molecular data from two nuclear (18S, 28S) and four mitochondrial (12S, 16S, Cytb, COI) genes can resolve the higher‐level relationships within the family. Our study is based on 76 Oriental species from 12 dolichopodid subfamilies and uses eight species of Empididae and Hybotidae as outgroups. Parsimony and likelihood analyses confirm the monophyly of the Dolichopodidae, as well as the monophyly of five of the ten subfamilies represented by more than two species [Sympycninae, Sciapodinae, Dolichopodinae, Hydrophorinae (excluding tribe Aphrosylini), Neurigoninae]. There is strong support for restoring the tribe Aphrosylini as a separate subfamily Aphrosylinae. The monophyly of Medeterinae, Peloropeodinae and Diaphorinae is dependent on which tree reconstruction technique is used, how indels are coded, and whether the fast‐evolving sites are excluded. Overall, we find that our sample of Oriental species is largely compatible with the subfamily concepts that were developed for the northern temperate fauna. However, our data provide little support for relationships between the subfamilies. Branch lengths, saturation, and distance plots suggest that this is probably the result of the rapid origin of dolichopodid subfamilies over a relatively short time. We find that genera that are difficult to place into subfamilies based on morphological characters are generally also difficult to place using molecular data. We predict that a dense, balanced taxon sample and protein‐encoding nuclear genes will be needed to resolve the higher‐level relationships in the Dolichopodidae. 相似文献
30.
STACEY LEE THOMPSON† MANUEL LAMOTHE PATRICK G. MEIRMANS‡ PIERRE PÉRINET§ NATHALIE ISABEL 《Molecular ecology》2010,19(1):132-145
As the evolutionary significance of hybridization is largely dictated by its extent beyond the first generation, we broadly surveyed patterns of introgression across a sympatric zone of two native poplars ( Populus balsamifera , Populus deltoides ) in Quebec, Canada within which European exotic Populus nigra and its hybrids have been extensively planted since the 1800s. Single nucleotide polymorphisms (SNPs) that appeared fixed within each species were characterized by DNA-sequencing pools of pure individuals. Thirty-five of these diagnostic SNPs were employed in a high-throughput assay that genotyped 635 trees of different age classes, sampled from 15 sites with various degrees of anthropogenic disturbance. The degree of admixture within sampled trees was then assessed through Bayesian clustering of genotypes. Hybrids were present in seven of the populations, with 2.4% of all sampled trees showing spontaneous admixture. Sites with hybrids were significantly more disturbed than pure stands, while hybrids comprised both immature juveniles and trees of reproductive age. All three possible F1s were detected. Advanced-generation hybrids were consistently biased towards P. balsamifera regardless of whether hybridization had occurred with P. deltoides or P. nigra. Gene exchange between P. deltoides and P. nigra was not detected beyond the F1 generation; however, detection of a trihybrid demonstrates that even this apparent reproductive isolation does not necessarily result in an evolutionary dead end. Collectively, results demonstrate the natural fertility of hybrid poplars and suggest that introduced genes could potentially affect the genetic integrity of native trees, similar to that arising from introgression between natives. 相似文献