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Sample records for abundance population structure

  1. Spatial variation in parasite abundance: evidence of geographical population structuring in southern garfish Hyporhamphus melanochir.

    PubMed

    Hutson, K S; Brock, E L; Steer, M A

    2011-01-01

    Southern garfish Hyporhamphus melanochir were examined for metazoan parasites from nine sites in three regions (Spencer Gulf, Gulf St Vincent and northern Kangaroo Island) in South Australia to document parasite assemblages, identify candidate species suitable for use as biological tags and investigate spatial variation in parasite abundance. Four ectoparasite and 10 endoparasite species were identified representing Cestoda, Trematoda, Monogenea, Nematoda, Acanthocephala, Copepoda and Isopoda. Lernaeenicus hemirhamphi, Micracanthorhynchina hemirhamphi, Mothocya halei and Philometra sp. were suggested for 'permanent' biological markers. Multivariate discriminant function analysis showed that most sites could be distinguished based on differences in parasite abundance. Four endoparasites (Conohelmins sp., Hysterothylacium sp., M. hemirhamphi and Philometra sp.) were most important for site characterization. Limited spatial variation in permanent endoparasite abundance among localities in northern Spencer Gulf provided evidence for a distinct northern Spencer Gulf population with little interregional mixing. In contrast, considerable spatial variation in permanent endoparasite abundance between localities sampled off Kangaroo Island implied limited local movement and suggested H. melanochir may comprise a metapopulation structure. These results largely align with recent evidence from otolith chemistry that indicates fine-scale geographical population structuring in South Australian waters. PMID:21235553

  2. Abundant mitochondrial DNA variation and world-wide population structure in humpback whales.

    PubMed

    Baker, C S; Perry, A; Bannister, J L; Weinrich, M T; Abernethy, R B; Calambokidis, J; Lien, J; Lambertsen, R H; Ramírez, J U; Vasquez, O

    1993-09-01

    Hunting during the last 200 years reduced many populations of mysticete whales to near extinction. To evaluate potential genetic bottlenecks in these exploited populations, we examined mitochondrial DNA control region sequences from 90 individual humpback whales (Megaptera novaeangliae) representing six subpopulations in three ocean basins. Comparisons of relative nucleotide and nucleotype diversity reveal an abundance of genetic variation in all but one of the oceanic subpopulations. Phylogenetic reconstruction of nucleotypes and analysis of maternal gene flow show that current genetic variation is not due to postexploitation migration between oceans but is a relic of past population variability. Calibration of the rate of control region evolution across three families of whales suggests that existing humpback whale lineages are of ancient origin. Preservation of preexploitation variation in humpback whales may be attributed to their long life-span and overlapping generations and to an effective, though perhaps not timely, international prohibition against hunting. PMID:8367488

  3. Artemia parthenogenetica (Branchiopoda: Anostraca) from the Large Aral Sea: Abundance, distribution, population structure and cyst production

    NASA Astrophysics Data System (ADS)

    Arashkevich, Elena G.; Sapozhnikov, P. V.; Soloviov, K. A.; Kudyshkin, T. V.; Zavialov, P. O.

    2009-03-01

    The brine shrimp Artemia parthenogenetica appeared in the Large Aral Sea (Central Asia) in 1998 when mineralization reached 63 ppt. Data on Artemia abundance and biomass, along with temperature and salinity measurements were collected in the western basin during 2002-2006, primarily in the autumn. During the study period, population density grew progressively, both in terms of number, from 250 to 1260 individuals per m 3, and in terms of biomass, from 0.3 to 1.3 g per m 3. In 2005, the population density and spatial distribution in the different parts of the sea (western and eastern basins and strait) was assessed. The horizontal distribution of the Artemia population was uniform in the deep central part of the western basin, although the distribution was quite patchy in the shallow coastal zone. Depth habitat of Artemia was restricted to the upper 20-25 m of depth, as the oxygen depletion and formation of anoxic layer prevented distribution of Artemia to the deeper waters. In autumn, all females reproduced oviparously, with an average clutch size of 30-35 eggs per female. The number of eggs in a clutch was positively correlated with female body length ( r2 = 0.36-0.44).

  4. Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration.

    PubMed

    Tatarenkov, A; Healey, C I M; Avise, J C

    2010-01-01

    Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent streams in Belize. The genetic data were complemented by a tagging study of movement within one stream. In the absence of physical dispersal barriers (waterfalls), population structure followed an isolation by distance (IBD) pattern. Genetic differentiation (F(ST) up to 0.07) was significant between and within creeks, despite high dispersal in the latter as judged by the tagging data. Such heterogeneity apparently was a result of genetic drift in local demes, due to small population sizes and highly skewed paternity. The IBD pattern was interrupted by waterfalls, boosting F(ST) above 0.30 between adjacent samples across these barriers. Overall, our results are helpful in understanding the interplay of evolutionary forces and population dynamics in a small fish living in a changeable habitat. PMID:20015140

  5. Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration.

    PubMed

    Tatarenkov, A; Healey, C I M; Avise, J C

    2010-01-01

    Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent streams in Belize. The genetic data were complemented by a tagging study of movement within one stream. In the absence of physical dispersal barriers (waterfalls), population structure followed an isolation by distance (IBD) pattern. Genetic differentiation (F(ST) up to 0.07) was significant between and within creeks, despite high dispersal in the latter as judged by the tagging data. Such heterogeneity apparently was a result of genetic drift in local demes, due to small population sizes and highly skewed paternity. The IBD pattern was interrupted by waterfalls, boosting F(ST) above 0.30 between adjacent samples across these barriers. Overall, our results are helpful in understanding the interplay of evolutionary forces and population dynamics in a small fish living in a changeable habitat.

  6. [Abundance, population structure and growth of the Atrina maura (Bivalvia: Pinnidae) in a tropical lagoon of the Mexican Pacific coast ].

    PubMed

    Ahumada-Sempoal, Miguel Angel; Serrano-Guzmán, Saúl Jaime; Ruiz-García, Noe

    2002-01-01

    The abundance, population structure, and growth of the Pen-shell Atrina maura in the Corralero-Alotengo tropical lagoon system in Oaxaca, Mexico, were studied from February to September of 1997. An abundance analysis showed significant temporal and spatial differences (Kruskal-Wallis, p < 0.001). Two spatial groups of abundance were found in the area, one from the mouth of the lagoon system to the middle of the Pen-shell bank, and the other between the middle of the Pen-shell bank and the head of the system. Three temporal periods of abundance were found (February-April-May; July-August; March-June-September). The distribution of population size showed that benthic recruitment of A. maura occurred from February to July. Length frequency of A. maura is commonly wide-ranging; nevertheless, in this study Pen-shell organisms with a valve length of 15 cm were frequently found. The growth rate length was 3.7 cm/month during the dry season (February to May), and 3.5 cm/month during the rainy season (June to September). Sex ratio was maintained at 1:1 from February to May, but males were dominant from June to August, and the minimum length for reproduction was registered at 10 cm valve length.

  7. [Relative abundance, population structure, habitat preferences and activity patterns of Tapirus bairdii (Perissodactyla: Tapiridae), in Chimalapas forest, Oaxaca, Mexico].

    PubMed

    Lira-Torres, Iván; Briones-Salas, Miguel; Sánchez-Rojas, Gerardo

    2014-12-01

    Baird's tapir (Tapirus bairdii) is endangered primarily because of habitat loss and fragmentation, and overhunting throughout its distribution range. One of the priority land areas for the conservation of this species is the Northern part of its range in the Chimalapas forest, Oaxaca. The aim of this research was to determine the relative abundance, population struc- ture, habitat preferences and activity patterns of Baird's tapir (Tapirus bairdii) in the Chimalapas forest, Oaxaca, Mexico, through the non-invasive technique of camera-trap sampling. A total of five sampling sessions were undertaken among 2009-2013, and used a total of 30 camera-traps in each period. The determinant factor of the sampling design was the hunting between two study areas. A total sampling effort of 9000 trap-days allowed to estimate an index of relative abundance (IRA) of 6.77 tapir photographs/1,000 trap-days (n = 61). IRA varied significantly between sampling stations (Mann-Whitney, p < 0.01). The frequency of Baird's tapir photos was higher in the dry season in tropical rain forest without hunting (χ2, p < 0.5). In the rainy season, the tropical rain forest and secondary vegetation habitats showed higher photo frequency than expected from random (χ2, p < 0.5). Considering population structure, a 95.08% of adult animals was obtained in photographic records (n = 58). Three types of activity pattern were observed, with more nocturnal records (88.33%; Kruskal-Wallis, p < 0.05). The Chimalapas forest appears to be the second most important terrestrial priority ecoregion, just after the Mayan Forest (Campeche, Chiapas, Quintana Roo), for the conservation of tapir populations, not only for Mexico but also for Central America. PMID:25720176

  8. [Relative abundance, population structure, habitat preferences and activity patterns of Tapirus bairdii (Perissodactyla: Tapiridae), in Chimalapas forest, Oaxaca, Mexico].

    PubMed

    Lira-Torres, Iván; Briones-Salas, Miguel; Sánchez-Rojas, Gerardo

    2014-12-01

    Baird's tapir (Tapirus bairdii) is endangered primarily because of habitat loss and fragmentation, and overhunting throughout its distribution range. One of the priority land areas for the conservation of this species is the Northern part of its range in the Chimalapas forest, Oaxaca. The aim of this research was to determine the relative abundance, population struc- ture, habitat preferences and activity patterns of Baird's tapir (Tapirus bairdii) in the Chimalapas forest, Oaxaca, Mexico, through the non-invasive technique of camera-trap sampling. A total of five sampling sessions were undertaken among 2009-2013, and used a total of 30 camera-traps in each period. The determinant factor of the sampling design was the hunting between two study areas. A total sampling effort of 9000 trap-days allowed to estimate an index of relative abundance (IRA) of 6.77 tapir photographs/1,000 trap-days (n = 61). IRA varied significantly between sampling stations (Mann-Whitney, p < 0.01). The frequency of Baird's tapir photos was higher in the dry season in tropical rain forest without hunting (χ2, p < 0.5). In the rainy season, the tropical rain forest and secondary vegetation habitats showed higher photo frequency than expected from random (χ2, p < 0.5). Considering population structure, a 95.08% of adult animals was obtained in photographic records (n = 58). Three types of activity pattern were observed, with more nocturnal records (88.33%; Kruskal-Wallis, p < 0.05). The Chimalapas forest appears to be the second most important terrestrial priority ecoregion, just after the Mayan Forest (Campeche, Chiapas, Quintana Roo), for the conservation of tapir populations, not only for Mexico but also for Central America.

  9. Effects of predation and habitat structure on the abundance and population structure of the rock shrimp Rhynchocinetes typus (Caridea) on temperate rocky reefs.

    PubMed

    Ory, Nicolas C; Dudgeon, D; Dumont, C P; Miranda, L; Thiel, M

    2012-01-01

    Human disturbances, such as overfishing, may disrupt predator-prey interactions and modify food webs. Underwater surveys were carried out at six shallow-water reef barrens in temperate waters of northern-central Chile from October to December 2010 to describe the effects of predation, habitat complexity (low, medium and high) and refuge availability on the abundance and population structure of the rock shrimp Rhynchocinetes typus (Rhynchocinetidae), an important mesoconsumer on subtidal hard substrata. Three sites were within managed (restricted access) areas for fishermen, and three were unmanaged (open-access). Field observations and tethering experiments were conducted to examine the relationship between fish and shrimp abundances, and the relative predation rates on shrimps. Direct effects of predation on R. typus body-size distribution were examined from shrimps collected in the field and fish stomachs. The presence and the abundance of R. typus increased with habitat reef complexity and refuge availability. Shrimp abundance was negatively related to fish abundance in managed areas, but not in open-access areas, where shrimp densities were the highest. Also, predation rates and body-size distribution of shrimps were unrelated, although fish consumed more large shrimps than should be expected from their distribution in the field. R. typus occurred most often in shelters with wide openings, offering limited protection against predators, but providing potential aggregation sites for shrimps. Overall, direct effects of predation on shrimp densities and population structure were weak, but indirect effects on shrimp distribution within reefs appear to have been mediated through behavioural responses. Our study highlights the need to assess both numerical and behavioural responses of prey to determine the effects of predator loss on mesoconsumer populations. PMID:24391278

  10. Effects of predation and habitat structure on the abundance and population structure of the rock shrimp Rhynchocinetes typus (Caridea) on temperate rocky reefs.

    PubMed

    Ory, Nicolas C; Dudgeon, D; Dumont, C P; Miranda, L; Thiel, M

    2012-01-01

    Human disturbances, such as overfishing, may disrupt predator-prey interactions and modify food webs. Underwater surveys were carried out at six shallow-water reef barrens in temperate waters of northern-central Chile from October to December 2010 to describe the effects of predation, habitat complexity (low, medium and high) and refuge availability on the abundance and population structure of the rock shrimp Rhynchocinetes typus (Rhynchocinetidae), an important mesoconsumer on subtidal hard substrata. Three sites were within managed (restricted access) areas for fishermen, and three were unmanaged (open-access). Field observations and tethering experiments were conducted to examine the relationship between fish and shrimp abundances, and the relative predation rates on shrimps. Direct effects of predation on R. typus body-size distribution were examined from shrimps collected in the field and fish stomachs. The presence and the abundance of R. typus increased with habitat reef complexity and refuge availability. Shrimp abundance was negatively related to fish abundance in managed areas, but not in open-access areas, where shrimp densities were the highest. Also, predation rates and body-size distribution of shrimps were unrelated, although fish consumed more large shrimps than should be expected from their distribution in the field. R. typus occurred most often in shelters with wide openings, offering limited protection against predators, but providing potential aggregation sites for shrimps. Overall, direct effects of predation on shrimp densities and population structure were weak, but indirect effects on shrimp distribution within reefs appear to have been mediated through behavioural responses. Our study highlights the need to assess both numerical and behavioural responses of prey to determine the effects of predator loss on mesoconsumer populations.

  11. Spatio-Temporal Variation in Age Structure and Abundance of the Endangered Snail Kite: Pooling across Regions Masks a Declining and Aging Population

    PubMed Central

    Kendall, William L.; Fletcher, Robert J.; Kitchens, Wiley M.

    2016-01-01

    While variation in age structure over time and space has long been considered important for population dynamics and conservation, reliable estimates of such spatio-temporal variation in age structure have been elusive for wild vertebrate populations. This limitation has arisen because of problems of imperfect detection, the potential for temporary emigration impacting assessments of age structure, and limited information on age. However, identifying patterns in age structure is important for making reliable predictions of both short- and long-term dynamics of populations of conservation concern. Using a multistate superpopulation estimator, we estimated region-specific abundance and age structure (the proportion of individuals within each age class) of a highly endangered population of snail kites for two separate regions in Florida over 17 years (1997–2013). We find that in the southern region of the snail kite—a region known to be critical for the long-term persistence of the species—the population has declined significantly since 1997, and during this time, it has increasingly become dominated by older snail kites (> 12 years old). In contrast, in the northern region—a region historically thought to serve primarily as drought refugia—the population has increased significantly since 2007 and age structure is more evenly distributed among age classes. Given that snail kites show senescence at approximately 13 years of age, where individuals suffer higher mortality rates and lower breeding rates, these results reveal an alarming trend for the southern region. Our work illustrates the importance of accounting for spatial structure when assessing changes in abundance and age distribution and the need for monitoring of age structure in imperiled species. PMID:27681854

  12. Carbon and oxygen abundances in stellar populations

    NASA Astrophysics Data System (ADS)

    Nissen, P. E.; Chen, Y. Q.; Carigi, L.; Schuster, W. J.; Zhao, G.

    2014-08-01

    Context. Carbon and oxygen abundances in stars are important in many fields of astrophysics including nucleosynthesis, stellar structure, evolution of galaxies, and formation of planetary systems. Still, our knowledge of the abundances of these elements in different stellar populations is uncertain because of difficulties in observing and analyzing atomic and molecular lines of C and O. Aims: Abundances of C, O, and Fe are determined for F and G main-sequence stars in the solar neighborhood with metallicities in the range -1.6 < [Fe/H] < +0.4 in order to study trends and possible systematic differences in the C/Fe, O/Fe, and C/O ratios for thin- and thick-disk stars as well as high- and low-alpha halo stars. In addition, we investigate if there is any connection between C and O abundances in stellar atmospheres and the occurrence of planets. Methods: Carbon abundances are determined from the λλ 5052,5380 C i lines and oxygen abundances from the λ7774 O i triplet and the forbidden [O i] line at 6300 Å. MARCS model atmospheres are applied and non-LTE corrections for the O i triplet are included. Results: Systematic differences between high- and low-alpha halo stars and between thin- and thick-disk stars are seen in the trends of [C/Fe] and [O/Fe]. The two halo populations and thick-disk stars show the same trend of [C/O] versus [O/H], whereas the thin-disk stars are shifted to higher [C/O] values. Furthermore, we find some evidence of higher C/O and C/Fe ratios in stars hosting planets than in stars for which no planets have been detected. Conclusions: The results suggest that C and O in both high- and low-alpha halo stars and in thick-disk stars are made mainly in massive (M> 8 M⊙) stars, whereas thin-disk stars have an additional carbon contribution from low-mass AGB and massive stars of high metallicity causing a rising trend of the C/O ratio with increasing metallicity. However, at the highest metallicities investigated ([Fe/H] ≃ + 0.4), C/O does not

  13. Spatial and temporal variation in the abundance, distribution and population structure of epibenthic megafauna in Port Foster, Deception Island

    NASA Astrophysics Data System (ADS)

    Cranmer, T. L.; Ruhl, H. A.; Baldwin, R. J.; Kaufmann, R. S.

    2003-06-01

    Abundance and spatial distribution of epibenthic megafauna were examined at Port Foster, Deception Island, five times between March 1999 and November 2000. Camera sled surveys and bottom trawls were used to identify and collect specimens, and camera sled photographs also were used to determine abundances and spatial distributions for each species. The ophiuroid Ophionotus victoriae, the regular echinoid Sterechinus neumayeri, and one or more species of Porifera were the most abundant taxa during this sampling period. Abundances of O. victoriae varied throughout the annual cycle, peaking in June 2000, and were correlated positively with sedimentation rates. In contrast, abundances of S. neumayeri were consistent throughout the sampling period, except for a peak in June 2000, during austral winter. Peak abundances for both species coincided with a large number of small individuals, indicating apparent recruitment events for O. victoriae and S. neumayeri during this time period. Poriferans, as a group, had statistically similar abundances during each sampling period. Low-abundance species tended to be aggregated on both small and large spatial scales, their distributions probably influenced by reproductive method, gregarious settlement, and food availability. The spatial distribution of S. neumayeri in June 2000 and O. victoriae was random across multiple spatial scales, perhaps in response to food availability and broad environmental tolerances, respectively.

  14. Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis

    PubMed Central

    Tout, Jessica; Siboni, Nachshon; Messer, Lauren F.; Garren, Melissa; Stocker, Roman; Webster, Nicole S.; Ralph, Peter J.; Seymour, Justin R.

    2015-01-01

    Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2–3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2–3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems. PMID:26042096

  15. Bacterial and archaeal symbionts in the South China Sea sponge Phakellia fusca: community structure, relative abundance, and ammonia-oxidizing populations.

    PubMed

    Han, Minqi; Liu, Fang; Zhang, Fengli; Li, Zhiyong; Lin, Houwen

    2012-12-01

    Many biologically active natural products have been isolated from Phakellia fusca, an indigenous sponge in the South China Sea; however, the microbial symbionts of Phakellia fusca remain unknown. The present investigations on sponge microbial community are mainly based on qualitative analysis, while quantitative analysis, e.g., relative abundance, is rarely carried out, and little is known about the roles of microbial symbionts. In this study, the community structure and relative abundance of bacteria, actinobacteria, and archaea associated with Phakellia fusca were revealed by 16S rRNA gene library-based sequencing and quantitative real time PCR (qRT-PCR). The ammonia-oxidizing populations were investigated based on amoA gene and anammox-specific 16S rRNA gene libraries. As a result, it was found that bacterial symbionts of sponge Phakellia fusca consist of Proteobacteria including Gamma-, Alpha-, and Delta-proteobacteria, Cyanobacteria with Gamma-proteobacteria as the predominant components. In particular, the diversity of actinobacterial symbionts in Phakellia fusca is high, which is composed of Corynebacterineae, Acidimicrobidae, Frankineae, Micrococcineae, and Streptosporangineae. All the observed archaea in sponge Phakellia fusca belong to Crenarchaeota, and the detected ammonia-oxidizing populations are ammonia-oxidizing archaea, suggesting the nitrification function of sponge archaeal symbionts. According to qRT-PCR analysis, bacterial symbionts dominated the microbial community, while archaea represented the second predominant symbionts, followed by actinobacteria. The revealed diverse prokaryotic symbionts of Phakellia fusca are valuable for the understanding and in-depth utilization of Phakellia fusca microbial symbionts. This study extends our knowledge of the community, especially the relative abundance of microbial symbionts in sponges.

  16. Population Structure, Abundance and Movement of Whale Sharks in the Arabian Gulf and the Gulf of Oman.

    PubMed

    Robinson, David P; Jaidah, Mohammed Y; Bach, Steffen; Lee, Katie; Jabado, Rima W; Rohner, Christoph A; March, Abi; Caprodossi, Simone; Henderson, Aaron C; Mair, James M; Ormond, Rupert; Pierce, Simon J

    2016-01-01

    Data on the occurrence of whale sharks, Rhincodon typus, in the Arabian Gulf and Gulf of Oman were collected by dedicated boat surveys and via a public-sightings scheme during the period from 2011 to 2014. A total of 422 individual whale sharks were photo-identified from the Arabian Gulf and the northern Gulf of Oman during that period. The majority of sharks (81%, n = 341) were encountered at the Al Shaheen area of Qatar, 90 km off the coast, with the Musandam region of Oman a secondary area of interest. At Al Shaheen, there were significantly more male sharks (n = 171) than females (n = 78; X2 = 17.52, P < 0.05). Mean estimated total length (TL) for sharks was 6.90 m ± 1.24 (median = 7 m; n = 296). Males (7.25 m ± 1.34; median = 8 m, n = 171) were larger than females (6.44 m ±1.09; median = 7 m, n = 78; Mann-Whitney U test, p < 0.01). Of the male sharks assessed for maturity 63% were mature (n = 81), with 50% attaining maturity by 7.29 m and 100% by 9.00 m. Two female sharks of >9 m individuals were visually assessed as pregnant. Connectivity among sharks sighted in Qatari, Omani and UAE waters was confirmed by individual spot pattern matches. A total of 13 identified sharks were re-sighted at locations other than that at which they were first sighted, including movements into and out of the Arabian Gulf through the Strait of Hormuz. Maximum likelihood techniques were used to model an estimated combined population for the Arabian Gulf and Gulf of Oman of 2837 sharks ± 1243.91 S.E. (95% C.I. 1720-6295). The Al Shaheen aggregation is thus the first site described as being dominated by mature males while the free-swimming pregnant females are the first reported from the Indian Ocean.

  17. Population Structure, Abundance and Movement of Whale Sharks in the Arabian Gulf and the Gulf of Oman

    PubMed Central

    Robinson, David P.; Jaidah, Mohammed Y.; Bach, Steffen; Lee, Katie; Jabado, Rima W.; Rohner, Christoph A.; March, Abi; Caprodossi, Simone; Henderson, Aaron C.; Mair, James M.; Ormond, Rupert; Pierce, Simon J.

    2016-01-01

    Data on the occurrence of whale sharks, Rhincodon typus, in the Arabian Gulf and Gulf of Oman were collected by dedicated boat surveys and via a public-sightings scheme during the period from 2011 to 2014. A total of 422 individual whale sharks were photo-identified from the Arabian Gulf and the northern Gulf of Oman during that period. The majority of sharks (81%, n = 341) were encountered at the Al Shaheen area of Qatar, 90 km off the coast, with the Musandam region of Oman a secondary area of interest. At Al Shaheen, there were significantly more male sharks (n = 171) than females (n = 78; X2 = 17.52, P < 0.05). Mean estimated total length (TL) for sharks was 6.90 m ± 1.24 (median = 7 m; n = 296). Males (7.25 m ± 1.34; median = 8 m, n = 171) were larger than females (6.44 m ±1.09; median = 7 m, n = 78; Mann-Whitney U test, p < 0.01). Of the male sharks assessed for maturity 63% were mature (n = 81), with 50% attaining maturity by 7.29 m and 100% by 9.00 m. Two female sharks of >9 m individuals were visually assessed as pregnant. Connectivity among sharks sighted in Qatari, Omani and UAE waters was confirmed by individual spot pattern matches. A total of 13 identified sharks were re-sighted at locations other than that at which they were first sighted, including movements into and out of the Arabian Gulf through the Strait of Hormuz. Maximum likelihood techniques were used to model an estimated combined population for the Arabian Gulf and Gulf of Oman of 2837 sharks ± 1243.91 S.E. (95% C.I. 1720–6295). The Al Shaheen aggregation is thus the first site described as being dominated by mature males while the free-swimming pregnant females are the first reported from the Indian Ocean. PMID:27362839

  18. Population Structure, Abundance and Movement of Whale Sharks in the Arabian Gulf and the Gulf of Oman.

    PubMed

    Robinson, David P; Jaidah, Mohammed Y; Bach, Steffen; Lee, Katie; Jabado, Rima W; Rohner, Christoph A; March, Abi; Caprodossi, Simone; Henderson, Aaron C; Mair, James M; Ormond, Rupert; Pierce, Simon J

    2016-01-01

    Data on the occurrence of whale sharks, Rhincodon typus, in the Arabian Gulf and Gulf of Oman were collected by dedicated boat surveys and via a public-sightings scheme during the period from 2011 to 2014. A total of 422 individual whale sharks were photo-identified from the Arabian Gulf and the northern Gulf of Oman during that period. The majority of sharks (81%, n = 341) were encountered at the Al Shaheen area of Qatar, 90 km off the coast, with the Musandam region of Oman a secondary area of interest. At Al Shaheen, there were significantly more male sharks (n = 171) than females (n = 78; X2 = 17.52, P < 0.05). Mean estimated total length (TL) for sharks was 6.90 m ± 1.24 (median = 7 m; n = 296). Males (7.25 m ± 1.34; median = 8 m, n = 171) were larger than females (6.44 m ±1.09; median = 7 m, n = 78; Mann-Whitney U test, p < 0.01). Of the male sharks assessed for maturity 63% were mature (n = 81), with 50% attaining maturity by 7.29 m and 100% by 9.00 m. Two female sharks of >9 m individuals were visually assessed as pregnant. Connectivity among sharks sighted in Qatari, Omani and UAE waters was confirmed by individual spot pattern matches. A total of 13 identified sharks were re-sighted at locations other than that at which they were first sighted, including movements into and out of the Arabian Gulf through the Strait of Hormuz. Maximum likelihood techniques were used to model an estimated combined population for the Arabian Gulf and Gulf of Oman of 2837 sharks ± 1243.91 S.E. (95% C.I. 1720-6295). The Al Shaheen aggregation is thus the first site described as being dominated by mature males while the free-swimming pregnant females are the first reported from the Indian Ocean. PMID:27362839

  19. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta.

    PubMed

    de Bakker, Didier M; Meesters, Erik H W G; van Bleijswijk, Judith D L; Luttikhuizen, Pieternella C; Breeuwer, Hans J A J; Becking, Leontine E

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s-1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12-0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02-0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to replenish

  20. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta

    PubMed Central

    de Bakker, Didier M.; Meesters, Erik H. W. G.; van Bleijswijk, Judith D. L.; Luttikhuizen, Pieternella C.; Breeuwer, Hans J. A. J.; Becking, Leontine E.

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s–1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12–0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02–0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to

  1. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta.

    PubMed

    de Bakker, Didier M; Meesters, Erik H W G; van Bleijswijk, Judith D L; Luttikhuizen, Pieternella C; Breeuwer, Hans J A J; Becking, Leontine E

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s-1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12-0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02-0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to replenish

  2. Effects of Fragment and Vegetation Structure on the Population Abundance of Ateles hybridus, Alouatta seniculus and Cebus albifrons in Magdalena Valley, Colombia.

    PubMed

    Marsh, Christopher; Link, Andres; King-Bailey, Gillian; Donati, Giuseppe

    2016-01-01

    Many primate species currently subsist in fragmented and anthropogenically disturbed habitats. Different threats arise depending on the species' life history strategy, dietary requirements and habitat preference. Additionally, anthropogenic disturbance is far from uniform and may affect individual forest fragments in a single landscape in differing ways. We studied the effects of fragmentation on three species of diurnal primate, Cebus albifrons, Alouatta seniculus and Ateles hybridus, in Magdalena Valley, Colombia. We tested the assumption that generalist species are more resilient than specialist species to habitat degradation by examining the fragments' vegetation and spatial structure and how these affected primate presence and abundance patterns. We found C. albifrons, a generalist, to be the most abundant species in 9 of 10 forest fragments, regardless of the level of habitat disturbance. A. hybridus, a large-bodied primate with a specialist diet, was either absent or low in abundance in fragments that had experienced recent disturbances and was found only in higher-quality fragments, regardless of the fragment size. A. seniculus, a species considered to have a highly flexible diet and the ability to survive in degraded habitat, was found in intermediate abundances between those of Cebus spp. and Ateles spp., and was more frequently found in high-quality fragments. PMID:27093602

  3. Comparative abundance and population structure of sympatric Afrotropical tortoises in six rainforest areas: the differential effects of ``traditional veneration'' and of ``subsistence hunting'' by local people

    NASA Astrophysics Data System (ADS)

    Luiselli, Luca

    2003-07-01

    Hinge-back tortoises are actively hunted by human populations in sub-Saharan Africa, and are currently threatened in wide areas of their ranges. The wide wetlands and moist rainforests of the Niger Delta (southeastern Nigeria, west Africa) house three sympatric species of hinge-back tortoises: Kinixys erosa, K. homeana, and K. belliana nogueyi. These tortoises are subjected to strong hunting pressure for several reasons (mainly domestic consumption), but in a few places in Bayelsa and Rivers States (eastern axis of the Niger Delta), they are traditionally venerated as "holy animals" bringing happiness. These few places may represent ideal laboratories for monitoring the effects of hundreds of years of "traditional conservation" on the wild populations of a tropical reptile. Here, I compare the apparent abundance, sex ratio, body sizes, microhabitats, and seasonal occurrence of free-ranging Kinixys populations inhabiting three of these "traditional sanctuaries" with the same ecological aspects of conspecifics from three neighbouring areas where the tortoises are actively hunted. K. homeana was the most common species at all sites, followed by K. erosa, whereas K. belliana was extremely rare. Adult sex ratio did not depart significantly from equality both in K. erosa and in K. homeana, and was not influenced by locality or by type of "management" (veneration or harvesting). The frequency of juveniles of K. homeana was significantly higher in areas with traditional veneration than in areas of harvesting, but the same pattern was not observed in K. erosa. There was a significant decrease in terms of the number of observed specimens between areas of traditional protection and areas of usual harvesting in all species, and this trend was more obvious in K. homeana than in K. erosa. The ratio "number of observed erosa/number of observed homeana" was not dependent on the presence of traditional veneration. Mean body sizes were not different in harvest areas and in

  4. "Capture" Me if You Can: Estimating Abundance of Dolphin Populations

    ERIC Educational Resources Information Center

    Thompson, Jessica; Curran, Mary Carla; Cox, Tara

    2016-01-01

    Animal populations are monitored over time to assess the effects of environmental disaster and disease, as well as the efficacy of laws designed to protect them. Determining the abundance of a species within a defined area is one method of monitoring a population. In "Capture" Me if You Can, middle school students will use data collected…

  5. Regularity underlies erratic population abundances in marine ecosystems

    PubMed Central

    Sun, Jie; Cornelius, Sean P.; Janssen, John; Gray, Kimberly A.; Motter, Adilson E.

    2015-01-01

    The abundance of a species' population in an ecosystem is rarely stationary, often exhibiting large fluctuations over time. Using historical data on marine species, we show that the year-to-year fluctuations of population growth rate obey a well-defined double-exponential (Laplace) distribution. This striking regularity allows us to devise a stochastic model despite seemingly irregular variations in population abundances. The model identifies the effect of reduced growth at low population density as a key factor missed in current approaches of population variability analysis and without which extinction risks are severely underestimated. The model also allows us to separate the effect of demographic stochasticity and show that single-species growth rates are dominantly determined by stochasticity common to all species. This dominance—and the implications it has for interspecies correlations, including co-extinctions—emphasizes the need for ecosystem-level management approaches to reduce the extinction risk of the individual species themselves. PMID:25972438

  6. Regularity underlies erratic population abundances in marine ecosystems.

    PubMed

    Sun, Jie; Cornelius, Sean P; Janssen, John; Gray, Kimberly A; Motter, Adilson E

    2015-06-01

    The abundance of a species' population in an ecosystem is rarely stationary, often exhibiting large fluctuations over time. Using historical data on marine species, we show that the year-to-year fluctuations of population growth rate obey a well-defined double-exponential (Laplace) distribution. This striking regularity allows us to devise a stochastic model despite seemingly irregular variations in population abundances. The model identifies the effect of reduced growth at low population density as a key factor missed in current approaches of population variability analysis and without which extinction risks are severely underestimated. The model also allows us to separate the effect of demographic stochasticity and show that single-species growth rates are dominantly determined by stochasticity common to all species. This dominance-and the implications it has for interspecies correlations, including co-extinctions-emphasizes the need for ecosystem-level management approaches to reduce the extinction risk of the individual species themselves.

  7. How selection structures species abundance distributions

    PubMed Central

    Magurran, Anne E.; Henderson, Peter A.

    2012-01-01

    How do species divide resources to produce the characteristic species abundance distributions seen in nature? One way to resolve this problem is to examine how the biomass (or capacity) of the spatial guilds that combine to produce an abundance distribution is allocated among species. Here we argue that selection on body size varies across guilds occupying spatially distinct habitats. Using an exceptionally well-characterized estuarine fish community, we show that biomass is concentrated in large bodied species in guilds where habitat structure provides protection from predators, but not in those guilds associated with open habitats and where safety in numbers is a mechanism for reducing predation risk. We further demonstrate that while there is temporal turnover in the abundances and identities of species that comprise these guilds, guild rank order is conserved across our 30-year time series. These results demonstrate that ecological communities are not randomly assembled but can be decomposed into guilds where capacity is predictably allocated among species. PMID:22787020

  8. Herbivory: effects on plant abundance, distribution and population growth

    PubMed Central

    Maron, John L; Crone, Elizabeth

    2006-01-01

    Plants are attacked by many different consumers. A critical question is how often, and under what conditions, common reductions in growth, fecundity or even survival that occur due to herbivory translate to meaningful impacts on abundance, distribution or dynamics of plant populations. Here, we review population-level studies of the effects of consumers on plant dynamics and evaluate: (i) whether particular consumers have predictably more or less influence on plant abundance, (ii) whether particular plant life-history types are predictably more vulnerable to herbivory at the population level, (iii) whether the strength of plant–consumer interactions shifts predictably across environmental gradients and (iv) the role of consumers in influencing plant distributional limits. Existing studies demonstrate numerous examples of consumers limiting local plant abundance and distribution. We found larger effects of consumers on grassland than woodland forbs, stronger effects of herbivory in areas with high versus low disturbance, but no systematic or unambiguous differences in the impact of consumers based on plant life-history or herbivore feeding mode. However, our ability to evaluate these and other patterns is limited by the small (but growing) number of studies in this area. As an impetus for further study, we review strengths and challenges of population-level studies, such as interpreting net impacts of consumers in the presence of density dependence and seed bank dynamics. PMID:17002942

  9. Dielectrophoretic capture of low abundance cell population using thick electrodes.

    PubMed

    Marchalot, Julien; Chateaux, Jean-François; Faivre, Magalie; Mertani, Hichem C; Ferrigno, Rosaria; Deman, Anne-Laure

    2015-09-01

    Enrichment of rare cell populations such as Circulating Tumor Cells (CTCs) is a critical step before performing analysis. This paper presents a polymeric microfluidic device with integrated thick Carbon-PolyDimethylSiloxane composite (C-PDMS) electrodes designed to carry out dielectrophoretic (DEP) trapping of low abundance biological cells. Such conductive composite material presents advantages over metallic structures. Indeed, as it combines properties of both the matrix and doping particles, C-PDMS allows the easy and fast integration of conductive microstructures using a soft-lithography approach while preserving O2 plasma bonding properties of PDMS substrate and avoiding a cumbersome alignment procedure. Here, we first performed numerical simulations to demonstrate the advantage of such thick C-PDMS electrodes over a coplanar electrode configuration. It is well established that dielectrophoretic force ([Formula: see text]) decreases quickly as the distance from the electrode surface increases resulting in coplanar configuration to a low trapping efficiency at high flow rate. Here, we showed quantitatively that by using electrodes as thick as a microchannel height, it is possible to extend the DEP force influence in the whole volume of the channel compared to coplanar electrode configuration and maintaining high trapping efficiency while increasing the throughput. This model was then used to numerically optimize a thick C-PDMS electrode configuration in terms of trapping efficiency. Then, optimized microfluidic configurations were fabricated and tested at various flow rates for the trapping of MDA-MB-231 breast cancer cell line. We reached trapping efficiencies of 97% at 20 μl/h and 78.7% at 80 μl/h, for 100 μm thick electrodes. Finally, we applied our device to the separation and localized trapping of CTCs (MDA-MB-231) from a red blood cells sample (concentration ratio of 1:10). PMID:26392836

  10. Dielectrophoretic capture of low abundance cell population using thick electrodes.

    PubMed

    Marchalot, Julien; Chateaux, Jean-François; Faivre, Magalie; Mertani, Hichem C; Ferrigno, Rosaria; Deman, Anne-Laure

    2015-09-01

    Enrichment of rare cell populations such as Circulating Tumor Cells (CTCs) is a critical step before performing analysis. This paper presents a polymeric microfluidic device with integrated thick Carbon-PolyDimethylSiloxane composite (C-PDMS) electrodes designed to carry out dielectrophoretic (DEP) trapping of low abundance biological cells. Such conductive composite material presents advantages over metallic structures. Indeed, as it combines properties of both the matrix and doping particles, C-PDMS allows the easy and fast integration of conductive microstructures using a soft-lithography approach while preserving O2 plasma bonding properties of PDMS substrate and avoiding a cumbersome alignment procedure. Here, we first performed numerical simulations to demonstrate the advantage of such thick C-PDMS electrodes over a coplanar electrode configuration. It is well established that dielectrophoretic force ([Formula: see text]) decreases quickly as the distance from the electrode surface increases resulting in coplanar configuration to a low trapping efficiency at high flow rate. Here, we showed quantitatively that by using electrodes as thick as a microchannel height, it is possible to extend the DEP force influence in the whole volume of the channel compared to coplanar electrode configuration and maintaining high trapping efficiency while increasing the throughput. This model was then used to numerically optimize a thick C-PDMS electrode configuration in terms of trapping efficiency. Then, optimized microfluidic configurations were fabricated and tested at various flow rates for the trapping of MDA-MB-231 breast cancer cell line. We reached trapping efficiencies of 97% at 20 μl/h and 78.7% at 80 μl/h, for 100 μm thick electrodes. Finally, we applied our device to the separation and localized trapping of CTCs (MDA-MB-231) from a red blood cells sample (concentration ratio of 1:10).

  11. Dielectrophoretic capture of low abundance cell population using thick electrodes

    PubMed Central

    Marchalot, Julien; Chateaux, Jean-François; Faivre, Magalie; Mertani, Hichem C.; Ferrigno, Rosaria; Deman, Anne-Laure

    2015-01-01

    Enrichment of rare cell populations such as Circulating Tumor Cells (CTCs) is a critical step before performing analysis. This paper presents a polymeric microfluidic device with integrated thick Carbon-PolyDimethylSiloxane composite (C-PDMS) electrodes designed to carry out dielectrophoretic (DEP) trapping of low abundance biological cells. Such conductive composite material presents advantages over metallic structures. Indeed, as it combines properties of both the matrix and doping particles, C-PDMS allows the easy and fast integration of conductive microstructures using a soft-lithography approach while preserving O2 plasma bonding properties of PDMS substrate and avoiding a cumbersome alignment procedure. Here, we first performed numerical simulations to demonstrate the advantage of such thick C-PDMS electrodes over a coplanar electrode configuration. It is well established that dielectrophoretic force (FDEP) decreases quickly as the distance from the electrode surface increases resulting in coplanar configuration to a low trapping efficiency at high flow rate. Here, we showed quantitatively that by using electrodes as thick as a microchannel height, it is possible to extend the DEP force influence in the whole volume of the channel compared to coplanar electrode configuration and maintaining high trapping efficiency while increasing the throughput. This model was then used to numerically optimize a thick C-PDMS electrode configuration in terms of trapping efficiency. Then, optimized microfluidic configurations were fabricated and tested at various flow rates for the trapping of MDA-MB-231 breast cancer cell line. We reached trapping efficiencies of 97% at 20 μl/h and 78.7% at 80 μl/h, for 100 μm thick electrodes. Finally, we applied our device to the separation and localized trapping of CTCs (MDA-MB-231) from a red blood cells sample (concentration ratio of 1:10). PMID:26392836

  12. Abundance trends and status of the Little Colorado River population of humpback chub

    USGS Publications Warehouse

    Coggins, L.G.; Pine, William E.; Walters, C.J.; Van Haverbeke, D. R.; Ward, D.; Johnstone, H.C.

    2006-01-01

    The abundance of the Little Colorado River population of federally listed humpback chub Gila cypha in Grand Canyon has been monitored since the late 1980s by means of catch rate indices and capture-recapture-based abundance estimators. Analyses of data from all sources using various methods are consistent and indicate that the adult population has declined since monitoring began. Intensive tagging led to a high proportion (>80%) of the adult population being marked by the mid-1990s. Analysis of these data using both closed and open abundance estimation models yields results that agree with catch rate indices about the extent of the decline. Survival rates for age-2 and older fish are age dependent but apparently not time dependent. Back-calculation of recruitment using the apparent 1990s population age structure implies periods of higher recruitment in the late 1970s to early 1980s than is now the case. Our analyses indicate that the U.S. Fish and Wildlife Service recovery criterion of stable abundance is not being met for this population. Also, there is a critical need to develop new abundance indexing and tagging methods so that early, reliable, and rapid estimates of humpback chub recruitment can be obtained to evaluate population responses to management actions designed to facilitate the restoration of Colorado River native fish communities. ?? Copyright by the American Fisheries Society 2006.

  13. A method for estimating abundance of mobile populations using telemetry and counts of unmarked animals

    USGS Publications Warehouse

    Clement, Matthew; O'Keefe, Joy M; Walters, Brianne

    2015-01-01

    While numerous methods exist for estimating abundance when detection is imperfect, these methods may not be appropriate due to logistical difficulties or unrealistic assumptions. In particular, if highly mobile taxa are frequently absent from survey locations, methods that estimate a probability of detection conditional on presence will generate biased abundance estimates. Here, we propose a new estimator for estimating abundance of mobile populations using telemetry and counts of unmarked animals. The estimator assumes that the target population conforms to a fission-fusion grouping pattern, in which the population is divided into groups that frequently change in size and composition. If assumptions are met, it is not necessary to locate all groups in the population to estimate abundance. We derive an estimator, perform a simulation study, conduct a power analysis, and apply the method to field data. The simulation study confirmed that our estimator is asymptotically unbiased with low bias, narrow confidence intervals, and good coverage, given a modest survey effort. The power analysis provided initial guidance on survey effort. When applied to small data sets obtained by radio-tracking Indiana bats, abundance estimates were reasonable, although imprecise. The proposed method has the potential to improve abundance estimates for mobile species that have a fission-fusion social structure, such as Indiana bats, because it does not condition detection on presence at survey locations and because it avoids certain restrictive assumptions.

  14. Negative binomial models for abundance estimation of multiple closed populations

    USGS Publications Warehouse

    Boyce, Mark S.; MacKenzie, Darry I.; Manly, Bryan F.J.; Haroldson, Mark A.; Moody, David W.

    2001-01-01

    Counts of uniquely identified individuals in a population offer opportunities to estimate abundance. However, for various reasons such counts may be burdened by heterogeneity in the probability of being detected. Theoretical arguments and empirical evidence demonstrate that the negative binomial distribution (NBD) is a useful characterization for counts from biological populations with heterogeneity. We propose a method that focuses on estimating multiple populations by simultaneously using a suite of models derived from the NBD. We used this approach to estimate the number of female grizzly bears (Ursus arctos) with cubs-of-the-year in the Yellowstone ecosystem, for each year, 1986-1998. Akaike's Information Criteria (AIC) indicated that a negative binomial model with a constant level of heterogeneity across all years was best for characterizing the sighting frequencies of female grizzly bears. A lack-of-fit test indicated the model adequately described the collected data. Bootstrap techniques were used to estimate standard errors and 95% confidence intervals. We provide a Monte Carlo technique, which confirms that the Yellowstone ecosystem grizzly bear population increased during the period 1986-1998.

  15. Beryllium and Boron abundances in population II stars

    NASA Technical Reports Server (NTRS)

    1995-01-01

    The scientific focus of this program was to undertake UV spectroscopic abundance analyses of extremely metal poor stars with attention to determining abundances of light elements such as beryllium and boron. The abundances are likely to reflect primordial abundances within the early galaxy and help to constrain models for early galactic nucleosynthesis. The general metal abundances of these stars are also important for understanding stellar evolution.

  16. Correlated variation and population differentiation in satellite DNA abundance among lines of Drosophila melanogaster.

    PubMed

    Wei, Kevin H-C; Grenier, Jennifer K; Barbash, Daniel A; Clark, Andrew G

    2014-12-30

    Tandemly repeating satellite DNA elements in heterochromatin occupy a substantial portion of many eukaryotic genomes. Although often characterized as genomic parasites deleterious to the host, they also can be crucial for essential processes such as chromosome segregation. Adding to their interest, satellite DNA elements evolve at high rates; among Drosophila, closely related species often differ drastically in both the types and abundances of satellite repeats. However, due to technical challenges, the evolutionary mechanisms driving this rapid turnover remain unclear. Here we characterize natural variation in simple-sequence repeats of 2-10 bp from inbred Drosophila melanogaster lines derived from multiple populations, using a method we developed called k-Seek that analyzes unassembled Illumina sequence reads. In addition to quantifying all previously described satellite repeats, we identified many novel repeats of low to medium abundance. Many of the repeats show population differentiation, including two that are present in only some populations. Interestingly, the population structure inferred from overall satellite quantities does not recapitulate the expected population relationships based on the demographic history of D. melanogaster. We also find that some satellites of similar sequence composition are correlated across lines, revealing concerted evolution. Moreover, correlated satellites tend to be interspersed with each other, further suggesting that concerted change is partially driven by higher order structure. Surprisingly, we identified negative correlations among some satellites, suggesting antagonistic interactions. Our study demonstrates that current genome assemblies vastly underestimate the complexity, abundance, and variation of highly repetitive satellite DNA and presents approaches to understand their rapid evolutionary divergence.

  17. Variability in population abundance is associated with thresholds between scaling regimes

    USGS Publications Warehouse

    Wardwell, D.; Allen, C.R.

    2009-01-01

    Discontinuous structure in landscapes may result in discontinuous, aggregated species body-mass patterns, reflecting the scales of structure available to animal communities within a landscape. The edges of these body-mass aggregations reflect transitions between available scales of landscape structure. Such transitions, or scale breaks, are theoretically associated with increased biological variability. We hypothesized that variability in population abundance is greater in animal species near the edge of body-mass aggregations than it is in species that are situated in the interior of body-mass aggregations. We tested this hypothesis by examining both temporal and spatial variability in the abundance of species in the bird community of the Florida Everglades sub-ecoregion, USA. Analyses of both temporal and spatial variability in population abundance supported our hypothesis. Our results indicate that variability within complex systems may be non-random, and is heightened where transitions in scales of process and structure occur. This is the first explicit test of the hypothetical relationship between increased population variability and scale breaks. ?? 2009 by the author(s).

  18. Community structure influences species' abundance along environmental gradients.

    PubMed

    Eloranta, Antti P; Helland, Ingeborg P; Sandlund, Odd T; Hesthagen, Trygve; Ugedal, Ola; Finstad, Anders G

    2016-01-01

    Species' response to abiotic environmental variation can be influenced by local community structure and interspecific interactions, particularly in restricted habitats such as islands and lakes. In temperate lakes, future increase in water temperature and run-off of terrestrial (allochthonous) dissolved organic carbon (DOC) are predicted to alter community composition and the overall ecosystem productivity. However, little is known about how the present community structure and abiotic environmental variation interact to affect the abundance of native fish populations. We used a space-for-time approach to study how local community structure interact with lake morphometric and climatic characteristics (i.e. temperature and catchment productivity) to affect brown trout (Salmo trutta L.) yield in 283 Norwegian lakes located in different biogeographical regions. Brown trout yield (based on data from standardized survey gill net fishing; g 100 m(-2) gill net night(-1)) was generally lower in lakes where other fish species were present than in lakes with brown trout only. The yield showed an overall negative relationship with increasing temperature and a positive relationship with lake shoreline complexity. Brown trout yield was also negatively correlated with DOC load (measured using Normalized Difference Vegetation Index as a proxy) and lake size and depth (measured using terrain slope as a proxy), but only in lakes where other fish species were present. The observed negative response of brown trout yield to increasing DOC load and proportion of the pelagic open-water area is likely due to restricted (littoral) niche availability and competitive dominance of more pelagic fishes such as Arctic charr (Salvelinus alpinus (L.)). Our study highlights that, through competitive interactions, the local community structure can influence the response of a species' abundance to variation in abiotic conditions. Changes in biomass and niche use of top predators (such as the brown

  19. Abundance anomalies in metal-poor stars from Population III supernova ejecta hydrodynamics

    NASA Astrophysics Data System (ADS)

    Sluder, Alan; Ritter, Jeremy S.; Safranek-Shrader, Chalence; Milosavljević, Miloš; Bromm, Volker

    2016-02-01

    We present a simulation of the long-term evolution of a Population III supernova remnant in a cosmological minihalo. Employing passive Lagrangian tracer particles, we investigate how chemical stratification and anisotropy in the explosion can affect the abundances of the first low-mass, metal-enriched stars. We find that reverse shock heating can leave the inner mass shells at entropies too high to cool, leading to carbon enhancement in the recollapsing gas. This hydrodynamic selection effect could explain the observed incidence of carbon-enhanced metal-poor stars at low metallicity. We further explore how anisotropic ejecta distributions, recently seen in direct numerical simulations of core-collapse explosions, may translate to abundances in metal-poor stars. We find that some of the observed scatter in the Population II abundance ratios can be explained by an incomplete mixing of supernova ejecta, even in the case of only one contributing enrichment event. We demonstrate that the customary hypothesis of fully mixed ejecta clearly fails if post-explosion hydrodynamics prefers the recycling of some nucleosynthetic products over others. Furthermore, to fully exploit the stellar-archaeological programme of constraining the Pop III initial mass function from the observed Pop II abundances, considering these hydrodynamical transport effects is crucial. We discuss applications to the rich chemical structure of ultrafaint dwarf satellite galaxies, to be probed in unprecedented detail with upcoming spectroscopic surveys.

  20. [Abundance of Trans-Volga population of the great bustard (Otis tarda L.)].

    PubMed

    Oparin, M L; Kondratenkov, I A; Oparina, O S

    2003-01-01

    We studied the abundance, spatial structure, and democratic parameters of the Trans-Volga population of great bustard as well as this species connection to the habitats during premigratory movements. The data were obtained by monitoring a test area of 1,200,000 hectares in 1998-2000. Time-related changes in the structure of great bustard habitats in Saratov Trans-Volga Region during the 20th century are described and the mechanisms underlying the changes in this species connection to the habitats under the influence of anthropogenic factors are proposed. PMID:14994471

  1. [Abundance of Trans-Volga population of the great bustard (Otis tarda L.)].

    PubMed

    Oparin, M L; Kondratenkov, I A; Oparina, O S

    2003-01-01

    We studied the abundance, spatial structure, and democratic parameters of the Trans-Volga population of great bustard as well as this species connection to the habitats during premigratory movements. The data were obtained by monitoring a test area of 1,200,000 hectares in 1998-2000. Time-related changes in the structure of great bustard habitats in Saratov Trans-Volga Region during the 20th century are described and the mechanisms underlying the changes in this species connection to the habitats under the influence of anthropogenic factors are proposed.

  2. Seasonal abundance of the microplankton population in the North Pacific central gyre

    NASA Astrophysics Data System (ADS)

    Beers, John R.; Reid, Freda M. H.; Stewart, Gene L.

    1982-02-01

    Population structure as numerical and biomas abundance was determined for the microplankton (˜ to 200 μm organisms) sampled throughout and just below the euphotic zone at five times of year other than fall in the North Pacific central gyre around 28°N, 155°W. Average total microplankton carbon of all strata varied by twofold or less over the cruises, conforming to the hypothesis of low heterogeneity of biomass in central oceanic gyral populations. For example, mean euphotic zone abundance ranged from 5.9 μg Cl -1 (late winter) to 10.5 μg Cl -1 (spring), averaging 7.9 μg Cl -1. Its variability and that of stations within cruises were similar. Microplankton did not show a maximum correlated with the chlorophyll α maximum seen near the base of the euphotic zone when there was thermal stratification within the euphotic zone. Nanoplankters consistently dominated the population. 'Monads and flagellates' and non-thecate dinoflagellates were the most abundant groups. Diatoms in the upper waters where temperature range was the widest were the most temporally variable. Statistically significant differences in the biomass of taxonomic groups between cruises were found in relatively few of the possible instances tested.

  3. Filling a void: abundance estimation of North American populations of arctic geese using hunter recoveries

    USGS Publications Warehouse

    Alisauskas, R.T.; Drake, K.L.; Nichols, J.D.; Thomson, David L.; Cooch, Evan G.; Conroy, Michael J.

    2009-01-01

    We consider use of recoveries of marked birds harvested by hunters, in conjunction with continental harvest estimates, for drawing inferences about continental abundance of a select number of goose species. We review assumptions of this method, a version of the Lincoln?Petersen approach, and consider its utility as a tool for making decisions about harvest management in comparison to current sources of information. Finally, we compare such estimates with existing count data, photographic estimates, or other abundance estimates. In most cases, Lincoln estimates are far higher than abundances assumed or perhaps accepted by many waterfowl biologists and managers. Nevertheless, depending on the geographic scope of inference, we suggest that this approach for abundance estimation of arctic geese may have usefulness for retrospective purposes or to assist with harvest management decisions for some species. Lincoln?s estimates may be as close or closer to truth than count, index, or photo data, and can be used with marking efforts currently in place for estimation of survival and harvest rates. Although there are bias issues associated with estimates of both harvest and harvest rate, some of the latter can be addressed with proper allocation of marks to spatially structured populations if subpopulations show heterogeneity in harvest rates.

  4. Estimating the abundance of mouse populations of known size: promises and pitfalls of new methods

    USGS Publications Warehouse

    Conn, P.B.; Arthur, A.D.; Bailey, L.L.; Singleton, G.R.

    2006-01-01

    Knowledge of animal abundance is fundamental to many ecological studies. Frequently, researchers cannot determine true abundance, and so must estimate it using a method such as mark-recapture or distance sampling. Recent advances in abundance estimation allow one to model heterogeneity with individual covariates or mixture distributions and to derive multimodel abundance estimators that explicitly address uncertainty about which model parameterization best represents truth. Further, it is possible to borrow information on detection probability across several populations when data are sparse. While promising, these methods have not been evaluated using mark?recapture data from populations of known abundance, and thus far have largely been overlooked by ecologists. In this paper, we explored the utility of newly developed mark?recapture methods for estimating the abundance of 12 captive populations of wild house mice (Mus musculus). We found that mark?recapture methods employing individual covariates yielded satisfactory abundance estimates for most populations. In contrast, model sets with heterogeneity formulations consisting solely of mixture distributions did not perform well for several of the populations. We show through simulation that a higher number of trapping occasions would have been necessary to achieve good estimator performance in this case. Finally, we show that simultaneous analysis of data from low abundance populations can yield viable abundance estimates.

  5. Effective population size and population subdivision in demographically structured populations.

    PubMed Central

    Laporte, Valérie; Charlesworth, Brian

    2002-01-01

    A fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age. This provides a general expression for the probability that a pair of alleles sampled from the population coalesce in the previous time interval. The effective population size is defined as the reciprocal of twice the product of generation time and the coalescence probability. Biologically explicit formulas for effective population size with discrete generations and separate sexes are derived for a variety of different modes of inheritance. The method is also applied to a nuclear gene in a population of partially self-fertilizing hermaphrodites. The effects of population subdivision on a demographically structured population are analyzed, using a matrix of net rates of movement of genes between different local populations. This involves weighting the migration probabilities of individuals of a given age/sex class by the contribution of this class to the leading left eigenvector of the matrix describing the movements of genes between age/sex classes. The effects of sex-specific migration and nonrandom distributions of offspring number on levels of genetic variability and among-population differentiation are described for different modes of inheritance in an island model. Data on DNA sequence variability in human and plant populations are discussed in the light of the results. PMID:12242257

  6. The existence and abundance of ghost ancestors in biparental populations.

    PubMed

    Gravel, Simon; Steel, Mike

    2015-05-01

    In a randomly-mating biparental population of size N there are, with high probability, individuals who are genealogical ancestors of every extant individual within approximately log2(N) generations into the past. We use this result of J. Chang to prove a curious corollary under standard models of recombination: there exist, with high probability, individuals within a constant multiple of log2(N) generations into the past who are simultaneously (i) genealogical ancestors of each of the individuals at the present, and (ii) genetic ancestors to none of the individuals at the present. Such ancestral individuals-ancestors of everyone today that left no genetic trace-represent 'ghost' ancestors in a strong sense. In this short note, we use simple analytical argument and simulations to estimate how many such individuals exist in finite Wright-Fisher populations. PMID:25703300

  7. Chemical abundances in LMC stellar populations. II. The bar sample

    NASA Astrophysics Data System (ADS)

    Van der Swaelmen, M.; Hill, V.; Primas, F.; Cole, A. A.

    2013-12-01

    Aims: This paper compares the chemical evolution of the Large Magellanic Cloud (LMC) to that of the Milky Way (MW) and investigates the relation between the bar and the inner disc of the LMC in the context of the formation of the bar. Methods: We obtained high-resolution and mid signal-to-noise ratio spectra with FLAMES/GIRAFFE at ESO/VLT and performed a detailed chemical analysis of 106 and 58 LMC field red giant stars (mostly older than 1 Gyr), located in the bar and the disc of the LMC respectively. To validate our stellar parameter determinations and abundance measurement procedures, we performed thorough tests using the well-known mildly metal-poor Milky-Way thick disc giant Arcturus (HD 124897, α Boo). We measured elemental abundances for O, Mg, Si, Ca, Ti (α-elements), Na (light odd element), Sc, V, Cr, Co, Ni, Cu (iron-peak elements), Y, Zr, Ba, La, and Eu (s- and r-elements). Results: We find that the α-element ratios [Mg/Fe] and [O/Fe] are lower in the LMC than in the MW while the LMC has similar [Si/Fe], [Ca/Fe], and [Ti/Fe] to the MW. As for the heavy elements, [Ba,La/Eu] exhibit a strong increase with increasing metallicity starting from [Fe/H] ≈ -0.8 dex, and the LMC has lower [Y + Zr/Ba + La] ratios than the MW. Cu is almost constant over all metallicities and about 0.5 dex lower in the LMC than in the MW. The LMC bar and inner disc exhibit differences in their [α/ Fe] (slightly larger scatter for the bar in the metallicity range [-1, -0.5]), their Eu (the bar trend is above the disc trend for [Fe/H] ≥ -0.5 dex), their Y and Zr, their Na and their V (offset between the bar and the disc distributions). Conclusions: Our results show that the chemical history of the LMC experienced a strong contribution from type Ia supernovae as well as a strong s-process enrichment from metal-poor AGB winds. Massive stars made a smaller contribution to the chemical enrichment compared to the MW. The observed differences between the bar and the disc speak in

  8. Distribution and abundance of zooplankton populations in Crater Lake, Oregon

    USGS Publications Warehouse

    Larson, G.L.; McIntire, C.D.; Buktenica, M.W.; Girdner, S.F.; Truitt, R.E.

    2007-01-01

    The zooplankton assemblages in Crater Lake exhibited consistency in species richness and general taxonomic composition, but varied in density and biomass during the period between 1988 and 2000. Collectively, the assemblages included 2 cladoceran taxa and 10 rotifer taxa (excluding rare taxa). Vertical habitat partitioning of the water column to a depth of 200 m was observed for most species with similar food habits and/or feeding mechanisms. No congeneric replacement was observed. The dominant species in the assemblages were variable, switching primarily between periods of dominance of Polyarthra-Keratella cochlearis and Daphnia. The unexpected occurrence and dominance of Asplanchna in 1991 and 1992 resulted in a major change in this typical temporal shift between Polyarthra-K. cochlearis and Daphnia. Following a collapse of the zooplankton biomass in 1993 that was probably caused by predation from Asplanchna, Kellicottia dominated the zooplankton assemblage biomass between 1994 and 1997. The decline in biomass of Kellicottia by 1998 coincided with a dramatic increase in Daphnia biomass. When Daphnia biomass declined by 2000, Keratella biomass increased again. Thus, by 1998 the assemblage returned to the typical shift between Keratella-Polyarthra and Daphnia. Although these observations provided considerable insight about the interannual variability of the zooplankton assemblages in Crater Lake, little was discovered about mechanisms behind the variability. When abundant, kokanee salmon may have played an important role in the disappearance of Daphnia in 1990 and 2000 either through predation, inducing diapause, or both. ?? 2007 Springer Science+Business Media B.V.

  9. Commonly rare and rarely common: comparing population abundance of invasive and native aquatic species.

    PubMed

    Hansen, Gretchen J A; Vander Zanden, M Jake; Blum, Michael J; Clayton, Murray K; Hain, Ernie F; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S; McIntyre, Peter B; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies.

  10. Commonly Rare and Rarely Common: Comparing Population Abundance of Invasive and Native Aquatic Species

    PubMed Central

    Hansen, Gretchen J. A.; Vander Zanden, M. Jake; Blum, Michael J.; Clayton, Murray K.; Hain, Ernie F.; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S.; McIntyre, Peter B.; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D.; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

  11. Commonly rare and rarely common: comparing population abundance of invasive and native aquatic species.

    PubMed

    Hansen, Gretchen J A; Vander Zanden, M Jake; Blum, Michael J; Clayton, Murray K; Hain, Ernie F; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S; McIntyre, Peter B; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

  12. Seasonal temperature and precipitation regulate brook trout young-of-the-year abundance and population dynamics

    USGS Publications Warehouse

    Kanno, Yoichiro; Pregler, Kasey C.; Hitt, Nathaniel P.; Letcher, Benjamin H.; Hocking, Daniel; Wofford, John E.B.

    2015-01-01

    Our results indicate that YOY abundance is a key driver of brook trout population dynamics that is mediated by seasonal weather patterns. A reliable assessment of climate change impacts on brook trout needs to account for how alternations in seasonal weather patterns impact YOY abundance and how such relationships may differ across the range of brook trout distribution.

  13. Abundance and Source Population of Suprathermal Heavy Ions in Corotating Interaction Regions

    NASA Astrophysics Data System (ADS)

    Jensema, R. J.; Desai, M. I.; Broiles, T. W.; Dayeh, M. A.

    2015-12-01

    In this study we analyze the abundances of suprathermal heavy ions in 75 Corotating Interaction Region (CIR) events between January 1st 1995 and December 31st 2008. We correlate the heavy ion abundances in these CIRs with those measured in the solar wind and suprathermal populations upstream of these events. Our analysis reveals that the CIR suprathermal heavy ion abundances vary by nearly two orders of magnitude over the solar activity cycle, with higher abundances (e.g., Fe/O) occurring during solar maximum and depleted values occurring during solar minimum. The abundances are also energy dependent, with larger abundances at higher energies, particularly during solar maximum. Following the method used by Mason et al. 2008, we correlate the CIR abundances with the corresponding solar wind and suprathermal values measured during 6-hour intervals for upstream periods spanning 10 days prior to the start of each CIR event. This correlation reveals that suprathermal heavy ions are better correlated with upstream suprathermal abundances measured at the same energy compared with the solar wind heavy ion abundances. Using the 6-hour averaging method, we also identified timeframes of maximum correlation between the CIR and the upstream suprathermal abundances, and find that the time of maximum correlation depends on the energy of the suprathermal ions. We discuss the implications of these results in terms of previous studies of CIR and suprathermal particles, and CIR seed populations and acceleration mechanisms.

  14. Population genetic structure and ecotoxicology.

    PubMed Central

    Guttman, S I

    1994-01-01

    Electrophoretic analyses of population genetic structure, both in the laboratory and in the field, have documented significant shifts in allozyme genotype frequencies in a variety of aquatic taxa as a result of environmental impacts. Studies are documented which indicate that contaminants may select for individuals with tolerant allozyme genotypes, causing the potential loss of individuals with sensitive genotypes. This may diminish the genetic variability and fitness of affected populations and make them more susceptible to extinction following a subsequent stress. Future research involving population genetic structure and ecotoxicology should focus on determining the mechanism of sensitivity, documenting multigenerational effects of chronic laboratory exposure on population genetic composition, investigating whether previously stressed and genetically impacted populations are more susceptible to further natural and/or anthropogenic stressors, and establishing the utility of population genetic structure as a sensitive monitor of impacts in aquatic systems and their subsequent remediation. PMID:7713044

  15. Performance of Baited Underwater Video: Does It Underestimate Abundance at High Population Densities?

    PubMed Central

    Stobart, Ben; Díaz, David; Álvarez, Federico; Alonso, Cristina; Mallol, Sandra; Goñi, Raquel

    2015-01-01

    Video survey techniques are now commonly used to estimate animal abundance under the assumption that estimates relate to true abundance, a key property needed to make video a valid survey tool. Using the spiny lobster Palinurus elephas as our model organism, we evaluate the effectiveness of baited underwater video (BUV) for estimating abundance in areas with widely different population density. We test three BUV abundance metrics and compare the results with an independently obtained abundance index from trammel-net surveys (Trammel). Video metrics used to estimate relative abundance include a value for total number of individuals per recording (TotN), the traditional maximum number of fish observed in a single video frame (MaxN), and the recently suggested alternative, the average of the mean MaxN from 5-minute periods throughout the duration of the recording (MeanN). This is the first video study of a wild population to include an estimate for TotN. Comparison of TotN with the other two BUV relative abundance metrics demonstrates that both of the latter lack resolution at high population densities. In spite of this, the three BUV metrics tested, as well as the independent estimate Trammel, distinguished high density areas from low density areas. Thus they could all be used to identify areas of differing population density, but MaxN and MeanN would not be appropriate metrics for studies aimed at documenting increases in abundance, such as those conducted to assess marine protected area effectiveness, as they are prone to sampling saturation. We also demonstrate that time of first arrival (T1) is highly correlated with all of the abundance indices; suggesting T1 may be a potentially useful index of abundance. However, these relationships require further investigation as our data suggests T1 may not adequately represent lobster abundance in areas of high density. PMID:26010738

  16. Performance of baited underwater video: does it underestimate abundance at high population densities?

    PubMed

    Stobart, Ben; Díaz, David; Álvarez, Federico; Alonso, Cristina; Mallol, Sandra; Goñi, Raquel

    2015-01-01

    Video survey techniques are now commonly used to estimate animal abundance under the assumption that estimates relate to true abundance, a key property needed to make video a valid survey tool. Using the spiny lobster Palinurus elephas as our model organism, we evaluate the effectiveness of baited underwater video (BUV) for estimating abundance in areas with widely different population density. We test three BUV abundance metrics and compare the results with an independently obtained abundance index from trammel-net surveys (Trammel). Video metrics used to estimate relative abundance include a value for total number of individuals per recording (TotN), the traditional maximum number of fish observed in a single video frame (MaxN), and the recently suggested alternative, the average of the mean MaxN from 5-minute periods throughout the duration of the recording (MeanN). This is the first video study of a wild population to include an estimate for TotN. Comparison of TotN with the other two BUV relative abundance metrics demonstrates that both of the latter lack resolution at high population densities. In spite of this, the three BUV metrics tested, as well as the independent estimate Trammel, distinguished high density areas from low density areas. Thus they could all be used to identify areas of differing population density, but MaxN and MeanN would not be appropriate metrics for studies aimed at documenting increases in abundance, such as those conducted to assess marine protected area effectiveness, as they are prone to sampling saturation. We also demonstrate that time of first arrival (T1) is highly correlated with all of the abundance indices; suggesting T1 may be a potentially useful index of abundance. However, these relationships require further investigation as our data suggests T1 may not adequately represent lobster abundance in areas of high density.

  17. Performance of baited underwater video: does it underestimate abundance at high population densities?

    PubMed

    Stobart, Ben; Díaz, David; Álvarez, Federico; Alonso, Cristina; Mallol, Sandra; Goñi, Raquel

    2015-01-01

    Video survey techniques are now commonly used to estimate animal abundance under the assumption that estimates relate to true abundance, a key property needed to make video a valid survey tool. Using the spiny lobster Palinurus elephas as our model organism, we evaluate the effectiveness of baited underwater video (BUV) for estimating abundance in areas with widely different population density. We test three BUV abundance metrics and compare the results with an independently obtained abundance index from trammel-net surveys (Trammel). Video metrics used to estimate relative abundance include a value for total number of individuals per recording (TotN), the traditional maximum number of fish observed in a single video frame (MaxN), and the recently suggested alternative, the average of the mean MaxN from 5-minute periods throughout the duration of the recording (MeanN). This is the first video study of a wild population to include an estimate for TotN. Comparison of TotN with the other two BUV relative abundance metrics demonstrates that both of the latter lack resolution at high population densities. In spite of this, the three BUV metrics tested, as well as the independent estimate Trammel, distinguished high density areas from low density areas. Thus they could all be used to identify areas of differing population density, but MaxN and MeanN would not be appropriate metrics for studies aimed at documenting increases in abundance, such as those conducted to assess marine protected area effectiveness, as they are prone to sampling saturation. We also demonstrate that time of first arrival (T1) is highly correlated with all of the abundance indices; suggesting T1 may be a potentially useful index of abundance. However, these relationships require further investigation as our data suggests T1 may not adequately represent lobster abundance in areas of high density. PMID:26010738

  18. An abundant population of small irregular satellites around Jupiter.

    PubMed

    Sheppard, Scott S; Jewitt, David C

    2003-05-15

    Irregular satellites have eccentric orbits that can be highly inclined or even retrograde relative to the equatorial planes of their planets. These objects cannot have formed by circumplanetary accretion, unlike the regular satellites that follow uninclined, nearly circular and prograde orbits. Rather, they are probably products of early capture from heliocentric orbits. Although the capture mechanism remains uncertain, the study of irregular satellites provides a window on processes operating in the young Solar System. Families of irregular satellites recently have been discovered around Saturn (thirteen members, refs 6, 7), Uranus (six, ref. 8) and Neptune (three, ref. 9). Because Jupiter is closer than the other giant planets, searches for smaller and fainter irregular satellites can be made. Here we report the discovery of 23 new irregular satellites of Jupiter, so increasing the total known population to 32. There are five distinct satellite groups, each dominated by one relatively large body. The groups were most probably produced by collisional shattering of precursor objects after capture by Jupiter.

  19. An abundant population of small irregular satellites around Jupiter.

    PubMed

    Sheppard, Scott S; Jewitt, David C

    2003-05-15

    Irregular satellites have eccentric orbits that can be highly inclined or even retrograde relative to the equatorial planes of their planets. These objects cannot have formed by circumplanetary accretion, unlike the regular satellites that follow uninclined, nearly circular and prograde orbits. Rather, they are probably products of early capture from heliocentric orbits. Although the capture mechanism remains uncertain, the study of irregular satellites provides a window on processes operating in the young Solar System. Families of irregular satellites recently have been discovered around Saturn (thirteen members, refs 6, 7), Uranus (six, ref. 8) and Neptune (three, ref. 9). Because Jupiter is closer than the other giant planets, searches for smaller and fainter irregular satellites can be made. Here we report the discovery of 23 new irregular satellites of Jupiter, so increasing the total known population to 32. There are five distinct satellite groups, each dominated by one relatively large body. The groups were most probably produced by collisional shattering of precursor objects after capture by Jupiter. PMID:12748634

  20. Phylogenetic structure and host abundance drive disease pressure in communities.

    PubMed

    Parker, Ingrid M; Saunders, Megan; Bontrager, Megan; Weitz, Andrew P; Hendricks, Rebecca; Magarey, Roger; Suiter, Karl; Gilbert, Gregory S

    2015-04-23

    Pathogens play an important part in shaping the structure and dynamics of natural communities, because species are not affected by them equally. A shared goal of ecology and epidemiology is to predict when a species is most vulnerable to disease. A leading hypothesis asserts that the impact of disease should increase with host abundance, producing a 'rare-species advantage'. However, the impact of a pathogen may be decoupled from host abundance, because most pathogens infect more than one species, leading to pathogen spillover onto closely related species. Here we show that the phylogenetic and ecological structure of the surrounding community can be important predictors of disease pressure. We found that the amount of tissue lost to disease increased with the relative abundance of a species across a grassland plant community, and that this rare-species advantage had an additional phylogenetic component: disease pressure was stronger on species with many close relatives. We used a global model of pathogen sharing as a function of relatedness between hosts, which provided a robust predictor of relative disease pressure at the local scale. In our grassland, the total amount of disease was most accurately explained not by the abundance of the focal host alone, but by the abundance of all species in the community weighted by their phylogenetic distance to the host. Furthermore, the model strongly predicted observed disease pressure for 44 novel host species we introduced experimentally to our study site, providing evidence for a mechanism to explain why phylogenetically rare species are more likely to become invasive when introduced. Our results demonstrate how the phylogenetic and ecological structure of communities can have a key role in disease dynamics, with implications for the maintenance of biodiversity, biotic resistance against introduced weeds, and the success of managed plants in agriculture and forestry.

  1. Impact of warming on abundance and occurrence of flatfish populations in the Bay of Biscay (France)

    NASA Astrophysics Data System (ADS)

    Hermant, Marie; Lobry, Jeremy; Bonhommeau, Sylvain; Poulard, Jean-Charles; Le Pape, Olivier

    2010-07-01

    The aim of the present study was to analyse the influence of warming on flatfish populations in the Bay of Biscay. 17 autumn cruises conducted from 1987 to 2006 over the whole shelf of the Bay of Biscay provided data for the abundance and occurrence of adults for twenty flatfish species. Trends in flatfish abundance were analysed with regard to geographic range of populations and interannual fluctuations in abundance were related to seawater temperature. Results showed significant trends in abundance and occurrence for 55% of the flatfish species in the Bay of Biscay. The response to warming of seawater was correlated to geographic ranges of species. While the abundance of the northern temperate species decreased, that of southern ones increased. Moreover, for 40% of the species which densities have significantly changed, abundances were correlated to temperatures in their year of birth, positively for southern species and negatively for northern ones. Last, the abundance of flatfish adults over the Bay of Biscay was compared to previous data on juveniles in the Bay of Vilaine, one of the estuarine nursery ground in this area. For the northern species which have disappeared, the decline in juvenile abundances preceded that of adults by several years, indicating that the recruitment is the process affected. We concluded on a major impact of warming to explain changes in flatfish species abundances. Nevertheless, the impact of fishing interacts with that of climate change because the exploited species appeared to be the most negatively affected.

  2. Abundance, distribution and size structure of Diadema antillarum (Echinodermata: Diadematidae) in South Eastern Cuban coral reefs.

    PubMed

    Martín Blanco, F; González Sansón, G; Pina Amargós, F; Clero Alonso, L

    2010-06-01

    The 1983-1984 mass mortality event of Diadema antillarum affected more than 93% of the total Caribbean population. Although there are no records about the status of Diadema populations before and after die-off on Cuban reefs, anecdotal information suggests that populations were struck. We analyzed spatial variation in the abundance and size structure of D. antillarum in 22 reefs sites in Jardines de la Reina, from June 2004 to September 2005. Counts of Diadema were performed in five 30x2 m transects at each sampling site and sampling time, and test diameters were measured in September 2005 at the same fore reefs. Abundances were higher at reef crests (mean densities 0.08-2.18 ind./m2), while reef slope populations reached a maximum site level of 0.13 ind./m2 at only one site and showed values up to three orders of magnitude lower than those from reef crests. Highest abundance occurred at the west margin of major channels between keys where larval recruitment seems to be favored by local oceanographic features and facilitated by the abundance of Echinometra lucunter. The size frequency distribution of D. antillarum indicates that recruitment began to be noticeable three years before September 2005, suggesting these populations were depleted in the past and they are recovering now.

  3. Abundance, distribution and size structure of Diadema antillarum (Echinodermata: Diadematidae) in South Eastern Cuban coral reefs.

    PubMed

    Martín Blanco, F; González Sansón, G; Pina Amargós, F; Clero Alonso, L

    2010-06-01

    The 1983-1984 mass mortality event of Diadema antillarum affected more than 93% of the total Caribbean population. Although there are no records about the status of Diadema populations before and after die-off on Cuban reefs, anecdotal information suggests that populations were struck. We analyzed spatial variation in the abundance and size structure of D. antillarum in 22 reefs sites in Jardines de la Reina, from June 2004 to September 2005. Counts of Diadema were performed in five 30x2 m transects at each sampling site and sampling time, and test diameters were measured in September 2005 at the same fore reefs. Abundances were higher at reef crests (mean densities 0.08-2.18 ind./m2), while reef slope populations reached a maximum site level of 0.13 ind./m2 at only one site and showed values up to three orders of magnitude lower than those from reef crests. Highest abundance occurred at the west margin of major channels between keys where larval recruitment seems to be favored by local oceanographic features and facilitated by the abundance of Echinometra lucunter. The size frequency distribution of D. antillarum indicates that recruitment began to be noticeable three years before September 2005, suggesting these populations were depleted in the past and they are recovering now. PMID:20527467

  4. Estimating the abundance of clustered animal population by using adaptive cluster sampling and negative binomial distribution

    NASA Astrophysics Data System (ADS)

    Bo, Yizhou; Shifa, Naima

    2013-09-01

    An estimator for finding the abundance of a rare, clustered and mobile population has been introduced. This model is based on adaptive cluster sampling (ACS) to identify the location of the population and negative binomial distribution to estimate the total in each site. To identify the location of the population we consider both sampling with replacement (WR) and sampling without replacement (WOR). Some mathematical properties of the model are also developed.

  5. Two distinct halo populations in the solar neighborhood: evidence from stellar abundance of beryllium

    NASA Astrophysics Data System (ADS)

    Tan, Kefeng; Zhao, Gang

    2014-01-01

    It is now generally believed that the Galaxy was formed through hierarchical merging, which means that different components of the Galaxy may have experienced different chemical evolution histories. Since alpha elements are mainly produced by core collapse supernovae, they are closely associated with the star formation history of the Galaxy. In this regard, Galactic components with different alpha elemental abundance patterns may show different behaviors in beryllium abundances since the production of beryllium is correlated with the cosmic rays and thus the supernovae. A recent study by Nissen & Schuster (2010) has revealed the existence of two distinct halo populations in the solar neighborhood based on the alpha elemental abundances and kinematics of 94 dwarf stars. We determined beryllium abundances for some of these stars and find systematic differences in beryllium abundances between these two halo populations. Our results consolidate the conclusion of two distinct halo populations in the solar neighborhood. Our results also show that beryllium abundance is a very good indicator of star formation rate, and could be used to trace the substructures of the Galactic halo.

  6. Climate change effects on soil microarthropod abundance and community structure

    SciTech Connect

    Kardol, Paul; Reynolds, W. Nicholas; Norby, Richard J; Classen, Aimee T

    2011-01-01

    Long-term ecosystem responses to climate change strongly depend on how the soil subsystem and its inhabitants respond to these perturbations. Using open-top chambers, we studied the response of soil microarthropods to single and combined effects of ambient and elevated atmospheric [CO{sub 2}], ambient and elevated temperatures and changes in precipitation in constructed old-fields in Tennessee, USA. Microarthropods were assessed five years after treatments were initiated and samples were collected in both November and June. Across treatments, mites and collembola were the most dominant microarthropod groups collected. We did not detect any treatment effects on microarthropod abundance. In November, but not in June, microarthropod richness, however, was affected by the climate change treatments. In November, total microarthropod richness was lower in dry than in wet treatments, and in ambient temperature treatments, richness was higher under elevated [CO{sub 2}] than under ambient [CO{sub 2}]. Differential responses of individual taxa to the climate change treatments resulted in shifts in community composition. In general, the precipitation and warming treatments explained most of the variation in community composition. Across treatments, we found that collembola abundance and richness were positively related to soil moisture content, and that negative relationships between collembola abundance and richness and soil temperature could be explained by temperature-related shifts in soil moisture content. Our data demonstrate how simultaneously acting climate change factors can affect the structure of soil microarthropod communities in old-field ecosystems. Overall, changes in soil moisture content, either as direct effect of changes in precipitation or as indirect effect of warming or elevated [CO{sub 2}], had a larger impact on microarthropod communities than did the direct effects of the warming and elevated [CO{sub 2}] treatments. Moisture-induced shifts in soil

  7. Genealogical histories in structured populations.

    PubMed

    Kumagai, Seiji; Uyenoyama, Marcy K

    2015-06-01

    In genealogies of genes sampled from structured populations, lineages coalesce at rates dependent on the states of the lineages. For migration and coalescence events occurring on comparable time scales, for example, only lineages residing in the same deme of a geographically subdivided population can have descended from a common ancestor in the immediately preceding generation. Here, we explore aspects of genealogical structure in a population comprising two demes, between which migration may occur. We use generating functions to obtain exact densities and moments of coalescence time, number of mutations, total tree length, and age of the most recent common ancestor of the sample. We describe qualitative features of the distribution of gene genealogies, including factors that influence the geographical location of the most recent common ancestor and departures of the distribution of internode lengths from exponential. PMID:25770971

  8. Efficient estimation of abundance for patchily distributed populations via two-phase, adaptive sampling.

    USGS Publications Warehouse

    Conroy, M.J.; Runge, J.P.; Barker, R.J.; Schofield, M.R.; Fonnesbeck, C.J.

    2008-01-01

    Many organisms are patchily distributed, with some patches occupied at high density, others at lower densities, and others not occupied. Estimation of overall abundance can be difficult and is inefficient via intensive approaches such as capture-mark-recapture (CMR) or distance sampling. We propose a two-phase sampling scheme and model in a Bayesian framework to estimate abundance for patchily distributed populations. In the first phase, occupancy is estimated by binomial detection samples taken on all selected sites, where selection may be of all sites available, or a random sample of sites. Detection can be by visual surveys, detection of sign, physical captures, or other approach. At the second phase, if a detection threshold is achieved, CMR or other intensive sampling is conducted via standard procedures (grids or webs) to estimate abundance. Detection and CMR data are then used in a joint likelihood to model probability of detection in the occupancy sample via an abundance-detection model. CMR modeling is used to estimate abundance for the abundance-detection relationship, which in turn is used to predict abundance at the remaining sites, where only detection data are collected. We present a full Bayesian modeling treatment of this problem, in which posterior inference on abundance and other parameters (detection, capture probability) is obtained under a variety of assumptions about spatial and individual sources of heterogeneity. We apply the approach to abundance estimation for two species of voles (Microtus spp.) in Montana, USA. We also use a simulation study to evaluate the frequentist properties of our procedure given known patterns in abundance and detection among sites as well as design criteria. For most population characteristics and designs considered, bias and mean-square error (MSE) were low, and coverage of true parameter values by Bayesian credibility intervals was near nominal. Our two-phase, adaptive approach allows efficient estimation of

  9. [Population structure and dynamics: the population matrix].

    PubMed

    Wang, C S; Gorter, D

    1990-08-01

    "This article shows an alternative way of presenting population data. The population matrix, constructed as an important part in the process of compiling socio-demographic accounts, demonstrates the close connection between stock and flow data, bringing both types of data consistently together." Official data for the Netherlands are used to illustrate the concept. (SUMMARY IN ENG) PMID:12342861

  10. Motor abundance and control structure in the golf swing.

    PubMed

    Morrison, A; McGrath, D; Wallace, E S

    2016-04-01

    Variability and control structure are under-represented areas of golf swing research. This study investigated the use of the abundant degrees of freedom in the golf swing of high and intermediate skilled golfers using uncontrolled manifold (UCM) analysis. The variance parallel to (VUCM) and orthogonal to (VOrth) the UCM with respect to the orientation and location of the clubhead were calculated. The higher skilled golfers had proportionally higher values of VUCM than lower skilled players for all measured outcome variables. Motor synergy was found in the control of the orientation of the clubhead and the combined outcome variables but not for clubhead location. Clubhead location variance zeroed-in on impact as has been previously shown, whereas clubhead orientation variance increased near impact. Both skill levels increased their control over the clubhead location leading up to impact, with more control exerted over the clubhead orientation in the early downswing. The results suggest that to achieve higher skill levels in golf may not lie simply in optimal technique, but may lie more in developing control over the abundant degrees of freedom in the body.

  11. Structure and Abundance of Nitrous Oxide Complexes in Earth's Atmosphere.

    PubMed

    Salmon, Steven R; de Lange, Katrina M; Lane, Joseph R

    2016-04-01

    We have investigated the lowest energy structures and binding energies of a series of atmospherically relevant nitrous oxide (N2O) complexes using explicitly correlated coupled cluster theory. Specifically, we have considered complexes with nitrogen (N2-N2O), oxygen (O2-N2O), argon (Ar-N2O), and water (H2O-N2O). We have calculated rotational constants and harmonic vibrational frequencies for the complexes and the constituent monomers. Statistical mechanics was used to determine the thermodynamic parameters for complex formation as a function of temperature and pressure. These results, in combination with relevant atmospheric data, were used to estimate the abundance of N2O complexes in Earth's atmosphere as a function of altitude. We find that the abundance of N2O complexes in Earth's atmosphere is small but non-negligible, and we suggest that N2O complexes may contribute to absorption of terrestrial radiation and be relevant for understanding the atmospheric fate of N2O.

  12. Motor abundance and control structure in the golf swing.

    PubMed

    Morrison, A; McGrath, D; Wallace, E S

    2016-04-01

    Variability and control structure are under-represented areas of golf swing research. This study investigated the use of the abundant degrees of freedom in the golf swing of high and intermediate skilled golfers using uncontrolled manifold (UCM) analysis. The variance parallel to (VUCM) and orthogonal to (VOrth) the UCM with respect to the orientation and location of the clubhead were calculated. The higher skilled golfers had proportionally higher values of VUCM than lower skilled players for all measured outcome variables. Motor synergy was found in the control of the orientation of the clubhead and the combined outcome variables but not for clubhead location. Clubhead location variance zeroed-in on impact as has been previously shown, whereas clubhead orientation variance increased near impact. Both skill levels increased their control over the clubhead location leading up to impact, with more control exerted over the clubhead orientation in the early downswing. The results suggest that to achieve higher skill levels in golf may not lie simply in optimal technique, but may lie more in developing control over the abundant degrees of freedom in the body. PMID:26784706

  13. The ornament-condition relationship varies with parasite abundance at population level in a female bird

    NASA Astrophysics Data System (ADS)

    Vergara, Pablo; Martínez-Padilla, Jesús; Redpath, Stephen M.; Mougeot, Francois

    2011-10-01

    Environmental heterogeneity is expected to create variation in the ornament-condition relationship. This topic has been studied in males with less attention being given to females. Here, we explore inter-population variation in the relationship between the size of a male-like trait, supra-orbital combs, and body mass in female red grouse Lagopus lagopus scoticus. We used the abundance of the nematode Trichostrongylus tenuis, a parasite with strong negative effects on this species, as a proxy of environmental conditions. We studied six populations over 5 years and showed that the comb size-body mass relationship varied with mean parasite abundance, with stronger ornament-condition relationships in populations with higher parasite infection levels. Our study supports the idea that environmental conditions, and in particular parasite infection levels, may affect the reliability of female ornaments as condition indicators.

  14. Optimal sampling design for estimating spatial distribution and abundance of a freshwater mussel population

    USGS Publications Warehouse

    Pooler, P.S.; Smith, D.R.

    2005-01-01

    We compared the ability of simple random sampling (SRS) and a variety of systematic sampling (SYS) designs to estimate abundance, quantify spatial clustering, and predict spatial distribution of freshwater mussels. Sampling simulations were conducted using data obtained from a census of freshwater mussels in a 40 X 33 m section of the Cacapon River near Capon Bridge, West Virginia, and from a simulated spatially random population generated to have the same abundance as the real population. Sampling units that were 0.25 m 2 gave more accurate and precise abundance estimates and generally better spatial predictions than 1-m2 sampling units. Systematic sampling with ???2 random starts was more efficient than SRS. Estimates of abundance based on SYS were more accurate when the distance between sampling units across the stream was less than or equal to the distance between sampling units along the stream. Three measures for quantifying spatial clustering were examined: Hopkins Statistic, the Clumping Index, and Morisita's Index. Morisita's Index was the most reliable, and the Hopkins Statistic was prone to false rejection of complete spatial randomness. SYS designs with units spaced equally across and up stream provided the most accurate predictions when estimating the spatial distribution by kriging. Our research indicates that SYS designs with sampling units equally spaced both across and along the stream would be appropriate for sampling freshwater mussels even if no information about the true underlying spatial distribution of the population were available to guide the design choice. ?? 2005 by The North American Benthological Society.

  15. Ultradiffuse galaxies: the high-spin tail of the abundant dwarf galaxy population

    NASA Astrophysics Data System (ADS)

    Amorisco, N. C.; Loeb, A.

    2016-06-01

    Recent observations have revealed the existence of an abundant population of faint, low surface brightness (SB) galaxies, which appear to be numerous and ubiquitous in nearby galaxy clusters, including the Virgo, Coma and Fornax clusters. With median stellar masses of dwarf galaxies, these ultradiffuse galaxies (UDGs) have unexpectedly large sizes, corresponding to a mean SB of 24 ≲ <μe>r mag-1 arcsec2 ≲ 27 within the effective radius. We show that the UDG population represents the tail of galaxies formed in dwarf-sized haloes with higher-than-average angular momentum. By adopting the standard model of disc formation - in which the size of galaxies is set by the spin of the halo - we recover both the abundance of UDGs as a function of the host cluster mass and the distribution of sizes within the UDG population. According to this model, UDGs are not failed L* galaxies, but genuine dwarfs, and their low SB is not uniquely connected to the harsh cluster environment. We therefore expect a correspondingly abundant population of UDGs in the field, with possibly different morphologies and colours.

  16. Comparing Population Patterns to Processes: Abundance and Survival of a Forest Salamander following Habitat Degradation

    PubMed Central

    Otto, Clint R. V.; Roloff, Gary J.; Thames, Rachael E.

    2014-01-01

    Habitat degradation resulting from anthropogenic activities poses immediate and prolonged threats to biodiversity, particularly among declining amphibians. Many studies infer amphibian response to habitat degradation by correlating patterns in species occupancy or abundance with environmental effects, often without regard to the demographic processes underlying these patterns. We evaluated how retention of vertical green trees (CANOPY) and coarse woody debris (CWD) influenced terrestrial salamander abundance and apparent survival in recently clearcut forests. Estimated abundance of unmarked salamanders was positively related to CANOPY (Canopy  = 0.21 (0.02–1.19; 95% CI), but not CWD (CWD  = 0.11 (−0.13–0.35) within 3,600 m2 sites, whereas estimated abundance of unmarked salamanders was not related to CANOPY (Canopy  = −0.01 (−0.21–0.18) or CWD (CWD  = −0.02 (−0.23–0.19) for 9 m2 enclosures. In contrast, apparent survival of marked salamanders within our enclosures over 1 month was positively influenced by both CANOPY and CWD retention (Canopy  = 0.73 (0.27–1.19; 95% CI) and CWD  = 1.01 (0.53–1.50). Our results indicate that environmental correlates to abundance are scale dependent reflecting habitat selection processes and organism movements after a habitat disturbance event. Our study also provides a cautionary example of how scientific inference is conditional on the response variable(s), and scale(s) of measure chosen by the investigator, which can have important implications for species conservation and management. Our research highlights the need for joint evaluation of population state variables, such as abundance, and population-level process, such as survival, when assessing anthropogenic impacts on forest biodiversity. PMID:24718498

  17. Population Genetic Structure of Aedes fluviatilis (Diptera: Culicidae)

    PubMed Central

    Multini, Laura Cristina; Suesdek, Lincoln; Marrelli, Mauro Toledo

    2016-01-01

    Although Aedes fluviatilis is an anthropophilic mosquito found abundantly in urban environments, its biology, epidemiological potential and genetic characteristics are poorly understood. Climate change and urbanization processes that result in environmental modifications benefit certain anthropophilic mosquito species such as Ae. fluviatilis, greatly increasing their abundance in urban areas. To gain a better understanding of whether urbanization processes modulate the genetic structure of this species in the city of São Paulo, we used eight microsatellite loci to genetically characterize Ae. fluviatilis populations collected in nine urban parks in the city of São Paulo. Our results show that there is high gene flow among the populations of this species, heterozygosity deficiency and low genetic structure and that the species may have undergone a recent population expansion. There are two main hypotheses to explain these findings: (i) Ae. fluviatilis populations have undergone a population expansion as a result of urbanization; and (ii) as urbanization of the city of São Paulo occurred recently and was quite intense, the structuring of these populations cannot be observed yet, apart from in the populations of Ibirapuera and Piqueri parks, where the first signs of structuring have appeared. We believe that the expansion found in Ae. fluviatilis populations is probably correlated with the unplanned urbanization of the city of São Paulo, which transformed green areas into urbanized areas, as well as the increasing population density in the city. PMID:27598889

  18. Population Genetic Structure of Aedes fluviatilis (Diptera: Culicidae).

    PubMed

    Multini, Laura Cristina; Wilke, André Barretto Bruno; Suesdek, Lincoln; Marrelli, Mauro Toledo

    2016-01-01

    Although Aedes fluviatilis is an anthropophilic mosquito found abundantly in urban environments, its biology, epidemiological potential and genetic characteristics are poorly understood. Climate change and urbanization processes that result in environmental modifications benefit certain anthropophilic mosquito species such as Ae. fluviatilis, greatly increasing their abundance in urban areas. To gain a better understanding of whether urbanization processes modulate the genetic structure of this species in the city of São Paulo, we used eight microsatellite loci to genetically characterize Ae. fluviatilis populations collected in nine urban parks in the city of São Paulo. Our results show that there is high gene flow among the populations of this species, heterozygosity deficiency and low genetic structure and that the species may have undergone a recent population expansion. There are two main hypotheses to explain these findings: (i) Ae. fluviatilis populations have undergone a population expansion as a result of urbanization; and (ii) as urbanization of the city of São Paulo occurred recently and was quite intense, the structuring of these populations cannot be observed yet, apart from in the populations of Ibirapuera and Piqueri parks, where the first signs of structuring have appeared. We believe that the expansion found in Ae. fluviatilis populations is probably correlated with the unplanned urbanization of the city of São Paulo, which transformed green areas into urbanized areas, as well as the increasing population density in the city. PMID:27598889

  19. Possible sources of the Population I lithium abundance and light-element evolution

    NASA Technical Reports Server (NTRS)

    Brown, Lawrence E.

    1992-01-01

    One-zone numerical models of Galactic chemical evolution of the light elements (lithium, beryllium, boron, and deuterium) with a broad sample of possible stellar lithium production sites and star formation histories, including the multiple merger model of Mathews and Schramm (1992), are examined. Models with high primordial lithium are constrained by observations of lithium and potassium in the interstellar medium of the LMC to have Li abundances close to the Population I value of about 10 exp -9. Li-7 production in intermediate- or high-mass stars (greater than 4 solar masses) is found to fit observations somewhat better than production in low-mass (1-5 solar masses) stars. Since elevated levels of lithium are commonly observed in intermediate-mass stars in the LMC, it is argued that this is indeed the major source of the Population I Li-7 abundance.

  20. Ecological niche structure and rangewide abundance patterns of species.

    PubMed

    Martínez-Meyer, Enrique; Díaz-Porras, Daniel; Peterson, A Townsend; Yáñez-Arenas, Carlos

    2013-02-23

    Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance-ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space. PMID:23134784

  1. Age and Abundance Discrimination in Old Stellar Populations Using Mid-Ultraviolet Colors

    NASA Astrophysics Data System (ADS)

    Dorman, Ben; O'Connell, Robert W.; Rood, Robert T.

    2003-07-01

    The rest-frame mid-ultraviolet spectral region (2000-3200 Å) is important in analyzing the stellar populations of the ``red envelope'' systems observed at high redshifts. Here we explore the usefulness of the mid-UV for determining ages and abundances of old populations. We work with a theoretical set of low-resolution spectra and broadband colors because tests show that these are at present more realistic than high-resolution models. A mid-UV to optical/IR wavelength baseline provides good separation of population components because the main-sequence turnoff dominates the integrated light between 2500 and 4000 Å. Mid-UV spectral features are not sensitive to the dwarf/giant mixture in the population, unlike those in the optical region. We find a 6 mag difference in the mid-UV continuum level (normalized at V) over the metallicity range -1.5abundance are 3-10 times larger than for the UBV region. Most of the spectral information on old populations therefore resides below 4000 Å. Measurement of a single mid-UV color is capable of placing a strong lower bound on the mean metallicity of an old population. We investigate the capability of UBV and mid-UV broadband colors to separately determine age and abundance, taking into account precision in the color measurements. We find that the mid-UV improves resolution in logt, logZ space by about a factor of 3 for a given observational precision. Contamination by hot, post-He flash evolutionary phases can seriously affect the mid-UV spectra of old populations. A simple estimate shows that contamination can reach over 80% in some cases. However, this is straightforward to remove as long as far-UV measurements are available. We find that extinction should have relatively small effects on parameters derived for old populations from the mid-UV. Finally, we show

  2. Linking TFT-LCD wastewater treatment performance to microbial population abundance of Hyphomicrobium and Thiobacillus spp.

    PubMed

    Fukushima, Toshikazu; Whang, Liang-Ming; Chen, Po-Chun; Putri, Dyah Wulandari; Chang, Ming-Yu; Wu, Yi-Ju; Lee, Ya-Ching

    2013-08-01

    This study investigated the linkage between performance of two full-scale membrane bioreactor (MBR) systems treating thin-film transistor liquid crystal display (TFT-LCD) wastewater and the population dynamics of dimethylsulfoxide (DMSO)/dimethylsulfide (DMS) degrading bacteria. High DMSO degradation efficiencies were achieved in both MBRs, while the levels of nitrification inhibition due to DMS production from DMSO degradation were different in the two MBRs. The results of real-time PCR targeting on DMSO/DMS degrading populations, including Hyphomicrobium and Thiobacillus spp., indicated that a higher DMSO oxidation efficiency occurred at a higher Hyphomicrobium spp. abundance in the systems, suggesting that Hyphomicrobium spp. may be more important for complete DMSO oxidation to sulfate compared with Thiobacillus spp. Furthermore, Thiobacillus spp. was more abundant during poor nitrification, while Hyphomicrobium spp. was more abundant during good nitrification. It is suggested that microbial population of DMSO/DMS degrading bacteria is closely linking to both DMSO/DMS degradation efficiency and nitrification performance. PMID:23628318

  3. Rainfall influences on ungulate population abundance in the Mara-Serengeti ecosystem.

    PubMed

    Ogutu, J O; Piepho, H-P; Dublin, H T; Bhola, N; Reid, R S

    2008-07-01

    1. Rainfall is the prime climatic factor underpinning the dynamics of African savanna ungulates, but no study has analysed its influence on the abundance of these ungulates at monthly to multiannual time scales. 2. We report relationships between rainfall and changes in age- and sex-structured abundances of seven ungulate species monitored monthly for 15 years using vehicle ground counts in the Maasai Mara National Reserve, Kenya. 3. Abundance showed strong and curvilinear relationships with current and cumulative rainfall, with older topi, Damaliscus korrigum (Ogilby); warthog, Phacochoerus aethiopicus (Pallas); waterbuck, Kobus ellipsyprimnus (Ogilby); and impala, Aepyceros melampus (Lichtenstein) responding to longer lags than younger animals, portraying carryover effects of prior habitat conditions. 4. The abundances of newborn calves were best correlated with monthly rainfall averaged over the preceding 5-6 months for topi, waterbuck, warthog, and 2 months for the migratory zebra Equus burchelli (Gray), but with seasonal rainfall averaged over 2-5 years for giraffe, Giraffa camelopardalis (L.); impala; and kongoni, Alcelaphus busephalus (Pallas). The cumulative late wet-season rainfall was the best predictor of abundance for quarter- to full-grown animals for most species. Monthly rainfall exerted both negative and positive effects on the abundances of zebra, impala and waterbuck. Ignoring age, both sexes responded similarly to rainfall. 5. Births were strongly seasonal only for warthog and topi, but peaked between August and December for most species. Hence abundance was strongly seasonal for young topi and warthog and the migratory zebra. Pronounced seasonality in births for warthog and topi obliterated otherwise strong relationships between abundance and rainfall when both month and rainfall were included in the same model. Aggregated density produced relationships with rainfall similar to those for fully grown animals, emphasizing the necessity of

  4. Population Signatures in Planetary Nebulae from Abundances of Fe-group and Neutron-Capture Elements

    NASA Astrophysics Data System (ADS)

    Dinerstein, Harriet L.; Geballe, Thomas R.; Sterling, N. C.

    2015-08-01

    There are two categories of elements for which abundances are measured in planetary nebulae (PNe). The first are species whose abundances may be modified by nuclear reactions in the star prior to PN formation, such as He, C, N, and nuclei made by slow neutron captures (Karakas & Lattanzio 2014, PASA, 31, 30). In contrast, elements unaffected by evolution should indicate the star’s initial composition. These include S, Ar, Cl, and (with certain exceptions) O and Ne, most of which are alpha species. A long-missing piece of the puzzle has been the abundances of the Fe-group elements. We cannot determine a meaningful elemental abundance from the gas-phase Fe lines seen in PNe, since Fe is heavily depleted into dust. Another approach is to use a different element as a proxy for Fe. Dinerstein & Geballe (2001, ApJ, 562, 515) identified a line at 3.625 μm as due to Zn, the least refractory Fe-group element. Observations of this line in Milky Way PNe yield -1 ≤ [Zn/H] ≤ 0 (Smith, Zijlstra, & Dinerstein 2014, MNRAS, 441, 3161; Dinerstein et al. 2015, in preparation). Substituting Zn for Fe, PNe can be placed in the [alpha/Fe] vs. [Fe/H] diagram used to characterize stellar populations. Dividing our sample into probable thin and thick disk members using the kinematic criterion of Peimbert’s Type II and III classes (1978, IAU Symp. 76, 215), we find that they occupy similar regions in [alpha/Fe] vs. [Fe/H] phase space as the stars of those populations. Elevated [alpha/Fe] values at subsolar [Fe/H], which tend to be higher for thick than thin disk PNe, cause degeneracies that make alpha species ambiguous metallicity indicators. This is important for self-enrichment studies, since if the initial abundance of an element is lower than projected from an alpha species, internal synthesis may be required to produce even a solar final abundance. Low observed abundances of the n-capture element Se suggest that many Type III PNe may have subsolar initial abundances of n

  5. Microbial abundance and community structure in a melting alpine snowpack.

    PubMed

    Lazzaro, Anna; Wismer, Andrea; Schneebeli, Martin; Erny, Isolde; Zeyer, Josef

    2015-05-01

    Snowmelt is a crucial period for alpine soil ecosystems, as it is related to inputs of nutrients, particulate matter and microorganisms to the underlying soil. Although snow-inhabiting microbial communities represent an important inoculum for soils, they have thus far received little attention. The distribution and structure of these microorganisms in the snowpack may be linked to the physical properties of the snowpack at snowmelt. Snow samples were taken from snow profiles at four sites (1930-2519 m a.s.l.) in the catchment of the Tiefengletscher, Canton Uri, Switzerland. Microbial (Archaea, Bacteria and Fungi) communities were investigated through T-RFLP profiling of the 16S and 18S rRNA genes, respectively. In parallel, we assessed physical and chemical parameters relevant to the understanding of melting processes. Along the snow profiles, density increased with depth due to compaction, while other physico-chemical parameters, such as temperature and concentrations of DOC and soluble ions, remained in the same range (e.g. <2 mg DOC L(-1), 5-30 μg NH4 (+)-N L(-1)) in all samples at all sites. Along the snow profiles, no major change was observed either in cell abundance or in bacterial and fungal diversity. No Archaea could be detected in the snow. Microbial communities, however, differed significantly between sites. Our results show that meltwater rearranges soluble ions and microbial communities in the snowpack.

  6. [Composition, abundance and distribution of populations of commercially important gastropods in La Guajira, Colombian Caribbean].

    PubMed

    Nieto-Bernal, Ramón; Luis, Chasqui; Rodriguez, Angélica María; Castro, Erick; Gil-Agudelo, Diego L

    2013-06-01

    In the continental Colombian Caribbean the conch resource exploitation and the status of snails populations has been poorly studied, which are reflected in the lack of fisheries management. This study assesses composition, population density and distribution of the gastropods species that make conch resource in La Guajira region. Underwater visual censuses for snails were performed between September-November 2009 in 145100x4m (400m2) transects, spanning a total area of 56920m2 between Riohacha and Cabo de la Vela. The study was complemented with the evaluation of composition, abundance and size of gastropods conch found in the discarded-by-fishermen shell mounds in 13 beaches. In October 2010 another 40 transects were evaluated (16 000 m2) from the Southern of Riohacha to the Camarones village (La Guajira). We found a total of 9911 snails belonging to 12 species, the most abundant being Strombus pugilis with 8 912 individuals and an average density of 1 538.4 +/- 3 662.6 ind./ha, followed by Vasum muricatum with 374 individuals and an average density of 51.8 +/- 91.2 ind./ha. Calculating the importance value index (IVI) for both living organisms as the empty shells on beaches, shows that Turbinella angulata is the most used species by artisanal fishermen in the region. Cassis madagascariensis and Cassis tuberosa are also important snail resources in the region (as suggested by the number of empty shells found in beaches), but its densities were low. Strombus gigas, with only three living organisms found in the area, presented the lowest abundance ever found in the Colombian Caribbean (0.52 +/- 3.6 ind./ha), showing that queen conch population in La Guajira cannot support commercial exploitation. The abundance of discarded S. gigas shells on beaches suggests resource exploitation in the recent past. Results remarks the urgency of implementing management plans for snail fisheries in the region.

  7. [Composition, abundance and distribution of populations of commercially important gastropods in La Guajira, Colombian Caribbean].

    PubMed

    Nieto-Bernal, Ramón; Luis, Chasqui; Rodriguez, Angélica María; Castro, Erick; Gil-Agudelo, Diego L

    2013-06-01

    In the continental Colombian Caribbean the conch resource exploitation and the status of snails populations has been poorly studied, which are reflected in the lack of fisheries management. This study assesses composition, population density and distribution of the gastropods species that make conch resource in La Guajira region. Underwater visual censuses for snails were performed between September-November 2009 in 145100x4m (400m2) transects, spanning a total area of 56920m2 between Riohacha and Cabo de la Vela. The study was complemented with the evaluation of composition, abundance and size of gastropods conch found in the discarded-by-fishermen shell mounds in 13 beaches. In October 2010 another 40 transects were evaluated (16 000 m2) from the Southern of Riohacha to the Camarones village (La Guajira). We found a total of 9911 snails belonging to 12 species, the most abundant being Strombus pugilis with 8 912 individuals and an average density of 1 538.4 +/- 3 662.6 ind./ha, followed by Vasum muricatum with 374 individuals and an average density of 51.8 +/- 91.2 ind./ha. Calculating the importance value index (IVI) for both living organisms as the empty shells on beaches, shows that Turbinella angulata is the most used species by artisanal fishermen in the region. Cassis madagascariensis and Cassis tuberosa are also important snail resources in the region (as suggested by the number of empty shells found in beaches), but its densities were low. Strombus gigas, with only three living organisms found in the area, presented the lowest abundance ever found in the Colombian Caribbean (0.52 +/- 3.6 ind./ha), showing that queen conch population in La Guajira cannot support commercial exploitation. The abundance of discarded S. gigas shells on beaches suggests resource exploitation in the recent past. Results remarks the urgency of implementing management plans for snail fisheries in the region. PMID:23885583

  8. Deer herbivory reduces web-building spider abundance by simplifying forest vegetation structure

    PubMed Central

    Chips, Michael J.; Carson, Walter P.

    2016-01-01

    Indirect ecological effects are a common feature of ecological systems, arising when one species affects interactions among two or more other species. We examined how browsing by white-tailed deer (Odocoileus virginianus) indirectly affected the abundance and composition of a web-building spider guild through their effects on the structure of the ground and shrub layers of northern hardwood forests. We examined paired plots consisting of deer-free and control plots in the Allegheny Plateau region Pennsylvania and Northern Highlands region of Wisconsin. We recorded the abundance of seven types of webs, each corresponding to a family of web-building spiders. We quantified vegetation structure and habitat suitability for the spiders by computing a web scaffold availability index (WSAI) at 0.5 m and 1.0 m above the ground. At Northern Highlands sites, we recorded prey availability. Spider webs were twice as abundant in deer-free plots compared to control plots, while WSAI was 7–12 times greater in deerfree plots. Prey availability was lower in deer-free plots. With the exception of funnel web-builders, all spider web types were significantly more abundant in deer-free plots. Both deer exclusion and the geographic region of plots were significant predictors of spider community structure. In closed canopy forests with high browsing pressure, the low density of tree saplings and shrubs provides few locations for web-building spiders to anchor webs. Recruitment of these spiders may become coupled with forest disturbance events that increase tree and shrub recruitment. By modifying habitat structure, deer appear to indirectly modify arthropod food web interactions. As deer populations have increased in eastern North America over the past several decades, the effects of deer on web-building spiders may be widespread. PMID:27703868

  9. Modeling structured population dynamics using data from unmarked individuals

    USGS Publications Warehouse

    Grant, Evan H. Campbell; Zipkin, Elise; Thorson, James T.; See, Kevin; Lynch, Heather J.; Kanno, Yoichiro; Chandler, Richard; Letcher, Benjamin H.; Royle, J. Andrew

    2014-01-01

    The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.

  10. In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake

    PubMed Central

    Salcher, Michaela M; Posch, Thomas; Pernthaler, Jakob

    2013-01-01

    The substrate partitioning of sympatric populations of freshwater bacterioplankton was studied via microautoradiography and fluorescence in situ hybridization. Fourteen radiolabeled tracers were used to assess microbial acquisition spectra of low-molecular-weight (LMW) organic compounds. The most abundant group, ac1 Actinobacteria, were highly active in leucine, thymidine and glucose assimilation, whereas Alphaproteobacteria from the LD12 lineage (the freshwater sister clade of SAR11) only weakly incorporated these tracers, but exhibited a distinct preference for glutamine and glutamate. Different Bacteroidetes showed contrasting uptake patterns: Flavobacteriales did not incorporate significant amounts of any LMW compound, and Cyclobacteriaceae were clearly specialized on leucine, glucose and arginine. Betaproteobacteria represented the most active and versatile bacterioplankton fraction and >90% of them could be assigned to eight species- to genus-like populations with contrasting substrate specialization. Limnohabitans sp. were the most abundant and active Betaproteobacteria, incorporating almost all tracers. While three closely related betaproteobacterial populations substantially differed in their uptake spectra, two more distantly related lineages had very similar preferences, and one population did not incorporate any tracer. The dominant phototrophic microorganism, the filamentous cyanobacterium Planktothrix rubescens, assimilated several substrates, whereas other (pico)cyanobacteria had no heterotrophic activity. The variable extent of specialization by the studied bacterial taxa on subsets of LMW compounds contrasts theoretical considerations about non-selective microbial substrate assimilation at oligotrophic conditions. This physiological niche separation might be one explanation for the coexistence of freshwater bacterioplankton species in a seemingly uniform environment. PMID:23235289

  11. Ecological niche structure and rangewide abundance patterns of species

    PubMed Central

    Martínez-Meyer, Enrique; Díaz-Porras, Daniel; Peterson, A. Townsend; Yáñez-Arenas, Carlos

    2013-01-01

    Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance–ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space. PMID:23134784

  12. Estimating snow leopard population abundance using photography and capture-recapture techniques

    USGS Publications Warehouse

    Jackson, R.M.; Roe, J.D.; Wangchuk, R.; Hunter, D.O.

    2006-01-01

    Conservation and management of snow leopards (Uncia uncia) has largely relied on anecdotal evidence and presence-absence data due to their cryptic nature and the difficult terrain they inhabit. These methods generally lack the scientific rigor necessary to accurately estimate population size and monitor trends. We evaluated the use of photography in capture-mark-recapture (CMR) techniques for estimating snow leopard population abundance and density within Hemis National Park, Ladakh, India. We placed infrared camera traps along actively used travel paths, scent-sprayed rocks, and scrape sites within 16- to 30-km2 sampling grids in successive winters during January and March 2003-2004. We used head-on, oblique, and side-view camera configurations to obtain snow leopard photographs at varying body orientations. We calculated snow leopard abundance estimates using the program CAPTURE. We obtained a total of 66 and 49 snow leopard captures resulting in 8.91 and 5.63 individuals per 100 trap-nights during 2003 and 2004, respectively. We identified snow leopards based on the distinct pelage patterns located primarily on the forelimbs, flanks, and dorsal surface of the tail. Capture probabilities ranged from 0.33 to 0.67. Density estimates ranged from 8.49 (SE = 0.22; individuals per 100 km2 in 2003 to 4.45 (SE = 0.16) in 2004. We believe the density disparity between years is attributable to different trap density and placement rather than to an actual decline in population size. Our results suggest that photographic capture-mark-recapture sampling may be a useful tool for monitoring demographic patterns. However, we believe a larger sample size would be necessary for generating a statistically robust estimate of population density and abundance based on CMR models.

  13. Field population abundance of leafhopper (Homoptera: Cicadelidae) and planthopper (Homoptera: Delphacidae) as affected by rice growth stages

    NASA Astrophysics Data System (ADS)

    Hafizal, M. M.; Idris, A. B.

    2013-11-01

    The leafhopper (Homoptera: Delphacidae) and planthopper (Homoptera: Cicadelidae) are considered as important rice pest in Asia including Malaysia. As phloem-feeders, they can cause loss to rice growth development and their population abundance is thought to be influenced by rice growth stages. This study was conducted to examine the population of Delphacidae and Cicadelidae between different rice growth stages, i.e. before and after rice planting periods. Monthly sampling was conducted in three sites in Kuala Selangor at before planting, vegetative, reproductive, maturing stages and post-harvest period using sweeping net and light traps. Population abundance of Delphacidae and Cicadelidae were found to be significantly different and positively correlated with different rice growth stages (p<0.05). Delphacidae was most abundance during maturing stages, while the abundance of Cicadelidae peaked during reproductive stage of rice growth. Differences in temporal abundance of the population of these two homopterans indicated adaptive feeding strategy to reduce food competition.

  14. Direct reciprocity in structured populations.

    PubMed

    van Veelen, Matthijs; García, Julián; Rand, David G; Nowak, Martin A

    2012-06-19

    Reciprocity and repeated games have been at the center of attention when studying the evolution of human cooperation. Direct reciprocity is considered to be a powerful mechanism for the evolution of cooperation, and it is generally assumed that it can lead to high levels of cooperation. Here we explore an open-ended, infinite strategy space, where every strategy that can be encoded by a finite state automaton is a possible mutant. Surprisingly, we find that direct reciprocity alone does not lead to high levels of cooperation. Instead we observe perpetual oscillations between cooperation and defection, with defection being substantially more frequent than cooperation. The reason for this is that "indirect invasions" remove equilibrium strategies: every strategy has neutral mutants, which in turn can be invaded by other strategies. However, reciprocity is not the only way to promote cooperation. Another mechanism for the evolution of cooperation, which has received as much attention, is assortment because of population structure. Here we develop a theory that allows us to study the synergistic interaction between direct reciprocity and assortment. This framework is particularly well suited for understanding human interactions, which are typically repeated and occur in relatively fluid but not unstructured populations. We show that if repeated games are combined with only a small amount of assortment, then natural selection favors the behavior typically observed among humans: high levels of cooperation implemented using conditional strategies.

  15. Genetics of single-cell protein abundance variation in large yeast populations

    NASA Astrophysics Data System (ADS)

    Albert, Frank W.; Treusch, Sebastian; Shockley, Arthur H.; Bloom, Joshua S.; Kruglyak, Leonid

    2014-02-01

    Variation among individuals arises in part from differences in DNA sequences, but the genetic basis for variation in most traits, including common diseases, remains only partly understood. Many DNA variants influence phenotypes by altering the expression level of one or several genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL). Traditional eQTL mapping requires large-scale genotype and gene expression data for each individual in the study sample, which limits sample sizes to hundreds of individuals in both humans and model organisms and reduces statistical power. Consequently, many eQTL are probably missed, especially those with smaller effects. Furthermore, most studies use messenger RNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics reported unexpected differences between eQTL and protein QTL (pQTL) for the same genes, but these studies have been even more limited in scope. Here we introduce a powerful method for identifying genetic loci that influence protein expression in the yeast Saccharomyces cerevisiae. We measure single-cell protein abundance through the use of green fluorescent protein tags in very large populations of genetically variable cells, and use pooled sequencing to compare allele frequencies across the genome in thousands of individuals with high versus low protein abundance. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci that we detected were clustered in `hotspots' that influence multiple proteins, and some hotspots were found to influence more than half of the proteins that we examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell

  16. Genetics of single-cell protein abundance variation in large yeast populations

    PubMed Central

    Albert, Frank W.; Treusch, Sebastian; Shockley, Arthur H.; Bloom, Joshua S.; Kruglyak, Leonid

    2014-01-01

    Variation among individuals arises in part from differences in DNA sequences, but the genetic basis for variation in most traits, including common diseases, remains only partly understood. Many DNA variants influence phenotypes by altering the expression level of one or multiple genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL) 1. Traditional eQTL mapping requires large-scale genotype and gene expression data for each individual in the study sample, which limits sample sizes to hundreds of individuals in both humans and model organisms and reduces statistical power 2–6. Consequently, many eQTL are likely missed, especially those with smaller effects 7. Further, most studies use mRNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics 8–13 reported surprising differences between eQTL and protein QTL (pQTL) for the same genes 9,10, but these studies have been even more limited in scope. Here, we introduce a powerful method for identifying genetic loci that influence protein expression in the yeast Saccharomyes cerevisiae. We measure single-cell protein abundance through the use of green-fluorescent-protein tags in very large populations of genetically variable cells, and use pooled sequencing to compare allele frequencies across the genome in thousands of individuals with high vs. low protein abundance. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci cluster at hotspot locations that influence multiple proteins—in some cases, more than half of those examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell physiology between yeast strains. PMID:24402228

  17. Abundance and phenology patterns of two pond-breeding salamanders determine species interactions in natural populations.

    PubMed

    Anderson, Thomas L; Hocking, Daniel J; Conner, Christopher A; Earl, Julia E; Harper, Elizabeth B; Osbourn, Michael S; Peterman, William E; Rittenhouse, Tracy A G; Semlitsch, Raymond D

    2015-03-01

    Phenology often determines the outcome of interspecific interactions, where early-arriving species often dominate interactions over those arriving later. The effects of phenology on species interactions are especially pronounced in aquatic systems, but the evidence is largely derived from experimental studies. We examined whether differences in breeding phenology between two pond-breeding salamanders (Ambystoma annulatum and A. maculatum) affected metamorph recruitment and demographic traits within natural populations, with the expectation that the fall-breeding A. annulatum would negatively affect the spring-breeding A. maculatum. We monitored populations of each species at five ponds over 4 years using drift fences. Metamorph abundance and survival of A. annulatum were affected by intra- and interspecific processes, whereas metamorph size and date of emigration were primarily influenced by intraspecific effects. Metamorph abundance, snout-vent length, date of emigration and survival for A. maculatum were all predicted by combinations of intra- and interspecific effects, but often showed negative relationships with A. annulatum metamorph traits and abundance. Size and date of metamorphosis were strongly correlated within each species, but in opposite patterns (negative for A. annulatum and positive for A. maculatum), suggesting that the two species use alternative strategies to enhance terrestrial survival and that these factors may influence their interactions. Our results match predictions from experimental studies that suggest recruitment is influenced by intra- and interspecific processes which are determined by phenological differences between species. Incorporating spatiotemporal variability when modeling population dynamics is necessary to understand the importance of phenology in species interactions, especially as shifts in phenology occur under climate change.

  18. Abundance and phenology patterns of two pond-breeding salamanders determine species interactions in natural populations.

    PubMed

    Anderson, Thomas L; Hocking, Daniel J; Conner, Christopher A; Earl, Julia E; Harper, Elizabeth B; Osbourn, Michael S; Peterman, William E; Rittenhouse, Tracy A G; Semlitsch, Raymond D

    2015-03-01

    Phenology often determines the outcome of interspecific interactions, where early-arriving species often dominate interactions over those arriving later. The effects of phenology on species interactions are especially pronounced in aquatic systems, but the evidence is largely derived from experimental studies. We examined whether differences in breeding phenology between two pond-breeding salamanders (Ambystoma annulatum and A. maculatum) affected metamorph recruitment and demographic traits within natural populations, with the expectation that the fall-breeding A. annulatum would negatively affect the spring-breeding A. maculatum. We monitored populations of each species at five ponds over 4 years using drift fences. Metamorph abundance and survival of A. annulatum were affected by intra- and interspecific processes, whereas metamorph size and date of emigration were primarily influenced by intraspecific effects. Metamorph abundance, snout-vent length, date of emigration and survival for A. maculatum were all predicted by combinations of intra- and interspecific effects, but often showed negative relationships with A. annulatum metamorph traits and abundance. Size and date of metamorphosis were strongly correlated within each species, but in opposite patterns (negative for A. annulatum and positive for A. maculatum), suggesting that the two species use alternative strategies to enhance terrestrial survival and that these factors may influence their interactions. Our results match predictions from experimental studies that suggest recruitment is influenced by intra- and interspecific processes which are determined by phenological differences between species. Incorporating spatiotemporal variability when modeling population dynamics is necessary to understand the importance of phenology in species interactions, especially as shifts in phenology occur under climate change. PMID:25413866

  19. Does White Clover (Trifolium repens) Abundance in Temperate Pastures Determine Sitona obsoletus (Coleoptera: Curculionidae) Larval Populations?

    PubMed Central

    McNeill, Mark R.; van Koten, Chikako; Cave, Vanessa M.; Chapman, David; Hodgson, Hamish

    2016-01-01

    To determine if host plant abundance determined the size of clover root weevil (CRW) Sitona obsoletus larval populations, a study was conducted over 4 years in plots sown in ryegrass (Lolium perenne) (cv. Nui) sown at either 6 or 30 kg/ha and white clover (Trifolium repens) sown at a uniform rate of 8 kg/ha. This provided a range of % white clover content to investigate CRW population establishment and impacts on white clover survival. Larval sampling was carried out in spring (October) when larval densities are near their spring peak at Lincoln (Canterbury, New Zealand) with % clover measured in autumn (April) and spring (September) of each year. Overall, mean larval densities measured in spring 2012–2015 were 310, 38, 59, and 31 larvae m-2, respectively. There was a significant decline in larval populations between 2012 and 2013, but spring populations were relatively uniform thereafter. The mean % white clover measured in autumns of 2012 to 2015 was 17, 10, 3, and 11%, respectively. In comparison, mean spring % white clover from 2012 to 2015, averaged c. 5% each year. Analysis relating spring (October) larval populations to % white clover measured in each plot in autumn (April) found the 2012 larval population to be statistically significantly larger in the ryegrass 6 kg/ha plots than 30 kg/ha plots. Thereafter, sowing rate had no significant effect on larval populations. From 2013 to 2015, spring larval populations had a negative relationship with the previous autumn % white clover with the relationship highly significant for the 2014 data. When CRW larval populations in spring 2013 to 2015 were predicted from the 2013 to 2015 autumn % white clover, respectively, based on their positive relationship in 2012, the predicted densities were substantially larger than those observed. Conversely, when 2015 spring larval data and % clover was regressed against 2012–2014 larval populations, observed densities tended to be higher than predicted, but the numbers came

  20. Does White Clover (Trifolium repens) Abundance in Temperate Pastures Determine Sitona obsoletus (Coleoptera: Curculionidae) Larval Populations?

    PubMed Central

    McNeill, Mark R.; van Koten, Chikako; Cave, Vanessa M.; Chapman, David; Hodgson, Hamish

    2016-01-01

    To determine if host plant abundance determined the size of clover root weevil (CRW) Sitona obsoletus larval populations, a study was conducted over 4 years in plots sown in ryegrass (Lolium perenne) (cv. Nui) sown at either 6 or 30 kg/ha and white clover (Trifolium repens) sown at a uniform rate of 8 kg/ha. This provided a range of % white clover content to investigate CRW population establishment and impacts on white clover survival. Larval sampling was carried out in spring (October) when larval densities are near their spring peak at Lincoln (Canterbury, New Zealand) with % clover measured in autumn (April) and spring (September) of each year. Overall, mean larval densities measured in spring 2012–2015 were 310, 38, 59, and 31 larvae m-2, respectively. There was a significant decline in larval populations between 2012 and 2013, but spring populations were relatively uniform thereafter. The mean % white clover measured in autumns of 2012 to 2015 was 17, 10, 3, and 11%, respectively. In comparison, mean spring % white clover from 2012 to 2015, averaged c. 5% each year. Analysis relating spring (October) larval populations to % white clover measured in each plot in autumn (April) found the 2012 larval population to be statistically significantly larger in the ryegrass 6 kg/ha plots than 30 kg/ha plots. Thereafter, sowing rate had no significant effect on larval populations. From 2013 to 2015, spring larval populations had a negative relationship with the previous autumn % white clover with the relationship highly significant for the 2014 data. When CRW larval populations in spring 2013 to 2015 were predicted from the 2013 to 2015 autumn % white clover, respectively, based on their positive relationship in 2012, the predicted densities were substantially larger than those observed. Conversely, when 2015 spring larval data and % clover was regressed against 2012–2014 larval populations, observed densities tended to be higher than predicted, but the numbers came

  1. Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA.

    PubMed

    Lodge, David M; Turner, Cameron R; Jerde, Christopher L; Barnes, Matthew A; Chadderton, Lindsay; Egan, Scott P; Feder, Jeffrey L; Mahon, Andrew R; Pfrender, Michael E

    2012-06-01

    Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, 'early detection and rapid response'; (ii) for conserving imperilled native species, 'protection of biodiversity hotspots'; and (iii) for assessing biosecurity risk, 'an ounce of prevention equals a pound of cure.' However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism's DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next-generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.

  2. Regional distribution shifts help explain local changes in wintering raptor abundance: implications for interpreting population trends.

    PubMed

    Paprocki, Neil; Heath, Julie A; Novak, Stephen J

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975-2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr(-1) and 7.74 km yr(-1) shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  3. Regional Distribution Shifts Help Explain Local Changes in Wintering Raptor Abundance: Implications for Interpreting Population Trends

    PubMed Central

    Paprocki, Neil; Heath, Julie A.; Novak, Stephen J.

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975–2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr−1 and 7.74 km yr−1 shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  4. Regional distribution shifts help explain local changes in wintering raptor abundance: implications for interpreting population trends.

    PubMed

    Paprocki, Neil; Heath, Julie A; Novak, Stephen J

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975-2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr(-1) and 7.74 km yr(-1) shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  5. Assessing small mammal abundance with track-tube indices and mark-recapture population estimates

    USGS Publications Warehouse

    Wiewel, A.S.; Clark, W.R.; Sovada, M.A.

    2007-01-01

    We compared track-tube sampling with mark-recapture livetrapping and evaluated a track-tube index, defined as the number of track tubes with identifiable small mammal tracks during a 4-night period, as a predictor of small mammal abundance estimates in North Dakota grasslands. Meadow voles (Microtus pennsylvanicus) were the most commonly recorded species by both methods, but were underrepresented in track-tube sampling, whereas 13-lined ground squirrels (Spermophilus tridecemlineatus) and Franklin's ground squirrels (S. franklinii) were overrepresented in track-tube sampling. Estimates of average species richness were lower from track tubes than from livetrapping. Regression models revealed that the track-tube index was at best a moderately good predictor of small mammal population estimates because both the form (linear versus curvilinear) and slope of the relationship varied between years. In addition, 95% prediction intervals indicated low precision when predicting population estimates from new track-tube index observations. Track tubes required less time and expense than mark-recapture and eliminated handling of small mammals. Using track tubes along with mark-recapture in a double sampling for regression framework would have potential value when attempting to estimate abundance of small mammals over large areas. ?? 2007 American Society of Mammalogists.

  6. Constraining Stellar Population Models. I. Age, Metallicity and Abundance Pattern Compilation for Galactic Globular Clusters

    NASA Astrophysics Data System (ADS)

    Roediger, Joel C.; Courteau, Stéphane; Graves, Genevieve; Schiavon, Ricardo P.

    2014-01-01

    We present an extensive literature compilation of age, metallicity, and chemical abundance pattern information for the 41 Galactic globular clusters (GGCs) studied by Schiavon et al. Our compilation constitutes a notable improvement over previous similar work, particularly in terms of chemical abundances. Its primary purpose is to enable detailed evaluations of and refinements to stellar population synthesis models designed to recover the above information for unresolved stellar systems based on their integrated spectra. However, since the Schiavon sample spans a wide range of the known GGC parameter space, our compilation may also benefit investigations related to a variety of astrophysical endeavors, such as the early formation of the Milky Way, the chemical evolution of GGCs, and stellar evolution and nucleosynthesis. For instance, we confirm with our compiled data that the GGC system has a bimodal metallicity distribution and is uniformly enhanced in the α elements. When paired with the ages of our clusters, we find evidence that supports a scenario whereby the Milky Way obtained its globular clusters through two channels: in situ formation and accretion of satellite galaxies. The distributions of C, N, O, and Na abundances and the dispersions thereof per cluster corroborate the known fact that all GGCs studied so far with respect to multiple stellar populations have been found to harbor them. Finally, using data on individual stars, we verify that stellar atmospheres become progressively polluted by CN(O)-processed material after they leave the main sequence. We also uncover evidence which suggests that the α elements Mg and Ca may originate from more than one nucleosynthetic production site. We estimate that our compilation incorporates all relevant analyses from the literature up to mid-2012. As an aid to investigators in the fields named above, we provide detailed electronic tables of the data upon which our work is based at http

  7. INTERACTIONS BETWEEN BYTHOTREPHES CEDERSTROEMI AND LEPTODORA KINDTII INFERRED FROM SEASONAL POPULATION ABUNDANCE PATTERNS IN LAKE MICHIGAMME, MICHIGAN, USA

    EPA Science Inventory


    Bythotrephes cederstroemi is a non-indigenous predaceous zooplankter invading North American freshwater lakes in the Great Lakes region. We present seasonal population abundance values for both Bythotrephes and Leptodora kindtii from Lake Michigamme, Michigan for the years ...

  8. A Rainfall- and Temperature-Driven Abundance Model for Aedes albopictus Populations

    PubMed Central

    Tran, Annelise; L’Ambert, Grégory; Lacour, Guillaume; Benoît, Romain; Demarchi, Marie; Cros, Myriam; Cailly, Priscilla; Aubry-Kientz, Mélaine; Balenghien, Thomas; Ezanno, Pauline

    2013-01-01

    The mosquito Aedes (Stegomyia) albopictus (Skuse) (Diptera: Culicidae) is an invasive species which has colonized Southern Europe in the last two decades. As it is a competent vector for several arboviruses, its spread is of increasing public health concern, and there is a need for appropriate monitoring tools. In this paper, we have developed a modelling approach to predict mosquito abundance over time, and identify the main determinants of mosquito population dynamics. The model is temperature- and rainfall-driven, takes into account egg diapause during unfavourable periods, and was used to model the population dynamics of Ae. albopictus in the French Riviera since 2008. Entomological collections of egg stage from six locations in Nice conurbation were used for model validation. We performed a sensitivity analysis to identify the key parameters of the mosquito population dynamics. Results showed that the model correctly predicted entomological field data (Pearson r correlation coefficient values range from 0.73 to 0.93). The model’s main control points were related to adult’s mortality rates, the carrying capacity in pupae of the environment, and the beginning of the unfavourable period. The proposed model can be efficiently used as a tool to predict Ae. albopictus population dynamics, and to assess the efficiency of different control strategies. PMID:23624579

  9. Ordering structured populations in multiplayer cooperation games

    PubMed Central

    Peña, Jorge; Wu, Bin; Traulsen, Arne

    2016-01-01

    Spatial structure greatly affects the evolution of cooperation. While in two-player games the condition for cooperation to evolve depends on a single structure coefficient, in multiplayer games the condition might depend on several structure coefficients, making it difficult to compare different population structures. We propose a solution to this issue by introducing two simple ways of ordering population structures: the containment order and the volume order. If population structure is greater than population structure in the containment or the volume order, then can be considered a stronger promoter of cooperation. We provide conditions for establishing the containment order, give general results on the volume order, and illustrate our theory by comparing different models of spatial games and associated update rules. Our results hold for a large class of population structures and can be easily applied to specific cases once the structure coefficients have been calculated or estimated. PMID:26819335

  10. Mountain goat abundance and population trends in the Olympic Mountains, Washington, 2011

    USGS Publications Warehouse

    Jenkins, Kurt; Happe, Patricia; Griffin, Paul C.; Beirne, Katherine; Hoffman, Roger; Baccus, William

    2011-01-01

    We conducted an aerial helicopter survey between July 18 and July 25, 2011, to estimate abundance and trends of introduced mountain goats (Oreamnos americanus) in the Olympic Mountains. The survey was the first since we developed a sightability correction model in 2008, which provided the means to estimate the number of mountain goats present in the surveyed areas and not seen during the aerial surveys, and to adjust for undercounting biases. Additionally, the count was the first since recent telemetry studies revealed that the previously defined survey zone, which was delineated at lower elevations by the 1,520-meter elevation contour, did not encompass all lands used by mountain goats during summer. We redefined the lower elevation boundary of survey units before conducting the 2011 surveys in an effort to more accurately estimate the entire mountain goat population. We surveyed 39 survey units, comprising 39 percent of the 59,615-hectare survey area. We estimated a mountain goat population of 344±44 (standard error, SE) in the expanded survey area. Based on this level of estimation uncertainty, the 95-percent confidence interval ranged from 258 to 430 mountain goats at the time of the survey. To permit comparisons of mountain goat populations between the 2004 and 2011 surveys, we recomputed population estimates derived from the 2004 survey using the newly developed bias correction methods, and we computed the 2004 and 2011 surveys based on comparable survey zone definitions (for example, using the boundaries of the 2004 survey). The recomputed estimates of mountain goat populations were 217±19 (SE) in 2004 and 303±41(SE) in 2011. The difference between the current 2011 population estimate (344±44[SE]) and the recomputed 2011 estimate (303±41[SE]) reflects the number of mountain goats counted in the expanded lower elevation portions of the survey zone added in 2011. We conclude that the population of mountain goats has increased in the Olympic Mountains at

  11. THE VERTICAL MOTIONS OF MONO-ABUNDANCE SUB-POPULATIONS IN THE MILKY WAY DISK

    SciTech Connect

    Bovy, Jo; Rix, Hans-Walter; Hogg, David W.; Zhang, Lan; Beers, Timothy C.; Lee, Young Sun

    2012-08-20

    We present the vertical kinematics of stars in the Milky Way's stellar disk inferred from Sloan Digital Sky Survey/Sloan Extension for Galactic Understanding and Exploration (SDSS/SEGUE) G-dwarf data, deriving the vertical velocity dispersion, {sigma}{sub z}, as a function of vertical height |z| and Galactocentric radius R for a set of 'mono-abundance' sub-populations of stars with very similar elemental abundances [{alpha}/Fe] and [Fe/H]. We find that all mono-abundance components exhibit nearly isothermal kinematics in |z|, and a slow outward decrease of the vertical velocity dispersion: {sigma}{sub z}(z, R | [{alpha}/Fe], [Fe/H]) Almost-Equal-To {sigma}{sub z}([{alpha}/Fe], [Fe/H]) Multiplication-Sign exp (- (R - R{sub 0})/7 kpc). The characteristic velocity dispersions of these components vary from {approx}15 km s{sup -1} for chemically young, metal-rich stars with solar [{alpha}/Fe], to {approx}> 50 km s{sup -1} for metal-poor stars that are strongly [{alpha}/Fe]-enhanced, and hence presumably very old. The mean {sigma}{sub z} gradient (d{sigma}{sub z}/dz) away from the mid-plane is only 0.3 {+-} 0.2 km s{sup -1} kpc{sup -1}. This kinematic simplicity of the mono-abundance components mirrors their geometric simplicity; we have recently found their density distribution to be simple exponentials in both the z- and R-directions. We find a continuum of vertical kinetic temperatures ({proportional_to}{sigma}{sup 2}{sub z}) as a function of ([{alpha}/Fe], [Fe/H]), which contribute to the total stellar surface-mass density approximately as {Sigma}{sub R{sub 0}}({sigma}{sup 2}{sub z}){proportional_to} exp(-{sigma}{sup 2}{sub z}). This and the existence of isothermal mono-abundance populations with intermediate dispersions (30-40 km s{sup -1}) reject the notion of a thin-thick-disk dichotomy. This continuum of disk components, ranging from old, 'hot', and centrally concentrated ones to younger, cooler, and radially extended ones, argues against models where the thicker

  12. Evolution in Stage-Structured Populations

    PubMed Central

    Barfield, Michael; Holt, Robert D.; Gomulkiewicz, Richard

    2016-01-01

    For many organisms, stage is a better predictor of demographic rates than age. Yet no general theoretical framework exists for understanding or predicting evolution in stage-structured populations. Here, we provide a general modeling approach that can be used to predict evolution and demography of stage-structured populations. This advances our ability to understand evolution in stage-structured populations to a level previously available only for populations structured by age. We use this framework to provide the first rigorous proof that Lande’s theorem, which relates adaptive evolution to population growth, applies to stage-classified populations, assuming only normality and that evolution is slow relative to population dynamics. We extend this theorem to allow for different means or variances among stages. Our next major result is the formulation of Price’s theorem, a fundamental law of evolution, for stage-structured populations. In addition, we use data from Trillium grandiflorum to demonstrate how our models can be applied to a real-world population and thereby show their practical potential to generate accurate projections of evolutionary and population dynamics. Finally, we use our framework to compare rates of evolution in age- versus stage-structured populations, which shows how our methods can yield biological insights about evolution in stage-structured populations. PMID:21460563

  13. Nitrogen abundances and multiple stellar populations in the globular clusters of the Fornax dSph

    SciTech Connect

    Larsen, Søren S.; Strader, Jay

    2014-12-10

    We use measurements of nitrogen abundances in red giants to search for multiple stellar populations in the four most metal-poor globular clusters (GCs) in the Fornax dwarf spheroidal galaxy (Fornax 1, 2, 3, and 5). New imaging in the F343N filter, obtained with the Wide Field Camera 3 on the Hubble Space Telescope, is combined with archival F555W and F814W observations to determine the strength of the NH band near 3370 Å. After accounting for observational errors, the spread in the F343N-F555W colors of red giants in the Fornax GCs is similar to that in M15 and corresponds to an abundance range of Δ[N/Fe] ∼ 2 dex, as observed also in several Galactic GCs. The spread in F555W-F814W is, instead, fully accounted for by observational errors. The stars with the reddest F343N-F555W colors (indicative of N-enhanced composition) have more centrally concentrated radial distributions in all four clusters, although the difference is not highly statistically significant within any individual cluster. From double-Gaussian fits to the color distributions, we find roughly equal numbers of 'N-normal' and 'N-enhanced' stars (formally ∼40% N-normal stars in Fornax 1, 3, and 5 and ∼60% in Fornax 2). We conclude that GC formation, in particular, regarding the processes responsible for the origin of multiple stellar populations, appears to have operated similarly in the Milky Way and in the Fornax dSph. Combined with the high ratio of metal-poor GCs to field stars in the Fornax dSph, this places an important constraint on scenarios for the origin of multiple stellar populations in GCs.

  14. Statistical analysis of polychaete population density: dynamics of dominant species and scaling properties in relative abundance fluctuations

    NASA Astrophysics Data System (ADS)

    Quiroz-Martinez, B.; Schmitt, F. G.; Dauvin, J.-C.

    2012-01-01

    We consider here the dynamics of two polychaete populations based on a 20 yr temporal benthic survey of two muddy fine sand communities in the Bay of Morlaix, Western English Channel. These populations display high temporal variability, which is analyzed here using scaling approaches. We find that population densities have heavy tailed probability density functions. We analyze the dynamics of relative species abundance in two different communities of polychaetes by estimating in a novel way a "mean square drift" coefficient which characterizes their fluctuations in relative abundance over time. We show the usefulness of using new tools to approach and model such highly variable population dynamics in marine ecosystems.

  15. Density-dependent state-space model for population-abundance data with unequal time intervals.

    PubMed

    Dennis, Brian; Ponciano, José Miguel

    2014-08-01

    The Gompertz state-space (GSS) model is a stochastic model for analyzing time-series observations of population abundances. The GSS model combines density dependence, environmental process noise, and observation error toward estimating quantities of interest in biological monitoring and population viability analysis. However, existing methods for estimating the model parameters apply only to population data with equal time intervals between observations. In the present paper, we extend the GSS model to data with unequal time intervals, by embedding it within a state-space version of the Ornstein-Uhlenbeck process, a continuous-time model of an equilibrating stochastic system. Maximum likelihood and restricted maximum likelihood calculations for the Ornstein-Uhlenbeck state-space model involve only numerical maximization of an explicit multivariate normal likelihood, and so the extension allows for easy bootstrapping, yielding confidence intervals for model parameters, statistical hypothesis testing of density dependence, and selection among sub-models using information criteria. Ecologists and managers previously drawn to models lacking density dependence or observation error because such models accommodated unequal time intervals (for example, due to missing data) now have an alternative analysis framework incorporating density dependence, process noise, and observation error.

  16. Density dependent state space model for population abundance data with unequal time intervals

    PubMed Central

    Dennis, Brian; Ponciano, José Miguel

    2014-01-01

    The Gompertz state-space (GSS) model is a stochastic model for analyzing time series observations of population abundances. The GSS model combines density dependence, environmental process noise, and observation error toward estimating quantities of interest in biological monitoring and population viability analysis. However, existing methods for estimating the model parameters apply only to population data with equal time intervals between observations. In the present paper, we extend the GSS model to data with unequal time intervals, by embedding it within a state-space version of the Ornstein-Uhlenbeck process, a continuous-time model of an equilibrating stochastic system. Maximum likelihood and restricted maximum likelihood calculations for the Ornstein-Uhlenbeck state-space model involve only numerical maximization of an explicit multivariate normal likelihood, and so the extension allows for easy bootstrapping, yielding confidence intervals for model parameters, statistical hypothesis testing of density dependence, and selection among sub-models using information criteria. Ecologists and managers previously drawn to models lacking density dependence or observation error because such models accommodated unequal time intervals (for example, due to missing data) now have an alternative analysis framework incorporating density dependence, process noise and observation error. PMID:25230459

  17. The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

    NASA Astrophysics Data System (ADS)

    Cardarelli, E.; Francis, C. A.

    2014-12-01

    Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

  18. Variation in Population Synchrony in a Multi-Species Seabird Community: Response to Changes in Predator Abundance.

    PubMed

    Robertson, Gail S; Bolton, Mark; Morrison, Paul; Monaghan, Pat

    2015-01-01

    Ecologically similar sympatric species, subject to typical environmental conditions, may be expected to exhibit synchronous temporal fluctuations in demographic parameters, while populations of dissimilar species might be expected to show less synchrony. Previous studies have tested for synchrony in different populations of single species, and those including data from more than one species have compared fluctuations in only one demographic parameter. We tested for synchrony in inter-annual changes in breeding population abundance and productivity among four tern species on Coquet Island, northeast England. We also examined how manipulation of one independent environmental variable (predator abundance) influenced temporal changes in ecologically similar and dissimilar tern species. Changes in breeding abundance and productivity of ecologically similar species (Arctic Sterna paradisaea, Common S. hirundo and Roseate Terns S. dougallii) were synchronous with one another over time, but not with a species with different foraging and breeding behaviour (Sandwich Terns Thalasseus sandvicensis). With respect to changes in predator abundance, there was no clear pattern. Roseate Tern abundance was negatively correlated with that of large gulls breeding on the island from 1975 to 2013, while Common Tern abundance was positively correlated with number of large gulls, and no significant correlations were found between large gull and Arctic and Sandwich Tern populations. Large gull abundance was negatively correlated with productivity of Arctic and Common Terns two years later, possibly due to predation risk after fledging, while no correlation with Roseate Tern productivity was found. The varying effect of predator abundance is most likely due to specific differences in the behaviour and ecology of even these closely-related species. Examining synchrony in multi-species assemblages improves our understanding of how whole communities react to long-term changes in the

  19. Variation in Population Synchrony in a Multi-Species Seabird Community: Response to Changes in Predator Abundance

    PubMed Central

    Robertson, Gail S.; Bolton, Mark; Morrison, Paul; Monaghan, Pat

    2015-01-01

    Ecologically similar sympatric species, subject to typical environmental conditions, may be expected to exhibit synchronous temporal fluctuations in demographic parameters, while populations of dissimilar species might be expected to show less synchrony. Previous studies have tested for synchrony in different populations of single species, and those including data from more than one species have compared fluctuations in only one demographic parameter. We tested for synchrony in inter-annual changes in breeding population abundance and productivity among four tern species on Coquet Island, northeast England. We also examined how manipulation of one independent environmental variable (predator abundance) influenced temporal changes in ecologically similar and dissimilar tern species. Changes in breeding abundance and productivity of ecologically similar species (Arctic Sterna paradisaea, Common S. hirundo and Roseate Terns S. dougallii) were synchronous with one another over time, but not with a species with different foraging and breeding behaviour (Sandwich Terns Thalasseus sandvicensis). With respect to changes in predator abundance, there was no clear pattern. Roseate Tern abundance was negatively correlated with that of large gulls breeding on the island from 1975 to 2013, while Common Tern abundance was positively correlated with number of large gulls, and no significant correlations were found between large gull and Arctic and Sandwich Tern populations. Large gull abundance was negatively correlated with productivity of Arctic and Common Terns two years later, possibly due to predation risk after fledging, while no correlation with Roseate Tern productivity was found. The varying effect of predator abundance is most likely due to specific differences in the behaviour and ecology of even these closely-related species. Examining synchrony in multi-species assemblages improves our understanding of how whole communities react to long-term changes in the

  20. Increased abundance of terrestrial isopod populations in terrestrial ecosystems contaminated with petrochemical wastes.

    PubMed

    Faulkner, B C; Lochmiller, R L

    2000-07-01

    Arthropods are integral components of the food chain, and because many reside in close association to the soil and its contaminants, their communities may be sensitive indicators of ecotoxicity. We examined the influence of petrochemical contaminants on the abundance of several taxonomic groups of macroarthropods, with an emphasis on isopods, residing on two reference sites and three petrochemical-contaminated sites at an abandoned oil refinery site in southwestern Oklahoma. Relative densities of surface-dwelling macroarthropod assemblages were significantly greater on contaminated sites than reference sites. Differences in terrestrial isopod populations were particularly remarkable and consistent across study sites, with densities approaching 180-fold greater on contaminated than reference sites. Similarity comparisons indicated that abundances and composition of macroarthropod assemblages sampled on the contaminated sites were more similar to one another than to the communities residing on reference sites. Although preliminary, these initial results support the hypothesis that macroarthropod assemblages, in particular isopods, are sensitive to soil contaminants and could be a valuable approach to evaluating the effects of petrochemical contamination of soils on terrestrial ecosystems.

  1. Plague outbreaks in prairie dog populations explained by percolation thresholds of alternate host abundance

    PubMed Central

    Salkeld, Daniel J.; Salathé, Marcel; Stapp, Paul; Jones, James Holland

    2010-01-01

    Highly lethal pathogens (e.g., hantaviruses, hendra virus, anthrax, or plague) pose unique public-health problems, because they seem to periodically flare into outbreaks before disappearing into long quiescent phases. A key element to their possible control and eradication is being able to understand where they persist in the latent phase and how to identify the conditions that result in sporadic epidemics or epizootics. In American grasslands, plague, caused by Yersinia pestis, exemplifies this quiescent–outbreak pattern, because it sporadically erupts in epizootics that decimate prairie dog (Cynomys ludovicianus) colonies, yet the causes of outbreaks and mechanisms for interepizootic persistence of this disease are poorly understood. Using field data on prairie community ecology, flea behavior, and plague-transmission biology, we find that plague can persist in prairie-dog colonies for prolonged periods, because host movement is highly spatially constrained. The abundance of an alternate host for disease vectors, the grasshopper mouse (Onychomys leucogaster), drives plague outbreaks by increasing the connectivity of the prairie dog hosts and therefore, permitting percolation of the disease throughout the primary host population. These results offer an alternative perspective on plague's ecology (i.e., disease transmission exacerbated by alternative hosts) and may have ramifications for plague dynamics in Asia and Africa, where a single main host has traditionally been considered to drive Yersinia ecology. Furthermore, abundance thresholds of alternate hosts may be a key phenomenon determining outbreaks of disease in many multihost-disease systems. PMID:20660742

  2. Tracing impacts of partner abundance in facultative pollination mutualisms: from individuals to populations.

    PubMed

    Geib, Jennifer C; Galen, Candace

    2012-07-01

    Partner abundance affects costs and benefits in obligate mutualisms, but its role in facultative partnerships is less clear. We address this gap in a pollination web consisting of two clovers (Trifolium) that differ in specialization on a bumble bee pollinator Bombus balteatus. We examine how pollination niche breadth affects plant responses to pollinator abundance, comparing early-flowering (specialized) and late-flowering (generalized) cohorts of T. parryi and early T. parryi to T. dasyphyllum, a pollination generalist. Co-pollinators disrupt the link between B. halteatus visitation and pollination rate for both clovers. Only for early-flowering T. parryi do visitation, pollination, and seed set increase with density of B. balteatus. Bumble bee density also alters timing of seed germination in T. parryi, with seeds from plants receiving augmented B. balteatus germinating sooner than seeds of open-pollinated counterparts. Benefits saturate at intermediate bumble bee densities. Despite strong effects of B. balteatus density on individual plant fitness components, population models suggest little impact of B. balteatus density on lamda in T. parryi or T. dasyphyllum. Findings show that functional redundancy in a pollinator guild mediates host-plant responses to partner density. Unexpected effects of pollinator density on life history schedule have implications for recruitment under pollinator decline. PMID:22919905

  3. Structural dynamics and ecology of flatfish populations

    NASA Astrophysics Data System (ADS)

    Bailey, Kevin M.

    1997-11-01

    The concept of structure in populations of marine fishes is fundamental to how we manage and conduct research on these resources. The degree of population structure ranges widely among flatfishes. Although we know that large populations tend to be subdivided into local populations, based on morphological, meristic and reproductive characteristics, these data often conflict with evidence on genetic stock structure, due to the scale and organization of movement within the metapopulation. Movement of individuals between local subpopulations and colonization events on a macroecological scale are probably important to some flatfish populations. Dispersal of larvae is known to be a major factor affecting population mixing. Some flatfishes have planktonic stages of long duration and for these species there is often, but not always, little population structure; gene flow sometimes may be limited by oceanographic features, such as eddies and fronts. At the juvenile stage dispersal can result in colonization of under-utilized habitats; however, for flatfishes with strong habitat requirements, this type of event may be less likely when suitable habitats are fragmented. Complex population structure has major implications for management, e.g. lumping harvested populations with little gene flow can have detrimental local effects. Moreover, the issue of population structure and movement influences the interpretation of research data, where populations are generally treated as closed systems. There is currently a strong need for a multidisciplinary approach to study fish population dynamics and the structure of their populations. This research should involve molecular geneticists, population geneticists, animal behaviourists and ecologists. Migration mechanisms, colonization and extinction events, gene flow and density-dependent movements are subject areas of great importance to managing large harvested populations, but our understanding of them at ecological scales, at least for

  4. Abundance Trends and Status of the Little Colorado River Population of Humpback Chub: An Update Considering 1989-2006 Data

    USGS Publications Warehouse

    Coggins,, Lewis G.

    2008-01-01

    EXECUTIVE SUMMARY In 1967, the humpback chub (Gila cypha) (HBC) was added to the federal list of endangered species and is today protected under the Endangered Species Act of 1973. Only six populations of humpback chub are currently known to exist, five in the Colorado River Basin above Lees Ferry, Arizona, and one in Grand Canyon, Arizona. The majority of Grand Canyon humpback chub are found in the Little Colorado River (LCR)-the largest tributary to the Colorado River in Grand Canyon-and the Colorado River near its confluence with the Little Colorado River. Monitoring and research of the Grand Canyon humpback chub population is overseen by the U.S. Geological Survey's (USGS) Grand Canyon Monitoring and Research Center (GCMRC) under the auspices of the Glen Canyon Dam Adaptive Management Program (GCDAMP), a Federal initiative to protect and improve resources downstream of Glen Canyon Dam. This report provides updated information on the status and trends of the LCR population in light of new information and refined assessment methodology. An earlier assessment of the LCR population (Coggins and others, 2006a) used data collected during 1989?2002; the assessment provided here includes that data and additional data collected through 2006. Catch-rate indices, closed population mark-recapture model abundance estimates, results from the original age-structured mark recapture (ASMR) model (Coggins and others, 2006b), and a newly refined ASMR model are presented. This report also seeks to (1) formally evaluate alternative stock assessment models using Pearson residual analyses and information theoretic procedures, (2) use mark-recapture data to estimate the relationship between HBC age and length, (3) translate uncertainty in the assignment of individual fish age to resulting estimates of recruitment and abundance from the ASMR model, and (4) evaluate past and present stock assessments considering the available data sources and analyses, recognizing the limitations

  5. Reproducibility of Vibrionaceae population structure in coastal bacterioplankton

    PubMed Central

    Szabo, Gitta; Preheim, Sarah P; Kauffman, Kathryn M; David, Lawrence A; Shapiro, Jesse; Alm, Eric J; Polz, Martin F

    2013-01-01

    How reproducibly microbial populations assemble in the wild remains poorly understood. Here, we assess evidence for ecological specialization and predictability of fine-scale population structure and habitat association in coastal ocean Vibrionaceae across years. We compare Vibrionaceae lifestyles in the bacterioplankton (combinations of free-living, particle, or zooplankton associations) measured using the same sampling scheme in 2006 and 2009 to assess whether the same groups show the same environmental association year after year. This reveals complex dynamics with populations falling primarily into two categories: (i) nearly equally represented in each of the two samplings and (ii) highly skewed, often to an extent that they appear exclusive to one or the other sampling times. Importantly, populations recovered at the same abundance in both samplings occupied highly similar habitats suggesting predictable and robust environmental association while skewed abundances of some populations may be triggered by shifts in ecological conditions. The latter is supported by difference in the composition of large eukaryotic plankton between years, with samples in 2006 being dominated by copepods, and those in 2009 by diatoms. Overall, the comparison supports highly predictable population-habitat linkage but highlights the fact that complex, and often unmeasured, environmental dynamics in habitat occurrence may have strong effects on population dynamics. PMID:23178668

  6. Landscape structure and the genetic effects of a population collapse.

    PubMed

    Caplins, Serena A; Gilbert, Kimberly J; Ciotir, Claudia; Roland, Jens; Matter, Stephen F; Keyghobadi, Nusha

    2014-12-01

    Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60-100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did not change. However, patch connectivity and local severity of the collapse interacted to determine allelic richness change within populations, indicating that patch connectivity can mediate genetic response to a demographic collapse. The collapse strongly affected spatial genetic structure, leading to a breakdown of isolation-by-distance and loss of landscape genetic pattern. Our study reveals important interactions between landscape structure and temporal demographic variability on the genetic diversity and genetic differentiation of populations. Projected future changes to both landscape and climate may lead to loss of genetic variability from the studied populations, and selection acting on adaptive variation will likely occur within the context of an increasing influence of genetic drift.

  7. Landscape structure and the genetic effects of a population collapse

    PubMed Central

    Caplins, Serena A.; Gilbert, Kimberly J.; Ciotir, Claudia; Roland, Jens; Matter, Stephen F.; Keyghobadi, Nusha

    2014-01-01

    Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60–100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did not change. However, patch connectivity and local severity of the collapse interacted to determine allelic richness change within populations, indicating that patch connectivity can mediate genetic response to a demographic collapse. The collapse strongly affected spatial genetic structure, leading to a breakdown of isolation-by-distance and loss of landscape genetic pattern. Our study reveals important interactions between landscape structure and temporal demographic variability on the genetic diversity and genetic differentiation of populations. Projected future changes to both landscape and climate may lead to loss of genetic variability from the studied populations, and selection acting on adaptive variation will likely occur within the context of an increasing influence of genetic drift. PMID:25320176

  8. Spatial structuring within a reservoir fish population: implications for management

    USGS Publications Warehouse

    Stewart, David R.; Long, James M.; Shoup, Daniel E.

    2014-01-01

    Spatial structuring in reservoir fish populations can exist because of environmental gradients, species-specific behaviour, or even localised fishing effort. The present study investigated whether white crappie exhibited evidence of improved population structure where the northern more productive half of a lake is closed to fishing to provide waterfowl hunting opportunities. Population response to angling was modelled for each substock of white crappie (north (protected) and south (unprotected) areas), the entire lake (single-stock model) and by combining simulations of the two independent substock models (additive model). White crappie in the protected area were more abundant, consisting of larger, older individuals, and exhibited a lower total annual mortality rate than in the unprotected area. Population modelling found that fishing mortality rates between 0.1 and 0.3 resulted in sustainable populations (spawning potential ratios (SPR) >0.30). The population in the unprotected area appeared to be more resilient (SPR > 0.30) at the higher fishing intensities (0.35–0.55). Considered additively, the whole-lake fishery appeared more resilient than when modelled as a single-panmictic stock. These results provided evidence of spatial structuring in reservoir fish populations, and we recommend model assessments used to guide management decisions should consider those spatial differences in other populations where they exist.

  9. Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest

    PubMed Central

    Ellison, Aaron M.; Jackson, Scott

    2015-01-01

    Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m2 and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that could

  10. Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest.

    PubMed

    Siddig, Ahmed A; Ellison, Aaron M; Jackson, Scott

    2015-01-01

    Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m(2) and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that

  11. Differences in ecological structure, function, and native species abundance between native and invaded Hawaiian streams.

    PubMed

    Holitzki, Tara M; MacKenzie, Richard A; Wiegner, Tracy N; McDermid, Karla J

    2013-09-01

    Poeciliids, one of the most invasive species worldwide, are found on almost every continent and have been identified as an "invasive species of concern" in the United States, New Zealand, and Australia. Despite their global prevalence, few studies have quantified their impacts on tropical stream ecosystem structure, function, and biodiversity. Utilizing Hawaiian streams as model ecosystems, we documented how ecological structure, function, and native species abundance differed between poeciliid-free and poeciliid-invaded tropical streams. Stream nutrient yields, benthic biofilm biomass, densities of macroinvertebrates and fish, and community structures of benthic algae, macroinvertebrates, and fish were compared between streams with and without established poeciliid populations on the island of Hawai'i, Hawaii, USA. Sum nitrate (sigmaNO3(-) = NO3(-) + NO2(-)), total nitrogen, and total organic carbon yields were eight times, six times, and five times higher, respectively, in poeciliid streams than in poeciliid-free streams. Benthic biofilm ash-free dry mass was 1.5x higher in poeciliid streams than in poeciliid-free streams. Percentage contributions of chironomids and hydroptilid caddisflies to macroinvertebrate densities were lower in poeciliid streams compared to poeciliid-free streams, while percentage contributions of Cheumatopsyche analis caddisflies, Dugesia sp. flatworms, and oligochaetes were higher. Additionally, mean densities of native gobies were two times lower in poeciliid streams than in poeciliid-free ones, with poeciliid densities being approximately eight times higher than native fish densities. Our results, coupled with the wide distribution of invasive poeciliids across Hawaii and elsewhere in the tropics, suggest that poeciliids may negatively impact the ecosystem structure, function, and native species abundance of tropical streams they invade. This underscores the need for increased public awareness to prevent future introductions and for

  12. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.)

    PubMed Central

    Fu, Peng-cheng; Zhang, Yan-Zhao; Ya, Hui-yuan

    2016-01-01

    Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1–6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+ T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop. PMID:26925343

  13. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.).

    PubMed

    Fu, Peng-Cheng; Zhang, Yan-Zhao; Ya, Hui-Yuan; Gao, Qing-Bo

    2016-01-01

    Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1-6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+ T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop.

  14. Population Structure and Quantitative Characters

    PubMed Central

    Rogers, Alan R.; Harpending, Henry C.

    1983-01-01

    A migration matrix model is used to investigate the behavior of neutral polygenic characters in subdivided populations. It is shown that gametic disequilibrium has a large effect on the variance among groups but none at all on its expectation. The variance of among-group variance is substantial and does not depend on the number of loci contributing to variance in the character. It is just as large for polygenic characters as for single loci with the same additive variance. This implies that one polygenic character contains exactly as much information about population relationships as one single-locus marker. The theory is compared with observed differentiation of dermatoglyphic and anthropometric characters among Bougainville islanders. PMID:17246186

  15. On the Apportionment of Population Structure

    PubMed Central

    Granot, Yaron; Tal, Omri; Rosset, Saharon; Skorecki, Karl

    2016-01-01

    Measures of population differentiation, such as FST, are traditionally derived from the partition of diversity within and between populations. However, the emergence of population clusters from multilocus analysis is a function of genetic structure (departures from panmixia) rather than of diversity. If the populations are close to panmixia, slight differences between the mean pairwise distance within and between populations (low FST) can manifest as strong separation between the populations, thus population clusters are often evident even when the vast majority of diversity is partitioned within populations rather than between them. For any given FST value, clusters can be tighter (more panmictic) or looser (more stratified), and in this respect higher FST does not always imply stronger differentiation. In this study we propose a measure for the partition of structure, denoted EST, which is more consistent with results from clustering schemes. Crucially, our measure is based on a statistic of the data that is a good measure of internal structure, mimicking the information extracted by unsupervised clustering or dimensionality reduction schemes. To assess the utility of our metric, we ranked various human (HGDP) population pairs based on FST and EST and found substantial differences in ranking order. EST ranking seems more consistent with population clustering and classification and possibly with geographic distance between populations. Thus, EST may at times outperform FST in identifying evolutionary significant differentiation. PMID:27505172

  16. Endoparasites in a Norwegian moose (Alces alces) population - Faunal diversity, abundance and body condition.

    PubMed

    Davidson, Rebecca K; Ličina, Tina; Gorini, Lucrezia; Milner, Jos M

    2015-04-01

    Many health surveillance programs for wild cervids do not include routine parasite screening despite evidence that gastrointestinal parasites can affect wildlife population dynamics by influencing host fecundity and survival. Slaughter weights of moose in some regions of Norway have been decreasing over recent decades but any role of parasites has not yet been considered. We investigated parasite faunal diversity of moose in Hedmark, SE Norway, by faecal analysis and identification of adult abomasal and caecal nematodes during the autumn hunting season. We related parasite prevalence and abundance to estimates of body condition, gender and age. We identified 11 parasite groups. Moose had high abomasal gastrointestinal nematode (GIN) burdens and all individuals were infected. Ostertagia antipini and Spiculopteragia alcis were the most prevalent abomasal GINs identified. O. leptospicularis and Telodorsagia circumcincta were also identified in the abomasa while a range of other GIN and Moniezia sp. eggs, and coccidia, Dictyocaulus sp. and Protostrongylid larvae were found in faeces. Female moose had higher mean abomasal nematode counts than males, particularly among adults. However, adult males had higher faecal egg counts than adult females which may reflect reduction in faecal volume with concentration of eggs among males during the rut. We found no strong evidence for the development of acquired immunity to abomasal nematodes with age, although there was a higher Protostrongylid and Moniezia infection prevalence in younger animals. High burdens of several parasites were associated with poor body condition in terms of slaughter weight relative to skeletal size but unrelated to visually evaluated fat reserves. Given findings from earlier experimental studies, our results imply sub-clinical effects of GI parasite infection on host condition. Managers should be aware that autumn faecal egg counts and field assessments of fat reserves may not be reliable indicators of

  17. Endoparasites in a Norwegian moose (Alces alces) population - Faunal diversity, abundance and body condition.

    PubMed

    Davidson, Rebecca K; Ličina, Tina; Gorini, Lucrezia; Milner, Jos M

    2015-04-01

    Many health surveillance programs for wild cervids do not include routine parasite screening despite evidence that gastrointestinal parasites can affect wildlife population dynamics by influencing host fecundity and survival. Slaughter weights of moose in some regions of Norway have been decreasing over recent decades but any role of parasites has not yet been considered. We investigated parasite faunal diversity of moose in Hedmark, SE Norway, by faecal analysis and identification of adult abomasal and caecal nematodes during the autumn hunting season. We related parasite prevalence and abundance to estimates of body condition, gender and age. We identified 11 parasite groups. Moose had high abomasal gastrointestinal nematode (GIN) burdens and all individuals were infected. Ostertagia antipini and Spiculopteragia alcis were the most prevalent abomasal GINs identified. O. leptospicularis and Telodorsagia circumcincta were also identified in the abomasa while a range of other GIN and Moniezia sp. eggs, and coccidia, Dictyocaulus sp. and Protostrongylid larvae were found in faeces. Female moose had higher mean abomasal nematode counts than males, particularly among adults. However, adult males had higher faecal egg counts than adult females which may reflect reduction in faecal volume with concentration of eggs among males during the rut. We found no strong evidence for the development of acquired immunity to abomasal nematodes with age, although there was a higher Protostrongylid and Moniezia infection prevalence in younger animals. High burdens of several parasites were associated with poor body condition in terms of slaughter weight relative to skeletal size but unrelated to visually evaluated fat reserves. Given findings from earlier experimental studies, our results imply sub-clinical effects of GI parasite infection on host condition. Managers should be aware that autumn faecal egg counts and field assessments of fat reserves may not be reliable indicators of

  18. The planetary nebulae populations in five galaxies: abundance patterns and evolution

    NASA Astrophysics Data System (ADS)

    Stasińska, G.; Richer, M. G.; McCall, M. L.

    1998-08-01

    We have collected photometric and spectroscopic data on planetary nebulae (PNe) in 5 galaxies: the Milky Way (bulge), M 31 (bulge), M 32, the LMC and the SMC. We have computed the abundances of O, Ne and N and compared them from one galaxy to another. In each Galaxy, the distribution of oxygen abundances has a large dispersion. The average O/H ratio is larger in the M 31 and the Galactic bulge PNe than in those in the Magellanic Clouds. In a given galaxy, it is also larger for PNe with [O III] luminosities greater than 100 L_⊙, which are likely to probe more recent epochs in the galaxy history. We find that the M 31 and the Galactic bulge PNe extend the very tight Ne/H-O/H correlation observed in the Galactic disk and Magellanic Clouds PNe towards higher metallicities. We note that the anticorrelation between N/O and O/H that was known to occur in the Magellanic Clouds and in the disk PNe is also marginally found in the PNe of the Galactic bulge. Furthermore, we find that high N/O ratios are higher for less luminous PNe. In M 32, all PNe have a large N/O ratio, indicating that the stellar nitrogen abundance is enhanced in this galaxy. We have also compared the PN evolution in the different galactic systems by constructing diagrams that are independent of abundances, and have found strikingly different behaviours of the various samples. In order to help in the interpretation of these data, we have constructed a grid of expanding, PN photoionization models in which the central stars evolve according to the evolutionary tracks of Bl{öcker (1995). These models show that the apparent spectroscopic properties of PNe are extremely dependent, not only on the central stars, but also on the masses and expansion velocities of the nebular envelopes. The main conclusion of the confrontation of the observed samples with the model grids is that the PN populations are indeed not the same in the various parent galaxies. Both stars and nebulae are different. In particular, the

  19. (Genetic structure of natural populations)

    SciTech Connect

    Not Available

    1988-01-01

    Our efforts in the first eight months were concentrated in obtaining a genomic clone of the copper-zinc superoxide dismutase (SOD) in Drosophila melanogaster and other Drosophila species. This we have now successfully accomplished. We seek to understand the role of SOD in radioresistance; how genetic variation in this enzyme is maintained in populations; and relevant aspects of its evolution that may contribute to these goals as well as to an understanding of molecular evolution in general. To accomplish these goals we are undertaking the following experiments: cloning and sequencing of (at least) one F allele, one S allele, and the null allele for SOD; cloning and sequencing SOD from species related to D. melanogaster; and cloning and sequencing the SOD gene from several independently sampled S and F alleles in D. melanogaster. We are also preparing to test the radioprotective effects of SOD. 67 refs.

  20. Spectra of late type dwarf stars of known abundance for stellar population models

    NASA Technical Reports Server (NTRS)

    Oconnell, R. W.

    1990-01-01

    The project consisted of two parts. The first was to obtain new low-dispersion, long-wavelength, high S/N IUE spectra of F-G-K dwarf stars with previously determined abundances, temperatures, and gravities. To insure high quality, the spectra are either trailed, or multiple exposures are taken within the large aperture. Second, the spectra are assembled into a library which combines the new data with existing IUE Archive data to yield mean spectral energy distributions for each important type of star. My principal responsibility is the construction and maintenance of this UV spectral library. It covers the spectral range 1200-3200A and is maintained in two parts: a version including complete wavelength coverage at the full spectral resolution of the Low Resolution cameras; and a selected bandpass version, consisting of the mean flux in pre-selected 20A bands. These bands are centered on spectral features or continuum regions of special utility - e.g. the C IV lambda 1550 or Mg II lambda 2800 feature. In the middle-UV region, special emphasis is given to those features (including continuum 'breaks') which are most useful in the study of F-G-K star spectra in the integrated light of old stellar populations.

  1. Consideraciones para la estimacion de abundancia de poblaciones de mamiferos. [Considerations for the estimation of abundance of mammal populations.

    USGS Publications Warehouse

    Walker, R.S.; Novare, A.J.; Nichols, J.D.

    2000-01-01

    Estimation of abundance of mammal populations is essential for monitoring programs and for many ecological investigations. The first step for any study of variation in mammal abundance over space or time is to define the objectives of the study and how and why abundance data are to be used. The data used to estimate abundance are count statistics in the form of counts of animals or their signs. There are two major sources of uncertainty that must be considered in the design of the study: spatial variation and the relationship between abundance and the count statistic. Spatial variation in the distribution of animals or signs may be taken into account with appropriate spatial sampling. Count statistics may be viewed as random variables, with the expected value of the count statistic equal to the true abundance of the population multiplied by a coefficient p. With direct counts, p represents the probability of detection or capture of individuals, and with indirect counts it represents the rate of production of the signs as well as their probability of detection. Comparisons of abundance using count statistics from different times or places assume that the p are the same for all times or places being compared (p= pi). In spite of considerable evidence that this assumption rarely holds true, it is commonly made in studies of mammal abundance, as when the minimum number alive or indices based on sign counts are used to compare abundance in different habitats or times. Alternatives to relying on this assumption are to calibrate the index used by testing the assumption of p= pi, or to incorporate the estimation of p into the study design.

  2. Population dynamics in a cyclic environment: consequences of cyclic food abundance on tawny owl reproduction and survival.

    PubMed

    Karell, Patrik; Ahola, Kari; Karstinen, Teuvo; Zolei, Aniko; Brommer, Jon E

    2009-09-01

    1. Understanding which factors regulate population dynamics may help us to understand how a population would respond to environmental change, and why some populations are declining. 2. In southern Finland, vole abundance shows a three-phased cycle of low, increase and decrease phases, but these have been fading out in recent years. During five such cycles (1981-1995), all tawny owls Strix aluco were censused in a 250-km(2) study area, and their reproduction and survival were monitored. 3. Males and females showed similar dynamics, but experienced breeders recruited more offspring and had higher survival than first breeders. Offspring recruitment, but not survival of breeding individuals varied in accordance with vole abundance. 4. The population's numerical response to prey abundance was primarily due to first-breeding individuals entering the population in the increase phase when immigration was the highest. First-breeding birds were younger, but experienced breeders were older in more favourable vole years. 5. A stage-specific matrix population model integrating survival and fecundity showed that, despite obvious variation in fecundity between vole cycle phases, this variation had limited importance for overall tawny owl population dynamics, but that the survival of experienced breeders during the low phase is most important for population growth. 6. Model and data agreed that the vole cycle drives the dynamics of this avian predator by limiting the recruitment of new breeders during the low phase. Population dynamics hence differ not only from the classic example of the species in a more temperate region in the UK where the number of territories is stable across years, but also from the dynamics of other avian vole predators in Fennoscandia where the recurring crash in vole abundance drastically lowers adult survival thereby creating vacancies. PMID:19493132

  3. Comparative population structure of cavity-nesting sea ducks

    USGS Publications Warehouse

    Pearce, John M.; Eadie, John M.; Savard, Jean-Pierre L.; Christensen, Thomas K.; Berdeen, James; Taylor, Eric J.; Boyd, Sean; Einarsson, Árni

    2014-01-01

    A growing collection of mtDNA genetic information from waterfowl species across North America suggests that larger-bodied cavity-nesting species exhibit greater levels of population differentiation than smaller-bodied congeners. Although little is known about nest-cavity availability for these species, one hypothesis to explain differences in population structure is reduced dispersal tendency of larger-bodied cavity-nesting species due to limited abundance of large cavities. To investigate this hypothesis, we examined population structure of three cavity-nesting waterfowl species distributed across much of North America: Barrow's Goldeneye (Bucephala islandica), Common Goldeneye (B. clangula), and Bufflehead (B. albeola). We compared patterns of population structure using both variation in mtDNA control-region sequences and band-recovery data for the same species and geographic regions. Results were highly congruent between data types, showing structured population patterns for Barrow's and Common Goldeneye but not for Bufflehead. Consistent with our prediction, the smallest cavity-nesting species, the Bufflehead, exhibited the lowest level of population differentiation due to increased dispersal and gene flow. Results provide evidence for discrete Old and New World populations of Common Goldeneye and for differentiation of regional groups of both goldeneye species in Alaska, the Pacific Northwest, and the eastern coast of North America. Results presented here will aid management objectives that require an understanding of population delineation and migratory connectivity between breeding and wintering areas. Comparative studies such as this one highlight factors that may drive patterns of genetic diversity and population trends.

  4. Structurally Resolved Abundances and Depletions in the Rho OPH Cloud

    NASA Astrophysics Data System (ADS)

    Seab, C.

    1995-07-01

    The mechanism that determines the pattern of depletion ofelements in the interstellar medium has been a problem for along time. It is clear that some of the most refractoryelements such as Si, Fe, and Mg, are heavily depleted onto theinterstellar grains. On the other hand, some elements such asS and Zn are normally either undepleted or very lightlydepleted. The difference between the two cases is notunderstood. We propose to address this question with adetailed study of the depletion patterns in the Rho Ophiuchicloud. This study is strongly based on a combination of thecapabilities of two modern instruments: the GHRS for high-resolution UV data, and the Ultra High Resolution Facility(UHRF) of the AAT. This instrument has been used to obtain NaI line profiles in the Rho Oph cloud with a resolution ofR=1,000,000. The combination of these two types of data willbe used to resolve the velocity structure of the elementdepletions in the cloud.

  5. Picoplankton and virioplankton abundance and community structure in Pearl River Estuary and Daya Bay, South China.

    PubMed

    Ni, Zhixin; Huang, Xiaoping; Zhang, Xia

    2015-06-01

    By using flow cytometry techniques, we investigated the abundance and composition of the heterotrophic prokaryotes, virioplankton and picophytoplankton community in the Pearl River Estuary and Daya Bay in the summer of 2012. We identified two subgroups of prokaryotes, high nucleic acid (HNA) and low nucleic acid (LNA), characterized by different nucleic acid contents. HNA abundance was significantly correlated with larger phytoplankton and Synechococcus (Syn) abundance, which suggested the important role of organic substrates released from primary producers on bacterial growth. Although LNA did not show any association with environmental variables, it was a vital component of the microbial community. In contrast to previous studies, the total virioplankton concentration had a poor relationship with nutrient availability. The positive relationship between large-sized phytoplankton abundance and the V-I population confirmed that V-I was a phytoplankton-infecting viral subgroup. Although the V-II group (bacteriophages) was dominant in the virioplankton community, it was not related with prokaryotic abundance, which indicated factors other than hosts controlling V-II abundance or the uncertainty of virus-host coupling. With respect to the picophytoplankton community, our results implied that river input exerted a strong limitation to Syn distribution in the estuary, while picoeukaryotes (Euk) were numerically less abundant and showed a quite different distribution pattern from that of Syn, and hence presented ecological properties distinct from Syn in our two studied areas.

  6. A Long-Term Comparison of Yellowstone Cutthroat Trout Abundance and Size Structure in Their Historical Range in Idaho.

    SciTech Connect

    Meyer, Kevin A.; Schill, Daniel J.; Elle, F. Steven

    2002-05-23

    We compared estimates of population abundance and size structure for Yellowstone cutthroat trout Oncorhynchus clarki bouvieri obtained by electrofishing 77 stream segments across southeastern Idaho in the 1980s and again in 1999-2000 to test whether populations of Yellowstone cutthroat trout had changed. Sites sampled in the 1980s were relocated in 1999-2000 by using maps and photographs or by finding original site-boundary stakes, so that the same reach of stream was sampled during both periods. Abundance of Yellowstone cutthroat trout longer than 10 cm did not change, averaging 41 fish/100 m of stream during both the 1980s and 1999-2000. The proportion of the total catch of trout composed of Yellowstone cutthroat trout also did not change, averaging 82% in the 1980s and 78% in 1999-2000. At the 48 sites where size structure could be estimated for both periods, the proportion of Yellowstone cutthroat trout that were 10-20 cm long declined slightly (74% versus 66%), but the change was due entirely to the shift in size structure at the Teton River sites. The number of sites that contained rainbow trout O. mykiss or cutthroat trout 3 rainbow trout hybrids rose from 23 to 37, but the average proportion of the catch composed of rainbow trout and hybrids did not increase (7% in both the 1980s and 1999-2000). Although the distribution and abundance of Yellowstone cutthroat trout have been substantially reduced in Idaho over the last century, our results indicate that Yellowstone cutthroat trout abundance and size structure in Idaho have remained relatively stable at a large number of locations for the last 10-20 years. The expanding distribution of rainbow trout and hybrids in portions of the upper Snake River basin, however, calls for additional monitoring and active management actions.

  7. Improving removal-based estimates of abundance by sampling a population of spatially distinct subpopulations

    USGS Publications Warehouse

    Dorazio, R.M.; Jelks, H.L.; Jordan, F.

    2005-01-01

     A statistical modeling framework is described for estimating the abundances of spatially distinct subpopulations of animals surveyed using removal sampling. To illustrate this framework, hierarchical models are developed using the Poisson and negative-binomial distributions to model variation in abundance among subpopulations and using the beta distribution to model variation in capture probabilities. These models are fitted to the removal counts observed in a survey of a federally endangered fish species. The resulting estimates of abundance have similar or better precision than those computed using the conventional approach of analyzing the removal counts of each subpopulation separately. Extension of the hierarchical models to include spatial covariates of abundance is straightforward and may be used to identify important features of an animal's habitat or to predict the abundance of animals at unsampled locations.

  8. Genetic structure of the world's polar bear populations

    USGS Publications Warehouse

    Paetkau, David; Amstrup, Steven C.; Born, E.W.; Calvert, W.; Derocher, A.E.; Garner, G.W.; Messier, F.; Stirling, I.; Taylor, M.K.; Wiig, O.; Strobeck, C.

    1999-01-01

    We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals.

  9. Non-LTE analysis of copper abundances for the two distinct halo populations in the solar neighborhood

    NASA Astrophysics Data System (ADS)

    Yan, H. L.; Shi, J. R.; Nissen, P. E.; Zhao, G.

    2016-01-01

    Context. Two distinct halo populations were found in the solar neighborhood by a series of works. They can be clearly separated by [α/Fe] and several other elemental abundance ratios including [Cu/Fe]. Very recently, a non-local thermodynamic equilibrium (non-LTE) study revealed that relatively large departures exist between LTE and non-LTE results in copper abundance analysis. The study also showed that non-LTE effects of neutral copper vary with stellar parameters and thus affect the [Cu/Fe] trend. Aims: We aim to derive the copper abundances for the stars from the sample of Nissen & Schuster (2010) with both LTE and non-LTE calculations. Based on our results, we study the non-LTE effects of copper and investigate whether the high-α population can still be distinguished from the low-α population in the non-LTE [Cu/Fe] results. Methods: Our differential abundance ratios are derived from the high-resolution spectra collected from VLT/UVES and NOT/FIES spectrographs. Applying the MAFAGS opacity sampling atmospheric models and spectrum synthesis method, we derive the non-LTE copper abundances based on the new atomic model with current atomic data obtained from both laboratory and theoretical calculations. Results: The copper abundances determined from non-LTE calculations are increased by 0.01 to 0.2 dex depending on the stellar parameters compared with the LTE results. The non-LTE [Cu/Fe] trend is much flatter than the LTE one in the metallicity range -1.6 < [ Fe / H ] < -0.8. Taking non-LTE effects into consideration, the high- and low-α stars still show distinguishable copper abundances, which appear even more clear in a diagram of non-LTE [Cu/Fe] versus [Fe/H]. Conclusions: The non-LTE effects are strong for copper, especially in metal-poor stars. Our results confirmed that there are two distinct halo populations in the solar neighborhood. The dichotomy in copper abundance is a peculiar feature of each population, suggesting that they formed in different

  10. Genetic structure among Fijian island populations.

    PubMed

    Shipley, Gerhard P; Taylor, Diana A; Tyagi, Anand; Tiwari, Geetanjali; Redd, Alan J

    2015-02-01

    We examined nine Y chromosome short tandem repeats (Y-STRs) and the mitochondrial DNA (mtDNA) hypervariable segment 1 region in the Fijian island populations of Viti Levu, Vanua Levu, Kadavu, the Lau islands and Rotuma. We found significant genetic structure among these populations for the Y-STRs, both with and without the Rotumans, but not for the mtDNA. We also found that all five populations exhibited the sex-biased admixture associated with areas settled by Austronesian-speaking people, with paternal lineages more strongly associated with Melanesian populations and maternal lineages more strongly associated with Polynesian populations. We also found that the Rotumans in the north and the Lau Islanders in the east were genetically more similar to Polynesian populations than were the other Fijians, but only for the mtDNA. For the Y-STRs, the Rotumans and the Lau Islanders were genetically as similar to Melanesian populations as were the other three populations. Of the five populations, the Rotumans were the most different in almost every regard. Although past genetic studies treated the Fijians as being genetically homogenous despite known geographic, phenotypic, cultural and linguistic variation, our findings show significant genetic variation and a need for a closer examination of individual island populations within Fiji, particularly the Rotumans, in order to better understand the process of the peopling of Fiji and of the surrounding regions.

  11. Synchronous centennial-scale variability in abundance of remote sardine populations in the Pacific

    NASA Astrophysics Data System (ADS)

    Kuwae, M.; Takashige, S.; Yamamoto, M.; Sagawa, T.; Takeoka, H.

    2012-12-01

    A number of studies have identified evidence for connections between Pacific climate decadal variability and variations in Pacific marine ecosystems which are typically shown in abundance of remote sardine and anchovy species off Japan, California, Peru, and Chile as well as Alaska salmon species. The variations in climate indices and abundance of sardine and anchovy species most likely have 50-70 year cycles and therefore these natural perturbations in climates and Pacific ecosystems should be considered for developing predictive models of fisheries productions and the managements. Despite the importance of natural perturbations for long-term predictions, one issue, whether synchronous centennial-variations in remote Pacific fisheries productions in response to climate variability exists in the past, has not been questioned, because there has never been long-term reconstructed time series in the western North Pacific. Here we present well preserved, fossil fish scale-based abundance record of Japanese sardine over the last 1100 years reconstructed from a seasonal anoxic basin in the western Seto Inland Sea near their spawning areas in the western North Pacific. A comparison of our record with other previous records clearly showed centennial-scale variations in abundance of sardine species off Japan, California, and Chile, characterized by centennial-scale alternations between low abundance regimes and high abundance regimes in which multidecadal fluctuations with large amplitudes occurred once or several times. High abundance regimes from 1450 to 1650 AD and after 1800 AD and a low abundance regime from 1650 to 1800 AD corresponded to low frequency patterns of PDO index reconstructed from tree-ring records in North America. This indicates that connections between Pacific climate variability and variations in Pacific marine ecosystems exist not only on multidecadal timescales but on centennial timescales. Three to four hundred-yr periodicity of the Pacific climate

  12. Population structure of ice-breeding seals.

    PubMed

    Davis, Corey S; Stirling, Ian; Strobeck, Curtis; Coltman, David W

    2008-07-01

    The development of population genetic structure in ice-breeding seal species is likely to be shaped by a combination of breeding habitat and life-history characteristics. Species that return to breed on predictable fast-ice locations are more likely to exhibit natal fidelity than pack-ice-breeding species, which in turn facilitates the development of genetic differentiation between subpopulations. Other aspects of life history such as geographically distinct vocalizations, female gregariousness, and the potential for polygynous breeding may also facilitate population structure. Based on these factors, we predicted that fast-ice-breeding seal species (the Weddell and ringed seal) would show elevated genetic differentiation compared to pack-ice-breeding species (the leopard, Ross, crabeater and bearded seals). We tested this prediction using microsatellite analysis to examine population structure of these six ice-breeding species. Our results did not support this prediction. While none of the Antarctic pack-ice species showed statistically significant population structure, the bearded seal of the Arctic pack ice showed strong differentiation between subpopulations. Again in contrast, the fast-ice-breeding Weddell seal of the Antarctic showed clear evidence for genetic differentiation while the ringed seal, breeding in similar habitat in the Arctic, did not. These results suggest that the development of population structure in ice-breeding phocid seals is a more complex outcome of the interplay of phylogenetic and ecological factors than can be predicted on the basis of breeding substrate and life-history characteristics.

  13. The Distribution and Abundance of an Island Population of Koalas (Phascolarctos cinereus) in the Far North of Their Geographic Range

    PubMed Central

    McGregor, Denise C.; Kerr, Sarah E.; Krockenberger, Andrew K.

    2013-01-01

    Koalas are an iconic species of charismatic megafauna, of substantial social and conservation significance. They are widely distributed, often at low densities, and individuals can be difficult to detect, making population surveys challenging and costly. Consequently, koala population estimates have been limited and the results inconsistent. The aims of this study were to estimate the distribution, relative abundance and population size of the koalas on Magnetic Island, far north Queensland. Population densities were estimated in 18 different vegetation types present on the island using a Fecal Standing Crop Method. Koala density ranged from 0.404 ha−1, recorded in forest red gum and bloodwood woodland, to absence from eight of the vegetation types surveyed. The second highest density of 0.297 koalas ha−1 was recorded in mixed eucalypt woodland, which covers 45% of the island. The total abundance of koalas on Magnetic Island, not including those present in urban areas, was estimated at 825±175 (SEM). The large variation in koala density across vegetation types reinforces the need for sampling stratification when calculating abundance over large areas, as uniformity of habitat quality cannot be assumed. In this context, koala populations also occur in low densities in areas generally regarded as poor quality koala habitat. These results highlight the importance of protecting vegetation communities not traditionally considered to have high conservation value to koalas, as these habitats may be essential for maintaining viable, widespread, low-density populations. The results from this study provide a baseline to assess future trends in koala distribution, density and abundance on Magnetic Island. PMID:23527258

  14. Fingerprints of anomalous primordial Universe on the abundance of large scale structures

    SciTech Connect

    Baghram, Shant; Abolhasani, Ali Akbar; Firouzjahi, Hassan; Namjoo, Mohammad Hossein E-mail: abolhasani@ipm.ir E-mail: MohammadHossein.Namjoo@utdallas.edu

    2014-12-01

    We study the predictions of anomalous inflationary models on the abundance of structures in large scale structure observations. The anomalous features encoded in primordial curvature perturbation power spectrum are (a): localized feature in momentum space, (b): hemispherical asymmetry and (c): statistical anisotropies. We present a model-independent expression relating the number density of structures to the changes in the matter density variance. Models with localized feature can alleviate the tension between observations and numerical simulations of cold dark matter structures on galactic scales as a possible solution to the missing satellite problem. In models with hemispherical asymmetry we show that the abundance of structures becomes asymmetric depending on the direction of observation to sky. In addition, we study the effects of scale-dependent dipole amplitude on the abundance of structures. Using the quasars data and adopting the power-law scaling k{sup n{sub A}-1} for the amplitude of dipole we find the upper bound n{sub A} < 0.6 for the spectral index of the dipole asymmetry. In all cases there is a critical mass scale M{sub c} in which for M M{sub c}) the enhancement in variance induced from anomalous feature decreases (increases) the abundance of dark matter structures in Universe.

  15. The population genetics of structural variation

    PubMed Central

    Conrad, Donald F; Hurles, Matthew E

    2009-01-01

    Population genetics is central to our understanding of human variation, and by linking medical and evolutionary themes, it enables us to understand the origins and impacts of our genomic differences. Despite current limitations in our knowledge of the locations, sizes and mutational origins of structural variants, our characterization of their population genetics is developing apace, bringing new insights into recent human adaptation, genome biology and disease. We summarize recent dramatic advances, describe the diverse mutational origins of chromosomal rearrangements and argue that their complexity necessitates a re-evaluation of existing population genetic methods. PMID:17597779

  16. Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

    PubMed

    Sawaya, Michael A; Stetz, Jeffrey B; Clevenger, Anthony P; Gibeau, Michael L; Kalinowski, Steven T

    2012-01-01

    We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains.

  17. Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

    PubMed

    Sawaya, Michael A; Stetz, Jeffrey B; Clevenger, Anthony P; Gibeau, Michael L; Kalinowski, Steven T

    2012-01-01

    We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains. PMID:22567089

  18. [New view on the population genetic structure of marine fish].

    PubMed

    Salmenkova, E A

    2011-11-01

    The view on homogeneous population genetic structure in many marine fish with high mobility has changed significantly during the last ten years. Molecular genetic population studies over the whole ranges of such species as Atlantic herring and Atlantic cod showed a complex picture of spatial differentiation both on the macrogeographic and, in many areas, on the microgeographic scale, although the differentiation for neutral molecular markers was low. It was established that the migration activity of such fish is constrained in many areas of the species range by hydrological and physicochemical transition zones (environmental gradients), as well as gyres in the spawning regions. Natal homing was recorded in a number of marine fish species. Existing in marine fish constraints of gene migration and a very high variance of reproductive success determine a significantly smaller proportion of effective reproductive size of their populations in the total population size, which generates more complex abundance dynamics than assumed earlier. The various constraints on gene migration and natal homing in marine fish promote the formation of local adaptations at ecologically important phenotypic traits. Effects of selection underlying adaptations are actively investigated in marine fish on the genomic level, using approaches of population genomics. The knowledge of adaptive intraspecific structure enables understanding the ecological and evolutionary processes, that influence biodiversity and providing spatial frames for conservation of genetic resources under commercial exploitation. Contemporary views on the population genetic and adaptive structures or biocomplexity in marine fish support and develop the main principles of the conception of systemic organization of the species and its regional populations, which were advanced by Yu.P. Altukhov and Yu.G. Rychkov.

  19. Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic

    USGS Publications Warehouse

    Sillett, Scott T.; Chandler, Richard B.; Royle, J. Andrew; Kéry, Marc; Morrison, Scott A.

    2012-01-01

    Population size and habitat-specific abundance estimates are essential for conservation management. A major impediment to obtaining such estimates is that few statistical models are able to simultaneously account for both spatial variation in abundance and heterogeneity in detection probability, and still be amenable to large-scale applications. The hierarchical distance-sampling model of J. A. Royle, D. K. Dawson, and S. Bates provides a practical solution. Here, we extend this model to estimate habitat-specific abundance and rangewide population size of a bird species of management concern, the Island Scrub-Jay (Aphelocoma insularis), which occurs solely on Santa Cruz Island, California, USA. We surveyed 307 randomly selected, 300 m diameter, point locations throughout the 250-km2 island during October 2008 and April 2009. Population size was estimated to be 2267 (95% CI 1613-3007) and 1705 (1212-2369) during the fall and spring respectively, considerably lower than a previously published but statistically problematic estimate of 12 500. This large discrepancy emphasizes the importance of proper survey design and analysis for obtaining reliable information for management decisions. Jays were most abundant in low-elevation chaparral habitat; the detection function depended primarily on the percent cover of chaparral and forest within count circles. Vegetation change on the island has been dramatic in recent decades, due to release from herbivory following the eradication of feral sheep (Ovis aries) from the majority of the island in the mid-1980s. We applied best-fit fall and spring models of habitat-specific jay abundance to a vegetation map from 1985, and estimated the population size of A. insularis was 1400-1500 at that time. The 20-30% increase in the jay population suggests that the species has benefited from the recovery of native vegetation since sheep removal. Nevertheless, this jay's tiny range and small population size make it vulnerable to natural

  20. Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic.

    PubMed

    Sillett, T Scott; Chandler, Richard B; Royle, J Andrew; Kery, Marc; Morrison, Scott A

    2012-10-01

    Population size and habitat-specific abundance estimates are essential for conservation management. A major impediment to obtaining such estimates is that few statistical models are able to simultaneously account for both spatial variation in abundance and heterogeneity in detection probability, and still be amenable to large-scale applications. The hierarchical distance-sampling model of J. A. Royle, D. K. Dawson, and S. Bates provides a practical solution. Here, we extend this model to estimate habitat-specific abundance and rangewide population size of a bird species of management concern, the Island Scrub-Jay (Aphelocoma insularis), which occurs solely on Santa Cruz Island, California, USA. We surveyed 307 randomly selected, 300 m diameter, point locations throughout the 250-km2 island during October 2008 and April 2009. Population size was estimated to be 2267 (95% CI 1613-3007) and 1705 (1212-2369) during the fall and spring respectively, considerably lower than a previously published but statistically problematic estimate of 12 500. This large discrepancy emphasizes the importance of proper survey design and analysis for obtaining reliable information for management decisions. Jays were most abundant in low-elevation chaparral habitat; the detection function depended primarily on the percent cover of chaparral and forest within count circles. Vegetation change on the island has been dramatic in recent decades, due to release from herbivory following the eradication of feral sheep (Ovis aries) from the majority of the island in the mid-1980s. We applied best-fit fall and spring models of habitat-specific jay abundance to a vegetation map from 1985, and estimated the population size of A. insularis was 1400-1500 at that time. The 20-30% increase in the jay population suggests that the species has benefited from the recovery of native vegetation since sheep removal. Nevertheless, this jay's tiny range and small population size make it vulnerable to natural

  1. Admixture, Population Structure, and F-Statistics.

    PubMed

    Peter, Benjamin M

    2016-04-01

    Many questions about human genetic history can be addressed by examining the patterns of shared genetic variation between sets of populations. A useful methodological framework for this purpose isF-statistics that measure shared genetic drift between sets of two, three, and four populations and can be used to test simple and complex hypotheses about admixture between populations. This article provides context from phylogenetic and population genetic theory. I review how F-statistics can be interpreted as branch lengths or paths and derive new interpretations, using coalescent theory. I further show that the admixture tests can be interpreted as testing general properties of phylogenies, allowing extension of some ideas applications to arbitrary phylogenetic trees. The new results are used to investigate the behavior of the statistics under different models of population structure and show how population substructure complicates inference. The results lead to simplified estimators in many cases, and I recommend to replace F3 with the average number of pairwise differences for estimating population divergence.

  2. Long-term Prairie Falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions

    USGS Publications Warehouse

    Steenhof, K.; Kochert, M.N.; Carpenter, L.B.; Lehman, R.N.

    1999-01-01

    We studied a nesting population of Prairie Falcons (Falco mexicanus) in the Snake River Birds of Prey National Conservation Area (NCA) from 1974-1997 to identify factors that influence abundance and reproduction. Our sampling period included two major droughts and associated crashes in Townsend's ground squirrel (Spermophilus townsendii) populations. The number of Prairie Falcon pairs found on long-term survey segments declined significantly from 1976-1997. Early declines were most severe at the eastern end of the NCA, where fires and agriculture have changed native shrubsteppe habitat. More recent declines occurred in the portion of canyon near the Orchard Training Area (OTA), where the Idaho Army National Guard conducts artillery firing and tank maneuvers. Overall Prairie Falcon reproductive rates were tied closely to annual indexes of ground squirrel abundance, but precipitation before and during the breeding season was related inversely to some measures of reproduction. Most reproductive parameters showed no significant trends over time, but during the 1990s, nesting success and productivity were lower in the stretch of canyon near the OTA than in adjacent areas. Extensive shrub loss, by itself, did not explain the pattern of declines in abundance and reproduction that we observed. Recent military training activities likely have interacted with fire and livestock grazing to create less than favorable foraging opportunities for Prairie Falcons in a large part of the NCA. To maintain Prairie Falcon populations in the NCA, managers should suppress wildfires, restore native plant communities, and regulate potentially incompatible land uses.

  3. Long-term prairie falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions

    USGS Publications Warehouse

    Steenhof, Karen; Kochert, Michael N.; Carpenter, L.B.; Lehman, Robert N.

    1999-01-01

    We studied a nesting population of Prairie Falcons( Falco mexicanus) in the Snake River Birds of Prey National Conservation Area (NCA) from 1974-1997 to identify factors that influence abundance and reproduction. Our sampling period included two major droughts and associated crashes in Townsenda??s ground squirrel (Spermophilus townsendii) populations. The number of Prairie Falcon pairs found on long-term survey segments declined significantly from 1976-1997. Early declines were most severe at the eastern end of the NCA, where fires and agriculture have changed native shrubsteppe habitat. More recent declines occurred in the portion of canyon near the Orchard Training Area (OTA), where the Idaho Army National Guard conducts artillery firing and tank maneuvers. Overall Prairie Falcon reproductive rates were tied closely to annual indexes of ground squirrel abundance, but precipitation before and during the breeding season was related inversely to some measures of reproduction. Most reproductive parameters showed no significant trends over time, but during the 199Os, nesting success and productivity were lower in the stretch of canyon near the OTA than in adjacent areas. Extensive shrub loss, by itself, did not explain the pattern of declines in abundance and reproduction that we observed. Recent military training activities likely have interacted with fire and livestock grazing to create less than favorable foraging opportunities for Prairie Falcons in a large part of the NCA. To maintain Prairie Falcon populations in the NCA, managers should suppress wildfires, restore native plant communities, and regulate potentially incompatible land uses.

  4. Effects of understory structure on the abundance, richness and diversity of Collembola (Arthropoda) in southern Brazil.

    PubMed

    Ribeiro-Troian, Vera R; Baldissera, Ronei; Hartz, Sandra M

    2009-01-01

    The purpose of this study was to investigate the effects of different landscape structures on the understory Collembola community. Four different forest physiognomies were compared: Pinus spp. plantation, Eucalyptus spp. plantation, Araucaria angustifolia plantation, and a remaining native Araucaria forest. Three areas containing two sampling units (25 mx2 m each) were selected in each forest physiognomy. Understory Collembola collection was done with a 1x1 m canvas sheet held horizontally below the vegetation, which was beaten with a 1 m long stick, seasonally from September 2003 to August 2004. We evaluated the influence of forest physiognomies on the abundance, richness and diversity of Collembola communities. It was also verified if the habitat structure of each physiognomy was associated with the composition of the Collembola community. A total number of 4,111 individuals were collected belonging to the families Entomobrydae and Tomocerida (Entomobryomorpha), and Sminthuridae (Symphypleona), and divided in 12 morphospecies. Pinus plantation presented the highest richness, abundance and diversity of Collembola and it was associated to diverse understory vegetation. The abundance of Entomobrydae and Sminthuridae was associated to the presence of bushes, while Tomoceridae abundance was associated to the presence of trees. The habitat structure, measured through understory vegetation density and composition, plays an important role on the determination of the structure and composition of the Collembola community.

  5. Abundance Trends and Status of the Little Colorado River Population of Humpback Chub: An Update Considering Data From 1989-2008

    USGS Publications Warehouse

    Coggins,, Lewis G.; Walters, Carl J.

    2009-01-01

    Mark-recapture methods have been used for the past two decades to assess trends in adult abundance and recruitment of the Little Colorado River (LCR) population of humpback chub. These methods indicate that the adult population declined through the 1980s and early 1990s but has been increasing for the past decade. Recruitment appears also to have increased, particularly in the 2003-4 period. Considering a range of assumed natural mortality-rates and magnitude of ageing error, it is unlikely that there are currently less than 6,000 adults or more than 10,000 adults. Our best estimate of the current adult (age 4 years or more) population is approximately 7,650 fish. Recent humpback chub assessments using the Age-Structured Mark-Recapture model (ASMR) and reported in 2006 (Melis and others, 2006) and 2008 (Coggins, 2008a,b) have provided abundance and recruitment trend estimates that have changed progressively over time as more data are considered by the model. The general pattern of change implies a less severe decline in adult abundance during the late 1980s through early 1990s, with attendant changes in recruitment supporting this demographic pattern. We have been concerned that these changes are not indicative of the true population and may be associated with a 'retrospective' bias as additional data are included in the ASMR model. To investigate this possibility, we developed a realistic individual-based simulation model (IBM) to generate replicate artificial data sets with similar characteristics to the true humpback chub data. The artificial data have known abundance trends and we analyzed these data with ASMR. On the basis of these simulations, we believe that errors in assigning age (and therefore brood-year) to fish based on their length are likely to have caused the retrospective bias pattern seen in the assessments and to have caused both less severe trends in the adult abundance estimates and progressively more severe downward bias in estimates of adult

  6. Hydrography and population genetic structure in brook charr (Salvelinus fontinalis, Mitchill) from eastern Canada.

    PubMed

    Hébert, C; Danzman, R G; Jones, M W; Bernatchez, L

    2000-07-01

    Despite the abundance of studies of genetic diversity in freshwater fishes, few have specifically addressed the role of habitat structure in partitioning genetic variance within and among populations. In this study, we analysed the variability of six microsatellite loci among 24 brook charr population samples in order to correlate hydrographic structure with genetic organization. These populations originated from three Canadian National parks (Kouchibouguac, Fundy and Forillon) that showed distinct hydrographic structure. Considering the general characteristics of these habitats, we formulated specific hypotheses in regard to genetic structure, which were principally based on the potential for gene flow and population size associated with each habitat. The hierarchical analysis of molecular variance and the genetic distances computed among populations revealed that habitat structure analyses constitute an important, but insufficient, predictor of genetic structure. We discuss the importance of habitat complexity on genetic structure in the context of management and conservation.

  7. Familial Identification: Population Structure and Relationship Distinguishability

    PubMed Central

    Rohlfs, Rori V.; Fullerton, Stephanie Malia; Weir, Bruce S.

    2012-01-01

    With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States. PMID:22346758

  8. Spatial population structure of Yellowstone bison

    USGS Publications Warehouse

    Olexa, E.M.; Gogan, P.J.P.

    2007-01-01

    Increases in Yellowstone National Park, USA, bison (Bison bison) numbers and shifts in seasonal distribution have resulted in more frequent movements of bison beyond park boundaries and development of an interagency management plan for the Yellowstone bison population. Implementation of the plan under the adaptive management paradigm requires an understanding of the spatial and temporal structure of the population. We used polythetic agglomerative hierarchical cluster analysis of radiolocations obtained from free-ranging bison to investigate seasonal movements and aggregations. We classified radiolocations into 4 periods: annual, peak rut (15 Jul-15 Sep), extended rut (1 Jun-31 Oct), and winter (1 Nov-31 May). We documented spatial separation of Yellowstone bison into 2 segments, the northern and central herds, during all periods. The estimated year-round exchange rate (4.85-5.83%) of instrumented bison varied with the fusion strategy employed. We did not observe exchange between the 2 segments during the peak rut and it varied during the extended rut (2.15-3.23%). We estimated a winter exchange of 4.85-7.77%. The outcome and effectiveness of management actions directed at Yellowstone bison may be affected by spatial segregation and herd affinity within the population. Reductions based on total population size, but not applied to the entire population, may adversely affect one herd while having little effect on the other. Similarly, management actions targeting a segment of the population may benefit from the spatial segregation exhibited.

  9. Purification, characterization and structural analysis of an abundant beta-1,3-glucanase from banana fruit.

    PubMed

    Peumans, W J; Barre, A; Derycke, V; Rougé, P; Zhang, W; May, G D; Delcour, J A; Van Leuven, F; Van Damme, E J

    2000-02-01

    An abundant, catalytically active beta-1,3-endoglucanase (EC 3.2.1. 39) has been isolated from the pulp of ripe bananas. Biochemical analysis of the purified protein, molecular modelling, and molecular cloning of the corresponding gene indicate that this banana enzyme closely resembles previously characterized plant beta-glucanases with respect to its amino-acid sequence, structure and biological activity. The results described in this paper demonstrate both the occurrence of an abundant active beta-1,3-endoglucanases in fruits and also readdress the question of the possible involvement of these enzymes in the ripening and/or softening process.

  10. Species abundance distribution and population dynamics in a two-community model of neutral ecology

    NASA Astrophysics Data System (ADS)

    Vallade, M.; Houchmandzadeh, B.

    2006-11-01

    Explicit formulas for the steady-state distribution of species in two interconnected communities of arbitrary sizes are derived in the framework of Hubbell’s neutral model of biodiversity. Migrations of seeds from both communities as well as mutations in both of them are taken into account. These results generalize those previously obtained for the “island-continent” model and they allow an analysis of the influence of the ratio of the sizes of the two communities on the dominance/diversity equilibrium. Exact expressions for species abundance distributions are deduced from a master equation for the joint probability distribution of species in the two communities. Moreover, an approximate self-consistent solution is derived. It corresponds to a generalization of previous results and it proves to be accurate over a broad range of parameters. The dynamical correlations between the abundances of a species in both communities are also discussed.

  11. Distribution and abundance of marine bird and pinniped populations within Port Foster, Deception Island, Antarctica

    NASA Astrophysics Data System (ADS)

    Kendall, Katrina A.; Ruhl, Henry A.; Wilson, Robert C.

    2003-06-01

    Seabirds and pinnipeds were surveyed during four cruises from March 1999 to November 2000 at Port Foster, Deception Island, Antarctica. Abundances and distributions of three species of pinnipeds, Arctocephalus gazella (Antarctic fur seals), Leptonychotes weddelli (Weddell seals), and Lobodon carcinophagus (crabeater seals), and 11 species of marine birds were documented within Port Foster. A. gazella was the dominant pinniped within Port Foster; its abundance has increased since the 1986/87 austral summer season. A. gazella were concentrated at the entrance to Port Foster. More pinnipeds were observed during the austral summer than during the spring. The most dominant seabird, Pygoscelis antarctica (chinstrap penguin), was concentrated along the rocky cliffs behind the beaches where A. gazella hauled out. Larus dominicanus (kelp gull) and Daption capense (cape petrel) were the most dominant flying seabirds. All other seabird species were more widely distributed around Port Foster than P. antarctica. There was no clear trend in abundances of seabirds over the study period. It is possible that the protected area of Port Foster provides refuge for vagrants of colonies along the outer periphery of the island and as a stopover point for migrating species.

  12. Improved Statistical Analysis of Low Abundance Phenomena in Bimodal Bacterial Populations

    PubMed Central

    Reinhard, Friedrich; van der Meer, Jan Roelof

    2013-01-01

    Accurate detection of subpopulation size determinations in bimodal populations remains problematic yet it represents a powerful way by which cellular heterogeneity under different environmental conditions can be compared. So far, most studies have relied on qualitative descriptions of population distribution patterns, on population-independent descriptors, or on arbitrary placement of thresholds distinguishing biological ON from OFF states. We found that all these methods fall short of accurately describing small population sizes in bimodal populations. Here we propose a simple, statistics-based method for the analysis of small subpopulation sizes for use in the free software environment R and test this method on real as well as simulated data. Four so-called population splitting methods were designed with different algorithms that can estimate subpopulation sizes from bimodal populations. All four methods proved more precise than previously used methods when analyzing subpopulation sizes of transfer competent cells arising in populations of the bacterium Pseudomonas knackmussii B13. The methods’ resolving powers were further explored by bootstrapping and simulations. Two of the methods were not severely limited by the proportions of subpopulations they could estimate correctly, but the two others only allowed accurate subpopulation quantification when this amounted to less than 25% of the total population. In contrast, only one method was still sufficiently accurate with subpopulations smaller than 1% of the total population. This study proposes a number of rational approximations to quantifying small subpopulations and offers an easy-to-use protocol for their implementation in the open source statistical software environment R. PMID:24205184

  13. Osprey distribution, abundance, and status in western North America: II. The Oregon population

    USGS Publications Warehouse

    Henny, C.J.; Collins, J.A.; Deibert, W.J.

    1978-01-01

    An estimated 308 ? 23 pairs of Ospreys nested in the survey area in Oregon in 1976. Major concentration centers include Crane Prairie Reservoir and the adjacent Deschutes National Forest, the coastal lakes and reservoirs between Florence and North Bend, the Rogue River, the Lane County reservoirs, and the Umpqua River. An estimated 47 percent of the Oregon population is nesting at reservoirs. Limited information is available concerning the long-term status of the Oregon population; however, the ability of the species to pioneer newly created reservoirs emphasizes that the population is utilizing new habitats.

  14. Estimating population abundance and mapping distribution of wintering sea ducks in coastal waters of the mid-Atlantic

    USGS Publications Warehouse

    Koneff, M.D.; Royle, J. Andrew; Forsell, D.J.; Wortham, J.S.; Boomer, G.S.; Perry, M.C.

    2005-01-01

    Survey design for wintering scoters (Melanitta sp.) and other sea ducks that occur in offshore waters is challenging because these species have large ranges, are subject to distributional shifts among years and within a season, and can occur in aggregations. Interest in winter sea duck population abundance surveys has grown in recent years. This interest stems from concern over the population status of some sea ducks, limitations of extant breeding waterfowl survey programs in North America and logistical challenges and costs of conducting surveys in northern breeding regions, high winter area philopatry in some species and potential conservation implications, and increasing concern over offshore development and other threats to sea duck wintering habitats. The efficiency and practicality of statistically-rigorous monitoring strategies for mobile, aggregated wintering sea duck populations have not been sufficiently investigated. This study evaluated a 2-phase adaptive stratified strip transect sampling plan to estimate wintering population size of scoters, long-tailed ducks (Clangua hyemalis), and other sea ducks and provide information on distribution. The sampling plan results in an optimal allocation of a fixed sampling effort among offshore strata in the U.S. mid-Atlantic coast region. Phase I transect selection probabilities were based on historic distribution and abundance data, while Phase 2 selection probabilities were based on observations made during Phase 1 flights. Distance sampling methods were used to estimate detection rates. Environmental variables thought to affect detection rates were recorded during the survey and post-stratification and covariate modeling were investigated to reduce the effect of heterogeneity on detection estimation. We assessed cost-precision tradeoffs under a number of fixed-cost sampling scenarios using Monte Carlo simulation. We discuss advantages and limitations of this sampling design for estimating wintering sea duck

  15. Population dynamics of some Pakistan mosquitoes: changes in adult relative abundance over time and space.

    PubMed

    Reisen, W K; Milby, M M

    1986-02-01

    Time series and spatial changes in the relative abundance of 14 mosquito species were described from weekly or biweekly collections at nine localities in Punjab province, Pakistan, from January 1976 to June 1980. Comparisons between indoor aspirator catches and outdoor mechanical sweeper collections enabled mosquito resting habits to be classified as: (1) endophilic (Anopheles culicifacies, An. fluviatilis, An. stephensi, An. subpictus); (2) partially exophilic (An. annularis, An. pulcherrimus, An. nigerrimus, Culex bitaeniorhynchus, Cx, pseudovishnui, Cx, quinquefasciatus, Cx. tritaeniorhynchus), or exophilic (Cx. fuscocephala, Aedes caspius, Mansonia uniformis). Temporal abundance patterns were grouped by seasonality, overwintering strategies and the magnitude of fluctuation. Seasonal patterns were: (1) unimodal-spring (Cx. quinquefasciatus, Ae. capius); (2) unimodal-monsoon (An. nigerrimus, An. subpictus, Cx. bitaeniorhynchus, Cx. fuscocephala); (3) bimodal-spring dominant (An. annularis, An. culcifacies, An. stephensi), and (4) bimodal-monsoon/post-monsoon dominant (An. fluviatilis, An. pulcherrimus, Cx. pseudovishnui, Cx. tritaeniorhynchus, Ma. uniformis). Mosquito overwintering strategies included: (1) adults with slowed reproductive activity (An. annularis, An. culicifacies, An. fluviatilis, An. pulcherrimus, An. stephensi, Cx. quinquefasciatus); (2) females with interrupted reproductive activity (An. nigerrimus, Cx. fuscocephala, Cx. pseudovishnui, Cx. tritaeniorhynchus); (3) immature stages (Ae. caspius, Ma. uniformis) and (4) annual extinction and re-introduction (An. subpictus). The magnitude of seasonal change was classified by the number of standard deviations from the overall mean exhibited by the annual maxima or minima: (1) stationary, less than 1 standard deviation (An. culicifacies, An. fluviatilis, Cx. bitaeniorhynchus, Ae. caspius), (2) fluctuating moderately, one to two standard deviations (An. annularis, An. nigerrimus, An. pulcherrimus, An

  16. Coronal Thermal Structure and Abundance of Super-Metal-Rich Late-Type Stars

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy; Mushotzky, Richard F. (Technical Monitor)

    2002-01-01

    This report covers the NASA grant NAG5-9943 for Cycle 1 XMM Guest Observer Program. The project is entitled 'Coronal Thermal Structure and Abundances of Super-Metal-Rich Late-Type Stars.' This observation is for grating spectroscopy of 30 Ari, a late-type star with very high metallicity (about twice solar). The goal is to use extreme cases to help understand how abundances change from the photosphere to the corona. The target was obtained by XMM-Newton on 2001 January 16 for 28000 sec. Data processing could not proceed until last fall because the SAS RGS software did not work. A poster was presented at the conference 'New Visions of the X-ray Universe in the XMM-Newton and Chandra Era,' held in Noordwijk 26-30 November 2001. The paper was entitled,'Coronal Abundances and Thermal Structure of the Super-Metal-Rich Star 30 Ari,'. The poster presented analysis of EPIC and RGS data to determine the individual abundances from the star and the emission measure distribution as a function of temperature. Results were compared with previous results on this star by our team using ASCA data.

  17. Population size and relative abundance of adult Alabama shad reaching jim woodruff lock and dam, Apalachicola River, Florida

    USGS Publications Warehouse

    Ely, Patrick C.; Young, S.P.; Isely, J.J.

    2008-01-01

    We estimated the population size of migrating Alabama shad Alosa alabamae below Jim Woodruff Lock and Dam in the Apalachicola River (located in the central panhandle of northwestern Florida) using mark-recapture and relative abundance techniques. After adjustment for tag loss, emigration, and mortality, the population size was estimated as 25,935 (95% confidence interval, 17,715-39,535) in 2005, 2,767 (838-5,031) in 2006, and 8,511 (5,211-14,674) in 2007. The cumulative catch rate from boat electrofishing averaged 20.47 Alabama shad per hour in 2005, 6.10 per hour in 2006, and 13.17 per hour in 2007. The relationship between population size (N) and electrofishing catch per unit effort (CPUE) was modeled by the equation N = -9008.2 + (electrofishing CPUE X 1616.4). Additionally, in 2007 the hook-and-line catch rate averaged 1.94 Alabama shad per rod hour. A predictive model relating the population size and hook-and-line CPUE of spawning American shad A. sapidissima was applied to Alabama shad hook-and-line CPUE and produced satisfactory results. Recent spawning populations of Alabama shad in the Apalachicola River are low relative to American shad populations in other southeastern U.S. rivers. ?? Copyright by the American Fisheries Society 2008.

  18. The Stellar Population Structure of the Galactic Disk

    NASA Astrophysics Data System (ADS)

    Bovy, Jo; Rix, Hans-Walter; Schlafly, Edward F.; Nidever, David L.; Holtzman, Jon A.; Shetrone, Matthew; Beers, Timothy C.

    2016-05-01

    The spatial structure of stellar populations with different chemical abundances in the Milky Way (MW) contains a wealth of information on Galactic evolution over cosmic time. We use data on 14,699 red-clump stars from the APOGEE survey, covering 4 {kpc}≲ R≲ 15 {kpc}, to determine the structure of mono-abundance populations (MAPs)—stars in narrow bins in [α /{Fe}] and [{Fe}/{{H}}]—accounting for the complex effects of the APOGEE selection function and the spatially variable dust obscuration. We determine that all MAPs with enhanced [α /{Fe}] are centrally concentrated and are well-described as exponentials with a scale length of 2.2+/- 0.2 {kpc} over the whole radial range of the disk. We discover that the surface-density profiles of low-[α /{Fe}] MAPs are complex: they do not monotonically decrease outwards, but rather display a peak radius ranging from ≈ 5 to ≈ 13 {kpc} at low [{Fe}/{{H}}]. The extensive radial coverage of the data allows us to measure radial trends in the thickness of each MAP. While high-[α /{Fe}] MAPs have constant scale heights, low-[α /{Fe}] MAPs flare. We confirm, now with high-precision abundances, previous results that each MAP contains only a single vertical scale height and that low-[{Fe}/{{H}}], low-[α /{Fe}] and high-[{Fe}/{{H}}], high-[α /{Fe}] MAPs have intermediate ({h}Z≈ 300{--}600 {pc}) scale heights that smoothly bridge the traditional thin- and thick-disk divide. That the high-[α /{Fe}], thick disk components do not flare is strong evidence against their thickness being caused by radial migration. The correspondence between the radial structure and chemical-enrichment age of stellar populations is clear confirmation of the inside-out growth of galactic disks. The details of these relations will constrain the variety of physical conditions under which stars form throughout the MW disk.

  19. Reef-scale trends in Florida Acropora spp. abundance and the effects of population enhancement

    PubMed Central

    Kerr, Katryna; Williams, Dana E.

    2016-01-01

    Since the listing of Acropora palmata and A. cervicornis under the US Endangered Species Act in 2006, increasing investments have been made in propagation of listed corals (primarily A. cervicornis, A. palmata to a much lesser extent) in offshore coral nurseries and outplanting cultured fragments to reef habitats. This investment is superimposed over a spatiotemporal patchwork of ongoing disturbances (especially storms, thermal bleaching, and disease) as well as the potential for natural population recovery. In 2014 and 2015, we repeated broad scale (>50 ha), low precision Acropora spp. censuses (i.e., direct observation by snorkelers documented via handheld GPS) originally conducted in appropriate reef habitats during 2005–2007 to evaluate the trajectory of local populations and the effect of population enhancement. Over the decade-long study, A. palmata showed a cumulative proportional decline of 0.4 –0.7x in colony density across all sites, despite very low levels of outplanting at some sites. A. cervicornis showed similar proportional declines at sites without outplanting. In contrast, sites that received A. cervicornis outplants showed a dramatic increase in density (over 13x). Indeed, change in A. cervicornis colony density was significantly positively correlated with cumulative numbers of outplants across sites. This study documents a substantive reef-scale benefit of Acropora spp. population enhancement in the Florida Keys, when performed at adequate levels, against a backdrop of ongoing population decline. PMID:27703862

  20. Use of the robust design to estimate seasonal abundance and demographic parameters of a coastal bottlenose dolphin (Tursiops aduncus) population.

    PubMed

    Smith, Holly C; Pollock, Ken; Waples, Kelly; Bradley, Stuart; Bejder, Lars

    2013-01-01

    As delphinid populations become increasingly exposed to human activities we rely on our capacity to produce accurate abundance estimates upon which to base management decisions. This study applied mark-recapture methods following the Robust Design to estimate abundance, demographic parameters, and temporary emigration rates of an Indo-Pacific bottlenose dolphin (Tursiops aduncus) population off Bunbury, Western Australia. Boat-based photo-identification surveys were conducted year-round over three consecutive years along pre-determined transect lines to create a consistent sampling effort throughout the study period and area. The best fitting capture-recapture model showed a population with a seasonal Markovian temporary emigration with time varying survival and capture probabilities. Abundance estimates were seasonally dependent with consistently lower numbers obtained during winter and higher during summer and autumn across the three-year study period. Specifically, abundance estimates for all adults and juveniles (combined) varied from a low of 63 (95% CI 59 to 73) in winter of 2007 to a high of 139 (95% CI 134 to148) in autumn of 2009. Temporary emigration rates (γ') for animals absent in the previous period ranged from 0.34 to 0.97 (mean  =  0.54; ±SE 0.11) with a peak during spring. Temporary emigration rates for animals present during the previous period (γ'') were lower, ranging from 0.00 to 0.29, with a mean of 0.16 (± SE 0.04). This model yielded a mean apparent survival estimate for juveniles and adults (combined) of 0.95 (± SE 0.02) and a capture probability from 0.07 to 0.51 with a mean of 0.30 (± SE 0.04). This study demonstrates the importance of incorporating temporary emigration to accurately estimate abundance of coastal delphinids. Temporary emigration rates were high in this study, despite the large area surveyed, indicating the challenges of sampling highly mobile animals which range over large spatial areas. PMID:24130781

  1. The Genetic Structure of the Swedish Population

    PubMed Central

    Humphreys, Keith; Grankvist, Alexander; Leu, Monica; Hall, Per; Liu, Jianjun; Ripatti, Samuli; Rehnström, Karola; Groop, Leif; Klareskog, Lars; Ding, Bo; Grönberg, Henrik; Xu, Jianfeng; Pedersen, Nancy L.; Lichtenstein, Paul; Mattingsdal, Morten; Andreassen, Ole A.; O'Dushlaine, Colm; Purcell, Shaun M.; Sklar, Pamela; Sullivan, Patrick F.; Hultman, Christina M.; Palmgren, Juni; Magnusson, Patrik K. E.

    2011-01-01

    Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with extensive geographical coverage, we analyzed the genetic structure of the Swedish population. We observed strong differences between the far northern counties and the remaining counties. The population of Dalarna county, in north middle Sweden, which borders southern Norway, also appears to differ markedly from other counties, possibly due to this county having more individuals with remote Finnish or Norwegian ancestry than other counties. An analysis of genetic differentiation (based on pairwise Fst) indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. Both the increased degree of homozygosity in the north and the large genetic differences between the south and the north may have arisen due to a small population in the north and the vast geographical distances between towns and villages in the north, in contrast to the more densely settled southern parts of Sweden. Our findings have implications for future genome-wide association studies (GWAS) with respect to the matching of cases and controls and the need for within-county matching. We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale. Thus, population stratification needs to be accounted for, even within a country like Sweden, which is often perceived to be relatively homogenous and a favourable resource for genetic mapping, otherwise inferences based on genetic data may lead to false conclusions

  2. Decline in abundance and health state of an Atlantic subtropical gorgonian population.

    PubMed

    Erni Cassola, Gabriel; Pacheco, Matheus S C; Barbosa, Moysés C; Hansen, Dennis M; Ferreira, Carlos E L

    2016-03-15

    Losses in coral cover have been widely reported for the Caribbean. In contrast, much less is known about the health state of the Brazilian reef fauna, which was declared as a priority for Atlantic biodiversity conservation due to its high degree of endemism. In the present study, we assessed the general health state of Phyllogorgia dilatata assemblages at the subtropical reefs of Arraial do Cabo (southeastern Brazil), where observations suggest that the abundance of this endemic gorgonian species has declined. We found that about 49% of the sampled colonies were dead, and 73% of the living colonies were affected by tissue loss. Tissue loss initially manifested as multifocal holes in the planar colonial coenenchyme and peripheral tissue retraction leaving denuded skeletal axes. In combination with other recent studies, our results raise the awareness for an increasingly threatened Southwestern Atlantic reef coral fauna. PMID:26822908

  3. Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8)

    PubMed Central

    Farag, Ibrahim F.; Davis, James P.; Youssef, Noha H.; Elshahed, Mostafa S.

    2014-01-01

    We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8). Our aim was to identify the putative ecological role(s) played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ∼1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples), and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples). While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as non-saline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions. PMID:24637619

  4. Responses of infaunal populations to benthoscape structure and the potential importance of transition zones

    USGS Publications Warehouse

    Zajac, R.N.; Lewis, R.S.; Poppe, L.J.; Twichell, D.C.; Vozarik, J.; DiGiacomo-Cohen, M. L.

    2003-01-01

    Relationships between population abundance and seafloor landscape, or benthoscape, structure were examined for 16 infaunal taxa in eastern Long Island Sound. Based on analyses of a side-scan sonar mosaic, the 19.4-km2 study area was comprised of six distinct large-scale (> km2) benthoscape elements, with varying levels of mesoscale (km2-m2) and small-scale (2) physical and biological habitat heterogeneity. Transition zones among elements varied from ~50 to 200 m in width, comprised ~32% of the benthoscape, and added to overall benthoscape heterogeneity. Population abundances of nine taxa varied significantly among the large-scale elements. Most species were found at high abundances only in one benthoscape element, but three had several foci of elevated abundances. Analyses of population responses to habitat heterogeneity at different spatial scales indicated that abundances of eight taxa varied significantly among spatial scales, but the significant scales were mixed among these species. Relatively large residual variations suggest significant amounts of mesoscale spatial variation were unaccounted for, varying from ~1 km2 to several m2. Responses to transition zones were mixed as well. Abundances of nine taxa varied significantly among transition zones and interiors of benthoscape elements, most with elevated abundances in transition zones. Our results show that infaunal populations exhibit complex and spatially varying patterns of abundance in relation to benthoscape structure and suggest that mesoscale variation may be particularly critical in this regard. Also, transition zones among benthoscape features add considerably to this variation and may be ecological important areas in seafloor environments.

  5. Origin and population structure of the Icelanders.

    PubMed

    Williams, J T

    1993-04-01

    The Norse and Celtic contributions to the founding population of Iceland have been estimated previously on a pan-Icelandic basis using gene frequency data for the entire island. Accounts of the settlement of Iceland, however, suggest that different regions received different proportions of Norse and Celtic settlers, indicating the need to incorporate geographic variation into Icelandic admixture studies. A formal likelihood ratio test rejects the null hypothesis of regional homogeneity in admixture proportions. Here, regional admixture estimates for Iceland are reported; they are in agreement with the settlement pattern inferred from historical accounts. The western, northern, and southern regions of Iceland exhibit a moderate Celtic component, consistent with historical indications that these regions were settled by Norse Vikings from the British Isles, accompanied by Celtic wives and slaves. Eastern Iceland, believed to have been settled chiefly by Vikings from Scandinavia, is characterized by a large Norse component of admixture. The northwestern peninsula is also found to be predominantly Norse. Regional genetic data are used to elucidate the contemporary population structure of Iceland. The observed structure correlates well with patterns of Icelandic geography, history, economy, marriage, urbanization, and internal migration. The northeastern region is strongly isolated, the urbanized areas of the north and southwest are representative of the overall population, and the remaining regions exhibit small-scale variation about the genetic central tendency. A high level of genetic homogeneity is indicated (RST = 0.0005), consistent with the high internal migration rate of the Icelanders. A regression of mean per-locus heterozygosity on distance from the gene frequency centroid reveals a greater than average external gene flow into the eastern region, whereas the northwestern peninsula has received less than average external gene flow. Iceland is compared with

  6. Linking CAI abundance to polarimetric response in a population of ancient asteroids

    NASA Astrophysics Data System (ADS)

    Devogele, Maxime; Tanga, Paolo; Bendjoya, Philippe; Rivet, Jean-Pierre; Surdej, Jean; Bus, Schelte J.; Sunshine, Jessica M.; Cellino, Alberto; Campins, Humberto; Licandro, Javier; Pinilla-Alonso, Noemi; Carry, Benoit

    2016-10-01

    Polarimetry constitutes one of the fundamental tools for characterizing the surface texture and composition of airless Solar System bodies. In 2006, polarimetric observations led to the discovery of a new type of asteroids, which displays a peculiar polarimetric response. These asteroids are collectively known as "Barbarians", from (234) Barbara the first discovered one.The most commonly accepted explanation for this perculiar polarization response seems to be the presence of a high percentage of fluffy-type Calcium Aluminium-rich Inclusions (CAIs), whose optical properties could produce the observed polarization. Their reflectance spectra also exibit an absorption feature in the near-infrared around 2.1-2.2 microns, that is characteristic of this peculiar group.Based on these results, we organized a systematic polarimetric and near-infrared observational campaign of known Barbarians or candidate asteroids. These campaigns include members of the family of 1040 Klumpkea, 2085 Henan and 729 Watsonia, which are known to contain Barbarian and/or L-type asteroids also suspected to have such a polarimetric behaviour. We have made use of the ToPo polarimeter at the 1m telescope of the Centre pédagogique Planète et Univers (C2PU, Observatoire de la Côte d'Azur, France). The spectroscopic observations in the near-infrared were obtained with the SpeX instrument at the NASA's InfraRed Telescope Facility (IRTF).By combining polarimetry and spectroscopy we find a correlation between the abundance of CAIs and the inversion angle of the phase-polarization curve of Barbarian asteroids. This is the first time that a direct link has been established between a specific polarimetric response and the surface composition of asteroids. In addition, we find a considerable variety of CAI abundance from one object to the other, consistent with a wide range of possible albedos. Since these asteroids constitute a reservoir of primitive Solar System material, understanding their origin can

  7. Effects of ocean acidification on population dynamics and community structure of crustose coralline algae.

    PubMed

    Ordoñez, Alexandra; Doropoulos, Christopher; Diaz-Pulido, Guillermo

    2014-06-01

    Calcification and growth of crustose coralline algae (CCA) are affected by elevated seawater pCO2 and associated changes in carbonate chemistry. However, the effects of ocean acidification (OA) on population and community-level responses of CCA have barely been investigated. We explored changes in community structure and population dynamics (size structure and reproduction) of CCA in response to OA. Recruited from an experimental flow-through system, CCA settled onto the walls of plastic aquaria and developed under exposure to one of three pCO2 treatments (control [present day, 389±6 ppm CO2], medium [753±11 ppm], and high [1267±19 ppm]). Elevated pCO2 reduced total CCA abundance and affected community structure, in particular the density of the dominant species Pneophyllum sp. and Porolithon onkodes. Meanwhile, the relative abundance of P. onkodes declined from 24% under control CO2 to 8.3% in high CO2 (65% change), while the relative abundance of Pneophyllum sp. remained constant. Population size structure of P. onkodes differed significantly across treatments, with fewer larger individuals under high CO2. In contrast, the population size structure and number of reproductive structures (conceptacles) per crust of Pneophyllum sp. was similar across treatments. The difference in the magnitude of the response of species abundance and population size structure between species may have the potential to induce species composition changes in the future. These results demonstrate that the impacts of OA on key coral reef builders go beyond declines in calcification and growth, and suggest important changes to aspects of population dynamics and community ecology.

  8. Distribution and abundance of fish populations in Harike wetland--a Ramsar site in India.

    PubMed

    Dua, Anish; Parkash, Chander

    2009-03-01

    Harike wetland was declared a Ramsar site in 1990. It is located at the confluence of two major rivers of Indus rivers system, the Beas and the Sutlej, but was never explored extensively for its existing fish biodiversity. Earlier only 27 fish species of commercial value were reported from the wetland. Acknowledging its importance for rich diversity fish assemblages in seven different reaches of Harike wetland were studied to determine their abundance and distribution. 61 fish species of 35 genera were recorded from Harike wetland during the present study. Cirrihinus mrigala and Cyprinus carpio belonging to family Cyprinidae were the dominant fish species. Lake and Riyasat having many microhabitats supported highest diversity of fishes (60 and 56 respectively) followed by Beas (20) Sutlej (14), Confluence (12), Reservoir (9) and Downstream (8). Among the IUCN designated threatened species, 1 Critically Endangered, 4 Endangered and 13 Vulnerable fish species of India are found in Harike wetland. Species diversity index, dominance, evenness and catch per unit effort were calculated to ascertain the fish distribution in Harike wetland. PMID:20121026

  9. SOLAR CYCLE ABUNDANCE VARIATIONS IN COROTATING INTERACTION REGIONS: EVIDENCE FOR A SUPRATHERMAL ION SEED POPULATION

    SciTech Connect

    Mason, G. M.; Desai, M. I.; Li, G.

    2012-04-01

    We have surveyed the heavy ion composition of corotating interaction regions (CIRs) over the recent solar minimum and combined this with our earlier survey to cover the 1998-2011 period encompassing a full solar cycle and onset of the new cycle. We find that the solar minimum CIR intensities and spectral forms are similar to those in active periods, indicating that the basic acceleration mechanism does not vary with solar activity for energies below a few MeV nucleon{sup -1}. However, the heavy ion abundances show a clear correlation with sunspot number, where heavy ions are more enhanced during active periods. Over the mass range He-Fe, the enhancement is organized by a power law in Q/M with exponent -1.9, with Fe/O varying by a factor of {approx}6. During solar minimum CIR Fe/O was {approx}0.05, well below the corresponding solar wind ratio. Previous studies have shown that rare ions (He{sup +}, {sup 3}He) enhanced in CIRs come from the suprathermal ion pool. The observations presented here extend this evidence, indicating that in addition to rare He{sup +} and {sup 3}He the CIR major heavy ion species are accelerated out of the suprathermal ion pool, not the bulk solar wind.

  10. Juxtaposition between host population structures: implications for disease transmission in a sympatric cervid community

    PubMed Central

    Vander Wal, Eric; Edye, Iain; Paquet, Paul C; Coltman, David W; Bayne, Erin; Brook, Ryan K; Andrés, José A

    2013-01-01

    Sympatric populations of phylogenetically related species are often vulnerable to similar communicable diseases. Although some host populations may exhibit spatial structure, other hosts within the community may have unstructured populations. Thus, individuals from unstructured host populations may act as interspecific vectors among discrete subpopulations of sympatric alternate hosts. We used a cervid-bovine tuberculosis (Mycobacterium bovis) system to investigate the landscape-scale potential for bovine tuberculosis transmission within a nonmigratory white-tailed deer (Odocoileus virginianus) and elk (Cervus canadensis) community. Using landscape population genetics, we tested for genetic and spatial structure in white-tailed deer. We then compared these findings with the sympatric elk population that is structured and which has structure that correlates spatially and genetically to physiognomic landscape features. Despite genetic structure that indicates the white-tailed deer population forms three sympatric clusters, the absence of spatial structure suggested that intraspecific pathogen transmission is not likely to be limited by physiognomic landscape features. The potential for intraspecific transmission among subpopulations of elk is low due to spatial population structure. Given that white-tailed deer are abundant, widely distributed, and exhibit a distinct lack of spatial population structure, white-tailed deer likely pose a greater threat as bovine tuberculosis vectors among elk subpopulations than elk. PMID:24187583

  11. Physiological tolerances account for range limits and abundance structure in an invasive slug.

    PubMed

    Lee, Jennifer E; Janion, Charlene; Marais, Elrike; Jansen van Vuuren, Bettine; Chown, Steven L

    2009-04-22

    Despite the importance of understanding the mechanisms underlying range limits and abundance structure, few studies have sought to do so. Here we use a terrestrial slug species, Deroceras panormitanum, that has invaded a remote, largely predator-free, Southern Ocean island as a model system to do so. Across Marion Island, slug density does not conform to an abundant centre distribution. Rather, abundance structure is characterized by patches and gaps. These are associated with this desiccation-sensitive species' preference for biotic and drainage line habitats that share few characteristics except for their high humidity below the vegetation surface. The coastal range margin has a threshold form, rapidly rising from zero to high density. Slugs do not occur where soil-exchangeable Na values are higher than 3000 mg kg(-1), and in laboratory experiments, survival is high below this value but negligible above it. Upper elevation range margins are a function of the inability of this species to survive temperatures below an absolute limit of -6.4 degrees C, which is regularly exceeded at 200 m altitude, above which slug density declines to zero. However, the linear decline in density from the coastal peak is probably also a function of a decline in performance or time available for activity. This is probably associated with an altitudinal decline in mean annual soil temperature. These findings support previous predictions made regarding the form of density change when substrate or climatic factors set range limits.

  12. Physiological tolerances account for range limits and abundance structure in an invasive slug

    PubMed Central

    Lee, Jennifer E.; Janion, Charlene; Marais, Elrike; Jansen van Vuuren, Bettine; Chown, Steven L.

    2009-01-01

    Despite the importance of understanding the mechanisms underlying range limits and abundance structure, few studies have sought to do so. Here we use a terrestrial slug species, Deroceras panormitanum, that has invaded a remote, largely predator-free, Southern Ocean island as a model system to do so. Across Marion Island, slug density does not conform to an abundant centre distribution. Rather, abundance structure is characterized by patches and gaps. These are associated with this desiccation-sensitive species' preference for biotic and drainage line habitats that share few characteristics except for their high humidity below the vegetation surface. The coastal range margin has a threshold form, rapidly rising from zero to high density. Slugs do not occur where soil-exchangeable Na values are higher than 3000 mg kg−1, and in laboratory experiments, survival is high below this value but negligible above it. Upper elevation range margins are a function of the inability of this species to survive temperatures below an absolute limit of −6.4°C, which is regularly exceeded at 200 m altitude, above which slug density declines to zero. However, the linear decline in density from the coastal peak is probably also a function of a decline in performance or time available for activity. This is probably associated with an altitudinal decline in mean annual soil temperature. These findings support previous predictions made regarding the form of density change when substrate or climatic factors set range limits. PMID:19324817

  13. Biotic Stress Shifted Structure and Abundance of Enterobacteriaceae in the Lettuce Microbiome

    PubMed Central

    Erlacher, Armin; Cardinale, Massimiliano; Grube, Martin; Berg, Gabriele

    2015-01-01

    Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health. PMID:25714833

  14. Biotic stress shifted structure and abundance of Enterobacteriaceae in the lettuce microbiome.

    PubMed

    Erlacher, Armin; Cardinale, Massimiliano; Grube, Martin; Berg, Gabriele

    2015-01-01

    Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health. PMID:25714833

  15. Tillage Management and Seasonal Effects on Denitrifier Community Abundance, Gene Expression and Structure over Winter.

    PubMed

    Tatti, Enrico; Goyer, Claudia; Burton, David L; Wertz, Sophie; Zebarth, Bernie J; Chantigny, Martin; Filion, Martin

    2015-10-01

    Tillage effects on denitrifier communities and nitrous oxide (N2O) emissions were mainly studied during the growing season. There is limited information for the non-growing season, especially in northern countries where winter has prolonged periods with sub-zero temperatures. The abundance and structure of the denitrifier community, denitrification gene expression and N2O emissions in fields under long-term tillage regimes [no-tillage (NT) vs conventional tillage (CT)] were assessed during two consecutive winters. NT exerted a positive effect on nirK and nosZ denitrifier abundance in both winters compared to CT. Moreover, the two contrasting managements had an opposite influence on nirK and nirS RNA/DNA ratios. Tillage management resulted in different denitrifier community structures during both winters. Seasonal changes were observed in the abundance and the structure of denitrifiers. Interestingly, the RNA/DNA ratios were greater in the coldest months for nirK, nirS and nosZ. N2O emissions were not influenced by management but changed over time with two orders of magnitude increase in the coldest month of both winters. In winter of 2009-2010, emissions were mainly as N2O, whereas in 2010-2011, when soil temperatures were milder due to persistent snow cover, most emissions were as dinitrogen. Results indicated that tillage management during the growing season induced differences in denitrifier community structure that persisted during winter. However, management did not affect the active cold-adapted community structure.

  16. Population Dynamics of Aphthona whitfieldi (Coleoptera: Chrysomelidae), Pest of Jatropha curcas, and Environmental Factors Favoring Its Abundance in Burkina Faso.

    PubMed

    Sawadogo, Alizèta; Nagalo, Estérer; Nacro, Souleymane; Rouamba, Mathurin; Kenis, Marc

    2015-01-01

    The flea beetle Aphthona whitfieldi Bryant (Coleoptera: Chrysomelidae) is the main pest of the bioenergy crop Jatropha curcas L. (Euphorbiaceae) in Burkina Faso and several other West African countries. Adults severely defoliate plants, resulting in seedling mortality, poor growth, and low yields. To study the population dynamics of the pest in the Sissili Province of Burkina Faso, 12 sites were monitored weekly during a year and 31 sites were inspected for damage at the peak period of insect abundance. The effect of cropping systems (hedge, intercropping, and monoculture) and surrounding vegetation on population densities of A. whitfieldi was assessed. Beetles were rarely found in the dry season and peaked in the second half of the rainy season. The cropping system did not significantly influence the abundance and attack level. In contrast, the close vicinity of fallow lands seems to increase damage levels. Many aspects of the biology and ecology of A. whitfieldi remain to be investigated before sustainable control methods can be developed. However, this study already allows us to propose recommendations for further research on management. PMID:26206896

  17. Abundance patterns of multiple populations in globular clusters: a chemical evolution model based on yields from AGB ejecta

    NASA Astrophysics Data System (ADS)

    D'Ercole, Annibale; D'Antona, Francesca; Ventura, Paolo; Vesperini, Enrico; McMillan, Stephen L. W.

    2010-09-01

    A large number of spectroscopic studies have provided evidence of the presence of multiple populations in globular clusters by revealing patterns in the stellar chemical abundances. This paper is aimed at studying the origin of these abundance patterns. We explore a model in which second generation (SG) stars form out of a mix of pristine gas and ejecta of the first generation of asymptotic giant branch stars. We first study the constraints imposed by the spectroscopic data of SG stars in globular clusters on the chemical properties of the asymptotic and super asymptotic giant branch ejecta. With a simple one-zone chemical model, we then explore the formation of the SG population abundance patterns focusing our attention on the Na-O, Al-Mg anticorrelations and on the helium distribution function (HDF). We carry out a survey of models and explore the dependence of the final SG chemical properties on the key parameters affecting the gas dynamics and the SG formation process. Finally, we use our chemical evolution framework to build specific models for NGC 2808 and M4, two Galactic globular clusters which show different patterns in the Na-O and Mg-Al anticorrelation and have different helium distributions. We find that the amount of pristine gas involved in the formation of SG stars is a key parameter to fit the observed O-Na and Mg-Al patterns. The HDF for these models is in general good agreement with the observed one. Our models, by shedding light on the role of different parameters and their interplay in determining the final SG chemical properties, illustrate the basic ingredients, constraints and problems encountered in this self-enrichment scenario which must be addressed by more sophisticated chemical and hydrodynamic simulations.

  18. Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

    PubMed

    Navarrete, Acacio Aparecido; Soares, Tielle; Rossetto, Raffaella; van Veen, Johannes Antonie; Tsai, Siu Mui; Kuramae, Eiko Eurya

    2015-09-01

    Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions. PMID:26184407

  19. High abundance of small zoobenthos around biogenic structures in tidal sediments of the Wadden Sea

    NASA Astrophysics Data System (ADS)

    Reise, K.

    1981-12-01

    On the tidal flats of the island of Sylt (eastern part of the North Sea) the quantity of micro- and meiofauna associated with shoots of seagrass (Zostera noltii), with infaunal bivalves (Macoma balthica), and with tubes and burrows of polychaetes (Pygospio elegans, Pectinaria koreni, Nereis diversicolor, Nereis virens, Arenicola marina) was found to add up to 5 to 33 % of the overall abundance. These structures, taken together, account for 10 to 50 % of the faunal abundance on an average tidal flat at Sylt. The quantitative effect of biogenic structures at the sediment surface (casts and funnels) is small compared to that of tubes and burrows penetrating the anaerobic subsurface layer. In providing stable oxic microenvironments these elite structures frequently bring together more individuals than occur in the entire reducing sediment below surface. Faunal composition of irrigated dwellings of large infauna is different from that of the oxic surface sediment. The common denominator of all elite structures of the subsurface is an oxic halo. Burrows without such a halo are unattractive. There is no evidence that owners of burrows prey on their smaller inmates.

  20. Exoplanet population inference and the abundance of Earth analogs from noisy, incomplete catalogs

    SciTech Connect

    Foreman-Mackey, Daniel; Hogg, David W.; Morton, Timothy D.

    2014-11-01

    No true extrasolar Earth analog is known. Hundreds of planets have been found around Sun-like stars that are either Earth-sized but on shorter periods, or else on year-long orbits but somewhat larger. Under strong assumptions, exoplanet catalogs have been used to make an extrapolated estimate of the rate at which Sun-like stars host Earth analogs. These studies are complicated by the fact that every catalog is censored by non-trivial selection effects and detection efficiencies, and every property (period, radius, etc.) is measured noisily. Here we present a general hierarchical probabilistic framework for making justified inferences about the population of exoplanets, taking into account survey completeness and, for the first time, observational uncertainties. We are able to make fewer assumptions about the distribution than previous studies; we only require that the occurrence rate density be a smooth function of period and radius (employing a Gaussian process). By applying our method to synthetic catalogs, we demonstrate that it produces more accurate estimates of the whole population than standard procedures based on weighting by inverse detection efficiency. We apply the method to an existing catalog of small planet candidates around G dwarf stars. We confirm a previous result that the radius distribution changes slope near Earth's radius. We find that the rate density of Earth analogs is about 0.02 (per star per natural logarithmic bin in period and radius) with large uncertainty. This number is much smaller than previous estimates made with the same data but stronger assumptions.

  1. Phytoplankton abundance and structural parameters of the critically endangered protected area Vaya Lake (Bulgaria)

    PubMed Central

    Dimitrova, Ralits; Nenova, Elena; Uzunov, Blagoy; Shishiniova, Maria; Stoyneva, Maya

    2014-01-01

    Vaya (Ramsar site, protected area and Natura 2000 site) is the biggest natural lake in Bulgaria and the shallowest Black Sea coastal lake, which during the last decades has undergone significant changes and was included as critically endangered in the Red List of Bulgarian Wetlands. Our studies were conducted during the summer and autumn months of three years – 2004–2006. The paper presents results on the phytoplankton abundance (numbers, biomass and carbon content) in combination with the indices of species diversity, evenness and dominance. Phytoplankton abundance was extremely high (average values of 1135 × 106 cells/L for the quantity and of 46 mg/L for the biomass) and increased in the end of the studied period (years 2005–2006), when decrease of species diversity and increase of the dominance index values were detected. The carbon content of the phytoplankton was at an average value of 9.7 mg/L and also increased from 2004 to 2006. Cyanoprokaryota dominated in the formation of the total carbon content of the phytoplankton, in its numbers (88%–97.8%), and in the biomass (62%–87.9%). All data on phytoplankton abundance and structural parameters in Vaya confirm the hypertrophic status of the lake and reflect the general negative trend in its development. PMID:26019571

  2. Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils.

    PubMed

    Dai, Yu; Wu, Zhen; Zhou, Qiheng; Zhao, Qun; Li, Ningning; Xie, Shuguang; Liu, Yong

    2015-10-01

    Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can be involved in biotransformation of ammonia to nitrite in soil ecosystems. However, the distribution of AOA and AOB in plateau soils and influential factors remain largely unclear. In the present study, the activity, abundance and structure of ammonia oxidizers in different soils on the Yunnan Plateau were assessed using potential nitrification rates (PNRs), quantitative PCR assay and clone library analysis, respectively. Wide variation was found in both AOA and AOB communities in plateau soils. PNRs showed a significant positive correlation with AOB abundance. Both were determined by the ratio of organic carbon to nitrogen (C/N) and total phosphorous (TP). AOB could play a more important role in ammonia oxidation. AOB community diversity was likely affected by soil total nitrogen (TN) and total organic carbon (TOC) and was usually higher than AOA community diversity. Moreover, Nitrososphaera- and Nitrosospira-like organisms, respectively, were the dominant AOA and AOB in plateau soils. AOA community structure was likely shaped by TP and C/N, while AOB community structure was determined by pH.

  3. The effects of mass flow on the temperature and abundance structure of the solar transition region

    NASA Technical Reports Server (NTRS)

    Woods, D. T.; Holzer, Thomas E.

    1991-01-01

    The density and temperature structure of a multicomponent plasma consisting of electrons, protons, ionized helium, and a trace minor ion species are computed. The equations of force and energy balance for this model are developed and solved. It is found that in the case of downflows the minor ion temperature can be significantly hotter than the electron temperature, and significant abundance enhancements are possible due to the slowdown of the minor species from the effect of the thermal force. A simple physical picture of the source of the thermal force is given.

  4. Population inertia and its sensitivity to changes in vital rates and population structure

    USGS Publications Warehouse

    Koons, D.N.; Holmes, R.R.; Grand, J.B.

    2007-01-01

    Because the (st)age structure of a population may rarely be stable, studies of transient population dynamics and population momentum are becoming ever more popular. Yet, studies of "population momentum" are restricted in the sense that they describe the inertia of population size resulting from a demographic transition to the stationary population growth rate. Although rarely mentioned, inertia in population size is a general phenomenon and can be produced by any demographic transition or perturbation. Because population size is of central importance in demography, conservation, and management, formulas relating the sensitivity of population inertia to changes in underlying vital rates and population structure could provide much-needed insight into the dynamics of populations with unstable (st)age structure. Here, we derive such formulas, which are readily computable, and provide examples of their potential use in studies of life history and applied arenas of population study. ?? 2007 by the Ecological Society of America.

  5. Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS): Stony Asteroids Abundant in the Background and Family Populations

    NASA Astrophysics Data System (ADS)

    Lucas, Michael P.; Emery, Joshua P.; Pinilla-Alonso, Noemi; Lindsay, Sean S.; Lorenzi, Vania

    2016-10-01

    The Hungaria region represents a "purgatory" for the closest, preserved samples of the material from which the terrestrial planets accreted. The Hungaria region harbors a collisional family of Xe-type asteroids, which are situated among a background of predominantly S-complex asteroids. Deciphering their surface composition may provide constraints on the nature of the primordial building blocks of the terrestrial planets. We hypothesize that planetesimals in the inner part of the primordial asteroid belt experienced partial- to full-melting and differentiation, the Hungaria region should retain any petrologically-evolved material that formed there.We have undertaken an observational campaign entitled the Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS) to record near-infrared (NIR) spectra to characterize taxonomy, surface mineralogy, and potential meteorite analogs. We used NIR instruments at two ground-based facilities (NASA IRTF; TNG). Our data set includes spectra of 82 Hungaria asteroids (61 background; 21 family), 65 were observed during HARTSS. We compare S-complex background asteroids to calibrations developed via laboratory analyses of ordinary chondrites, and to our analyses (EPMA, XRD, VIS+NIR spectra) of 11 primitive achondrite (acapulcoite-lodranite clan) meteorites.We find that stony S-complex asteroids dominate the Hungaria background population (~80%). Background objects exhibit considerable spectral diversity, when quantified by spectral band parameter measurements, translates to a variety of surface compositions. Two main meteorite groups are represented within the Hungaria background: unmelted, nebular L chondrites (and/or L chondrites), and partially-melted primitive achondrites. H-chondrite mineralogies appear to be absent from the Hungaria background. Xe-type Hungaria family members exhibit spectral homogeneity, consistent with the hypothesis that the family was derived from the disruption of a parent body analogous to an enstatite

  6. Divergent patterns of abundance and age-class structure of headwater stream tadpoles in burned and unburned watersheds

    USGS Publications Warehouse

    Hossack, B.R.; Corn, P.S.; Fagre, D.B.

    2006-01-01

    Wildfire is a potential threat to many species with narrow environmental tolerances like the Rocky Mountain tailed frog (Ascaphus montanus Mittleman and Myers, 1949), which inhabits a region where the frequency and intensity of wildfires are expected to increase. We compared pre- and post-fire counts of tadpoles in eight streams in northwestern Montana to determine the effects of wildfire on A. montanus. All streams were initially sampled in 2001, 2 years before four of them burned in a large wildfire, and were resampled during the 2 years following the fire. Counts of tadpoles were similar in the two groups of streams before the fire. After the fire, tadpoles were almost twice as abundant in unburned streams than in burned streams. The fire seemed to have the greatest negative effect on abundance of age-1 tadpoles, which was reflected in the greater variation in same-stream age-class structure compared with those in unburned streams. Despite the apparent effect on tadpoles, we do not expect the wildfire to be an extirpation threat to populations in the streams that we sampled. Studies spanning a chronosequence of fires, as well as in other areas, are needed to assess the effects of fires on streams with A. montanus and to determine the severity and persistence of these effects.

  7. Mesh size effects on assessments of planktonic hydrozoan abundance and assemblage structure

    NASA Astrophysics Data System (ADS)

    Nogueira Júnior, Miodeli; Pukanski, Luis Eduardo de M.; Souza-Conceição, José M.

    2015-04-01

    The choice of appropriate mesh-size is paramount to accurately quantify planktonic assemblages, however there is no such information available for hydrozoans. Here planktonic hydrozoan abundance and assemblage structure were compared using 200 and 500 μm meshes at Babitonga estuary (S Brazil), throughout a year cycle. Species richness and Shannon-Wiener diversity were higher in the 200 μm mesh, while evenness was typically higher in the 500 μm. Assemblage structure was significantly different between meshes (PERMANOVA, P < 0.05; n = 72 pairs of samples) both regarding taxa and size composition. These discrepancies are due to significant underestimation of small hydromedusae by the coarse mesh, like Obelia spp., young Liriope tetraphylla, Podocoryna loyola and others. Yet, larger taxa like Eucheilota maculata and adult L. tetraphylla were more abundant in the coarse mesh on some occasions and others such as Blackfordia virginica and Muggiaea kochi were similarly represented in both meshes. Overall collection efficiency of the coarse mesh (CE500) was 14.4%, with monthly averages between 1.6% and 43.0%, in July (winter) and January (summer) respectively. Differences between the meshes were size-dependent; CE500 was ~ 0.3% for hydrozoans sizing < 0.5 mm, ~ 21% for those between 1 and 2 mm, ~ 56% for those between 2 and 4 mm, and nearly 100% for larger ones, reaching up to 312% for hydrozoans > 8 mm in October. These results suggest that both meshes have their drawbacks and the best choice would depend on the objectives of each study. Nevertheless species richness, total abundances and most taxa were better represented by the 200 μm mesh, suggesting that it is more appropriate to quantitatively sample planktonic hydrozoan assemblages.

  8. Population Genetic Structure of a Microalgal Species under Expansion

    PubMed Central

    Lebret, Karen; Kritzberg, Emma S.; Rengefors, Karin

    2013-01-01

    Biological invasions often cause major perturbations in the environment and are well studied among macroorganisms. Less is known about invasion by free-living microbes. Gonyostomum semen (Raphidophyceae) is a freshwater phytoplankton species that has increased in abundance in Northern Europe since the 1980's and has expanded its habitat range. In this study, we aimed to determine the genetic population structure of G. semen in Northern Europe and to what extent it reflects the species' recent expansion. We sampled lakes from 12 locations (11 lakes) in Norway, Sweden and Finland. Multiple strains from each location were genotyped using Amplified Fragment Length Polymorphism (AFLP). We found low differentiation between locations, and low gene diversity within each location. Moreover, there was an absence of genetic isolation with distance (Mantel test, p = 0.50). According to a Bayesian clustering method all the isolates belonged to the same genetic population. Together our data suggest the presence of one metapopulation and an overall low diversity, which is coherent with a recent expansion of G. semen. PMID:24349300

  9. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils.

    PubMed

    Siles, José A; Cajthaml, Tomas; Minerbi, Stefano; Margesin, Rosa

    2016-03-01

    In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated.

  10. Simultaneous mapping of chemical abundances and magnetic field structure in Ap stars

    NASA Astrophysics Data System (ADS)

    Lueftinger, T.

    2014-11-01

    Magnetic A stars represent about 5 highly ordered, very stable and often very strong magnetic fields. They frequently show variations in both brightness and spectral line profiles that are synchronised to stellar rotation. Those variations are believed to be produced by atomic diffusion operating in the stellar atmospheres which have become stabilized by multi-kG magnetic fields. In recent years, with the development and application of the Doppler and magnetic-Doppler imaging techniques and the availability of high-precision spectroscopic and spectropolarimetric data, it has became possible to map the chemical abundances and magnetic field structures of Ap stars simultaneously and in increasing detail, based on full Stokes vector observations. I review the state-of-the-art understanding pf Ap star spots and their relation to magnetic fields, the development of Doppler and magnetic-Doppler imaging into one of the most powerful remote sensing methods for astrophysics, and the physics of Ap stars atmospheres that we can deduce from simultaneous mapping of magnetic field structure and chemical abundances.

  11. Soil biota community structure and abundance under agricultural intensification and extensification.

    PubMed

    Postma-Blaauw, Maria B; de Goede, Ron G M; Bloem, Jaap; Faber, Jack H; Brussaard, Lijbert

    2010-02-01

    Understanding the impacts of agricultural intensification and extensification on soil biota communities is useful in order to preserve and restore biological diversity in agricultural soils and enhance the role of soil biota in agroecosystem functioning. Over four consecutive years, we investigated the effects of agricultural intensification and extensification (including conversion of grassland to arable land and vice versa, increased and decreased levels of mineral fertilization, and monoculture compared to crop rotation) on major soil biota group abundances and functional diversity. We integrated and compared effects across taxonomic levels to identify sensitive species groups. Conversion of grassland to arable land negatively affected both abundances and functional diversity of soil biota. Further intensification of the cropping system by increased fertilization and reduced crop diversity exerted smaller and differential effects on different soil biota groups. Agricultural intensification affected abundances of taxonomic groups with larger body size (earthworms, enchytraeids, microarthropods, and nematodes) more negatively than smaller-sized taxonomic groups (protozoans, bacteria, and fungi). Also functional group diversity and composition were more negatively affected in larger-sized soil biota (earthworms, predatory mites) than in smaller-sized soil biota (nematodes). Furthermore, larger soil biota appeared to be primarily affected by short-term consequences of conversion (disturbance, loss of habitat), whereas smaller soil biota were predominantly affected by long-term consequences (probably loss of organic matter). Reestablishment of grassland resulted in increased abundances of soil biota groups, but since not all groups increased in the same measure, the community structure was not completely restored. We concluded that larger-sized soil biota are more sensitive to agricultural intensification than smaller-sized soil biota. Furthermore, since larger

  12. Effects of bioaugmentation in para-nitrophenol-contaminated soil on the abundance and community structure of ammonia-oxidizing bacteria and archaea.

    PubMed

    Chi, Xiang-Qun; Liu, Kun; Zhou, Ning-Yi

    2015-07-01

    Pseudomonas sp. strain WBC-3 mineralizes the priority pollutant para-nitrophenol (PNP) and releases nitrite (NO2 (-)), which is probably involved in the nitrification. In this study, the rate of PNP removal in soil bioaugmented with strain WBC-3 was more accelerated with more NO2 (-) accumulation than in uninoculated soils. Strain WBC-3 survived well and remained stable throughout the entire period. Real-time polymerase chain reaction (real-time PCR) indicated a higher abundance of ammonia-oxidizing bacteria (AOB) than ammonia-oxidizing archaea (AOA), suggesting that AOB played a greater role in nitrification in the original sampled soil. Real-time PCR and multivariate analysis based on the denaturing gradient gel electrophoresis showed that PNP contamination did not significantly alter the abundance and community structure of ammonia oxidizers except for inhibiting the AOB abundance. Bioaugmentation of PNP-contaminated soil showed a significant effect on AOB populations and community structure as well as AOA populations. In addition, ammonium (NH4 (+)) variation was found to be the primary factor affecting the AOB community structure, as determined by the correlation between the community structures of ammonia oxidizers and environmental factors. It is here proposed that the balance between archaeal and bacterial ammonia oxidation could be influenced significantly by the variation in NH4 (+) levels as caused by bioaugmentation of contaminated soil by a pollutant containing nitrogen.

  13. Current land bird distribution and trends in population abundance between 1982 and 2012 on Rota, Mariana Islands

    USGS Publications Warehouse

    Camp, Richard J.; Brinck, Kevin W.; Gorresen, P. Marcos; Amidon, Fred A.; Radley, Paul M.; Berkowitz, S. Paul; Banko, Paul C.

    2015-01-01

    The western Pacific island of Rota is the fourth largest human-inhabited island in the Mariana archipelago and designated an Endemic Bird Area. Between 1982 and 2012, 12 point-transect distance-sampling surveys were conducted to assess bird population status. Surveys did not consistently sample the entire island; thus, we used a ratio estimator to estimate bird abundances in strata not sampled during every survey. Trends in population size were reliably estimated for 11 of 13 bird species, and 7 species declined over the 30-y time series, including the island collared-dove Streptopelia bitorquata, white-throated ground-dove Gallicolumba xanthonura, Mariana fruit-dove Ptilinopus roseicapilla, collared kingfisher Todiramphus chloris orii, Micronesian myzomela Myzomela rubratra, black drongo Dicrurus macrocercus, and Mariana crow Corvus kubaryi. The endangered Mariana crow (x̄  =  81 birds, 95% CI 30–202) declined sharply to fewer than 200 individuals in 2012, down from 1,491 birds in 1982 (95% CI  =  815–3,115). Trends increased for white tern Gygis alba, rufous fantail Rhipidura rufifrons mariae, and Micronesian starling Aplonis opaca. Numbers of the endangered Rota white-eye Zosterops rotensis declined from 1982 to the late 1990s but returned to 1980s levels by 2012, resulting in an overall stable trend. Trends for the yellow bittern Ixobrychus sinensis were inconclusive. Eurasian tree sparrow Passer montanus trends were not assessed; however, their numbers in 1982 and 2012 were similar. Occupancy models of the 2012 survey data revealed general patterns of land cover use and detectability among 12 species that could be reliably modeled. Occupancy was not assessed for the Eurasian tree sparrow because of insufficient detections. Based on the 2012 survey, bird distribution and abundance across Rota revealed three general patterns: 1) range restriction, including Mariana crow, Rota white-eye, and Eurasian tree sparrow; 2) widespread distribution, low

  14. Modeling wetland blackbird populations as a function of waterfowl abundance in the prairie pothole region of the United States and Canada

    USGS Publications Warehouse

    Forcey, G.M.; Linz, G.M.; Thogmartin, W.E.; Bleier, W.J.

    2008-01-01

    Blackbirds share wetland habitat with many waterfowl species in Bird Conservation Region 11 (BCR 11), the prairie potholes. Because of similar habitat preferences, there may be associations between blackbird populations and populations of one or more species of waterfowl in BCR11. This study models populations of red-winged blackbirds and yellow-headed blackbirds as a function of multiple waterfowl species using data from the North American Breeding Bird Survey within BCR11. For each blackbird species, we created a global model with blackbird abundance modeled as a function of 11 waterfowl species; nuisance effects (year, route, and observer) also were included in the model. Hierarchical Poisson regression models were fit using Markov chain Monte Carlo methods in WinBUGS 1.4.1. Waterfowl abundances were weakly associated with blackbird numbers, and no single waterfowl species showed a strong correlation with any blackbird species. These findings suggest waterfowl abundance from a single species is not likely a good bioindicator of blackbird abundance; however, a global model provided good fit for predicting red-winged blackbird abundance. Increased model complexity may be required for accurate predictions of blackbird abundance; the amount of data required to construct appropriate models may limit this approach for predicting blackbird abundance in the prairie potholes. Copyright ?? Taylor & Francis Group, LLC.

  15. Competing pressures on populations: long-term dynamics of food availability, food quality, disease, stress and animal abundance.

    PubMed

    Chapman, Colin A; Schoof, Valérie A M; Bonnell, Tyler R; Gogarten, Jan F; Calmé, Sophie

    2015-05-26

    Despite strong links between sociality and fitness that ultimately affect the size of animal populations, the particular social and ecological factors that lead to endangerment are not well understood. Here, we synthesize approximately 25 years of data and present new analyses that highlight dynamics in forest composition, food availability, the nutritional quality of food, disease, physiological stress and population size of endangered folivorous red colobus monkeys (Procolobus rufomitratus). There is a decline in the quality of leaves 15 and 30 years following two previous studies in an undisturbed area of forest. The consumption of a low-quality diet in one month was associated with higher glucocorticoid levels in the subsequent month and stress levels in groups living in degraded forest fragments where diet was poor was more than twice those in forest groups. In contrast, forest composition has changed and when red colobus food availability was weighted by the protein-to-fibre ratio, which we have shown positively predicts folivore biomass, there was an increase in the availability of high-quality trees. Despite these changing social and ecological factors, the abundance of red colobus has remained stable, possibly through a combination of increasing group size and behavioural flexibility.

  16. Competing pressures on populations: long-term dynamics of food availability, food quality, disease, stress and animal abundance.

    PubMed

    Chapman, Colin A; Schoof, Valérie A M; Bonnell, Tyler R; Gogarten, Jan F; Calmé, Sophie

    2015-05-26

    Despite strong links between sociality and fitness that ultimately affect the size of animal populations, the particular social and ecological factors that lead to endangerment are not well understood. Here, we synthesize approximately 25 years of data and present new analyses that highlight dynamics in forest composition, food availability, the nutritional quality of food, disease, physiological stress and population size of endangered folivorous red colobus monkeys (Procolobus rufomitratus). There is a decline in the quality of leaves 15 and 30 years following two previous studies in an undisturbed area of forest. The consumption of a low-quality diet in one month was associated with higher glucocorticoid levels in the subsequent month and stress levels in groups living in degraded forest fragments where diet was poor was more than twice those in forest groups. In contrast, forest composition has changed and when red colobus food availability was weighted by the protein-to-fibre ratio, which we have shown positively predicts folivore biomass, there was an increase in the availability of high-quality trees. Despite these changing social and ecological factors, the abundance of red colobus has remained stable, possibly through a combination of increasing group size and behavioural flexibility. PMID:25870398

  17. Competing pressures on populations: long-term dynamics of food availability, food quality, disease, stress and animal abundance

    PubMed Central

    Chapman, Colin A.; Schoof, Valérie A. M.; Bonnell, Tyler R.; Gogarten, Jan F.; Calmé, Sophie

    2015-01-01

    Despite strong links between sociality and fitness that ultimately affect the size of animal populations, the particular social and ecological factors that lead to endangerment are not well understood. Here, we synthesize approximately 25 years of data and present new analyses that highlight dynamics in forest composition, food availability, the nutritional quality of food, disease, physiological stress and population size of endangered folivorous red colobus monkeys (Procolobus rufomitratus). There is a decline in the quality of leaves 15 and 30 years following two previous studies in an undisturbed area of forest. The consumption of a low-quality diet in one month was associated with higher glucocorticoid levels in the subsequent month and stress levels in groups living in degraded forest fragments where diet was poor was more than twice those in forest groups. In contrast, forest composition has changed and when red colobus food availability was weighted by the protein-to-fibre ratio, which we have shown positively predicts folivore biomass, there was an increase in the availability of high-quality trees. Despite these changing social and ecological factors, the abundance of red colobus has remained stable, possibly through a combination of increasing group size and behavioural flexibility. PMID:25870398

  18. Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides

    PubMed Central

    Teixeira, Marcus M.

    2016-01-01

    During the past 20 years, a general picture of the genetic diversity and population structure of Coccidioides, the causal agent of coccidioidomycosis (Valley fever), has emerged. The genus consists of 2 genetically diverse species, C. immitis and C. posadasii, each of which contains 1 or more distinct populations with limited gene flow. Genotypic data indicate that C. immitis is divided into 2 subpopulations (central and southern California populations) and C. posadasii is divided into 3 subpopulations (Arizona, Mexico, and Texas/South America populations). However, admixture within and among these populations and the current paucity of environmental isolates limit our understanding of the population genetics of Coccidioides. We assessed population structure of Coccidioides in Arizona by analyzing 495 clinical and environmental isolates. Our findings confirm the population structure as previously described and indicate a finer scale population structure in Arizona. Environmental isolates appear to have higher genetic diversity than isolates from human patients. PMID:27191589

  19. [Effects of different fertilization regimes on abundance and community structure of the nirK-type denitrifying bacteria in greenhouse vegetable soils].

    PubMed

    Zeng, Xi-Bai; Wang, Ya-Nan; Wang, Yu-Zhong; Bai, Ling-Yu; Li, Lian-Fang; Duan, Ran; Su, Shi-Ming; Wu, Cui-Xia

    2014-02-01

    The community structure and abundance of nirK-type denitrifying bacteria in different soil layers (0-20 cm and 20-40 cm) under various fertilization regimes in Wuwei, Gansu Province were investigated by the combination of terminal restriction fragment length polymorphism (T-RFLP) and real-time quantitative PCR. Results showed that the nirK-type denitrifying bacteria community structure was significantly affected by fertilization regimes, especially for 70, 156 and 190 bp T-RFs that represented the dominant populations in greenhouse soil. Fertilization regimes significantly influenced the abundance of nirK gene in the 0-20 cm soil layer with the highest abundance of nirK gene copy number (2.16 x 10(7) copies x g(-1) soil) detected in the manure treatment (M), which was 2.04 and 2.02 times of that in the control (CK) and chemical fertilizer (NPK) treatments, respectively. Both the dominant population and abundance of nirK-type denitrifying bacteria in the greenhouse soil were significantly different between the 0-20 cm and 20-40 cm soil layers, and the nirK-type denitrifying bacteria community structure and abundance in the greenhouse soil were obviously different from that in the field. Soil pH, soil organic matter content and nitrate-N content had the greatest influence on the bacterial community composition. Phylogenetic analysis indicated that there were not only anaerobic nirK-type denitrifying bacteria in greenhouse soil, but also aerobic denitrifying bacteria, such as Rhizobium, Ochrobactrum, Agrobacterium. PMID:24830252

  20. Developing STR databases on structured populations: the native South Siberian population versus the Russian population.

    PubMed

    Zhivotovsky, Lev A; Malyarchuk, Boris A; Derenko, Miroslava V; Wozniak, Marcin; Grzybowski, Tomasz

    2009-09-01

    Developing a forensic DNA database on a population that consists of local ethnic groups separated by physical and cultural barriers is questionable as it can be genetically subdivided. On the other side, small sizes of ethnic groups, especially in alpine regions where they are sub-structured further into small villages, prevent collecting a large sample from each ethnic group. For such situations, we suggest to obtain both a total population database on allele frequencies across ethnic groups and a list of theta-values between the groups and the total data. We have genotyped 558 individuals from the native population of South Siberia, consisting of nine ethnic groups, at 17 autosomal STR loci of the kit packages AmpFlSTR SGM Plus i, Cyrillic AmpFlSTR Profiler Plus. The groups differentiate from each other with average theta-values of around 1.1%, and some reach up to three to four percent at certain loci. There exists between-village differentiation as well. Therefore, a database for the population of South Siberia is composed of data on allele frequencies in the pool of ethnic groups and data on theta-values that indicate variation in allele frequencies across the groups. Comparison to additional data on northeastern Asia (the Chukchi and Koryak) shows that differentiation in allele frequencies among small groups that are separated by large geographic distance can be even greater. In contrast, populations of Russians that live in large cities of the European part of Russia are homogeneous in allele frequencies, despite large geographic distance between them, and thus can be described by a database on allele frequencies alone, without any specific information on theta-values.

  1. Understanding cooperative behavior in structurally disordered populations

    NASA Astrophysics Data System (ADS)

    Xu, C.; Zhang, W.; Du, P.; Choi, C. W.; Hui, P. M.

    2016-06-01

    The effects of an inhomogeneous competing environment on the extent of cooperation are studied within the context of a site-diluted evolutionary snowdrift game on a square lattice, with the occupied sites representing the players, both numerically and analytically. The frequency of cooperation ℱ C generally shows a non-monotonic dependence on the fraction of occupied sites ρ, for different values of the payoff parameter r. Slightly diluting a lattice leads to a lower cooperation for small and high values of r. For a range of r, however, dilution leads to an enhanced cooperation. An analytic treatment is developed for ℱC I + ℱC II, with ℱC I emphasizing the importance of the small clusters of players especially for ℱC II from the other players is shown to be inadequate. A local configuration approximation (LCA) that treats the local competing configurations as the variables and amounts to include spatial correlation up to the neighborhood of a player's neighbors is developed. Results of ℱ C ( ρ) and the number of different local configurations from LCA are in good agreement with simulation results. A transparent physical picture of the dynamics stemming from LCA is also presented. The theoretical approach provides a framework that can be readily applied to competing agent-based models in structurally ordered and disordered populations.

  2. Biodiversity at the plant-soil interface: microbial abundance and community structure respond to litter mixing.

    PubMed

    Chapman, Samantha K; Newman, Gregory S

    2010-03-01

    The interactive effects of diversity in plants and microbial communities at the litter interface are not well understood. Mixtures of plant litter from different species often decompose differently than when individual species decompose alone. Previously, we found that litter mixtures of multiple conifers decomposed more rapidly than expected, but litter mixtures that included conifer and aspen litter did not. Understanding the mechanisms underlying these diversity effects may help explain existing anomalous decay dynamics and provide a glimpse into the elusive linkage between plant diversity and the fungi and bacteria that carry out decomposition. We examined the microbial communities on litter from individual plant species decomposing both in mixture and alone. We assessed two main hypotheses to explain how the decomposer community could stimulate mixed-litter decomposition above predicted rates: either by being more abundant, or having a different or more diverse community structure than when microbes decompose a single species of litter. Fungal, bacterial and total phospholipid fatty acid microbial biomass increased by over 40% on both conifer and aspen litter types in mixture, and microbial community composition changed significantly when plant litter types were mixed. Microbial diversity also increased with increasing plant litter diversity. While our data provide support for both the increased abundance hypothesis and the altered microbial community hypothesis, microbial changes do not translate to predictably altered litter decomposition and may only produce synergisms when mixed litters are functionally similar.

  3. Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.

    PubMed

    Qiu, Yu-Qing; Tian, Xue; Zhang, Shihua

    2015-01-01

    Metagenomic research uses sequencing technologies to investigate the genetic biodiversity of microbiomes presented in various ecosystems or animal tissues. The composition of a microbial community is highly associated with the environment in which the organisms exist. As large amount of sequencing short reads of microorganism genomes obtained, accurately estimating the abundance of microorganisms within a metagenomic sample is becoming an increasing challenge in bioinformatics. In this paper, we describe a hierarchical taxonomy tree-based mixture model (HTTMM) for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree. In this model, genome-specific short reads and homologous short reads among genomes can be distinguished and represented by leaf and intermediate nodes in the taxonomy tree, respectively. We adopt an expectation-maximization algorithm to solve this model. Using simulated and real-world data, we demonstrate that the proposed method is superior to both flat mixture model and lowest common ancestry-based methods. Moreover, this model can reveal previously unaddressed homologous genomes.

  4. Helium abundance and ionization structure in the Orion nebula: radio recombination lines observations

    NASA Astrophysics Data System (ADS)

    Poppi, S.; Tsivilev, A. P.; Cortiglioni, S.; Palumbo, G. G. C.; Sorochenko, R. L.

    2007-03-01

    Results of the Ori A HII region mapping based on hydrogen (H), helium (He) and carbon (C) Radio Recombination lines (RRL) are presented. Observations were made with the same angular resolution (2') using the 32 m VLBI dish of Medicina (Italy, 22.4 GHz) and the Pushchino RT-22 dish (Russia, 36.5 GHz). The behaviour of the ionized helium abundance, y^+, with distance from the center shows that the He+ zone size is smaller than that of H^+. Such a behaviour is different for the core and for the envelope, as well as for different directions from the center. The helium abundance, N(He)/N(H)=10.0(± 0.8)%, is measured. Derived line radial velocities, their widths and y+ data support the well-known "blister-type" structure of this HII region. LTE electron temperatures (7800-9600 K) are also measured. Appendices (Figs. 15, 16 and Sect. 4.1 "Carbon RRLs") are only available in electronic form at http://www.aanda.org

  5. Effects of coconut and fish oils on ruminal methanogenesis, fermentation, and abundance and diversity of microbial populations in vitro.

    PubMed

    Patra, A K; Yu, Z

    2013-03-01

    Coconut (CO) and fish (FO) oils were previously shown to inhibit rumen methanogenesis and biohydrogenation, which mitigates methane emission and helps improve beneficial fatty acids in meat and milk. This study aimed at investigating the comparative effects of CO and FO on the methanogenesis, fermentation, and microbial abundances and diversity in vitro rumen cultures containing different doses (0, 3.1, and 6.2 mL/L) of each oil and 400mg feed substrate using rumen fluid from lactating dairy cows as inocula. Increasing doses of CO and FO quadratically decreased concentrations of methane, but hydrogen concentrations were only increased quadratically by CO. Both oils linearly decreased dry matter and neutral detergent fiber digestibility of feeds but did not affect the concentration of total volatile fatty acids. However, CO reduced acetate percentage and acetate to propionate ratio and increased the percentages of propionate and butyrate to a greater extent than FO. Ammonia concentration was greater for CO than FO. As determined by quantitative real-time PCR, FO had greater inhibition to methanogens than CO, but the opposite was true for protozoal, Ruminococcus flavefaciens, and Fibrobacter succinogenes. Ruminococcus albus was not affected by either oil. Denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial and archaeal community composition were changed differently by oil type. Based on Pareto-Lorenz evenness curve analysis of the DGGE profiles, CO noticeably changed the functional organization of archaea compared with FO. In conclusion, although both CO and FO decreased methane concentrations to a similar extent, the mode of reduction and the effect on abundances and diversity of archaeal and bacterial populations differed between the oils. Thus, the use of combination of CO and FO at a low dose may additively lower methanogenesis in the rumen while having little adverse effect on rumen fermentation. PMID:23332846

  6. Camera Traps on Wildlife Crossing Structures as a Tool in Gray Wolf (Canis lupus) Management - Five-Years Monitoring of Wolf Abundance Trends in Croatia.

    PubMed

    Šver, Lidija; Bielen, Ana; Križan, Josip; Gužvica, Goran

    2016-01-01

    The conservation of gray wolf (Canis lupus) and its coexistence with humans presents a challenge and requires continuous monitoring and management efforts. One of the non-invasive methods that produces high-quality wolf monitoring datasets is camera trapping. We present a novel monitoring approach where camera traps are positioned on wildlife crossing structures that channel the animals, thereby increasing trapping success and increasing the cost-efficiency of the method. In this way we have followed abundance trends of five wolf packs whose home ranges are intersected by a motorway which spans throughout the wolf distribution range in Croatia. During the five-year monitoring of six green bridges we have recorded 28 250 camera-events, 132 with wolves. Four viaducts were monitored for two years, recording 4914 camera-events, 185 with wolves. We have detected a negative abundance trend of the monitored Croatian wolf packs since 2011, especially severe in the northern part of the study area. Further, we have pinpointed the legal cull as probable major negative influence on the wolf pack abundance trends (linear regression, r2 > 0.75, P < 0.05). Using the same approach we did not find evidence for a negative impact of wolves on the prey populations, both wild ungulates and livestock. We encourage strict protection of wolf in Croatia until there is more data proving population stability. In conclusion, quantitative methods, such as the one presented here, should be used as much as possible when assessing wolf abundance trends. PMID:27327498

  7. Camera Traps on Wildlife Crossing Structures as a Tool in Gray Wolf (Canis lupus) Management - Five-Years Monitoring of Wolf Abundance Trends in Croatia

    PubMed Central

    Križan, Josip; Gužvica, Goran

    2016-01-01

    The conservation of gray wolf (Canis lupus) and its coexistence with humans presents a challenge and requires continuous monitoring and management efforts. One of the non-invasive methods that produces high-quality wolf monitoring datasets is camera trapping. We present a novel monitoring approach where camera traps are positioned on wildlife crossing structures that channel the animals, thereby increasing trapping success and increasing the cost-efficiency of the method. In this way we have followed abundance trends of five wolf packs whose home ranges are intersected by a motorway which spans throughout the wolf distribution range in Croatia. During the five-year monitoring of six green bridges we have recorded 28 250 camera-events, 132 with wolves. Four viaducts were monitored for two years, recording 4914 camera-events, 185 with wolves. We have detected a negative abundance trend of the monitored Croatian wolf packs since 2011, especially severe in the northern part of the study area. Further, we have pinpointed the legal cull as probable major negative influence on the wolf pack abundance trends (linear regression, r2 > 0.75, P < 0.05). Using the same approach we did not find evidence for a negative impact of wolves on the prey populations, both wild ungulates and livestock. We encourage strict protection of wolf in Croatia until there is more data proving population stability. In conclusion, quantitative methods, such as the one presented here, should be used as much as possible when assessing wolf abundance trends. PMID:27327498

  8. Inferring population structure and demographic history using Y-STR data from worldwide populations.

    PubMed

    Xu, Hongyang; Wang, Chuan-Chao; Shrestha, Rukesh; Wang, Ling-Xiang; Zhang, Manfei; He, Yungang; Kidd, Judith R; Kidd, Kenneth K; Jin, Li; Li, Hui

    2015-02-01

    The Y chromosome is one of the best genetic materials to explore the evolutionary history of human populations. Global analyses of Y chromosomal short tandem repeats (STRs) data can reveal very interesting world population structures and histories. However, previous Y-STR works tended to focus on small geographical ranges or only included limited sample sizes. In this study, we have investigated population structure and demographic history using 17 Y chromosomal STRs data of 979 males from 44 worldwide populations. The largest genetic distances have been observed between pairs of African and non-African populations. American populations with the lowest genetic diversities also showed large genetic distances and coancestry coefficients with other populations, whereas Eurasian populations displayed close genetic affinities. African populations tend to have the oldest time to the most recent common ancestors (TMRCAs), the largest effective population sizes and the earliest expansion times, whereas the American, Siberian, Melanesian, and isolated Atayal populations have the most recent TMRCAs and expansion times, and the smallest effective population sizes. This clear geographic pattern is well consistent with serial founder model for the origin of populations outside Africa. The Y-STR dataset presented here provides the most detailed view of worldwide population structure and human male demographic history, and additionally will be of great benefit to future forensic applications and population genetic studies.

  9. Inferring population structure and demographic history using Y-STR data from worldwide populations.

    PubMed

    Xu, Hongyang; Wang, Chuan-Chao; Shrestha, Rukesh; Wang, Ling-Xiang; Zhang, Manfei; He, Yungang; Kidd, Judith R; Kidd, Kenneth K; Jin, Li; Li, Hui

    2015-02-01

    The Y chromosome is one of the best genetic materials to explore the evolutionary history of human populations. Global analyses of Y chromosomal short tandem repeats (STRs) data can reveal very interesting world population structures and histories. However, previous Y-STR works tended to focus on small geographical ranges or only included limited sample sizes. In this study, we have investigated population structure and demographic history using 17 Y chromosomal STRs data of 979 males from 44 worldwide populations. The largest genetic distances have been observed between pairs of African and non-African populations. American populations with the lowest genetic diversities also showed large genetic distances and coancestry coefficients with other populations, whereas Eurasian populations displayed close genetic affinities. African populations tend to have the oldest time to the most recent common ancestors (TMRCAs), the largest effective population sizes and the earliest expansion times, whereas the American, Siberian, Melanesian, and isolated Atayal populations have the most recent TMRCAs and expansion times, and the smallest effective population sizes. This clear geographic pattern is well consistent with serial founder model for the origin of populations outside Africa. The Y-STR dataset presented here provides the most detailed view of worldwide population structure and human male demographic history, and additionally will be of great benefit to future forensic applications and population genetic studies. PMID:25159112

  10. Molecular identification and relative abundance of cryptic Lophodermium species in natural populations of Scots pine, Pinus sylvestris L.

    PubMed

    Reignoux, Sabrina N A; Green, Sarah; Ennos, Richard A

    2014-01-01

    The multi-locus phylogenetic species recognition approach and population genetic analysis of Amplified Fragment Length Polymorphism (AFLP) markers were used to delineate Lophodermium taxa inhabiting needles of Scots pine (Pinus sylvestris) in native pinewoods within Scotland. These analyses revealed three major lineages corresponding to the morphological species Lophodermium seditiosum and Lophodermium conigenum, fruiting on broken branches, and Lophodermium pinastri, fruiting on naturally fallen needles. Within L. pinastri three well supported sister clades were found representing cryptic taxa designated L. pinastri I, L. pinastri II, and L. pinastri III. Significant differences in mean growth rate in culture were found among the cryptic taxa. Taxon-specific primers based on ITS sequences were designed and used to classify over 500 Lophodermium isolates, derived from fallen needles of P. sylvestris in three Scottish and one French pinewood site, into the three L. pinastri cryptic taxa. Highly significant differences in the relative abundance of the three taxa were found among the Scottish pinewood sites, and between the French and all of the Scottish sites.

  11. Abundance-area relationships in bird assemblages along an Afrotropical elevational gradient: space limitation in montane forest selects for higher population densities.

    PubMed

    Ferenc, Michal; Fjeldså, Jon; Sedláček, Ondřej; Motombi, Francis Njie; Djomo Nana, Eric; Mudrová, Karolína; Hořák, David

    2016-05-01

    The usual positive inter-specific relationship between range size and abundance of local populations can have notable exceptions in Afrotropical montane areas, where range-restricted bird species are unusually abundant. We tested how the area occupied locally by passerines and their geographic range size relate to local abundances along a tropical elevational gradient of Mt Cameroon, West-Central Africa. Data on bird assemblages were collected at six forested elevations (350, 650, 1100, 1500, 1850 m, 2200 m a.s.l.) using a standardised point count at 16 locations per elevation. Elevational ranges of birds were compiled from published sources and their geographic range sizes were determined as the occupancy of 1° x 1° grid cells. The observed relationship between local abundance and geographic range size within the entire passerine assemblage on Mt Cameroon disagrees with the most frequently reported positive pattern. However, the patterns differ among elevations, with positive trends of the abundance-range size relationship in lowland changing to negative trends towards higher elevations. Interestingly, the total assemblage abundances do not differ much among elevations and population size estimates of species occupying different parts of the gradient remain relatively constant. These patterns are caused by relatively high abundances of montane species, which might be a result of long-term ecological specialization and/or competitive release in species-poor montane locations and possibly facilitated by an extinction filter. Our data suggest that montane species' abilities to maintain dense populations might compensate for less area available near mountain tops and help these populations to circumvent extinction. PMID:26801494

  12. Osprey distribution, abundance, and status in western North America: III. The Baja California and Gulf of California population

    USGS Publications Warehouse

    Henny, C.J.; Anderson, D.W.

    1979-01-01

    -An estimated 810 ? 55 pairs (minimum estimate) of ospreys (Pandion haliaetus) were nesting in the study area during our survey (24 March-l April 1977). Approximately 174 pairs nested along the Pacific side of Baja California, 255 pairs along the gulf side, 187 pairs on the Midriff Islands, and 194 pairs in coastal Sonora and Sinaloa. Most nested on cliffs adjacent to the sea (59%); some nested on cactus in flat terrain (26%). Seven per cent nested on the ground, three percent nested in mangroves and other trees in the southern portion of the study area,.and four percent nested on man-made structures. The extreme northwestern Baja California population that was extirpated early in this century has not recovered. However, several populations immediately to the south along the Pacific Coast now appear stationary. Pesticide residues in osprey eggs from Mexico were among the lowest reported for the species in North America.

  13. Fish passage and abundance around grade control structures on incised streams

    USGS Publications Warehouse

    Thomas, J.T.; Papanicolaou, A.N.; Pierce, C.L.; Dermisis, D.C.; Litvan, M.E.; Larson, C.J.

    2009-01-01

    This paper summarizes research from separate studies of fish passage over weirs (Larson et al., 2004; Litvan, 2006; Litvan, et al., 2008a-c) and weir hydraulics (Papanicolaou and Dermisis, 2006; Papanicolaou and Dermisis, in press). Channel incision in the deep loess region of western Iowa has caused decreased biodiversity because streams have high sediment loads, altered flow regimes, lost habitat, and lost lateral connectivity with their former floodplains. In-stream grade control structures (GCS) are built to prevent further erosion, protect infrastructure, and reduce sediment loads. However, GCS can have a detrimental impact on fisheries abundance and migration, biodiversity, and longitudinal connectivity. Fish mark-recapture studies were performed on stretches of streams with and without GCS. GCS with vertical or 1:4 (rise/run) downstream slopes did not allow fish migration, but GCS with slopes ??? 1:15 did. GCS sites were characterized by greater proportions of pool habitat, maximum depths, fish biomass, slightly higher index of biotic integrity (IBI) scores, and greater macroinvertebrate abundance and diversity than non-GCS sites. After modification of three GCS, IBI scores increased and fish species exhibiting truncated distributions before were found throughout the study area. Another study examined the hydraulic performance of GCS to facilitate unimpeded fish passage by determining the mean and turbulent flow characteristics in the vicinity of the GCS via detailed, non-intrusive field tests. Mean flow depth (Y) and velocity (V) atop the GCS were critical for evaluating GCS performance. Turbulent flow measurements illustrated that certain GCS designs cause sudden constrictions which form eddies large enough to disorient fish. GCS with slopes ??? 1:15 best met the minimum requirements to allow catfish passage of a flow depth of ??? 0.31 m and a mean flow velocity of ??? 1.22 m/s. ?? 2009 ASCE.

  14. Rare Variation Facilitates Inferences of Fine-Scale Population Structure in Humans

    PubMed Central

    O’Connor, Timothy D.; Fu, Wenqing; Mychaleckyj, Josyf C.; Logsdon, Benjamin; Auer, Paul; Carlson, Christopher S.; Leal, Suzanne M.; Smith, Joshua D.; Rieder, Mark J.; Bamshad, Michael J.; Nickerson, Deborah A.; Akey, Joshua M.

    2015-01-01

    Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale resequencing studies have shown an abundance of rare variation in humans, which may be particularly useful for making inferences of fine-scale population structure. To this end, we used an information theory framework and extensive coalescent simulations to rigorously quantify the informativeness of rare and common variation to detect signatures of fine-scale population structure. We show that rare variation affords unique insights into patterns of recent population structure. Furthermore, to empirically assess our theoretical findings, we analyzed high-coverage exome sequences in 6,515 European and African American individuals. As predicted, rare variants are more informative than common polymorphisms in revealing a distinct cluster of European–American individuals, and subsequent analyses demonstrate that these individuals are likely of Ashkenazi Jewish ancestry. Our results provide new insights into the population structure using rare variation, which will be an important factor to account for in rare variant association studies. PMID:25415970

  15. Vegetation in water-limited environments prioritizes photosynthesis over structural development when water is most abundant

    NASA Astrophysics Data System (ADS)

    Mccoll, K. A.; Konings, A. G.; Entekhabi, D.; Piles, M.; Alemohammad, S.

    2013-12-01

    Changes in rainfall variability due to climate change may shift some vegetated regions to water-limited conditions. It is unclear how this shift will affect vegetation phenology. To gain insight into the relationship between global vegetation phenology and water stress, we use global L-band scatterometer observations from NASA's Aquarius satellite to estimate RVI (Radar Vegetation Index; approximately, a measure of vegetation structure), global MODIS (MODerate Resolution Imaging Spectroradiometer) observations of NDVI (Normalized Difference Vegetation Index; approximately, a measure of vegetation function) and MERRA (Modern-Era Retrospective analysis for Research and Applications) reanalysis outputs of precipitation (P) and net radiation (Rn). We estimate the time of year at which each timeseries reaches a maximum, and observe consistent lags between peaks in NDVI and RVI over water-limited ecosystems that are not present in energy-limited ecosystems. We hypothesize that, in water-limited ecosystems, plants prioritize photosynthesis when water is most abundant and delay structural development until the dry season. In contrast, in energy-limited ecosystems, plants are able to both photosynthesize and generate woody biomass concurrently. The temporal variability of precipitation and net radiation, therefore, qualitatively influences the temporal dynamics of plant biomass allocation.

  16. Population II Li-6 as a probe of nucleosynthesis and stellar structure and evolution

    NASA Technical Reports Server (NTRS)

    Steigman, Gary; Fields, Brian D.; Olive, Keith A.; Schramm, David N.; Walker, Terry P.

    1993-01-01

    We discuss the importance of Population II Li-6 as a diagnostic for models of primordial nucleosynthesis, cosmic-ray nucleosyntheses in the early Galaxy, and the structure and evolution of metal-poor solar-type stars. The observation of Li-6 in the subdwarf HD 84937 is shown to be consistent with the existing Population II LiBeB data within the context of a simple three-component model: (1) standard big bang nucleosynthesis, (2) Population II cosmic-ray nucleosynthesis, (3) standard (nonrotating) stellar LiBeB depletion. If this interpretation is correct, we predict a potentially detectable boron abundance for this star: about 2 x 10 exp -12. Subsequent Population II LiBeB observations, and in particular further observations of Population II Li-6, are shown to be crucial to our understanding of the primordial and early galactic creation and destruction mechanisms for light elements.

  17. Detecting declines in the abundance of a bull trout (Salvelinus confluentus) population: Understanding the accuracy, precision, and costs of our efforts

    USGS Publications Warehouse

    Al-Chokhachy, R.; Budy, P.; Conner, M.

    2009-01-01

    Using empirical field data for bull trout (Salvelinus confluentus), we evaluated the trade-off between power and sampling effort-cost using Monte Carlo simulations of commonly collected mark-recapture-resight and count data, and we estimated the power to detect changes in abundance across different time intervals. We also evaluated the effects of monitoring different components of a population and stratification methods on the precision of each method. Our results illustrate substantial variability in the relative precision, cost, and information gained from each approach. While grouping estimates by age or stage class substantially increased the precision of estimates, spatial stratification of sampling units resulted in limited increases in precision. Although mark-resight methods allowed for estimates of abundance versus indices of abundance, our results suggest snorkel surveys may be a more affordable monitoring approach across large spatial scales. Detecting a 25% decline in abundance after 5 years was not possible, regardless of technique (power = 0.80), without high sampling effort (48% of study site). Detecting a 25% decline was possible after 15 years, but still required high sampling efforts. Our results suggest detecting moderate changes in abundance of freshwater salmonids requires considerable resource and temporal commitments and highlight the difficulties of using abundance measures for monitoring bull trout populations.

  18. Geometrical Structures of Chemically Decomposed Thick and Thin Disk Populations

    NASA Astrophysics Data System (ADS)

    Kawata, D.; Brook, C. B.; Rahimi, A.; Gibson, B. K.

    2016-10-01

    We summarize the thick and thin disk formation commonly seen in cosmological N-body simulations. As suggested in Brook et al. (2004), a hierarchical clustering scenario causes multiple minor gas-rich mergers, and leads to the formation of a kinematically hot disk, thick disk population, at a high redshift. Once the mergers become less significant at a later epoch, the thin disk population starts building up. Because in this scenario the thick disk population forms intensively at high redshift through multiple gas-rich mergers, the thick disk population is compact and has systematically higher [α/Fe] abundance than the thin disk population. We discuss that the thick disk population would be affected by the formation of the thin disk and suffer from the radial migration, which helps the thick disk population to be observed in the solar neighborhood. In addition, we show that the current cosmological simulations also naturally predict that the thin disk population is flaring at the outer region. As shown in Rahimi et al. (2014), at high vertical height from the disk plane, the compact thick disk population (low metallicity and high [α/Fe]) is dominant in the inner region and the flaring thin disk population (high metallicity and low [α/Fe]) contributes more in the outer region. This helps to explain the positive radial metallicity gradient and negative radial [α/Fe] gradient observed at high vertical height in the Milky Way stellar disk.

  19. Genetic structure of Tribolium castaneum (Coleptera: Tenebrionidae) populations in mills

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The red flour beetle, Tribolium castaneum, is primarily found associated with human structures such as wheat and rice mills, which are spatially isolated resource patches with apparently limited immigration that could produce genetically structured populations. We investigated genetic diversity and...

  20. Population Structure and Genetic Diversity of Native and Invasive Populations of Solanum rostratum (Solanaceae)

    PubMed Central

    Zhao, Jiali; Solís-Montero, Lislie; Lou, Anru; Vallejo-Marín, Mario

    2013-01-01

    Aims We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1) determine the level of genetic diversity across the studied regions; (2) explore the likely origins of invasive populations in China; and (3) investigate whether there is the evidence of multiple introductions into China. Methods We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China. Important Findings We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (FIS) or population differentiation (FST). Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China. PMID:24224008

  1. Population structure of a parasitic plant and its perennial host.

    PubMed

    Mutikainen, P; Koskela, T

    2002-10-01

    Characterization of host and parasite population genetic structure and estimation of gene flow among populations are essential for the understanding of parasite local adaptation and coevolutionary interactions between hosts and parasites. We examined two aspects of population structure in a parasitic plant, the greater dodder (Cuscuta europaea) and its host plant, the stinging nettle (Urtica dioica), using allozyme data from 12 host and eight parasite populations. First, we examined whether hosts exposed to parasitism in the past contain higher levels of genetic variation. Second, we examined whether host and parasite populations differ in terms of population structure and if their population structures are correlated. There was no evidence that host populations differed in terms of gene diversity or heterozygosity according to their history of parasitism. Host populations were genetically more differentiated (F(ST) = 0.032) than parasite populations (F(ST) = 0.009). Based on these F(ST) values, gene flow was high for both host and parasite. Such high levels of gene flow could counteract selection for local adaptation of the parasite. We found no significant correlation between geographic and genetic distance (estimated as pairwise F(ST)), either for the host or for the parasite. Furthermore, host and parasite genetic distance matrices were uncorrelated, suggesting that sites with genetically similar host populations are unlikely to have genetically similar parasite populations. PMID:12242649

  2. Population structure and genetic diversity of moose in Alaska.

    PubMed

    Schmidt, Jennifer I; Hundertmark, Kris J; Bowyer, R Terry; McCracken, Kevin G

    2009-01-01

    Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P < 0.001) with F(ST) < 0.109 and R(ST) < 0.125. Results of analyses from STRUCTURE indicated 2 prominent population groups, a mix of moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P < 0.01). Finally, there was no evidence of bottlenecks either at the population level or overall. We conclude that weak population structure occurs among moose in Alaska with population expansion from interior Alaska westward toward the coast.

  3. Abundance coefficients, a new method for measuring microorganism relative abundance

    USGS Publications Warehouse

    Forester, R.M.

    1977-01-01

    A new method of measuring the relative abundance of microorganisms by using a set of interrelated coefficients, termed 'abundance coefficients' or 'AC', is proposed. These coefficients provide a means of recording abundance for geometric density categories, and each density measurement represents an approximation of the Poisson parameter ??t. The AC is the natural logarithm of a 'characteristic value,' which is a particular number for each geometric density category. The 'characteristic values' are based upon a probabilistic error statement derived from the Poisson formula, and they present evidence for separation of the geometric category boundaries by e = 2.71828. The proposed AC provide a means for recording species abundance in a manner suitable for arithmetic manipulation, for population structure studies, and for the determination of practical limits for defining the presence or absence of a species. Further, these coefficients provide for both intrasample and intersample abundance comparisons. ?? 1977 Plenum Publishing Corporation.

  4. Abundance of intrinsic structural disorder in the histone H1 subtypes.

    PubMed

    Kowalski, Andrzej

    2015-12-01

    The intrinsically disordered proteins consist of partially structured regions linked to the unstructured stretches, which consequently form the transient and dynamic conformational ensembles. They undergo disorder to order transition upon binding their partners. Intrinsic disorder is attributed to histones H1, perceived as assemblers of chromatin structure and the regulators of DNA and proteins activity. In this work, the comparison of intrinsic disorder abundance in the histone H1 subtypes was performed both by the analysis of their amino acid composition and by the prediction of disordered stretches, as well as by identifying molecular recognition features (MoRFs) and ANCHOR protein binding regions (APBR) that are responsible for recognition and binding. Both human and model organisms-animals, plants, fungi and protists-have H1 histone subtypes with the properties typical of disordered state. They possess a significantly higher content of hydrophilic and charged amino acid residues, arranged in the long regions, covering over half of the whole amino acid residues in chain. Almost complete disorder corresponds to histone H1 terminal domains, including MoRFs and ANCHOR. Those motifs were also identified in a more ordered histone H1 globular domain. Compared to the control (globular and fibrous) proteins, H1 histones demonstrate the increased folding rate and a higher proportion of low-complexity segments. The results of this work indicate that intrinsic disorder is an inherent structural property of histone H1 subtypes and it is essential for establishing a protein conformation which defines functional outcomes affecting on DNA- and/or partner protein-dependent cell processes.

  5. FIFI-LS [OIII] Spectrosopy of Nearby Infrared Bright Galaxies: Tracing Stellar Populations, the O/N Abundance Ratio, and absolute abundances

    NASA Astrophysics Data System (ADS)

    Stacey, Gordon

    We propose to map the [OIII] 52 um line emission from the central regions of five infrared bright, nearby star forming galaxies, NGC 1808, NGC 1365, NGC 3256, NGC 4945, and Arp 299. These data will be used together with publically available [OIII] 88 um, [NII] 122 um, and [NIII] 57 um line detections from Herschel/PACS and H radio recombination line interferometric observations to constrain the ionized gas density and mass, the hardness of the stellar radiation fields (hence most massive star on the main sequence), the O/N ratio (reflecting the numbers of cycles for star formation) and the ionized gas phase N/H and O/H abundances which measure the star formation efficiency integrated over time. We will also use the Herschel archival [OI] 63 and 146 um, and [CII] 158 um imaging to characterize the neutral ISM and the strength of the FUV (6-13.6 eV) stellar radiation fields. Together we will have a continuous measure of the stellar UV radiation fields from 6 to 54 eV thereby constraining the numbers of upper main sequence stars. The proposed FIFI-LS [OIII] 52 um line observations are the lynch-pin that holds the technique together. These measurements provide a local benchmark for our line-ratio techniques that can be applied to similar studies of high-z galaxies where it is expected that stellar radiation fields will be harder, and the O/N radio will be larger for the lowest metallicity galaxies. Therefore, the proposed observations are fundamentally important to our understanding of the star formation process over cosmic time.

  6. Extensive population genetic structure in the giraffe

    PubMed Central

    Brown, David M; Brenneman, Rick A; Koepfli, Klaus-Peter; Pollinger, John P; Milá, Borja; Georgiadis, Nicholas J; Louis, Edward E; Grether, Gregory F; Jacobs, David K; Wayne, Robert K

    2007-01-01

    Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations. PMID:18154651

  7. High Prevalence of HIV Low Abundance Drug-Resistant Variants in a Treatment-Naive Population in North Rift Kenya.

    PubMed

    Cheriro, Winfrida; Kiptoo, Michael; Kikuvi, Gideon; Mining, Simeon; Emonyi, Wilfred; Songok, Elijah

    2015-12-01

    The advent of antiretroviral treatment (ART) has resulted in a dramatic reduction in AIDS-related morbidity and mortality. However, the emergence and spread of antiretroviral drug resistance (DR) threaten to negatively impact treatment regimens and compromise efforts to control the epidemic. It is recommended that surveillance of drug resistance occur in conjunction with scale-up efforts to ensure that appropriate first-line therapy is offered relative to the resistance that exists. However, standard resistance testing methods used in Sub-Saharan Africa rely on techniques that do not include low abundance DR variants (LADRVs) that have been documented to contribute to treatment failure. The use of next generation sequencing (NGS) has been shown to be more sensitive to LADRVS. We have carried out a preliminary investigation using NGS to determine the prevalence of LDRVS among a drug-naive population in North Rift Kenya. Antiretroviral-naive patients attending a care clinic in North Rift Kenya were requested to provide and with consent provided blood samples for DR analysis. DNA was extracted and amplified and nested PCR was conducted on the pol RT region using primers tagged with multiplex identifiers (MID). Resulting PCR amplicons were purified, quantified, and pyrosequenced using a GS FLX Titanium PicoTiterPlate (Roche). Valid pyrosequencing reads were aligned with HXB-2 and the frequency and distribution of nucleotide and amino acid changes were determined using an in-house Perl script. DR mutations were identified using the IAS-USA HIV DR mutation database. Sixty samples were successfully sequenced of which 26 were subtype A, 9 were subtype D, 2 were subtype C, and the remaining were recombinants. Forty-six (76.6%) had at least one drug resistance mutation, with 25 (41.6%) indicated as major and the remaining 21 (35%) indicated as minor. The most prevalent mutation was NRTI position K219Q/R (11/46, 24%) followed by NRTI M184V (5/46, 11%) and NNRTI K103N (4/46, 9

  8. High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations.

    PubMed

    Zhang, Yu; Tian, Zhe; Liu, Miaomiao; Shi, Zhou Jason; Hale, Lauren; Zhou, Jizhong; Yang, Min

    2015-08-01

    To evaluate the potential effects of antibiotics on ammonia-oxidizing microbes, multiple tools including quantitative PCR (qPCR), 454-pyrosequencing, and a high-throughput functional gene array (GeoChip) were used to reveal the distribution of ammonia-oxidizing archaea (AOA) and archaeal amoA (Arch-amoA) genes in three wastewater treatment systems receiving spiramycin or oxytetracycline production wastewaters. The qPCR results revealed that the copy number ratios of Arch-amoA to ammonia-oxidizing bacteria (AOB) amoA genes were the highest in the spiramycin full-scale (5.30) and pilot-scale systems (1.49 × 10(-1)), followed by the oxytetracycline system (4.90 × 10(-4)), with no Arch-amoA genes detected in the control systems treating sewage or inosine production wastewater. The pyrosequencing result showed that the relative abundance of AOA affiliated with Thaumarchaeota accounted for 78.5-99.6% of total archaea in the two spiramycin systems, which was in accordance with the qPCR results. Mantel test based on GeoChip data showed that Arch-amoA gene signal intensity correlated with the presence of spiramycin (P < 0.05). Antibiotics explained 25.8% of variations in amoA functional gene structures by variance partitioning analysis. This study revealed the selection of AOA in the presence of high concentrations of spiramycin in activated sludge systems.

  9. Evolutionary dynamics of general group interactions in structured populations

    NASA Astrophysics Data System (ADS)

    Li, Aming; Broom, Mark; Du, Jinming; Wang, Long

    2016-02-01

    The evolution of populations is influenced by many factors, and the simple classical models have been developed in a number of important ways. Both population structure and multiplayer interactions have been shown to significantly affect the evolution of important properties, such as the level of cooperation or of aggressive behavior. Here we combine these two key factors and develop the evolutionary dynamics of general group interactions in structured populations represented by regular graphs. The traditional linear and threshold public goods games are adopted as models to address the dynamics. We show that for linear group interactions, population structure can favor the evolution of cooperation compared to the well-mixed case, and we see that the more neighbors there are, the harder it is for cooperators to persist in structured populations. We further show that threshold group interactions could lead to the emergence of cooperation even in well-mixed populations. Here population structure sometimes inhibits cooperation for the threshold public goods game, where depending on the benefit to cost ratio, the outcomes are bistability or a monomorphic population of defectors or cooperators. Our results suggest, counterintuitively, that structured populations are not always beneficial for the evolution of cooperation for nonlinear group interactions.

  10. Evolutionary dynamics of general group interactions in structured populations.

    PubMed

    Li, Aming; Broom, Mark; Du, Jinming; Wang, Long

    2016-02-01

    The evolution of populations is influenced by many factors, and the simple classical models have been developed in a number of important ways. Both population structure and multiplayer interactions have been shown to significantly affect the evolution of important properties, such as the level of cooperation or of aggressive behavior. Here we combine these two key factors and develop the evolutionary dynamics of general group interactions in structured populations represented by regular graphs. The traditional linear and threshold public goods games are adopted as models to address the dynamics. We show that for linear group interactions, population structure can favor the evolution of cooperation compared to the well-mixed case, and we see that the more neighbors there are, the harder it is for cooperators to persist in structured populations. We further show that threshold group interactions could lead to the emergence of cooperation even in well-mixed populations. Here population structure sometimes inhibits cooperation for the threshold public goods game, where depending on the benefit to cost ratio, the outcomes are bistability or a monomorphic population of defectors or cooperators. Our results suggest, counterintuitively, that structured populations are not always beneficial for the evolution of cooperation for nonlinear group interactions. PMID:26986362

  11. Towards a landscape scale management of pesticides: ERA using changes in modelled occupancy and abundance to assess long-term population impacts of pesticides.

    PubMed

    Topping, Chris J; Craig, Peter S; de Jong, Frank; Klein, Michael; Laskowski, Ryszard; Manachini, Barbara; Pieper, Silvia; Smith, Rob; Sousa, José Paulo; Streissl, Franz; Swarowsky, Klaus; Tiktak, Aaldrik; van der Linden, Ton

    2015-12-15

    Pesticides are regulated in Europe and this process includes an environmental risk assessment (ERA) for non-target arthropods (NTA). Traditionally a non-spatial or field trial assessment is used. In this study we exemplify the introduction of a spatial context to the ERA as well as suggest a way in which the results of complex models, necessary for proper inclusion of spatial aspects in the ERA, can be presented and evaluated easily using abundance and occupancy ratios (AOR). We used an agent-based simulation system and an existing model for a widespread carabid beetle (Bembidion lampros), to evaluate the impact of a fictitious highly-toxic pesticide on population density and the distribution of beetles in time and space. Landscape structure and field margin management were evaluated by comparing scenario-based ERAs for the beetle. Source-sink dynamics led to an off-crop impact even when no pesticide was present off-crop. In addition, the impacts increased with multi-year application of the pesticide whereas current ERA considers only maximally one year. These results further indicated a complex interaction between landscape structure and pesticide effect in time, both in-crop and off-crop, indicating the need for NTA ERA to be conducted at landscape- and multi-season temporal-scales. Use of AOR indices to compare ERA outputs facilitated easy comparison of scenarios, allowing simultaneous evaluation of impacts and planning of mitigation measures. The landscape and population ERA approach also demonstrates that there is a potential to change from regulation of a pesticide in isolation, towards the consideration of pesticide management at landscape scales and provision of biodiversity benefits via inclusion and testing of mitigation measures in authorisation procedures.

  12. Towards a landscape scale management of pesticides: ERA using changes in modelled occupancy and abundance to assess long-term population impacts of pesticides.

    PubMed

    Topping, Chris J; Craig, Peter S; de Jong, Frank; Klein, Michael; Laskowski, Ryszard; Manachini, Barbara; Pieper, Silvia; Smith, Rob; Sousa, José Paulo; Streissl, Franz; Swarowsky, Klaus; Tiktak, Aaldrik; van der Linden, Ton

    2015-12-15

    Pesticides are regulated in Europe and this process includes an environmental risk assessment (ERA) for non-target arthropods (NTA). Traditionally a non-spatial or field trial assessment is used. In this study we exemplify the introduction of a spatial context to the ERA as well as suggest a way in which the results of complex models, necessary for proper inclusion of spatial aspects in the ERA, can be presented and evaluated easily using abundance and occupancy ratios (AOR). We used an agent-based simulation system and an existing model for a widespread carabid beetle (Bembidion lampros), to evaluate the impact of a fictitious highly-toxic pesticide on population density and the distribution of beetles in time and space. Landscape structure and field margin management were evaluated by comparing scenario-based ERAs for the beetle. Source-sink dynamics led to an off-crop impact even when no pesticide was present off-crop. In addition, the impacts increased with multi-year application of the pesticide whereas current ERA considers only maximally one year. These results further indicated a complex interaction between landscape structure and pesticide effect in time, both in-crop and off-crop, indicating the need for NTA ERA to be conducted at landscape- and multi-season temporal-scales. Use of AOR indices to compare ERA outputs facilitated easy comparison of scenarios, allowing simultaneous evaluation of impacts and planning of mitigation measures. The landscape and population ERA approach also demonstrates that there is a potential to change from regulation of a pesticide in isolation, towards the consideration of pesticide management at landscape scales and provision of biodiversity benefits via inclusion and testing of mitigation measures in authorisation procedures. PMID:26318547

  13. A spatial age-structured model for describing sea lamprey (Petromyzon marinus) population dynamics

    USGS Publications Warehouse

    Robinson, Jason M.; Wilberg, Michael J.; Adams, Jean V.; Jones, Michael L.

    2013-01-01

    The control of invasive sea lampreys (Petromyzon marinus) presents large scale management challenges in the Laurentian Great Lakes. No modeling approach has been developed that describes spatial dynamics of lamprey populations. We developed and validated a spatial and age-structured model and applied it to a sea lamprey population in a large river in the Great Lakes basin. We considered 75 discrete spatial areas, included a stock-recruitment function, spatial recruitment patterns, natural mortality, chemical treatment mortality, and larval metamorphosis. Recruitment was variable, and an upstream shift in recruitment location was observed over time. From 1993–2011 recruitment, larval abundance, and the abundance of metamorphosing individuals decreased by 80, 84, and 86%, respectively. The model successfully identified areas of high larval abundance and showed that areas of low larval density contribute significantly to the population. Estimated treatment mortality was less than expected but had a large population-level impact. The results and general approach of this work have applications for sea lamprey control throughout the Great Lakes and for the restoration and conservation of native lamprey species globally.

  14. Population Structure of Montastraea cavernosa on Shallow versus Mesophotic Reefs in Bermuda.

    PubMed

    Goodbody-Gringley, Gretchen; Marchini, Chiara; Chequer, Alex D; Goffredo, Stefano

    2015-01-01

    Mesophotic coral reef ecosystems remain largely unexplored with only limited information available on taxonomic composition, abundance and distribution. Yet, mesophotic reefs may serve as potential refugia for shallow-water species and thus understanding biodiversity, ecology and connectivity of deep reef communities is integral for resource management and conservation. The Caribbean coral, Montastraea cavernosa, is considered a depth generalist and is commonly found at mesophotic depths. We surveyed abundance and size-frequency of M. cavernosa populations at six shallow (10m) and six upper mesophotic (45m) sites in Bermuda and found population structure was depth dependent. The mean surface area of colonies at mesophotic sites was significantly smaller than at shallow sites, suggesting that growth rates and maximum colony surface area are limited on mesophotic reefs. Colony density was significantly higher at mesophotic sites, however, resulting in equal contributions to overall percent cover. Size-frequency distributions between shallow and mesophotic sites were also significantly different with populations at mesophotic reefs skewed towards smaller individuals. Overall, the results of this study provide valuable baseline data on population structure, which indicate that the mesophotic reefs of Bermuda support an established population of M. cavernosa. PMID:26544963

  15. Population Structure of Montastraea cavernosa on Shallow versus Mesophotic Reefs in Bermuda

    PubMed Central

    Goodbody-Gringley, Gretchen; Marchini, Chiara; Chequer, Alex D.; Goffredo, Stefano

    2015-01-01

    Mesophotic coral reef ecosystems remain largely unexplored with only limited information available on taxonomic composition, abundance and distribution. Yet, mesophotic reefs may serve as potential refugia for shallow-water species and thus understanding biodiversity, ecology and connectivity of deep reef communities is integral for resource management and conservation. The Caribbean coral, Montastraea cavernosa, is considered a depth generalist and is commonly found at mesophotic depths. We surveyed abundance and size-frequency of M. cavernosa populations at six shallow (10m) and six upper mesophotic (45m) sites in Bermuda and found population structure was depth dependent. The mean surface area of colonies at mesophotic sites was significantly smaller than at shallow sites, suggesting that growth rates and maximum colony surface area are limited on mesophotic reefs. Colony density was significantly higher at mesophotic sites, however, resulting in equal contributions to overall percent cover. Size-frequency distributions between shallow and mesophotic sites were also significantly different with populations at mesophotic reefs skewed towards smaller individuals. Overall, the results of this study provide valuable baseline data on population structure, which indicate that the mesophotic reefs of Bermuda support an established population of M. cavernosa. PMID:26544963

  16. Population Structure of Montastraea cavernosa on Shallow versus Mesophotic Reefs in Bermuda.

    PubMed

    Goodbody-Gringley, Gretchen; Marchini, Chiara; Chequer, Alex D; Goffredo, Stefano

    2015-01-01

    Mesophotic coral reef ecosystems remain largely unexplored with only limited information available on taxonomic composition, abundance and distribution. Yet, mesophotic reefs may serve as potential refugia for shallow-water species and thus understanding biodiversity, ecology and connectivity of deep reef communities is integral for resource management and conservation. The Caribbean coral, Montastraea cavernosa, is considered a depth generalist and is commonly found at mesophotic depths. We surveyed abundance and size-frequency of M. cavernosa populations at six shallow (10m) and six upper mesophotic (45m) sites in Bermuda and found population structure was depth dependent. The mean surface area of colonies at mesophotic sites was significantly smaller than at shallow sites, suggesting that growth rates and maximum colony surface area are limited on mesophotic reefs. Colony density was significantly higher at mesophotic sites, however, resulting in equal contributions to overall percent cover. Size-frequency distributions between shallow and mesophotic sites were also significantly different with populations at mesophotic reefs skewed towards smaller individuals. Overall, the results of this study provide valuable baseline data on population structure, which indicate that the mesophotic reefs of Bermuda support an established population of M. cavernosa.

  17. Demographic connectivity for ursid populations at wildlife crossing structures in Banff National Park.

    PubMed

    Sawaya, Michael A; Clevenger, Anthony P; Kalinowski, Steven T

    2013-08-01

    Wildlife crossing structures are one solution to mitigating the fragmentation of wildlife populations caused by roads, but their effectiveness in providing connectivity has only been superficially evaluated. Hundreds of grizzly (Ursus arctos) and black bear (Ursus americanus) passages through under and overpasses have been recorded in Banff National Park, Alberta, Canada. However, the ability of crossing structures to allow individual and population-level movements across road networks remains unknown. In April 2006, we initiated a 3-year investigation into whether crossing structures provide demographic connectivity for grizzly and black bears in Banff National Park. We collected hair with multiple noninvasive methods to obtain genetic samples from grizzly and black bears around the Bow Valley. Our objectives were to determine the number of male and female grizzly and black bears that use crossing structures; examine spatial and temporal patterns of crossings; and estimate the proportions of grizzly and black bear populations in the Bow Valley that use crossing structures. Fifteen grizzly (7 female, 8 male) and 17 black bears (8 female, 9 male) used wildlife crossing structures. The number of individuals detected at wildlife crossing structures was highly correlated with the number of passages in space and time. Grizzly bears used open crossing structures (e.g., overpasses) more often than constricted crossings (e.g., culverts). Peak use of crossing structures for both bear species occurred in July, when high rates of foraging activity coincide with mating season. We compared the number of bears that used crossings with estimates of population abundance from a related study and determined that substantial percentages of grizzly (15.0% in 2006, 19.8% in 2008) and black bear (17.6% in 2006, 11.0% in 2008) populations used crossing structures. On the basis of our results, we concluded wildlife crossing structures provide demographic connectivity for bear populations

  18. Demographic connectivity for ursid populations at wildlife crossing structures in Banff National Park.

    PubMed

    Sawaya, Michael A; Clevenger, Anthony P; Kalinowski, Steven T

    2013-08-01

    Wildlife crossing structures are one solution to mitigating the fragmentation of wildlife populations caused by roads, but their effectiveness in providing connectivity has only been superficially evaluated. Hundreds of grizzly (Ursus arctos) and black bear (Ursus americanus) passages through under and overpasses have been recorded in Banff National Park, Alberta, Canada. However, the ability of crossing structures to allow individual and population-level movements across road networks remains unknown. In April 2006, we initiated a 3-year investigation into whether crossing structures provide demographic connectivity for grizzly and black bears in Banff National Park. We collected hair with multiple noninvasive methods to obtain genetic samples from grizzly and black bears around the Bow Valley. Our objectives were to determine the number of male and female grizzly and black bears that use crossing structures; examine spatial and temporal patterns of crossings; and estimate the proportions of grizzly and black bear populations in the Bow Valley that use crossing structures. Fifteen grizzly (7 female, 8 male) and 17 black bears (8 female, 9 male) used wildlife crossing structures. The number of individuals detected at wildlife crossing structures was highly correlated with the number of passages in space and time. Grizzly bears used open crossing structures (e.g., overpasses) more often than constricted crossings (e.g., culverts). Peak use of crossing structures for both bear species occurred in July, when high rates of foraging activity coincide with mating season. We compared the number of bears that used crossings with estimates of population abundance from a related study and determined that substantial percentages of grizzly (15.0% in 2006, 19.8% in 2008) and black bear (17.6% in 2006, 11.0% in 2008) populations used crossing structures. On the basis of our results, we concluded wildlife crossing structures provide demographic connectivity for bear populations

  19. The abundant symmetry structure of hierarchies of nonlinear equations obtained by reciprocal links

    NASA Astrophysics Data System (ADS)

    Carillo, Sandra; Fuchssteiner, Benno

    1989-07-01

    Explicit computation for a Kawamoto-type equation shows that there is a rich associated symmetry structure for four separate hierarchies of nonlinear integrodifferential equations. Contrary to the general belief that symmetry groups for nonlinear evolution equations in 1+1 dimensions have to be Abelian, it is shown that, in this case, the symmetry group is noncommutative. Its semisimple part is isomorphic to the affine Lie algebra A(1)1 associated to sl(2,C). In two of the additional hierarchies that were found, an explicit dependence of the independent variable occurs. Surprisingly, the generic invariance for the Kawamoto-type equation obtained in Rogers and Carillo [Phys. Scr. 36, 865 (1987)] via a reciprocal link to the Möbius invariance of the singularity equation of the Kaup-Kupershmidt (KK) equation only holds for one of the additional hierarchies of symmetry groups. Thus the generic invariance is not a universal property for the complete symmetry group of equations obtained by reciprocal links. In addition to these results, the bi-Hamiltonian formulation of the hierarchy is given. A direct Bäcklund transformation between the (KK) hierarchy and the hierarchy of singularity equation for the Caudrey-Dodd-Gibbon-Sawada-Kotera equation is exhibited: This shows that the abundant symmetry structure found for the Kawamoto equation must exist for all fifth-order equations, which are known to be completely integrable since these equations are connected either by Bäcklund transformations or reciprocal links. It is shown that similar results must hold for all hierarchies emerging out of singularity hierarchies via reciprocal links. Furthermore, general aspects of the results are discussed.

  20. Constraining the Thermal Structure, Abundances, and Dynamics of the Exoplanet HD 209458b

    NASA Astrophysics Data System (ADS)

    Zellem, Robert; Griffith, Caitlin A.; Lewis, Nikole K.; Swain, Mark R.; Knutson, Heather A.

    2014-11-01

    HD 209458b has been extensively studied from the UV to IR as it is one of the brightest of the transiting exoplanets and has a large planet-to-star contrast. However its thermal profile and abundances remain constrained to at best 3 orders of magnitude (Line et al. 2014), largely due to a lack of spectral coverage. We expand HD 209458b’s wavelength coverage with ground and space observations. Our ground H, K, and L-band secondary eclipse spectroscopy, which explores HD 209458b’s emission mechanisms, is motivated by multiple detections of bright 3.3 μm emission on HD 189733b, resembling the CH4 ν3 band and potentially non-LTE fluorescence (Swain et al. 2010; Waldmann et al. 2012). CH4 fluorescence has previously been observed on Titan (Kim et al. 2000), Saturn, and Jupiter (Drossart et al. 1999; Brown et al. 2003), thereby likening exoplanets to their Solar System counterparts. We find that the hotter HD 209458b lacks to ~3σ a bright 3.3 μm feature as seen on HD 189733b, which is consistent with thermochemical equilibrium predictions (Moses et al. 2011). We measure HD 209458b’s longitudinally-varying thermal structure with Spitzer/IRAC full-orbit phase curve observations, and revise a previous 4.5 μm emission measurement downward by ˜35%. This change is significant because the high 4.5 and 5.8 μm brightness temperatures were interpreted as a thermal inversion (e.g., Line et al. 2014). While our 4.5 μm photometric emission point does not require an inversion, the shape of the phase curve, particularly the location and brightness temperature of the hot spot, suggests that HD 209458b has a dayside inversion. However the nightside is much cooler than predicted by a GCM. This discrepancy is potentially due to the GCM lacking quenching where vertical mixing outpaces reaction rates, causing increased CO and CH4 abundances at higher altitudes. We explore evidence for CH4 quenching with IRAC 3.6 micron data, which overlap the wings of the CH4 ν3 band, allowing

  1. Constraining the Thermal Structure, Abundances, and Dynamics of the Exoplanet HD 209458b

    NASA Astrophysics Data System (ADS)

    Zellem, Robert; Griffith, Caitlin Ann; Lewis, Nikole; Swain, Mark R.; Knutson, Heather

    2015-01-01

    HD 209458b has been extensively studied from the UV to IR as it is one of the brightest of the transiting exoplanets and has a large planet-to-star contrast. However its thermal profile and abundances remain constrained to at best 3 orders of magnitude (Line et al. 2014), largely due to a lack of spectral coverage. We expand HD 209458b's wavelength coverage with ground and space observations. Our ground H, K, and L-band secondary eclipse spectroscopy, which explores HD 209458b's emission mechanisms, is motivated by multiple detections of bright 3.3 μm emission on HD 189733b, resembling the CH4 ν3 band and potentially non-LTE fluorescence (Swain et al. 2010; Waldmann et al. 2012). CH4 fluorescence has previously been observed on Titan (Kim et al. 2000), Saturn, and Jupiter (Drossart et al. 1999; Brown et al. 2003), thereby likening exoplanets to their Solar System counterparts. We find that the hotter HD 209458b lacks to ~3σ a bright 3.3 μm feature as seen on HD 189733b, which is consistent with thermochemical equilibrium predictions (Moses et al. 2011). We measure HD 209458b's longitudinally-varying thermal structure with Spitzer/IRAC full-orbit phase curve observations, and revise a previous 4.5 μm emission measurement downward by ˜35%. This change is significant because the high 4.5 and 5.8 μm brightness temperatures were interpreted as a thermal inversion (e.g., Line et al. 2014). While our 4.5 μm photometric emission point does not require an inversion, the shape of the phase curve, particularly the location and brightness temperature of the hot spot, suggests that HD 209458b has a dayside inversion. However the nightside is much cooler than predicted by a GCM. This discrepancy is potentially due to the GCM lacking quenching where vertical mixing outpaces reaction rates, causing increased CO and CH4 abundances at higher altitudes. We explore evidence for CH4 quenching with IRAC 3.6 micron data, which overlap the wings of the CH4 ν3 band, allowing us to

  2. Selection of Cooperation in Spatially Structured Populations

    NASA Astrophysics Data System (ADS)

    Yang, Hyunmo; Ghim, Cheol-Min

    The social dilemma games give rise to an emergence of cooperation in which altruistic individuals survive the natural selection at higher rate than random chance. We try to extend our understanding of this spatial reciprocity by including the impact of degree-degree correlation on the propensity toward prosocial behaviour in an otherwise well-mixed population. In a stochastic death-birth process with weak selection, we find that the disassortative degree mixing, or negative correlation between the degrees of neighbouring nodes significantly promotes the fixation of cooperators whereas the assortative mixing acts to suppress it. This is consistent with the fact that the spatial heterogeneity weakens the average tendency of a population to cooperate, which we describe in a unified scheme of the effective isothermality in coarse-grained networks. We also discuss the individual-level incentives that indirectly foster restructuring the social networks toward the more cooperative topologies.

  3. [Marriage structure of Yakut populations: migrations].

    PubMed

    Kucher, A I; Danilova, A L; Koneva, L A; Nogovitsina, A N

    2010-05-01

    Rural and urban settlements of the Republic of Sakha (Yakutia) are characterized by intense marriage migrations: both indigenous residents of different uluses (districts) of the republic (7-30%) and migrants from outside Yakutia (7-29%) contract marriages in five administrative centers analyzed in this respect. All the populations studied are characterized by a wide geographic range of the birthplaces of persons contracted marriages there (from 14 to 24 uluses of Yakutia), without any predominant migration flow from one district to another. The proportion of homolocal marriages among indigenous ethnic groups (Evenks, Evens, and Yukagirs) is as high as 75-100%; this proportion among Yakuts varies from 26 to 68%; heterolocal marriages are more characteristic of Russian immigrants (41-95%). Positive assortative marriages among persons with the same birthplaces have been found in all populations except for Momsky ulus. PMID:20583606

  4. Diversity, Abundance and Community Structure of Benthic Macro- and Megafauna on the Beaufort Shelf and Slope

    PubMed Central

    Nephin, Jessica; Juniper, S. Kim; Archambault, Philippe

    2014-01-01

    Diversity and community patterns of macro- and megafauna were compared on the Canadian Beaufort shelf and slope. Faunal sampling collected 247 taxa from 48 stations with box core and trawl gear over the summers of 2009–2011 between 50 and 1,000 m in depth. Of the 80 macrofaunal and 167 megafaunal taxa, 23% were uniques, present at only one station. Rare taxa were found to increase proportional to total taxa richness and differ between the shelf ( 100 m) where they tended to be sparse and the slope where they were relatively abundant. The macrofauna principally comprised polychaetes with nephtyid polychaetes dominant on the shelf and maldanid polychaetes (up to 92% in relative abundance/station) dominant on the slope. The megafauna principally comprised echinoderms with Ophiocten sp. (up to 90% in relative abundance/station) dominant on the shelf and Ophiopleura sp. dominant on the slope. Macro- and megafauna had divergent patterns of abundance, taxa richness ( diversity) and diversity. A greater degree of macrofaunal than megafaunal variation in abundance, richness and diversity was explained by confounding factors: location (east-west), sampling year and the timing of sampling with respect to sea-ice conditions. Change in megafaunal abundance, richness and diversity was greatest across the depth gradient, with total abundance and richness elevated on the shelf compared to the slope. We conclude that megafaunal slope taxa were differentiated from shelf taxa, as faunal replacement not nestedness appears to be the main driver of megafaunal diversity across the depth gradient. PMID:25007347

  5. Effects of soil tillage and management of crop residues on soil properties: abundance, biomass and diversity of earthworms, soil structure and nutrient evolutions

    NASA Astrophysics Data System (ADS)

    lemtiri, Aboulkacem

    2013-04-01

    The living soil is represented by soil biota that interacts with aboveground biota and with the abiotic environment, soil structure, soil reaction, organic matter, nutrient contents, aso. Maintenance of soil organic matter through integrated soil fertility management is an important issue to conciliate soil quality and agricultural productivity. Earthworms are key actors in soil structure formation through the production of casts and the incorporation of soil organic matter in the soil. Research is still needed about the interactive effects of various tillage and crop residue management practices on earthworm populations and physical and chemical properties of soil. To investigate the impacts of two tillage management systems and two cropping systems on earthworm populations, soil structure evolution and nutrient dynamics, we carried out a three years study in an experimental field. The aims of this experimentation, were to assess the effects of the tillage systems (ploughing versus reduced tillage) and the availability of crop residues (export versus no export) on (i) the abundance, biomass and diversity of earthworms, on the soil structure and on the temporal variation of water extractable nutrients and organic carbon. The first results show that tillage management did significantly affect earthworm abundance and biomass. However, crop residue management did not affect abundance, biomass and diversity of earthworms. Regarding soil physical properties, the tillage affected the compaction profiles within the top 30cm. The analysis of nutrient and organic carbon dynamics show divergent trends (decrease of calcium and magnesium, increase of hot water extractable carbon and phosphorus…) but no clear effect of the studied factors could be identified. The question of the initial soil variability raised as a crucial point in the discussion.

  6. The spatial structure of hunter access determines the local abundance of forest elephants (Loxodonta africana cyclotis).

    PubMed

    Yackulic, Charles B; Strindberg, Samantha; Maisels, Fiona; Blake, Stephen

    2011-06-01

    In many previously remote regions in the world, increasing and often unregulated access is leading to dramatic increases in hunting pressure and declines in the densities of prey species, sometimes to the point of local extinction. Not surprisingly, numerous studies have found a correlation between the distance to the closest access point and prey densities. Here we hypothesized that, for many wide-ranging species, local abundances are reduced by hunting associated with multiple access points as opposed to just the closest access points. We also hypothesized that the distribution of hunter access determines both patterns of occupancy and abundance in occupied areas and that these two patterns (occupancy and abundance) respond to access at different spatial scales. Using data on the distribution of abundances of African forest elephant (Loxodonta africana cyclotis) in and around five national parks in Central Africa, we tested these hypotheses using a model comparison framework. We found that models including an index based on the distance to multiple roads outperformed models including other access-based covariates, including a model based on distance to the closest road only. We also found that models that allowed us to model occupancy and abundance separately outperformed simpler models. Occupancy responds to access at the same scale as previous estimates of average maximum displacement in the subspecies, while the scale of the response of abundance is more ambiguous, but appears to be greater. Lastly, we show that incorporating indices based on multiple access points and modeling abundance and occupancy has important practical consequences for our understanding of overall regional abundances and the distribution of abundances within regions.

  7. Hierarchical spatial structure of genetically variable nucleopolyhedroviruses infecting cyclic populations of western tent caterpillars.

    PubMed

    Cooper, Dawn; Cory, Jenny S; Myers, Judith H

    2003-04-01

    The cyclic population dynamics of western tent caterpillars, Malacosoma californicum pluviale, are associated with epizootics of a nucleopolyhedrovirus, McplNPV. Given the dynamic fluctuations in host abundance and levels of viral infection, host resistance and virus virulence might be expected to change during different phases of the cycle. As a first step in determining if McplNPV virulence and population structure change with host density, we used restriction fragment length polymorphism (RFLP) analysis to examine the genetic diversity of McplNPV infecting western tent caterpillar populations at different spatial scales. Thirteen dominant genetic variants were identified in 39 virus isolates (individual larvae) collected from field populations during one year of low host density, and another distinct variant was discovered among nine additional isolates in two subsequent years of declining host density. The distribution of these genetic variants was not random and indicated that the McplNPV population was structured at several spatial levels. A high proportion of the variation could be explained by family grouping, which suggested that isolates collected within a family were more likely to be the same than isolates compared among populations. Additionally, virus variants from within populations (sites) were more likely to be the same than isolates collected from tent caterpillar populations on different islands. This may indicate that there is limited mixing of virus among tent caterpillar families and populations when host population density is low. Thus there is potential for the virus to become locally adapted to western tent caterpillar populations in different sites. However, no dominant genotype was observed at any site. Whether and how selection acts on the genetically diverse nucleopolyhedrovirus populations as host density changes will be investigated over the next cycle of tent caterpillar populations.

  8. Very Low Population Structure in a Highly Mobile and Wide-Ranging Endangered Bird Species.

    PubMed

    Kvistad, Lynna; Ingwersen, Dean; Pavlova, Alexandra; Bull, James K; Sunnucks, Paul

    2015-01-01

    The loss of biodiversity following fragmentation and degradation of habitat is a major issue in conservation biology. As competition for resources increases following habitat loss and fragmentation, severe population declines may occur even in common, highly mobile species; such demographic decline may cause changes within the population structure of the species. The regent honeyeater, Anthochaera phrygia, is a highly nomadic woodland bird once common in its native southeast Australia. It has experienced a sharp decline in abundance since the late 1970s, following clearing of large areas of its preferred habitat, box-ironbark woodland, within the last 200 years. A captive breeding program has been established as part of efforts to restore this species. This study used genetic data to examine the range-wide population structure of regent honeyeaters, including spatial structure, its change through time, sex differences in philopatry and mobility, and genetic differences between the captive and wild populations. There was low genetic differentiation between birds captured in different geographic areas. Despite the recent demographic decline, low spatial structure appears to have some temporal consistency. Both sexes appear to be highly mobile, and there does not seem to be significant genetic differentiation between the captive and wild populations. We conclude that management efforts for survival of this species, including habitat protection, restoration, and release of captive-bred birds into the wild, can treat the species as effectively a single genetic population.

  9. Very Low Population Structure in a Highly Mobile and Wide-Ranging Endangered Bird Species

    PubMed Central

    Kvistad, Lynna; Ingwersen, Dean; Pavlova, Alexandra; Bull, James K.; Sunnucks, Paul

    2015-01-01

    The loss of biodiversity following fragmentation and degradation of habitat is a major issue in conservation biology. As competition for resources increases following habitat loss and fragmentation, severe population declines may occur even in common, highly mobile species; such demographic decline may cause changes within the population structure of the species. The regent honeyeater, Anthochaera phrygia, is a highly nomadic woodland bird once common in its native southeast Australia. It has experienced a sharp decline in abundance since the late 1970s, following clearing of large areas of its preferred habitat, box-ironbark woodland, within the last 200 years. A captive breeding program has been established as part of efforts to restore this species. This study used genetic data to examine the range-wide population structure of regent honeyeaters, including spatial structure, its change through time, sex differences in philopatry and mobility, and genetic differences between the captive and wild populations. There was low genetic differentiation between birds captured in different geographic areas. Despite the recent demographic decline, low spatial structure appears to have some temporal consistency. Both sexes appear to be highly mobile, and there does not seem to be significant genetic differentiation between the captive and wild populations. We conclude that management efforts for survival of this species, including habitat protection, restoration, and release of captive-bred birds into the wild, can treat the species as effectively a single genetic population. PMID:26649426

  10. Very Low Population Structure in a Highly Mobile and Wide-Ranging Endangered Bird Species.

    PubMed

    Kvistad, Lynna; Ingwersen, Dean; Pavlova, Alexandra; Bull, James K; Sunnucks, Paul

    2015-01-01

    The loss of biodiversity following fragmentation and degradation of habitat is a major issue in conservation biology. As competition for resources increases following habitat loss and fragmentation, severe population declines may occur even in common, highly mobile species; such demographic decline may cause changes within the population structure of the species. The regent honeyeater, Anthochaera phrygia, is a highly nomadic woodland bird once common in its native southeast Australia. It has experienced a sharp decline in abundance since the late 1970s, following clearing of large areas of its preferred habitat, box-ironbark woodland, within the last 200 years. A captive breeding program has been established as part of efforts to restore this species. This study used genetic data to examine the range-wide population structure of regent honeyeaters, including spatial structure, its change through time, sex differences in philopatry and mobility, and genetic differences between the captive and wild populations. There was low genetic differentiation between birds captured in different geographic areas. Despite the recent demographic decline, low spatial structure appears to have some temporal consistency. Both sexes appear to be highly mobile, and there does not seem to be significant genetic differentiation between the captive and wild populations. We conclude that management efforts for survival of this species, including habitat protection, restoration, and release of captive-bred birds into the wild, can treat the species as effectively a single genetic population. PMID:26649426

  11. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    PubMed

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.

  12. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    PubMed

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations. PMID:23450090

  13. Fluvial processes and local lithology controlling abundance, structure, and composition of mussel beds

    PubMed Central

    Vannote, Robin L.; Minshall, G. Wayne

    1982-01-01

    In the Salmon River Canyon, Idaho, the fresh-water pearl mussel, Margaritifera falcata, attains maximum density and age in river reaches where large block-boulders structurally stabilize cobbles and interstitial gravels. We hypothesize that block-boulders prevent significant bed scour during major floods, and these boulder-sheltered mussel beds, although rare, may be critical for population recruitment elsewhere within the river, especially after periodic flood scour of less protected mussel habitat. Mussel shells in Indian middens adjacent to these boulder-stabilized areas suggest that prehistoric tribes selectively exploited the high-density old-aged mussel beds. Locally, canyon reaches are aggrading with sand and gravel, and M. falcata is being replaced by Gonidea angulata. PMID:16593208

  14. The population genomics of begomoviruses: global scale population structure and gene flow

    PubMed Central

    2010-01-01

    Background The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people. Results We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations. Conclusions Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could facilitate population genetics studies

  15. How population structure shapes neighborhood segregation.

    PubMed

    Bruch, Elizabeth E

    2014-03-01

    This study provides a framework for understanding how population composition conditions the relationship between individuals' choices about group affiliation and aggregate patterns of social separation or integration. The substantive focus is the role of income inequality in racial residential segregation. The author identifies three population parameters--between-group inequality, within-group inequality, and relative group size--that determine how income inequality between race groups affects racial segregation. She uses data from the Panel Study of Income Dynamics to estimate models of individual-level residential mobility and incorporates these estimates into agent-based models. She then simulates segregation dynamics under alternative assumptions about (1) the relative size of minority groups and (2) the degree of correlation between race and income among individuals. The author finds that income inequality can have offsetting effects at the high and low ends of the income distribution. She demonstrates the empirical relevance of the simulation results using fixed-effects, metro-level regressions applied to 1980-2000 U.S. census data.

  16. Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

    PubMed

    Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

    2014-01-01

    Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations

  17. Comparative population genetic structures and local adaptation of two mutualists.

    PubMed

    Anderson, Bruce; Olivieri, Isabelle; Lourmas, Mathieu; Stewart, Barbara A

    2004-08-01

    Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations. PMID:15446426

  18. Host genetics and population structure effects on parasitic disease.

    PubMed

    Williams-Blangero, Sarah; Criscione, Charles D; VandeBerg, John L; Correa-Oliveira, Rodrigo; Williams, Kimberly D; Subedi, Janardan; Kent, Jack W; Williams, Jeff; Kumar, Satish; Blangero, John

    2012-03-19

    Host genetic factors exert significant influences on differential susceptibility to many infectious diseases. In addition, population structure of both host and parasite may influence disease distribution patterns. In this study, we assess the effects of population structure on infectious disease in two populations in which host genetic factors influencing susceptibility to parasitic disease have been extensively studied. The first population is the Jirel population of eastern Nepal that has been the subject of research on the determinants of differential susceptibility to soil-transmitted helminth infections. The second group is a Brazilian population residing in an area endemic for Trypanosoma cruzi infection that has been assessed for genetic influences on differential disease progression in Chagas disease. For measures of Ascaris worm burden, within-population host genetic effects are generally more important than host population structure factors in determining patterns of infectious disease. No significant influences of population structure on measures associated with progression of cardiac disease in individuals who were seropositive for T. cruzi infection were found.

  19. Comparative population genetic structures and local adaptation of two mutualists.

    PubMed

    Anderson, Bruce; Olivieri, Isabelle; Lourmas, Mathieu; Stewart, Barbara A

    2004-08-01

    Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations.

  20. Isonymy and the genetic structure of Albanian populations.

    PubMed

    Mikerezi, Ilia; Pizzetti, Paola; Lucchetti, Enzo; Ekonomi, Milva

    2003-12-01

    It is well known that in systems of surname transmission through the paternal line, surnames simulate neutral gene alleles belonging to the Y chromosome. This property of surnames was used to analyze the genetic structure of Albanian populations. Two large samples of surnames belonging to two different periods of time were analyzed. The analysis of indicators of population structure showed that geographical distance has an important effect on surname distribution. It seems that isolation by distance and genetic drift have been still important factors in the determination of the genetic structure of the Albanian population. PMID:14746137

  1. Genomic diversity, population structure, and migration following rapid range expansion in the Balsam poplar, Populus balsamifera.

    PubMed

    Keller, Stephen R; Olson, Matthew S; Silim, Salim; Schroeder, William; Tiffin, Peter

    2010-03-01

    Rapid range expansions can cause pervasive changes in the genetic diversity and structure of populations. The postglacial history of the Balsam Poplar, Populus balsamifera, involved the colonization of most of northern North America, an area largely covered by continental ice sheets during the last glacial maximum. To characterize how this expansion shaped genomic diversity within and among populations, we developed 412 SNP markers that we assayed for a range-wide sample of 474 individuals sampled from 34 populations. We complemented the SNP data set with DNA sequence data from 11 nuclear loci from 94 individuals, and used coalescent analyses to estimate historical population size, demographic growth, and patterns of migration. Bayesian clustering identified three geographically separated demes found in the Northern, Central, and Eastern portions of the species' range. These demes varied significantly in nucleotide diversity, the abundance of private polymorphisms, and population substructure. Most measures supported the Central deme as descended from the primary refuge of diversity. Both SNPs and sequence data suggested recent population growth, and coalescent analyses of historical migration suggested a massive expansion from the Centre to the North and East. Collectively, these data demonstrate the strong influence that range expansions exert on genomic diversity, both within local populations and across the range. Our results suggest that an in-depth knowledge of nucleotide diversity following expansion requires sampling within multiple populations, and highlight the utility of combining insights from different data types in population genomic studies.

  2. Determining population structure and hybridization for two iris species

    PubMed Central

    Hamlin, Jennafer A P; Arnold, Michael L

    2014-01-01

    Identifying processes that promote or limit gene flow can help define the ecological and evolutionary history of a species. Furthermore, defining those factors that make up “species boundaries” can provide a definition of the independent evolutionary trajectories of related taxa. For many species, the historic processes that account for their distribution of genetic variation remain unresolved. In this study, we examine the geographic distribution of genetic diversity for two species of Louisiana Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how populations are structured and if population structure coincides with potential barriers to gene flow. We also asked whether there is evidence of hybridization between these two species outside Louisiana hybrid zones. We used a genotyping-by-sequencing approach and sampled a large number of single nucleotide polymorphisms across these species' genomes. Two different population assignment methods were used to resolve population structure in I. brevicaulis; however, there was considerably less population structure in I. fulva. We used a species tree approach to infer phylogenies both within and between populations and species. For I. brevicaulis, the geography of the collection locality was reflected in the phylogeny. The I. fulva phylogeny reflected much less structure than detected for I. brevicaulis. Lastly, combining both species into a phylogenetic analysis resolved two of six populations of I. brevicaulis that shared alleles with I. fulva. Taken together, our results suggest major differences in the level and pattern of connectivity among populations of these two Louisiana Iris species. PMID:24683457

  3. Population dynamics of bowfin in a south Georgia reservoir: latitudinal comparisons of population structure, growth, and mortality

    USGS Publications Warehouse

    Porter, Nicholas J.; Bonvechio, Timothy F.; McCormick, Joshua L.; Quist, Michael

    2014-01-01

    The objectives of this study were to evaluate the population dynamics of bowfin (Amia calva) in Lake Lindsay Grace, Georgia, and to compare those dynamics to other bowfin populations. Relative abundance of bowfin sampled in 2010 in Lake Lindsay Grace was low and variable (mean±SD; 2.7±4.7 fish per hour of electrofishing). Total length (TL) of bowfin collected in Lake Lindsay Grace varied from 233–683 mm. Age of bowfin in Lake Lindsay Grace varied from 0–5 yr. Total annual mortality (A) was estimated at 68%. Both sexes appeared to be fully mature by age 2 with gonadosomatic index values above 8 for females and close to 1 for males. The majority of females were older, longer, and heavier than males. Bowfin in Lake Lindsay Grace had fast growth up to age 4 and higher total annual mortality than the other populations examined in this study. A chi-square test indicated that size structure of bowfin from Lake Lindsay Grace was different than those of a Louisiana population and two bowfin populations from the upper Mississippi River. To further assess bowfin size structure, we proposed standard length (i.e., TL) categories: stock (200 mm, 8 inches), quality (350 mm, 14 inches), preferred (460 mm, 18 inches), memorable (560 mm, 22, inches), and trophy (710 mm, 28 inches). Because our knowledge of bowfin ecology is limited, additional understanding of bowfin population dynamics provides important insight that can be used in management of bowfin across their distribution.

  4. Evolution of extortion in structured populations.

    PubMed

    Szolnoki, Attila; Perc, Matjaž

    2014-02-01

    Extortion strategies can dominate any opponent in an iterated prisoner's dilemma game. But if players are able to adopt the strategies performing better, extortion becomes widespread and evolutionary unstable. It may sometimes act as a catalyst for the evolution of cooperation, and it can also emerge in interactions between two populations, yet it is not the evolutionarily stable outcome. Here we revisit these results in the realm of spatial games. We find that pairwise imitation and birth-death dynamics return known evolutionary outcomes. Myopic best response strategy updating, on the other hand, reveals counterintuitive solutions. Defectors and extortioners coarsen spontaneously, which allows cooperators to prevail even at prohibitively high temptations to defect. Here extortion strategies play the role of a Trojan horse. They may emerge among defectors by chance, and once they do, cooperators become viable as well. These results are independent of the interaction topology, and they highlight the importance of coarsening, checkerboard ordering, and best response updating in evolutionary games.

  5. Evolution of extortion in structured populations

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Perc, Matjaž

    2014-02-01

    Extortion strategies can dominate any opponent in an iterated prisoner's dilemma game. But if players are able to adopt the strategies performing better, extortion becomes widespread and evolutionary unstable. It may sometimes act as a catalyst for the evolution of cooperation, and it can also emerge in interactions between two populations, yet it is not the evolutionarily stable outcome. Here we revisit these results in the realm of spatial games. We find that pairwise imitation and birth-death dynamics return known evolutionary outcomes. Myopic best response strategy updating, on the other hand, reveals counterintuitive solutions. Defectors and extortioners coarsen spontaneously, which allows cooperators to prevail even at prohibitively high temptations to defect. Here extortion strategies play the role of a Trojan horse. They may emerge among defectors by chance, and once they do, cooperators become viable as well. These results are independent of the interaction topology, and they highlight the importance of coarsening, checkerboard ordering, and best response updating in evolutionary games.

  6. Accounting for Subgroup Structure in Line-Transect Abundance Estimates of False Killer Whales (Pseudorca crassidens) in Hawaiian Waters

    PubMed Central

    Bradford, Amanda L.; Forney, Karin A.; Oleson, Erin M.; Barlow, Jay

    2014-01-01

    For biological populations that form aggregations (or clusters) of individuals, cluster size is an important parameter in line-transect abundance estimation and should be accurately measured. Cluster size in cetaceans has traditionally been represented as the total number of individuals in a group, but group size may be underestimated if group members are spatially diffuse. Groups of false killer whales (Pseudorca crassidens) can comprise numerous subgroups that are dispersed over tens of kilometers, leading to a spatial mismatch between a detected group and the theoretical framework of line-transect analysis. Three stocks of false killer whales are found within the U.S. Exclusive Economic Zone of the Hawaiian Islands (Hawaiian EEZ): an insular main Hawaiian Islands stock, a pelagic stock, and a Northwestern Hawaiian Islands (NWHI) stock. A ship-based line-transect survey of the Hawaiian EEZ was conducted in the summer and fall of 2010, resulting in six systematic-effort visual sightings of pelagic (n = 5) and NWHI (n = 1) false killer whale groups. The maximum number and spatial extent of subgroups per sighting was 18 subgroups and 35 km, respectively. These sightings were combined with data from similar previous surveys and analyzed within the conventional line-transect estimation framework. The detection function, mean cluster size, and encounter rate were estimated separately to appropriately incorporate data collected using different methods. Unlike previous line-transect analyses of cetaceans, subgroups were treated as the analytical cluster instead of groups because subgroups better conform to the specifications of line-transect theory. Bootstrap values (n = 5,000) of the line-transect parameters were randomly combined to estimate the variance of stock-specific abundance estimates. Hawai’i pelagic and NWHI false killer whales were estimated to number 1,552 (CV = 0.66; 95% CI = 479–5,030) and 552 (CV = 1.09; 95% CI = 97–3

  7. Accounting for subgroup structure in line-transect abundance estimates of false killer whales (Pseudorca crassidens) in Hawaiian waters.

    PubMed

    Bradford, Amanda L; Forney, Karin A; Oleson, Erin M; Barlow, Jay

    2014-01-01

    For biological populations that form aggregations (or clusters) of individuals, cluster size is an important parameter in line-transect abundance estimation and should be accurately measured. Cluster size in cetaceans has traditionally been represented as the total number of individuals in a group, but group size may be underestimated if group members are spatially diffuse. Groups of false killer whales (Pseudorca crassidens) can comprise numerous subgroups that are dispersed over tens of kilometers, leading to a spatial mismatch between a detected group and the theoretical framework of line-transect analysis. Three stocks of false killer whales are found within the U.S. Exclusive Economic Zone of the Hawaiian Islands (Hawaiian EEZ): an insular main Hawaiian Islands stock, a pelagic stock, and a Northwestern Hawaiian Islands (NWHI) stock. A ship-based line-transect survey of the Hawaiian EEZ was conducted in the summer and fall of 2010, resulting in six systematic-effort visual sightings of pelagic (n = 5) and NWHI (n = 1) false killer whale groups. The maximum number and spatial extent of subgroups per sighting was 18 subgroups and 35 km, respectively. These sightings were combined with data from similar previous surveys and analyzed within the conventional line-transect estimation framework. The detection function, mean cluster size, and encounter rate were estimated separately to appropriately incorporate data collected using different methods. Unlike previous line-transect analyses of cetaceans, subgroups were treated as the analytical cluster instead of groups because subgroups better conform to the specifications of line-transect theory. Bootstrap values (n = 5,000) of the line-transect parameters were randomly combined to estimate the variance of stock-specific abundance estimates. Hawai'i pelagic and NWHI false killer whales were estimated to number 1,552 (CV = 0.66; 95% CI = 479-5,030) and 552 (CV = 1.09; 95% CI = 97

  8. Accounting for subgroup structure in line-transect abundance estimates of false killer whales (Pseudorca crassidens) in Hawaiian waters.

    PubMed

    Bradford, Amanda L; Forney, Karin A; Oleson, Erin M; Barlow, Jay

    2014-01-01

    For biological populations that form aggregations (or clusters) of individuals, cluster size is an important parameter in line-transect abundance estimation and should be accurately measured. Cluster size in cetaceans has traditionally been represented as the total number of individuals in a group, but group size may be underestimated if group members are spatially diffuse. Groups of false killer whales (Pseudorca crassidens) can comprise numerous subgroups that are dispersed over tens of kilometers, leading to a spatial mismatch between a detected group and the theoretical framework of line-transect analysis. Three stocks of false killer whales are found within the U.S. Exclusive Economic Zone of the Hawaiian Islands (Hawaiian EEZ): an insular main Hawaiian Islands stock, a pelagic stock, and a Northwestern Hawaiian Islands (NWHI) stock. A ship-based line-transect survey of the Hawaiian EEZ was conducted in the summer and fall of 2010, resulting in six systematic-effort visual sightings of pelagic (n = 5) and NWHI (n = 1) false killer whale groups. The maximum number and spatial extent of subgroups per sighting was 18 subgroups and 35 km, respectively. These sightings were combined with data from similar previous surveys and analyzed within the conventional line-transect estimation framework. The detection function, mean cluster size, and encounter rate were estimated separately to appropriately incorporate data collected using different methods. Unlike previous line-transect analyses of cetaceans, subgroups were treated as the analytical cluster instead of groups because subgroups better conform to the specifications of line-transect theory. Bootstrap values (n = 5,000) of the line-transect parameters were randomly combined to estimate the variance of stock-specific abundance estimates. Hawai'i pelagic and NWHI false killer whales were estimated to number 1,552 (CV = 0.66; 95% CI = 479-5,030) and 552 (CV = 1.09; 95% CI = 97

  9. Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid.

    PubMed Central

    Kyrkjeeide, Magni Olsen; Hassel, Kristian; Flatberg, Kjell Ivar; Shaw, A. Jonathan; Yousefi, Narjes; Stenøien, Hans K.

    2016-01-01

    Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum. PMID:26859563

  10. Predicting meningococcal disease outbreaks in structured populations.

    PubMed

    Ranta, J; Mäkelä, P H; Arjas, E

    2004-03-30

    Rational decision making on whether some form of intervention would be necessary to control the spread of a meningococcal epidemic is based on predictions concerning its potential natural progression. Unfortunately, reliable predictions are difficult to make during the early stages of an outbreak. A stochastic discrete time epidemic model was applied to adaptively predict the development of outbreaks of meningococcal disease in 'closed' populations such as military garrisons or boarding schools, which are further divided into subgroups called 'units'. The performance of the adaptive method was assessed by using 3 simulated epidemics representing substantially different realizations in a 'garrison' of 20 units, with 68 men in each. Predictions of the weekly number of disease cases, of the number of carriers, and of the number of new infections were computed. Simulations suggest that predictions based only on the observed numbers of disease cases are generally inaccurate. These predictions can be improved if temporal observations on asymptomatic carriers in different units are utilized together with observed time series of the disease. A sample of 15 per cent from all units can be sufficient for a major improvement if the alternative is to obtain a full sample of only some units. Exploiting fully such information requires computer intensive Markov chain Monte Carlo methods. PMID:15027081

  11. HOW POPULATION STRUCTURE SHAPES NEIGHBORHOOD SEGREGATION*

    PubMed Central

    Bruch, Elizabeth E.

    2014-01-01

    This study investigates how choices about social affiliation based on one attribute can exacerbate or attenuate segregation on another correlated attribute. The specific application is the role of racial and economic factors in generating patterns of racial residential segregation. I identify three population parameters—between-group inequality, within-group inequality, and relative group size—that determine how income inequality between race groups affects racial segregation. I use data from the Panel Study of Income Dynamics to estimate models of individual-level residential mobility, and incorporate these estimates into agent-based models. I then simulate segregation dynamics under alternative assumptions about: (1) the relative size of minority groups; and (2) the degree of correlation between race and income among individuals. I find that income inequality can have offsetting effects at the high and low ends of the income distribution. I demonstrate the empirical relevance of the simulation results using fixed-effects, metro-level regressions applied to 1980-2000 U.S. Census data. PMID:25009360

  12. Evolution of extortion in structured populations.

    PubMed

    Szolnoki, Attila; Perc, Matjaž

    2014-02-01

    Extortion strategies can dominate any opponent in an iterated prisoner's dilemma game. But if players are able to adopt the strategies performing better, extortion becomes widespread and evolutionary unstable. It may sometimes act as a catalyst for the evolution of cooperation, and it can also emerge in interactions between two populations, yet it is not the evolutionarily stable outcome. Here we revisit these results in the realm of spatial games. We find that pairwise imitation and birth-death dynamics return known evolutionary outcomes. Myopic best response strategy updating, on the other hand, reveals counterintuitive solutions. Defectors and extortioners coarsen spontaneously, which allows cooperators to prevail even at prohibitively high temptations to defect. Here extortion strategies play the role of a Trojan horse. They may emerge among defectors by chance, and once they do, cooperators become viable as well. These results are independent of the interaction topology, and they highlight the importance of coarsening, checkerboard ordering, and best response updating in evolutionary games. PMID:25353531

  13. Social and population structure in the ant Cataglyphis emmae.

    PubMed

    Jowers, Michael J; Leniaud, Laurianne; Cerdá, Xim; Alasaad, Samer; Caut, Stephane; Amor, Fernando; Aron, Serge; Boulay, Raphaël R

    2013-01-01

    Dispersal has consequences not only for individual fitness, but also for population dynamics, population genetics and species distribution. Social Hymenoptera show two contrasting colony reproductive strategies, dependent and independent colony foundation modes, and these are often associated to the population structures derived from inter and intra-population gene flow processes conditioned by alternative dispersal strategies. Here we employ microsatellite and mitochondrial markers to investigate the population and social genetic structure and dispersal patterns in the ant Cataglyphis emmae at both, local and regional scales. We find that C. emmae is monogynous and polyandrous. Lack of detection of any population viscosity and population structure with nuclear markers at the local scale suggests efficient dispersal, in agreement with a lack of inbreeding. Contrasting demographic differences before and during the mating seasons suggest that C. emmae workers raise sexuals in peripheric nest chambers to reduce intracolonial conflicts. The high genetic differentiation recovered from the mtDNA haplotypes, together with the significant correlation of such to geographic distance, and presence of new nuclear alleles between areas (valleys) suggest long-term historical isolation between these regions, indicative of limited dispersal at the regional scale. Our findings on the ecological, social and population structure of this species increases our understanding of the patterns and processes involved under independent colony foundation. PMID:24039827

  14. Social and Population Structure in the Ant Cataglyphis emmae

    PubMed Central

    Jowers, Michael J.; Leniaud, Laurianne; Cerdá, Xim; Alasaad, Samer; Caut, Stephane; Amor, Fernando; Aron, Serge; Boulay, Raphaël R.

    2013-01-01

    Dispersal has consequences not only for individual fitness, but also for population dynamics, population genetics and species distribution. Social Hymenoptera show two contrasting colony reproductive strategies, dependent and independent colony foundation modes, and these are often associated to the population structures derived from inter and intra-population gene flow processes conditioned by alternative dispersal strategies. Here we employ microsatellite and mitochondrial markers to investigate the population and social genetic structure and dispersal patterns in the ant Cataglyphis emmae at both, local and regional scales. We find that C. emmae is monogynous and polyandrous. Lack of detection of any population viscosity and population structure with nuclear markers at the local scale suggests efficient dispersal, in agreement with a lack of inbreeding. Contrasting demographic differences before and during the mating seasons suggest that C. emmae workers raise sexuals in peripheric nest chambers to reduce intracolonial conflicts. The high genetic differentiation recovered from the mtDNA haplotypes, together with the significant correlation of such to geographic distance, and presence of new nuclear alleles between areas (valleys) suggest long-term historical isolation between these regions, indicative of limited dispersal at the regional scale. Our findings on the ecological, social and population structure of this species increases our understanding of the patterns and processes involved under independent colony foundation. PMID:24039827

  15. Heterogeneous road networks have no apparent effect on the genetic structure of small mammal populations.

    PubMed

    Grilo, Clara; Del Cerro, Irene; Centeno-Cuadros, Alejandro; Ramiro, Victor; Román, Jacinto; Molina-Vacas, Guillem; Fernández-Aguilar, Xavier; Rodríguez, Juan; Porto-Peter, Flávia; Fonseca, Carlos; Revilla, Eloy; Godoy, José A

    2016-09-15

    Roads are widely recognized to represent a barrier to individual movements and, conversely, verges can act as potential corridors for the dispersal of many small mammals. Both barrier and corridor effects should generate a clear spatial pattern in genetic structure. Nevertheless, the effect of roads on the genetic structure of small mammal populations still remains unclear. In this study, we examine the barrier effect that different road types (4-lane highway, 2-lane roads and single-lane unpaved roads) may have on the population genetic structure of three species differing in relevant life history traits: southern water vole Arvicola sapidus, the Mediterranean pine vole Microtus duodecimcostatus and the Algerian mouse Mus spretus. We also examine the corridor effect of highway verges on the Mediterranean pine vole and the Algerian mouse. We analysed the population structure through pairwise estimates of FST among subpopulations bisected by roads, identified genetic clusters through Bayesian assignment approaches, and used simple and partial Mantel tests to evaluate the relative barrier or corridor effect of roads. No strong evidences were found for an effect of roads on population structure of these three species. The barrier effect of roads seems to be site-specific and no corridor effect of verges was found for the pine vole and Algerian mouse populations. The lack of consistent results among species and for each road type lead us to believe that the ability of individual dispersers to use those crossing structures or the habitat quality in the highway verges may have a relatively higher influence on gene flow among populations than the presence of crossing structures per se. Further research should include microhabitat analysis and the estimates of species abundance to understand the mechanisms that underlie the genetic structure observed at some sites. PMID:27219505

  16. Heterogeneous road networks have no apparent effect on the genetic structure of small mammal populations.

    PubMed

    Grilo, Clara; Del Cerro, Irene; Centeno-Cuadros, Alejandro; Ramiro, Victor; Román, Jacinto; Molina-Vacas, Guillem; Fernández-Aguilar, Xavier; Rodríguez, Juan; Porto-Peter, Flávia; Fonseca, Carlos; Revilla, Eloy; Godoy, José A

    2016-09-15

    Roads are widely recognized to represent a barrier to individual movements and, conversely, verges can act as potential corridors for the dispersal of many small mammals. Both barrier and corridor effects should generate a clear spatial pattern in genetic structure. Nevertheless, the effect of roads on the genetic structure of small mammal populations still remains unclear. In this study, we examine the barrier effect that different road types (4-lane highway, 2-lane roads and single-lane unpaved roads) may have on the population genetic structure of three species differing in relevant life history traits: southern water vole Arvicola sapidus, the Mediterranean pine vole Microtus duodecimcostatus and the Algerian mouse Mus spretus. We also examine the corridor effect of highway verges on the Mediterranean pine vole and the Algerian mouse. We analysed the population structure through pairwise estimates of FST among subpopulations bisected by roads, identified genetic clusters through Bayesian assignment approaches, and used simple and partial Mantel tests to evaluate the relative barrier or corridor effect of roads. No strong evidences were found for an effect of roads on population structure of these three species. The barrier effect of roads seems to be site-specific and no corridor effect of verges was found for the pine vole and Algerian mouse populations. The lack of consistent results among species and for each road type lead us to believe that the ability of individual dispersers to use those crossing structures or the habitat quality in the highway verges may have a relatively higher influence on gene flow among populations than the presence of crossing structures per se. Further research should include microhabitat analysis and the estimates of species abundance to understand the mechanisms that underlie the genetic structure observed at some sites.

  17. Geographic patterns in relative abundances and population trends of breeding and wintering loggerhead shrikes in North America

    USGS Publications Warehouse

    Sauer, J.R.; Orsillo, S.; Peterjohn, B.G.; Yosef, Reuven; Lohrer, Fred E.

    1995-01-01

    In North America, the Breeding Bird Survey and the Christmas Bird Count provide data that are collected at sites visited each year, and the site-specific data can be placed in a Geographic Information System and smoothed to produce contour maps of relative abundance and trend for the United States and southern Canada. We develop these contour maps for Loggerhead Shrike (Lanius ludovicianus) data from both surveys, and compare the patterns derived from each survey to evaluate the consistency of trends and relative abundances within physiographic strata. Patterns in relative abundance seem to be associated with strata, especially in the breeding season, but trends are often heterogeneous within strata. Because of limitations of the surveys and observed geographic patterns of shrike trends in the survey data, we suggest that there is no natural scale for the analysis of shrike-habitat associations.

  18. Earthworm ecology affects the population structure of their Verminephrobacter symbionts.

    PubMed

    Viana, Flávia; Jensen, Christopher Erik; Macey, Michael; Schramm, Andreas; Lund, Marie Braad

    2016-05-01

    Earthworms carry species-specific Verminephrobacter symbionts in their nephridia (excretory organs). The symbionts are vertically transmitted via the cocoon, can only colonize the host during early embryonic development, and have co-speciated with their host for about 100 million years. Although several studies have addressed Verminephrobacter diversity between worm species, the intra-species diversity of the symbiont population has never been investigated. In this study, symbiont population structure was examined by using a multi-locus sequence typing (MLST) approach on Verminephrobacter isolated from two contrasting ecological types of earthworm hosts: the high population density, fast reproducing compost worms, Eisenia andrei and Eisenia fetida, and the low-density, slow reproducing Aporrectodea tuberculata, commonly found in garden soils. Three distinct populations were investigated for both types and, according to MLST analysis of 193 Verminephrobacter isolates, the symbiont community in each worm individual was very homogeneous. The more solitary A. tuberculata carried unique symbiont populations in 9 out of 10 host individuals, whereas the symbiont populations in the social compost worms were homogeneous across host individuals from the same population. These data suggested that host ecology shaped the population structure of Verminephrobacter symbionts. The homogeneous symbiont populations in the compost worms led to the hypothesis that Verminephrobacter could be transferred bi-parentally or via leaky horizontal transmission in high-density, frequently mating worm populations. PMID:27040820

  19. Genetic Variation and Population Structure in Native Americans

    PubMed Central

    Ramachandran, Sohini; Ray, Nicolas; Bedoya, Gabriel; Rojas, Winston; Parra, Maria V; Molina, Julio A; Gallo, Carla; Mazzotti, Guido; Poletti, Giovanni; Hill, Kim; Hurtado, Ana M; Labuda, Damian; Klitz, William; Barrantes, Ramiro; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, Maria Luiza; Tsuneto, Luiza T; Llop, Elena; Rothhammer, Francisco; Excoffier, Laurent; Feldman, Marcus W; Rosenberg, Noah A; Ruiz-Linares, Andrés

    2007-01-01

    We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas. PMID:18039031

  20. Genetic variation and population structure in native Americans.

    PubMed

    Wang, Sijia; Lewis, Cecil M; Jakobsson, Mattias; Ramachandran, Sohini; Ray, Nicolas; Bedoya, Gabriel; Rojas, Winston; Parra, Maria V; Molina, Julio A; Gallo, Carla; Mazzotti, Guido; Poletti, Giovanni; Hill, Kim; Hurtado, Ana M; Labuda, Damian; Klitz, William; Barrantes, Ramiro; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, Maria Luiza; Tsuneto, Luiza T; Llop, Elena; Rothhammer, Francisco; Excoffier, Laurent; Feldman, Marcus W; Rosenberg, Noah A; Ruiz-Linares, Andrés

    2007-11-01

    We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas. PMID:18039031

  1. Plasmodium vivax Diversity and Population Structure across Four Continents

    PubMed Central

    Koepfli, Cristian; Rodrigues, Priscila T.; Antao, Tiago; Orjuela-Sánchez, Pamela; Van den Eede, Peter; Gamboa, Dionicia; van Hong, Nguyen; Bendezu, Jorge; Erhart, Annette; Barnadas, Céline; Ratsimbasoa, Arsène; Menard, Didier; Severini, Carlo; Menegon, Michela; Nour, Bakri Y. M.; Karunaweera, Nadira; Mueller, Ivo; Ferreira, Marcelo U.; Felger, Ingrid

    2015-01-01

    Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60–80% in Latin American populations, suggesting that typing of 2–6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11–0.16) between South American and all other populations, and lowest (0.04–0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations. PMID:26125189

  2. Plasmodium vivax Diversity and Population Structure across Four Continents.

    PubMed

    Koepfli, Cristian; Rodrigues, Priscila T; Antao, Tiago; Orjuela-Sánchez, Pamela; Van den Eede, Peter; Gamboa, Dionicia; van Hong, Nguyen; Bendezu, Jorge; Erhart, Annette; Barnadas, Céline; Ratsimbasoa, Arsène; Menard, Didier; Severini, Carlo; Menegon, Michela; Nour, Bakri Y M; Karunaweera, Nadira; Mueller, Ivo; Ferreira, Marcelo U; Felger, Ingrid

    2015-01-01

    Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999-2008. Diversity was highest in South-East Asia (mean allelic richness 10.0-12.8), intermediate in the South Pacific (8.1-9.9) Madagascar and Sudan (7.9-8.4), and lowest in South America and Central Asia (5.5-7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60-80% in Latin American populations, suggesting that typing of 2-6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11-0.16) between South American and all other populations, and lowest (0.04-0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations.

  3. Practical Bias Correction in Aerial Surveys of Large Mammals: Validation of Hybrid Double-Observer with Sightability Method against Known Abundance of Feral Horse (Equus caballus) Populations

    PubMed Central

    2016-01-01

    Reliably estimating wildlife abundance is fundamental to effective management. Aerial surveys are one of the only spatially robust tools for estimating large mammal populations, but statistical sampling methods are required to address detection biases that affect accuracy and precision of the estimates. Although various methods for correcting aerial survey bias are employed on large mammal species around the world, these have rarely been rigorously validated. Several populations of feral horses (Equus caballus) in the western United States have been intensively studied, resulting in identification of all unique individuals. This provided a rare opportunity to test aerial survey bias correction on populations of known abundance. We hypothesized that a hybrid method combining simultaneous double-observer and sightability bias correction techniques would accurately estimate abundance. We validated this integrated technique on populations of known size and also on a pair of surveys before and after a known number was removed. Our analysis identified several covariates across the surveys that explained and corrected biases in the estimates. All six tests on known populations produced estimates with deviations from the known value ranging from -8.5% to +13.7% and <0.7 standard errors. Precision varied widely, from 6.1% CV to 25.0% CV. In contrast, the pair of surveys conducted around a known management removal produced an estimated change in population between the surveys that was significantly larger than the known reduction. Although the deviation between was only 9.1%, the precision estimate (CV = 1.6%) may have been artificially low. It was apparent that use of a helicopter in those surveys perturbed the horses, introducing detection error and heterogeneity in a manner that could not be corrected by our statistical models. Our results validate the hybrid method, highlight its potentially broad applicability, identify some limitations, and provide insight and guidance

  4. Trends in sea otter population abundance in western Prince William Sound, Alaska: Progress toward recovery following the 1989 Exxon Valdez oil spill

    USGS Publications Warehouse

    Bodkin, J.L.; Ballachey, B.E.; Esslinger, G.G.

    2011-01-01

    Sea otters in western Prince William Sound (WPWS) and elsewhere in the Gulf of Alaska suffered widespread mortality as a result of oiling following the 1989 T/V Exxon Valdez oil spill. Following the spill, extensive efforts have been directed toward identifying and understanding long-term consequences of the spill and the process of recovery. We conducted annual aerial surveys of sea otter abundance from 1993 to 2009 (except for 2001 and 2006) in WPWS. We observed an increasing trend in population abundance at the scale of WPWS through 2000 at an average annual rate of 4 percent: however, at northern Knight Island where oiling was heaviest and sea otter mortality highest, no increase in abundance was evident by 2000. We continued to see significant increase in abundance at the scale of WPWS between 2001 and 2009, with an average annual rate of increase from 1993 to 2009 of 2.6 percent. We estimated the 2009 population size of WPWS to be 3,958 animals (standard error=653), nearly 2,000 animals more than the first post-spill estimate in 1993. Surveys since 2003 also have identified a significant increasing trend at the heavily oiled site in northern Knight Island, averaging about 25 percent annually and resulting in a 2009 estimated population size of 116 animals (standard error=19). Although the 2009 estimate for northern Knight Island remains about 30 percent less than the pre-spill estimate of 165 animals, we interpret this trend as strong evidence of a trajectory toward recovery of spill-affected sea otter populations in WPWS.

  5. Distribution, Abundance, and Population Dynamics of Northern Squawfish, Walleye, Smallmouth Bass, and Channel Catfish in John Day Reservoir, 1986 Annual Report.

    SciTech Connect

    Beamesderfer, Raymond C.

    1987-04-01

    John Day Reservoir was sampled from 25 March to 1 September 1986 using gill nets, trap nets, boat electrofishers, hook and line, and an angler survey to collect 4945 northern squawfish Ptychocheilus oregonesis, 602 walleye Stizostedion vitreum 2894 smallmouth bass Micropterus dolomieui, and 563 channel catfish Icatalurus punctatus. Distribution, abundance and population parameters of each species were examined. One year growth, mortality, and relative year class strength was described.

  6. Statistical validation of structured population models for Daphnia magna

    PubMed Central

    Adoteye, Kaska; Banks, H.T.; Cross, Karissa; Eytcheson, Stephanie; Flores, Kevin B.; LeBlanc, Gerald A.; Nguyen, Timothy; Ross, Chelsea; Smith, Emmaline; Stemkovski, Michael; Stokely, Sarah

    2016-01-01

    In this study we use statistical validation techniques to verify density-dependent mechanisms hypothesized for populations of Daphnia magna. We develop structured population models that exemplify specific mechanisms, and use multi-scale experimental data in order to test their importance. We show that fecundity and survival rates are affected by both time-varying density-independent factors, such as age, and density-dependent factors, such as competition. We perform uncertainty analysis and show that our parameters are estimated with a high degree of confidence. Further, we perform a sensitivity analysis to understand how changes in fecundity and survival rates affect population size and age-structure. PMID:26092608

  7. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient

    PubMed Central

    Vangestel, C; Mergeay, J; Dawson, D A; Callens, T; Vandomme, V; Lens, L

    2012-01-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients. PMID:22588131

  8. Diversity, abundance and community network structure in sporocarp-associated beetle communities of the central Appalachian Mountains.

    PubMed

    Epps, Mary Jane; Arnold, A Elizabeth

    2010-01-01

    Although arthropods are abundant and diverse in and on macrofungal sporocarps, their associations with fungi seldom have been described at a community level. We examined sporocarp-associated beetle communities in two primary sites in the Appalachian Mountains and foothills, assessing beetle diversity and abundance in relation to study site, sampling season (early vs. late summer), and sporocarp characteristics such as taxonomic position, dry mass and age. From 758 sporocarps representing >180 species we recovered 15404 adult beetles representing 72 species and 15 families, primarily Staphylinidae (> 98% of individuals and of 64% morphospecies). The probability of sporocarp colonization by beetles, beetle abundance and diversity differed among fungal species and were positively associated with sporocarp dry mass. Sporocarp age was positively correlated with beetle diversity and abundance (as measured in a focal species, Megacollybia platyphylla, Tricholomataceae), and its effects were independent of dry mass. Many beetle species were generalists, visiting a wide breadth of fungi in both the Agaricales and Polyporales; however, several beetle taxa showed evidence of specialization on particular fungal hosts. Host association data were used to examine the structure underlying sporocarp-beetle associations. Here we present the first evidence of nested community structure in the sporocarp-beetle interaction network. PMID:20648747

  9. Population genetic structure of Aedes albopictus in Penang, Malaysia.

    PubMed

    Zawani, M K N; Abu, H A; Sazaly, A B; Zary, S Y; Darlina, M N

    2014-10-07

    The mosquito Aedes albopictus is indigenous to Southeast Asian and is a vector for arbovirus diseases. Studies examining the population genetics structure of A. albopictus have been conducted worldwide; however, there are no documented reports on the population genetic structure of A. albopictus in Malaysia, particularly in Penang. We examined the population genetics of A. albopictus based on a 445-base pair segment of the mitochondrial DNA cytochrome oxidase 1 gene among 77 individuals from 9 localities representing 4 regions (Seberang Perai Utara, Seberang Perai Tengah, Northeast, and Southwest) of Penang. A total of 37 haplotypes were detected, including 28 unique haplotypes. The other 9 haplotypes were shared among various populations. These shared haplotypes reflect the weak population genetic structure of A. albopictus. The phylogenetic tree showed a low bootstrap value with no genetic structure, which was supported by minimum spanning network analysis. Analysis of mismatch distribution showed poor fit of equilibrium distribution. The genetic distance showed low genetic variation, while pairwise FST values showed no significant difference between all regions in Penang except for some localities. High haplotype diversity and low nucleotide diversity was observed for cytochrome oxidase 1 mtDNA. We conclude that there is no population genetic structure of A. albopictus mosquitoes in the Penang area.

  10. Population genetic structure of Theileria parva field isolates from indigenous cattle populations of Uganda.

    PubMed

    Muwanika, Vincent; Kabi, Fredrick; Masembe, Charles

    2016-03-01

    Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control. PMID:26613662

  11. Detecting Heterogeneity in Population Structure Across the Genome in Admixed Populations.

    PubMed

    McHugh, Caitlin; Brown, Lisa; Thornton, Timothy A

    2016-09-01

    The genetic structure of human populations is often characterized by aggregating measures of ancestry across the autosomal chromosomes. While it may be reasonable to assume that population structure patterns are similar genome-wide in relatively homogeneous populations, this assumption may not be appropriate for admixed populations, such as Hispanics and African-Americans, with recent ancestry from two or more continents. Recent studies have suggested that systematic ancestry differences can arise at genomic locations in admixed populations as a result of selection and nonrandom mating. Here, we propose a method, which we refer to as the chromosomal ancestry differences (CAnD) test, for detecting heterogeneity in population structure across the genome. CAnD can incorporate either local or chromosome-wide ancestry inferred from SNP genotype data to identify chromosomes harboring genomic regions with ancestry contributions that are significantly different than expected. In simulation studies with real genotype data from phase III of the HapMap Project, we demonstrate the validity and power of CAnD. We apply CAnD to the HapMap Mexican-American (MXL) and African-American (ASW) population samples; in this analysis the software RFMix is used to infer local ancestry at genomic regions, assuming admixing from Europeans, West Africans, and Native Americans. The CAnD test provides strong evidence of heterogeneity in population structure across the genome in the MXL sample ([Formula: see text]), which is largely driven by elevated Native American ancestry and deficit of European ancestry on the X chromosomes. Among the ASW, all chromosomes are largely African derived and no heterogeneity in population structure is detected in this sample. PMID:27440868

  12. Stage-Structured Population Dynamics of AEDES AEGYPTI

    NASA Astrophysics Data System (ADS)

    Yusoff, Nuraini; Budin, Harun; Ismail, Salemah

    Aedes aegypti is the main vector in the transmission of dengue fever, a vector-borne disease affecting world population living in tropical and sub-tropical countries. Better understanding of the dynamics of its population growth will help in the efforts of controlling the spread of this disease. In looking at the population dynamics of Aedes aegypti, this paper explored the stage-structured modeling of the population growth of the mosquito using the matrix population model. The life cycle of the mosquito was divided into five stages: eggs, larvae, pupae, adult1 and adult2. Developmental rates were obtained for the average Malaysian temperature and these were used in constructing the transition matrix for the matrix model. The model, which was based only on temperature, projected that the population of Aedes aegypti will blow up with time, which is not realistic. For further work, other factors need to be taken into account to obtain a more realistic result.

  13. Inference of population structure using dense haplotype data.

    PubMed

    Lawson, Daniel John; Hellenthal, Garrett; Myers, Simon; Falush, Daniel

    2012-01-01

    The advent of genome-wide dense variation data provides an opportunity to investigate ancestry in unprecedented detail, but presents new statistical challenges. We propose a novel inference framework that aims to efficiently capture information on population structure provided by patterns of haplotype similarity. Each individual in a sample is considered in turn as a recipient, whose chromosomes are reconstructed using chunks of DNA donated by the other individuals. Results of this "chromosome painting" can be summarized as a "coancestry matrix," which directly reveals key information about ancestral relationships among individuals. If markers are viewed as independent, we show that this matrix almost completely captures the information used by both standard Principal Components Analysis (PCA) and model-based approaches such as STRUCTURE in a unified manner. Furthermore, when markers are in linkage disequilibrium, the matrix combines information across successive markers to increase the ability to discern fine-scale population structure using PCA. In parallel, we have developed an efficient model-based approach to identify discrete populations using this matrix, which offers advantages over PCA in terms of interpretability and over existing clustering algorithms in terms of speed, number of separable populations, and sensitivity to subtle population structure. We analyse Human Genome Diversity Panel data for 938 individuals and 641,000 markers, and we identify 226 populations reflecting differences on continental, regional, local, and family scales. We present multiple lines of evidence that, while many methods capture similar information among strongly differentiated groups, more subtle population structure in human populations is consistently present at a much finer level than currently available geographic labels and is only captured by the haplotype-based approach. The software used for this article, ChromoPainter and fineSTRUCTURE, is available from http://www.paintmychromosomes.com/.

  14. Emergence and Abundance of Western Corn Rootworm (Coleoptera: Chrysomelidae) in Bt Cornfields With Structured and Seed Blend Refuges.

    PubMed

    Hughson, Sarah A; Spencer, Joseph L

    2015-02-01

    To slow evolution of western corn rootworm (Diabrotica virgifera virgifera LeConte) resistance to Bt (Bacillus thuringiensis Berliner) corn hybrids, non-Bt "refuges" must be planted within or adjacent to Bt cornfields, allowing susceptible insects to develop without exposure to Bt toxins. Bt-susceptible adults from refuges are expected to find and mate with resistant adults that have emerged from Bt corn, reducing the likelihood that Bt-resistant offspring are produced. The spatial and temporal distribution of adults in four refuge treatments (20, 5, and 0% structured refuges and 5% seed blend) and adjacent soybean fields was compared from 2010 to 2012. Adult emergence (adults/trap/day) from refuge corn in structured refuge treatments was greater than that from Bt corn, except during the post-pollination period of corn phenology when emergence from refuge and Bt plants was often the same. Abundance of free-moving adults was greatest in and near refuge rows in structured refuge treatments during vegetative and pollination periods. By post-pollination, adult abundance became evenly distributed. In contrast, adult abundance in 5% seed blends and 0% refuges was evenly distributed, or nearly so, across plots throughout the season. The persistent concentration of adults in refuge rows suggests that structured refuge configurations may not facilitate the expected mixing of adults from refuge and Bt corn. Seed blends produce uniform distributions of adults across the field that may facilitate mating between Bt and refuge adults and ultimately delay the evolution of Bt resistance. PMID:26470111

  15. Population structure of the thornback ray ( Raja clavata L.) in British waters

    NASA Astrophysics Data System (ADS)

    Chevolot, Malia; Ellis, Jim R.; Hoarau, Galice; Rijnsdorp, Adriaan D.; Stam, Wytze T.; Olsen, Jeanine L.

    2006-11-01

    Prior to the 1950s, thornback ray ( Raja clavata L.) was common and widely distributed in the seas of Northwest Europe. Since then, it has decreased in abundance and geographic range due to over-fishing. The sustainability of ray populations is of concern to fisheries management because their slow growth rate, late maturity and low fecundity make them susceptible to exploitation as victims of by-catch. We investigated the population genetic structure of thornback rays from 14 locations in the southern North Sea, English Channel and Irish Sea. Adults comprised < 4% of the total sampling despite heavy sampling effort over 47 hauls; thus our results apply mainly to sexually immature individuals. Using five microsatellite loci, weak but significant population differentiation was detected with a global FST = 0.013 ( P < 0.001). Pairwise Fst was significant for 75 out of 171 comparisons. Although earlier tagging studies suggest restricted foraging distances from home areas, the absence of genetic differentiation between some distant populations suggests that a substantial fraction of individuals migrate over wide areas. Autumn/winter locations appear to have a lower level of differentiation than spring/summer, which could be due to seasonal migration. Management and conservation of thornback ray populations will be challenging as population structure appears to be dynamic in space and time.

  16. Pulses of movement across the sea ice: population connectivity and temporal genetic structure in the arctic fox.

    PubMed

    Norén, Karin; Carmichael, Lindsey; Fuglei, Eva; Eide, Nina E; Hersteinsson, Pall; Angerbjörn, Anders

    2011-08-01

    Lemmings are involved in several important functions in the Arctic ecosystem. The Arctic fox (Vulpes lagopus) can be divided into two discrete ecotypes: "lemming foxes" and "coastal foxes". Crashes in lemming abundance can result in pulses of "lemming fox" movement across the Arctic sea ice and immigration into coastal habitats in search for food. These pulses can influence the genetic structure of the receiving population. We have tested the impact of immigration on the genetic structure of the "coastal fox" population in Svalbard by recording microsatellite variation in seven loci for 162 Arctic foxes sampled during the summer and winter over a 5-year period. Genetic heterogeneity and temporal genetic shifts, as inferred by STRUCTURE simulations and deviations from Hardy-Weinberg proportions, respectively, were recorded. Maximum likelihood estimates of movement as well as STRUCTURE simulations suggested that both immigration and genetic mixture are higher in Svalbard than in the neighbouring "lemming fox" populations. The STRUCTURE simulations and AMOVA revealed there are differences in genetic composition of the population between summer and winter seasons, indicating that immigrants are not present in the reproductive portion of the Svalbard population. Based on these results, we conclude that Arctic fox population structure varies with time and is influenced by immigration from neighbouring populations. The lemming cycle is likely an important factor shaping Arctic fox movement across sea ice and the subsequent population genetic structure, but is also likely to influence local adaptation to the coastal habitat and the prevalence of diseases.

  17. [Effects of macro-jellyfish abundance dynamics on fishery resource structure in the Yangtze River estuary and its adjacent waters].

    PubMed

    Shan, Xiu-Juan; Zhuang, Zhi-Meng; Jin, Xian-Shi; Dai, Fang-Qun

    2011-12-01

    Based on the bottom trawl survey data in May 2007 and May and June 2008, this paper analyzed the effects of the abundance dynamics of macro-jellyfish on the species composition, distribution, and abundance of fishery resource in the Yangtze River estuary and its adjacent waters. From May 2007 to June 2008, the average catch per haul and the top catch per haul of macro-jellyfish increased, up to 222.2 kg x h(-1) and 1800 kg x h(-1) in June 2008, respectively. The macro-jellyfish were mainly distributed in the areas around 50 m isobath, and not beyond 100 m isobath where was the joint front of the coastal waters of East China Sea, Yangtze River runoff, and Taiwan Warm Current. The main distribution area of macro-jellyfish in June migrated northward, as compared with that in May, and the highest catches of macro-jellyfish in May 2007 and May 2008 were found in the same sampling station (122.5 degrees E, 28.5 degrees N). In the sampling stations with higher abundance of macro-jellyfish, the fishery abundance was low, and the fishery species also changed greatly, mainly composed by small-sized species (Trachurus japonicus, Harpadon nehereus, and Acropoma japonicum) and pelagic species (Psenopsis anomala, Octopus variabilis) and Trichiurus japonicus, and P. anomala accounted for 23.7% of the total catch in June 2008. Larimichthys polyactis also occupied higher proportion of the total catch in sampling stations with higher macro-jellyfish abundance, but the demersal species Lophius litulon was not found, and a few crustaceans were collected. This study showed that macro-jellyfish had definite negative effects on the fishery community structure and abundance in the Yangtze River estuary fishery ecosystem, and further, changed the energy flow patterns of the ecosystem through cascading trophic interactions. Therefore, macro-jellyfish was strongly suggested to be an independent ecological group when the corresponding fishery management measures were considered.

  18. Human gut microbiota community structures in urban and rural populations in Russia

    PubMed Central

    Tyakht, Alexander V.; Kostryukova, Elena S.; Popenko, Anna S.; Belenikin, Maxim S.; Pavlenko, Alexander V.; Larin, Andrey K.; Karpova, Irina Y.; Selezneva, Oksana V.; Semashko, Tatyana A.; Ospanova, Elena A.; Babenko, Vladislav V.; Maev, Igor V.; Cheremushkin, Sergey V.; Kucheryavyy, Yuriy A.; Shcherbakov, Petr L.; Grinevich, Vladimir B.; Efimov, Oleg I.; Sas, Evgenii I.; Abdulkhakov, Rustam A.; Abdulkhakov, Sayar R.; Lyalyukova, Elena A.; Livzan, Maria A.; Vlassov, Valentin V.; Sagdeev, Renad Z.; Tsukanov, Vladislav V.; Osipenko, Marina F.; Kozlova, Irina V.; Tkachev, Alexander V.; Sergienko, Valery I.; Alexeev, Dmitry G.; Govorun, Vadim M.

    2013-01-01

    The microbial community of the human gut has a crucial role in sustaining host homeostasis. High-throughput DNA sequencing has delineated the structural and functional configurations of gut metagenomes in world populations. The microbiota of the Russian population is of particular interest to researchers, because Russia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Here we conduct a shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects, which reveals novel microbial community structures. The communities from several rural regions display similarities within each region and are dominated by the bacterial taxa associated with the healthy gut. Functional analysis shows that the metabolic pathways exhibiting differential abundance in the novel types are primarily associated with the trade-off between the Bacteroidetes and Firmicutes phyla. The specific signatures of the Russian gut microbiota are likely linked to the host diet, cultural habits and socioeconomic status. PMID:24036685

  19. Population genetic structure of mussels from the Baltic Sea

    NASA Astrophysics Data System (ADS)

    Bulnheim, H.-P.; Gosling, E.

    1988-03-01

    In a macrogeographic survey, the population genetic structure of mussels from various regions of the Baltic Sea, a large semi-enclosed brackish-water basin, was examined with reference to Mytilus edulis and M. galloprovincialis samples from the North Sea, Irish coast and southern Portugal. Electrophoretically detectable variation was analysed at 6 polymorphic enzyme loci ( Ap, Est-D, Lap-2, Odh, Pgi and Pgm). Evidence was provided of a remarkably large amount of biochemical genetic differentiation among ecologically and morphologically divergent mussel populations in the Baltic. Patterns of allele frequencies in low-salinity populations from the area of the Baltic Proper were demonstrated to be widely homogeneous but contrast strongly with those of the western Baltic, the latter resembling populations from marine habitats of the North Sea. Associated with a pronounced salinity gradient, the spatial heterogeneity in gene-pool structure is indicated by steep clines of allele frequency changes in the area of the eastern Danish isles. The adaptive significance of the observed allozymic variation is suggested. From genetic distance estimates, the subdivision of population structure is discussed in relation to the significant amount of differentiation detected within Mytilus populations to date and to the evolutionary time required for the divergence of Baltic mussel populations. The allozymic data provide evidence for the genetic distinctiveness of mussels from the low-salinity areas of the Baltic. Their position at the specific or subspecific level of classification requires further consideration.

  20. River mainstem thermal regimes influence population structuring within an Appalachian brook trout population

    USGS Publications Warehouse

    Aunins, Aaron W.; Petty, J. Todd; King, Timothy L.; Schilz, Mariya; Mazik, Patricia M.

    2015-01-01

    Brook trout (Salvelinus fontinalis) often exist as highly differentiated populations, even at small spatial scales, due either to natural or anthropogenic sources of isolation and low rates of dispersal. In this study, we used molecular approaches to describe the unique population structure of brook trout inhabiting the Shavers Fork watershed, located in eastern West Virginia, and contrast it to nearby populations in tributaries of the upper Greenbrier River and North Fork South Branch Potomac Rivers. Bayesian and maximum likelihood clustering methods identified minimal population structuring among 14 collections of brook trout from throughout the mainstem and tributaries of Shavers Fork, highlighting the role of the cold-water mainstem for connectivity and high rates of effective migration among tributaries. In contrast, the Potomac and Greenbrier River collections displayed distinct levels of population differentiation among tributaries, presumably resulting from tributary isolation by warm-water mainstems. Our results highlight the importance of protecting and restoring cold-water mainstem habitats as part of region-wide brook trout conservation efforts. In addition, our results from Shavers Fork provide a contrast to previous genetic studies that characterize Appalachian brook trout as fragmented isolates rather than well-mixed populations. Additional study is needed to determine whether the existence of brook trout as genetically similar populations among tributaries is truly unique and whether connectivity among brook trout populations can potentially be restored within other central Appalachian watersheds.

  1. Genetic structure of Aedes aegypti populations determined using pairwise comparisons.

    PubMed

    Patarro, T de F; Guirado, M M; Ravazzi, L M; Bicudo, H E M de C

    2013-01-01

    The biological characteristics of Aedes aegypti (Diptera, Culicidae), which is a vector of dengue and yellow fever, make this organism a good model for studying population structure and the events that may influence it under the effect of human activity. We assessed the genetic variability of five A. aegypti populations using RAPD-PCR technique and six primers. Four populations were from Brazil and one was from the USA. A total of 165 polymorphic DNA loci were generated. Considering the six primers and the five populations, the mean value of inter-population genetic diversity (Gst) was 0.277, which is considered high according to the Wright classification. However, pairwise comparisons of the populations gave variable Gst values ranging from 0.044 to 0.289. This variation followed the population's geographic distance to some extent but was also influenced by human activity. The lowest Gst values were obtained in the comparison of populations from cities with intensive commercial and medical contacts. These mosquito populations were previously classified as insecticide resistant, susceptible, or with decreased susceptibility; this parameter apparently had an effect on the Gst values obtained in the pairwise comparisons.

  2. Population connectivity and genetic structure of burbot (Lota lota) populations in the Wind River Basin, Wyoming

    USGS Publications Warehouse

    Underwood, Zachary E.; Mandeville, Elizabeth G.; Walters, Annika W.

    2016-01-01

    Burbot (Lota lota) occur in the Wind River Basin in central Wyoming, USA, at the southwestern extreme of the species’ native range in North America. The most stable and successful of these populations occur in six glacially carved mountain lakes on three different tributary streams and one large main stem impoundment (Boysen Reservoir) downstream from the tributary populations. Burbot are rarely found in connecting streams and rivers, which are relatively small and high gradient, with a variety of potential barriers to upstream movement of fish. We used high-throughput genomic sequence data for 11,197 SNPs to characterize the genetic diversity, population structure, and connectivity among burbot populations on the Wind River system. Fish from Boysen Reservoir and lower basin tributary populations were genetically differentiated from those in the upper basin tributary populations. In addition, fish within the same tributary streams fell within the same genetic clusters, suggesting there is movement of fish between lakes on the same tributaries but that populations within each tributary system are isolated and genetically distinct from other populations. Observed genetic differentiation corresponded to natural and anthropogenic barriers, highlighting the importance of barriers to fish population connectivity and gene flow in human-altered linked lake-stream habitats.

  3. Computer Simulation of Sexual Selection on Age-Structured Populations

    NASA Astrophysics Data System (ADS)

    Martins, S. G. F.; Penna, T. J. P.

    Using computer simulations of a bit-string model for age-structured populations, we found that sexual selection of older males is advantageous, from an evolutionary point of view. These results are in opposition to a recent proposal of females choosing younger males. Our simulations are based on findings from recent studies of polygynous bird species. Since secondary sex characters are found mostly in males, we could make use of asexual populations that can be implemented in a fast and efficient way.

  4. Correlations in the population structure of music, genes and language.

    PubMed

    Brown, Steven; Savage, Patrick E; Ko, Albert Min-Shan; Stoneking, Mark; Ko, Ying-Chin; Loo, Jun-Hun; Trejaut, Jean A

    2014-01-01

    We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers.

  5. From inclusive fitness to fixation probability in homogeneous structured populations.

    PubMed

    Taylor, Peter D; Day, Troy; Wild, Geoff

    2007-11-01

    The methods of inclusive fitness provide a powerful analysis of the action of selection on social behaviour. The key component of this analysis is the concept of relatedness R. In infinite populations, a standard method of calculating relatedness coefficients is through coefficients of consanguinity using the notion of genetic identity by descent. In this paper, we show that this approach can also be made to work in finite populations and we assume here that the population has a homogeneous structure, such as an island model. We demonstrate that, under the assumption that genetic effects are small and additive, the resulting formulation of inclusive fitness is equivalent to other significant measures of selection in finite populations, including the change in average allele frequency and fixation probability. The results are illustrated for a model of the evolution of cooperation in a finite island population.

  6. Correlations in the population structure of music, genes and language

    PubMed Central

    Brown, Steven; Savage, Patrick E.; Ko, Albert Min-Shan; Stoneking, Mark; Ko, Ying-Chin; Loo, Jun-Hun; Trejaut, Jean A.

    2014-01-01

    We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers. PMID:24225453

  7. [Age structure and growth characteristic of Castanopsis fargesii population].

    PubMed

    Song, Kun; Da, Liang-jun; Yang, Tong-hui; Yang, Xu-feng

    2007-02-01

    In this paper, the age structure and growth characteristics of Castanopsis fargesii population in a shade-tolerant broadleaved evergreen forest were studied, aimed to understand more about the regeneration patterns and dynamics of this population. The results showed that the age structure of C. fargesii population was of sporadic type, with two death peaks of a 30-year gap. This population had a good plasticity in growth to light condition. Because there were no significant differences in light condition under the canopy in vertical, the saplings came into their first suppression period when they were 5-8 years old, with a height growth rate less than 0. 1 m x a(-1) lasting for 10 years. The beginning time of the first growth suppression period was by the end of the first death peak of the population, and the ending time of the first growth suppression period was at the beginning of the second death peak of the population, demonstrating that growth characteristic was the key factor affecting the age structure of C. fargesii.

  8. Genotypic structure of a Drosophila population for adult locomotor activity

    SciTech Connect

    Grechanyi, G.V.; Korzun, V.M.

    1995-01-01

    Analysis of the variation of adult locomotor activity in four samples taken at different times from a natural population of Drosophila melanogaster showed that the total variation of this trait is relatively stable in time and has a substantial genetic component. Genotypic structure of the population for locomotor activity is characterized by the presence of large groups of genotypes with high and low values of this trait. A possible explanation for the presence of such groups in a population is cyclic density-dependent selection.

  9. Age-structured optimal control in population economics.

    PubMed

    Feichtinger, Gustav; Prskawetz, Alexia; Veliov, Vladimir M

    2004-06-01

    This paper brings both intertemporal and age-dependent features to a theory of population policy at the macro-level. A Lotka-type renewal model of population dynamics is combined with a Solow/Ramsey economy. We consider a social planner who maximizes an aggregate intertemporal utility function which depends on per capita consumption. As control policies we consider migration and saving rate (both age-dependent). By using a new maximum principle for age-structured control systems we derive meaningful results for the optimal migration and saving rate in an aging population. The model used in the numerical calculations is calibrated for Austria.

  10. Newly rare or newly common: evolutionary feedbacks through changes in population density and relative species abundance, and their management implications

    PubMed Central

    Lankau, Richard A; Strauss, Sharon Y

    2011-01-01

    Environmental management typically seeks to increase or maintain the population sizes of desirable species and to decrease population sizes of undesirable pests, pathogens, or invaders. With changes in population size come long-recognized changes in ecological processes that act in a density-dependent fashion. While the ecological effects of density dependence have been well studied, the evolutionary effects of changes in population size, via changes in ecological interactions with community members, are underappreciated. Here, we provide examples of changing selective pressures on, or evolution in, species as a result of changes in either density of conspecifics or changes in the frequency of heterospecific versus conspecific interactions. We also discuss the management implications of such evolutionary responses in species that have experienced rapid increases or decreases in density caused by human actions. PMID:25567977

  11. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure.

    PubMed

    Möbius, Wolfram; Murray, Andrew W; Nelson, David R

    2015-12-01

    As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle's shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call 'geometry-enhanced genetic drift', complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects expected from

  12. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure

    PubMed Central

    Möbius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2015-01-01

    As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle’s shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call ‘geometry-enhanced genetic drift’, complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects

  13. Error, population structure and the origin of diverse sign systems.

    PubMed

    Grassly, N C; Von Haeseler, A; Krakauer, D C

    2000-10-01

    Evolutionary models of communication are used to shed some light on the selective pressures involved in the evolution of simple referential signals, and the constraints hindering the emergence of signs. Error-prone communication results from errors in transmission (in which individuals learn the wrong associations) and communication (in which signs are mistaken for one another). We demonstrate how both classes of errors are required to generate diversity and subsequently impose limits on the sign repertoire within a population. We then explore the influence of geographic structuring of a population on the evolution of a shared sign system and the importance of such structure for the maintenance of sign diversity. Deceit tends to erode conventional signs systems thereby reducing signal diversity, we demonstrate that population structure can act as a hedge against deceit, thereby ensuring the persistence of sign systems. PMID:10988022

  14. Genetic Population Structure of Tectura paleacea: Implications for the Mechanisms Regulating Population Structure in Patchy Coastal Habitats

    PubMed Central

    Begovic, Emina; Lindberg, David R.

    2011-01-01

    The seagrass limpet Tectura paleacea (Gastropoda; Patellogastropoda) belongs to a seagrass obligate lineage that has shifted from the Caribbean in the late Miocene, across the Isthmus of Panama prior to the closing of the Panamanian seaway, and then northward to its modern Baja California – Oregon distribution. To address whether larval entrainment by seagrass beds contributes to population structuring, populations were sampled at six California/Oregon localities approximately 2 degrees latitude apart during two post-settlement periods in July 2002 and June 2003. Partial cytochrome oxidase b (Cytb) sequences were obtained from 20 individuals (10 per year) from each population in order to determine the levels of population subdivision/connectivity. From the 120 individuals sequenced, there were eighty-one unique haplotypes, with the greatest haplotype diversity occurring in southern populations. The only significant genetic break detected was consistent with a peri-Point Conception (PPC) biogeographic boundary while populations north and south of Point Conception were each panmictic. The data further indicate that populations found south of the PPC biogeographic boundary originated from northern populations. This pattern of population structure suggests that seagrass patches are not entraining the larvae of T. paleacea by altering flow regimes within their environment; a process hypothesized to produce extensive genetic subdivision on fine geographic scales. In contrast to the haplotype data, morphological patterns vary significantly over very fine geographic scales that are inconsistent with the observed patterns of genetic population structure, indicating that morphological variation in T. paleacea might be attributed to differential ecophenotypic expression in response to local habitat variability throughout its distribution. These results suggest that highly localized conservation efforts may not be as effective as large-scale conservation efforts in near

  15. Effects of Chemical Abundances on the Structure and Dynamics of the Solar Atmosphere

    NASA Astrophysics Data System (ADS)

    Demarque, Pierre; Basu, S.; Robinson, F.; Hunter, C.; Kallinger, T.

    2008-05-01

    This paper presents a comparison between two three-dimensional radiative hydrodynamical (3D RHD) simulations of the solar outer layers using the Grevesse & Sauval (1998; GS98) and the Asplund, Grevesse & Sauval (2005; AGS05) mixtures, respectively. The AGS05 mixture is a revision of the solar abundance mixture using a model atmosphere based on the stratification and dynamics of a solar 3D RHD simulation performed with the GS98 mixture, using the code of Stein & Nordlund (1989, 1998). Our simulations use the same code, and physically realistic treatment of radiative opacities and equation of state as Robinson et al. (2003). A comparison between our GS98 and AGS05 3D simulations shows differences both in the mean vertical temperature gradient and in the turbulent velocity field in the line forming region of the solar atmosphere. The whole superadiabatic layer (SAL) in the AGS05 simulation, including its peak, is shifted outward with respect to the GS98 SAL. Turbulent velocities, critical for absorption line profile calculations, are larger in the AGS05 simulation by about 10%. Since opacities for the AGS05 mixture are lower than those for the GS98 mixture, the T-τ relations derived from the two simulations are different. At 5000K, τ obtained from the GS98 simulation is about 30% larger than that obtained from the AGS05 simulation. These results show the importance of preserving self consistency in the chemical abundances between the model atmosphere and the 3D HRD simulation. When deriving the solar abundances, one must iterate the chemical composition in the model atmosphere, and hence in the 3D simulation on which the atmosphere is based. This research was supported in part by NASA/ATP grant NAG5-13299 (PD and FR) and NSF grant ATM 0348837 to SB.

  16. The chemical abundances of the stellar populations in the Leo I and II dSph galaxies

    NASA Astrophysics Data System (ADS)

    Bosler, Tammy L.; Smecker-Hane, Tammy A.; Stetson, Peter B.

    2007-06-01

    We have obtained calcium abundances and radial velocities for 102 red giant branch (RGB) stars in the Leo I dwarf spheroidal galaxy (dSph) and 74 RGB stars in the Leo II dSph using the low-resolution spectrograph (LRIS) on the Keck I 10-m telescope. We report on the calcium abundances [Ca/H] derived from the strengths of the CaII triplet absorption lines at 8498, 8542 and 8662 Å in the stellar spectra using a new empirical CaII triplet calibration to [Ca/H]. The two galaxies have different average [Ca/H] values of -1.34 +/- 0.02 for Leo I and -1.65 +/- 0.02 for Leo II with intrinsic abundance dispersions of 1.2 and 1.0 dex, respectively. The typical random and total errors in derived abundances are 0.10 and 0.17 dex per star. For comparison to the existing literature, we also converted our CaII measurements to [Fe/H] on the scale of Carretta and Gratton (1997) though we discuss why this may not be the best determinant of metallicity; Leo I has a mean [Fe/H] = -1.34 and Leo II has a mean [Fe/H] = -1.59. The metallicity distribution function of Leo I is approximately Gaussian in shape with an excess at the metal-rich end, while that of Leo II shows an abrupt cut-off at the metal-rich end. The lower mean metallicity of Leo II is consistent with the fact that it has a lower luminosity, hence lower the total mass than Leo I; thus, the evolution of Leo II may have been affected more by mass lost in galactic winds. Our direct and independent measurement of the metallicity distributions in these dSph will allow a more accurate star-formation histories to be derived from future analysis of their colour-magnitude diagrams(CMDs). Data presented herein were obtained at the W.M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. E

  17. Moist convection and the vertical structure and water abundance of Jupiter's atmosphere

    NASA Technical Reports Server (NTRS)

    Del Genio, Anthony D.; Mcgrattan, Kevin B.

    1990-01-01

    The cumulative effects of an ensemble of moist convective plumes on a conditionally unstable atmosphere are predicted by a model of moist convection on Jupiter in which the heating/cooling and drying/moistening of the environment occur through (1) compensating subsidence, (2) detrainment of updraft air at cloud tops, and (3) the evaporation and melting of falling condensate. Parahydrogen is transported as a passive tracer. Pure moist convective, mixed moist-dry convective, and primarily dry convective regimes are possible, depending on the assumed deep-water abundance, efficiency of condensate evaporation, and initial temperature profile.

  18. Spatial population structure of a specialist leaf-mining moth.

    PubMed

    Gripenberg, Sofia; Ovaskainen, Otso; Morriën, Elly; Roslin, Tomas

    2008-07-01

    1. The spatial structure of natural populations may profoundly influence their dynamics. Depending on the frequency of movements among local populations and the consequent balance between local and regional population processes, earlier work has attempted to classify metapopulations into clear-cut categories, ranging from patchy populations to sets of remnant populations. In an alternative, dichotomous scheme, local populations have been classified as self-sustaining populations generating a surplus of individuals (sources) and those depending on immigration for persistence (sinks). 2. In this paper, we describe the spatial population structure of the leaf-mining moth Tischeria ekebladella, a specialist herbivore of the pedunculate oak Quercus robur. We relate moth dispersal to the distribution of oaks on Wattkast, a small island (5 km(2)) off the south-western coast of Finland. 3. We build a spatially realistic metapopulation model derived from assumptions concerning the behaviour of individual moths, and show that the model is able to explain part of the variation in observed patterns of occurrence and colonization. 4. While the species was always present on large trees, a considerable proportion of the local populations associated with small oaks showed extinction-recolonization dynamics. The vast majority of moth individuals occur on large trees. 5. According to model predictions, the dominance of local vs. regional processes in tree-specific moth dynamics varies drastically across the landscape. Most local populations may be defined broadly as 'sinks', as model simulations suggest that in the absence of immigration, only the largest oaks will sustain viable moth populations. Large trees in areas of high oak density will contribute most to the overall persistence of the metapopulation by acting as sources of moths colonizing other trees. 6. No single 'metapopulation type' will suffice to describe the oak-moth system. Instead, our study supports the notion that

  19. Habitat-specific size structure variations in periwinkle populations ( Littorina littorea) caused by biotic factors

    NASA Astrophysics Data System (ADS)

    Eschweiler, Nina; Molis, Markus; Buschbaum, Christian

    2009-06-01

    Shell size distribution patterns of marine gastropod populations may vary considerably across different environments. We investigated the size and density structure of genetically continuous periwinkle populations ( Littorina littorea) on an exposed rocky and a sheltered sedimentary environment on two nearby islands in the south-eastern North Sea (German Bight). On the sedimentary shore, periwinkle density (917 ± 722 individuals m-2) was about three times higher than on the rocky shore (296 ± 168 individuals m-2). Mean (9.8 ± 3.9 mm) and maximum (22 mm) shell size of L. littorea on the sedimentary shore were smaller than on the rocky shore (21.5 ± 4.2 and 32 mm, respectively), where only few small snails were found. Additionally, periwinkle shells were thicker and stronger on the rocky than on the sedimentary shore. To ascertain mechanisms responsible for differences in population structures, we examined periwinkles in both environments for growth rate, predation pressure, infection with a shell boring polychaete ( Polydora ciliata) and parasitic infestation by trematodes. A crosswise transplantation experiment revealed better growth conditions on the sedimentary than on the rocky shore. However, crab abundance and prevalence of parasites and P. ciliata in adult snails were higher on the sedimentary shore. Previous investigations showed that crabs prefer large periwinkles infested with P. ciliata. Thus, we suggest that parasites and shell boring P. ciliata in conjunction with an increased crab predation pressure are responsible for low abundances of large periwinkles on the sedimentary shore while high wave exposure may explain low densities of juvenile L. littorea on the rocky shore. We conclude that biotic factors may strongly contribute to observed differences in size structure of the L. littorea populations studied on rocky and sedimentary shores.

  20. Nematode diversity, abundance and community structure 50 years after the formation of the volcanic island of Surtsey

    NASA Astrophysics Data System (ADS)

    Ilieva-Makulec, K.; Bjarnadottir, B.; Sigurdsson, B. D.

    2014-10-01

    The soil nematode fauna can give important insights into soil development and other habitat changes that occur during primary succession. We investigated the generic composition, density, distribution and community structure of nematodes 50 years after the formation of a pristine volcanic island, Surtsey, Iceland. Part of the island has received additional nutrient inputs from seagulls breeding there since 1985, while the reminder has been much less affected and is at present found at a different successional sere. In total, 25 genera of nematodes were identified, of which 14 were reported on Surtsey for the first time. Nematode communities were more diverse in the more infertile area outside the gull colony, where 24 genera were found, compared to 18 inside. The trophic structure of the nematode communities showed relatively higher abundance of fungal feeders in the infertile areas, but relatively more bacterial- and plant-feeders inside the colony. Nematode abundance in surface soil was, however, significantly higher within the gull colony, with 16.7 ind. cm-2 compared to 3.6 ind. cm-2 outside. A multivariate analysis indicated that the nematode abundance and distribution on Surtsey were most strongly related to the soil C : N ratio, soil acidity, plant cover and biomass, soil temperature and soil depth.

  1. Analysis of the c-src gene product structure, abundance, and protein kinase activity in human neuroblastoma and glioblastoma cells.

    PubMed

    O'Shaughnessy, J; Deseau, V; Amini, S; Rosen, N; Bolen, J B

    1987-01-01

    We have compared in different human neuroblastoma cell lines and human glioblastoma cells the expression level, structure, and tyrosine-specific protein kinase activity of pp60c-src. Our results show that not all human neuroblastoma cell lines express pp60c-src molecules with amino-terminal structural alterations. In neuroblastoma cells which possess pp60c-src with altered gel migration, the diminished polyacrylamide gel mobility of pp60c-src was found not to be dependent upon amino-terminal phosphorylations since extensive treatment of these molecules with phosphatase did not significantly change their gel migration properties. Similar differences in gel migration were observed when RNA from the various neuroblastoma and glioblastoma cells was translated in vitro using either rabbit reticulocyte or wheat germ lysates. White the level of c-src mRNA in the different cells analyzed was found to be similar, the abundance of pp60c-src in these same cells was found to vary by as much as 12-fold. This suggests that the abundance of pp60c-src in human neuroendocrine tumors is regulated through post-transcriptional and/or post-translational events which may be related to the stage of neuronal differentiation of the cells. Based upon determination of pp60c-src abundance by immunoblot analysis, we demonstrate that pp60c-src molecules derived from human neuroblastoma and glioblastoma cells have very similar in vitro protein kinase activities.

  2. Population models for passerine birds: structure, parameterization, and analysis

    USGS Publications Warehouse

    Noon, B.R.; Sauer, J.R.; McCullough, D.R.; Barrett, R.H.

    1992-01-01

    Population models have great potential as management tools, as they use infonnation about the life history of a species to summarize estimates of fecundity and survival into a description of population change. Models provide a framework for projecting future populations, determining the effects of management decisions on future population dynamics, evaluating extinction probabilities, and addressing a variety of questions of ecological and evolutionary interest. Even when insufficient information exists to allow complete identification of the model, the modelling procedure is useful because it forces the investigator to consider the life history of the species when determining what parameters should be estimated from field studies and provides a context for evaluating the relative importance of demographic parameters. Models have been little used in the study of the population dynamics of passerine birds because of: (1) widespread misunderstandings of the model structures and parameterizations, (2) a lack of knowledge of life histories of many species, (3) difficulties in obtaining statistically reliable estimates of demographic parameters for most passerine species, and (4) confusion about functional relationships among demographic parameters. As a result, studies of passerine demography are often designed inappropriately and fail to provide essential data. We review appropriate models for passerine bird populations and illustrate their possible uses in evaluating the effects of management or other environmental influences on population dynamics. We identify environmental influences on population dynamics. We identify parameters that must be estimated from field data, briefly review existing statistical methods for obtaining valid estimates, and evaluate the present status of knowledge of these parameters.

  3. Temporal changes in population structure of a marine planktonic diatom.

    PubMed

    Tesson, Sylvie V M; Montresor, Marina; Procaccini, Gabriele; Kooistra, Wiebe H C F

    2014-01-01

    A prevailing question in phytoplankton research addresses changes of genetic diversity in the face of huge population sizes and apparently unlimited dispersal capabilities. We investigated population genetic structure of the pennate planktonic marine diatom Pseudo-nitzschia multistriata at the LTER station MareChiara in the Gulf of Naples (Italy) over four consecutive years and explored possible changes over seasons and from year to year. A total of 525 strains were genotyped using seven microsatellite markers, for a genotypic diversity of 75.05%, comparable to that found in other Pseudo-nitzschia species. Evidence from Bayesian clustering analysis (BA) identified two genetically distinct clusters, here interpreted as populations, and several strains that could not be assigned with ≥ 90% probability to either population, here interpreted as putative hybrids. Principal Component Analysis (PCA) recovered these two clusters in distinct clouds with most of the putative hybrids located in-between. Relative proportions of the two populations and the putative hybrids remained similar within years, but changed radically between 2008 and 2009 and between 2010 and 2011, when the 2008-population apparently became the dominant one again. Strains from the two populations are inter-fertile, and so is their offspring. Inclusion of genotypes of parental strains and their offspring shows that the majority of the latter could not be assigned to any of the two parental populations. Therefore, field strains classified by BA as the putative hybrids could be biological hybrids. We hypothesize that P. multistriata population dynamics in the Gulf of Naples follows a meta-population-like model, including establishment of populations by cell inocula at the beginning of each growth season and remixing and dispersal governed by moving and mildly turbulent water masses.

  4. Temporal Changes in Population Structure of a Marine Planktonic Diatom

    PubMed Central

    Tesson, Sylvie V. M.; Montresor, Marina; Procaccini, Gabriele; Kooistra, Wiebe H. C. F.

    2014-01-01

    A prevailing question in phytoplankton research addresses changes of genetic diversity in the face of huge population sizes and apparently unlimited dispersal capabilities. We investigated population genetic structure of the pennate planktonic marine diatom Pseudo-nitzschia multistriata at the LTER station MareChiara in the Gulf of Naples (Italy) over four consecutive years and explored possible changes over seasons and from year to year. A total of 525 strains were genotyped using seven microsatellite markers, for a genotypic diversity of 75.05%, comparable to that found in other Pseudo-nitzschia species. Evidence from Bayesian clustering analysis (BA) identified two genetically distinct clusters, here interpreted as populations, and several strains that could not be assigned with ≥90% probability to either population, here interpreted as putative hybrids. Principal Component Analysis (PCA) recovered these two clusters in distinct clouds with most of the putative hybrids located in-between. Relative proportions of the two populations and the putative hybrids remained similar within years, but changed radically between 2008 and 2009 and between 2010 and 2011, when the 2008-population apparently became the dominant one again. Strains from the two populations are inter-fertile, and so is their offspring. Inclusion of genotypes of parental strains and their offspring shows that the majority of the latter could not be assigned to any of the two parental populations. Therefore, field strains classified by BA as the putative hybrids could be biological hybrids. We hypothesize that P. multistriata population dynamics in the Gulf of Naples follows a meta-population-like model, including establishment of populations by cell inocula at the beginning of each growth season and remixing and dispersal governed by moving and mildly turbulent water masses. PMID:25506926

  5. Abundance, diversity, and seasonal population dynamics of aquatic Coleoptera and Heteroptera in rice fields: effects of direct seeding management.

    PubMed

    Watanabe, Kohei; Koji, Shinsaku; Hidaka, Kazumasa; Nakamura, Koji

    2013-10-01

    Recent introduction of modern drainage systems has produced intensely dry conditions in rice farmlands and has degraded habitats for aquatic animals. In this study, we compared water beetle (Coleoptera) and water bug (Heteroptera) communities within rice fields cultivated under different management regimes: V-furrow no-till direct-seeding (DS) and conventional regimes. In DS fields, rice is sown in well-drained fields, and flooding is performed a month later than in conventional rice fields. DS fields are then continuously flooded until harvesting; unlike in conventional fields, where midseason drainage is performed in summer. We observed that DS fields supported higher densities of water beetles and water bugs than conventional fields, probably because of the high compatibility between the flooding period and the reproductive season of the insects. The species richness of water beetles was higher in DS fields than in conventional fields. Overall, DS fields showed higher water beetle and water bug abundance, but the effect was variable for individual species: seven species were more abundant in DS than in conventional fields, whereas two species showed opposite tendencies. Considering the differential responses among species to the management regimes, a mosaic of DS and conventional fields is preferable to either field alone for the conservation of aquatic insects in rice agroecosystems.

  6. Abundance, diversity, and seasonal population dynamics of aquatic Coleoptera and Heteroptera in rice fields: effects of direct seeding management.

    PubMed

    Watanabe, Kohei; Koji, Shinsaku; Hidaka, Kazumasa; Nakamura, Koji

    2013-10-01

    Recent introduction of modern drainage systems has produced intensely dry conditions in rice farmlands and has degraded habitats for aquatic animals. In this study, we compared water beetle (Coleoptera) and water bug (Heteroptera) communities within rice fields cultivated under different management regimes: V-furrow no-till direct-seeding (DS) and conventional regimes. In DS fields, rice is sown in well-drained fields, and flooding is performed a month later than in conventional rice fields. DS fields are then continuously flooded until harvesting; unlike in conventional fields, where midseason drainage is performed in summer. We observed that DS fields supported higher densities of water beetles and water bugs than conventional fields, probably because of the high compatibility between the flooding period and the reproductive season of the insects. The species richness of water beetles was higher in DS fields than in conventional fields. Overall, DS fields showed higher water beetle and water bug abundance, but the effect was variable for individual species: seven species were more abundant in DS than in conventional fields, whereas two species showed opposite tendencies. Considering the differential responses among species to the management regimes, a mosaic of DS and conventional fields is preferable to either field alone for the conservation of aquatic insects in rice agroecosystems. PMID:24073897

  7. Effects of Flow on Structure and Abundances in Multispecies Solar Coronal Loops

    NASA Astrophysics Data System (ADS)

    Lenz, Dawn D.

    2004-03-01

    We investigate the effects of large-scale bulk flows on coronal abundances using a multispecies numerical model. The model assumes that electrons, protons, and helium are in thermal equilibrium and constitute the bulk of the coronal plasma. Thermal diffusion and Coulomb friction are included. Temperature profiles for the bulk component and for each ion species are assumed, so the model reduces to a solution of mass and force balance for each component. We further assume that the bulk component has an upward bulk velocity at the base, and that ion flow speeds along field lines are negligible relative to the bulk flow. Coulomb coupling of the electrons and ions induces drag that counteracts the tendency of the ions to gravitationally settle. In regions of small ∇T, such as the outer regions of the corona, Coulomb drag is the only significant force counteracting gravitational settling in this model. We find that relatively modest bulk flows of tens of km s-1 can enhance ion abundances by 2-3 orders of magnitude over their values in low- or no-flow cases.

  8. Abundance and structure of microbial loop components (bacteria and protists) in lakes of different trophic status.

    PubMed

    Ryszard, Chrost J; Tomasz, Adamczewski; Kalinowska, Krystyna; Skowronska, Agnieszka

    2009-09-01

    The abundance, biomass, size distribution, and taxonomic composition of bacterial and protistan (heterotrophic and autotrophic nanoflagellates and ciliates) communities were investigated in six lakes of Masurian Lake District (north-eastern Poland) differing in trophic state. Samples were taken from the trophogenic water layer during summer stratification periods in the years of 2004 and 2006. Image analysis techniques with fluorescent in situ hybridization (FISH) as well as [3H]-methyl-thymidine incorporation methods were applied to analyze differences in the composition and activity of bacterial communities. The greatest differences in trophic parameters were found between the humic lake and remaining non-humic ones. The same bacterial and heterotrophic nanoflagellate (HNF) cell size classes dominated in all the studied lakes. However, distinct increases in the contributions of large bacterial (>1.0 microm) and HNF (>10 microm) cells were observed in eutrophic lakes. The bacterial community was dominated by the beta-Proteobacteria group, which accounted for 27% of total DAPI counts. Ciliate communities were largely composed of Oligotrichida. Positive correlations between bacteria and protists, as well as between nanoflagellates (both heterotrophic and autotrophic) and ciliates, suggest that concentrations of food sources may be important in determining the abundance of protists in the studied lakes.

  9. Ethnicity and population structure in personal naming networks.

    PubMed

    Mateos, Pablo; Longley, Paul A; O'Sullivan, David

    2011-01-01

    Personal naming practices exist in all human groups and are far from random. Rather, they continue to reflect social norms and ethno-cultural customs that have developed over generations. As a consequence, contemporary name frequency distributions retain distinct geographic, social and ethno-cultural patterning that can be exploited to understand population structure in human biology, public health and social science. Previous attempts to detect and delineate such structure in large populations have entailed extensive empirical analysis of naming conventions in different parts of the world without seeking any general or automated methods of population classification by ethno-cultural origin. Here we show how 'naming networks', constructed from forename-surname pairs of a large sample of the contemporary human population in 17 countries, provide a valuable representation of cultural, ethnic and linguistic population structure around the world. This innovative approach enriches and adds value to automated population classification through conventional national data sources such as telephone directories and electoral registers. The method identifies clear social and ethno-cultural clusters in such naming networks that extend far beyond the geographic areas in which particular names originated, and that are preserved even after international migration. Moreover, one of the most striking findings of this approach is that these clusters simply 'emerge' from the aggregation of millions of individual decisions on parental naming practices for their children, without any prior knowledge introduced by the researcher. Our probabilistic approach to community assignment, both at city level as well as at a global scale, helps to reveal the degree of isolation, integration or overlap between human populations in our rapidly globalising world. As such, this work has important implications for research in population genetics, public health, and social science adding new

  10. Ethnicity and population structure in personal naming networks.

    PubMed

    Mateos, Pablo; Longley, Paul A; O'Sullivan, David

    2011-01-01

    Personal naming practices exist in all human groups and are far from random. Rather, they continue to reflect social norms and ethno-cultural customs that have developed over generations. As a consequence, contemporary name frequency distributions retain distinct geographic, social and ethno-cultural patterning that can be exploited to understand population structure in human biology, public health and social science. Previous attempts to detect and delineate such structure in large populations have entailed extensive empirical analysis of naming conventions in different parts of the world without seeking any general or automated methods of population classification by ethno-cultural origin. Here we show how 'naming networks', constructed from forename-surname pairs of a large sample of the contemporary human population in 17 countries, provide a valuable representation of cultural, ethnic and linguistic population structure around the world. This innovative approach enriches and adds value to automated population classification through conventional national data sources such as telephone directories and electoral registers. The method identifies clear social and ethno-cultural clusters in such naming networks that extend far beyond the geographic areas in which particular names originated, and that are preserved even after international migration. Moreover, one of the most striking findings of this approach is that these clusters simply 'emerge' from the aggregation of millions of individual decisions on parental naming practices for their children, without any prior knowledge introduced by the researcher. Our probabilistic approach to community assignment, both at city level as well as at a global scale, helps to reveal the degree of isolation, integration or overlap between human populations in our rapidly globalising world. As such, this work has important implications for research in population genetics, public health, and social science adding new

  11. Structure of the New England herring gull population

    USGS Publications Warehouse

    Kadlec, J.A.; Drury, W.H.

    1968-01-01

    Measurements of the rates of population increase, reproduction, and mortality together with an observed age ratio, were used to analyze the population of the Herring Gull in New England. Data from sporadic censuses prior to this study, aerial censuses by the authors, and National Audubon Society Christmas Bird Count indicated that the New England breeding population has been doubling every 12 to 15 years since the early 1900's. This increase has involved founding new colonies and expanding the breeding range There is evidence that 15 to 30% of the adults do not breed in any given year. Sixty-one productivity measurements on 43 islands from 1963 through 1966, involving almost 13,000 nests, showed that from 0.8 to 1.4 young/breeding pair/year is the usual range of rate of production. The age distribution in the population was determined by classifying Herring Gulls by plumage category on an aerial census of the coast from Tampico, Mexico, to Cape Sable, Nova Scotia. Of the 622,000 gulls observed, 68% were adults, 17% were second- and third-year birds, and 15% were first-year birds. Mortality rates derived from band recovery data were too high to be consistent with the observed rate of population growth, productivity, and age structure. Loss of bands increasing to the rate of about 20%/year 5 years after banding eliminates most of the discrepancy. The age structure and rate of population increase indicate a mortality rate of 4 to 9% for gulls 2 years old or older, compared with the 25 to 30% indicated by band recoveries. The population structure we have developed fits everything we have observed about Herring Gull population dynamics, except mortality based on band recoveries.

  12. Effects of Adaptation of In vitro Rumen Culture to Garlic Oil, Nitrate, and Saponin and Their Combinations on Methanogenesis, Fermentation, and Abundances and Diversity of Microbial Populations

    PubMed Central

    Patra, Amlan K.; Yu, Zhongtang

    2015-01-01

    This study investigated the effects of garlic oil (0.25 g/L), nitrate (5 mM), and quillaja saponin (0.6 g/L), alone and in binary or ternary combinations, on methanogenesis, rumen fermentation, and abundances of select microbial populations using in vitro rumen cultures. Potential adaptation to these compounds was also examined by repeated transfers of the cultures on alternate days until day 18. All treatments except saponin alone significantly decreased methanogenesis. Ternary combinations of garlic oil, nitrate, and saponin additively/synergistically suppressed methane production by 65% at day 2 and by 40% at day 18. Feed digestion was not adversely affected by any of the treatments at day 2, but was decreased by the combinations (binary and ternary) of garlic oil with the other inhibitors at days 10 and 18. Saponin, alone or in combinations, and garlic oil alone lowered ammonia concentration at day 2, while nitrate increased ammonia concentration at days 10 and 18. Total volatile fatty acid concentration was decreased by garlic oil alone or garlic oil-saponin combination. Molar proportions of acetate and propionate were affected to different extents by the different treatments. The abundances of methanogens were similar among treatments at day 2; however, garlic oil and its combination with saponin and/or nitrate at day 10 and all treatments except saponin at day 18 significantly decreased the abundances of methanogens. All the inhibitors, either alone or in combinations, did not adversely affect the abundances of total bacteria or Ruminococcus flavefaciens. However, at day 18 the abundances of Fibrobacter succinogenes and Ruminococcus albus were lowered in the presence of garlic oil and saponin, respectively. The results suggest that garlic oil-nitrate-saponin combination (at the doses used in this study) can effectively decreases methanogenesis in the rumen, but its efficacy may decrease while inhibition to feed digestion can increase over time. PMID:26733975

  13. Population genetic structure and long-distance dispersal among seabird populations: implications for colony persistence.

    PubMed

    Bicknell, A W J; Knight, M E; Bilton, D; Reid, J B; Burke, T; Votier, S C

    2012-06-01

    Dramatic local population decline brought about by anthropogenic-driven change is an increasingly common threat to biodiversity. Seabird life history traits make them particularly vulnerable to such change; therefore, understanding population connectivity and dispersal dynamics is vital for successful management. Our study used a 357-base pair mitochondrial control region locus sequenced for 103 individuals and 18 nuclear microsatellite loci genotyped for 245 individuals to investigate population structure in the Atlantic and Pacific populations of the pelagic seabird, Leach's storm-petrel Oceanodroma leucorhoa leucorhoa. This species is under intense predation pressure at one regionally important colony on St Kilda, Scotland, where a disparity between population decline and predation rates hints at immigration from other large colonies. AMOVA, F(ST), Φ(ST) and Bayesian cluster analyses revealed no genetic structure among Atlantic colonies (Global Φ(ST) = -0.02 P > 0.05, Global F(ST) = 0.003, P > 0.05, STRUCTURE K = 1), consistent with either contemporary gene flow or strong historical association within the ocean basin. The Pacific and Atlantic populations are genetically distinct (Global Φ(ST) = 0.32 P < 0.0001, Global F(ST) = 0.04, P < 0.0001, STRUCTURE K = 2), but evidence for interocean exchange was found with individual exclusion/assignment and population coalescent analyses. These findings highlight the importance of conserving multiple colonies at a number of different sites and suggest that management of this seabird may be best viewed at an oceanic scale. Moreover, our study provides an illustration of how long-distance movement may ameliorate the potentially deleterious impacts of localized environmental change, although direct measures of dispersal are still required to better understand this process. PMID:22548276

  14. Demography and genetic structure of a recovering grizzly bear population

    USGS Publications Warehouse

    Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

    2009-01-01

    Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

  15. Population Structure and Inbreeding From Pedigree Analysis of Purebred Dogs

    PubMed Central

    Calboli, Federico C. F.; Sampson, Jeff; Fretwell, Neale; Balding, David J.

    2008-01-01

    Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, >90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Ψ for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare. PMID:18493074

  16. Population and colony structure of the carpenter ant Camponotus floridanus.

    PubMed

    Gadau, J; Heinze, J; Hölldobler, B; Schmid, M

    1996-12-01

    The colony and population structure of the carpenter ant, Camponotus floridanus, were investigated by multilocus DNA fingerprinting using simple repeat motifs as probes [e.g. (GATA)4]. The mating frequency of 15 queens was determined by comparing the fingerprint patterns of the queen and 17-33 of her progeny workers. C. floridanus queens are most probably singly mated, i.e. this species is monandrous and monogynous (one queen per colony). C. floridanus occurs in all counties of mainland Florida and also inhabits most of the Key islands in the southern part of Florida. We tested whether the two mainland populations and the island populations are genetically isolated. Wright's FST and Nei's D-value of genetic distance were calculated from intercolonial bandsharing-coefficients. The population of C. floridanus is substructured (FST = 0.19 +/- 0.09) and the highest degree of genetic distance was found between one of the mainland populations and the island populations (D = 0.35). Our fingerprinting technique could successfully be transferred to 12 other Camponotus species and here also revealed sufficient variability to analyse the genetic structure. In three of these species (C. ligniperdus, C. herculeanus and C. gigas) we could determine the mating frequency of the queen in one or two colonies, respectively.

  17. The genetic structure of a relict population of wood frogs

    USGS Publications Warehouse

    Scherer, Rick; Muths, Erin; Noon, Barry; Oyler-McCance, Sara

    2012-01-01

    Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and this result was further supported by factorial component analysis. In addition, an estimate of FST (FST = 0.0675, P value \\0.0001) supported the genetic differentiation of the two clusters. Estimates of migration rates among the two subpopulations were low, as were estimates of genetic variability. Conservation of the population of wood frogs may be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.

  18. Population and colony structure of the carpenter ant Camponotus floridanus.

    PubMed

    Gadau, J; Heinze, J; Hölldobler, B; Schmid, M

    1996-12-01

    The colony and population structure of the carpenter ant, Camponotus floridanus, were investigated by multilocus DNA fingerprinting using simple repeat motifs as probes [e.g. (GATA)4]. The mating frequency of 15 queens was determined by comparing the fingerprint patterns of the queen and 17-33 of her progeny workers. C. floridanus queens are most probably singly mated, i.e. this species is monandrous and monogynous (one queen per colony). C. floridanus occurs in all counties of mainland Florida and also inhabits most of the Key islands in the southern part of Florida. We tested whether the two mainland populations and the island populations are genetically isolated. Wright's FST and Nei's D-value of genetic distance were calculated from intercolonial bandsharing-coefficients. The population of C. floridanus is substructured (FST = 0.19 +/- 0.09) and the highest degree of genetic distance was found between one of the mainland populations and the island populations (D = 0.35). Our fingerprinting technique could successfully be transferred to 12 other Camponotus species and here also revealed sufficient variability to analyse the genetic structure. In three of these species (C. ligniperdus, C. herculeanus and C. gigas) we could determine the mating frequency of the queen in one or two colonies, respectively. PMID:8981768

  19. Globalization and the population structure of Toxoplasma gondii.

    PubMed

    Lehmann, Tovi; Marcet, Paula L; Graham, Doug H; Dahl, Erica R; Dubey, J P

    2006-07-25

    Toxoplasma gondii is a protozoan parasite that infects nearly all mammal and bird species worldwide. Usually asymptomatic, toxoplasmosis can be severe and even fatal to many hosts, including people. Elucidating the contribution of genetic variation among parasites to patterns of disease transmission and manifestations has been the goal of many studies. Focusing on the geographic component of this variation, we show that most genotypes are locale-specific, but some are found across continents and are closely related to each other, indicating a recent radiation of a pandemic genotype. Furthermore, we show that the geographic structure of T. gondii is extraordinary in having one population that is found in all continents except South America, whereas other populations are generally confined to South America, and yet another population is found worldwide. Our evidence suggests that South American and Eurasian populations have evolved separately until recently, when ships populated by rats, mice, and cats provided T. gondii with unprecedented migration opportunities, probably during the transatlantic slave trade. Our results explain several enigmatic features of the population structure of T. gondii and demonstrate how pervasive, prompt, and elusive the impact of human globalization is on nature.

  20. Heterogeneity of macrozoobenthic assemblages within a Zostera noltii seagrass bed: diversity, abundance, biomass and structuring factors

    NASA Astrophysics Data System (ADS)

    Blanchet, Hugues; de Montaudouin, Xavier; Lucas, Aurélien; Chardy, Pierre

    2004-09-01

    The macrobenthic fauna community of a 70-km 2Zostera noltii seagrass bed (Arcachon bay, France) was studied by sampling 49 stations systematically. A total of 126 taxa were identified. Cluster Analysis based on χ2 distance showed that in this apparently homogeneous habitat, four distinct macrobenthic communities could be identified. Multiple Discriminant Analysis highlighted the major contribution of the overlying water mass as a forcing variable, and, to a lesser extent, of tidal level and Z. noltii's below-ground parts. Seven stations did not constitute any conspicuous group, and were characterized by a low biomass of leaf (<28 g DW m -2), considered as the lowest value to constitute a Z. noltii community. Less than 24% of the seagrass bed was situated in more oceanic waters and at a quite low tidal level. In this relatively stable environment, the macrofauna community was characterized by a high species richness (mean = 39) and a moderate density and high biomass (12 638 individuals m -2 and 25 g AFDW m -2, respectively). Annelids dominated, particularly the oligochaetes. When physical constraints increased (emersion or brackish water conditions), diversity decreased, abundance and biomass increased. The seagrass bed (55%) was flooded with highly fluctuating waters in term of temperature and salinity, here species richness was low (mean = 27) but abundance and biomass were high (24 384 individuals m -2 and 28 g AFDW m -2, respectively), with a dominance of molluscs. The meadow (7%) was in external waters but at a higher tidal level (2.4 m vs 1.8 m above medium low tide level). This community was characterized by the particularly high density (41 826 individuals m -2) and dominance of oligochaetes (79% of total abundance). Species richness was high (mean = 37) here. A fourth community, extending over 12% of the meadow was dominated by the gastropod Hydrobia ulvae but could not be linked to a specific forcing variable. This study confirmed the almost

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

    PubMed

    Chen, Shan-Yuan; Duan, Zi-Yuan; Sha, Tao; Xiangyu, Jinggong; Wu, Shi-Fang; Zhang, Ya-Ping

    2006-07-19

    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.

  2. Dissecting simulated disc galaxies - I. The structure of mono-age populations

    NASA Astrophysics Data System (ADS)

    Martig, Marie; Minchev, Ivan; Flynn, Chris

    2014-08-01

    We study seven simulated disc galaxies, three with a quiescent merger history, and four with mergers in their last 9 Gyr of evolution. We compare their structure at z = 0 by decomposing them into `mono-age populations' (MAPs) of stars within 500 Myr age bins. All studied galaxies undergo a phase of merging activity at high redshift, so that stars older than 9 Gyr are found in a centrally concentrated component, while younger stars are mostly found in discs. We find that most MAPs have simple exponential radial and vertical density profiles, with a scaleheight that typically increases with age. Because a large range of merger histories can create populations with simple structures, this suggests that the simplicity of the structure of mono-abundance populations observed in the Milky Way by Bovy et al. is not necessarily a direct indicator of a quiescent history for the Milky Way. Similarly, the anticorrelation between scalelength and scaleheight does not necessarily imply a merger-free history. However, mergers produce discontinuities between thin and thick disc components, and jumps in the age-velocity relation. The absence of a structural discontinuity between thin and thick disc observed in the Milky Way would seem to be a good indicator that no merger with a mass ratio larger than 1:15-1:10 occurred in the last 9 Gyr. Mergers at higher redshift might nevertheless be necessary to produce the thickest, hottest components of the Milky Way's disc.

  3. Evolutionary snowdrift game incorporating costly punishment in structured populations

    NASA Astrophysics Data System (ADS)

    Chan, Nat W. H.; Xu, C.; Tey, Siew Kian; Yap, Yee Jiun; Hui, P. M.

    2013-01-01

    The role of punishment and the effects of a structured population in promoting cooperation are important issues. Within a recent model of snowdrift game (SG) incorporating a costly punishing strategy (P), we study the effects of a population connected through a square lattice. The punishers, who carry basically a cooperative (C) character, are willing to pay a cost α so as to punish a non-cooperative (D) opponent by β. Depending on α, β, the cost-to-benefit ratio r in SG, and the initial conditions, the system evolves into different phases that could be homogeneous or inhomogeneous. The spatial structure imposes geometrical constraint on how one agent is affected by neighboring agents. Results of extensive numerical simulations, both for the steady state and the dynamics, are presented. Possible phases are identified and discussed, and isolated phases in the r-β space are identified as special local structures of strategies that are stable due to the lattice structure. In contrast to a well-mixed population where punishers are suppressed due to the cost of punishment, the altruistic punishing strategy can flourish and prevail for appropriate values of the parameters, implying an enhancement in cooperation by imposing punishments in a structured population. The system could evolve to a phase corresponding to the coexistence of C, D, and P strategies at some particular payoff parameters, and such a phase is absent in a well-mixed population. The pair approximation, a commonly used analytic approach, is extended from a two-strategy system to a three-strategy system. We show that the pair approximation can, at best, capture the numerical results only qualitatively. Due to the improper way of including spatial correlation imposed by the lattice structure, the approximation does not give the frequencies of C, D, and P accurately and fails to give the homogeneous AllD and AllP phases.

  4. Microsatellite and Wolbachia analysis in Rhagoletis cerasi natural populations: population structuring and multiple infections.

    PubMed

    Augustinos, Antonios A; Asimakopoulou, Anastasia K; Moraiti, Cleopatra A; Mavragani-Tsipidou, Penelope; Papadopoulos, Nikolaos T; Bourtzis, Kostas

    2014-05-01

    Rhagoletis cerasi (Diptera: Tephritidae) is a major pest of sweet and sour cherries in Europe and parts of Asia. Despite its economic significance, there is a lack of studies on the genetic structure of R. cerasi populations. Elucidating the genetic structure of insects of economic importance is crucial for developing phenological-predictive models and environmental friendly control methods. All natural populations of R. cerasi have been found to harbor the endosymbiont Wolbachia pipientis, which widely affects multiple biological traits contributing to the evolution of its hosts, and has been suggested as a tool for the biological control of insect pests and disease vectors. In the current study, the analysis of 18 R. cerasi populations collected in Greece, Germany, and Russia using 13 microsatellite markers revealed structuring of R. cerasi natural populations, even at close geographic range. We also analyzed the Wolbachia infection status of these populations using 16S rRNA-, MLST- and wsp-based approaches. All 244 individuals screened were positive for Wolbachia. Our results suggest the fixation of the wCer1 strain in Greece while wCer2, wCer4, wCer5, and probably other uncharacterized strains were also detected in multiply infected individuals. The role of Wolbachia and its potential extended phenotypes needs a thorough investigation in R. cerasi. Our data suggest an involvement of this symbiont in the observed restriction in the gene flow in addition to a number of different ecological factors. PMID:24963388

  5. Microsatellite and Wolbachia analysis in Rhagoletis cerasi natural populations: population structuring and multiple infections

    PubMed Central

    Augustinos, Antonios A; Asimakopoulou, Anastasia K; Moraiti, Cleopatra A; Mavragani-Tsipidou, Penelope; Papadopoulos, Nikolaos T; Bourtzis, Kostas

    2014-01-01

    Rhagoletis cerasi (Diptera: Tephritidae) is a major pest of sweet and sour cherries in Europe and parts of Asia. Despite its economic significance, there is a lack of studies on the genetic structure of R. cerasi populations. Elucidating the genetic structure of insects of economic importance is crucial for developing phenological-predictive models and environmental friendly control methods. All natural populations of R. cerasi have been found to harbor the endosymbiont Wolbachia pipientis, which widely affects multiple biological traits contributing to the evolution of its hosts, and has been suggested as a tool for the biological control of insect pests and disease vectors. In the current study, the analysis of 18 R. cerasi populations collected in Greece, Germany, and Russia using 13 microsatellite markers revealed structuring of R. cerasi natural populations, even at close geographic range. We also analyzed the Wolbachia infection status of these populations using 16S rRNA-, MLST- and wsp-based approaches. All 244 individuals screened were positive for Wolbachia. Our results suggest the fixation of the wCer1 strain in Greece while wCer2, wCer4, wCer5, and probably other uncharacterized strains were also detected in multiply infected individuals. The role of Wolbachia and its potential extended phenotypes needs a thorough investigation in R. cerasi. Our data suggest an involvement of this symbiont in the observed restriction in the gene flow in addition to a number of different ecological factors. PMID:24963388

  6. Triiodothyronine expands the lactotroph and maintains the lactosomatotroph population, whereas thyrotrophin-releasing hormone augments thyrotroph abundance in aggregate cell cultures of postnatal rat pituitary gland.

    PubMed

    Pals, K; Vankelecom, H; Denef, C

    2006-03-01

    In the present study, we used a three-dimensional pituitary cell culture system from early postnatal rats to examine the in vitro developmental potential of triiodothyronine (T3) and thyrotrophin-releasing hormone (TRH). Cell types were identified at the hormone mRNA level by single-cell reverse transcription-polymerase chain reaction and any change in abundance was further examined by immunofluorescence staining of the corresponding hormone protein. In aggregates from 14-day-old rats, long-term (12-16 days) treatment with T3 (0.5 nM) increased the abundance of cells expressing prolactin mRNA (PRLmRNA cells) by 2.5-fold and lowered that of nonhormonal cells and thyroid-stimulating hormone beta (TSHbeta)mRNA cells. The abundance of growth hormone (GH)mRNA cells decreased during culture compared to that in the freshly dispersed pituitary gland and T3 did not significantly affect this cell population. Cells coexpressing PRL mRNA and GH mRNA virtually disappeared during culture but reappeared in the presence of T3. T3 increased the abundance of PRL-immunoreactive (ir) cells in aggregates from 14-day-old rats, as well as in aggregates from newborn and 1-week-old rats. As estimated by bromodeoxyuridine (BrdU) labelling, a 3-day treatment with T3 enhanced the number of PRL-ir cells that had incorporated BrdU, but did not yet expand the total population of PRL-ir cells. Long-term treatment with TRH (100 nM) did not affect the proportion of PRLmRNA or GHmRNA cells, but consistently increased the proportional number of TSHbeta(mRNA) and TSHbeta-ir cells. The present data confirm the findings obtained in recent in vivo loss of function genetic studies suggesting that T3 plays a prominent role in postnatal expansion of the lactotroph population and that TRH is important for thyrotroph development. The data suggest that the effect of T3 is brought about by a direct action on the pituitary gland through a cell proliferation mechanism. T3 also appears to support the

  7. A general abundance problem for all self-enrichment scenarios for the origin of multiple populations in globular clusters

    NASA Astrophysics Data System (ADS)

    Bastian, Nate; Cabrera-Ziri, Ivan; Salaris, Maurizio

    2015-05-01

    A number of stellar sources have been advocated as the origin of the enriched material required to explain the abundance anomalies seen in ancient globular clusters (GCs). Most studies to date have compared the yields from potential sources [asymptotic giant branch stars (AGBs), fast rotating massive stars (FRMS), high-mass interacting binaries (IBs), and very massive stars (VMS)] with observations of specific elements that are observed to vary from star-to-star in GCs, focusing on extreme GCs such as NGC 2808, which display large He variations. However, a consistency check between the results of fitting extreme cases with the requirements of more typical clusters, has rarely been done. Such a check is particularly timely given the constraints on He abundances in GCs now available. Here, we show that all of the popular enrichment sources fail to reproduce the observed trends in GCs, focusing primarily on Na, O and He. In particular, we show that any model that can fit clusters like NGC 2808, will necessarily fail (by construction) to fit more typical clusters like 47 Tuc or NGC 288. All sources severely overproduce He for most clusters. Additionally, given the large differences in He spreads between clusters, but similar spreads observed in Na-O, only sources with large degrees of stochasticity in the resulting yields will be able to fit the observations. We conclude that no enrichment source put forward so far (AGBs, FRMS, IBs, VMS - or combinations thereof) is consistent with the observations of GCs. Finally, the observed trends of increasing [N/Fe] and He spread with increasing cluster mass cannot be resolved within a self-enrichment framework, without further exacerbating the mass-budget problem.

  8. Population Structure of Barley Landrace Populations and Gene-Flow with Modern Varieties

    PubMed Central

    Bellucci, Elisa; Bitocchi, Elena; Rau, Domenico; Nanni, Laura; Ferradini, Nicoletta; Giardini, Alessandro; Rodriguez, Monica; Attene, Giovanna; Papa, Roberto

    2013-01-01

    Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments. PMID:24386303

  9. The subtle role of climate change on population genetic structure in Canada lynx.

    PubMed

    Row, Jeffrey R; Wilson, Paul J; Gomez, Celine; Koen, Erin L; Bowman, Jeff; Thornton, Daniel; Murray, Dennis L

    2014-07-01

    Anthropogenically driven climatic change is expected to reshape global patterns of species distribution and abundance. Given recent links between genetic variation and environmental patterns, climate change may similarly impact genetic population structure, but we lack information on the spatial and mechanistic underpinnings of genetic-climate associations. Here, we show that current genetic variability of Canada lynx (Lynx canadensis) is strongly correlated with a winter climate gradient (i.e. increasing snow depth and winter precipitation from west-to-east) across the Pacific-North American (PNO) to North Atlantic Oscillation (NAO) climatic systems. This relationship was stronger than isolation by distance and not explained by landscape variables or changes in abundance. Thus, these patterns suggest that individuals restricted dispersal across the climate boundary, likely in the absence of changes in habitat quality. We propose habitat imprinting on snow conditions as one possible explanation for this unusual phenomenon. Coupling historical climate data with future projections, we also found increasingly diverging snow conditions between the two climate systems. Based on genetic simulations using projected climate data (2041-2070), we predicted that this divergence could lead to a threefold increase in genetic differentiation, potentially leading to isolated east-west populations of lynx in North America. Our results imply that subtle genetic structure can be governed by current climate and that substantive genetic differentiation and related ecological divergence may arise from changing climate patterns.

  10. Task-specific stability of abundant systems: Structure of variance and motor equivalence.

    PubMed

    Mattos, D; Schöner, G; Zatsiorsky, V M; Latash, M L

    2015-12-01

    Our main goal was to test a hypothesis that transient changes in performance of a steady-state task would result in motor equivalence. We also estimated effects of visual feedback on the amount of reorganization of motor elements. Healthy subjects performed two variations of a four-finger pressing task requiring accurate production of total pressing force (F TOT) and total moment of force (M TOT). In the Jumping-Target task, a sequence of target jumps required transient changes in either F TOT or M TOT. In the Step-Perturbation task, the index finger was lifted by 1cm for 0.5s leading to a change in both F TOT and M TOT. Visual feedback could have been frozen for one of these two variables in both tasks. Deviations in the space of finger modes (hypothetical commands to individual fingers) were quantified in directions of unchanged F TOT and M TOT (motor equivalent - ME) and in directions that changed F TOT and M TOT (non-motor equivalence - nME). Both the ME and nME components increased when the performance changed. After transient target jumps leading to the same combination of F TOT and M TOT, the changes in finger modes had a large residual ME component with only a very small nME component. Without visual feedback, an increase in the nME component was observed without consistent changes in the ME component. Results from the Step-Perturbation task were qualitatively similar. These findings suggest that both external perturbations and purposeful changes in performance trigger a reorganization of elements of an abundant system, leading to large ME change. These results are consistent with the principle of motor abundance corroborating the idea that a family of solutions is facilitated to stabilize values of important performance variables. PMID:26434623

  11. Genetic Structure of Daphnia galeata Populations in Eastern China

    PubMed Central

    Wolinska, Justyna; Ma, Xiaolin; Yang, Zhong; Hu, Wei; Yin, Mingbo

    2015-01-01

    This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes. PMID:25768727

  12. The Decay of Genetic Variability in Geographically Structured Populations*

    PubMed Central

    Nagylaki, Thomas

    1974-01-01

    The geographical structure of a population distributed continuously and homogeneously along an infinite linear habitat is explored. The analysis is restricted to a single locus in the absence of selection, and every mutant is assumed to be new to the population. An explicit formula is derived for the probability that two homologous genes separated by a given distance at any time t are the same allele. The ultimate rate of approach to equilibrium is shown to be t-3/2e-2ut, where u is the mutation rate. An approximation is given for the stationary probability of allelism in an infinite two-dimensional population, which, unlike previous expressions, is finite everywhere. For a finite habitat of arbitrary shape and any number of dimensions, it is proved that if the population density is very high, then asymptotically the transient part of the probability of allelism is spatially uniform and decays at the rate e-[2u+1/(2N)]t, where N is the total population size. Thus, in this respect the population behaves as if it were panmictic. The dependence of the amount of local gene frequency differentiation on population density and habitat size and dimensionality is discussed. PMID:4528770

  13. Population structure and cultural geography of a folktale in Europe

    PubMed Central

    Ross, Robert M.; Greenhill, Simon J.; Atkinson, Quentin D.

    2013-01-01

    Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture. PMID:23390109

  14. Population structure and cultural geography of a folktale in Europe.

    PubMed

    Ross, Robert M; Greenhill, Simon J; Atkinson, Quentin D

    2013-04-01

    Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture.

  15. Population genetic structure of the people of Qatar.

    PubMed

    Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W; Fuller, Jennifer; Hackett, Neil R; Crystal, Ronald G; Clark, Andrew G

    2010-07-01

    People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari.

  16. Inference of population structure and patterns of gene flow in canine heartworm (Dirofilaria immitis).

    PubMed

    Belanger, Diana H; Perkins, Susan L; Rockwell, Robert F

    2011-08-01

    Understanding the genetic variation within a parasitic species is crucial to implementing successful control programs and preventing the dispersal of drug resistance alleles. We examined the population genetics and structure of canine heartworm (Dirofilaria immitis) by developing a panel of 11 polymorphic microsatellite loci for this abundant parasite. In total, 192 individual nematodes were opportunistically sampled from 9 geographic regions in the United States and Mexico and genotyped. Population genetic analyses indicate the presence of 4 genetic clusters. The canine heartworm samples used in this study were characterized by low heterozygosity, with eastern and central North America experiencing high levels of reciprocal gene flow. Geographic barriers impede the movement of vectors and infected hosts west of the Rocky Mountains and south of the Central Mexican Plateau. This, combined with corridors of contiguous habitat, could influence the spread of drug resistance alleles. PMID:21506823

  17. Evolutionary dynamics for persistent cooperation in structured populations

    NASA Astrophysics Data System (ADS)

    Li, Yan; Liu, Xinsheng; Claussen, Jens Christian; Guo, Wanlin

    2015-06-01

    The emergence and maintenance of cooperative behavior is a fascinating topic in evolutionary biology and social science. The public goods game (PGG) is a paradigm for exploring cooperative behavior. In PGG, the total resulting payoff is divided equally among all participants. This feature still leads to the dominance of defection without substantially magnifying the public good by a multiplying factor. Much effort has been made to explain the evolution of cooperative strategies, including a recent model in which only a portion of the total benefit is shared by all the players through introducing a new strategy named persistent cooperation. A persistent cooperator is a contributor who is willing to pay a second cost to retrieve the remaining portion of the payoff contributed by themselves. In a previous study, this model was analyzed in the framework of well-mixed populations. This paper focuses on discussing the persistent cooperation in lattice-structured populations. The evolutionary dynamics of the structured populations consisting of three types of competing players (pure cooperators, defectors, and persistent cooperators) are revealed by theoretical analysis and numerical simulations. In particular, the approximate expressions of fixation probabilities for strategies are derived on one-dimensional lattices. The phase diagrams of stationary states, and the evolution of frequencies and spatial patterns for strategies are illustrated on both one-dimensional and square lattices by simulations. Our results are consistent with the general observation that, at least in most situations, a structured population facilitates the evolution of cooperation. Specifically, here we find that the existence of persistent cooperators greatly suppresses the spreading of defectors under more relaxed conditions in structured populations compared to that obtained in well-mixed populations.

  18. Population Structure Shapes Copy Number Variation in Malaria Parasites

    PubMed Central

    Cheeseman, Ian H.; Miller, Becky; Tan, John C.; Tan, Asako; Nair, Shalini; Nkhoma, Standwell C.; De Donato, Marcos; Rodulfo, Hectorina; Dondorp, Arjen; Branch, Oralee H.; Mesia, Lastenia Ruiz; Newton, Paul; Mayxay, Mayfong; Amambua-Ngwa, Alfred; Conway, David J.; Nosten, François; Ferdig, Michael T.; Anderson, Tim J. C.

    2016-01-01

    If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen. PMID:26613787

  19. Population Structure Shapes Copy Number Variation in Malaria Parasites.

    PubMed

    Cheeseman, Ian H; Miller, Becky; Tan, John C; Tan, Asako; Nair, Shalini; Nkhoma, Standwell C; De Donato, Marcos; Rodulfo, Hectorina; Dondorp, Arjen; Branch, Oralee H; Mesia, Lastenia Ruiz; Newton, Paul; Mayxay, Mayfong; Amambua-Ngwa, Alfred; Conway, David J; Nosten, François; Ferdig, Michael T; Anderson, Tim J C

    2016-03-01

    If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.

  20. Population Structure, Genetic Variation, and Linkage Disequilibrium in Perennial Ryegrass Populations Divergently Selected for Freezing Tolerance.

    PubMed

    Kovi, Mallikarjuna Rao; Fjellheim, Siri; Sandve, Simen R; Larsen, Arild; Rudi, Heidi; Asp, Torben; Kent, Matthew Peter; Rognli, Odd Arne

    2015-01-01

    Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L.), and freezing tolerance is a complex trait of major agronomical importance in northern and central Europe. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. The plant material investigated in this study was an experimental synthetic population derived from pair-crosses among five European perennial ryegrass genotypes, representing adaptations to a range of climatic conditions across Europe. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF], and 27 of Unselected [US]) from the second generation of the two divergently selected populations and an unselected (US) control population were genotyped using 278 genome-wide SNPs derived from perennial ryegrass transcriptome sequences. Our studies investigated the genetic diversity among the three experimental populations by analysis of molecular variance and population structure, and determined that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD) decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two F st outlier methods; finite island model (fdist) by LOSITAN and hierarchical structure model using ARLEQUIN, both detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation, and abiotic stress. These six candidate loci under directional selection for freezing tolerance might be potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  1. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa.

    PubMed

    Khanyile, Khulekani S; Dzomba, Edgar F; Muchadeyi, Farai C

    2015-01-01

    Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective

  2. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

    PubMed Central

    Khanyile, Khulekani S.; Dzomba, Edgar F.; Muchadeyi, Farai C.

    2015-01-01

    Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective

  3. Impact of the 2010 Deepwater Horizon oil spill on population size and genetic structure of horse flies in Louisiana marshes.

    PubMed

    Husseneder, Claudia; Donaldson, Jennifer R; Foil, Lane D

    2016-01-01

    The greenhead horse fly, Tabanus nigrovittatus Macquart, is frequently found in coastal marshes of the Eastern United States. The greenhead horse fly larvae are top predators in the marsh and thus vulnerable to changes in the environment, and the adults potentially are attracted to polarized surfaces like oil. Therefore, horse fly populations could serve as bioindicators of marsh health and toxic effects of oil intrusion. In this study, we describe the impact of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico on tabanid population abundance and genetics as well as mating structure. Horse fly populations were sampled biweekly from oiled and unaffected locations immediately after the oil spill in June 2010 until October 2011. Horse fly abundance estimates showed severe crashes of tabanid populations in oiled areas. Microsatellite genotyping of six pristine and seven oiled populations at ten polymorphic loci detected genetic bottlenecks in six of the oiled populations in association with fewer breeding parents, reduced effective population size, lower number of family clusters and fewer migrants among populations. This is the first study assessing the impact of oil contamination at the level of a top arthropod predator of the invertebrate community in salt marshes. PMID:26755069

  4. Impact of the 2010 Deepwater Horizon oil spill on population size and genetic structure of horse flies in Louisiana marshes

    PubMed Central

    Husseneder, Claudia; Donaldson, Jennifer R.; Foil, Lane D.

    2016-01-01

    The greenhead horse fly, Tabanus nigrovittatus Macquart, is frequently found in coastal marshes of the Eastern United States. The greenhead horse fly larvae are top predators in the marsh and thus vulnerable to changes in the environment, and the adults potentially are attracted to polarized surfaces like oil. Therefore, horse fly populations could serve as bioindicators of marsh health and toxic effects of oil intrusion. In this study, we describe the impact of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico on tabanid population abundance and genetics as well as mating structure. Horse fly populations were sampled biweekly from oiled and unaffected locations immediately after the oil spill in June 2010 until October 2011. Horse fly abundance estimates showed severe crashes of tabanid populations in oiled areas. Microsatellite genotyping of six pristine and seven oiled populations at ten polymorphic loci detected genetic bottlenecks in six of the oiled populations in association with fewer breeding parents, reduced effective population size, lower number of family clusters and fewer migrants among populations. This is the first study assessing the impact of oil contamination at the level of a top arthropod predator of the invertebrate community in salt marshes. PMID:26755069

  5. Impact of the 2010 Deepwater Horizon oil spill on population size and genetic structure of horse flies in Louisiana marshes.

    PubMed

    Husseneder, Claudia; Donaldson, Jennifer R; Foil, Lane D

    2016-01-12

    The greenhead horse fly, Tabanus nigrovittatus Macquart, is frequently found in coastal marshes of the Eastern United States. The greenhead horse fly larvae are top predators in the marsh and thus vulnerable to changes in the environment, and the adults potentially are attracted to polarized surfaces like oil. Therefore, horse fly populations could serve as bioindicators of marsh health and toxic effects of oil intrusion. In this study, we describe the impact of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico on tabanid population abundance and genetics as well as mating structure. Horse fly populations were sampled biweekly from oiled and unaffected locations immediately after the oil spill in June 2010 until October 2011. Horse fly abundance estimates showed severe crashes of tabanid populations in oiled areas. Microsatellite genotyping of six pristine and seven oiled populations at ten polymorphic loci detected genetic bottlenecks in six of the oiled populations in association with fewer breeding parents, reduced effective population size, lower number of family clusters and fewer migrants among populations. This is the first study assessing the impact of oil contamination at the level of a top arthropod predator of the invertebrate community in salt marshes.

  6. Effects of structural complexity enhancement on eastern red-backed salamander (Plethodon cinereus) populations in northern hardwood forests

    USGS Publications Warehouse

    McKenny, H.C.; Keeton, W.S.; Donovan, T.M.

    2006-01-01

    Managing for stand structural complexity in northern hardwood forests has been proposed as a method for promoting microhabitat characteristics important to eastern red-backed salamanders (Plethodon cinereus). We evaluated the effects of alternate, structure-based silvicultural systems on red-backed salamander populations at two research sites in northwestern Vermont. Treatments included two uneven-aged approaches (single-tree selection and group-selection) and one unconventional approach, termed "structural complexity enhancement" (SCE), that promotes development of late-successional structure, including elevated levels of coarse woody debris (CWD). Treatments were applied to 2 ha units and were replicated two to four times depending on treatment. We surveyed red-backed salamanders with a natural cover search method of transects nested within vegetation plots 1 year after logging. Abundance estimates corrected for detection probability were calculated from survey data with a binomial mixture model. Abundance estimates differed between study areas and were influenced by forest structural characteristics. Model selection was conducted using Akaike Information Criteria, corrected for over-dispersed data and small sample size (QAICc). We found no difference in abundance as a response to treatment as a whole, suggesting that all of the uneven-aged silvicultural systems evaluated can maintain salamander populations after harvest. However, abundance was tied to specific structural habitat attributes associated with study plots within treatments. The most parsimonious model of habitat covariates included site, relative density of overstory trees, and density of more-decayed and less-decayed downed CWD. Abundance responded positively to the density of downed, well-decayed CWD and negatively to the density of poorly decayed CWD and to overstory relative density. CWD volume was not a strong predictor of salamander abundance. We conclude that structural complexity enhancement

  7. Vertical changes in abundance, biomass and community structure of copepods down to 3000 m in the southern Bering Sea

    NASA Astrophysics Data System (ADS)

    Homma, Tomoe; Yamaguchi, Atsushi

    2010-08-01

    Vertical changes in abundance, biomass and community structure of copepods down to 3000 m depth were studied at a single station of the Aleutian Basin of the Bering Sea (53°28'N, 177°00'W, depth 3779 m) on the 14th June 2006. Both abundance and biomass of copepods were greatest near the surface layer and decreased with increase in depth. Abundance and biomass of copepods integrated over 0-3000 m were 1,390,000 inds. m -2 and 5056 mg C m -2, respectively. Copepod carcasses occurred throughout the layer, and the carcass:living specimen ratio was the greatest in the oxygen minimum layer (750-100 m, the ratio was 2.3). A total of 72 calanoid copepod species belonging to 34 genera and 15 families occurred in the 0-3000 m water column (Cyclopoida, Harpacticoida and Poecilostomatoida were not identified to species level). Cluster analysis separated calanoid copepod communities into 5 groups (A-E). Each group was separated by depth, and the depth range of each group was at 0-75 m (A), 75-500 m (B), 500-750 m (C), 750-1500 m (D) and 1500-3000 m (E). Copepods were divided into four types based on the feeding pattern: suspension feeders, suspension feeders in diapause, detritivores and carnivores. In terms of abundance the most dominant group was suspension feeders (mainly Cyclopoida) in the epipelagic zone, and detritivores (mainly Poecilostomatoida) were dominant in the meso- and bathypelagic zones. In terms of biomass, suspension feeders in diapause (calanoid copepods Neocalanus spp. and Eucalanus bungii) were the major component (ca. 10-45%), especially in the 250-3000 m depth. These results are compared with the previous studies in the same region and that down to greater depths in the worldwide oceans.

  8. Genetic structure of a lotic population of Burkholderia (Pseudomonas) cepacia

    SciTech Connect

    Wise, M.G.; Shimkets, L.J.; McArthur, J.V.

    1995-05-01

    The genetic structure of a population of Burkholderia (Pseudomonas) cepacia isolated from a southeastern blackwater stream was investigated by using multilocus enzyme electrophoresis to examine the allelic variation in eight structural gene loci. Overall, 213 isolates were collected at transect points along the stream continuum, from both the sediments along the bank and the water column. Multilocus enzyme electrophoresis analysis revealed 164 distinct electrophoretic types, and the mean genetic diversity of the entire population was 0.574. Genetic diversity values did not vary spatially along the stream continuum. From a canonical discriminant analysis, Mahalonobis distances (measurements of genetic similarity between populations) revealed significant differences among the subpopulations at the sediment sampling points, suggesting bacterial adaptation to a heterogeneous (or patchy) microgeographical environment. Multilocus linkage disequilibrium analysis of the isolates revealed only limited association between alleles, suggesting frequent recombination, relative to binary fission, in this population. Furthermore, the dendrogram created from the data of this study and the allele mismatch distribution are typical of a population characterized by extensive genetic mixing. We suggest that B. cepacia be added to the growing list of bacteria that are not obligatorily clonal. 41 refs., 5 figs., 3 tabs.

  9. How detectable is predation in stage-structured populations? Insights from a simulation-testing analysis.

    PubMed

    Oken, Kiva L; Essington, Timothy E

    2015-01-01

    The potential of predation to structure marine food webs is widely acknowledged. However, available tools to detect the regulation of prey population dynamics by predation are limited, partly because available population data often aggregate a population's age structure into a single biomass or abundance metric. Additionally, many food webs are relatively complex, with prey species subject to different assemblages of predators throughout their ontogeny. The goal of this study was to evaluate the extent to which stage-structured predation could be reliably detected from time series of total biomass of predators and prey. We simulated age-structured populations of four mid-trophic-level fish species with distinct life-history traits, exposed them to variable predation at different life stages and fit production models to resulting population biomass to determine how reliably the effects of predators could be detected. Predation targeting early life history and juvenile life stages generally led to larger fluctuations in annual production and was therefore more detectable. However, ecologically realistic levels of observation error and environmental stochasticity masked most predator signals. The addition of predation at a second life stage sharply decreased the ability to detect the effect of each predator. We conclude that the absence of detectable species interactions from biomass time series may be partly due to the interactive effects of environmental variability and complex food web linkages and life histories. We also note that predation signals are most robust for predator-prey systems where predators primarily act on mortality of submature life-history stages. Simulation testing can be applied widely to evaluate the statistical power of analyses to detect predation effects.

  10. Population structure and genetic analysis of narrow-clawed crayfish (Astacus leptodactylus) populations in Turkey.

    PubMed

    Akhan, Suleyman; Bektas, Yusuf; Berber, Selcuk; Kalayci, Gokhan

    2014-10-01

    The genetic differentiation among Turkish populations of the narrow-clawed crayfish was investigated using a partial sequence of cytochrome oxidase subunit I gene (585 bp) of 183 specimens from 17 different crayfish populations. Median joining network and all phylogenetic analyses disclosed a strong haplotype structure with three prominent clades diverged by a range between 20 and 50 mutations and substantial inter-group pairwise sequence divergence (5.19-6.95 %), suggesting the presence of three distinct clades within the Anatolian populations of Astacus leptodactylus. The divergence times among the three clades of Turkish A. leptodactylus are estimated to be 4.96-3.70 Mya using a molecular clock of 1.4 % sequence divergence per million years, pointing to a lower Pliocene separation. The high level of genetic variability (H d = 95.8 %, π = 4.17 %) and numerous private haplotypes suggest the presence of refugial populations in Anatolia unaffected by Pleistocene habitat restrictions. The pattern of genetic variation among Turkish A. leptodactylus populations, therefore, suggests that the unrevealed intraspecific genetic structure is independent of geographic tendency and congruent with the previously reported geographic distribution and number of subspecies (A. l. leptodactylus and A. l. salinus) of A. leptodactylus.

  11. Coronal Thermal Structure and Abundance of Super-Metal-Rich Late-Type Stars

    NASA Technical Reports Server (NTRS)

    Brickhouse, N.; Mushotzky, Richard F. (Technical Monitor)

    2001-01-01

    This observation is for grating spectroscopy of 30 Ari, a late-type star with very high metallicity. The goal is to use extreme cases to help understand how abundances change from the photosphere to the corona. The only progress is to report to date is preparation for the analysis of the data. The SAO team has produced spectral model predictions for comparison with the observed spectra. The target was obtained by X-ray Multimirror Mission (XMM)-Newton on 2001 January 16 for 28000 sec. Pipeline processing is difficult and the data have not yet been available. Furthermore, we have been cautioned that the data cannot be correctly processed until at least September of this year, as there are problems with the RGS software to extract the spectrum. We have attended two workshops this summer in which results from XMM on late-type stellar coronae were presented including SMM results from GT team members. We noted that only members of the instrument teams are in a position to analyze XMM data.

  12. Sexual networks: measuring sexual selection in structured, polyandrous populations.

    PubMed

    McDonald, Grant C; James, Richard; Krause, Jens; Pizzari, Tommaso

    2013-03-01

    Sexual selection is traditionally measured at the population level, assuming that populations lack structure. However, increasing evidence undermines this approach, indicating that intrasexual competition in natural populations often displays complex patterns of spatial and temporal structure. This complexity is due in part to the degree and mechanisms of polyandry within a population, which can influence the intensity and scale of both pre- and post-copulatory sexual competition. Attempts to measure selection at the local and global scale have been made through multi-level selection approaches. However, definitions of local scale are often based on physical proximity, providing a rather coarse measure of local competition, particularly in polyandrous populations where the local scale of pre- and post-copulatory competition may differ drastically from each other. These limitations can be solved by social network analysis, which allows us to define a unique sexual environment for each member of a population: 'local scale' competition, therefore, becomes an emergent property of a sexual network. Here, we first propose a novel quantitative approach to measure pre- and post-copulatory sexual selection, which integrates multi-level selection with information on local scale competition derived as an emergent property of networks of sexual interactions. We then use simple simulations to illustrate the ways in which polyandry can impact estimates of sexual selection. We show that for intermediate levels of polyandry, the proposed network-based approach provides substantially more accurate measures of sexual selection than the more traditional population-level approach. We argue that the increasing availability of fine-grained behavioural datasets provides exciting new opportunities to develop network approaches to study sexual selection in complex societies.

  13. Molecular Population Genetic Structure in the Piping Plover

    USGS Publications Warehouse

    Miller, Mark P.; Haig, Susan M.; Gratto-Trevor, Cheri L.; Mullins, Thomas D.

    2009-01-01

    The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect

  14. Sexual networks: measuring sexual selection in structured, polyandrous populations

    PubMed Central

    McDonald, Grant C.; James, Richard; Krause, Jens; Pizzari, Tommaso

    2013-01-01

    Sexual selection is traditionally measured at the population level, assuming that populations lack structure. However, increasing evidence undermines this approach, indicating that intrasexual competition in natural populations often displays complex patterns of spatial and temporal structure. This complexity is due in part to the degree and mechanisms of polyandry within a population, which can influence the intensity and scale of both pre- and post-copulatory sexual competition. Attempts to measure selection at the local and global scale have been made through multi-level selection approaches. However, definitions of local scale are often based on physical proximity, providing a rather coarse measure of local competition, particularly in polyandrous populations where the local scale of pre- and post-copulatory competition may differ drastically from each other. These limitations can be solved by social network analysis, which allows us to define a unique sexual environment for each member of a population: ‘local scale’ competition, therefore, becomes an emergent property of a sexual network. Here, we first propose a novel quantitative approach to measure pre- and post-copulatory sexual selection, which integrates multi-level selection with information on local scale competition derived as an emergent property of networks of sexual interactions. We then use simple simulations to illustrate the ways in which polyandry can impact estimates of sexual selection. We show that for intermediate levels of polyandry, the proposed network-based approach provides substantially more accurate measures of sexual selection than the more traditional population-level approach. We argue that the increasing availability of fine-grained behavioural datasets provides exciting new opportunities to develop network approaches to study sexual selection in complex societies. PMID:23339246

  15. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population

    DOE PAGES

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; Dugard, Christopher K.; Held, Michael A.; Klimek, John F.; Shreve, Jacob T.; Fowler, Matthew; Ziebell, Angela; Davis, Mark F.; et al

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 x 3 Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yieldmore » was shared. A genome-wide association study for lignin abundance and sugar yield of the 282- member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. Finally, these results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.« less

  16. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population

    SciTech Connect

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; Dugard, Christopher K.; Held, Michael A.; Klimek, John F.; Shreve, Jacob T.; Fowler, Matthew; Ziebell, Angela; Davis, Mark F.; Decker, Stephen R.; Turner, Geoffrey B.; Mosier, Nathan S.; Springer, Nathan M.; Thimmapuram, Jyothi; Weil, Clifford F.; McCann, Maureen C.; Carpita, Nicholas C.

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 x 3 Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282- member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. Finally, these results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.

  17. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population.

    PubMed

    Penning, Bryan W; Sykes, Robert W; Babcock, Nicholas C; Dugard, Christopher K; Held, Michael A; Klimek, John F; Shreve, Jacob T; Fowler, Matthew; Ziebell, Angela; Davis, Mark F; Decker, Stephen R; Turner, Geoffrey B; Mosier, Nathan S; Springer, Nathan M; Thimmapuram, Jyothi; Weil, Clifford F; McCann, Maureen C; Carpita, Nicholas C

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 × Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282-member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. These results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.

  18. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population1[W][OPEN

    PubMed Central

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; Dugard, Christopher K.; Held, Michael A.; Klimek, John F.; Shreve, Jacob T.; Fowler, Matthew; Ziebell, Angela; Davis, Mark F.; Decker, Stephen R.; Turner, Geoffrey B.; Mosier, Nathan S.; Springer, Nathan M.; Thimmapuram, Jyothi; Weil, Clifford F.; McCann, Maureen C.; Carpita, Nicholas C.

    2014-01-01

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 × Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282-member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. These results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass. PMID:24972714

  19. Models of earth structure inferred from neodymium and strontium isotopic abundances

    PubMed Central

    Wasserburg, G. J.; DePaolo, D. J.

    1979-01-01

    A simplified model of earth structure based on the Nd and Sr isotopic characteristics of oceanic and continental tholeiitic flood basalts is presented, taking into account the motion of crustal plates and a chemical balance for trace elements. The resulting structure that is inferred consists of a lower mantle that is still essentially undifferentiated, overlain by an upper mantle that is the residue of the original source from which the continents were derived. PMID:16592688

  20. A Spatial Framework for Understanding Population Structure and Admixture.

    PubMed

    Bradburd, Gideon S; Ralph, Peter L; Coop, Graham M

    2016-01-01

    Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build "geogenetic maps," which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix. PMID:26771578

  1. Population structure of the giant garter snake, Thamnophis gigas

    USGS Publications Warehouse

    Paquin, M.M.; Wylie, G.D.; Routman, E.J.

    2006-01-01

    The giant garter snake, Thamnophis gigas, is a threatened species endemic to California's Central Valley. We tested the hypothesis that current watershed boundaries have caused genetic differentiation among populations of T. gigas. We sampled 14 populations throughout the current geographic range of T. gigas and amplified 859 bp from the mitochondrial gene ND4 and one nuclear microsatellite locus. DNA sequence variation from the mitochondrial gene indicates there is some genetic structuring of the populations, with high F ST values and unique haplotypes occurring at high frequency in several populations. We found that clustering populations by watershed boundary results in significant between-region genetic variance for mtDNA. However, analysis of allele frequencies at the microsatellite locus NSU3 reveals very low F ST values and little between-region variation in allele frequencies. The discordance found between mitochondrial and microsatellite data may be explained by aspects of molecular evolution and/or T. gigas life history characteristics. Differences in effective population size between mitochondrial and nuclear DNA, or male-biased gene flow, result in a lower migration rate of mitochondrial haplotypes relative to nuclear alleles. However, we cannot exclude homoplasy as one explanation for homogeneity found for the single microsatellite locus. The mitochondrial nucleotide sequence data supports conservation practices that identify separate management units for T. gigas. ?? Springer 2006.

  2. Population structure of loggerhead shrikes in the California Channel Islands.

    PubMed

    Eggert, Lori S; Mundy, Nicholas I; Woodruff, David S

    2004-08-01

    The loggerhead shrike (Lanius ludovicianus), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi, was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi, was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity.

  3. Types of marriages, population structure and genetic disease.

    PubMed

    Machado, T M B; Bomfim, T F; Souza, L V; Soares, N; Santos, F L; Acosta, A X; Abe-Sandes, K

    2013-07-01

    A high occurrence rate of consanguineous marriages may favour the onset and increased frequency of autosomal recessive diseases in a population. The population of Monte Santo, Bahia, Brazil, has a high frequency of rare genetic diseases such as mucopolysaccharidosis type VI, whose observed frequency in this population is 1:5000, while the incidence of this disease recorded in other regions of the world varies from 1:43,261 in Turkey to 1:1,505,160 in Switzerland. To verify the influence of consanguineous marriage on the increased frequency of observed genetic diseases in this population, the population structure and frequency of different types of marriage during different time periods were evaluated. A total of 9765 marriages were found in an analysis of parish marriage records from the city. Over three periods, 1860-1895, 1950-1961 and 1975-2010, the inbreeding rates were 37.1%, 13.2% and 4.2% respectively. Although there was a high rate of inbreeding, endogamic marriages were the dominant marriage type in all three periods. In the most recent period, there was an increase in the number of exogamous marriages and those among immigrants, but most of these occurred among individuals from cities that neighbour Monte Santo. The low rate of migration and high frequency of endogamic and consanguineous marriages show that growth of this population is predominantly internal and could explain the occurrence, and increase in frequency, of recessive genetic diseases in the city.

  4. A Spatial Framework for Understanding Population Structure and Admixture

    PubMed Central

    Bradburd, Gideon S.; Ralph, Peter L.; Coop, Graham M.

    2016-01-01

    Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build “geogenetic maps,” which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix. PMID:26771578

  5. Genetic diversity and population structure of Yucca filamentosa (Agavaceae).

    PubMed

    Massey, L; Hamrick, J

    1998-03-01

    Using 19 allozyme loci we studied genetic diversity in 18 populations of Yucca filamentosa (Agavaceae) from the southeastern United States. Of the 19 loci surveyed, 17 (89.5%) were polymorphic in at least one of the populations sampled. There was considerable variation among populations in the percentage of polymorphic loci (range = 31.6-84.2%, mean = 67.6%). Similar heterogeneity among populations was observed for mean number of alleles per polymorphic locus (range = 2.0-3.0; mean = 2.48) and mean expected heterozygosity (range = 0.113-0.288; mean = 0.213). On average, 83% of the total genetic diversity was found within populations. Duplications of three allozyme loci were detected in several populations. The life-history characteristics of Y. filamentosa (a long-lived, semiwoody, predominantly outcrossing monocot with a large geographical range) may contribute to the maintenance of such high levels of genetic diversity. These results contradict expectations of the genetic structure of Y. filamentosa based on observations of the dispersal and pollination behavior of its sole pollinator, Tegeticula yuccasella, the yucca moth. PMID:21684917

  6. Genetic diversity and population structure of Yucca filamentosa (Agavaceae).

    PubMed

    Massey, L; Hamrick, J

    1998-03-01

    Using 19 allozyme loci we studied genetic diversity in 18 populations of Yucca filamentosa (Agavaceae) from the southeastern United States. Of the 19 loci surveyed, 17 (89.5%) were polymorphic in at least one of the populations sampled. There was considerable variation among populations in the percentage of polymorphic loci (range = 31.6-84.2%, mean = 67.6%). Similar heterogeneity among populations was observed for mean number of alleles per polymorphic locus (range = 2.0-3.0; mean = 2.48) and mean expected heterozygosity (range = 0.113-0.288; mean = 0.213). On average, 83% of the total genetic diversity was found within populations. Duplications of three allozyme loci were detected in several populations. The life-history characteristics of Y. filamentosa (a long-lived, semiwoody, predominantly outcrossing monocot with a large geographical range) may contribute to the maintenance of such high levels of genetic diversity. These results contradict expectations of the genetic structure of Y. filamentosa based on observations of the dispersal and pollination behavior of its sole pollinator, Tegeticula yuccasella, the yucca moth.

  7. Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars.

    PubMed

    Glassmire, Andrea E; Jeffrey, Christopher S; Forister, Matthew L; Parchman, Thomas L; Nice, Chris C; Jahner, Joshua P; Wilson, Joseph S; Walla, Thomas R; Richards, Lora A; Smilanich, Angela M; Leonard, Michael D; Morrison, Colin R; Simbaña, Wilmer; Salagaje, Luis A; Dodson, Craig D; Miller, Jim S; Tepe, Eric J; Villamarin-Cortez, Santiago; Dyer, Lee A

    2016-10-01

    Chemically mediated plant-herbivore interactions contribute to the diversity of terrestrial communities and the diversification of plants and insects. While our understanding of the processes affecting community structure and evolutionary diversification has grown, few studies have investigated how trait variation shapes genetic and species diversity simultaneously in a tropical ecosystem. We investigated secondary metabolite variation among subpopulations of a single plant species, Piper kelleyi (Piperaceae), using high-performance liquid chromatography (HPLC), to understand associations between plant phytochemistry and host-specialized caterpillars in the genus Eois (Geometridae: Larentiinae) and associated parasitoid wasps and flies. In addition, we used a genotyping-by-sequencing approach to examine the genetic structure of one abundant caterpillar species, Eois encina, in relation to host phytochemical variation. We found substantive concentration differences among three major secondary metabolites, and these differences in chemistry predicted caterpillar and parasitoid community structure among host plant populations. Furthermore, E. encina populations located at high elevations were genetically different from other populations. They fed on plants containing high concentrations of prenylated benzoic acid. Thus, phytochemistry potentially shapes caterpillar and wasp community composition and geographic variation in species interactions, both of which can contribute to diversification of plants and insects.

  8. Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars.

    PubMed

    Glassmire, Andrea E; Jeffrey, Christopher S; Forister, Matthew L; Parchman, Thomas L; Nice, Chris C; Jahner, Joshua P; Wilson, Joseph S; Walla, Thomas R; Richards, Lora A; Smilanich, Angela M; Leonard, Michael D; Morrison, Colin R; Simbaña, Wilmer; Salagaje, Luis A; Dodson, Craig D; Miller, Jim S; Tepe, Eric J; Villamarin-Cortez, Santiago; Dyer, Lee A

    2016-10-01

    Chemically mediated plant-herbivore interactions contribute to the diversity of terrestrial communities and the diversification of plants and insects. While our understanding of the processes affecting community structure and evolutionary diversification has grown, few studies have investigated how trait variation shapes genetic and species diversity simultaneously in a tropical ecosystem. We investigated secondary metabolite variation among subpopulations of a single plant species, Piper kelleyi (Piperaceae), using high-performance liquid chromatography (HPLC), to understand associations between plant phytochemistry and host-specialized caterpillars in the genus Eois (Geometridae: Larentiinae) and associated parasitoid wasps and flies. In addition, we used a genotyping-by-sequencing approach to examine the genetic structure of one abundant caterpillar species, Eois encina, in relation to host phytochemical variation. We found substantive concentration differences among three major secondary metabolites, and these differences in chemistry predicted caterpillar and parasitoid community structure among host plant populations. Furthermore, E. encina populations located at high elevations were genetically different from other populations. They fed on plants containing high concentrations of prenylated benzoic acid. Thus, phytochemistry potentially shapes caterpillar and wasp community composition and geographic variation in species interactions, both of which can contribute to diversification of plants and insects. PMID:27279551

  9. Dimensions of global population projections: what do we know about future population trends and structures?

    PubMed

    Lutz, Wolfgang; K C, Samir

    2010-09-27

    The total size of the world population is likely to increase from its current 7 billion to 8-10 billion by 2050. This uncertainty is because of unknown future fertility and mortality trends in different parts of the world. But the young age structure of the population and the fact that in much of Africa and Western Asia, fertility is still very high makes an increase by at least one more billion almost certain. Virtually, all the increase will happen in the developing world. For the second half of the century, population stabilization and the onset of a decline are likely. In addition to the future size of the population, its distribution by age, sex, level of educational attainment and place of residence are of specific importance for studying future food security. The paper provides a detailed discussion of different relevant dimensions in population projections and an evaluation of the methods and assumptions used in current global population projections and in particular those produced by the United Nations and by IIASA. PMID:20713384

  10. fastSTRUCTURE: variational inference of population structure in large SNP data sets.

    PubMed

    Raj, Anil; Stephens, Matthew; Pritchard, Jonathan K

    2014-06-01

    Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, allowing us to build on recent advances in optimization theory to develop fast inference tools. In addition, we propose useful heuristic scores to identify the number of populations represented in a data set and a new hierarchical prior to detect weak population structure in the data. We test the variational algorithms on simulated data and illustrate using genotype data from the CEPH-Human Genome Diversity Panel. The variational algorithms are almost two orders of magnitude faster than STRUCTURE and achieve accuracies comparable to those of ADMIXTURE. Furthermore, our results show that the heuristic scores for choosing model complexity provide a reasonable range of values for the number of populations represented in the data, with minimal bias toward detecting structure when it is very weak. Our algorithm, fastSTRUCTURE, is freely available online at http://pritchardlab.stanford.edu/structure.html.

  11. Demographic analysis from summaries of an age-structured population

    USGS Publications Warehouse

    Link, W.A.; Royle, J. Andrew; Hatfield, J.S.

    2003-01-01

    Demographic analyses of age-structured populations typically rely on life history data for individuals, or when individual animals are not identified, on information about the numbers of individuals in each age class through time. While it is usually difficult to determine the age class of a randomly encountered individual, it is often the case that the individual can be readily and reliably assigned to one of a set of age classes. For example, it is often possible to distinguish first-year from older birds. In such cases, the population age structure can be regarded as a latent variable governed by a process prior, and the data as summaries of this latent structure. In this article, we consider the problem of uncovering the latent structure and estimating process parameters from summaries of age class information. We present a demographic analysis for the critically endangered migratory population of whooping cranes (Grus americana), based only on counts of first-year birds and of older birds. We estimate age and year-specific survival rates. We address the controversial issue of whether management action on the breeding grounds has influenced recruitment, relating recruitment rates to the number of seventh-year and older birds, and examining the pattern of variation through time in this rate.

  12. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

    PubMed Central

    Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R.; Luke, Sarah H.; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package “traitor” to facilitate assessments of missing trait data. PMID:26881747

  13. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure

    PubMed Central

    Ho, Adrian; van den Brink, Erik; Reim, Andreas; Krause, Sascha M. B.; Bodelier, Paul L. E.

    2016-01-01

    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a ‘tipping point’ where activity no longer recovered if disturbance persists and increase in frequency. PMID:26779148

  14. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure.

    PubMed

    Ho, Adrian; van den Brink, Erik; Reim, Andreas; Krause, Sascha M B; Bodelier, Paul L E

    2015-01-01

    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a 'tipping point' where activity no longer recovered if disturbance persists and increase in frequency.

  15. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R; Luke, Sarah H; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data. PMID:26881747

  16. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R; Luke, Sarah H; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data.

  17. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure.

    PubMed

    Ho, Adrian; van den Brink, Erik; Reim, Andreas; Krause, Sascha M B; Bodelier, Paul L E

    2015-01-01

    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a 'tipping point' where activity no longer recovered if disturbance persists and increase in frequency. PMID:26779148

  18. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments

    PubMed Central

    Li, Xi; Zhang, Miaomiao; Liu, Feng; Li, Yong; He, Yang; Zhang, Shunan; Wu, Jinshui

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different waters were treated by M. elatinoides in microcosms for one month. The five waters included tap water (Control), swine wastewater (SW), 50% diluted swine wastewater (50% SW), and two synthetic wastewaters: 200 mg NH4+-N L−1 (200 NH4+-N) and 400 mg NH4+-N L−1 (400 NH4+-N). The most dramatic changes were in NH4+-N and total N (TN) concentrations, with average removal rates of 84% and 90%, respectively, in the treatments containing swine wastewater. On days 7, 14, and 28, the dissolved oxygen (DO) increased by 81.8%, 210.4% and 136.5%, respectively, compared with on day 0, in the swine wastewater. The results also showed that the bacterial amoA (AOB) copy numbers in the sediments of the treatments were significantly higher than those of archaeal amoA (AOA) copy numbers (p = 0.015). In addition, the high DO concentrations in swine wastewater responded well to the high abundance of AOB. The AOA and AOB community distributions were positively related with NO3-N and were negatively related with DO in swine wastewater treatments. In summary, our experimental results suggested that the M. elatinoides purification system could improve the activity of ammonia-oxidizing microorganisms and consequently might contribute to the significant N removal from the swine wastewater. PMID:26444015

  19. Galactic chemical evolution and solar s-process abundances: Dependence on the {sup 13}C-pocket structure

    SciTech Connect

    Bisterzo, S.; Travaglio, C.; Gallino, R.; Wiescher, M.; Käppeler, F. E-mail: sarabisterzo@gmail.com

    2014-05-20

    We study the s-process abundances (A ≳ 90) at the epoch of the solar system formation. Asymptotic giant branch yields are computed with an updated neutron capture network and updated initial solar abundances. We confirm our previous results obtained with a Galactic chemical evolution (GCE) model: (1) as suggested by the s-process spread observed in disk stars and in presolar meteoritic SiC grains, a weighted average of s-process strengths is needed to reproduce the solar s distribution of isotopes with A > 130; and (2) an additional contribution (of about 25%) is required in order to represent the solar s-process abundances of isotopes from A = 90 to 130. Furthermore, we investigate the effect of different internal structures of the {sup 13}C pocket, which may affect the efficiency of the {sup 13}C(α, n){sup 16}O reaction, the major neutron source of the s process. First, keeping the same {sup 13}C profile adopted so far, we modify by a factor of two the mass involved in the pocket; second, we assume a flat {sup 13}C profile in the pocket, and we test again the effects of the variation of the mass of the pocket. We find that GCE s predictions at the epoch of the solar system formation marginally depend on the size and shape of the {sup 13}C pocket once a different weighted range of {sup 13}C-pocket strengths is assumed. We obtain that, independently of the internal structure of the {sup 13}C pocket, the missing solar system s-process contribution in the range from A = 90 to 130 remains essentially the same.

  20. Decreasing Abundance, Increasing Diversity and Changing Structure of the Wild Bee Community (Hymenoptera: Anthophila) along an Urbanization Gradient

    PubMed Central

    Fortel, Laura; Henry, Mickaël; Guilbaud, Laurent; Guirao, Anne Laure; Kuhlmann, Michael; Mouret, Hugues; Rollin, Orianne; Vaissière, Bernard E.

    2014-01-01

    Background Wild bees are important pollinators that have declined in diversity and abundance during the last decades. Habitat destruction and fragmentation associated with urbanization are reported as part of the main causes of this decline. Urbanization involves dramatic changes of the landscape, increasing the proportion of impervious surface while decreasing that of green areas. Few studies have investigated the effects of urbanization on bee communities. We assessed changes in the abundance, species richness, and composition of wild bee community along an urbanization gradient. Methodology/Principal Findings Over two years and on a monthly basis, bees were sampled with colored pan traps and insect nets at 24 sites located along an urbanization gradient. Landscape structure within three different radii was measured at each study site. We captured 291 wild bee species. The abundance of wild bees was negatively correlated with the proportion of impervious surface, while species richness reached a maximum at an intermediate (50%) proportion of impervious surface. The structure of the community changed along the urbanization gradient with more parasitic species in sites with an intermediate proportion of impervious surface. There were also greater numbers of cavity-nesting species and long-tongued species in sites with intermediate or higher proportion of impervious surface. However, urbanization had no effect on the occurrence of species depending on their social behavior or body size. Conclusions/Significance We found nearly a third of the wild bee fauna known from France in our study sites. Indeed, urban areas supported a diverse bee community, but sites with an intermediate level of urbanization were the most speciose ones, including greater proportion of parasitic species. The presence of a diverse array of bee species even in the most urbanized area makes these pollinators worthy of being a flagship group to raise the awareness of urban citizens about

  1. Venus cloud structure and water vapor abundance from Mariner 10 observations

    NASA Technical Reports Server (NTRS)

    Taylor, F. W.

    1976-01-01

    Observations of the Venus atmosphere with the infrared radiometer on Mariner 10 have been analyzed by Taylor (1975) in terms of the vertical distribution of opacity at wavelengths near 11 microns and 45 microns in the thermal infrared. In this paper, we discuss models of the Venus atmosphere which are consistent with the inferred opacity structure. Either a two-layer cloud structure, or a single cloud deck overlaid by a layer containing approximately 40 precipitable microns of water vapor, would have the required limb-darkening characteristics at the wavelengths of observation.

  2. Visualizing spatial population structure with estimated effective migration surfaces.

    PubMed

    Petkova, Desislava; Novembre, John; Stephens, Matthew

    2016-01-01

    Genetic data often exhibit patterns broadly consistent with 'isolation by distance'-a phenomenon where genetic similarity decays with geographic distance. In a heterogeneous habitat, this may occur more quickly in some regions than in others: for example, barriers to gene flow can accelerate differentiation between neighboring groups. We use the concept of 'effective migration' to model the relationship between genetics and geography. In this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to visualize variation in effective migration across a habitat from geographically indexed genetic data. Our approach uses a population genetic model to relate effective migration rates to expected genetic dissimilarities. We illustrate its potential and limitations using simulations and data from elephant, human and Arabidopsis thaliana populations. The resulting visualizations highlight important spatial features of population structure that are difficult to discern using existing methods for summarizing genetic variation.

  3. Visualizing spatial population structure with estimated effective migration surfaces

    PubMed Central

    Petkova, Desislava; Novembre, John; Stephens, Matthew

    2015-01-01

    Genetic data often exhibit patterns broadly consistent with “isolation by distance” – a phenomenon where genetic similarity decays with geographic distance. In a heterogeneous habitat this may occur more quickly in some regions than others: for example, barriers to gene flow can accelerate differentiation between neighboring groups. We use the concept of “effective migration” to model the relationship between genetics and geography: in this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to visualize variation in effective migration across the habitat from geographically indexed genetic data. Our approach uses a population genetic model to relate effective migration rates to expected genetic dissimilarities. We illustrate its potential and limitations using simulations and data from elephant, human and A. thaliana populations. The resulting visualizations highlight important spatial features of population structure that are difficult to discern using existing methods for summarizing genetic variation. PMID:26642242

  4. Ionization structure and chemical abundances of the Wolf-Rayet nebula NGC 6888 with integral field spectroscopy

    NASA Astrophysics Data System (ADS)

    Fernández-Martín, A.; Vílchez, J. M.; Pérez Montero, E.

    2013-05-01

    n this work we search for the observational footprints of the interactions between the interstellar medium and stellar winds in the Wolf-Rayet nebula NGC 6888 in order to understand its ionization structure, chemical composition, and kinematics. We collected a set of integral field spectroscopy observations across NGC 6888, obtained with PPAK in the optical range performing both 2D and 1D analyses. Attending to the 2D analysis in the north-east part of the nebula, we generated maps of the extinction structure and electron density. We produced diagnostic diagrams and statistical frequency distributions of the radial velocity. Nine integrated spectra were generated over the whole nebula. We measured line intensities to obtain physical parameters and chemical abundances. We inferred that nearly all the zones present an oxygen abundance slightly below the solar values. The derived N/H appears enhanced up to a factor of 6. Helium presents an enrichment in most of the integrated zones, too. Finally, we proposed a scheme of irregular and/or broken shells for NGC 6888 to explain the features observed.

  5. Rivers influence the population genetic structure of bonobos (Pan paniscus).

    PubMed

    Eriksson, J; Hohmann, G; Boesch, C; Vigilant, L

    2004-11-01

    Bonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current-day barriers, but not when straight-line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.

  6. Demographic History, Population Structure