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  • 1
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    The global diversity of birds in space and time (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-11-06
    Description: Current global patterns of biodiversity result from processes that operate over both space and time and thus require an integrated macroecological and macroevolutionary perspective. Molecular time trees have advanced our understanding of the tempo and mode of diversification and have identified remarkable adaptive radiations across the tree of life. However, incomplete joint phylogenetic and geographic sampling has limited broad-scale inference. Thus, the relative prevalence of rapid radiations and the importance of their geographic settings in shaping global biodiversity patterns remain unclear. Here we present, analyse and map the first complete dated phylogeny of all 9,993 extant species of birds, a widely studied group showing many unique adaptations. We find that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present. This acceleration is due to a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers. Importantly, species characterized with very high past diversification rates are interspersed throughout the avian tree and across geographic space. Geographically, the major differences in diversification rates are hemispheric rather than latitudinal, with bird assemblages in Asia, North America and southern South America containing a disproportionate number of species from recent rapid radiations. The contribution of rapidly radiating lineages to both temporal diversification dynamics and spatial distributions of species diversity illustrates the benefits of an inclusive geographical and taxonomical perspective. Overall, whereas constituent clades may exhibit slowdowns, the adaptive zone into which modern birds have diversified since the Cretaceous may still offer opportunities for diversification.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jetz, W -- Thomas, G H -- Joy, J B -- Hartmann, K -- Mooers, A O -- England -- Nature. 2012 Nov 15;491(7424):444-8. doi: 10.1038/nature11631. Epub 2012 Oct 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, Connecticut 06520-8106, USA. walter.jetz@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23123857" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Birds/*classification/genetics/physiology ; *Phylogeny
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    The ability of potassium solubilizing rhizo-bacteria isolated from maize rhizosphere for microbial fertilizer (2018)
    Institute of Physics (IOP)
    Details
    Publication Date: 2018-12-08
    Description: Potassium is an essential macro nutrient for plants but most of them are not available because it is fixed in the soil in primary or secondary silicate minerals such as K-feldspar or 2:1 type clay form, so trigger the excessive use of potassium fertilizer that can damage the environment. Potassium solubilizing rhizo-bacteria (KSRB) which is a microbial fertilizer can overcome this problem by changing the non available into available soilpotassium. This is a promising strategy for improving of plant absorption of potassium and reducing the use of chemical fertilizers. The objective of this study was to evaluated the ability of fifteen KSRB isolates that isolated from maize rhizosphere to dissolve potassium. Potassium dissolution activity by KSRB isolate was observed using Khandeparkar’s selection ratio (modified) by measuring the diameter of the clear zone around the colony compared with the colony diameter on Aleksandrov solid medium (K-feldspar powder as sole potassium source) ...
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
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  • 3
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    Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-04
    Description: Primer IDs ( pIDs ) are random oligonucleotide tags used in next-generation sequencing to identify sequences that originate from the same template. These tags are produced by degenerate primers during the reverse transcription of RNA molecules into cDNA. The use of pIDs helps to track the number of RNA molecules carried through amplification and sequencing, and allows resolution of inconsistencies between reads sharing a pID. Three potential issues complicate the above applications. First, multiple cDNAs may share a pID by chance; we found that while preventing any cDNAs from sharing a pID may be unfeasible, it is still practical to limit the number of these collisions. Secondly, a pID must be observed in at least three sequences to allow error correction; as such, pIDs observed only one or two times must be rejected. If the sequencing product contains copies from a high number of RT templates but produces few reads, our findings indicate that rejecting such pIDs will discard a great deal of data. Thirdly, the use of pIDs could influence amplification and sequencing. We examined the effects of several intrinsic and extrinsic factors on sequencing reads at both the individual and ensemble level.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-05
    Description: Viral phylogenetic methods contribute to understanding how HIV spreads in populations, and thereby help guide the design of prevention interventions. So far, most analyses have been applied to well-sampled concentrated HIV-1 epidemics in wealthy countries. To direct the use of phylogenetic tools to where the impact of HIV-1 is greatest, the Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium generates full-genome viral sequences from across sub-Saharan Africa. Analyzing these data presents new challenges, since epidemics are principally driven by heterosexual transmission and a smaller fraction of cases is sampled. Here, we show that viral phylogenetic tools can be adapted and used to estimate epidemiological quantities of central importance to HIV-1 prevention in sub-Saharan Africa. We used a community-wide methods comparison exercise on simulated data, where participants were blinded to the true dynamics they were inferring. Two distinct simulations captured generalized HIV-1 epidemics, before and after a large community-level intervention that reduced infection levels. Five research groups participated. Structured coalescent modeling approaches were most successful: phylogenetic estimates of HIV-1 incidence, incidence reductions, and the proportion of transmissions from individuals in their first 3 months of infection correlated with the true values (Pearson correlation 〉 90%), with small bias. However, on some simulations, true values were markedly outside reported confidence or credibility intervals. The blinded comparison revealed current limits and strengths in using HIV phylogenetics in challenging settings, provided benchmarks for future methods’ development, and supports using the latest generation of phylogenetic tools to advance HIV surveillance and prevention.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    The global diversity of birds in space and time (2012)
    Springer Nature
    Details
    Publication Date: 2012-10-31
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 6
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    Predominance of squid (Gonatus spp.) in the diet of Greenland halibut (Reinhardtius hippoglossoides) on the deep slope of the northeast Newfoundland continental shelf (1998)
    Elsevier
    In:  Fisheries Research, 36 (2-3). pp. 267-273.
    Details
    Publication Date: 2021-04-29
    Description: The feeding ecology of Greenland halibut (Reinhardtius hippoglossoides) on the deep slope of the northeast Newfoundland continental shelf was investigated based on stomach analysis. Stomach samples were collected from the spring 1992 Canadian bottom trawl fishery at depths of 1000–1250 m. The squid, Gonatus spp., predominated in the diet, representing the first known instance of reliance of Greenland halibut upon this bathypelagic squid as prey in Canadian waters. A change from predation primarily upon pelagic prey, reported in earlier studies, may be related to annual variability in abundance and distribution of both Greenland halibut and its principal pelagic fish prey species, capelin (Mallotus villosus). Seasonal effects may account for the absence of epipelagic, juvenile Gonatus spp. from the diet. There was a linear size relationship in observed predation which may reflect a common size-related depth distribution pattern between predator and prey or, more likely, prey selectivity. At larger sizes, Greenland halibut switched from Gonatus spp. to groundfish as its principal prey. The importance of Gonatus spp. in the deep continental slope trophic web is reviewed.
    Type: Article , PeerReviewed
    Format: text
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