@article{FischerMayerSchollImholtetal.2018,
  author    = {Fischer, Stefan and Mayer-Scholl, Anne and Imholt, Christian and Spierling, Nastasja G. and Heuser, Elisa and Schmidt, Sabrina and Reil, Daniela and Rosenfeld, Ulrike M. and Jacob, Jens and N{\"o}ckler, Karsten and Ulrich, Rainer G.},
  title     = {Leptospira genomospecies and sequence type prevalence in small mammal populations in Germany},
  series = {Vector-Borne and Zoonotic Diseases},
  volume    = {18},
  journal   = {Vector-Borne and Zoonotic Diseases},
  number    = {4},
  publisher = {Liebert},
  address   = {New Rochelle},
  issn      = {1530-3667},
  doi       = {10.1089/vbz.2017.2140},
  pages     = {188 -- 199},
  year      = {2018},
  abstract  = {Leptospirosis is a worldwide emerging infectious disease caused by zoonotic bacteria of the genus Leptospira. Numerous mammals, including domestic and companion animals, can be infected by Leptospira spp., but rodents and other small mammals are considered the main reservoir. The annual number of recorded human leptospirosis cases in Germany (2001-2016) was 25-166. Field fever outbreaks in strawberry pickers, due to infection with Leptospira kirschneri serovar Grippotyphosa, were reported in 2007 and 2014. To identify the most commonly occurring Leptospira genomospecies, sequence types (STs), and their small mammal host specificity, a monitoring study was performed during 2010-2014 in four federal states of Germany. Initial screening of kidney tissues of 3,950 animals by PCR targeting the lipl32 gene revealed 435 rodents of 6 species and 89 shrews of three species positive for leptospiral DNA. PCR-based analyses resulted in the identification of the genomospecies L. kirschneri (62.7\%), Leptospira interrogans (28.3\%), and Leptospira borgpetersenii (9.0\%), which are represented by four, one, and two STs, respectively. The average Leptospira prevalence was highest (approximate to 30\%) in common voles (Microtus arvalis) and field voles (Microtus agrestis). Both species were exclusively infected with L. kirschneri. In contrast, in bank voles (Myodes glareolus) and yellow-necked mice (Apodemus flavicollis), DNA of all three genomospecies was detected, and in common shrews (Sorex araneus) DNA of L. kirschneri and L. borgpetersenii was identified. The association between individual infection status and demographic factors varied between species; infection status was always positively correlated to body weight. In conclusion, the study confirmed a broad geographical distribution of Leptospira in small mammals and suggested an important public health relevance of common and field voles as reservoirs of L. kirschneri. Furthermore, the investigations identified seasonal, habitat-related, as well as individual influences on Leptospira prevalence in small mammals that might impact public health.},
  language  = {en}
}
@article{CornettiValenteDunningetal.2015,
  author    = {Cornetti, Luca and Valente, Luis M. and Dunning, Luke T. and Quan, Xueping and Black, Richard A. and Hebert, Olivier and Savolainen, Vincent},
  title     = {The Genome of the "Great Speciator" Provides Insights into Bird Diversification},
  series = {Genome biology and evolution},
  volume    = {7},
  journal   = {Genome biology and evolution},
  number    = {9},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1759-6653},
  doi       = {10.1093/gbe/evv168},
  pages     = {2680 -- 2691},
  year      = {2015},
  abstract  = {Among birds, white-eyes (genusZosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the 'great speciator." The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation.},
  language  = {en}
}
@article{MarionMcInernyPageletal.2012,
  author    = {Marion, Glenn and McInerny, Greg J. and Pagel, J{\"o}rn and Catterall, Stephen and Cook, Alex R. and Hartig, Florian and O\&rsquo, and Hara, Robert B.},
  title     = {Parameter and uncertainty estimation for process-oriented population and distribution models: data, statistics and the niche},
  series = {JOURNAL OF BIOGEOGRAPHY},
  volume    = {39},
  journal   = {JOURNAL OF BIOGEOGRAPHY},
  number    = {12},
  publisher = {WILEY-BLACKWELL},
  address   = {HOBOKEN},
  issn      = {0305-0270},
  doi       = {10.1111/j.1365-2699.2012.02772.x},
  pages     = {2225 -- 2239},
  year      = {2012},
  abstract  = {The spatial distribution of a species is determined by dynamic processes such as reproduction, mortality and dispersal. Conventional static species distribution models (SDMs) do not incorporate these processes explicitly. This limits their applicability, particularly for non-equilibrium situations such as invasions or climate change. In this paper we show how dynamic SDMs can be formulated and fitted to data within a Bayesian framework. Our focus is on discrete state-space Markov process models which provide a flexible framework to account for stochasticity in key demographic processes, including dispersal, growth and competition. We show how to construct likelihood functions for such models (both discrete and continuous time versions) and how these can be combined with suitable observation models to conduct Bayesian parameter inference using computational techniques such as Markov chain Monte Carlo. We illustrate the current state-of-the-art with three contrasting examples using both simulated and empirical data. The use of simulated data allows the robustness of the methods to be tested with respect to deficiencies in both data and model. These examples show how mechanistic understanding of the processes that determine distribution and abundance can be combined with different sources of information at a range of spatial and temporal scales. Application of such techniques will enable more reliable inference and projections, e.g. under future climate change scenarios than is possible with purely correlative approaches. Conversely, confronting such process-oriented niche models with abundance and distribution data will test current understanding and may ultimately feedback to improve underlying ecological theory.},
  language  = {en}
}
@misc{NathanHorvitzHeetal.2011,
  author    = {Nathan, Ran and Horvitz, Nir and He, Yanping and Kuparinen, Anna and Schurr, Frank Martin and Katul, Gabriel G.},
  title     = {Spread of North American wind-dispersed trees in future environments},
  series = {Ecology letters},
  volume    = {14},
  journal   = {Ecology letters},
  number    = {3},
  publisher = {Wiley-Blackwell},
  address   = {Malden},
  issn      = {1461-023X},
  doi       = {10.1111/j.1461-0248.2010.01573.x},
  pages     = {211 -- 219},
  year      = {2011},
  abstract  = {P>Despite ample research, understanding plant spread and predicting their ability to track projected climate changes remain a formidable challenge to be confronted. We modelled the spread of North American wind-dispersed trees in current and future (c. 2060) conditions, accounting for variation in 10 key dispersal, demographic and environmental factors affecting population spread. Predicted spread rates vary substantially among 12 study species, primarily due to inter-specific variation in maturation age, fecundity and seed terminal velocity. Future spread is predicted to be faster if atmospheric CO2 enrichment would increase fecundity and advance maturation, irrespective of the projected changes in mean surface windspeed. Yet, for only a few species, predicted wind-driven spread will match future climate changes, conditioned on seed abscission occurring only in strong winds and environmental conditions favouring high survival of the farthest-dispersed seeds. Because such conditions are unlikely, North American wind-dispersed trees are expected to lag behind the projected climate range shift.},
  language  = {en}
}