High conservation combined with high plasticity: genomics and evolution of Borrelia bavariensis

BackgroundBorrelia bavariensis is one of the agents of Lyme Borreliosis (or Lyme disease) in Eurasia. The genome of the Borrelia burgdorferi sensu lato species complex, that includes B. bavariensis, is known to be very complex and fragmented making the assembly of whole genomes with next-generation sequencing data a challenge.ResultsWe present a genome reconstruction for 33 B. bavariensis isolates from Eurasia based on long-read (Pacific Bioscience, for three isolates) and short-read (Illumina) data. We show that the combination of both sequencing techniques allows proper genome reconstruction of all plasmids in most cases but use of a very close reference is necessary when only short-read sequencing data is available. B. bavariensis genomes combine a high degree of genetic conservation with high plasticity: all isolates share the main chromosome and five plasmids, but the repertoire of other plasmids is highly variable. In addition to plasmid losses and gains through horizontal transfer, we also observe several fusions between plasmids. Although European isolates of B. bavariensis have little diversity in genome content, there is some geographic structure to this variation. In contrast, each Asian isolate has a unique plasmid repertoire and we observe no geographically based differences between Japanese and Russian isolates. Comparing the genomes of Asian and European populations of B. bavariensis suggests that some genes which are markedly different between the two populations may be good candidates for adaptation to the tick vector, (Ixodes ricinus in Europe and I. persulcatus in Asia).ConclusionsWe present the characterization of genomes of a large sample of B. bavariensis isolates and show that their plasmid content is highly variable. This study opens the way for genomic studies seeking to understand host and vector adaptation as well as human pathogenicity in Eurasian Lyme Borreliosis agents.Peer reviewe

Can Life History Trade-Offs Explain the Evolution of Short Stature in Human Pygmies? A Response to Migliano et al. (2007)

Walker et al. [“Growth rates and life histories in twenty-two small scale societies,” Am. J. Hum. Biol. 18:295–311 (2006)] used life history theory to develop an innovative explanation for human diversity in stature. Short stature could have been selected for in some human populations as a result of the advantage of an earlier growth cessation and earlier reproduction in a context of high mortality. Migliano et al. [“Life history trade-offs explain the evolution of human pygmies,” Proc. Natl. Acad. Sci. USA 104:20,216–20,219 (2007)] recently published an important article that tested this hypothesis to explain short stature in human pygmy populations. However innovative this work may be, we believe that some of the data and results presented are controversial if not questionable. As problematic points we note (1) the use of an arbitrary threshold of height (155 cm) to categorize populations into pygmies and nonpygmies; (2) the use of demographic data from Philippine pygmy groups that have experienced dramatic cultural and environmental changes in the last 20 years, and (3) the use of demographic data concerning African pygmy groups because good systematic data on these groups are not available. Finally, we report here mathematical errors and loopholes in the optimization model developed by Migliano and colleagues. In this paper we suggest alternative trade-offs that can be used to explain Migliano’s results on more reliable bases

The role of GHR and IGF1 genes in the genetic determination of African pygmies’ short stature

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Host dispersal shapes the population structure of a tick-borne bacterial pathogen

Birds are hosts for several zoonotic pathogens. Because of their high mobility, especially of longdistance migrants, birds can disperse these pathogens, affecting their distribution and phylogeography. We focused on Borrelia burgdorferi sensu lato, which includes the causative agents of Lyme borreliosis, as an example for tick-borne pathogens, to address the role of birds as propagation hosts of zoonotic agents at a large geographical scale. We collected ticks from passerine birds in 11 European countries. B. burgdorferi s.l. prevalence in Ixodes spp. was 37% and increased with latitude. The fieldfare Turdus pilaris and the blackbird T. merula carried ticks with the highest Borrelia prevalence (92 and 58%, respectively), whereas robin Erithacus rubecula ticks were the least infected (3.8%). Borrelia garinii was the most prevalent genospecies (61%), followed by B. valaisiana (24%), B. afzelii (9%), B. turdi (5%) and B. lusitaniae (0.5%). A novel Borrelia genospecies “Candidatus Borrelia aligera” was also detected. Multilocus sequence typing (MLST) analysis of B. garinii isolates together with the global collection of B. garinii genotypes obtained from the Borrelia MLST public database revealed that: (a) there was little overlap among genotypes from different continents, (b) there was no geographical structuring within Europe, and (c) there was no evident association pattern detectable among B. garinii genotypes from ticks feeding on birds, questing ticks or human isolates. These findings strengthen the hypothesis that the population structure and evolutionary biology of tick-borne pathogens are shaped by their host associations and the movement patterns of these hosts.This study received financial support from Fundação para a Ciência e a Tecnologia by the strategic program of MARE (MARE ‐ UID/MAR/04292/2013) and the fellowship to Ana Cláudia Norte (SFRH/BPD/108197/2015), and the Portuguese National Institute of Health. Raivo Mänd, Tomi Trilar, Tapio Eeva, Tomas Grim and Dieter Heylen were supported by the Estonian Research Council (research grant # IUT34‐8), the Slovenian Research Agency ‐programme “Communities, relations and communications in the ecosystems” (No. P1‐0255), the Academy of Finland (project 265859), the Internal Grant Agency of Palacky University (PrF_2014_018, PrF_2015_018, PrF_2013_018) and the Marie Sklodowska‐Curie Actions (EU‐Horizon 2020, Individual Global Fellowship, project no 799609), respectively

Host dispersal shapes the population structure of a tick‐borne bacterial pathogen

Abstract Birds are hosts for several zoonotic pathogens. Because of their high mobility, especially of longdistance migrants, birds can disperse these pathogens, affecting their distribution and phylogeography. We focused on Borrelia burgdorferi sensu lato, which includes the causative agents of Lyme borreliosis, as an example for tick‐borne pathogens, to address the role of birds as propagation hosts of zoonotic agents at a large geographical scale. We collected ticks from passerine birds in 11 European countries. B. burgdorferi s.l. prevalence in Ixodes spp. was 37% and increased with latitude. The fieldfare Turdus pilaris and the blackbird T. merula carried ticks with the highest Borrelia prevalence (92 and 58%, respectively), whereas robin Erithacus rubecula ticks were the least infected (3.8%). Borrelia garinii was the most prevalent genospecies (61%), followed by B. valaisiana (24%), B. afzelii (9%), B. turdi (5%) and B. lusitaniae (0.5%). A novel Borrelia genospecies “Candidatus Borrelia aligera” was also detected. Multilocus sequence typing (MLST) analysis of B. garinii isolates together with the global collection of B. garinii genotypes obtained from the Borrelia MLST public database revealed that: (a) there was little overlap among genotypes from different continents, (b) there was no geographical structuring within Europe, and (c) there was no evident association pattern detectable among B. garinii genotypes from ticks feeding on birds, questing ticks or human isolates. These findings strengthen the hypothesis that the population structure and evolutionary biology of tick‐borne pathogens are shaped by their host associations and the movement patterns of these hosts