Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
- MeSH
- Bacteroidetes classification genetics virology MeSH
- Bacteriophages classification genetics MeSH
- DNA, Viral genetics MeSH
- Feces virology MeSH
- Phylogeny MeSH
- Phylogeography MeSH
- Genetic Variation MeSH
- Biological Coevolution * MeSH
- Humans MeSH
- Primates virology MeSH
- Gastrointestinal Microbiome * MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Here, we present a study of the Pipistrellus pipistrellus species complex, a highly diversified bat group with a radiation centre in the Mediterranean biodiversity hotspot. The study sample comprised 583 animals from 118 localities representatively covering the bats' range in the western Palearctic. We used fast-evolving markers (the mitochondrial D-loop sequence and 11 nuclear microsatellites) to describe the phylogeography, demography and population structure of this model taxon and address details of its diversification. The overall pattern within this group includes a mosaic of phylogenetically basal, often morphologically distant, relatively small and mostly allopatric demes in the Mediterranean Basin, as well as two sympatric sibling species in the large continental part of the range. The southern populations exhibit constant size, whereas northern populations show a demographic trend of growth associated with range expansion during the Pleistocene climate oscillations. There is evidence of isolation by distance and female philopatry in P. pipistrellus sensu stricto. Although the northern populations are reproductively isolated, we detected introgression events among several Mediterranean lineages. This pattern implies incomplete establishment of reproductive isolating mechanisms in these populations as well as the existence of a past reinforcement stage in the continental siblings. The occurrence of reticulations in the radiation centre among morphologically and ecologically derived relict demes suggests that adaptive unequal gene exchange within hybridizing populations could play a role in speciation and adaptive radiation within this group.
- MeSH
- Chiroptera classification genetics MeSH
- Phylogeography methods MeSH
- Microsatellite Repeats genetics MeSH
- DNA, Mitochondrial genetics MeSH
- Genetics, Population methods MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Mediterranean Region MeSH
The theory of classical and cryptic Pleistocene refugia is based mainly on historical changes in temperature, and the refugia are usually defined within a latitudinal gradient. However, the gradient of oceanic-continental climate (i.e. longitudinal) was also significantly variable during glacial cycles with important biotic consequences. Range-wide phylogeography of the European ground squirrel (EGS) was used to interpret the evolutionary and palaeogeographical history of the species in Europe and to shed light on its glacial-interglacial dynamic. The EGS is a steppe-inhabiting species and the westernmost member of the genus in the Palaearctic region. We have analysed 915 specimens throughout the present natural range by employing mitochondrial DNA sequences (cytochrome b gene) and 12 nuclear microsatellite markers. The reconstructed phylogeography divides the species into two main geographical groups, with deep substructuring within both groups. Bulgaria is the centre of the ancestral area, and it also has the highest genetic diversity within the species. The northernmost group of the EGS survived in the southern part of Pannonia throughout several glacial-interglacial cycles. Animals from this population probably repeatedly colonized areas further to the north and west during the glacial periods, while in the interglacial periods, the EGS distribution contracted back to this Pannonian refugium. The EGS thus represents a species with a glacial expansion/interglacial contraction palaeogeographical dynamics, and the Pannonian and southeastern Balkanian steppes are supported as cryptic refugia of continental climate during Pleistocene interglacials.
- MeSH
- Cytochromes b genetics MeSH
- Phylogeny * MeSH
- Phylogeography MeSH
- Genetic Variation MeSH
- Ice Cover * MeSH
- Microsatellite Repeats genetics MeSH
- DNA, Mitochondrial genetics MeSH
- Evolution, Molecular MeSH
- Molecular Sequence Data MeSH
- Climate MeSH
- Genetics, Population * MeSH
- Sciuridae genetics physiology MeSH
- Sequence Analysis, DNA MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Europe MeSH
Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) are the principal vectors of Leishmania spp. (Kinetoplastida: Trypanosomatidae) worldwide. The subgenus Adlerius is taxonomically challenging and currently comprises about 20 species with a wide geographic distribution from eastern Asia to southeastern Europe. Some species are confirmed or suspected vectors of Leishmania donovani/infantum, L. major, and L. tropica, and are thus of high medical and veterinary relevance. A single record of Phlebotomus (Adlerius) simici in Austria from 2018 marks its sporadic northernmost and westernmost occurrence, with the origin of its appearance remaining unclear. To better understand Adlerius diversification and particularly post-glacial spread of Ph. simici to northern parts of Europe, we combined phylogenetic analyses with climatic suitability modelling. Divergence time estimates well supported the currently observed geographic distribution of the studied species and revealed several taxonomic challenges in the subgenus. We clearly delineated three distinct genetic and geographic Ph. simici lineages and phylogeographically assessed diversification that were well supported by climatic models. This study provides a comprehensive phylogenetic analysis of the subgenus Adlerius, enhancing our understanding of the diversification in relation to changing climate of this understudied group, and we present new insights into the post-glacial spread of Ph. simici, a suspected vector of L. infantum.
- MeSH
- Phylogeny * MeSH
- Phylogeography * MeSH
- Insect Vectors genetics classification MeSH
- Phlebotomus * classification genetics MeSH
- Climate MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Europe MeSH
We examined the global phylogeography of gypsy moth (Lymantria dispar L.) using molecular data based on mitochondrial and nuclear genes. Populations from all biogeographic regions of the native and introduced range of L. dispar, were sampled to fully document intraspecific and subspecies variation, identify potential cryptic species, and to clarify the relationships among major phylogeographic lineages. We recovered three major mtDNA lineages of L. dispar: Transcaucasia; East Asia + Japan; and Europe + Central Asia. The circumscription of these lineages is only partially consistent with the current taxonomic concept (i.e., L. dispar dispar; L. dispar asiatica; L. dispar japonica), with the following important discrepancies: (1) north-central Asian populations, including topotypical populations of L. dispar asiatica, may be more closely related to European rather than Asian segregates, which would require the synonymization of the taxon asiatica and establishment of a new name; (2) the Japanese populations (L. d. japonica) are not distinct from east Asian populations; (3) the presence of a distinct, unnamed mitogenomic lineage endemic to the Trancaucasus region. We demonstrated that the population from Transcaucasia contains the highest mitochondrial haplotype diversity among L. dispar, potentially indicative of an ancestral area for the entire dispar-group. Our study corroborates the endemic Hokkaido, Japan taxon Lymantria umbrosa (Butler) as the sister group to all other L. dispar populations, but the applicability of the names umbrosa versus hokkaidoensis Goldschmidt needs to be re-evaluated. The ancestral area analysis suggest that Japan was likely colonized via Sakhalin ∼1 Mya, in contrast to previous studies which have suggested colonization of the Japanese archipelago via the Korean Peninsula. Lastly, mitogenomic variation within L. dispar is incongruent with phylogenies based on nuclear DNA, as nDNA gene phylogenies did not recover the three major mtDNA lineages, and also failed to recover L. dispar and L. umbrosa as reciprocally monophyletic.
- MeSH
- Bayes Theorem MeSH
- Biological Evolution * MeSH
- Cell Nucleus genetics MeSH
- Phylogeny MeSH
- Phylogeography * MeSH
- Genome, Mitochondrial MeSH
- Haplotypes genetics MeSH
- DNA, Mitochondrial genetics MeSH
- Moths classification genetics MeSH
- Likelihood Functions MeSH
- DNA Barcoding, Taxonomic MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Understanding how species responded to past climate change can provide information about how they may respond to the current global warming. Here we show how a European reptile species responded to the last natural global warming event at the Pleistocene-Holocene transition that led to the Holocene climatic optimum approximately 5000-8000 years ago. The Aesculapian snake, Zamenis longissimus, is a thermophilous species whose present-day distribution in the southern half of Europe is a remnant of much wider range during the Holocene climatic optimum when populations occurred as far north as Denmark. These northern populations went extinct as the climate cooled, and presently the species is extinct from all central Europe, except few relic populations in locally suitable microhabitats in Germany and the Czech Republic. Our phylogenetic and demographic analyses identified two major clades that expanded from their respective western and eastern refugia after the last glacial maximum (18,000-23,000 years ago) and contributed approximately equally to the present range. Snakes from the relic northern populations carried the Eastern clade, showing that it was primarily the snakes from the eastern, probably Balkan, refugium that occupied the central and northern Europe during the Holocene climatic optimum. Two small, deep-branching clades were identified in near the Black Sea and in Greece. These clades provide evidence for two additional refugia, which did not successfully contribute to the colonization of Europe. If, as our results suggest, some populations responded to the mid-Holocene global warming by shifting their ranges further north than other populations of the same species, knowing what populations were able to expand in different species may provide information about what populations will be important for the species' ability to cope with the current global warming.
- MeSH
- Colubridae classification genetics MeSH
- Phylogeny MeSH
- Phylogeography MeSH
- Haplotypes MeSH
- DNA, Mitochondrial genetics MeSH
- Evolution, Molecular MeSH
- Climate MeSH
- Likelihood Functions MeSH
- Sequence Analysis, DNA MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Europe MeSH
Pleistocene glaciations had significant effects on the distribution and evolution of species inhabiting the Holarctic region. Phylogeographic studies concerning the entire region are still rare. Here, we compared global phylogeographic patterns of one boreo-montane and one boreo-temperate butterflies with largely overlapping distribution ranges across the Northern Hemisphere, but with different levels of range fragmentation and food specialization. We reconstructed the global phylogeographic history of the boreo-montane specialist Boloria eunomia (n = 223) and of the boreo-temperate generalist Boloria selene (n = 106) based on mitochondrial and nuclear DNA markers, and with species distribution modelling (SDM). According to the genetic structures obtained, both species show a Siberian origin and considerable split among populations from Nearctic and Palaearctic regions. According to SDMs and molecular data, both butterflies could inhabit vast areas during the moderate glacials. In the case of B. selene, high haplotype diversity and low geographic structure suggest long-lasting interconnected gene flow among populations. A stronger geographic structuring between populations was identified in the specialist B. eunomia, presumably due to the less widespread, heterogeneously distributed food resources, associated with cooler and more humid climatic conditions. Populations of both species show opposite patterns across major parts of North America and in the case of B. eunomia also across Asia. Our data underline the relevance to cover entire distribution ranges to reconstruct the correct phylogeographic history of species.
Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease.
- MeSH
- Dysentery, Bacillary epidemiology history microbiology MeSH
- Drug Resistance, Bacterial MeSH
- Global Health MeSH
- History, 19th Century MeSH
- History, 20th Century MeSH
- History, 21st Century MeSH
- Phylogeography * MeSH
- Genome, Bacterial MeSH
- Humans MeSH
- Molecular Epidemiology MeSH
- Evolution, Molecular * MeSH
- Sequence Analysis, DNA MeSH
- Serogroup * MeSH
- Shigella dysenteriae classification genetics isolation & purification MeSH
- Check Tag
- History, 19th Century MeSH
- History, 20th Century MeSH
- History, 21st Century MeSH
- Humans MeSH
- Publication type
- Journal Article MeSH
- Historical Article MeSH
The isolation of populations in the Iberian, Italian and Balkan peninsulas during the ice ages define four main paradigms that explain much of the known distribution of intraspecific genetic diversity in Europe. In this study we investigated the phylogeography of a wide-spread bat species, the bent-winged bat, Miniopterus schreibersii around the Mediterranean basin and in the Caucasus. Environmental Niche Modeling (ENM) analysis was applied to predict both the current distribution of the species and its distribution during the last glacial maximum (LGM). The combination of genetics and ENM results suggest that the populations of M. schreibersii in Europe, the Caucasus and Anatolia went extinct during the LGM, and the refugium for the species was a relatively small area to the east of the Levantine Sea, corresponding to the Mediterranean coasts of present-day Syria, Lebanon, Israel, and northeastern and northwestern Egypt. Subsequently the species first repopulated Anatolia, diversified there, and afterwards expanded into the Caucasus, continental Europe and North Africa after the end of the LGM. The fossil record in Iberia and the ENM results indicate continuous presence of Miniopterus in this peninsula that most probably was related to the Maghrebian lineage during the LGM, which did not persist afterwards. Using our results combined with similar findings in previous studies, we propose a new paradigm explaining the general distribution of genetic diversity in Europe involving the recolonization of the continent, with the main contribution from refugial populations in Anatolia and the Middle East. The study shows how genetics and ENM approaches can complement each other in providing a more detailed picture of intraspecific evolution.
- MeSH
- Models, Biological MeSH
- Chiroptera classification genetics MeSH
- Phylogeny MeSH
- Phylogeography MeSH
- Genetic Variation MeSH
- DNA, Mitochondrial isolation & purification metabolism MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Balkan Peninsula MeSH
- Europe MeSH
- Africa, Northern MeSH
- Middle East MeSH
Over the years, researchers have used presumptively neutral molecular variation to infer the origins of current species' distributions in northern latitudes (especially Europe). However, several reported examples of genic and chromosomal replacements suggest that end-glacial colonizations of particular northern areas may have involved genetic input from different source populations at different times, coupled with competition and selection. We investigate the functional consequences of differences between two bank vole (Clethrionomys glareolus) haemoglobins deriving from different glacial refugia, one of which partially replaced the other in Britain during end-glacial climate warming. This allows us to examine their adaptive divergence and hence a possible role of selection in the replacement. We determine the amino acid substitution Ser52Cys in the major expressed β-globin gene as the allelic difference. We use structural modelling to reveal that the protein environment renders the 52Cys thiol a highly reactive functional group and we show its reactivity in vitro. We demonstrate that possessing the reactive thiol in haemoglobin increases the resistance of bank vole erythrocytes to oxidative stress. Our study thus provides striking evidence for physiological differences between products of genic variants that spread at the expense of one another during colonization of an area from different glacial refugia.
- MeSH
- Arvicolinae classification genetics metabolism MeSH
- Phylogeography MeSH
- Genetic Variation MeSH
- Hemoglobins chemistry genetics metabolism MeSH
- Molecular Sequence Data MeSH
- Amino Acid Substitution MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- United Kingdom MeSH
