Phylogeography of the Pygmy Rain Frog (Pristimantis ridens) across the lowland wet forests of isthmian Central America

We used a phylogeographic approach to elucidate the evolutionary history of a lineage of frogs, known as Pristimantis (formerly Eleutherodactylus) ridens (Anura: Brachycephalidae), restricted to the wet forests occurring along the Caribbean versant of isthmian Central America as well as the disjunct wet forest on the Pacific slope of Costa Rica. We placed our phylogeographic study of P. ridens within a larger molecular phylogenetic analysis of Central American Pristimantis. All phylogenetic inferences were based on a 1455 base pair fragment of mitochondrial DNA, containing the complete ND2 gene and five flanking tRNA genes. Our reconstruction of the intraspecific phylogeny of P. ridens yielded a basal trichotomy dating to an estimated 12+ million years ago (Ma), consisting of central Panama, western Panama, and Costa Rica plus Honduras. Thus, the presence of P. ridens appears to predate the completion of the Isthmus 3.1Ma. Using a parametric bootstrap (SOWH) test, we evaluated four a priori zoogeographic hypotheses for the origin and spread of P. ridens. This analysis suggested that the P. ridens populations on the Caribbean versant of Costa Rica were established by Pacific versant ancestors only recently, in contrast to the very old lineages found in Panama. Our results support a model of Miocene colonization, long-term geographic stasis, followed by rapid dispersal across the Caribbean lowlands during the Pliocene or Pleistocene.     

Amblyomma variegatum and associated diseases in the Caribbean: strategies for control and eradication in Guadeloupe

Amblyomma variegatum, introduced into Guadelopue 150 years ago, has recently spread in the Lesser Antilles and threatens North America. Two important diseases are associated with the tick: heartwater and dermatophilosis. Heartwater occurs in Guadeloupe, Marie-Galante and Antigua; acute dermatophilosis exists almost everywhere the tick is present. Both are very pathogenic for upgraded or newly-infested cattle. After 15 years of A. variegatum control in Guadeloupe, a balance is established between a tick population maintained at a low level by spraying acaricides and an animal population either completely resistant to heartwater and dermatophilosis (creole cattle) or regularly treated against ticks (upgraded cattle). An eradication campaign against A. variegatum in Guadeloupe, to avoid the spread of the associated diseases, appears technically difficult but possible, economically profitable, but socially completely utopian. We suggest for Guadeloupe a reinforced control of the tick with a persistent acaricide, hoping that a general decrease of the tick infestation rate on cattle will eliminate heartwater and acute dermatophilosis.     

The coevolution of ixodid ticks and terrestrial vertebrates

Paleontologic and zoogeographic data speak in favour of Mesozoic origin of ixodid ticks. The absence of strict restrictions for the feeding on unusual species of hosts has caused the domination of polyphagy and oligophagy over monophagy among ixodid ticks. The same peculiarities of ixodid ecology are responsible for a restricted part or absence of phylogenetic parallelism with hosts in their evolution. Primary food relations with reptiles are, apparently, preserved only in the genus Aponomma and in many species of Amblyomma while hosts for most species of other genera are mammals and, to a lesser extent, birds. The number of potential hosts in these species can be much greater than that of real ones. Restrictions in the distribution of some species are connected rather with direct effect of unfavourable environmental factors on their nonparasitic stages of the life cycle than with the absence of suitable hosts. During the evolution of natural landscapes and at a shorter stages under the influence of successions or anthropogenic factors ixodids easily adapt themselves to feeding on new species of hosts. So the differentiation of primary and secondary hosts of these parasites is rather difficult.     

Human endogenous retroviruses in the primate lineage and their influence on host genomes

Primates emerged about 60 million years ago. Since that time various primate-targeting retroviruses have integrated in the germ line of primate species, and some drifted to fixation. After germ line fixation, continued activity of proviruses resulted in intragenomic spread of so-called endogenous retroviruses (ERVs). Variant ERVs emerged, amplified in the genome and profoundly altered genome structures and potentially functionality. Importantly, ERVs are genome modifiers of exogenous origin. The human genome contains about 8% of sequences of retroviral origin. The human ERVs (HERVs) comprise many distinct families that amplified to copy numbers of up to several thousand. We review here the evolution of several well-characterized HERV families in the human lineage since initial germ line fixation. It is apparent that endogenous retroviruses profoundly affected the genomes of species in the evolutionary lineage leading to Homo sapiens.     

The incidence of the tick parasite Ixodes uriae in Kittiwake Rissa tridactyla colonies in relation to the age of the colony, and a mechanism of infecting new colonies

Kittiwakes Rissa tridactyla (683 chicks and 64 adults) were examined for ectoparasites in three breeding areas: Isle of May (Firth of Forth, Scotland; eight colonies of approximately known age of occupation on natural sites), North Shields and Gateshead (Tyne and Wear, England; well established colonies of known age on buildings). All the 208 ticks collected were Ixodes uriae. On the Isle of May, a colony which had only been established for 7 years was already infested by ticks. Tick incidence increased significantly with the length of colonization of the area during the first 30 years. Age of colonization did not have an effect after 30 years. In Gateshead only a single adult among the 127 birds examined had a tick. No ticks were found on the 106 chicks born at North Shields checked in 1987 or in 1988. However, among nine visiting newly-fledged chicks from neighbouring colonies caught at the North Shields colony, six had either ticks or scars of previous infestation. Some visiting chicks remained for several days in the host colony and were even fed by the owners of visited nests. Ixodes uriae may thus spread from one colony to another during visits of newly-fledged infested chicks to neighbouring colonies. The absence of any infestation in old colonies (38 years in North Shields and 17 years in Gateshead) on buildings that are regularly visited by newly fledged infested chicks, suggests that buildings may lack the rock refuges necessary for tick survival from one year to the next. In this respect Kittiwake colonies on buildings are rather atypical.     

Reflections on a journey: a retrospective of the ISCB Student Council symposium series

This article describes the motivation, origin and evolution of the student symposia series organised by the ISCB Student Council. The meeting series started thirteen years ago in Madrid and has spread to four continents. The article concludes with the highlights of the most recent edition of annual Student Council Symposium held in conjunction with the 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology, in Prague, in July 2017.     

The impact of human conflict on the genetics of Mastomys natalensis and Lassa virus in West Africa

Environmental changes have been shown to play an important role in the emergence of new human diseases of zoonotic origin. The contribution of social factors to their spread, especially conflicts followed by mass movement of populations, has not been extensively investigated. Here we reveal the effects of civil war on the phylogeography of a zoonotic emerging infectious disease by concomitantly studying the population structure, evolution and demography of Lassa virus and its natural reservoir, the rodent Mastomys natalensis, in Guinea, West Africa. Analysis of nucleoprotein gene sequences enabled us to reconstruct the evolutionary history of Lassa virus, which appeared 750 to 900 years ago in Nigeria and only recently spread across western Africa (170 years ago). Bayesian demographic inferences revealed that both the host and the virus populations have gone recently through severe genetic bottlenecks. The timing of these events matches civil war-related mass movements of refugees and accompanying environmental degradation. Forest and habitat destruction and human predation of the natural reservoir are likely explanations for the sharp decline observed in the rodent populations, the consequent virus population decline, and the coincident increased incidence of Lassa fever in these regions. Interestingly, we were also able to detect a similar pattern in Nigeria coinciding with the Biafra war. Our findings show that anthropogenic factors may profoundly impact the population genetics of a virus and its reservoir within the context of an emerging infectious disease.     

Bayesian Phylogeography of Crimean-Congo Hemorrhagic Fever Virus in Europe

Crimean-Congo hemorrhagic fever (CCHF) is a zoonosis mainly transmitted by ticks that causes severe hemorrhagic fever and has a mortality rate of 5-60%. The first outbreak of CCHF occurred in the Crimean peninsula in 1944-45 and it has recently emerged in the Balkans and eastern Mediterranean. In order to reconstruct the origin and pathway of the worldwide dispersion of the virus at global and regional (eastern European) level, we investigated the phylogeography of the infection by analysing 121 publicly available CCHFV S gene sequences including two recently characterised Albanian isolates. The spatial and temporal phylogeny was reconstructed using a Bayesian Markov chain Monte Carlo approach, which estimated a mean evolutionary rate of 2.96 x 10^-4 (95%HPD=1.6 and 4.7 x 10^-4) substitutions/site/year for the analysed fragment. All of the isolates segregated into seven highly significant clades that correspond to the known geographical clades: in particular the two new isolates from northern Albania clustered significantly within the Europe 1 clade. Our phylogeographical reconstruction suggests that the global CCHFV clades originated about one thousand years ago from a common ancestor probably located in Africa. The virus then spread to Asia in the XV century and entered Europe on at least two occasions: the first in the early 1800s, when a still circulating but less or non-pathogenic virus emerged in Greece and Turkey, and the second in the early 1900s, when a pathogenic CCHFV strain began to spread in eastern Europe. The most probable location for the origin of this European clade 1 was Russia, but Turkey played a central role in spreading the virus throughout Europe. Given the close proximity of the infected areas, our data suggest that the movement of wild and domestic ungulates from endemic areas was probably the main cause of the dissemination of the virus in eastern Europe.     

Immunology of the tick-host interaction and the control of ticks and tick-borne diseases.

The first experimental vaccination against ticks was carried out 60 years ago. Since then, progress has been slow, although the recent commercial release of a recombinant vaccine against Boophilus microplus is significant. The nature of naturally acquired protective immunity against ticks is poorly understood, particularly in the important, domesticated ruminant hosts. Characterization of the antigens of naturally acquired immunity remains limited, although more has been achieved with 'concealed' antigens. Crucial questions remain about the true impact of tick-induced immunosuppression and the effect of immunity on the transmission of tick-borne diseases, despite some fascinating and important recent results, as discussed here by Peter Willadsen and Frans Jongejan.     

中国瓢蜡蝉科昆虫区系分析(半翅目:蜡蝉总科)

为了解中国瓢蜡蝉科昆虫的区系结构及起源特性,本文对中国已知瓢蜡蝉科昆虫3族45属187种进行区系分析,结果表明:中国瓢蜡蝉科昆虫在世界动物地理区划中计3式区系型;东洋界区系型呈现主导优势,计179种,占总数95.72%;中国动物地理区划中计14式区系型,其中华南区系型所占比重最大,计121种,占总数64.71%;华南区成为现生中国瓢蜡蝉的集中与分化中心,并与华中区的联系最强;中国瓢蜡蝉科昆虫具有较强的北方起源性,这与大陆漂移和板块运动密切相关,且燕山运动等地质事件造就了该类昆虫属种水平的分异与演化;该科族级水平演化关系为:瓢蜡蝉族Issini Spinola,1839最为原始,铲头瓢蜡蝉族Parahiraciini ChengYang,1991次之,球瓢蜡蝉族Hemisphaeriini Melichar,1906最为进化;通过聚类分析,中国瓢蜡蝉科昆虫区系可分成3个区:即A区(东北区+华北区+蒙新区)、B区(华南区+华中区+西南区)和C区(青藏区),这可能与中国动物地理区划复杂的地理环境以及瓢蜡蝉自身飞行能力较差等原因相关。     

Mitochondrial DNA variation in house mice, Mus domesticus (Rutty)

This article summarizes knowledge of house mouse diversity based on restriction analysis of mtDNA from 202 individuals representing 83 localities in Europe, North Africa, the Middle East, and the Americas. It begins by describing the variation among 34 newly collected European mice and relating the 15 new types of mtDNA found in them to the 37 types known from previous work. None of the new types represent deep new branches in the tree. Moreover, the order of branching in the tree reinforces the view that mice north of the Alps have southern origins. Two possible time scales are under consideration for the process of colonization of north-western Europe. According to one hypothesis, which assumes that the mtDNA clock in mice ticks at the standard mammalian rate, commensal mice colonized Europe north of the Alps roughly 30 000–70 000 years ago, perhaps in concert with the spread of anatomically modern Homo sapiens . Another hypothesis, which requires accelerated mtDNA evolution in mice, would have the colonization take place 5000–6000 years ago, or even more recently, following the spread of agriculture. The study also shows that mtDNAs closely resembling those M. domesticus mtDNAs that introgressed into the Danish and Swedish populations of M. musculus are widespread in M. domesticus populations of the region near the hybrid zone between these two species in Germany.     

Substantial rise in the prevalence of Lyme borreliosis spirochetes in a region of western Germany over a 10-year period

More than a decade after a study on the transmission cycle of Borrelia burgdorferi sensu lato in the Siebengebirge, a nature reserve near Bonn, Germany, questing nymphal and adult Ixodes ricinus ticks were collected again in three selected areas of the same low mountain range and examined for infection with B. burgdorferi sensu lato. Between May and October 2001, a total of 1,754 ticks were collected by blanket dragging; 374 ticks were analyzed for B. burgdorferi sensu lato by both an immunofluorescence assay (IFA) and at least two different PCR tests, whereas 171 ticks were analyzed by PCR only. By combining all assays, an average of 14% of the ticks tested positive for B. burgdorferi sensu lato, 5.5, 15.8, and 21.8% in the three collection areas. Of the nymphs and adults examined, 12.9 and 21.1%, respectively, were found to be spirochete infected. A lower total infection prevalence was obtained by IFA (14.4%) than by a nested PCR approach (16.5%), but both were higher than that obtained by a simple PCR approach (11.9%). Compared with data collected over a decade ago, the mean infection prevalence of B. burgdorferi sensu lato in the ticks was significantly higher for all three biotopes, whereas a similar pattern of habitat-specific infection prevalence was observed. Genotyping of B. burgdorferi sensu lato revealed high relative prevalences of B. valaisiana (identified in 43.1% of infected ticks) and B. garinii (32.3%), whereas B. afzelii (12.3%) and B. burgdorferi sensu stricto (1.5%) were relatively rare. We conclude that B. burgdorferi sensu lato infection has increased in this region over the last 15 years due to presently unknown changes in ecological conditions, perhaps related to climate change or wildlife management.     

Detection of <Emphasis Type="Italic">Francisella tularensis</Emphasis> in ticks and identification of their genotypes using multiple-locus variable-number tandem repeat analysis

Background  

Tularemia was reported in China over 50 years ago, however, many epidemical characteristics remain unclear. In the present study, the prevalence of Francisella tularensis in ticks was investigated during an epidemiological surveillance in China and then we measured their genetic diversity by conducting multiple-locus variable- number tandem repeat analysis (MLVA).     

Phylogeny, Evolution and Historical Zoogeography of Ticks: A Review of Recent Progress

There has been much progress in our understanding of the phylogeny and evolution of ticks, particularly hard ticks, in the past 5 years. Indeed, a consensus about the phylogeny of the hard ticks has emerged. Our current working hypothesis for the phylogeny of ticks is quite different to the working hypothesis of 5 years ago. So that the classification reflects our knowledge of ticks, several changes to the nomenclature of ticks are imminent. One subfamily, the Hyalomminae, will probably be sunk, yet another, the Bothriocrotoninae n. subfamily, will be created. Bothriocrotoninae n. subfamily, and Bothriocroton n. genus, are being created to house an early-diverging (‘basal’) lineage of endemic Australian ticks that used to be in the genus Aponomma (ticks of reptiles). There has been progress in our understanding of the subfamily Rhipicephalinae. The genus Rhipicephalus is almost certainly paraphyletic with respect to the genus Boophilus. Thus, the genus Boophilus will probably become a subgenus of Rhipicephalus. This change to the nomenclature, unlike other options, will keep the name Boophilus in common usage. Rhipicephalus (Boophilus) microplus may still called B. microplus, and Rhipicephalus (Boophilus) annulatus may still be called B. annulatus, but the nomenclature will have been changed to reflect our knowledge of the phylogeny and evolution of these ticks. New insights into the historical zoogeography of ticks will also be presented. This revised version was published online in July 2006 with corrections to the Cover Date.     

Population-Based Passive Tick Surveillance and Detection of Expanding Foci of Blacklegged Ticks Ixodes scapularis and the Lyme Disease Agent Borrelia burgdorferi in Ontario,Canada

We identified ticks submitted by the public from 2008 through 2012 in Ontario, Canada, and tested blacklegged ticks Ixodes scapularis for Borrelia burgdorferi and Anaplasma phagocytophilum. Among the 18 species of ticks identified, I. scapularis, Dermacentor variabilis, Ixodes cookei and Amblyomma americanum represented 98.1% of the 14,369 ticks submitted. Rates of blacklegged tick submission per 100,000 population were highest in Ontario''s Eastern region; D. variabilis in Central West and Eastern regions; I. cookei in Eastern and South West regions; and A. americanum had a scattered distribution. Rates of blacklegged tick submission per 100,000 population were highest from children (0–9 years old) and older adults (55–74 years old). In two health units in the Eastern region (i.e., Leeds, Grenville & Lanark District and Kingston-Frontenac and Lennox & Addington), the rate of submission for engorged and B. burgdorferi-positive blacklegged ticks was 47× higher than the rest of Ontario. Rate of spread for blacklegged ticks was relatively faster and across a larger geographic area along the northern shore of Lake Ontario/St. Lawrence River, compared with slower spread from isolated populations along the northern shore of Lake Erie. The infection prevalence of B. burgdorferi in blacklegged ticks increased in Ontario over the study period from 8.4% in 2008 to 19.1% in 2012. The prevalence of B. burgdorferi-positive blacklegged ticks increased yearly during the surveillance period and, while increases were not uniform across all regions, increases were greatest in the Central West region, followed by Eastern and South West regions. The overall infection prevalence of A. phagocytophilum in blacklegged ticks was 0.3%. This study provides essential information on ticks of medical importance in Ontario, and identifies demographic and geographic areas for focused public education on the prevention of tick bites and tick-borne diseases.     

Overview of the origins and history of the five major cucurbit crops: issues for ancient DNA analysis of archaeological specimens

The gourd family, Cucurbitaceae, contains five vegetable crops of worldwide importance, the pumpkins and squash (Cucurbita spp.), watermelons (Citrullus lanatus), melons (Cucumis melo) and cucumbers (Cucumis sativus). Here is presented a synopsis of the origin and history of these cucurbit crops. Historical records of the use of cucurbits by people take the form of archaeobotanical finds, iconography and literature. The weight of the evidence indicates that Cucurbita spp. were first cultivated in the Americas at least 10,000 years ago, and that by 1492 ce a number of cultivar-groups of pumpkins and squash had been developed by indigenous American peoples. Watermelons were cultivated in northeastern Africa at least 4,000 years ago, first probably as a source of fresh water. Melons and cucumbers are native to Asia, probably initially cultivated for the use of the young fruits as vegetables. Melons spread to eastern Africa at an early date, but cucumbers are probably a more recent domesticate and spread westwards later, reaching Europe in early medieval times. Sequencing of cucurbit plant genomes and advances in ancient DNA research offer much promise for obtaining an improved assessment of cucurbit crop origins, specifically the genetic constitution and geographical home of ancestral source populations. Next-generation genomic sequencing, if applied to an appropriate array of archaeological cucurbit remains and modern germplasm, could contribute much to the understanding of the history and evolution under domestication of cucurbit crops.     

Proto-Uto-Aztecan: A Community of Cultivators in Central Mexico?

Authorities on the origin and history of Uto-Aztecan have held that speakers of the protolanguage were foragers who lived in upland regions of Arizona, New Mexico, and the adjacent areas of the Mexican states of Sonora and Chihuahua about 5,000 years ago. New lexical evidence supports a different view, that speakers of the protolanguage were maize cultivators. The Proto-Uto-Aztecan speech community was probably located in Mesoamerica and spread northward into the present range because of demographic pressure associated with cultivation. The chronology for the spread and differentiation of the family should then correspond to the chronology for the northward spread of maize cultivation from Mesoamerica into the U.S. Southwest, between 4500 and 3000 B.P. [ Uto-Aztecan, cultivation, Mesoamerican, historical linguistics, migration ]