Inferring population history from microsatellite and enzyme data in serially introduced cane toads, Bufo marinus

Much progress has been made on inferring population history from molecular data. However, complex demographic scenarios have been considered rarely or have proved intractable. The serial introduction of the South-Central American cane Load Bufo marinas in various Caribbean and Pacific islands involves four major phases: a possible genetic admixture during the first introduction, a bottleneck associated with founding, a transitory, population boom, and finally, a demographic stabilization. A large amount of historical and demographic information is available for those introductions and can be combined profitably with molecular data. We used a Bayesian approach to combine this information With microsatellite (10 loci) and enzyme (22 loci) data and used a rejection algorithm to simultaneously estimate the demographic parameters describing the four major phases of the introduction history,. The general historical trends supported by microsatellites and enzymes were similar. However, there was a stronger support for a larger bottleneck at introductions for microsatellites than enzymes and for a more balanced genetic admixture for enzymes than for microsatellites. Verb, little information was obtained from either marker about the transitory population boom observed after each introduction. Possible explanations for differences in resolution of demographic events and discrepancies between results obtained with microsatellites and enzymes were explored. Limits Of Our model and method for the analysis of nonequilibrium populations were discussed.

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC.

Genomic evidence for the Pleistocene and recent population history of Native Americans

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative “Paleoamerican” relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Genetic characterization, population history and evolutionary medicine perspective in two native south american populations: Yanesha and Wichi

Two Amerindian populations from the Peruvian Amazon (Yanesha) and from rural lowlands of the Argentinean Gran Chaco (Wichi) were analyzed. They represent two case study of the South American genetic variability. The Yanesha represent a model of population isolated for long-time in the Amazon rainforest, characterized by environmental and altitudinal stratifications. The Wichi represent a model of population living in an area recently colonized by European populations (the Criollos are the population of the admixed descendents), whose aim is to depict the native ancestral gene pool and the degree of admixture, in relation to the very high prevalence of Chagas disease. The methods used for the genotyping are common, concerning the Y chromosome markers (male lineage) and the mitochondrial markers (maternal lineage). The determination of the phylogeographic diagnostic polymorphisms was carried out by the classical techniques of PCR, restriction enzymes, sequencing and specific mini-sequencing. New method for the detection of the protozoa Trypanosoma cruzi was developed by means of the nested PCR. The main results show patterns of genetic stratification in Yanesha forest communities, referable to different migrations at different times, estimated by Bayesian analyses. In particular Yanesha were considered as a population of transition between the Amazon basin and the Andean Cordillera, evaluating the potential migration routes and the separation of clusters of community in relation to different genetic bio-ancestry. As the Wichi, the gene pool analyzed appears clearly differentiated by the admixed sympatric Criollos, due to strict social practices (deeply analyzed with the support of cultural anthropological tools) that have preserved the native identity at a diachronic level. A pattern of distribution of the seropositivity in relation to the different phylogenetic lineages (the adaptation in evolutionary terms) does not appear, neither Amerindian nor European, but in relation to environmental and living conditions of the two distinct subpopulations.

Molecular genetic investigation of the Neolithic population history in the western Carpathian Basin

Der Fokus dieser Dissertation ist die populationsgenetische Analyse der neolithischen Bevölkerungswechsel in den 6.-5. Jahrtausende vor Christus, die im westlichen Karpatenbecken stattfanden. Die Zielsetzung der Studie war, mittels der Analyse von mitochondrialer und Y-chromosomaler aDNA, den Genpool der sechs neolithischen und kupferzeitlichen Populationen zu untersuchen und die daraus resultierenden Ergebnisse mit anderen prähistorischen und modernen genetischen Daten zu vergleichen.rnInsgesamt wurden 323 Individuen aus 32 ungarischen, kroatischen und slowakischen Fundplätzen beprobt und bearbeitet in den archäogenetischen Laboren der Johannes Gutenberg-Universität in Mainz. Die DNA Ergebnisse wurden mit verschiedenen populationsgenetischen Methoden ausgewertet. Vergleichsdaten von prähistorischen und modernen eurasiatischen Populationen wurden dazu gesammelt.rnDie HVS-I Region der mitochondrialen DNA konnten bei 256 Individuen reproduziert und authentifiziert werden (mit einer Erfolgsrate von 85.9%). Die Typisierung der HVS-II Region war in 80 Fällen erfolgreich. Testend alle gut erhaltene Proben, die Y-chromosomale Haplogruppe konnte in 33 männlichen Individuen typisiert werden.rnDie neolithischen, mitochondrialen Haplogruppen deuten auf eine hohe Variabilität des maternalen Genpools hin. Sowohl die mitochondrialen als auch die Y-chromosomalen Daten lassen Rückschlüsse auf eine nah-östliche bzw. südwestasiatische Herkunft der frühen Bauern zu. Die Starčevo- und linearbandkermaischen-Populationen in westlichem Karpatenbecken (letztere abgekürzt als LBKT) und die linearbandkermaischen-Population in Mitteleuropa (LBK) haben so starke genetische Ähnlichkeit, dass die Verbreitung der LBK nach Mitteleuropa mit vorangegangenen Wanderungsereignissen zu erklären ist. Die Transdanubische aDNA Daten zeigen hohe Affinität zu den publizierten prähistorischen aDNA Datensätzen von Mitteleuropa aus den 6.-4. Jahrtausende vor Chr. Die maternal-genetische Variabilität der Starčevo-Population konnte auch innerhalb der nachfolgenden Populationen Transdanubiens festgestellt werden. Nur kleinere Infiltrationen und Immigrationsereignissen konnten während der Vinča-, LBKT-, Sopot- und Balaton-Lasinja-Kultur in Transdanubien identifiziert werden. Zwischen den transdanubischen Regionen konnten mögliche genetische Unterschiede nur in der LBKT und in der Lengyel-Periode beobachtet werden, als sich die nördlichen Gruppen von den südlichen Populationen trennten. rnDie festgestellte Heterogenität der mtDNA in Zusammenhang mit der Y-chromosomalen Homogenität in den Starčevo- und LBK-Populationen, weisen auf patrilokale Residenzregeln und patrilineare Abstammungsregeln in den ersten Bauergemeinschaften hin. rnObwohl die hier präsentierten Daten einen großen Fortschritt in der Forschung von aDNA und Neolithikum des Karpatenbeckens und Mitteleuropas bedeuten, werfen sie auch mehrere Fragen auf, deren Beantwortung durch zukünftige Genomforschungen erbracht werden könnte.

Genetics and the population history of Europe

Analysis of genetic variation among modern individuals is providing insight into prehistoric events. Comparisons of levels and patterns of genetic diversity with the predictions of models based on archeological evidence suggest that the spread of early farmers from the Levant was probably the main episode in the European population history, but that both older and more recent processes have left recognizable traces in the current gene pool.

Phylogeographic Triangulation: Using Predator-Prey-Parasite Interactions to Infer Population History from Partial Genetic Information

Phylogeographic studies, which infer population history and dispersal movements from intra-specific spatial genetic variation, require expensive and time-consuming analyses that are not always feasible, especially in the case of rare or endangered species. On the other hand, comparative phylogeography of species involved in close biotic interactions may show congruent patterns depending on the specificity of the relationship. Consequently, the phylogeography of a parasite that needs two hosts to complete its life cycle should reflect population history traits of both hosts. Population movements evidenced by the parasite’s phylogeography that are not reflected in the phylogeography of one of these hosts may thus be attributed to the other host. Using the wild rabbit (Oryctolagus cuniculus) and a parasitic tapeworm (Taenia pisiformis) as an example, we propose comparing the phylogeography of easily available organisms such as game species and their specific heteroxenous parasites to infer population movements of definitive host/predator species, independently of performing genetic analyses on the latter. This may be an interesting approach for indirectly studying the history of species whose phylogeography is difficult to analyse directly.

Microsatellite allele sequencing in population analyses of the South American cactophilic species Drosophila antonietae (Diptera: Drosophilidae)

Drosophila antonietae belongs to the Drosophila buzzatii cluster, a cactophilic group of species naturally endemic to South America. Morphological and genetic analyses indicate that its populations are the most homogenous in the cluster and that the diversity observed is mainly a result of variation within populations. Seven polymorphic microsatellite loci were described for this species and used in the present study to investigate the genetic diversity of natural populations of D. antonietae by both length and sequence variation. The study aimed to understand how homoplasy and null alleles affect inferences about the population history of this species and to obtain an accurate interpretation of population inferences where these loci could be applied. The results provide useful information on the interpretation of genetic data derived from the microsatellite loci described for D. antonietae and on evolutionary aspects of cactophilic Drosophila. Importantly, the results indicate that size homoplasy and null alleles do not represent significant problems for the population genetics analyses because the large amount of variability at microsatellite loci compensate the low frequency of these problems in the populations. (C) 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 573-584.

Comparative population genomics in animals uncovers the determinants of genetic diversity.

Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinants of this variation, and particularly the relative influences of species biology and ecology versus population history, are still largely mysterious. Here we show that the diversity of a species is predictable, and is determined in the first place by its ecological strategy. We investigated the genome-wide diversity of 76 non-model animal species by sequencing the transcriptome of two to ten individuals in each species. The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones. Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies.

The Phylogeographic History of the New World Screwworm Fly, Inferred by Approximate Bayesian Computation Analysis

Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC) analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred between the North/Central American and South American populations in the end of the Last Glacial Maximum (15,300-19,000 YBP). The second split occurred between the North and South Amazonian populations in the transition between the Pleistocene and the Holocene eras (9,100-11,000 YBP). The species also experienced population expansion. Phylogenetic analysis likewise suggests this north to south colonization and Maxent models suggest an increase in the number of suitable areas in South America from the past to present. We found that the phylogeographic patterns observed in C. hominivorax cannot be explained only by climatic oscillations and can be connected to host population histories. Interestingly we found these patterns are very coincident with general patterns of ancient human movements in the Americas, suggesting that humans might have played a crucial role in shaping the distribution and population structure of this insect pest. This work presents the first hypothesis test regarding the processes that shaped the current phylogeographic structure of C. hominivorax and represents an alternate perspective on investigating the problem of insect pests. © 2013 Fresia et al.

The genetic history of Italians: new-insights from uniparentally-inherited markers

Genetic differences among human groups can be ascribed both to the broad-scale extents of pre-historical and historical migrations and to the fine-scale impacts of socio-cultural and geographic heterogeneity. In this thesis, the genetic information provided by uniparental markers were exploited to address different aspects of the Italian population history, by combining macro- and micro-geographic investigations at different spatial and temporal scales. To firstly assess the overall Italian variability, Y-chromosome and mtDNA markers were deeply typed in ~900 individuals from continental Italy, Sicily and Sardinia. Sex-biased patterns and contrasting demographic histories were observed for males and females. Differential European and Mediterranean contributions were invoked to explain the paternal genetic sub-structure observed in peninsular Italy, compared to the homogeneous maternal genetic landscape. If Neolithic showed to be one principal determinant of the detected paternal structure, local insights into specific Italian regional contexts highlighted the importance of Post-Neolithic contributions. Among them, migrations from the Balkans (particularly Greece) during late Metal Ages, played a relevant role in the cultural and genetic transitions occurred in Sicily and Southern Italy. On a finer geographic and temporal perspective, the more recent layers of Italian genetic history and some aspects of the gene-culture interaction were assessed by exploring the genetic variability within two “marginal populations”: Arbereshe of Southern Italy and Partecipanza in Northern Italy. The Arbereshe are Albanian-speaking communities settled in Sicily and Calabria since the end of Middle Ages. Despite sharing common genetic and cultural backgrounds, these groups revealed diverging micro-evolutionary histories, implying different founding events and different patterns of cultural isolation and local admixture. Partecipanza is an idiosyncratic institution of Medieval origin aimed at sharing and devolving collective lands. This case-study exemplified that socio-economic stratification within the same population may induce sex-biased genetic structuring and the maintenance of otherwise hidden historical genetic traces.

All cause and disease specific mortality in patients with knee or hip osteoarthritis: population based cohort study

Objective To examine all cause and disease specific mortality in patients with osteoarthritis of the knee or hip. Design Population based cohort study. Setting General practices in the southwest of England. Participants 1163 patients aged 35 years or over with symptoms and radiological confirmation of osteoarthritis of the knee or hip. Main outcome measures Age and sex standardised mortality ratios and multivariable hazard ratios of death after a median of 14 years’ follow-up. Results Patients with osteoarthritis had excess all cause mortality compared with the general population (standardised mortality ratio 1.55, 95% confidence interval 1.41 to 1.70). Excess mortality was observed for all disease specific causes of death but was particularly pronounced for cardiovascular (standardised mortality ratio 1.71, 1.49 to 1.98) and dementia associated mortality (1.99, 1.22 to 3.25). Mortality increased with increasing age (P for trend <0.001), male sex (adjusted hazard ratio 1.59, 1.30 to 1.96), self reported history of diabetes (1.95, 1.31 to 2.90), cancer (2.28, 1.50 to 3.47), cardiovascular disease (1.38, 1.12 to 1.71), and walking disability (1.48, 1.17 to 1.86). However, little evidence existed for increased mortality associated with previous joint replacement, obesity, depression, chronic inflammatory disease, eye disease, or presence of pain at baseline. The more severe the walking disability, the higher was the risk of death (P for trend <0.001). Conclusion Patients with osteoarthritis are at higher risk of death compared with the general population. History of diabetes, cancer, or cardiovascular disease and the presence of walking disability are major risk factors. Management of patients with osteoarthritis and walking disability should focus on effective treatment of cardiovascular risk factors and comorbidities, as well as on increasing physical activity.