Demography,genealogy and genetics. The reproductive process in the populations of two French Mountain Valleys from the seventeenth to the twentieth century

An exhaustive analysis of registers of births, deaths, and marriages is used to reconstitute genealogies, both ascending and descending, for all individuals who lived in two mountain valleys: the Valserine valley (in the French Jura), which is studied from the end of the seventeenth century to the present, and the Vallouise valley (in the French Alps) studied from the seventeenth to the nieteenth centuries. This genealogical approach makes it possible to trace the reproductive process in the populations whose members lived in the valley for several generations. The Vallouise valley forms an important demographic isolate; nearly 98 per cent of those born between 1820 and 1849 were descendants of ancestors who had lived in the valley two centuries earlier. By contrast, there has been continuous immigration into the Valserine valley, which has resulted in a constant renewal of the gene pool. Only 18 per cent of the gene pool of individuals living in this valley two centuries later was contributed by those who lived in the valley and who were born before 1750.     

High levels of Paleolithic Y-chromosome lineages characterize Serbia

Whether present-day European genetic variation and its distribution patterns can be attributed primarily to the initial peopling of Europe by anatomically modern humans during the Paleolithic, or to latter Near Eastern Neolithic input is still the subject of debate. Southeastern Europe has been a crossroads for several cultures since Paleolithic times and the Balkans, specifically, would have been part of the route used by Neolithic farmers to enter Europe. Given its geographic location in the heart of the Balkan Peninsula at the intersection of Central and Southeastern Europe, Serbia represents a key geographical location that may provide insight to elucidate the interactions between indigenous Paleolithic people and agricultural colonists from the Fertile Crescent. In this study, we examine, for the first time, the Y-chromosome constitution of the general Serbian population. A total of 103 individuals were sampled and their DNA analyzed for 104 Y-chromosome bi-allelic markers and 17 associated STR loci. Our results indicate that approximately 58% of Serbian Y-chromosomes (I1-M253, I2a-P37.2 and R1a1a-M198) belong to lineages believed to be pre-Neolithic. On the other hand, the signature of putative Near Eastern Neolithic lineages, including E1b1b1a1-M78, G2a-P15, J1-M267, J2-M172 and R1b1a2-M269 accounts for 39% of the Y-chromosome. Haplogroup frequency distributions in Western and Eastern Europe reveal a spotted landscape of paleolithic Y chromosomes, undermining continental-wide generalizations. Furthermore, an examination of the distribution of Y-chromosome filiations in Europe indicates extreme levels of Paleolithic lineages in a region encompassing Serbia, Bosnia-Herzegovina and Croatia, possibly the result of Neolithic migrations encroaching on Paleolithic populations against the Adriatic Sea.     

Does organismal pedigree impact the magnitude of topological congruence among gene trees for unlinked loci?

One of the fundamental assumptions in the multi-locus approach to phylogeographic studies is that unlinked loci have independent genealogies. For this reason, congruence among gene trees from unlinked loci is normally interpreted as support for the existence of external forces that may have concordantly shaped the topology of multiple gene trees. However, it is also important to address and quantify the possibility that gene trees within a given species are all inherently constrained to some degree by their shared organismal pedigree, and thus in this strict sense are not entirely independent. Here we demonstrate by computer simulations that gene trees from a shared pedigree tend to display higher topological concordance than do gene trees from independent pedigrees with the same demographic parameters, but we also show that these constraining effects are normally minor in comparison to the much higher degree of topological concordance that can routinely emerge from external phylogeographic shaping forces. The topology-constraining effect of a shared pedigree decreases as effective population size increases, and becomes almost negligible in a random mating population of more than 1,000 individuals. Moreover, statistical detection of the pedigree effect requires a relatively large number of unlinked loci that far exceed what is typically used in current phylogeographic studies. Thus, with the possible exception of extremely small populations, multiple unlinked genes within a pedigree can indeed be assumed, for most practical purposes, to have independent genealogical histories.     

Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae)

Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g., incomplete lineage sorting) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here, we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 ultraconserved element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with >1,200 species. We sampled representatives of all tribes within the group and >80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests. We show that within-locus partitioning improves gene tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.     

The genealogical process of neutral genes with mutation in geographically structured populations

The genealogical process of neutral genes with mutation in geographically structured populations is investigated. Following Watterson [24], the sampled genes are partitioned into two types, old equivalence classes and new equivalence classes. The model is described by a bivariate continuous time Markov chain as an interactive particle system. Some results are obtained in the two-population model and the stepping stone model with symmetric nearest-neighbour migration.     

A Feel for Genealogy: ‘Family Treeing’ in the North of England

Family history research is popular in England. As a social practice it straddles social class and is confined to neither the middle nor the working classes, but shows an enthusiastic and flourishing interest in the workings of social class and in micro-histories of the region. This article focuses on experts in family history research in a region of the north west of England where it is referred to colloquially as ‘family treeing’. Here family treeing is inflected by a post-industrial landscape and recent social and economic transformations with attendant threats to working-class life and dignity. Family treeing is about caring for the dead, but it is also, significantly, about caring for the living, and not only kin. It is an active practice of belonging both to people and places, and entails constant acts of reciprocity.     

Host specificity and genealogy of the louse Polyplax serrata on field mice, Apodemus species: a case of parasite duplication or colonisation?

The genealogy, population structure and population dynamics of the sucking louse Polyplax serrata were analysed across four host species of the genus Apodemus. An analysis of 126 sequences of cytochrome c oxidase subunit I using phylogenetic approaches and haplotype networking revealed a clear structure of European samples, forming three distinct and genetically distant clades with different host specificities. Although a clear connection was detected between the host and parasite genealogies/phylogenies, a uniform pattern of co-speciation was not found. For example, a dramatic shift in the degree of host specificity was demonstrated for two related louse lineages living in sympatry and sharing one of their host species. While one of the louse lineages frequently parasitised two different host taxa (Apodemus sylvaticus and Apodemus flavicollis), the other louse lineage was strictly specific to A. flavicollis. The estimate of divergence time between the two louse lineages indicates that they may have arisen due to parasite duplication on A. flavicollis.     

Inbreeding, pedigree size, and the most recent common ancestor of humanity

How many generations ago did the common ancestor of all present-day individuals live, and how does inbreeding affect this estimate? The number of ancestors within family trees determines the timing of the most recent common ancestor of humanity. However, mating is often non-random and inbreeding is ubiquitous in natural populations. Rates of pedigree growth are found for multiple types of inbreeding. This data is then combined with models of global population structure to estimate biparental coalescence times. When pedigrees for regular systems of mating are constructed, the growth rates of inbred populations contain Fibonacci n-step constants. The timing of the most recent common ancestor depends on global population structure, the mean rate of pedigree growth, mean fitness, and current population size. Inbreeding reduces the number of ancestors in a pedigree, pushing back global common ancestry times. These results are consistent with the remarkable findings of previous studies: all humanity shares common ancestry in the recent past.     

The domestication process of the Modern Rose: genetic structure and allelic composition of the rose complex

Genetic variability among 100 old cultivated rose varieties from 13 horticultural groups was estimated by arbitrary primed (AP) PCR. Using five long (20-mer) PCR primers, 58 polymorphic DNA fragments were produced, of which 55 were highly discriminant, allowing differentiation of the quasi-totality of the 100 cultivars. A dendrogram was constructed displaying the relative genetic similarities between cultivars estimated from the presence/absence of PCR fragments. It shows the relationships between the Chinese and European founder roses, hybrid groups of the first (Bourbons, Noisettes, Portlands) and second (Hybrid Perpetuals and Teas) generations, and the most modern Hybrid Teas, produced during the history of domestication. Principal components analysis (PCA) of the same data demonstrates the occurrence of a continuous gradient of the European/Chinese allele ratio, and a considerable reduction of genetic variability superimposed with the progress of domestication. The two complementary analyses are in good agreement with the horticultural literature. They also give access to DNA fragments potentially linked to genes involved in the control of the main morphogenetic characters of various groups. Received: 10 January 2000 / Accepted: 30 April 2000     

The birth process with immigration,and the genealogical structure of large populations

This paper studies a version of the birth and immigration process in which families are followed in the order of their appearance. This age structure is related to a number of results from population genetics, in particular the genealogical structure of the infinitely-many neutral alleles model. The asymptotic behavior of this genealogy is an easy consequence of the structure of the age-ordered family size process.