Relaxed molecular clocks for dating historical plant dispersal events

Age estimation from molecular sequences has emerged as a powerful tool for inferring when a plant lineage arrived in a particular area. Knowing the tenure of lineages within a region is key to understanding the evolution of traits, the evolution of biotic interactions, and the evolution of floras. New analytical methods model change in substitution rates along individual branches of a phylogenetic tree by combining molecular data with time constraints, usually from fossils. These "relaxed clock" approaches can be applied to several gene regions that need not all have the same substitution rates, and they can also incorporate multiple simultaneous fossil calibrations. Since 1995, at least 100 plant biogeographic studies have used molecular-clock dating, and about a fifth has used relaxed clocks. Many of these report evidence of long-distance dispersal. Meta-analyses of studies from the same geographic region can identify directional biases because of prevailing wind or water currents and the relative position and size of landmasses.     

Genetic structure of Podocarpus nubigena (Podocarpaceae) provides evidence of Quaternary and ancient historical events

Evolution of ancient lineages inhabiting austral latitudes of the southern Andes has taken place in response to historical processes occurring at distinct spatial and temporal scales. We tested the hypothesis that distribution patterns of genetic polymorphisms within Podocarpus nubigena Lindl. (Podocarpaceae) were shaped by contemporary events acting at local scales such as Quaternary glaciations as well as pre-Quaternary palaeogeographical features of the landscape. We predict that such cold hardy species was able to survive locally in refugia during ice ages. As a result of local long-lasting persistence, its gene pool may also reflect the pre-Quaternary palaeogeography of southern South America. We collected fresh leaves from 30 randomly selected individuals at 14 populations. Leaf tissue was analyzed by isozyme electrophoresis using 12 putative loci most of which (92%) were polymorphic in at least one population. Elevated total genetic diversity was recorded H_T = 0.275 which was similarly high throughout populations with an overall significant mean among-population isolation (F_ST = 18%). Multivariate cluster and Bayesian analyses yielded significant latitudinal divergence at 43°S associated to a palaeobasin that produced a barrier for gene flow. Populations south of 43°S and those growing in lowland areas on Quaternary substrates of the North Patagonian Massif (Q NPM) present the highest genetic diversity suggesting long-lasting persistence. In contrast, northern mountain populations on pre-Quaternary substrates (pre-Q NPM) hold reduced genetic variation due to altitudinal movements in response to climate shifts. We suggest that palaeogeography of southern South America in addition to Neogene glaciations have shaped the genetic makeup of such ancient lineage as Podocarpus.     

Chromosome breakage: a possible mechanism for diverse genetic events in outbred populations.

Evidence is summarised to support the hypothesis that genetic characteristics frequently assayed in natural populations, including mutator activity, sterility, male recombination, and distortion of segregation, may often be expressions of the same general event--chromosome breakage in outbred populations.     

Afghanistan's ethnic groups share a Y-chromosomal heritage structured by historical events

Afghanistan has held a strategic position throughout history. It has been inhabited since the Paleolithic and later became a crossroad for expanding civilizations and empires. Afghanistan's location, history, and diverse ethnic groups present a unique opportunity to explore how nations and ethnic groups emerged, and how major cultural evolutions and technological developments in human history have influenced modern population structures. In this study we have analyzed, for the first time, the four major ethnic groups in present-day Afghanistan: Hazara, Pashtun, Tajik, and Uzbek, using 52 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y-chromosome. A total of 204 Afghan samples were investigated along with more than 8,500 samples from surrounding populations important to Afghanistan's history through migrations and conquests, including Iranians, Greeks, Indians, Middle Easterners, East Europeans, and East Asians. Our results suggest that all current Afghans largely share a heritage derived from a common unstructured ancestral population that could have emerged during the Neolithic revolution and the formation of the first farming communities. Our results also indicate that inter-Afghan differentiation started during the Bronze Age, probably driven by the formation of the first civilizations in the region. Later migrations and invasions into the region have been assimilated differentially among the ethnic groups, increasing inter-population genetic differences, and giving the Afghans a unique genetic diversity in Central Asia.     

Habitat barriers limit gene flow and illuminate historical events in a wide-ranging carnivore, the American puma

We examined the effects of habitat discontinuities on gene flow among puma (Puma concolor) populations across the southwestern USA. Using 16 microsatellite loci, we genotyped 540 pumas sampled throughout the states of Utah, Colorado, Arizona, and New Mexico, where a high degree of habitat heterogeneity provides for a wide range of connective habitat configurations between subpopulations. We investigated genetic structuring using complementary individual- and population-based analyses, the latter employing a novel technique to geographically cluster individuals without introducing investigator bias. The analyses revealed genetic structuring at two distinct scales. First, strikingly strong differentiation between northern and southern regions within the study area suggests little migration between them. Second, within each region, gene flow appears to be strongly limited by distance, particularly in the presence of habitat barriers such as open desert and grasslands. Northern pumas showed both reduced genetic diversity and greater divergence from a hypothetical ancestral population based on Bayesian clustering analyses, possibly reflecting a post-Pleistocene range expansion. Bayesian clustering results were sensitive to sampling density, which may complicate inference of numbers of populations when using this method. The results presented here build on those of previous studies, and begin to complete a picture of how different habitat types facilitate or impede gene flow among puma populations.     

Molecular dating of a marine species,Eriocheir japonica (Decapoda: Grapsidae), corroborates cenozoic tectonic events and sea level fluctuation

Changes of coastal topography for Cenozoic Himalayan orogeny complicated the phylogeographical structure of marine species and deepened their divergences. To test the association between divergence and Cenozoic tectonic events, we analyzed the phylogeographical structure of Eriocheir japonica by combining molecular data and geographical environment events. The four distinct lineages obtained through phylogenetic reconstruction and network analysis demonstrated the significant genetic divergence among geographical populations. Furthermore, the divergence time between E. j. japonica in Japan and E. j. sinensis in China was about 10.5–11.5 mya, which was coincident with the opening of the Sea of Japan. The north-south divergence time (15.5–17.5 mya) was in the range of the occurrence of the Himalaya movement. We hypothesize that coastal topography, including the formation of Taiwan in the Himalaya movement and the opening of the Sea of Japan, contributed to the geographical subspeciation of marine species. Mitten crabs were inferred to originate from one ancient population with the oldest haplotype H6 and subsequently divide into northern and southern populations. Furthermore, the Japan lineage derived from northern population in China for the opening of the Sea of Japan.     

Genetic effective size of a wild primate population: influence of current and historical demography

A comprehensive assessment of the determinants of effective population size (N(e)) requires estimates of variance in lifetime reproductive success and past changes in census numbers. For natural populations, such information can be best obtained by combining longitudinal data on individual life histories and genetic marker-based inferences of demographic history. Independent estimates of the variance effective size (N(ev), obtained from life-history data) and the inbreeding effective size (N((eI), obtained from genetic data) provide a means of disentangling the effects of current and historical demography. The purpose of this study was to assess the demographic determinants of N(e) in one of the most intensively studied natural populations of a vertebrate species: the population of savannah baboons (Papio cynocephalus) in the Amboseli Basin, southern Kenya. We tested the hypotheses that N(eV) < N < N(eI) (where N = population census number) due to a recent demographic bottleneck. N(eV) was estimated using a stochastic demographic model based on detailed life-history data spanning a 28-year period. Using empirical estimates of age-specific rates of survival and fertility for both sexes, individual-based simulations were used to estimate the variance in lifetime reproductive success. The resultant values translated into an N(eV)/N estimate of 0.329 (SD = 0.116, 95% CI = 0.172-0.537). Historical N(eI), was estimated from 14-locus microsatellite genotypes using a coalescent-based simulation model. Estimates of N(eI) were 2.2 to 7.2 times higher than the contemporary census number of the Amboseli baboon population. In addition to the effects of immigration, the disparity between historical N(eI) and contemporary N is likely attributable to the time lag between the recent drop in census numbers and the rate of increase in the average probability of allelic identity-by-descent. Thus, observed levels of genetic diversity may primarily reflect the population's prebottleneck history rather than its current demography.     

Genetic and Molecular Mapping of Chromosome Region 85a in Drosophila Melanogaster

Chromosome region 85A contains at least 12 genetic complementation groups, including the genes dhod, pink and hunchback. In order to better understand the organization of this chromosomal segment and to permit molecular studies of these genes, we have carried out a genetic analysis coupled with a chromosome walk to isolate the DNA containing these genes. Complementation tests with chromosomal deficiencies permitted unambiguous ordering of most of the complementation groups identified within the 85A region. Recombinant bacteriophage clones were isolated that collectively span over 120 kb of 85A DNA and these were used to produce a molecular map of the region. The breakpoint sites of a number of 85A chromosome rearrangements were localized on the molecular map, thereby delimiting regions of the DNA that contain the various genetic complementation groups.     

Interference in Genetic Crossing over and Chromosome Mapping

This paper proposes a general model for interference in genetic crossing over. The model assumes serial occurrence of chiasmata, visualized as a renewal process along the paired (or pairing) chromosomes. This process is described as an underlying Poisson process in which the 1st, n + 1th, 2n + 1th, etc., events are to be interpreted as realized chiasmata. Chromatid interference is described in terms of the probabilities that two successive chiasmata involve two, three or four different chromatids. Several characteristics of this model, e.g., the cytological and genetic mapping function and the density of chiasmata along the chromosomes, are discussed. Some aspects of other interference models are briefly discussed.     

Genetic Studies of Autistic Disorder and Chromosome 7

Genome-wide scans have suggested that a locus on 7q is involved in the etiology of autistic disorder (AD). We have identified an AD family in which three sibs inherited from their mother a paracentric inversion in the chromosome 7 candidate region (inv(7)(q22-q31.2)). Clinically, the two male sibs have AD, while the female sib has expressive language disorder. The mother carries the inversion, but does not express AD. Haplotype data on the family suggest that the chromosomal origin of the inversion was from the children's maternal grandfather. Based on these data, we have genotyped 76 multiplex (>/=2 AD affecteds/family) families for markers in this region of 7q. Two-point linkage analysis yielded a maximum heterogeneity lod score of 1.47 and maximum lod score (MLS) of 1.03 at D7S495. Multipoint MLS and NPL analyses resulted in peak scores of 1.77 at D7S2527 and 2.01 at D7S640. Examination of affected sibpairs revealed significant paternal (P = 0.007), but not maternal (P = 0. 75), identity-by-descent sharing at D7S640. Significant linkage disequilibrium was detected with paternal (P = 0.02), but not maternal (P = 0.15), transmissions at D7S1824 in multiplex and singleton families. There was also evidence for an increase in recombination in the region (D7S1817 to D7S1824) in the AD families versus non-AD families (P = 0.03, sex-averaged; and P = 0.01, sex-specific). These results provide further evidence for the presence of an AD locus on chromosome 7q, as well as provide evidence suggesting that this locus may be paternally expressed.     

Landscape history,calcareous fen development and historical events in the Slovak Eastern Carpathians

We explored interactions among human activities, landscape development and changes in biotic proxies in two small calcareous spring fens in the Slovak Eastern Carpathians. These date back to cal. a.d. 930. Results of pollen, plant macrofossil, and mollusc analyses were compared with the settlement history. The regional pollen record reflected historical events and changes in the settlement density very well at both study sites. The natural mixed fir-beech-spruce forests with fern undergrowth were suppressed and replaced by light-demanding trees in the periods of high human impact (e.g. Wallachian colonization). The study area was affected several times by wars and raids followed by a consequent decline in the settlement density. Some of these events are well reflected in the pollen records that document tree recovery and decline of cereals, weeds, and pasture indicators. In comparison, only some landscape changes were reflected in the local fen development. Both spring fens originated after deforestation, Ro?kovce around a.d. 1347 and Mirol'a around a.d. 929. The most pronounced change involving the water regime stabilization and undisturbed development of plant and mollusc communities took place after the decline in human impact. We conclude that humans were the main drivers of landscape transformation in the last millennium; they directly created spring-fen ecosystems through deforestation and influenced fen species composition through husbandry activities.     

Horka, a Dominant Mutation of Drosophila, Induces Nondisjunction And, through Paternal Effect, Chromosome Loss and Genetic Mosaics

Fs(3) Horka (Horka) was described as a dominant female-sterile mutation of Drosophila melanogaster. Genetic and cytological data show that Horka induces mostly equational nondisjunction during spermatogenesis but not chromosome loss and possesses a dominant paternal effect: the X, second, third and the fourth chromosomes, but not the Y, are rendered unstable while undergoing spermatogenesis and may be lost in the descending zygotes. The frequency of Horka-induced chromosome loss is usually 2-4% but varies with the genetic background and can be over 20%. The X chromosome loss occurs during the gonomeric and the initial cleavage divisions. Loss of the X and fourth chromosomes shows no correlation. We propose, based on similarities in the mutant phenotypes with the chromosome destabilizing mutations nonclaret disjunctional and paternal loss, that the normal Horka(+) product is required for function of the centromeres and/or nearby regions. Horka is a convenient tool for the generation of gynandromorphs, autosome mosaics and for the study of gene expression in mosaics.     

Physical and Genetic Map of the Pasteurella multocida A:1 Chromosome

A physical and genetic map of the Pasteurella multocida A:1 genome was generated by using the restriction enzymes ApaI, CeuI, and NotI. The positions of 23 restriction sites and 32 genes, including 5 rrn operons, were localized on the 2.35-Mbp single circular chromosome. This report presents the first genetic and physical map for this genus.