Demographic history and genetic diversity in West Indian Coereba flaveola populations

The bananaquit (Coereba flaveola) has been well studied throughout the Caribbean region from a phylogenetic perspective. However, data concerning the population genetics and long-term demography of this bird species are lacking. In this study, we focused on three populations within the Lesser Antilles and one on Puerto Rico and assessed genetic and demographic processes, using five nuclear and two mitochondrial markers. We found that genetic diversity of bananaquits on Puerto Rico exceeds that on the smaller islands (Dominica, Guadeloupe and Grenada); this might reflect either successive founder events from Puerto Rico to Grenada, or more rapid drift in smaller populations subsequent to colonization. Population growth rate estimates showed no evidence of rapid expansion and migration was indicated only between populations from the closest islands of Dominica and Guadeloupe. Overall, our results suggest that a "demographic fission" model, considering only mutation and drift, but without migration, can be applied to these bananaquit populations in the West Indies.     

Demographic processes shaping genetic variation

Demographic processes modulate genome-wide levels and patterns of genetic variation via impacting effective population size independently of natural selection. Such processes include the perturbation of population distributions from external events shaping habitat landscape and internal factors shaping the probability of contemporaneous alleles in a population (coalescence). Several patterns have recently emerged: spatial and temporal heterogeneity in population structure have different influences on the persistence of new mutations and genetic variation, multi-locus analyses indicate that gene flow continues to occur during speciation and the incorporation of demographic processes into models of molecular evolution and association genetics approaches has improved statistical power to detect deviations from neutral-equilibrium expectations and decreased false positive rates.     

Rocks and clocks: linking geologic history and rates of genetic differentiation in anchialine organisms

The geologic history of a region can significantly impact the development of its flora and fauna, with past events shaping community patterns and evolutionary trajectories of species. In this context, islands are excellent “natural laboratories” for studying the fundamental processes of evolution due to their discrete geographical nature and dynamic geologic histories. An island system meeting these criteria is the Hawaiian Archipelago, which is ideal for testing how island geologic history influences the processes leading to population genetic variation and differentiation. One Hawaiian endemic whose evolutionary history is closely tied to the geology of the islands is the anchialine atyid shrimp Halocaridina, whose mitochondrial cytochrome oxidase I (COI) gene is hypothesized to be evolving at the rate of 20% per million years. To validate this rapid evolutionary rate, time since divergence estimates between geographically close, yet genetically distinct, populations were calculated for Halocaridina from anchialine habitats on the islands of Hawai’i, Maui, and O’ahu. On the younger (i.e., <1.5 million years) islands of Hawai’i and Maui, where all anchialine habitats occur in basalt, application of the Halocaridina molecular clock identified a strong correlation between levels of genetic divergence and the geologic age of the region inhabited by those populations. In contrast, this relationship weakened when similar analyses were conducted for Halocaridina from limestone anchialine habitats on the older (i.e., >2.75 million years) island of O’ahu. These results suggest geologic age, basin origin and/or composition are important factors that should be taken into consideration when conducting molecular clock analyses on anchialine flora and fauna as well as island populations in general.     

Demographic history and the low genetic diversity in Dipteryx alata (Fabaceae) from Brazilian Neotropical savannas

Genetic effects of habitat fragmentation may be undetectable because they are generally a recent event in evolutionary time or because of confounding effects such as historical bottlenecks and historical changes in species'' distribution. To assess the effects of demographic history on the genetic diversity and population structure in the Neotropical tree Dipteryx alata (Fabaceae), we used coalescence analyses coupled with ecological niche modeling to hindcast its distribution over the last 21 000 years. Twenty-five populations (644 individuals) were sampled and all individuals were genotyped using eight microsatellite loci. All populations presented low allelic richness and genetic diversity. The estimated effective population size was small in all populations and gene flow was negligible among most. We also found a significant signal of demographic reduction in most cases. Genetic differentiation among populations was significantly correlated with geographical distance. Allelic richness showed a spatial cline pattern in relation to the species'' paleodistribution 21 kyr BP (thousand years before present), as expected under a range expansion model. Our results show strong evidences that genetic diversity in D. alata is the outcome of the historical changes in species distribution during the late Pleistocene. Because of this historically low effective population size and the low genetic diversity, recent fragmentation of the Cerrado biome may increase population differentiation, causing population decline and compromising long-term persistence.     

Mitochondrial evidence for multiple radiations in the evolutionary history of small apes

Background  

Gibbons or small apes inhabit tropical and subtropical rain forests in Southeast Asia and adjacent regions, and are, next to great apes, our closest living relatives. With up to 16 species, gibbons form the most diverse group of living hominoids, but the number of taxa, their phylogenetic relationships and their phylogeography is controversial. To further the discussion of these issues we analyzed the complete mitochondrial cytochrome b gene from 85 individuals representing all gibbon species, including most subspecies.     

Demographic and genetic invasion history of a 9-year-old roadside population of Bunias orientalis L. (Brassicaceae)

The population history of a 9-year-old roadside population of the invasive plant Bunias orientalis was reconstructed by demographic analysis including size, position, age (determined by herbchronology) and RAPD-PCR patterns of individual plants. We evaluated emerging patterns of population growth and genetic structure during a full period of population development under typical site conditions (anthropogenic disturbance) and their possible consequences for the invasion potential of the species. The population has grown rapidly and continuously (though with slowing geometric population increase) during the 9 years since its foundation, filling the space available in the study area. Genetic variation (RAPD markers) was already high in the founder cohorts and remained at the same level throughout population development (variance fluctuations <15%). Both results may be related to the mowing management at the site which seems to promote population growth of B. orientalis relative to other co-occuring species and to prevent the genetic drift and the development of spatial genetic structure that would be expected under isolation-by-distance models. Large founder plants had comparatively low genetic variance and were more closely related to younger cohorts than were small founder plants, indicating that selection acted during population development. Overall, the current anthropogenic disturbance regimes may contribute to high genetic variability by artificially increasing gene flow and thereby promoting the adaptability of invasive species to the often unpredictable conditions at disturbed sites. Our approach using retrospective demographic investigation allows the detection of spatio-temporal microscale patterns in genetic and phenotypic variation. Thus it allows a thorough understanding of local invasions of perennial herbaceous plants. Received: 23 November 1998 / Accepted: 14 April 1999     

Demographic history of european populations of Arabidopsis thaliana

The model plant species Arabidopsis thaliana is successful at colonizing land that has recently undergone human-mediated disturbance. To investigate the prehistoric spread of A. thaliana, we applied approximate Bayesian computation and explicit spatial modeling to 76 European accessions sequenced at 876 nuclear loci. We find evidence that a major migration wave occurred from east to west, affecting most of the sampled individuals. The longitudinal gradient appears to result from the plant having spread in Europe from the east ~10,000 years ago, with a rate of westward spread of ~0.9 km/year. This wave-of-advance model is consistent with a natural colonization from an eastern glacial refugium that overwhelmed ancient western lineages. However, the speed and time frame of the model also suggest that the migration of A. thaliana into Europe may have accompanied the spread of agriculture during the Neolithic transition.     

Demographic and genetic interrelationships among the Gavlis of Dharwad

Lot of work has been done in recent years on the genetics of isolated and small population groups. But J. Sutter (1963) notes that these studies have not yielded satisfactory results, because these investigators have applied the formulae and models constructed by the mathematicians which are based on the assumption of panmixia, whereas panmixia cannot occur in human populations especially if the population is very small. Sometimes we speak of genetic drift and selection without taking into account the fact that the population at the same time is controlled by two most important demographic parameters of fertility and mortality which can alter genetic drift and selection. The geneticists are primarily interested in fertility. They want to determine, for any given couple, the number of offspring reaching the age of reproduction. One might therefore assume that the measurement of fertility should play a major role in population genetics. Thus, there is an urgent need for the establishment of meaningful relationship between demography and population genetics. In view of the above facts, an attempt is made in the present study to analyse the “Demographic and Genetic Interrelationships among the Gavlis of Dharwad” so as to throw light on some of the complex genetic issues like endogamy, inbreeding and selection potential.     

Conflict between genetic and phenotypic differentiation: the evolutionary history of a 'lost and rediscovered' shorebird

Understanding and resolving conflicts between phenotypic and genetic differentiation is central to evolutionary research. While phenotypically monomorphic species may exhibit deep genetic divergences, some morphologically distinct taxa lack notable genetic differentiation. Here we conduct a molecular investigation of an enigmatic shorebird with a convoluted taxonomic history, the White-faced Plover (Charadrius alexandrinus dealbatus), widely regarded as a subspecies of the Kentish Plover (C. alexandrinus). Described as distinct in 1863, its name was consistently misapplied in subsequent decades until taxonomic clarification ensued in 2008. Using a recently proposed test of species delimitation, we reconfirm the phenotypic distinctness of dealbatus. We then compare three mitochondrial and seven nuclear DNA markers among 278 samples of dealbatus and alexandrinus from across their breeding range and four other closely related plovers. We fail to find any population genetic differentiation between dealbatus and alexandrinus, whereas the other species are deeply diverged at the study loci. Kentish Plovers join a small but growing list of species for which low levels of genetic differentiation are accompanied by the presence of strong phenotypic divergence, suggesting that diagnostic phenotypic characters may be encoded by few genes that are difficult to detect. Alternatively, gene expression differences may be crucial in producing different phenotypes whereas neutral differentiation may be lagging behind.     

Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.)

Tomato (Solanum lycopersicum L.) has undergone intensive selection during and following domestication. We investigated population structure and genetic differentiation within a collection of 70 tomato lines representing contemporary (processing and fresh-market) varieties, vintage varieties and landraces. The model-based Bayesian clustering software, STRUCTURE, was used to detect subpopulations. Six independent analyses were conducted using all marker data (173 markers) and five subsets of markers based on marker type (single-nucleotide polymorphisms, simple sequence repeats and insertion/deletions) and location (exon and intron sequences) within genes. All of these analyses consistently separated four groups predefined by market niche and age into distinct subpopulations. Furthermore, we detected at least two subpopulations within the processing varieties. These subpopulations correspond to historical patterns of breeding conducted for specific production environments. We found no subpopulation within fresh-market varieties, vintage varieties and landraces when using all marker data. High levels of admixture were shown in several varieties representing a transition in the demarcation between processing and fresh-market breeding. The genetic clustering detected by using the STRUCTURE software was confirmed by two statistics, pairwise F(st) (θ) and Nei's standard genetic distance. We also identified a total of 19 loci under positive selection between processing, fresh-market and vintage germplasm by using an F(st)-outlier method based on the deviation from the expected distribution of F(st) and heterozygosity. The markers and genome locations we identified are consistent with known patterns of selection and linkage to traits that differentiate the market classes. These results demonstrate how human selection through breeding has shaped genetic variation within cultivated tomato.     

A universal microsatellite multiplex kit for genetic analysis of great apes

DNA profiling with microsatellite markers is a commonly used genetic method of studying the great apes. An efficient method of generating the genetic data is amplification of multiple microsatellites in a single PCR reaction. Here we describe a PCR multiplex in which 9 genetic markers can be amplified simultaneously, thereby saving time, expenses and DNA. This marker system can discriminate between all the great ape species except bonobos and chimpanzees. Furthermore, the cumulative probability of identity values were low for all 4 species tested.     

Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations

To infer the role of natural selection in shaping standing genetic diversity, it is necessary to assess the genomewide impact of demographic history on nucleotide diversity. In this study we analyzed sequence diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent nucleotide diversity, which was approximately 0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, rho, were 0.0064 and 0.0294, respectively. The summary statistics of nucleotide diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.     

Demographic parameters and life history of chimpanzees at Bossou, Guinea

Demographic parameters of wild chimpanzees at Bossou, Guinea, are presented and compared with those of other populations. The population size of Bossou chimpanzees has been stable over the last 26 years, except during two incidents of partial deforestation. The annual birth rate for a female (mean = 0.194, but 0.165 when the infant survived more than 4 years) and interbirth interval are not much different from those of other study sites. The primiparous age of Bossou chimpanzees, however, is far younger (mean = 10.9 years) than for all other known wild chimpanzee populations. The infant and juvenile survival rate is also the highest (female = 0.64, male = 0.52 for the first 8 years). As a result, the lifetime reproductive success of Bossou chimpanzees is estimated to be highest among long-term study sites. The rate of disappearance from Bossou dramatically increases during the adolescent stage, and most young chimpanzees disappear before or around maturation. Probably because the environmental capacity for chimpanzees at Bossou is at its limit, many young independent males, as well as females, have to disperse, though others may die. For chimpanzee alpha males of other populations, mature males may be needed as collaborators to defend resources. In the case of Bossou, however, a lack of adjacent groups, conspecific competitors, predators, and perhaps medium-sized mammals as prey for group hunting may eliminate this need of the alpha male for other males. The reasons why all males of other chimpanzee populations persist in being philopatric for life and maintain kin-related male bonds differing from most mammal species, including humans, are discussed.     

Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum

The Antarctic silverfish Pleuragramma antarcticum (Nototheniidae) is the most abundant pelagic fish inhabiting Antarctic waters. In this study we investigated, through partial sequencing of the D-loop mitochondrial region, samples collected at four different locations in the Southern Ocean, three in the Atlantic and one in the Pacific sector. Sampling was replicated in two different years at two locations. Sequence analysis showed a remarkably high polymorphism, with 110 haplotypes over the 256 investigated specimens, and about 80% of haplotypes occurring only once. Neutrality tests indicated that all samples were not at mutation-drift equilibrium, and suggested a past population expansion. This result was supported by the presence of a star-like topology in the D-loop gene tree, and by results of mismatch distribution. The start of the expansion was dated, using a specifically calibrated clock, between 111 and 126 thousand years ago. This value corresponds to the start of the cooling period that led to the last glaciation peak, and is in close agreement with a recently suggested range expansion for pelagic Antarctic ecosystems. Analysis of molecular variation indicated a small, though highly significant, value of differentiation between samples. This result, together with the lack of association between clades and geographical locations, indicates a weak population structure for the species.