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Colonization models and initial genetic diversity in the Americas.

The mode and tempo of colonization of the Americas established the initial pattern of continental genetic diversity. Despite a long history of study, the process of settlement remains controversial in terms of date, rate, and pattern. While there is agreement that Asia was the source population, several different models have been proposed for the colonization process. A classic model postulates a rapid spread of population ("blitzkrieg") from a small band of hunters entering through the corridor between the continental ice sheets circa 11,000 years B.P. Colonization occurred as a wave of expansion across the land masses of North and South America. An alternative model envisions the original colonists initially limiting settlement to the coastline, using boats, and entering the Americas at an earlier date, circa 13,500 B.P. Range expansion along this linear habitat from North to South America could be rapid without requiring population saturation of entire continental regions. These models have markedly different implications for genetic variation among Native Americans. The blitzkrieg colonization process would have generated multiple founder effects leading to extreme loss of genetic variation. Computer simulation of this model shows nearly complete fixation in 30 generations. Simulation of the coastal model, on the other hand, requires less extreme demographic assumptions and maintains substantial genetic variability after 100 generations. Although with the coastal model continental interiors are occupied less rapidly than with the blitzkrieg model, the coastal model allows earlier entry and rapid expansion to the southern limits of the hemisphere.

Emigration and Immigration↗

Controlling for the effects of history and nonequilibrium conditions in gene flow estimates in northern bullfrog (Rana catesbeiana) populations.

Nonequilibrium conditions due to either allopatry followed by secondary contact or recent range expansion can confound measurements of gene flow among populations in previously glaciated regions. We determined the scale at which gene flow can be estimated among breeding aggregations of bullfrogs (Rana catesbeiana) at the northern limit of their range in Ontario, Canada, using seven highly polymorphic DNA microsatellite loci. We first identified breeding aggregations that likely share a common history, determined from the pattern of allelic richness, factorial correspondence analysis, and a previously published mtDNA phylogeography, and then tested for regional equilibrium by evaluating the association between pairwise F(ST) and geographic distance. Regional breeding aggregations in eastern Ontario separated by <100 km were determined to be at or near equilibrium. High levels of gene flow were measured using traditional F-statistics and likelihood estimates of Nm. Similarly high levels of recent migration (past one to three generations) were estimated among the breeding aggregations using nonequilibrium methods. We also show that, in many cases, breeding aggregations separated by up to tens of kilometers are not genetically distinct enough to be considered separate genetic populations. These results have important implications both for the identification of independent "populations" and in assessing the effect of scale in detecting patterns of genetic equilibrium and gene flow.

Animals↗

Mitochondrial haplotype distribution, seed dispersal and patterns of postglacial expansion of ponderosa pine.

Maternally inherited mtDNA in a secondary contact zone of ponderosa pine revealed a cline less than 10 km wide - much narrower than previously described. A survey of 76 populations gave no evidence either of intermixing or of a mosaic contact zone. Such sharp contact zones are consistent with diffusive range expansion, rather than long distance colonization. However, evidence for long distance seed dispersal events was found in two populations where haplotypes were observed far from their main area of occurrence. The results suggest a small number of long distance colonists with diffusive dispersal from these centres.

Biological Evolution↗

Evolution in invasive plants: implications for biological control.

Evidence is increasing that invasive plants can undergo rapid adaptive evolution during the process of range expansion. Here, we argue that evolutionary change during invasions will also affect plant-antagonist interactions and, thus, will have important implications for biological control programmes targeted at invasive plants. We explore how altered selection in the new range might influence the evolution of plant defence (resistance and tolerance) and life history. The degree to which such evolutionary processes might affect biological control efficacy is largely unexplored. We hope that, by testing the hypotheses that we propose here, a closer link can be established between biological control and evolutionary biology, to the benefit of both disciplines.

Journal Article↗

The colonization history and present-day population structure of the european great tit (Parus major major)

The colonization history and present-day population structure of the European subspecies of the great tit Parus major major were studied using mitochondrial control region sequences. One major haplotype was found in all but one of the eight sampled populations from Spain to northern Finland. The other haplotypes differed from the common one by just a few substitutions; the overall nucleotide diversity was 0.00187 and haplotype diversity 0.8633. No population structuring was detected. The mismatch distribution followed the expected distribution of an expanding population. The estimated time to the most recent common ancestor coincides with the last glacial period. The results suggest that P. m. major survived the last glacial period in a single isolated refuge probably by the Mediterranean Sea. This was followed by rapid colonization of the European continent and population growth. The most recent range expansion northwards is still occurring. Gene flow between the sampled populations is extensive. It is aided by juvenile dispersal, long-distance movements of juvenile flocks and partial migration in the northern parts of the great tit's range.

Journal Article↗

Geographic distribution and recombination of genomic fragments on the short arm of chromosome 2 of Arabidopsis thaliana.

Range expansion from Pleistocene refugia and anthropogenic influences contribute to the present distribution pattern of Arabidopsis thaliana. We scored a genome-wide set of CAPSs and found two markers with an east-west geographic distribution across the Eurasian range of the species. Regions around the two SNPs were sequenced in 98 accessions, including newly collected plants from Middle Asia and Western Siberia. These regions correspond to a gene ( approximately 1500 bp) and a non-coding region ( approximately 500 bp) 300 kbp apart on chromosome 2. Nucleotide diversities, pi, of the two sequenced fragments were 0.0032 and 0.0130. The haplotypes of both sequences belonged to one of two groups: a rather uniform "Asian" and a more variable "European" haplotype group, on the basis of non-disjunct clusters of SNPs. Recombination between "Asian" and "European" haplotypes occurs where they meet. Especially in the "European" haplotype, many rare SNP variants representing independent mutations are scattered among the shared haplotype-specific SNPs. This agrees with previous suggestions of two large haplotype groups in A. thaliana and the post-glacial colonization of central Europe from the east and the west. A clear correlation between climatic factors and the haplotype distribution may reflect the dispersal history rather than local climate adaptation. The pattern of SNP variation within the contiguous sequences explains why only a minority of SNPs selected across the genome show evidence of this geographic pattern.

Arabidopsis↗

Involvement of the calcium inward current in cardiac impulse propagation: induction of unidirectional conduction block by nifedipine and reversal by Bay K 8644.

In general, the fast sodium inward current (INa) is regarded as the main inward current ensuring fast and safe excitation of the normally polarized working myocardium. However, under conditions of locally delayed excitation in the millisecond range, the slow inward current (ICa) might additionally contribute to the success of impulse propagation. This hypothesis was tested in patterned growth cultures of neonatal rat ventricular myocytes, which consisted of narrow cell strands connected to large rectangular cell monolayers, where INa or ICa could be modified in the narrow cell strand adjacent to the expansion by a microsuperfusion system. As assessed during antegrade (strand-->expansion) propagation under control conditions using a system for multiple site optical recording of transmembrane voltage (MSORTV), this cell pattern gave either rise to local activation delays at the expansion ranging from 0.5 to 4 ms (dcontrol), or it induced undirectional conduction blocks (UCBs) in the antegrade direction. Irrespective of the size of dcontrol, suppression of the sodium current with tetrodotoxin confined to the cell strand adjacent to the expansion invariably induced UCB in the antegrade direction. If dcontrol was > 1 ms, UCB could also be elicited by suppression of ICa alone with nifedipine. Conversely, if UCB was present under control conditions, the inclusion of Bay K 8644 in the microsuperfusion established successful bidirectional conduction. These results suggest that ICa can be critically important for the success of impulse propagation across abrupt expansions of excitable tissue even if INa is not concurrently depressed.

3-Pyridinecarboxylic acid, 1,4-dihydro-2,6-dimethy↗

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.

Animals↗

The role of ecologic diversification in sibling speciation of Empidonax flycatchers (Tyrannidae): multigene evidence from mtDNA.

Avian genera characterized by sibling species with distinctive habitat preferences present an evolutionary enigma in view of the more commonplace occurrence of syntopic congeners that differ strikingly in colour and pattern. No existing theory has explained the evolutionary background that led to these differences. Here we propose that great phenotypic similarity among some groups of sibling species limits their coexistence and that clues to their radiation can be seen in patterns of geographical occurrence. To illustrate our thesis we focused on the New World flycatcher genus Empidonax, a group of 15 species notorious for their great phenotypic similarity. Using 3069 base pairs of mitochondrial DNA from four genes, we produced a complete molecular phylogeny that identified four clades, three of which represent close relatives. The fourth clade includes only E. virescens, which apparently has no close living relatives. The majority of species, including many distant relatives, are completely (58.1%) or essentially (6.7%) allopatric in breeding distribution and exhibit striking ecological segregation into distinctive climate-vegetation zones. Even where ranges overlap, occupancy of the same habitat by different species is rare. Phylogenetic and distributional patterns in Empidonax suggest a peripatric model of stepwise colonization and then range expansion of small groups of pioneers during glacial periods into initially enlarging, distinctive habitats destined to be widespread during interglacials. Vicariance is not indicated in the absence of barriers of appropriate age and geographical position. Rapoport's rule that northern species have larger ranges than southern species is strongly supported.

Animals↗

Population structure and population history of Anopheles dirus mosquitoes in Southeast Asia.

Separating the confounding effects of long-term population history from gene flow can be difficult. Here, we address the question of what inferences about gene flow can be made from mitochondrial sequence data in three closely related species of mosquitoes, Anopheles dirus species A, C, and D, from southeast Asia. A total of 84 sequences of 923 bp of the mitochondrial cytochrome oxidase I gene were obtained from 14 populations in Thailand, Myanmar, and Bangladesh. The genealogy of sequences obtained from two populations of AN: dirus C indicates no contemporary gene flow between them. The F(ST) value of 0.421 therefore probably represents a recent common history, perhaps involving colonization events. Anopheles dirus A and D are parapatric, yet no differentiation was seen either within or between species. The starlike genealogy of their haplotypes, smooth unimodal mismatch distributions, and excess of low frequency mutations indicate population expansion in An. dirus A and D. This, rather than widespread gene flow, explains their low within-species F(ST) values (0.018 and 0.022). The greater genetic diversity of An. dirus D suggests that expansion occurred first in species D and subsequently in species A. The current geographical separation and low hybrid fitness of these species also argue against ongoing interspecific gene flow. They suggest instead either historical introgression of mtDNA from An. dirus D into species A followed by independent range expansions, or a selective sweep of mtDNA that originated in An. dirus D. While not excluding contemporary gene flow, historical population processes are sufficient to explain the data in An. dirus A and D. The genealogical relationships between haplotypes could not be used to make inferences of gene flow because of extensive homoplasy due to hypervariable sites and possibly also recombination. However, it is concluded that this approach, rather than the use of fixation indices, is required in the future to understand contemporary gene flow in these mosquitoes. The implications of these results for understanding gene flow in another important and comparable group of malaria vector mosquitoes in Africa, the An. gambiae complex, are also discussed.

Animals↗

Patterns of trait divergence between populations of the meadow grasshopper, Chorthippus parallelus.

To understand the process of speciation, we need to identify the evolutionary phenomena associated with divergence between populations of the same species. A powerful approach is to compare patterns of trait differences between populations differing in their evolutionary histories. A recent study of genetic divergence between populations of the meadow grasshopper Chorthippus parallelus, from different locations around Europe has allowed us to use this species to investigate which aspects of evolutionary history are associated with divergence in morphology and mating signals. During the last glaciation C. parallelus was confined to a number of refugia in southern Europe and has subsequently recolonized the northern part of the continent. This process of isolation followed by range expansion has created populations differing markedly in their evolutionary pasts--some have been isolated from one another for thousands of years, others have undergone repeated founder events, and others now live in sympatry with a closely related species. Using laboratory-reared grasshoppers from 12 different populations with a range of evolutionary histories, we quantify differences in morphology, chemical signals, and male calling-song. The observed pattern of divergence between these populations is then compared with the pattern predicted by hypotheses about what drives divergence. This comparison reveals that long periods in allopatry and processes associated with repeated founder events are both strongly associated with divergence.

Animals↗

Delayed population explosion of an introduced butterfly.

1. The causes of lagged population and geographical range expansions after species introductions are poorly understood, and there are relatively few detailed case studies. 2. We document the 29-year history of population dynamics and structure for a population of Euphydryas gillettii Barnes that was introduced to the Colorado Rocky Mountains, USA in 1977. 3. The population size remained low (< 200 individuals) and confined to a single habitat patch (approximately 2.25 ha) to 1998. These values are similar to those of many other populations within the natural geographical range of the species. 4. However, by 2002 the population increased dramatically to > 3000 individuals and covered approximately 70 ha, nearly all to the south of the original site. The direction of population expansion was the same as that of predominant winds. 5. By 2004, the butterfly's local distribution had retracted mainly to three habitat patches. It thus exhibited a 'surge/contraction' form of population growth. Searches within 15 km of the original site yielded no other new populations. 6. In 2005, butterfly numbers crashed, but all three habitat patches remained occupied. The populations within each patch did not decrease in the same proportions, suggesting independent dynamics that are characteristic of metapopulations. 7. We postulate that this behaviour results, in this species, in establishment of satellite populations and, given appropriate habitat structure, may result in lagged or punctuated expansions of introduced populations.

Animals↗

Phylogeography and conservation genetics of the Columbia spotted frog (Rana luteiventris; Amphibia, Ranidae).

The Columbia spotted frog (Rana luteiventris) has a widespread distribution in western Canada and the western US, although the southern reach of its range is highly fragmented into several isolated populations. Threats from various factors have raised concerns regarding the long-term survival of many small, isolated populations. Here, we report a study designed to determine the phylogeographic and conservation genetic parameters of R. luteiventris in the western US. Mitochondrial DNA (mtDNA) sequences were examined for phylogeographic structuring using phylogenetic reconstruction methods, coupled with networking and nested clade analyses. These methods permitted a distinction to be made between historic and demographic forces acting to generate geographical patterning of genetic variation. Phylogenetic analysis revealed four geographically correlated monophyletic clades. Three of these clades correspond to well-defined, nonoverlapping geographical locations in the fragmented portion of the range. The other is comprised of all samples collected from the contiguous range and includes one isolate from northern Wyoming. Networking and nested clade analyses confirmed these results and revealed that historical processes, such as range expansion and vicariance, rather than recurrent gene flow are likely responsible for observed patterns of genetic variation. A measure of genetic variation (theta = 4N(e)mu) revealed that R. luteiventris populations in Utah have a relatively low amount of genetic variation compared with populations in the continuous portion of the range.

Animals↗

Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations.

Human social organization can deeply affect levels of genetic diversity. This fact implies that genetic information can be used to study social structures, which is the basis of ethnogenetics. Recently, methods have been developed to extract this information from genetic data gathered from subdivided populations that have gone through recent spatial expansions, which is typical of most human populations. Here, we perform a Bayesian analysis of mitochondrial and Y chromosome diversity in three matrilocal and three patrilocal groups from northern Thailand to infer the number of males and females arriving in these populations each generation and to estimate the age of their range expansion. We find that the number of male immigrants is 8 times smaller in patrilocal populations than in matrilocal populations, whereas women move 2.5 times more in patrilocal populations than in matrilocal populations. In addition to providing genetic quantification of sex-specific dispersal rates in human populations, we show that although men and women are exchanged at a similar rate between matrilocal populations, there are far fewer men than women moving into patrilocal populations. This finding is compatible with the hypothesis that men are strictly controlling male immigration and promoting female immigration in patrilocal populations and that immigration is much less regulated in matrilocal populations.

Bayes Theorem↗

Patterns of diversification in two African forest shrews: Sylvisorex johnstoni and Sylvisorex ollula (Soricidae, Insectivora) in relation to paleo-environmental changes.

We analysed the phylogeographic patterns of two congeneric and syntopic species of forest shrews and compared them with biogeographical scenarios proposed for the Central African tropical forest. Our results, based on 82 partial 16s rRNA mitochondrial sequences, suggest that both species must have originated in the Plio-Pleistocene and that their haplotype distributions could reflect the effect of forest fragmentation and expansion associated with paleoclimatic fluctuations during the Pleistocene. However, it seems that the two species responded very differently to environmental changes. While Sylvisorex johnstoni populations exhibit ancient haplotype segregation that may even represent currently unrecognised allopatric species, Sylvisorex ollula haplotypes are much less differentiated and suggest that this taxon has undergone a recent range expansion. The observed differences between these taxa may be explained by their presumably different ecological requirements and colonisation abilities, which in turn may be the result of a significant difference in body size between the two species. In conclusion, our results suggest that it is necessary to incorporate several ecologically well-documented species in studies that attempt to infer evolutionary processes from phylogeographic patterns

Africa, Central↗

Impact of target lesion calcification on coronary stent expansion after rotational atherectomy.

BACKGROUND: Calcified lesions carry the risk of suboptimal stent expansion. The purpose of this study was to investigate the impact of target lesion calcification on intracoronary ultrasound (ICUS) guided stent expansion after rotational atherectomy. METHODS: Stent expansion was assessed by ICUS in 39 patients with the aid of the proximal stent/proximal reference lumen, the minimal stent/mean reference lumen, and the minimal stent/minor reference lumen ratios as well as the symmetry index. Thirty-nine stent implantations in uncalcified lesions served for comparison. RESULTS: Relative stent expansion ranged between 76.3% +/- 6.7% and 98.4% +/- 16.4%. Categorization according to an ICUS-derived arc of superficial lesion calcium of <180 degrees (average 102 +/- 74 degrees) or >180 degrees (average 248 +/- 71 degrees) revealed decreased stent symmetry in calcified lesions >180 degrees compared with the control group (P <.05). Despite a trend toward less expansion with increasing calcium load, no significant differences of the lumen area ratios between the study groups was present. CONCLUSION: Rotational atherectomy before ICUS-guided stent implantation enables adequate stent expansion even in significant superficial target lesion calcification.

Aged↗

Age-related persistent clonal expansions of CD28(-) cells: phenotypic and molecular TCR analysis reveals both CD4(+) and CD4(+)CD8(+) cells with identical CDR3 sequences.

In a small group of subjects we had identified persistent expansions (range 6-72%) of CD4(+)CD8(+) double-positive (DP) peripheral blood (PB) cells which express the CD8 alpha/alpha homodimer. Here, DP cells present in a larger cohort were further investigated and found by FACS analysis to express a single or a dominant TCRBV family. In these subjects, with a mean age of about 64 years, expansions of CD4(+) cells with the same TCRBV family specificity as in the respective DP cells also were consistently detected. TCR heterogeneity of the dominant TCRBV family was specifically evaluated: The amplified CDR3 region was cloned and found to consist of one single or two largely dominant sequence patterns. Furthermore, cloning of the CDR3 region from FACS-sorted DP, CD4(+), or CD8(+) cells indicates that both DP and CD4(+), but not CD8(+) cells, isolated from the same individual possess a striking identity of the CDR3 regions. As indicated by FACS analysis, the clonally expanded cells occur in the CD4(+)CD28(-) cells. Taken together, these results suggest that expanded CD4(+)CD28(-) cells might also acquire CD8 alpha/alpha expression and become DP and imply that CD4 clonality is a more frequent phenomenon than previously suspected. In conclusion, the persistent expansions described in this report represent a novel group of age-related benign clonal expansions of still undefined significance of a rare CD28(-) T cell subset.

Adult↗

Phylogeographic study reveals the origin and evolutionary history of a Rhododendron species complex in Taiwan.

This study infers a single origin and a once-widespread distribution of the Rhododendron pseudochrysanthum species complex in Taiwan based on chloroplast DNA (cpDNA) variation. In total, 124 individuals from five endemic Rhododendron species were used for amplifications of two chloroplast intergenic spacers: trnL-trnF and atpB-rbcL. The haplotype and nucleotide diversities were much lower for the R. pseudochrysanthum complex, comprised of the species R. pseudochrysanthum, R. morii, Rhododendron rubropunctatum, and Rhododendron hyperythrum, than for Rhododendron formosanum. Two measures of pairwise population differentiation, N(ST) and F(ST), consistently revealed mostly non-significant levels of genetic divergence between populations of the R. pseudochrysanthum complex. No genetic difference was found among the four species of the R. pseudochrysanthum complex by analysis of molecular variance (AMOVA), which is concordant with the parsimonious topology of cpDNA haplotypes for the complex. Nested clade analysis (NCA) of the cpDNA haplotypes indicated that restricted gene flow with isolation-by-distance characterized the recolonization pattern of the R. pseudochrysanthum complex. In contrast, the NCA analysis indicated a contiguous range expansion for cpDNA haplotypes of R. formosanum. This research suggests a once-widespread distribution of the R. pseudochrysanthum complex probably via north-to-south colonization of mid-elevations during low-temperature periods of the Pleistocene. Population fragmentation followed the warmer climate which began in the Holocene and resulted in the present-day range contraction into high elevations.

DNA, Chloroplast↗