Severe Bottleneck Research Articles

Microsatellite Analysis of Three Subspecies of Elk (Cervus elaphus) in California

A total of 676 elk (Cervus elaphus) were genotyped at 16 tetranucleotide microsatellite loci to evaluate genetic differences among 3 subspecies of elk in California: tule (C. e. nannodes), Roosevelt (C. e. roosevelti), and Rocky Mountain (C. e. nelsoni) elk. Of the 13 populations analyzed, 5 represented tule elk herds, 3 were Roosevelt elk, 2 were Rocky Mountain elk, and 3 were of uncertain taxonomic status. Overall, populations averaged between 7 and 8 alleles per locus, with observed heterozygosity values ranging from 0.33 to 0.58 per population. Tule elk, which experienced a severe bottleneck in the 1870s, had consistently less genetic diversity than the other subspecies. All 3 subspecies were significantly differentiated, with the greatest genetic distance seen between the tule and Roosevelt subspecies. Assignment of individuals to subspecies using microsatellite data was nearly 100% accurate. Despite the past population bottleneck, significant differences were found among the tule elk herds. Assignment testing of elk from Modoc, Siskiyou, and Shasta counties to determine subspecific status of individuals suggested that these populations contained both Roosevelt and Rocky Mountain elk and their hybrids, indicating that these elk subspecies interbreed where subspecies coexist.

Population genetics of Scirtothrips perseae: tracing the origin of a recently introduced exotic pest of Californian avocado orchards, using mitochondrial and microsatellite DNA markers

AbstractThe Californian avocado industry has recently been impacted by the establishment of three exotic arthropod pests that are native to Mexico and Central America. Establishment of all three pests is thought to have resulted from illegal movement of host plants (avocado) into California. To identify likely sources and routes of entry of such pest invasions, we examined the population genetics of the most recent invader, avocado thrips [Scirtothrips perseae Nakahara (Thysanoptera: Thripidae)], using mitochondrial DNA (mtDNA) and microsatellite markers. The mtDNA sequences revealed three geographically distinct and divergent lineages, of which the mtDNA haplotypes of Californian individuals were most closely related to populations in the center of the pest's native range. Analysis of allele frequencies at four microsatellite loci added resolution, indicating Coatepec Harinas, Mexico, as the most likely source of the Californian population. Statistically, we did not detect any bottleneck in population size associated with the invasion of California. However, estimates of the effective population size of the invading population suggest that a severe bottleneck occurred, indicating that the quantity of host‐plant material entering California was small. Our findings implicate Coatepec Harinas, a large avocado germplasm and breeding center, as the most likely source of the introduced Californian population of S. perseae and as a likely source of previous and future avocado pest introductions. Efforts to identify natural enemies of S. perseae for biological control should focus on Coatepec Harinas and immediate surrounds. Moreover, identification of the source of invasive pests enables the establishment and enforcement of plant quarantine and free‐trade protocols.

Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtusa: implications for management and conservation

We investigated 25 natural populations of Chamaecyparis obtusa using 51 cleaved amplified polymorphic sequence (CAPS) markers, which were developed using information on sequence-tagged sites (STS) in Cryptomeria japonica. Most CAPS markers have codominant expression patterns, and are suitable for population studies because of their robustness and convenience. We estimated various genetic diversity parameters, including average heterozygosity (H(e)) and allelic richness and found that the more peripheral populations tended to have lower genetic diversity than central populations, in agreement with a previous theoretical study. The overall genetic differentiation between populations was low, but statistically significant (G(ST)=0.039), and similar to the level reported in a previous allozyme study. We attempted to detect non-neutral loci associated with local adaptation to clarify the relationship between the fixation index (F(ST)) and H(e) values for each locus and found seven candidates non-neutral loci. Phylogenetic tree analysis of the populations and Bayesian clustering analysis revealed a pattern of gradually increasing isolation of populations with increasing geographical distance. Three populations had a high degree of linkage disequilibrium, which we attribute to severe bottlenecks due to human disturbance or competition with other species during their migration from refugia after the most recent glaciation. We concluded that the small populations in western Japan and in Kanto district are more important, from a conservation perspective, than the populations in central Japan, due to their genetic divergence, relatively small sizes and restricted areas.

Genetic variation in Holocene bowhead whales from Svalbard

Bowhead whales (Balaena mysticetus) are distributed in the Arctic in five putative stocks. All stocks have been heavily depleted due to centuries of exploitation. In the present study, nucleotide sequence variation of the mitochondrial control region was determined from bone remains of 99 bowhead whales. The bones, 14C dated from recent to more than 50,000 bp, were collected on Svalbard (Spitsbergen) and are expected to relate to ancestors of the today nearly extinct Spitsbergen stock. Fifty-eight haplotypes were found, a few being frequent but many only found in one individual. The most abundant haplotypes of the Spitsbergen stock are the same as those most abundant in the extant Bering-Chukchi-Beaufort (BCB) Seas stock of bowhead whales. Although F(ST) indicates a slight but statistically significant genetic differentiation between the Spitsbergen and the BCB stocks this was not considered informative due to the very high levels of genetic diversity of mitochondrial DNA haplotypes in both bowhead whale stocks. Other measures such as K(ST) also indicated very low genetic differentiation between the two populations. Nucleotide diversity and haplotype diversity showed only minor differences between the Spitsbergen and BCB stocks. The data suggest that the historic Spitsbergen stock--before the severe bottleneck caused by whaling--did not have substantially more genetic variation than the extant BCB stock. The similar haplotypes of the Holocene Svalbard samples and the current BCB stock indicate significant migration between these two stocks and question the current designation of five distinct stocks of bowhead whales in the Arctic.

Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei: Cyprinidae)

The origins and phylogenetic patterns were assessed for G. przewalskii and G. eckloni by analyzing the complete mtDNA cytochrome b gene sequence (1140bp). Phylogenetic analyses further supported that there were three mtDNA lineages (A-C) identified in G. przewalskii and G. eckloni, demonstrating that outer rakers of the first gill have little significance in the phylogeny of the Gymnocypris fishes. The network established showed that G. eckloni of the Yellow River specific haplotype A1 was a founder and it radiated all haplotypes of G. przewalskii which suggested G. przewalskii might only originate from one of two maternals of G. eckloni from the Yellow River. Fs test and mismatch analysis showed at least two expansion events in the population of G. przewalskii about 0.2734 Ma and 0.0658 Ma, while G. eckloni from Qaidam Basin could have experienced severe bottleneck effect about 0.0693 Ma. The population expansion was detected in subclades A1 and A21 with the most recent common ancestor (TMRCA) about 0.2308 +/- 0.01 Ma and 0.1319 +/- 0.015 Ma, respectively, which were within the geological age range of Gonghe Movement event that caused the separation of Lake Qinghai from the upper Yellow River. These results suggested the effect of the fish diversification by rapid uplift of the Qinghai-Tibetan Plateau in the Late Pleistocene.

Conservation genetics of the imperilled Barbary red deer in Tunisia

AbstractBarbary red deer Cervus elaphus barbarus from three areas in Tunisia (n=30) were analysed for genetic variability at 13 microsatellite loci and 680 bp of the mitochondrial control region. Barbary red deer, the only African deer taxon, are presently confined to a small area along the Tunisian–Algerian border and underwent a severe bottleneck in the middle of the 20th century with, on the Tunisian side, possibly only seven animals left. The genetic data showed signs of inbreeding and reflected the bottleneck event. Variability was on the lower end of the range previously reported for red deer (number of haplotypes=two, observed and expected heterozygosity 0.46 and 0.78, respectively) but not as low as might have been feared in view of the population's demographic history. The three sampling sites – among them the reserve at El Feidja from which, apart from Algerian immigrants, all extant Tunisian red deer originate – did not show any sign of genetic differentiation. The Tunisian red deer can thus probably be considered a single, genetically homogeneous population. Implications for management and conservation of the genetic findings are discussed.

Grinding up Wheat: A Massive Loss of Nucleotide Diversity Since Domestication

Several demographic and selective events occurred during the domestication of wheat from the allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated wheat has since been affected by other historical events. We analyzed nucleotide diversity at 21 loci in a sample of 101 individuals representing 4 taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum, and bread wheats) to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent with a single domestication event and identify 2 genetically different groups of bread wheat. The wild group is not highly polymorphic, with only 212 polymorphic sites among the 21,720 bp sequenced, and, during domestication, diversity was further reduced in cultivated forms--by 69% in bread wheat and 84% in durum wheat--with considerable differences between loci, some retaining no polymorphism at all. Coalescent simulations were performed and compared with our data to estimate the intensity of the bottlenecks associated with domestication and subsequent selection. Based on our 21-locus analysis, the average intensity of domestication bottleneck was estimated at about 3--giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes departed from the empirical distribution of most loci, suggesting that they might have been selected during domestication or breeding. We detected a departure from the null model of demographic bottleneck for the hypothetical gene HgA. However, the atypical pattern of polymorphism at this locus might reveal selection on the linked locus Gsp1A, which may affect grain softness--an important trait for end-use quality in wheat.

Combined ecological niche modelling and molecular phylogeography revealed the evolutionary history of Hordeum marinum (Poaceae) — niche differentiation, loss of genetic diversity, and speciation in Mediterranean Quaternary refugia

The Hordeum marinum species group consists of two annual grasses of western Eurasian saline meadows or marshes. The two grasses split in the Quaternary about two million years ago. Hordeum marinum and the diploid of Hordeum gussoneanum (2x) co-occur throughout the Mediterranean basin, while the autotetraploid cytotype of H. gussoneanum (4x) overlaps with its diploid progenitor geographically only in the utmost Eastern Mediterranean, extending from there eastwards into Asia. Using chloroplast sequences of the trnL-F region, six newly developed chloroplast microsatellite loci, ecological predictive models based on climate data, and the present geographical distribution of the two species we analysed differentiation processes in the H. marinum group. The chloroplast data indicated clear differences in the history of both species. For H. marinum we found a subdivision between genetically variable populations from the Iberian Peninsula and the more uniform populations from the remaining Mediterranean. As an explanation, we assume Pleistocene fragmentation of an earlier widespread population and survival in an Iberian and a Central Mediterranean glacial refuge. Chloroplast variation was completely absent within the cytotypes of H. gussoneanum, indicating a severe and recent genetic bottleneck. Due to this lack of chloroplast variation only the combination of ecological habitat modelling with molecular data analyses allowed conclusions about the history of this taxon. The distribution areas of the two cytotypes of H. gussoneanum overlap today in parts of Turkey, indicating an area with similar climate conditions during polyploid formation. However, after its origin the polyploid cytotype underwent a pronounced ecological shift, compared to its diploid progenitor, allowing it to colonize mountainous inland habitats between the Mediterranean basin and Afghanistan. The extant sympatric occurrence of H. marinum and H. gussoneanum 2x in the Mediterranean region is interpreted as a result of secondary contact after fast Holocene range expansion out of different ice age refugia.

Molecular evidence for a recent founder event in the UK populations of the Adonis blue butterfly (Polyommatus bellargus)

Contrary to accepted theories of post-glacial colonisation of the UK approximately 10,000 year BP (yBP), historical population data for Polyommatus bellargus suggests the butterfly was either extremely rare or not present before 1775. We examined the phylogeography of the species by sequencing the ‘hypervariable’ mitochondrial control region of UK and French butterflies. Overall, 22 polymorphic nucleotide sites were identified within the control region. French specimens were highly variable, with 17 polymorphic sites, whereas most UK specimens were monomorphic. Average nucleotide diversity was 0.026 (SD 0.016, n = 8) in France, whilst the UK values ranged from 0.00 (n = 6) (for every UK population outside Dorset, n = 43) to 0.01 (SD 0.008, n = 7) (Dorset). The mean number of pairwise differences among the French samples was 7.42, whilst the UK values ranged from 0.00 (all populations except Dorset) to 0.295 (Dorset). One French haplotype differed from the predominant UK version by just a single nucleotide substitution. It seems implausible that the species can have been resident in the UK for 10,000 years without accumulating variation at this mitochondrial region. Thus, the results suggest that either a severe genetic bottleneck or founder event has occurred recently in the UK.

Genetic diversity and historical population structure of Schizopygopsis pylzovi (Teleostei: Cyprinidae) in the Qinghai–Tibetan Plateau

Summary1. Complete sequences of 1140 base pair of the cytochrome b gene from 133 specimens were obtained from nine localities including the inflow drainage system, isolated lakes and outflow drainage system in Qinghai–Tibetan Plateau to assess genetic diversity and to infer population histories of the freshwater fish Schizopygopsis pylzovi.2. Nucleotide diversities (π) were moderate (0.0024–0.0045) in populations from the outflow drainage system and Tuosuo Lake, but low (0.0018–0.0021) in populations from Qiadam Basin. It is probable that the low intra‐population variability is related with the paleoenvironmental fluctuation in Qiadam Basin, suggesting that the populations from Qiadam Basin have experienced severe bottleneck events in history.3. Phylogenetic tree topologies indicate that the individuals from different populations did not form reciprocal monophyly, but the populations from the adjacent drainages cluster geographically. Most population pairwise FST tests were significant, with non‐significant pairwise tests between Tuosu Lake and Tuosuo Lake in the north‐west of the Qinghai–Tibetan Plateau. Analysis of molecular variance (amova) indicates that the significant genetic variation was explained at the levels of catchments within and among, not among specific boundaries or inflow and outflow drainage systems.4. The nested clade phylogeographical analysis indicates that historical processes are very important in the observed geographical structuring of S. pylzovi, and the contemporary population structure and differentiation of S. pylzovi may be consistent with the historical tectonic events occurred in the course of uplifts of the Qinghai–Tibetan Plateau. Fluctuations of the ecogeographical environment and major hydrographic formation might have promoted contiguous range expansion of freshwater fish populations, whereas the geological barriers among drainages have resulted in the fragmentation of population and restricted the gene flow among populations.5. The significantly large negative Fs‐value (−24.91, P < 0.01) of Fu's Fs‐test and the unimodal mismatch distribution indicate that the species S. pylzovi underwent a sudden population expansion after the historical tectonic event of the Gonghe Movement.6. The results of this study indicate that each population from the Qinghai–Tibetan Plateau should be managed and conserved separately and that efforts should be directed towards preserving the genetic integrity of each group.

HISTORICAL RANGE EXPANSION DETERMINES THE PHYLOGENETIC DIVERSITY INTRODUCED DURING CONTEMPORARY SPECIES INVASION

For a species rapidly expanding its geographic range, such as during biological invasion, most alleles in the introduced range will have their evolutionary origins in the native range. Yet, the way in which historical processes occurring over evolutionary time in the native range contribute to the diversity sampled during contemporary invasion is largely unknown. We used chloroplast DNA (cpDNA) gene genealogies and coalescent methods to study two congeneric plants, Silene latifolia and S. vulgaris. We examined how phylogenetic diversity was shaped by demographic growth and historical range expansions in the native European range, and how this history affected the diversity sampled during their recent invasion of North America. Genealogies from both species depart from neutrality, likely as a result of demographic expansion in the ancestral range, the timing of which corresponds to shortly after each species originated. However, the species differ in the spatial distribution of cpDNA lineages across the native range. Silene latifolia shows a highly significant phylogeographic structure that most likely reflects different avenues of the post-glacial expansion into northern Europe from Mediterranean refugia. By contrast, cpDNA lineages in S. vulgaris have been widely scattered across Europe during, or since, the most recent post-glacial expansion. These different evolutionary histories resulted in dramatic differences in how phylogenetic diversity was sampled during invasion of North America. In S. latifolia, relatively few, discrete invasion events from a structured native range resulted in a rather severe genetic bottleneck, but also opportunities for admixture among previously isolated lineages. In S. vulgaris, lack of genetic structure was accompanied by more representative sampling of phylogenetic diversity during invasion, and reduced potential for admixture. Our results provide clear insights into how historical processes may feed forward to influence the phylogenetic diversity of species invading new geographic ranges.

Efficient repeated low-dose intravaginal infection with X4 and R5 SHIVs in rhesus macaque: Implications for HIV-1 transmission in humans

We examined the effect of inoculum dose on SHIV transmission and infection. We found that repeated low-dose intravaginal exposure with either R5-SHIV SF162P3 or X4-SHIV SF33A results in infections that are blunted and rapidly controlled. Interestingly, although the transmission rate after all repeated exposures is comparable for the two viruses, the probability of low-dose vaginal transmission is greater for the X4 than R5 virus. Furthermore, X4-SHIV SF33A replication predominates in low-dose dually-exposed macaques, suggesting that it is better at establishing a systemic infection following transmission. However, X4-SHIV SF33A advantage in transmission and infection is not observed in macaques inoculated intravenously with low-dose mixed inoculum. The finding that although matched in tissue culture infectious dose, the X4 inoculum is more complex leads us to hypothesize that the greater genetic heterogeneity of the X4 virus population may have rendered it less susceptible to the severe bottleneck effects imposed by IVAG inoculation with small doses, allowing for greater probability of transmission and establishment of a generalized infection. These data have implications for HIV-1 transmission and infection in humans.

Hybridization between white‐headed ducks and introduced ruddy ducks in Spain

The ruddy duck, Oxyura jamaicensis, was introduced to Great Britain in the mid-20th century and has recently spread to other Western European countries. In Spain, ruddy ducks hybridize with the globally endangered white-headed duck, Oxyura leucocephala. We assessed the effects of hybridization on the Spanish white-headed ducks, which constitute 25% of the global population of this species, using a panel of eight nuclear intron markers, 10 microsatellite loci, and mtDNA control region sequences. These data allowed parental individuals, F(1) hybrids, and the progeny of backcrossing to be reliably distinguished. We show that hybrids between the two species are fertile and produce viable offspring in backcrosses with both parental species. To date, however, we found no extensive introgression of ruddy duck genes into the Spanish white-headed duck population, probably due to the early implementation of an effective ruddy duck and hybrid control programme. We also show that genetic diversity in the expanding European ruddy duck population, which was founded by just seven individuals, exceeds that of the native Spanish white-headed duck population, which recently recovered from a severe bottleneck. Unless effective control of ruddy ducks is continued, genetic introgression will compromise the unique behavioural and ecological adaptations of white-headed ducks and consequently their survival as a genetically and evolutionary distinct species.

Multilocus Analysis of Nucleotide Variation of Oryza sativa and Its Wild Relatives: Severe Bottleneck during Domestication of Rice

Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationship and demographic history of O. sativa and its close relatives (Oryza rufipogon and Oryza nivara), we investigated nucleotide diversity data from 10 unlinked nuclear loci in species-wide samples of these species. The results indicated that O. rufipogon and O. nivara possessed comparable levels of nucleotide variation ((sil) = 0.0077 approximately 0.0095) compared with the relatives of other crops. In contrast, nucleotide diversity of O. sativa was as low as (sil) = 0.0024 and even lower ((sil) = 0.0021 for indica and 0.0011 for japonica), if we consider the 2 subspecies separately. Overall, only 20-10% of the diversity in the wild species was retained in 2 subspecies of the cultivated rice (indica and japonica), respectively. Because statistic tests did not reject the assumption of neutrality for all 10 loci, we further used coalescent to simulate bottlenecks under various lengths and population sizes to better understand the domestication process. Consistent with the dramatic reduction in nucleotide diversity, we detected a severe domestication bottleneck and demonstrated that the sequence diversity currently found in the rice genome could be explained by a founding population of 1,500 individuals if the initial domestication event occurred over a 3,000-year period. Phylogenetic analyses revealed close genetic relationships and ambiguous species boundary of O. rufipogon and O. nivara, providing additional evidence to treat them as 2 ecotypes of a single species. Lowest linkage disequilibrium (LD) was found in the perennial O. rufipogon where the r(2) value dropped to a negligible level within 400 bp, and the highest in the japonica rice where LD extended to the entirely sequenced region ( approximately 900 bp), implying that LD mapping by genome scans may not be feasible in wild rice due to the high density of markers needed.

A Comparison of the Variability Spectra of Two Genomic Loci in a European Group of Individuals Reveals Fundamental Differences Pointing to Selection or a Population Bottleneck

Knowledge about the variability spectra of neutrally evolving sequences in a population is a prerequisite for the identification of genes, which may have been under positive selection during recent human evolution. Here, we report the results of a re-sequencing project of a presumably neutrally evolving chromosome 22 locus with a severely reduced recombination frequency in a group of 24 individuals of German origin. The comparison of these data with the results of a similar analysis of a chromosome 17 locus revealed striking differences, although the same group of individuals was used. For the chromosome 17 locus two well-separated groups of sequences, a positive value of Tajima's D and a TMRCA of 700,000 years were observed. In contrast, the sequences from the chromosome 22 locus were found to be relatively homogeneous, with no deep splits between subgroups; the obtained value for Tajima's D was negative and the TMRCA was only 260,000 years. These discrepancies may be explained by selection or demographic processes. Regarding demography, the most plausible explanation is the assumption of a severe bottleneck in the history of the European population: in the case of the chromosome 17 locus two ancient lineages passed this bottleneck; for the chromosome 22 locus it was only one ancient lineage.

Surviving with low genetic diversity: the case of albatrosses

Low genetic diversity is predicted to negatively impact species viability and has been a central concern for conservation. In contrast, the possibility that some species may thrive in spite of a relatively poor diversity has received little attention. The wandering and Amsterdam albatrosses (Diomedea exulans and Diomedea amsterdamensis) are long-lived seabirds standing at an extreme along the gradient of life strategies, having traits that may favour inbreeding and low genetic diversity. Divergence time of the two species is estimated at 0.84 Myr ago from cytochrome b data. We tested the hypothesis that both albatrosses inherited poor genetic diversity from their common ancestor. Within the wandering albatross, per cent polymorphic loci and expected heterozygosity at amplified fragment length polymorphisms were approximately one-third of the minimal values reported in other vertebrates. Genetic diversity in the Amsterdam albatross, which is recovering from a severe bottleneck, was about twice as low as in the wandering albatross. Simulations supported the hypothesis that genetic diversity in albatrosses was already depleted prior to their divergence. Given the generally high breeding success of these species, it is likely that they are not suffering much from their impoverished diversity. Whether albatrosses are unique in this regard is unknown, but they appear to challenge the classical view about the negative consequences of genetic depletion on species survival.

Multilocus dataset reveals demographic histories of two peat mosses in Europe

BackgroundRevealing the past and present demographic history of populations is of high importance to evaluate the conservation status of species. Demographic data can be obtained by direct monitoring or by analysing data of historical and recent collections. Although these methods provide the most detailed information they are very time consuming. Another alternative way is to make use of the information accumulated in the species' DNA over its history. Recent development of the coalescent theory makes it possible to reconstruct the demographic history of species using nucleotide polymorphism data. To separate the effect of natural selection and demography, multilocus analysis is needed because these two forces can produce similar patterns of polymorphisms. In this study we investigated the amount and pattern of sequence variability of a Europe wide sample set of two peat moss species (Sphagnum fimbriatum and S. squarrosum) with similar distributions and mating systems but presumably contrasting historical demographies using 3 regions of the nuclear genome (appr. 3000 bps). We aimed to draw inferences concerning demographic, and phylogeographic histories of the species.ResultsAll three nuclear regions supported the presence of an Atlantic and Non-Atlantic clade of S. fimbriatum suggesting glacial survival of the species along the Atlantic coast of Europe. Contrarily, S. squarrosum haplotypes showed three clades but no geographic structure at all. Maximum likelihood, mismatch and Bayesian analyses supported a severe historical bottleneck and a relatively recent demographic expansion of the Non-Atlantic clade of S. fimbriatum, whereas size of S. squarrosum populations has probably decreased in the past. Species wide molecular diversity of the two species was nearly the same with an excess of replacement mutations in S. fimbriatum. Similar levels of molecular diversity, contrasting phylogeographic patterns and excess of replacement mutations in S. fimbriatum compared to S. squarrosum mirror unexpected differences in the demography and population history of the species.ConclusionThis study represents the first detailed European wide phylodemographic investigation on bryophytes and shows how pattern of nucleotide polymorphism can reveal unexpected differences in the population history of haploid plants with seemingly similar characteristics.

Identification of Selective Sweeps Using a Dynamically Adjusted Number of Linked Microsatellites

There is currently large interest in distinguishing the signatures of genetic variation produced by demographic events from those produced by natural selection. We propose a simple multilocus statistical test to identify candidate sites of selective sweeps with high power. The test is based on the variability profile measured in an array of linked microsatellites. We also show that the analysis of flanking markers drastically reduces the number of false positives among the candidates that are identified in a genomewide survey of unlinked loci and find that this property is maintained in many population-bottleneck scenarios. However, for a certain range of intermediately severe population bottlenecks we find genomic signatures that are very similar to those produced by a selective sweep. While in these worst-case scenarios the power of the proposed test remains high, the false-positive rate reaches values close to 50%. Hence, selective sweeps may be hard to identify even if multiple linked loci are analyzed. Nevertheless, the integration of information from multiple linked loci always leads to a considerable reduction of the false-positive rate compared to a genome scan of unlinked loci. We discuss the application of this test to experimental data from Drosophila melanogaster.

Phylogenomic Analysis of the L1 Retrotransposons in Deuterostomia

L1 retrotransposons constitute the largest single component of mammalian genomes. In contrast to the single remaining lineage of L1 retrotransposons in mammalian genomes, some teleost fishes contain a highly diverse L1 retrotransposon repertoire. Major evolutionary changes in L1 retrotransposon repertoires have therefore taken place in the land vertebrates (Tetrapoda). The lack of sequence data for L1 retrotransposons in the basal living Tetrapoda lineages prompted an investigation of their distribution and evolution in the genomes of the key tetrapod lineages, amphibians and reptiles, and in lungfishes. In this study, we combined genome database searches with PCR analysis to demonstrate that L1 retrotransposons are present in the genomes of lungfishes, amphibians, and lepidosaurs. Phylogenomic analysis shows that the genomes of Deuterostomia possess three highly divergent groups of L1 retrotransposons, with distinct distribution patterns. The analysis of L1 diversity shows the presence of a very large number of diverse L1 families, each with very low copy numbers, at the time of the origin of tetrapods. During the evolution of synapsids, all but one L1 lineage have been lost. This study establishes that the loss of L1 diversity and explosion in copy numbers occurred in the synapsid ancestors of mammals, and was most probably caused by severe population bottlenecks.

Multilocus Patterns of Nucleotide Diversity, Linkage Disequilibrium and Demographic History of Norway Spruce [Picea abies (L.) Karst

DNA polymorphism at 22 loci was studied in an average of 47 Norway spruce [Picea abies (L.) Karst.] haplotypes sampled in seven populations representative of the natural range. The overall nucleotide variation was limited, being lower than that observed in most plant species so far studied. Linkage disequilibrium was also restricted and did not extend beyond a few hundred base pairs. All populations, with the exception of the Romanian population, could be divided into two main domains, a Baltico-Nordic and an Alpine one. Mean Tajima's D and Fay and Wu's H across loci were both negative, indicating the presence of an excess of both rare and high-frequency-derived variants compared to the expected frequency spectrum in a standard neutral model. Multilocus neutrality tests based on D and H led to the rejection of the standard neutral model and exponential growth in the whole population as well as in the two main domains. On the other hand, in all three cases the data are compatible with a severe bottleneck occurring some hundreds of thousands of years ago. Hence, demographic departures from equilibrium expectations and population structure will have to be accounted for when detecting selection at candidate genes and in association mapping studies, respectively.