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PubMed2002

Longer life spans and delayed maturation in wild-derived mice.

Nearly all the experimental mice used in aging research are derived from lineages that have been selected for many generations for adaptation to laboratory breeding conditions and are subsequently inbred. To see if inbreeding and laboratory adaptation might have altered the frequencies of genes that influence life span, we have developed three lines of mice (Idaho [Id], Pohnpei [Po], and Majuro [Ma]) from wild-trapped progenitors, and have compared them with a genetically heterogeneous mouse stock (DC) representative of the laboratory-adapted gene pool. Mean life span of the Id stock exceeded that of the DC stock by 24% (P < 0.00002), and maximal life span, estimated as mean longevity of the longest-lived 10% of the mice, was also increased by 16% (P < 0.003). Mice of the Ma stock also had a significantly longer maximal longevity than DC mice (9%, P = 0.04). The longest-lived Id mouse died at the age of 1450 days, which appears to exceed the previous longevity record for fully fed, non-mutant mice. The life table of the Po mice resembled that of the DC controls. Ma and Id mice differ from DC mice in several respects: both are shorter and lighter, and females of both stocks, particularly Id, are much slower to reach sexual maturity. As young adults, Id mice have lower levels of insulin-like growth factor 1 (IGF-I), leptin, and glycosylated hemoglobin compared with DC controls, implicating several biochemical pathways as potential longevity mediators. The results support the idea that inadvertent selection for rapid maturation and large body size during the adaptation of the common stocks of laboratory mice may have forced the loss of natural alleles that retard the aging process. Genes present in the Id and Ma stocks may be valuable tools for the analysis of the physiology and biochemistry of aging in mice.

Animals↗
PubMed2002

QTL clusters reflect character associations in wild and cultivated rice.

The genetic basis of character association related to differentiation found in the primary gene pool of rice was investigated based on the genomic distribution of quantitative trait loci (QTLs). Major evolutionary trends in cultivated rice of Asiatic origin ( Oryza sativa) and its wild progenitor ( O. rufipogon) are: (1) differentiation from wild to domesticated types (domestication), (2) ecotype differentiation between the perennial and annual types in wild races, and (3) the Indica versus Japonica type differentiation in cultivated races. Using 125 recombinant inbred lines (RILs) derived from a cross between an Indica cultivar of O. sativa and a strain of O. rufipogon carrying some Japonica-like characteristics, we mapped 147 markers, mostly RFLPs, on 12 chromosomes. Thirty-seven morphological and physiological quantitative traits were evaluated, and QTLs for 24 traits were detected. The mapped loci showed a tendency to form clusters that are composed of QTLs of the domestication-related traits as well as Indica/Japonica diagnostic traits. QTLs for perennial/annual type differences did not cluster. This cluster phenomenon could be considered "multifactorial linkages" followed by natural selection favoring co-adapted traits. Further, it is possible that the clustering phenomenon is partly due to pleiotropy of some unknown key factor(s) controlling various traits through diverse metabolic pathways. Chromosomal regions where QTL clusters were found coincided with the regions harboring genes or gene blocks where the frequency of cultivar-derived alleles in RILs is higher than expected. This distortion may be partly due to unconscious selection favoring cultivated plant type during the establishment of RILs.

Journal Article↗
PubMed2003

Microarray analyses of Xylella fastidiosa provide evidence of coordinated transcription control of laterally transferred elements.

Genetically distinct strains of the plant bacterium Xylella fastidiosa (Xf) are responsible for a variety of plant diseases, accounting for severe economic damage throughout the world. Using as a reference the genome of Xf 9a5c strain, associated with citrus variegated chlorosis (CVC), we developed a microarray-based comparison involving 12 Xf isolates, providing a thorough assessment of the variation in genomic composition across the group. Our results demonstrate that Xf displays one of the largest flexible gene pools characterized to date, with several horizontally acquired elements, such as prophages, plasmids, and genomic islands (GIs), which contribute up to 18% of the final genome. Transcriptome analysis of bacteria grown under different conditions shows that most of these elements are transcriptionally active, and their expression can be influenced in a coordinated manner by environmental stimuli. Finally, evaluation of the genetic composition of these laterally transferred elements identified differences that may help to explain the adaptability of Xf strains to infect such a wide range of plant species.

Chromosome Mapping↗
PubMed1991

Estimation of gene diversity at the b locus of the constant region of the immunoglobulin light chain in natural populations of European rabbit (Oryctolagus cuniculus) in Portugal, Andalusia and on the Azorean Islands.

The minimal gene diversity at a locus of the antibody constant region, as estimated in natural populations of rabbit, revealed levels of heterozygosity similar to those reported for the major histocompatibility complex in human and murine populations. Sera of 416 wild rabbits were collected on the Iberian peninsula and on three islands of the Azorean archipelago and analyzed for the occurrence of the serological markers of the b locus of the immunoglobulin light chain. All four serotypes present in domestic rabbits were found in Portugal. They represented less than 50% of the gene pool. In Andalusia this was less than 15% and on the Azorean islands less than 10%. The pronounced and systematic hierarchy in allele frequencies, previously found in populations from the more recent distribution area of the species, was not observed. On the peninsula, the frequencies of the "domestic" alleles were similar, averaging 10%. The Portuguese sample revealed a total heterozygosity of at least 87%. This high value was supported by at least 11 serologically different alleles, none of them occurring at frequencies above 20%. These data are in agreement with an Iberian origin of the European rabbit and strongly suggest the coalescence of b locus allelic lines drawn from Iberian and western populations. The role of balancing selection in the evolution of the b locus polymorphism was further emphasized.

Alleles↗
PubMed2004

Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations.

The molecular basis of more than 25 genetic diseases has been described in Ashkenazi Jewish populations. Most of these diseases are characterized by one or two major founder mutations that are present in the Ashkenazi population at elevated frequencies. One explanation for this preponderance of recessive diseases is accentuated genetic drift resulting from a series of dispersals to and within Europe, endogamy, and/or recent rapid population growth. However, a clear picture of the manner in which neutral genetic variation has been affected by such a demographic history has not yet emerged. We have examined a set of 32 binary markers (single nucleotide polymorphisms; SNPs) and 10 microsatellites on the non-recombining portion of the Y chromosome (NRY) to investigate the ways in which patterns of variation differ between Ashkenazi Jewish and their non-Jewish host populations in Europe. This set of SNPs defines a total of 20 NRY haplogroups in these populations, at least four of which are likely to have been part of the ancestral Ashkenazi gene pool in the Near East, and at least three of which may have introgressed to some degree into Ashkenazi populations after their dispersal to Europe. It is striking that whereas Ashkenazi populations are genetically more diverse at both the SNP and STR level compared with their European non-Jewish counterparts, they have greatly reduced within-haplogroup STR variability, especially in those founder haplogroups that migrated from the Near East. This contrasting pattern of diversity in Ashkenazi populations is evidence for a reduction in male effective population size, possibly resulting from a series of founder events and high rates of endogamy within Europe. This reduced effective population size may explain the high incidence of founder disease mutations despite overall high levels of NRY diversity.

Chromosomes, Human, Y↗
PubMed1993

Genetic relationships of European populations reflect their ethnohistorical affinities.

From 420 records of ethnic locations and movements since 2000 B.C., we computed vectors describing the proportions which peoples of the various European language families contributed to the gene pools within 85 land-based 5 x 5-degree quadrats in Europe. Using these language family vectors, we computed ethnohistorical affinities as arc distances between all pairs of the 85 quadrats. These affinities are significantly correlated with genetic distances based on 26 genetic systems, even when geographic distances, a common causative factor, are held constant. Thus, the ethnohistorical distances explain a significant amount of the genetic variation observed in modern populations. Randomizations of the records by chronology result in loss of significance for the observed partial correlation between genetics and ethnohistory, when geography is held constant. However, a randomization of records by location only results in reduced significance. Thus, while the historical sequence of the movements does not seem to matter in Europe, their geographic locations do. We discuss the implications of these findings.

Alleles↗
PubMed2005

The effect of the Neolithic expansion on European molecular diversity.

We performed extensive and realistic simulations of the colonization process of Europe by Neolithic farmers, as well as their potential admixture and competition with local Palaeolithic hunter-gatherers. We find that minute amounts of gene flow between Palaeolithic and Neolithic populations should lead to a massive Palaeolithic contribution to the current gene pool of Europeans. This large Palaeolithic contribution is not expected under the demic diffusion (DD) model, which postulates that agriculture diffused over Europe by a massive migration of individuals from the Near East. However, genetic evidence in favour of this model mainly consisted in the observation of allele frequency clines over Europe, which are shown here to be equally probable under a pure DD or a pure acculturation model. The examination of the consequence of range expansions on single nucleotide polymorphism (SNP) diversity reveals that an ascertainment bias consisting of selecting SNPs with high frequencies will promote the observation of genetic clines (which are not expected for random SNPs) and will lead to multimodal mismatch distributions. We conclude that the different patterns of molecular diversity observed for Y chromosome and mitochondrial DNA can be at least partly owing to an ascertainment bias when selecting Y chromosome SNPs for studying European populations.

Chromosomes, Human, Y↗
PubMed1976

A contribution to the study of linkage disequilibrium in Drosophila melanogaster.

Linkage disequilibrium was detected in 12 out of 30 cases involivng gene alleles and inversions in three cage populations and in a natural population of Drosophila melanogaster from Greece. The cage populations possessed practically the same gene pool at their origin and were maintained simultaneously under the effects of the ecological factors "food medium" and "humidity". It is dicussed that the correlation of the same direction found between the frequencies of nonallelic elements of Adh locus and In (2L) 22D-34A or In (2R)52A-56F in such different populations as American, Japanese (Mukai et al;, 1971, 1974; Langley et al., 1974) and Greek, as well as cage populations under different environmental conditions, could be attributed to the effect of epistatic selection. Moreover, it seems that the In(2L)22D-34A has a tendency to interact genetically with the alpha-Gpdh locus, particularly when the populations are maintained under crowding conditions. However, further data are needed to assess whether other cases of the observed nonrandom associations can be better explained as transient associations generated by random drift, or as the result of epistatic selection.

Alcohol Oxidoreductases↗
PubMed2005

Roles played by esterase activity and by a sodium channel mutation involved in pyrethroid resistance in populations of Boophilus microplus (Acari: Ixodidae) collected from Yucatan, Mexico.

Pyrethroid resistance in Boophilus microplus (Canestrini) (Acari: Ixodidae) was studied by correlating discriminating-dose (DD) bioassay results and esterase activity or the frequency of a sodium channel mutation known to be involved in pyrethroid resistance in nine field strains of B. microplus from Yucatan, Mexico. Two tick strains (P67 and B74) were identified as susceptible to cypermethrin, deltamethrin, and flumethrin by DD, one strain (P65) was susceptible to cypermethrin and resistant to deltamethrin and flumethrin, and six strains were resistant to cypermethrin, delta-methrin, and flumethrin (T11, M10, C54, R49, B71, and T66). By using polymerase chain reaction, only 6.0 and 6.2% of resistance allele (R) was found in the susceptible strains (P67 and B74, respectively). In the T66 strain, with 100% of larval survival to the DD of pyrethroids as measured by the larval packet test (LPT), 98.0% of the gene pool contained the R allele. Positive correlations between the larval survival and the percentage of the R allele were found (deltamethrin r2 = 0.8875, P < 0.01; cypermethrin r2 = 0.8563, P < 0.01; and flumethrin r2 = 0.8491, P < 0.01). There were no significant correlations between the level of larval survival and esterase-based hydrolytic activity. It was concluded that within the B. microplus populations studied, resistance to flumethrin, deltamethrin, or cypermethrin was because of the novel sodium channel mutation (Phe-->Ile amino acid substitution in the S6 transmembrane segment of domain III), and there was a correlation between tick mortality by pyrethroid exposure (larval survival) and the presence of R allele. It was not determined whether enhanced esterase-based hydrolytic activity was involved in pyrethroid resistance in the populations tested.

Animals↗
PubMed2000

Shattered: Medawar's test tubes and their enduring legacy of chaos.

Medawar's 1952 paper 'An Unsolved Problem of Biology' underlies most subsequent theoretical work regarding the evolution of aging; it concludes that aging is accidental and could not have evolved; this prevents reconciling the growing body of evidence suggesting the existence of multiple, evolved, aging systems. The paper features a well-known thought experiment using test tubes to show why aging could not evolve. Medawar assumes that constant, random, breakage sufficiently represents lethal forces of nature; however, famine, drought, predation, disease, and accidents each uniquely affect populations. Predation is the only evolving force that continually invents new ways to kill members of the prey populations; thus all prey defenses to predation will eventually be defeated. Defenses to non-evolving or non-obligate lethal forces, however, should quickly evolve. Thus unevolving, identical test tubes cannot adequately represent biological populations. The example also ignores population booms and busts which often occur in nature. By ignoring these issues, Medawar examines only one population age distribution skewed towards younger individuals in predator-dominated environments while ignoring predator-free populations skewed towards older individuals after population crashes. Further, Medawar's test tubes lack meaningful competition for finite resources, and ignore declining fertility which occurs in all aging species. Medawar concludes that older individuals are too few in number to influence the population's gene pool for or against aging. This conclusion is found to be incorrect when variations in the age of reproductive senescence are introduced into a predator-free population.A new thought experiment with competing strains of algae corrects for these issues and shows that aging evolved and is retained so that groups retain enough genetic variability to allow for rapid evolution of a defense to novel predation. The example shows reasons why the rate of aging is directly linked to the reproductive rate, litter size, metabolic rate, reproductive senescence, and fixed body size. It also suggests that in the absence of predation, immortality would quickly evolve if not for the evolution of highly-conserved aging systems. Prior analysis of aging evolution is incorrect due to theorists' rejection of the idea of group selection. It is believed to be 'impossible' to select for mutations that are bad for the individual but good for the group. However, mutations that are neutral to young individuals which are only deleterious if expressed at older ages can accumulate in early-mortality, predator-dominated environments. Removing the predator allows deleterious mutation expression. Positive group selection then occurs amongst traits that are negative to the individual. Further, group selection is a universal force that occurs between local, non-breeding groups and not, as theorists propose, between distant groups of potentially interbreeding species. Local survivors migrate to replace extinct, related species. The antagonistic pleiotropy theory, which was created to salvage the idea of accidental aging, is examined and shown to be untenable. The hypothetical antagonistic pleiotropy genes that are beneficial to young while detrimental to old individuals, predicted to exist in the 1950s, are unlikely to exist, have not, and likely will not be found in sufficient quantity to participate in the aging process.

Aging↗
PubMed2007

Identification of soluble CD14 as an endogenous agonist for Toll-like receptor 2 on human astrocytes by genome-scale functional screening of glial cell derived proteins.

Human astrocytes express a limited repertoire of Toll-like receptor (TLR) family members including TLR1-4, which are expressed on the cell surface. Also, TLR3 but not TLR4 activation on astrocytes induces expression of several factors involved in neuroprotection and down-regulation of inflammation rather than in the onset of traditional pro-inflammatory reactions. The notion that astrocyte TLR may thus play a role not only in host defense but also in tissue repair responses prompted us to examine the possibility that endogenous TLR agonists could be expressed in the human central nervous system to regulate the apparently dual astrocyte functions during trauma or inflammation. As a potential source of endogenous agonists, a cDNA library derived from several human brain tumor cell lines was used. Gene pools of this library were transfected into COS-7 cells and the expression products were screened for their ability to induce TLR activation in human primary astrocytes. The screening resulted in the identification of soluble CD14. By using a panel of TLR-transfected HEK293 cells, we found that signaling by soluble CD14 was TLR2 dependent. Moreover, the CD14-triggered TLR2-mediated response in astrocytes lead to the production of CXCL8, IL-6, and IL12p40, whereas typical TLR-induced pro-inflammatory cytokines, like TNF-alpha and IL-1beta, were not produced at detectable levels. In conclusion, our data indicate that apart from its well-known ability to act as a co-receptor for TLR-dependent signaling by peptidoglycans or LPS, soluble CD14 can also act as a direct agonist for TLR2.

Adult↗
PubMed2000

A tumor-infiltrating lymphocyte from a melanoma metastasis with decreased expression of melanoma differentiation antigens recognizes MAGE-12.

Twenty separate tumor infiltrating lymphocyte (TIL) bulk cultures and a tumor cell line were originated simultaneously from a fine needle aspiration biopsy of a metastasis in a patient with melanoma (F001) previously immunized with the HLA-A*0201-associated gp100:209-217(210 M) peptide. None of the TIL recognized gp100. However, 12 recognized autologous (F001-MEL) and allogeneic melanoma cells expressing the HLA haplotype A*0201, B*0702, Cw*0702. Further characterization of F001-MEL demonstrated loss of gp100/PMel17, severely decreased expression of other melanoma differentiation Ags and retained expression of tumor-specific Ags. Transfection of HLA class I alleles into B*0702/Cw*0702-negative melanoma cell lines identified HLA-Cw*0702 as the restriction element for F001-TIL. A cDNA library from F001-MEL was used to transfect IFN-alpha-stimulated 293 human embryonal kidney (293-HEK) cells expressing HLA-Cw*0702. A 100-gene pool was identified that induced recognition of 293-HEK cells by F001-TIL. Subsequent cloning of the pool identified a cDNA sequence homologous, except for one amino acid (aa 187 D-->A), to MAGE-12. Among 25 peptide sequences from MAGE-12 with the HLA-Cw*0702 binding motif, MAGE-12:170-178 (VRIGHLYIL) induced IFN-gamma release by F001-TIL when pulsed on F001-EBV-B cells at concentrations as low as 10 pg/ml. Peptide sequences from MAGE-1, 2, 3, 4a, and 6 aligned to MAGE-12:170-178 were not recognized by F001-TIL. In summary a TIL recognizing a MAGE protein was developed from an HLA-A*0201 expressing tumor with strongly reduced expression of melanoma differentiation Ags. Persisting tumor-specific Ag expression maintained tumor immune competence suggesting that tumor-specific Ags/melanoma differentiation Ags may complement each other in the context of melanoma Ag-specific vaccination.

Alleles↗
PubMed2005

Admixture analysis of a rural population of the state of Guerrero, Mexico.

We studied 156 individuals of Native American descent from the city of Tlapa in the state of Guerrero in western Mexico. Most individuals' ethnicity was either Nahua, Mixtec, or Tlapanec, but self-identified Mestizos and individuals of mixed ethnicities were also included in the sample. We typed 24 autosomal, one Y-chromosome, and four mitochondrial ancestry-informative markers (AIMs) to estimate group and individual admixture proportions, and determine whether the admixture process involved directional gene flow between parental groups. When genetically defined (GD) Mestizos were excluded from the analysis, Native American ancestry represented approximately 98% of the population's gene pool, while European and West African ancestry represented approximately 1% each. Maternally inherited markers also showed an exceptionally high Native American contribution (98.5%), as did the paternally inherited marker, DYS199 (90.7%). We did not detect genetic structure in this population using these AIMs, which appears consistent with the homogeneity of the sample in terms of admixture proportions. The addition of GD Mestizos to the sample did not produce a considerable change in admixture estimates, but it had a major effect on population structure. These results show that the population of Tlapa in Guerrero, Mexico, has experienced little admixture with Europeans and/or West Africans. They also show that the impact of a small number of admixed individuals on an otherwise homogeneous population might have profound implications on subsequent ancestry/phenotype analysis and mapping strategies. We suggest that heterogeneity is a major characteristic of Mexican populations and, as a consequence, should not be disregarded when designing epidemiological studies of Mexican and Mexican American populations.

Black People↗
PubMed2006

The population biology of bacterial plasmids: a hidden Markov model approach.

Horizontal plasmid transfer plays a key role in bacterial adaptation. In harsh environments, bacterial populations adapt by sampling genetic material from a horizontal gene pool through self-transmissible plasmids, and that allows persistence of these mobile genetic elements. In the absence of selection for plasmid-encoded traits it is not well understood if and how plasmids persist in bacterial communities. Here we present three models of the dynamics of plasmid persistence in the absence of selection. The models consider plasmid loss (segregation), plasmid cost, conjugative plasmid transfer, and observation error. Also, we present a stochastic model in which the relative fitness of the plasmid-free cells was modeled as a random variable affected by an environmental process using a hidden Markov model (HMM). Extensive simulations showed that the estimates from the proposed model are nearly unbiased. Likelihood-ratio tests showed that the dynamics of plasmid persistence are strongly dependent on the host type. Accounting for stochasticity was necessary to explain four of seven time-series data sets, thus confirming that plasmid persistence needs to be understood as a stochastic process. This work can be viewed as a conceptual starting point under which new plasmid persistence hypotheses can be tested.

Bacteria↗
PubMed2006

Does disturbance and restoration of alpine grassland soils affect the genetic structure and diversity of bacterial and N2-fixing populations?

Responses of bacterial communities to disturbance and restoration processes were investigated on alpine grassland soil. Bulk soil, rhizosphere soil and two soil separates, i.e. sand-size (2000-200 microm) and silt-size (50-2 microm) were sampled from undisturbed grassland soil to soil under restoration for 1 month, 1 year, 4 years and 13 years after disturbance. Automated ribosomal intergenic spacer analysis (ARISA) and restriction fragment length polymorphism (RFLP) of nifH gene pools were used to assay genetic structure of the bacterial communities and N2-fixing guild. According to the distribution of ARISA band length in bacterial phyla, the dominance of ARISA bands below 400 bp showed that Gram-positive bacteria would be predominant in the studied grassland soil when not disturbed. Disturbance affected the genetic structure of bacterial community and of N2-fixing guild in relation to their location within the selected habitats. Shifts in IGS and nifH profiles of bulk soil metagenome were larger than those observed from sand-size- and silt-size-fractions, accounting for 40-50% of the variance in the profiles. Restoration of the genetic structure of telluric bacteria community and N2-fixing populations was found to be influenced by the spatial heterogeneity of the soil and niche diversification. Particular bacterial genetic structure within distinct habitats were evidenced and must be defined as subdivisions of the meta-community of bulk soil. Scale of soil microbial diversity/stability relationships is discussed with special attention to disconnected bacterial habitat compared with whole soil with multiple niches.

Bacteria↗
PubMed2000

Y chromosomes traveling south: the cohen modal haplotype and the origins of the Lemba--the "Black Jews of Southern Africa".

The Lemba are a traditionally endogamous group speaking a variety of Bantu languages who live in a number of locations in southern Africa. They claim descent from Jews who came to Africa from "Sena." "Sena" is variously identified by them as Sanaa in Yemen, Judea, Egypt, or Ethiopia. A previous study using Y-chromosome markers suggested both a Bantu and a Semitic contribution to the Lemba gene pool, a suggestion that is not inconsistent with Lemba oral tradition. To provide a more detailed picture of the Lemba paternal genetic heritage, we analyzed 399 Y chromosomes for six microsatellites and six biallelic markers in six populations (Lemba, Bantu, Yemeni-Hadramaut, Yemeni-Sena, Sephardic Jews, and Ashkenazic Jews). The high resolution afforded by the markers shows that Lemba Y chromosomes are clearly divided into Semitic and Bantu clades. Interestingly, one of the Lemba clans carries, at a very high frequency, a particular Y-chromosome type termed the "Cohen modal haplotype," which is known to be characteristic of the paternally inherited Jewish priesthood and is thought, more generally, to be a potential signature haplotype of Judaic origin. The Bantu Y-chromosome samples are predominantly (>80%) YAP+ and include a modal haplotype at high frequency. Assuming a rapid expansion of the eastern Bantu, we used variation in microsatellite alleles in YAP+ sY81-G Bantu Y chromosomes to calculate a rough date, 3,000-5,000 years before the present, for the start of their expansion.

Africa, Southern↗
PubMed2004

Stocking impact and migration pattern in an anadromous brown trout (Salmo trutta) complex: where have all the stocked spawning sea trout gone?

We examined polymorphism at seven microsatellite loci among sea trout (Salmo trutta) (n = 846) collected from three areas in the Limfjord (Denmark). We then assessed their potential population source by comparing, using a mixed stock analysis (MSA) Bayesian framework, their genetic composition to that of brown trout collected from 32 tributaries pooled into nine geographical regions (n = 3801) and two hatcheries (n = 222) used for stocking. For each of the three regional sea trout groups (western, central and eastern Limfjord, n = 91, n = 426, n = 329, respectively), MSA was conducted with (i) all individuals in the group, (ii) with the subset of spawning sea trout only and (iii) with the subset of foraging, nonspawning individuals only, a subset that consisted primarily of sea trout caught during their first year at sea. For all three regional sea trout groups, a higher proportion of individuals (regardless of whether they were foraging or spawning) appear to have originated from the rivers that drain locally, than from the rivers that drain in other parts of the Limfjord. This suggests (1) that sea trout, at least during their first year at sea, undertake limited migrations within the Limfjord system and (2) that sea trout on their spawning run were caught close to their natal rivers. The proportion of sea trout of hatchery origin varied widely among all three Limfjord areas and broadly reflected regional stocking histories, with high proportions of sea trout of domestic origin in the east (39.3%), where stocking with domestic trout was practised intensely at the time of sampling, and in the west (57.2%), where a programme of coastal stocking of post smolts took place over several years in the early 1990s. In contrast, in the central Limfjord, where stocking with domestic trout was largely abandoned in the early 1990s, the proportion of sea trout of domestic origin was only 8.5%. Interestingly, for all three regional sea trout groups, virtually no sea trout of hatchery origin were found among the spawning individuals, which were on average larger than the nonspawning sea trout. These results suggest that stocked domestic brown trout that become anadromous experience high mortality at sea and are therefore largely absent among the larger, spawning individuals. We conclude that sea trout of domestic origin exhibit much reduced ability to reproduce and are unlikely to contribute significantly to the local gene pool largely because of a relatively high mortality at sea before the onset of maturity.

Animal Migration↗
PubMed2003

Genetic diversity of forest arabica coffee (Coffea arabica L.) in Ethiopia as revealed by random amplified polymorphic DNA (RAPD) analysis.

Genetic diversity within the forest Coffea arabica L. gene pool in Ethiopia has not been extensively examined with molecular markers. In the present study, a total of 75 polymorphic RAPD bands generated by twelve random primers were used to assess genetic diversity among 144 genotypes representing 16 C. arabica populations. The number of polymorphic bands detected with each primer ranged from 2 to 9 with a mean of 6.25 bands per primer. Banding patterns ranged in percentage polymorphism from 37% to 73% with an overall mean of 56% for the populations analyzed. The amount of genetic variation among populations estimated by Shannon-Weaver diversity index was (H = 0.30). The within population and between populations differentiation values were 0.65 and 0.35, respectively. Genetic differentiations within and between zones of sample collection sites were 0.80 and 0.20, respectively. Within population average similarities estimated by simple matching coefficients ranged from 0.72 to 0.85, with an overall average of 0.78. In the cluster analysis that used individual samples as operational taxonomic units, most of the representatives of the same population failed to cluster before they joined members of other populations. Nevertheless, most of the populations were clustered on the basis of their geographic closeness and an east west differentiation was observed at approximately 75% similarity. The results obtained provide information on how to select sites for in situ conservation of C. arabica germplasm.

Coffea↗