Lack Of Genetic Variation Research Articles

Rediscovery of pycnidia inThamnolia vermicularis: implications for chemotype occurrence and distribution

AbstractThamnolia vermicularisis a globally widespread arctic-alpine lichen with two distinct chemotypes. The intermixing of these chemotypes at the local scale and lack of genetic variation between them is puzzling given the apparent absence of specialized reproductive structures. Apothecia and conidiomata were originally reported forThamnoliain the second half of the 19th century, but putative apothecia proved to be parasitic in origin. This study presents conclusive microscopic evidence for the existence of pycnidial conidiomata containing conidia on thalli ofThamnolia vermicularisfrom geographically widespread locations. Sequences of the internal transcribed spacer (ITS) region of ribosomal DNA from excised pycnidial conidiomata matched that of thallus tips from individualThamnoliathalli. Our examination of the historic literature found that the occurrence of pycnidial conidiomata was never disproved, but this information was lost from the post-1920s English-language literature. Our rediscovery of pycnidial conidiomata indicates thatThamnolia vermicularispossesses a reproductive strategy with the potential for long-distance dispersal of multitudes of mitotically produced conidia, providing a plausible explanation for the cosmopolitan distribution of the species and the low levels of genetic variation among populations. Reversible processes, for example alternative splicing, warrant consideration as explanations for chemotype intermixing.

Allograft Outcomes in Outbred Mice

Inbreeding depression and lack of genetic diversity in inbred mice could mask unappreciated causes of graft failure or remove barriers to tolerance induction. To test these possibilities, we performed heart transplantation between outbred or inbred mice. Unlike untreated inbred mice in which all allografts were rejected acutely (6-16 days posttransplantation), untreated outbred mice had heterogeneous outcomes, with grafts failing early (<4 days posttransplantation), acutely (6-24 days) or undergoing chronic rejection (>75 days). Blocking T cell costimulation induced long-term graft acceptance in both inbred and outbred mice, but did not prevent the early graft failure observed in the latter. Further investigation of this early phenotype established that it is dependent on the donor, and not the recipient, being outbred and that it is characterized by hemorrhagic necrosis and neutrophilic vasculitis in the graft without preformed, high titer antidonor antibodies in the recipient. Complement or neutrophil depletion prevented early failure of outbred grafts, whereas transplanting CD73-deficient inbred hearts, which are highly susceptible to ischemia-reperfusion injury, recapitulated the early phenotype. Therefore, outbred mice could provide broader insight into donor and recipient determinants of allograft outcomes but their hybrid vigor and genetic diversity do not constitute a uniform barrier to tolerance induction.

New insights into character evolution, hybridization and diversity of Indian Nymphaea (Nymphaeaceae): evidence from molecular and morphological data

A comprehensive reassessment of Indian Nymphaea (Nymphaeaceae) based on morphology, RAPD and nucleotide sequence data of the ITS, trnK intron, matK and rbcL gene was conducted. Although considerable morphological variations have been reported, pollen colour and rhizome shape are two characters which have not been mentioned in previous studies. The transformation from yellow to white coloured pollen may have evolved independently and is probably associated with a strong selective pressure acted upon by the animal pollinators on white pollen of N. pubescens and N. rubra. Rhizome shape could easily discriminate among subgenera; the difference in shape (triangular, globular and cylindrical) probably highlights the success in their distribution. Our studies using RAPD revealed high genetic variability among individuals of N. caerulea. This may be attributed to the breeding system followed, which could be an outcrossing species. But the lack of genetic diversity in N. tetragona is probably due to founder events, whereby a solitary founder individual from China could have resulted in the establishment of this single population of ∼25–30 individuals with no detectable variations. Molecular cloning of the ITS region of N. rubra, necessitated by the presence of additional signals in the sequencing chromatogram, confirmed the origin of this plant taxon through hybridization involving N. lotus and N. pubescens as the parental species.

Genetic diversity of the endangered Chinese endemic herb Dayaoshania cotinifolia (Gesneriaceae) revealed by simple sequence repeat (SSR) markers

Abstract Dayaoshania cotinifolia W.T. Wang is a critically endangered perennial herb endemic to southern China. Simple sequence repeat (SSR) markers were employed to assess genetic diversity in two populations of D. cotinifolia . Eight primer pairs generated a total of 36 alleles, with a mean of 4.5 alleles per locus. The expected heterozygosity ( H e = 0.416) and observed heterozygosity ( H o = 0.508) indicated a moderate level of genetic diversity, though the genetic differentiation between the populations was low ( F st = 0.014), a result that was supported by a higher gene flow ( N m = 18.000). No severe bottleneck effect was detected in the two populations. Thus, the endangered status of this species is most likely due to anthropologic effects rather than a lack of genetic diversity. In situ conservation strategies should be promoted, and the sizes of the populations should be increased through artificial breeding.

Genetic diversity and population structure in wild Sichuan rhesus macaques

Because wild rhesus macaque (Macaca mulatta) populations have suffered major declines, there is a growing need to characterize their genetic and population structure in order to protect the genetic integrity of this species. In this study, we genotyped a sample comprising 120 wild rhesus macaques from six sites in Sichuan Province for 30 nuclear microsatellite (STR) loci using an ABI 3130xl genetic analyzer. Bayesian analyses and PCA clearly differentiated monkeys from Heishui from those at other sites. The samples from all six sites exhibited high gene diversity suggesting that the Sichuan wild rhesus macaque populations are not threatened by a lack of genetic diversity. Deviation from Hardy-Weinberg equilibrium was more frequent in the Danba and Heishui populations. This may be due to the more fragmented habitat and less disturbance by humans in this area that foster greater subpopulation structuring than occurs in eastern China. We suggest that this population subdivision is the result of both long-term geographic barriers and human activity.

The ‘paradigm of extremes’: extremely low genetic diversity in an extremely narrow endemic species, Coristospermum huteri (Umbelliferae)

Low levels of genetic diversity in endemic species are generally attributable to the small size of their populations. This lack of genetic variability will, predictably, be more evident in those species that occur in only one or a very few localities with a total population consisting of a few dozen individuals, or sometimes fewer (i.e. ‘extremely narrow endemics’, ENEs). We used allozyme electrophoresis to survey the genetic variability of Coristospermum huteri, an endemic species from the island of Majorca (Balearic Islands, W. Mediterranean Basin) with a single natural population of about 100 individuals. As expected, allozyme variability was virtually nil for this species (P = 8.3 %, A = 1.08, H e = 0.022), which seems to be a general rule for ENEs (mean H e = 0.057). A founder effect associated with a dispersal event from the continent is probably behind the lack of genetic diversity in this highly threatened species. Preservation of the mountain summit where the plant is found (Puig Major) is essential for the survival of C. huteri, and would also guarantee the conservation of other ENEs and rare and threatened species.

Genetic factors affecting food‐plant specialization of an oligophagous seed predator

Several ecological and genetic factors affect the diet specialization of insect herbivores. The evolution of specialization may be constrained by lack of genetic variation in herbivore performance on different food-plant species. By traditional view, trade-offs, that is, negative genetic correlations between the performance of the herbivores on different food-plant species favour the evolution of specialization. To investigate whether there is genetic variation or trade-offs in herbivore performance between different food plants that may influence specialization of the oligophagous seed-eating herbivore, Lygaeus equestris (Heteroptera), we conducted a feeding trial in laboratory using four food-plant species. Although L. equestris is specialized on Vincetoxicum hirundinaria (Apocynaceae) to some degree, it occasionally feeds on alternative food-plant species. We did not find significant negative genetic correlations between mortality, developmental time and adult biomass of L.equestris on the different food-plant species. We found genetic variation in mortality and developmental time of L. equestris on some of the food plants, but not in adult biomass. Our results suggest that trade-offs do not affect adaptation and specialization of L. equestris to current and novel food-plant species, but the lack of genetic variation may restrict food-plant utilization. As food-plant specialization of herbivores may have wide-ranging effects, for instance, on coevolving plant-herbivore interactions and speciation, it is essential to thoroughly understand the factors behind the specialization process. Our findings provide valuable information about the role of genetic factors in food-plant specialization of this oligophagous herbivore.

Recovery of a nearly extinct Galápagos tortoise despite minimal genetic variation

A species of Galápagos tortoise endemic to Española Island was reduced to just 12 females and three males that have been bred in captivity since 1971 and have produced over 1700 offspring now repatriated to the island. Our molecular genetic analyses of juveniles repatriated to and surviving on the island indicate that none of the tortoises sampled in 1994 had hatched on the island versus 3% in 2004 and 24% in 2007, which demonstrates substantial and increasing reproduction in situ once again. This recovery occurred despite the parental population having an estimated effective population size <8 due to a combination of unequal reproductive success of the breeders and nonrandom mating in captivity. These results provide guidelines for adapting breeding regimes in the parental captive population and decreasing inbreeding in the repatriated population. Using simple morphological data scored on the sampled animals, we also show that a strongly heterogeneous distribution of tortoise sizes on Española Island observed today is due to a large variance in the number of animals included in yearly repatriation events performed in the last 40 years. Our study reveals that, at least in the short run, some endangered species can recover dramatically despite a lack of genetic variation and irregular repatriation efforts.

Historical and modern neutral genetic variability in Mednyi Arctic foxes passed through a severe bottleneck

AbstractSmall isolated populations often show lower genetic variability. Demographic bottlenecks lead to loss of genetic variation too. Arctic foxes (Vulpes lagopus) have been isolated since the Pleistocene on Mednyi and Bering Islands (Commander Islands). In 1970–1980, the Mednyi population passed through a severe bottleneck due to a mange outbreak. Previous studies showed lack of genetic diversity in the contemporary Mednyi population that could be due to the long history of isolation and/or the recent bottleneck. To test both factors, we analyzed the mtDNA D‐loop fragment and five microsatellites in pre‐bottleneck Mednyi museum samples. Also, contemporary Mednyi, Bering and mainland Alaskan Arctic foxes were analyzed. Registered genetic variability in historical Mednyi was higher than in contemporary Mednyi Arctic foxes, but lower than in contemporary the Bering population. Our data confirms that the bottleneck reduced an already depleted polymorphism in Mednyi Arctic foxes. Lack of genetic variability could be a reason why the Mednyi population did not recover following the outbreak of mange.

The evolutionary potential of Baker's weediness traits in the common morning glory, Ipomoea purpurea (Convolvulaceae)

Many reports have cited Baker's list of weediness traits, or those that exemplify the "ideal" weed, yet few have considered the evolutionary potential of such traits as a group. Thus, it is unknown whether constraints on the evolution of increased weediness, such as a lack of genetic variation or genetic correlations between the traits, are present. Ipomoea purpurea, the common morning glory, is a problematic weed that exhibits many of Baker's ideal weed traits. We used progeny from a half/full-sib breeding design in a series of three greenhouse experiments to assess the presence of genetic variation, narrow sense heritabilities, and genetic correlations in Baker's growth, competition, and fitness "weediness" traits in two populations of I. purpurea. We uncovered genetic variation underlying reproductive fitness traits and competitive ability in at least one population, but no evidence of genetic variation underlying growth rate in either population. Genetic correlations between many of the weediness characters differed significantly from zero; however, their direction and/or magnitude differed between populations. We found that increased weediness in the common morning glory is more likely to occur through selection on reproductive output and competitive ability rather than through selection on growth rate. Assessing Baker's traits in a quantitative genetics framework can provide a solid perspective on their evolutionary potential and a unique framework within which to determine how weeds will respond to different environmental stresses and/or scenarios of global climate change.

Molecular Diversity Revealed by AFLP Markers in Upland Cotton Genotypes

Cotton is an important fiber crop grown over tropical and subtropical regions worldwide. The narrow genetic base of the cotton germplasm being used in breeding programs is one of the factors in failing to achieve appreciable amount of progress in improving fiber traits. Molecular markers have been successfully applied to estimate genetic diversity, besides their use in advancing the breeding cycle. Sixty upland genotypes from a cooperative regional testing program were screened with AFLP markers. Louisiana genotypes possessed coarse fibers, medium staple, and strong fibers, while heat tolerant genotypes showed high variability for these traits. The pairwise kinship estimates ranged between 0.1–0.88, while the PIC values ranged from 0.15–0.30, accounting for most of the shared ancestral alleles. The estimates of genetic diversity were in the range of 0.1–0.34. PCoA, and correspondence and UPGMA clustering methods showed no obvious grouping of the genotypes in line with their geographical origin. Some of genotypes, such as AU 5367, Acala 1517-99, and LA 05307025, were highly diverse from rest of the population. The DICE distance estimates among all the 60 genotypes reached a maximum of less than 0.15, indicating the relative lack of genetic diversity in this group of genotypes based on the markers used in this study.

Population genetics of introduced and native populations of the green mussel, Perna viridis: determining patterns of introduction

Genetic variation can be used to determine routes of introduction of non-native species and whether introduced populations lost variation during establishment. The present study sought to determine whether multiple, geographically isolated non-native populations of the green mussel, Perna viridis, were the product of a stepping stone expansion of a single introduction or from multiple independent introductions from the native range. Measurements of genetic variation were compared among five introduced populations and three populations from within the native range. We sequenced 650 bp of the mitochondrial gene cytochrome oxidase I from 280 samples from five introduced populations and another 190 samples from three native populations. Haplotype frequencies of all introduced populations were not significantly different from each other, but virtually all populations differed from samples taken from the native range. Measurements of genetic variation tended to suggest that introduced populations had less variation than most native populations and there was no evidence for admixture in any of the introduced populations. The genetic data and Monte Carlo simulations both provide compelling evidence of a stepping-stone pattern of introduction of P. viridis from the native range to Trinidad, and from Trinidad to other locations in the Caribbean and United States. The lack of genetic variation in introduced populations suggests that the initial introduction was relatively small and the lack of admixture suggests a single original source population.

A recent transposition of river involving Paraná and São Francisco basins: Effects on the genetic variability and structure of the neotropical fish Parauchenipterus galeatus (Siluriformes, Auchenipteridae)

This study analyzed sequences of the control region of mitochondrial DNA (D-loop) in three populations of Parauchenipterus galeatus from the basins of the Paraná, São Francisco, and Piumhi rivers, of which the last river being a region that suffered transposition river. A fragment of 850 base pairs was obtained with a total of 65 polymorphic sites. The data discuss aspects related to the genetic distance between the populations through the phylogenetic reconstruction methods (neighbor-joining, maximum-likelihood, and Bayesian analysis). Moreover, the data suggest that the Piumhi River population (transposition region) has recently gone through a significant bottleneck effect, which must be directly related to the anthropic action that occurred in this region, since the drainage the old existing swamp was necessary for the construction of the transposition channel potentially leading this population in to the current lack of genetic diversity.

SSR FINGERPRINTING OF BLACK RASPBERRY CULTIVARS SHOWS DISCREPANCIES IN IDENTIFICATION

Breeding progress in black raspberry (Rubus occidentalis L.) has been limited by a lack of genetic diversity in elite germplasm. Black raspberry cultivars are noted for showing very few differences, and seedlings for a lack of segregation for important traits. Genetic fingerprinting using microsatellite, or simple sequence repeat (SSR) markers, can reliably identify unique clones and evaluate diversity in black raspberry cultivars. Twenty-one black raspberry cultivars were sampled from the USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon. Black raspberry clones were also sampled from nurseries, grower’s fields, and other black raspberry breeding programs for comparison. These genotypes were compared using 18 polymorphic SSR primer pairs. The black raspberries 'Bristol,' 'Jewel,' and 'Mac Black' had consistent SSR fingerprints between sources. However, plants being sold as 'Black Hawk' and 'Cumberland' had the same fingerprint as 'Jewel'. Plants of 'Bristol', 'Cumberland', 'Munger', 'New Logan', 'Plum Farmer' and 'Shuttleworth' in the NCGR collection had identical fingerprints. Eleven unique SSR fingerprints were found among plants being grown or sold as ‘Munger’, though there was one predominant fingerprint for this cultivar. 'Allen' and 'John Robertson' were each represented by three different fingerprints from three different sources, and 'Earlysweet' and 'Jewel' had SSR alleles at multiple loci that cannot be explained by their reported pedigrees. While overall genetic diversity in black raspberry cultivars is low, discrepancies in the naming of clones appear to be widespread in commercial and research plantings. Future work in this area should focus on sampling additional independent sources of plant material and evaluating clones to determine the extent of performance differences. Further SSR development in black raspberry may be needed to fingerprint some unique clones.

Family history of malignant and benign thyroid diseases and risk of thyroid cancer: a population-based case–control study in New Caledonia

Exceptionally high incidence rates of thyroid cancer have been observed in New Caledonia, particularly in Melanesian women, but familial aggregation of thyroid diseases in this population is unknown. We study the association between family history of malignant or benign thyroid diseases and non-medullary thyroid cancer in this country. We conducted a population-based case-control study including 332 cases with papillary or follicular carcinoma diagnosed in 1993-1999 and 412 controls, matched by sex and 5-year age-group. Thyroid cancer was associated with a history of thyroid cancer in first-degree relatives (odds ratio (OR), 3.2; 95% CI, 1.6-6.2) and with a family history of multinodular goiter (OR, 3.6; 95% CI, 1.9-7.0). The ORs did not change by age at diagnosis and with the number of affected relatives. The study provides evidence that the familial component of thyroid cancer is particularly strong in men. Thyroid cancer was not associated with a family history of thyroid diseases in Melanesians from the Loyalty Islands, the area with the highest incidence rates for thyroid cancer, possibly indicating a high frequency of genetic susceptibility variants and lack of genetic variation in this population subgroup. Overall our findings confirm an elevated risk of thyroid cancer in individuals with a family history of malignant or benign thyroid diseases, particularly in Melanesians where familial aggregation of thyroid cancer had never been investigated before. The study of genetic variants in candidate susceptibility genes for thyroid cancer may help clarifying the absence of an association in the subgroup of Melanesians from the Loyalty Islands.

Genetic diversity in wild and cultivated black raspberry (Rubus occidentalis L.) evaluated by simple sequence repeat markers

Breeding progress in black raspberry (Rubus occidentalis L.) has been limited by a lack of genetic diversity in elite germplasm. Black raspberry cultivars have been noted for showing very few phenotypic differences and seedlings from crosses between cultivars for a lack of segregation for important traits. Despite these challenges, little molecular work has been done to explore genetic diversity and relationships in wild and cultivated black raspberry germplasm. Microsatellite, or simple sequence repeat (SSR), markers are highly polymorphic codominant markers useful for studying genetic diversity, population genetics, genetic fingerprinting and other applications. We examined genetic diversity in 148 wild and cultivated black raspberry accessions using 21 polymorphic SSR markers. Black raspberry cultivars clustered tightly and showed higher than expected heterozygosity while that of wild accessions was low. Relationships between wild black raspberry accessions were poorly resolved and regional clusters were mostly absent from our analysis. Our results indicated that wild black raspberry germplasm is a relatively untapped resource available for future breeding.

The role of founder effects on the genetic structure of the invasive bullfrog (Lithobates catesbeianaus) in China

Founder effects and genetic drift can reduce the genetic diversity and alter the genetic composition of introduced species during the processes of population establishment and spread. Thus, founder effects are of particular concern for introduced commercial populations (usually founded from few individuals) and for the natural populations they interact with. Bullfrogs were initially introduced in China for aquaculture purposes and escapes from farms have established many feral populations. Most of the bullfrog farms currently operative have been founded from a limited number of descendents from the original introductions, providing an excellent framework to elucidate the importance of founder effects and genetic diversity in the establishment and persistence of invasive species introduced for commercial purposes. We sequenced a region of the mitochondrial cytochrome b gene in 510 samples collected from feral and farm individuals across China and compared them to populations in their native range. Only two haplotypes (H43 and H7) were identified, and H43 identified in this study for the first time was present at high frequency in both feral and commercial populations. We show a significant difference in the relative frequency of the two identified haplotypes in commercial and feral populations, and suggest that sequential founding events are responsible for the emerging widely distributed new haplotype and the observed differences in genetic structure between bullfrog populations. Our findings indicate that lack of genetic diversity does not necessarily impair the colonizing ability of invasive species and highlight the potential threat posed by introduced commercial populations, given their unique genetic makeup.

Lack of genetic diversity in Crimean‐Congo hemorrhagic fever viruses in Turkey: Assessment of present and future patterns of disease

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne zoonosis which is common in Africa, Asia, Eastern Europe, and the Balkan Peninsula. CCHF has been reported in Turkey with high frequency since 2002. The aim of the present study was to investigate the genetic diversity and genetic relationship between CCHF virus (CCHFV) isolates derived from infected patients over a 2-year period (2009 and 2010) in several provinces of Turkey. Serum samples (n = 48) were selected from CCHFV RNA positive patients and subjected to sequence analysis of the gene regions encoding the S (48 samples) and M (14 samples) segments. The nucleotide sequence alignments showed that the nucleic acid relatedness of CCHFV isolates ranged from 95.7% to 100% and from 93.7% to 100% for S and M segments, respectively. Phylogenetic analysis of both segment sequences revealed that CCHFV isolates circulating in Turkey belonged to the European lineage I and were closely related to the viruses found in the Eastern European-Russian and Balkan Peninsula. The M gene segment-based phylogenetic analysis suggested that 2/14 CCHFV isolates (KYSR3159/09 and YZGT714/10) had additional genetic variations. The results of the present study confirmed that the CCHFV isolates present in Turkey associated with human disease had high genetic homology in S segment, but some variability in the M segment of the RNA.

The genetic crisis of the Mexican Bolson Tortoise (Gopherus flavomarginatus: Testudinidae)

Gopherusflavomarginatus(Testudinidae) is endemic to a series of discontinuous, isolated basins collectively known as the Bolson de Mapimí in the Chihuahuan Desert. Its numbers declined after catastrophic levels of exploitation during the mid-20th century. However currently, the Bolson Tortoise appears to be on a path to recovery owing to intensive, sustained conservation efforts. We sequenced an 842-bp-long fragment of the D-loop from 76 individuals distributed throughout the species’ range. The results revealed only two haplotypes. An AMOVA showed that 95% of the variance occurred among populations, whereas the remaining 5% was explained by genetic differences within populations. Tectonic processes together with ecological transformation during the Pleistocene and Holocene may be responsible for the reduction in this species’ genetic variation. A bottleneck during which a significant percentage of the haplotype diversity was lost would result in genetic homogeneity. Although there is demographic growth, the lack of genetic diversity is indicative of the potential crisis that the Bolson Tortoise is facing, and awareness must be brought to this situation.

Separate introductions but lack of genetic variability in the invasive clam Corbicula spp. in Swiss lakes

This study documents the spread of the invasive clam Corbicula spp. in Switzerland since its first record in the River Rhine in 1995. Clams were newly recorded in several Swiss lowland lakes whose interconnecting rivers have not yet been colonized. We present evidence for separate introductions of an identical haplotype of Corbicula fluminea into five lakes in Switzerland in the years 2003–2010 based on the mitochondrial DNA-sequence of the COI in specimens sampled. This suggests passive dispersal of the clam by human activities and/or waterfowl. All but one of the 72 genetically analysed individuals were assigned to a single haplotype FW5 and to the species name C. fluminea. Recent records of specimens, which were not genetically analysed, displayed all the shell morphology of C. fluminea, confirming the dominance of this clam in Swiss rivers and lakes.