Patterns Of Molecular Variation Research Articles

Frequency of Major Transmitted Integrase Resistance in Poland Remains Low Despite Change in Subtype Variability.

With the widespread use of integrase inhibitors and the expanding use of long-acting cabotegravir in both pre-exposure prophylaxis and antiretroviral treatment, molecular surveillance on the transmission of integrase resistance has regained clinical significance. This study aimed to determine the frequency of INSTI-transmitted drug resistance mutations (DRMs) among treatment-naïve individuals in Poland from 2016 to 2023. INSTI resistance was analyzed in 882 antiretroviral treatment-naïve individuals using Sanger sequencing. Integrase DRMs were defined based on the Stanford HIV drug resistance database scores. Phylogeny was used to investigate subtyping and clustering. For the analysis of time-trends, logistic regression was used. Major (E138K and R263K) integrase mutations were detected in 0.45% of cases with minor resistance observed in 14.85%, most commonly (13.95%) E157Q. Overall, no major clusters of transmitted drug resistance were identified, and the transmission of E157Q showed a decreasing trend (p < 0.001). While the frequency of sub-subtype A6 increased, it was predominantly found among migrants and associated with L74 mutations. The frequency of major integrase-transmitted DRMs remains low, despite the changes in subtype variability. Surveillance of changing HIV molecular variation patterns is vital from the perspective of the optimal use of integrase inhibitors, especially due to expanding long-acting cabotegravir implementation.

Enumeration of binary trees compatible with a perfect phylogeny

Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy—a rooted, binary, timed tree, with tips corresponding to individual sequences. Under the infinitely-many-sites mutation model, mutations are randomly superimposed along the branches of the genealogy, so that every mutation occurs at a chromosomal site that has not previously mutated; if a mutation occurs at an interior branch, then all individuals descending from that branch carry the mutation. The implication is that observed patterns of molecular variation from this model impose combinatorial constraints on the hidden state space of genealogies. In particular, observed molecular variation can be represented in the form of a perfect phylogeny, a tree structure that fully encodes the mutational differences among sequences. For a sample of n sequences, a perfect phylogeny might not possess n distinct leaves, and hence might be compatible with many possible binary tree structures that could describe the evolutionary relationships among the n sequences. Here, we investigate enumerative properties of the set of binary ranked and unranked tree shapes that are compatible with a perfect phylogeny, and hence, the binary ranked and unranked tree shapes conditioned on an observed pattern of mutations under the infinitely-many-sites mutation model. We provide a recursive enumeration of these shapes. We consider both perfect phylogenies that can be represented as binary and those that are multifurcating. The results have implications for computational aspects of the statistical inference of evolutionary parameters that underlie sets of molecular sequences.

Exome sequencing of deer mice on two California Channel Islands identifies potential adaptation to strongly contrasting ecological conditions.

Understanding the forces that drive genotypic and phenotypic change in wild populations is a central goal of evolutionary biology. We examined exome variation in populations of deer mice from two of the California Channel Islands: Peromyscus maniculatus elusus from Santa Barbara Island and P. m. santacruzae from Santa Cruz Island exhibit significant differences in olfactory predator recognition, activity timing, aggressive behavior, morphology, prevalence of Sin Nombre virus, and population densities. We characterized variation in protein‐coding regions using exome capture and sequencing of 25 mice from Santa Barbara Island and 22 mice from Santa Cruz Island. We identified and examined 386,256 SNPs using three complementary methods (BayeScan, pcadapt, and LFMM). We found strong differences in molecular variation between the two populations and 710 outlier SNPs in protein‐coding genes that were detected by all three methods. We identified 35 candidate genes from this outlier set that were related to differences in phenotypes between island populations. Enrichment analyses demonstrated that patterns of molecular variation were associated with biological processes related to response to chemical stimuli and regulation of immune processes. Candidate genes associated with olfaction (Gfy, Tlr2, Vmn13r2, numerous olfactory receptor genes), circadian activity (Cry1), anxiety (Brca1), immunity (Cd28, Eif2ak4, Il12a, Syne1), aggression (Cyp19a, Lama2), and body size (Bc16, Syne1) exhibited non‐synonymous mutations predicted to have moderate to large effects. Variation in olfaction‐related genes, including a stop codon in the Santa Barbara Island population, suggests loss of predator‐recognition traits at the molecular level, consistent with a lack of behavioral aversion to fox feces. These findings also suggest that divergent pathogen prevalence and population density may have influenced adaptive immunity and behavioral phenotypes, such as reduced aggression. Overall, our study indicates that ecological differences between islands are associated with signatures of selection in protein‐coding genes underlying phenotypes that promote success in those environments.

Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes

BackgroundGoat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats.ResultsA high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows.ConclusionsAfter domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.

Genetic, Bio-Agronomic, and Nutritional Characterization of Kale (Brassica Oleracea L. var. Acephala) Diversity in Apulia, Southern Italy

Kale (Brassica oleracea L. var. acephala) is a widely appreciated vegetable with a century-old history of cultivation in Italy. The present study was addressed to the collection and characterization of kale germplasm traditionally cultivated in Apulia, Southern Italy, nowadays at risk of genetic erosion. In total, nineteen Apulian kale accessions were acquired. Genotyping by means of simple sequence repeat (SSR) DNA markers led to the identification of highly informative primer combinations and highlighted significant patterns of molecular variation among accessions. Consistently, significant differences were observed with respect to morpho-agronomic traits, including yield and harvesting time, and the content of bioactive compounds, namely total phenols, flavonoids, and anthocyanins, associated with antioxidant activity. Overall, this study led to the establishment of an ex situ collection of great importance to preserve endangered Apulian kale germplasm and to provide seed access to potential growers. Meanwhile, it offers a first characterization of Apulian kale, useful to promote its consumption and valorisation through breeding programmes.

Testing hypotheses on suprageneric relationships and morphological evolution in the Leucobryaceae (Bryophyta)

We studied suprageneric relationships and patterns of morphological character evolution within the moss family Leucobryaceae, based on phylogenetic analyses of markers from all three genomes and representatives from 11 out of 14 genera. Three main lineages are strongly supported within the Leucobryaceae, which display different morphologies of the leaf costa, two dicranoid clades (Campylopus clade and Dicranodontium clade) and a leucobryoid clade. Character evolution analyses resolved the leucobryoid morphology as a synapomorphy for the leucobryoid clade and provided data to evaluate generic circumscriptions within the family. Patterns of molecular variation, species richness, geographical distribution, ecological amplitude and variation in costa structure seem to covary: The two lineages with the most modified morphologies (deviating from the basic dicranoid type; Campylopus and leucobryoid clades) are also the most molecularly variable, species diverse, and occupy the broadest distributions and widest variety of habitats. Most sampled genera have clear morpho-molecular circumscriptions, except Campylopodiella, Dicranodontium and Leucobryum. For the latter, two alternative topologies were resolved (Leucobryum monophyletic or the Asian genera Cladopodanthus and Schistomitrium nested within Leucobryum).

Microsatellite DNA analysis of population structure in Cornops aquaticum (Orthoptera: Acrididae), over a cline for three Robertsonian translocations

The grasshopper Cornops aquaticum occurs between Mexico (23°N) and Uruguay and Central Argentina (35°S). It was recently introduced as a pest control agent of the neotropical water-hyacinth Eichhornia crassipes in South Africa. The information about the amount and distribution of genetic variability of the native populations may optimise the results of biological control programmes. Here we analyse microsatellite variability at the south of C. aquaticum’s distribution, coinciding with a cline for three polymorphic Robertsonian translocations along the Parana River in order to: (1) estimate the amount of intrapopulation variation and its correlation with geographic/climatic variables, (2) infer interpopulation genetic variation and assess connectivity between local populations and (3) compare chromosome, morphometric and molecular variation patterns to analyse the probable causes involved in the maintenance of intraspecific variation. Our sample of 170 individuals of C. aquaticum from seven Argentine populations between latitudes 27°S to 34°S showed 211 alleles across seven microsatellite loci. Genetic diversity was estimated through average number of alleles, allelic richness, expected heterozygosity and observed heterozygosity. The analysis of molecular variance showed significant genetic differentiation among populations. Pairwise comparisons of FST/RST and Bayesian population assignment method and the discriminant analysis of principal components revealed that the two southernmost populations are more differentiated. Genetic diversity is negatively correlated with Southern latitude and with Robertsonian translocation frequencies. Our results showed that the Parana River’s middle course populations are genetically undifferentiated and more genetically diverse than the highly chromosomally polymorphic downstream ones. The chromosomal polymorphisms are associated with increased body size in the direction in which larger size is adaptive. This may be relevant for C. aquaticum’s role as a pest control agent, since chromosome variability would enhance the ability of the species for a successful settlement in its new habitats, especially in temperate regions of the world.

Abstract 1535: Next generation sequencing of brain metastasis in non-small cell lung cancer

Abstract Introduction: Molecular analysis of non-small cell lung cancer (NSCLC) has provided a detailed classification of NSCLC. Activating mutations in the EGFR gene are both prognostic and predictive in that they are associated with improved survival irrespective of therapy and are associated with a significant response to EGFR tyrosine kinase inhibitors (TKIs) such as gefitinib or erlotinib. Patients with EGFR mutations show a significant improvement in progression free survival compared to standard chemotherapy. In addition, a recent study showed that ALK gene rearrangement was significantly associated with pericardial spread and pleural disease and those patients with either ALK gene rearrangements or EGFR mutations were predisposed to liver metastasis. These results support the hypothesis that the dominant molecular oncogenes in NSCLC are associated with different biological behaviors which manifest as distinct patterns of metastatic spread at the time of diagnosis. To date, no pattern of molecular variation has been linked to brain metastasis. Here we use next generation sequencing to identify a pattern of genomic variation associated with the development of brain metastases in NSCLC. Methods: Three patient groups were analyzed: samples from NSCLC patients who did not develop metastasis (n = 8), samples from NSCLC patients who developed metastasis not associated with the central nervous system (n = 7), and brain metastasis samples of NSCLC patients (n = 16). DNA was isolated, and libraries prepared using Qiagen's Comprehensive Cancer Panel which focuses on 160 cancer-related genes. Libraries were sequenced on the Illumina NextSeq 500. Alignment was done using SoftGenetic's NextGENe with subsequent biological interpretation with Ingenuity Variant Analysis. Results: At the variant level, a missense mutation in CDK12 (chr1:37686934) was found in 7 of the 16 cases with brain metastasis while only 1 of 8 cases with no metastasis and 0 of 7 cases with non-CNS metastasis had the variant. However, no other variants were found in ≥6 cases of brain metastasis and 1 or less of the control cases. After filtering variants that occurred in more than 1 control (no metastasis or non-CNS metastasis), the TP53 gene was altered in 11 of the 16 cases with brain metastasis. This included 14 different variants with none of these variants present in the controls. Additionally, BRCA1 and CDK12 had variants in 9 cases with brain metastasis, but the variant was also present in 1 of the controls. Taken together, all 16 cases contained alterations in at least 1 gene involved in PI3K/AKT signaling including variants in JAK1, MTOR, TP53, TSC1, and TSC2. Conclusion: This pilot study has delivered valuable results to better characterize the pattern of genomic variants in NSCLC. While no single variant was associated with brain metastasis, this study implicates PI3K/AKT signaling and, in particular, variants of TP53 as crucial for determining the potential development of NSCLC brain metastasis. Citation Format: Bryan Thibodeau, Paola Yumpo Cardenas, Samreen Ahmed, Marc Dunn, Matthew Johnson, George Wilson. Next generation sequencing of brain metastasis in non-small cell lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1535.

Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect.

Comparative population genetics in asexual vs. sexual species offers the opportunity to investigate the impact of asexuality on genome evolution. Here, we analyse coding sequence polymorphism and divergence patterns in the fascinating Lineus ribbon worms, a group of marine, carnivorous nemerteans with unusual regeneration abilities, and in which asexual reproduction by fissiparity is documented. The population genomics of the fissiparous L.pseudolacteus is characterized by an extremely high level of heterozygosity and unexpectedly elevated πN /πS ratio, in apparent agreement with theoretical expectations under clonal evolution. Analysis of among-species allele sharing and read-count distribution, however, reveals that L.pseudolacteus is a triploid hybrid between Atlantic populations of L.sanguineus and L.lacteus. We model and quantify the relative impact of hybridity, polyploidy and asexuality on molecular variation patterns in L.pseudolacteus and conclude that (i) the peculiarities of L.pseudolacteus population genomics result in the first place from hybridization and (ii) the accumulation of new mutations through the Meselson effect is more than compensated by processes of heterozygosity erosion, such as gene conversion or gene copy loss. This study illustrates the complexity of the evolutionary processes associated with asexuality and identifies L.pseudolacteus as a promising model to study the first steps of polyploid genome evolution in an asexual context.

The impact of Yangtze River discharge on the genetic structure of a population of the rock bream, Oplegnathus fasciatus

ABSTRACTAs a rocky reef species, Oplegnathus fasciatus displays significant geographic differences that may be congruent with patterns of molecular variation. We used 10 polymorphism microsatellite loci to characterize the genetic structure and test the impact of ocean currents and the Yangtze River on the population genetic connectivity of the rock bream, O. fasciatus, sampled from Jiaonan (JN), Zhoushan (ZS) and Taiwan (TW). The average number of alleles was 17.78, with a total of 160 alleles, and the average allele value in the East China Sea (ZS = 13.70) was higher than that in the Yellow Sea (JN = 6.70). The individuals at the ZS location showed the highest expected heterozygosity (He = 0.86), Nei's genetic diversity (H = 0.84) and Shannon genetic diversity (I = 2.21). Genetic bottleneck tests showed that individuals had experienced a recent bottleneck effect in the JN location. AMOVA analysis showed that 12.19% of genetic variation existed among populations, indicating significant population genetic differentiation in the species. The values of the population pairwise differentiation index (Fst and Φpt) ranged from 0.01 to 0.29. The UPGMA tree showed two diverged genealogical branches corresponding to sampling localities (Clade A = JN, Clade B = ZS and TW) in the species. The AMOVA and STRUCTURE analyses suggested that O. fasciatus may be composed of two stocks in the examined range, and the freshwater discharge from the Yangtze River might act as a physical barrier to genetic exchange between north and south China stocks of the species.

Coalescent Times and Patterns of Genetic Diversity in Species with Facultative Sex: Effects of Gene Conversion, Population Structure, and Heterogeneity

Many diploid organisms undergo facultative sexual reproduction. However, little is currently known concerning the distribution of neutral genetic variation among facultative sexual organisms except in very simple cases. Understanding this distribution is important when making inferences about rates of sexual reproduction, effective population size, and demographic history. Here we extend coalescent theory in diploids with facultative sex to consider gene conversion, selfing, population subdivision, and temporal and spatial heterogeneity in rates of sex. In addition to analytical results for two-sample coalescent times, we outline a coalescent algorithm that accommodates the complexities arising from partial sex; this algorithm can be used to generate multisample coalescent distributions. A key result is that when sex is rare, gene conversion becomes a significant force in reducing diversity within individuals. This can reduce genomic signatures of infrequent sex (i.e., elevated within-individual allelic sequence divergence) or entirely reverse the predicted patterns. These models offer improved methods for assessing null patterns of molecular variation in facultative sexual organisms.

Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole-rat, Heterocephalus glaber.

The role of genetic relatedness in the evolution of eusociality has been the topic of much debate, especially when contrasting eusocial insects with vertebrates displaying reproductive altruism. The naked mole-rat, Heterocephalus glaber, was the first described eusocial mammal. Although this discovery was based on an ecological constraints model of eusocial evolution, early genetic studies reported high levels of relatedness in naked mole-rats, providing a compelling argument that low dispersal rates and consanguineous mating (inbreeding as a mating system) are the driving forces for the evolution of this eusocial species. One caveat to accepting this long-held view is that the original genetic studies were based on limited sampling from the species' geographic distribution. A growing body of evidence supports a contrary view, with the original samples not representative of the species-rather reflecting a single founder event, establishing a small population south of the Athi River. Our study is the first to address these competing hypotheses by examining patterns of molecular variation in colonies sampled from north and south of the Athi and Tana rivers, which based on our results, serve to isolate genetically distinct populations of naked mole-rats. Although colonies south of the Athi River share a single mtDNA haplotype and are fixed at most microsatellite loci, populations north of the Athi River are considerably more variable. Our findings support the position that the low variation observed in naked mole-rat populations south of the Athi River reflects a founder event, rather than a consequence of this species' unusual mating system.

Phylogeography and genetic structure of a Tertiary relict tree species, Tapiscia sinensis (Tapisciaceae): implications for conservation.

The phylogeography of plant species in sub-tropical China remains largely unclear. This study used Tapiscia sinensis, an endemic and endangered tree species widely but disjunctly distributed in sub-tropical China, as a model to reveal the patterns of genetic diversity and phylogeographical history of Tertiary relict plant species in this region. The implications of the results are discussed in relation to its conservation management. Samples were taken from 24 populations covering the natural geographical distribution of T. sinensis. Genetic structure was investigated by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA). Phylogenetic relationships among haplotypes were constructed with maximum parsimony and haplotype network methods. Historical population expansion events were tested with pairwise mismatch distribution analysis and neutrality tests. Species potential range was deduced by ecological niche modelling (ENM). A low level of genetic diversity was detected at the population level. A high level of genetic differentiation and a significant phylogeographical structure were revealed. The mean divergence time of the haplotypes was approx. 1·33 million years ago. Recent range expansion in this species is suggested by a star-like haplotype network and by the results from the mismatch distribution analysis and neutrality tests. Climatic oscillations during the Pleistocene have had pronounced effects on the extant distribution of Tapiscia relative to the Last Glacial Maximum (LGM). Spatial patterns of molecular variation and ENM suggest that T. sinensis may have retreated in south-western and central China and colonized eastern China prior to the LGM. Multiple montane refugia for T. sinense existing during the LGM are inferred in central and western China. The populations adjacent to or within these refugia of T. sinense should be given high priority in the development of conservation policies and management strategies for this endangered species.

The relations between recombination rate and patterns of molecular variation and evolution in Drosophila.

Genetic recombination affects levels of variability and the efficacy of selection because natural selection acting at one site affects evolutionary processes at linked sites. The variation in local recombination rates across the Drosophila genome provides excellent material for testing hypotheses concerning the evolutionary consequences of recombination. The current state of knowledge from studies of Drosophila genomics and population genetics is reviewed here. Selection at linked sites has influenced the relations between recombination rates and patterns of molecular variation and evolution, such that higher rates of recombination are associated with both higher levels of variability and a greater efficacy of selection. It seems likely that background selection against deleterious mutations is a major factor contributing to these patterns in genome regions in which crossing over is rare or absent, whereas selective sweeps of positively selected mutations probably play an important role in regions with crossing over.

The demography and population genomics of evolutionary transitions to self-fertilization in plants.

The evolution of self-fertilization from outcrossing has occurred on numerous occasions in flowering plants. This shift in mating system profoundly influences the morphology, ecology, genetics and evolution of selfing lineages. As a result, there has been sustained interest in understanding the mechanisms driving the evolution of selfing and its environmental context. Recently, patterns of molecular variation have been used to make inferences about the selective mechanisms associated with mating system transitions. However, these inferences can be complicated by the action of linked selection following the transition. Here, using multilocus simulations and comparative molecular data from related selfers and outcrossers, we demonstrate that there is little evidence for strong bottlenecks associated with initial transitions to selfing, and our simulation results cast doubt on whether it is possible to infer the role of bottlenecks associated with reproductive assurance in the evolution of selfing. They indicate that the effects of background selection on the loss of diversity and efficacy of selection occur rapidly following the shift to high selfing. Future comparative studies that integrate explicit ecological and genomic details are necessary for quantifying the independent and joint effects of selection and demography on transitions to selfing and the loss of genetic diversity.

Cranial variation amongst independent lineages of the alligator snapping turtle (Macrochelys temminckii)

Recent interest in diagnoses and relationships between lineages of the alligator snapping turtle (Macrochelys temminckii) present conflicting patterns of molecular variation across the taxon's range. This study uses geometric morphometric techniques to test molecular hypotheses. We analyse alligator snapping turtle cranial variation amongst populations (i.e. drainages) with the hypothesis that populations of turtles recovered as monophyletic by previous molecular studies are more similar to each other in cranial shape. Dorsal, lateral and ventral cranial shape analyses corroborate the uniqueness of populations recovered by molecular genetic hypotheses. Additionally, analyses reveal near equal separation between drainages that were assigned to monophyletic clades by previous phylogenetic studies. These results reveal the potential for more independent lineages that have yet to be diagnosed, and unique cranial shapes are described for our three most heavily sampled drainages.

Unravelling the evolutionary history of Eucalyptus cordata (Myrtaceae) using molecular markers

We studied the evolutionary processes shaping the genetic diversity in the naturally fragmented Eucalyptus cordata, a rare homoblastic tree endemic to the island of Tasmania. A genome-wide scan showed that E. cordata and the endangered heteroblastic E. morrisbyi were closely related, suggesting a neotenous origin of E. cordata from an endemic heteroblastic ancestor. Bayesian cluster analysis based on nuclear microsatellites assayed in 567 E. cordata and E. morrisbyi individuals revealed five genetic clusters. Two clusters comprised populations that correspond to putative ancestral gene pools linking E. cordata and E. morrisbyi. Another cluster included populations that transgressed the drowned Derwent River valley, suggestive of a wider glacial distribution. However, the majority of individuals occurred in the two genetic clusters distributed in the south-west and north-east of the range of E. cordata. The elevated genetic diversity in populations comprising these clusters suggests that they represent two recently fragmented cores of the distribution. Genetic evidence suggests that the newly described, localised E. cordata subspecies quadrangulosa has been recently selected from within the morphologically diverse, south-western cluster. We argue that multiple phases of isolation and drift have led to the contemporary pattern of molecular variation and the scattering of relictual and more recently derived populations across the species distribution.

Failed species, innominate forms, and the vain search for species limits: cryptic diversity in dusky salamanders (Desmognathus) of eastern Tennessee

AbstractCytochrome B sequences and allozymes reveal complex patterns of molecular variation in dusky salamander (Desmognathus) populations in eastern Tennessee. One group of allozymically distinctive populations, which we refer to as the Sinking Creek form (SCF), combines morphological attributes of Desmognathus fuscus with cytB sequences characteristic of Desmognathus carolinensis. This form is abruptly replaced by D. fuscus just north of Johnson City, TN with no evidence of either sympatry or gene exchange. To the south, allozymic markers indicate a broad zone of admixture with populations characterized by distinct cytB sequences and that may or may not be ultimately referable to Desmognathus conanti. A third distinctive group of populations, which we refer to as the Lemon Gap form (LGF), occurs in the foothills of the Great Smoky and southern Bald Mountains and exchanges genes with Desmognathus santeetlah along the escarpment of the Great Smokies, D. carolinensis in the southern Bald Mountains, and populations of a different haplotype clade in the Ridge and Valley. We treat all these as innominate forms that may represent “failed species,” recognizing that it may never be possible to reconcile species limits with patterns of phylogeny, morphology, and gene exchange in these salamanders.

Assessment of genetic diversity of Tunisian Barbary fig (Opuntia ficus indica) cultivars by RAPD markers and morphological traits

In this work, we report the analysis of genetic diversity of Tunisian Opuntia ficus indica ecotypes using morphological parameters and RAPD markers. Morphological evaluation showed phenotypic variation among the accessions studied. The used phenotypic traits appear a good descriptors for Barbary fig varieties. The subsequent RAPD banding patterns exhibited large number of polymorphic bands. Ten primers were screened to assess their ability to detect polymorphisms within 28 Tunisian Barbary fig cultivars and revealed 41 polymorphic RAPD markers. The percentage of polymorphic bands (73.21%) and the resolving power (Rp) (24.17) showed the efficiency of the used primers. The revealed RAPD markers permit to distinguish all considered cultivars and resolve homonymy problem. UPGMA dendrogram and principal component analysis were performed to access patterns of diversity among cultivars and its structuration. In fact the cultivars distribution occurs independently of their geographic origin. The overall distribution pattern of molecular variation suggested that about 92.58% of the total variance was accounted within group. The remaining 7.42% of the variation was hierarchically structured between components due to differentiation among groups. A positive and significant correlation was evidenced between morphological descriptors and RAPD markers. Wide phenotypic and molecular diversity was found in local cactus germplasm indicating a considerable potential for improving this crop. The combined analysis of phenotypic and molecular markers was also a valuable tool for assessing the genetic diversity in cacti.

Frequent adaptation and the McDonald–Kreitman test

Population genomic studies have shown that genetic draft and background selection can profoundly affect the genome-wide patterns of molecular variation. We performed forward simulations under realistic gene-structure and selection scenarios to investigate whether such linkage effects impinge on the ability of the McDonald-Kreitman (MK) test to infer the rate of positive selection (α) from polymorphism and divergence data. We find that in the presence of slightly deleterious mutations, MK estimates of α severely underestimate the true rate of adaptation even if all polymorphisms with population frequencies under 50% are excluded. Furthermore, already under intermediate rates of adaptation, genetic draft substantially distorts the site frequency spectra at neutral and functional sites from the expectations under mutation-selection-drift balance. MK-type approaches that first infer demography from synonymous sites and then use the inferred demography to correct the estimation of α obtain almost the correct α in our simulations. However, these approaches typically infer a severe past population expansion although there was no such expansion in the simulations, casting doubt on the accuracy of methods that infer demography from synonymous polymorphism data. We propose a simple asymptotic extension of the MK test that yields accurate estimates of α in our simulations and should provide a fruitful direction for future studies.