Persistence Of Lineages Research Articles

Persistence of HIV-1 Env-Specific Plasmablast Lineages in Plasma Cells after Vaccination in Humans

SummaryInduction of persistent HIV-1 Envelope (Env) specific antibody (Ab) is a primary goal of HIV vaccine strategies; however, it is unclear whether HIV Env immunization in humans induces bone marrow plasma cells, the presumed source of long-lived systemic Ab. To define the features of Env-specific plasma cells after vaccination, samples were obtained from HVTN 105, a phase I trial testing the same gp120 protein immunogen, AIDSVAX B/E, used in RV144, along with a DNA immunogen in various prime and boost strategies. Boosting regimens that included AIDSVAX B/E induced robust peripheral blood plasmablast responses. The Env-specific immunoglobulin repertoire of the plasmablasts is dominated by VH1 gene usage and targeting of the V3 region. Numerous plasmablast-derived immunoglobulin lineages persisted in the bone marrow >8 months after immunization, including in the CD138+ long-lived plasma cell compartment. These findings identify a cellular linkage for the development of sustained Env-specific Abs following vaccination in humans.

Can fine-scale habitats of limestone outcrops be considered litho-refugia for dry forest tree lineages?

In the neotropical region, seasonally dry tropical forests (SDTF) are commonly associated with scatterly distributed limestone outcrops, known for harbouring high numbers of endemic species and genera. In the context of lacking knowledge on fine-scale vegetation and environmental heterogeneity of these geoecosystems and having a limestone outcrop in eastern Brazil as a case study, we address the question: how important are limestone outcrops for SDTF tree community composition, structure, function and evolution? We distinguished five habitats related to position and distance to the outcrop, and within each of 25 sampled plots (five per habitat), we identified and measured the diameter of all living tree individuals and collected soil samples for chemical and textural analyses. We investigated taxonomic and phylogenetic substitution across the habitats and fitted linear models to test the effects of habitat type, soil fertility and texture on taxonomic/structural, functional and phylogenetic parameters. We found striking taxonomic and phylogenetic differentiation among the habitats, especially related to recent diversification, with soil fertility and texture largely accounting for variations in all analysed parameters. Given the predominant roles of vicariance and in situ diversification believed to have given rise to the current patterns of endemism and diversity of eastern Brazil SDTF, we argue that the conditions presented by limestone outcrops, including aridity and high fertility, may have favoured the persistence of SDTF lineages during the Quaternary environmental changes, highlighting their role as litho-refugia. In order to complete this biogeographic puzzle, we encourage other fine-scale assessments of outcrop-associated SDTF from the phylogenetic viewpoint.

Building mountain biodiversity: Geological and evolutionary processes.

Mountain regions are unusually biodiverse, with rich aggregations of small-ranged species that form centers of endemism. Mountains play an array of roles for Earth's biodiversity and affect neighboring lowlands through biotic interchange, changes in regional climate, and nutrient runoff. The high biodiversity of certain mountains reflects the interplay of multiple evolutionary mechanisms: enhanced speciation rates with distinct opportunities for coexistence and persistence of lineages, shaped by long-term climatic changes interacting with topographically dynamic landscapes. High diversity in most tropical mountains is tightly linked to bedrock geology-notably, areas comprising mafic and ultramafic lithologies, rock types rich in magnesium and poor in phosphate that present special requirements for plant physiology. Mountain biodiversity bears the signature of deep-time evolutionary and ecological processes, a history well worth preserving.

Fine-scale to Flora-wide Phylogenetic Perspectives on Californian Plant Diversity, Endemism, and Conservation

The California Floristic Province (CA-FP) encompasses North America’s Mediterranean-type climatic region and is a global biodiversity hotspot in temperate North America. Fine-scale phylogenetic studies and increasing scrutiny of morphological, ecological, and geographic variation in the CA-FP vascular flora continue to reveal novel, often cryptic diversity warranting taxonomic attention. The prevalence of such discoveries warrants caution about potential for loss of undescribed or unrecognized biodiversity from human-related impacts, including insufficiently informed conservation-related actions (e.g., genetic augmentation or assisted migration). Broader-scale molecular phylogenetic studies have yielded other examples of more extensive CA-FP diversification than previously resolved. For example, clades uniting CA-FP taxa not earlier thought to be such close relatives have been discovered in a wide diversity of tribes of composites and legumes. This understanding adds additional weight to the conclusions of Raven and Axelrod (1978) that in situ evolution, especially since the pronounced mid-Miocene transition toward summer-drying, has been a major factor in the origins of Californian vascular plant diversity. The importance of paleo-endemism in gymnosperms and (especially woody) angiosperms of the CA-FP flora also has been corroborated and refined by molecular phylogenetic studies, with improved understanding of the timing of divergence and relationships of isolated lineages, such as the extinct island-endemic Hesperelaea A. Gray (Oleaceae). On a regional scale, studies of spatial patterns of Californian species richness, phylogenetic diversity, and phylogenetic endemism by the California Plant Phylodiversity Project (CPPP) have reinforced the floristic importance of areas of high topographic complexity, or environmental heterogeneity more generally, where relatively high levels of habitat diversity, speciation, and lineage persistence may be expected. The CPPP’s finding that particularly young plant lineages and significantly high phylogenetic endemism are concentrated in drier regions of the CA-FP and in the adjacent Californian deserts has corroborated earlier preliminary findings and aligns with Stebbins’s (1952) hypothesis of aridity as an evolutionary stimulus. A recent conservation gap analysis by the CPPP incorporating flora-wide phylogenetic and geographic occurrence data plus land-protection status and habitat-integrity information for California has demonstrated the potential of an integrative, evolutionary approach for identifying high-priority land conservation targets.

Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000\u20132016

Multidrug-resistant (MDR) Salmonella enterica has been deemed a high-priority pathogen by the World Health Organization. Two hundred and sixty-four Salmonella enterica isolates recovered over a 16-year period (2000 to 2016) from the poultry and swine production chains, in Brazil, were investigated by whole-genome sequencing (WGS). Most international lineages belonging to 28 serovars, including, S. enterica serovars S. Schwarzengrund ST96, S. Typhimurium ST19, S. Minnesota ST548, S. Infantis ST32, S. Heidelberg ST15, S. Newport ST45, S. Brandenburg ST65 and S. Kentucky ST198 displayed MDR and virulent genetic backgrounds. In this regard, resistome analysis revealed presence of qnrE1 (identified for the first time in S. Typhimurium from food chain), qnrB19, qnrS1, blaCTX-M-8, blaCTX-M-2 and blaCMY-2 genes, as well as gyrA mutations; whereas ColpVC, IncHI2A, IncHI2, IncFIA, Incl1, IncA/C2, IncR, IncX1 and po111 plasmids were detected. In addition, phylogenetic analysis revealed multiple independent lineages such as S. enterica serovars S. Infantis, S. Schwarzengrund, S. Minnesota, S. Kentucky and S. Brandenburg. In brief, ocurrence and persistence of international lineages of S. enterica serovars in food production chain is supported by conserved genomes and wide virulome and resistome.

Founder effects on trans-generational dynamics of closed inbreeding lineages of the predatory mite Phytoseiulus persimilis.

Both close inbreeding and distant outbreeding may reduce fitness below the level of individuals with intermediate parental relatedness. In the haplodiploid plant-inhabiting predatory mite Phytoseiulus persimilis, which is patchily distributed within and among host plants, fitness is indeed reduced in the short term, i.e. by a single generation of inbreeding. However, in the medium to long term (multiple generations), distant out-breeding should provide for favorable demographic founder effects in isolated populations. We tested this prediction in isolated experimental lineages founded by females mated to a sibling (close inbreeding), a male from the same population (intermediate relatedness) or a male from another population (distant outbreeding) and monitored lineage growth and persistence over four generations. Cross-generationally, lineages founded by distantly outbred females performed the best, i.e. produced the most descendants. However, this was solely due to superior performance from the F2 generation onwards, whereas in the F1 generation, lineages founded by females mated to males from their own population (intermediate relatedness) performed the best, as predicted from short-term in- and out-breeding depression effects. At the genetic level, this result was most likely due to distantly outbred founders introducing higher allelic variability and lower homozygosity levels, counterbalancing inbreeding depression, which inevitably occurs in isolated lineages, from the F2 generation onwards.

Phylogenetic diversity in the Western Ghats biodiversity hotspot reflects environmental filtering and past niche diversification of trees

AbstractAimWe examined how contrasted climatic conditions influenced the ecological and phylogenetic diversity of tropical trees at the regional scale. Beyond the basic expectation of greater environmental filtering in currently stressful contexts, we addressed how biogeographic history and past climates contributed to shaping the distribution and diversity of extant taxa.LocationEvergreen forests of Western Ghats, India.MethodsWe evaluated the relative importance of niche‐based, historical, and spatial processes on community phylogenetic structure and turnover in 297 plots including 459 species. If niche conservatism prevails, we expected greater phylogenetic clustering under harsher or historically less stable climates, and overdispersion in opposite conditions. To test the role of environmental filtering in shaping local communities, we assessed species’ climatic niches and congruence between niche and phylogenetic diversity. To assess the imprint of ancient versus recent evolutionary constraints, we calculated mean pair‐wise (MPD) and nearest‐taxon (MNTD) phylogenetic distances, respectively.ResultsWe found non‐random phylogenetic structure depending on both current and past climatic variation. Basal community phylogenetic structure (MPD) was related to niche diversity and varied according to hydric stress: (a) northern environments filtered more closely related species, while (b) phylogenetic overdispersion suggested greater niche differentiation in stable, least‐seasonal southern habitats and at high elevations. Terminal phylogenetic structure (MNTD) did not show overdispersion. Phylogenetic turnover was driven by current abiotic factors, not space.Main conclusionsThe patterns of ecological and phylogenetic diversity likely reflect the Miocene climate shift to increasing seasonality northwards. Phylogenetic clustering under hydric stress or historical instability suggests the influence of functional conservatism, whereas overdispersion in southern forests supports the persistence of old lineages in an ancient rain forest refugium as an evolutionary museum. Overdispersion in fragmented montane forests reflects a mixture of biogeographically distinct species pools, both tropical and temperate, that characterise environmentally contrasted cores and fringes. Low phylogenetic turnover along the seasonality gradient suggests recent ecological diversification across forests with contrasted rainfall seasonality.

Molecular phylogenetics and historical biogeography of the tribe Lilieae (Liliaceae): bi-directional dispersal between biodiversity hotspots in Eurasia.

The role played by the Qinghai-Tibet Plateau (QTP) in the organismal diversification and biogeography of plants in the Northern Hemisphere has attracted much attention from evolutionary biologists. Here we use tribe Lilieae (Liliaceae), including primarily temperate and alpine lineages with disjunct distributions in the North Temperate Zone, as a case study to shed light upon these processes. Using 191 taxa (five outgroup taxa) comprising more than 60 % of extant Lilieae species across the entire geographical range, we analyse phylogenetic relationships based on three plastid markers (matK, rbcL, rpl16) and nuclear ITS. Divergence time estimation and ancestral range reconstruction were further inferred. The results support a monophyletic Lilieae divided into four clades. Lilium is nested within Fritillaria, which is paraphyletic and partitioned into two clades, New World and Old World, in the chloroplast DNA (cpDNA) analysis. Incongruences between the ITS and cpDNA trees may be explained by divergent ITS paralogues and hybridization. Lilieae originated around 40-49 (28-67) Mya and probably diversified in the QTP region with four major clades that were established during the Oligocene and the Early Miocene. Uplift of the QTP and climatic changes probably drove early diversification of Lilieae in the QTP region. A rapid radiation occurred during the Late Miocene and the Pleistocene, coinciding temporally with recent orogenic process in the QTP region and climatic oscillations. Several lineages dispersed out of the QTP. Lineage persistence and explosive radiation were important processes for establishing high species diversity of Lilieae in the QTP region. Both long-distance dispersal and migration across Beringia probably contributed to the modern distribution range of Lilieae. Our study shows that biotic interchanges between the QTP region and Irano-Turanian region and the Mediterranean Basin were bi-directional, suggesting the latter was a secondary centre of diversity.

Aspergillus flavus resident in Kenya: High genetic diversity in an ancient population primarily shaped by clonal reproduction and mutation-driven evolution.

Aspergillus flavus has long been considered to be an asexual species. Although a sexual stage was recently reported for this species from in vitro studies, the amount of recombination ongoing in natural populations and the genetic distance across which meiosis occurs is largely unknown. In the current study, genetic diversity, reproduction and evolution of natural A. flavus populations endemic to Kenya were examined. A total of 2744 isolates recovered from 629 maize-field soils across southern Kenya in two consecutive seasons were characterized at 17 SSR loci, revealing high genetic diversity (9-72 alleles/locus and 2140 haplotypes). Clonal reproduction and persistence of clonal lineages predominated, with many identical haplotypes occurring in multiple soil samples and both seasons. Genetic analyses predicted three distinct lineages with linkage disequilibrium and evolutionary relationships among haplotypes within each lineage suggesting mutation-driven evolution followed by clonal reproduction. Low genetic differentiation among adjacent communities reflected frequent short distance dispersal.

Patterns and drivers of species diversity in the Indo‐Pacific red seaweed Portieria

AbstractAimBiogeographical processes underlying Indo‐Pacific biodiversity patterns have been relatively well studied in marine shallow water invertebrates and fishes, but have been explored much less extensively in seaweeds, despite these organisms often displaying markedly different patterns. Using the marine red alga Portieria as a model, we aim to gain understanding of the evolutionary processes generating seaweed biogeographical patterns. Our results will be evaluated and compared with known patterns and processes in animals.LocationIndo‐Pacific marine region.MethodsSpecies diversity estimates were inferred using DNA‐based species delimitation methods. Historical biogeographical patterns were inferred based on a six‐gene time‐calibrated phylogeny, distribution data of 802 specimens, and probabilistic modelling of geographical range evolution. The importance of geographical isolation for speciation was further evaluated by population genetic analyses at the intraspecific level.ResultsWe delimited 92 candidate species, most with restricted distributions, suggesting low dispersal capacity. Highest species diversity was found in the Indo‐Malay Archipelago (IMA). Our phylogeny indicates that Portieria originated during the late Cretaceous in the area that is now the Central Indo‐Pacific. The biogeographical history of Portieria includes repeated dispersal events to peripheral regions, followed by long‐term persistence and diversification of lineages within those regions, and limited dispersal back to the IMA.Main conclusionsOur results suggest that the long geological history of the IMA played an important role in shaping Portieria diversity. High species richness in the IMA resulted from a combination of speciation at small spatial scales, possibly as a result of increased regional habitat diversity from the Eocene onwards, and species accumulation via dispersal and/or island integration through tectonic movement. Our results are consistent with the biodiversity feedback model, in which biodiversity hotspots act as both “centres of origin” and “centres of accumulation,” and corroborate previous findings for invertebrates and fish that there is no single unifying model explaining the biological diversity within the IMA.

Does the evolution of self-fertilization rescue populations or increase the risk of extinction?

As a major evolutionary transition in seed plants, the evolution of plant mating systems has been much debated in evolutionary ecology. Over the last 10 years, well-established patterns of evolution have emerged. On the one hand, experimental studies have shown that self-fertilization is likely to evolve in a few generations (microevolution) as a response to rapid environmental change (e.g. pollinator decline), eventually rescuing a population. On the other, phylogenetic studies have demonstrated that repeated evolution towards self-fertilization (macroevolution) leads to a higher risk of lineage extinction and is thus likely to be disadvantageous in the long term. In either case - the short-term or long-term evolution of self-fertilization (selfing) - these findings indicate that a mating system is not neutral with respect to population or lineage persistence. They also suggest that selfing can have contrasting effects depending on time scale. This raises the question of whether mating system evolution can rescue populations facing environmental change. In this review, empirical and theoretical evidence of the direct and indirect effects of mating systems on population demography and lineage persistence were analysed. A simple theoretical evolutionary rescue model was also developed to investigate the potential for evolutionary rescue through selfing. Demographic studies consistently show a short-term advantage of selfing provided by reproductive assurance, but a long-term disadvantage for selfing lineages, suggesting indirect genomic consequences of selfing (e.g. mutation load and lower adaptability). However, our theoretical evolutionary rescue model found that even in the short term, while mating system evolution can lead to evolutionary rescue, it can also lead to evolutionary suicide, due to the inherent frequency-dependent selection of mating system traits. These findings point to the importance of analysing the demographic consequences of self-fertilization in order to predict the effect of selfing on population persistence as well as take into account the indirect genomic consequences of selfing. The pace at which processes such as inbreeding depression, purging, reproductive assurance and genomic rearrangements occur after the selfing transition is the key to clarifying whether or not selfing will result in evolutionary rescue.

The influence of biogeographic history on the functional and phylogenetic diversity of passerine birds in savannas and forests of the Brazilian Amazon.

Passeriformes is the largest and most diverse avian order in the world and comprises the Passeri and Tyranni suborders. These suborders constitute a monophyletic group, but differ in their ecology and history of occupation of South America. We investigated the influence of biogeographic history on functional and phylogenetic diversities of Passeri and Tyranni in forest and savanna habitats in the Brazilian Amazon. We compiled species composition data for 34 Passeriformes assemblages, 12 in savannas and 22 in forests. We calculated the functional (Rao's quadratic entropy, FDQ) and phylogenetic diversities (mean pairwise distance, MPD, and mean nearest taxon distance, MNTD), and the functional beta diversity to investigate the potential role of biogeographic history in shaping ecological traits and species lineages of both suborders. The functional diversity of Passeri was higher than for Tyranni in both habitats. The MPD for Tyranni was higher than for Passeri in forests; however, there was no difference between the suborders in savannas. In savannas, Passeri presented higher MNTD than Tyranni, while in forest areas, Tyranni assemblages showed higher MNTD than Passeri. We found a high functional turnover (~75%) between Passeri and Tyranni in both habitats. The high functional diversity of Passeri in both habitats is due to the high diversity of ecological traits exhibited by species of this group, which enables the exploitation of a wide variety of resources and foraging strategies. The higher Tyranni MPD and MNTD in forests is likely due to Tyranni being older settlers in this habitat, resulting in the emergence and persistence of more lineages. The higher Passeri MNTD in savannas can be explained by the existence of a larger number of different Passeri lineages adapted to this severe habitat. The high functional turnover between the suborders in both habitats suggests an ecological strategy to avoid niche overlap.

The origins of diversity in ancient landscapes: Deep phylogeographic structuring in a pseudoscorpion (Pseudotyrannochthoniidae: Pseudotyrannochthonius) reflects Plio-Pleistocene climate fluctuations

Southwestern Australia is one of the global biodiversity hotspots. Like many other hotspots, comparatively few data are available explaining speciation patterns in endemic animal lineages, which hampers conservation efforts and a deeper understanding of how diversity is generated and maintained. I investigated the phylogeographic structure of an ancient arachnid species, the pseudoscorpion Pseudotyrannochthonius giganteus Beier, 1971, endemic to the mesic eucalypt forests of southwestern Australia. This species is habitat-restricted and has morphologically divergent populations in epigean (forest) and hypogean (karst) habitats. Phylogenetic, molecular clock and population genetic analyses of mitochondrial (COI mtDNA) and nuclear (ITS2 rDNA) data revealed a complex population structure, with six allopatric lineages separated by vicariant barriers, such as rivers. These lineages diverged between the late Miocene and Pliocene epochs, characterised by increasingly intense climatic cycles between mesic/warm and arid/cold. Surprisingly, specimens from caves were genetically similar to those from forests, indicating subterranean isolation has not driven diversification. Instead, genetic diversity is clustered in a small area, coinciding with the highest rainfall and lowest seasonality in Western Australia. Future climates, warmer and drier than today, will likely lead to range retraction towards this area and mimic past variations that have shaped contemporary diversity. Southwestern Australia is an ancient, stable landscape that allowed for persistence of ancient lineages, such as P. giganteus. Historic climatic fluctuations have driven diversification, generating highly structured species and localised centres of endemism. Other ancient landscapes, e.g. South Africa’s Cape Provinces, are expected to share similarly complex patterns of invertebrate biodiversity. Unravelling these is essential to informed conservation decision making.

Phylogeny and antimicrobial resistance in Neisseria gonorrhoeae isolates from Rio de Janeiro, Brazil

Resistance in Neisseria gonorrhoeae is a global public health challenge. However, little is known about N. gonorrhoeae isolates from Brazil. In this study, we characterized 116N. gonorrhoeae isolates obtained in Rio de Janeiro between 2006 and 2015 according to antimicrobial susceptibility profiles, resistance mechanisms, and clonal diversity. We determined antimicrobial minimal inhibitory concentrations by agar dilution, and whole genome sequencing was conducted to investigate alleles related to resistance, determine multilocus sequence typing profiles, and group isolates based on core genome single nucleotide polymorphisms. Resistance to penicillin, tetracycline, ciprofloxacin, and azithromycin was observed since 2006. Resistance to penicillin was mediated by β-lactamase plasmids and chromosomal mutations in ponA and porB genes, and tetracycline resistance was mediated by TetM plasmids, and porB and rspJ mutations. Ciprofloxacin resistant isolates presented cumulative point mutations in the quinolone resistance-determining region (QRDR) of gyrA and parC. Alterations in rrl genes encoding 23S rRNA, mtrR, and the mtrR promoter region were responsible for resistance to azithromycin. Phylogenetic analysis identified seven main clades, which included isolates with similar resistance profiles that mainly belonged to a limited number of sequence types that occurred during different years. Our results demonstrated high penicillin, tetracycline, and ciprofloxacin resistance rates associated with the persistence of successful resistant gonococcal lineages, and the polyclonal emergence of azithromycin resistance. Moreover, we reinforce the importance of surveillance to monitor the evolution of this scenario and to allow the early detection of possible changes to azithromycin and ceftriaxone as effective treatment options in the city.

Population genomics and geographical parthenogenesis in Japanese harvestmen (Opiliones, Sclerosomatidae, Leiobunum).

Naturally occurring population variation in reproductive mode presents an opportunity for researchers to test hypotheses regarding the evolution of sex. Asexual reproduction frequently assumes a geographical pattern, in which parthenogenesis‐dominated populations are more broadly dispersed than their sexual conspecifics. We evaluate the geographical distribution of genomic signatures associated with parthenogenesis using nuclear and mitochondrial DNA sequence data from two Japanese harvestman sister taxa, Leiobunum manubriatum and Leiobunum globosum. Asexual reproduction is putatively facultative in these species, and female‐biased localities are common in habitat margins. Past karyotypic and current cytometric work indicates L. globosum is entirely tetraploid, while L. manubriatum may be either diploid or tetraploid. We estimated species phylogeny, genetic differentiation, diversity, and mitonuclear discordance in females collected across the species range in order to identify range expansion toward marginal habitat, potential for hybrid origin, and persistence of asexual lineages. Our results point to northward expansion of a tetraploid ancestor of L. manubriatum and L. globosum, coupled with support for greater male gene flow in southern L. manubriatum localities. Specimens from localities in the Tohoku and Hokkaido regions were indistinct, particularly those of L. globosum, potentially due to little mitochondrial differentiation or haplotypic variation. Although L. manubriatum overlaps with L. globosum across its entire range, L. globosum was reconstructed as monophyletic with strong support using mtDNA, and marginal support with nuclear loci. Ultimately, we find evidence for continued sexual reproduction in both species and describe opportunities to clarify the rate and mechanism of parthenogenesis.

Effective purifying selection in ancient asexual oribatid mites

Sex is beneficial in the long term because it can prevent mutational meltdown through increased effectiveness of selection. This idea is supported by empirical evidence of deleterious mutation accumulation in species with a recent transition to asexuality. Here, we study the effectiveness of purifying selection in oribatid mites which have lost sex millions of years ago and diversified into different families and species while reproducing asexually. We compare the accumulation of deleterious nonsynonymous and synonymous mutations between three asexual and three sexual lineages using transcriptome data. Contrasting studies of young asexual lineages, we find evidence for strong purifying selection that is more effective in asexual as compared to sexual oribatid mite lineages. Our results suggest that large populations likely sustain effective purifying selection and facilitate the escape of mutational meltdown in the absence of sex. Thus, sex per se is not a prerequisite for the long-term persistence of animal lineages.

Micropathogen Community Analysis in Hyalomma rufipes via High-Throughput Sequencing of Small RNAs.

Ticks are important vectors in the transmission of a broad range of micropathogens to vertebrates, including humans. Because of the role of ticks in disease transmission, identifying and characterizing the micropathogen profiles of tick populations have become increasingly important. The objective of this study was to survey the micropathogens of Hyalomma rufipes ticks. Illumina HiSeq2000 technology was utilized to perform deep sequencing of small RNAs (sRNAs) extracted from field-collected H. rufipes ticks in Gansu Province, China. The resultant sRNA library data revealed that the surveyed tick populations produced reads that were homologous to St. Croix River Virus (SCRV) sequences. We also observed many reads that were homologous to microbial and/or pathogenic isolates, including bacteria, protozoa, and fungi. As part of this analysis, a phylogenetic tree was constructed to display the relationships among the homologous sequences that were identified. The study offered a unique opportunity to gain insight into the micropathogens of H. rufipes ticks. The effective control of arthropod vectors in the future will require knowledge of the micropathogen composition of vectors harboring infectious agents. Understanding the ecological factors that regulate vector propagation in association with the prevalence and persistence of micropathogen lineages is also imperative. These interactions may affect the evolution of micropathogen lineages, especially if the micropathogens rely on the vector or host for dispersal. The sRNA deep-sequencing approach used in this analysis provides an intuitive method to survey micropathogen prevalence in ticks and other vector species.

Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex.

The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture data set and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O.beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes. Here, we showed that these mtDNA lineages likely formed in allopatry during the Pleistocene, but responded differentially to climatic changes that occurred since the last interglacial (~120,000years ago). We find that the Northern lineage maintained a stable range throughout this period, correlating with genetic distinctiveness among all genetic markers and low migration rates with the other lineages. In contrast, our results suggested that the Southern lineage expanded from Baja California Sur during the Late Pleistocene to overlap and potentially swamp a contracting Central lineage. High rates of intraspecific gene flow between Southern lineage individuals among expansion origin and expansion edge populations largely eroded Central ancestry from autosomal markers. However, male-biased dispersal in this system preserved signals of this past hybridization and introgression event in matrilineal-biased X-chromosome and mtDNA markers. Our results highlight the importance of range stability in maintaining the persistence of phylogeographic lineages, whereas unstable range dynamics can increase the tendency for lineages to merge upon secondary contact.

Isolation and gene flow in a speciation continuum in newts

Because reproductive isolation often evolves gradually, differentiating lineages may retain the potential for genetic exchange for prolonged periods, providing an opportunity to quantify and to understand the fundamental role of gene flow during speciation. Here we delimit evolutionary lineages, reconstruct the phylogeny and infer gene flow in newts of the Lissotriton vulgaris species complex based on 74 nuclear markers sampled from 127 localities. We demonstrate that distinct lineages along the speciation continuum in newts exchange nontrivial amounts of genes, affecting their evolutionary trajectories. By integrating a wide array of methods, we delimit nine evolutionary lineages and show that two principal factors have driven their genetic differentiation: time since the last common ancestor determining levels of shared ancestral polymorphism, and shifts in geographic distributions determining the extent of secondary contact. Post-divergence gene flow, indicative of evolutionary non-independence, has been most extensive in Central Europe, while four southern European lineages have acquired the population-genetic hallmarks of independent species (L. graecus, L. kosswigi, L. lantzi, L. schmidtleri). We obtained strong statistical support for widespread mtDNA introgression following secondary contact, previously suggested by discordance between mtDNA phylogeny and morphology. Our study reveals long-term evolutionary persistence of evolutionary lineages that may periodically exchange genes with one another: although some of these lineages may become extinct or fuse, others will acquire complete reproductive isolation and will carry signatures of this complex history in their genomes.

Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution.

Most studies on seasonal influenza A/H3N2 virus adaptation have focused on the main antigenic gene, hemagglutinin. However, there is increasing evidence that the genome-wide genetic background of novel antigenic variants can influence these variants’ emergence probabilities and impact their patterns of dominance in the population. This suggests that non-antigenic genes may be important in shaping the viral evolutionary dynamics. To better understand the role of selection on non-antigenic genes in the adaptive evolution of seasonal influenza viruses, we have developed a simple population genetic model that considers a virus with one antigenic and one non-antigenic gene segment. By simulating this model under different regimes of selection and reassortment, we find that the empirical patterns of lineage turnover for the antigenic and non-antigenic gene segments are best captured when there is both limited viral coinfection and selection operating on both gene segments. In contrast, under a scenario of only neutral evolution in the non-antigenic gene segment, we see persistence of multiple lineages for long periods of time in that segment, which is not compatible with observed molecular evolutionary patterns. Further, we find that reassortment, occurring in coinfected individuals, can increase the speed of viral adaptive evolution by primarily reducing selective interference and genetic linkage effects. Together, these findings suggest that, for influenza, with six internal or non-antigenic gene segments, the evolutionary dynamics of novel antigenic variants are likely to be influenced by the genome-wide genetic background as a result of linked selection among both beneficial and deleterious mutations.