Genetic continuity of Indo-Iranian speakers since the Iron Age in southern Central Asia.

Since prehistoric times, southern Central Asia has been at the crossroads of the movement of people, culture, and goods. Today, the Central Asian populations are divided into two cultural and linguistic groups: the Indo-Iranian and the Turko-Mongolian groups. Previous genetic studies unveiled that migrations from East Asia contributed to the spread of Turko-Mongolian populations in Central Asia and the partial replacement of the Indo-Iranian populations. However, little is known about the origin of the latters. To shed light on this, we compare the genetic data on two current-day Indo-Iranian populations - Yaghnobis and Tajiks - with genome-wide data from published ancient individuals. The present Indo-Iranian populations from Central Asia display a strong genetic continuity with Iron Age samples from Turkmenistan and Tajikistan. We model Yaghnobis as a mixture of 93% Iron Age individual from Turkmenistan and 7% from Baikal. For the Tajiks, we observe a higher Baikal ancestry and an additional admixture event with a South Asian population. Our results, therefore, suggest that in addition to a complex history, Central Asia shows a remarkable genetic continuity since the Iron Age, with only limited gene flow.

Interspecific Gene Flow and Mitochondrial Genome Capture during the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae).

Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean Anolis lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, Anolis opalinus, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting (ILS). Here, we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene tree, species tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene tree recovers the same relationships previously inferred for this group, which is strikingly different from the species tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model (MSCM), so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group; however, coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of Anolis is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent, adaptive radiations. [Adaptive radiation; hybridization; introgression; multispecies network coalescent; posterior predictive simulation.].

Circular RNA HIPK3 exacerbates diabetic nephropathy and promotes proliferation by sponging miR-185.

PURPOSE: The aim of the present study was to investigate expression levels of circular RNA HIPK3 (circHIPK3) in mice with diabetic nephropathy (DN) and the role of circHIPK3 in rat mesangial cells (MCs). METHODS: Quantitative real-time polymerase chain reaction was performed to detect expression levels of circHIPK3, miR-185, cyclin D1, proliferating cell nuclear antigen (PCNA), transforming growth factor-ß1 (TGF-ß1), collagen Ⅰ (Col. Ⅰ), and fibronectin (FN) in mice with DN and rat mesangial cells. Luciferase assay was performed to investigate the binding sites of circHIPK3 and miR-185. Silencing cells of circHIPK3 and miR-185 were constructed using cell transfection assay. RESULTS: Our results revealed that the levels of 24-hour urinary albumin and urinary 8-hydroxy-2'-deoxyguanosine (8-OH-dG) from diabetic mice increased considerably. Up-regulation of circHIPK3 was observed in the renal tissues of mice with DN. Similarly, circHIPK3 expression in rat mesangial cells increased significantly in a microenvironment of high glucose. A loss-of-function experiment indicated that down-regulation of circHIPK3 inhibited cell proliferation and significantly decreased mRNA abundance of cyclin D1, PCNA, TGF-ß1, Col. I, and FN in MCs. Luciferase assay demonstrated that circHIPK3 can specifically sponge miR-185, and silencing of miR-185 can reverse the effects of knocking down circHIPK3 on cell proliferation and mRNA abundance of cyclin D1, PCNA, TGF-ß1, Col. I, and FN in MCs. CONCLUSION: Overall, circHIPK3 exhibits a promotive function in DN by sponging miR-185 and this evidence suggests that circHIPK3 might be a biomarker or therapeutic target for DN.

HIV/AIDS epidemic in the State of Amazonas: characteristics and trends from 2001 to 2012

A scoping review was conducted to describe the epidemiological characteristics of the human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) epidemic in the State of Amazonas, Brazil, from 2001 to 2012, and temporary patterns were estimated from surveillance data. The results suggest that in its third decade, the Amazon HIV/AIDS epidemic is far from being stabilized and displays rising AIDS incidence and mortality rates and late diagnoses. The data suggest that AIDS cases are hitting mostly young adults and have recently shifted toward men, both homosexual and heterosexual. AIDS cases among the indigenous people have remained stable and low. However, the epidemic has disseminated to the interior of the state, which adds difficulties to its control, given the geographical isolation, logistical barriers, and culturally and ethnically diverse population. Antiretroviral (ARV) therapy has been decentralized, but peripheral ARV services are still insufficient and too distant from people who need them. Recently, the expansion of point-of-care (POC) rapid HIV testing has been contributing to overcoming logistical barriers. Other new POC devices, such as the PIMA CD4 analyzer, will bring the laboratory to the patient. AIDS uniquely coexists with other tropical infections, sharing their epidemiological profiles. The increased demand for HIV/AIDS care services can only be satisfied through increased decentralization to peripheral health units, which can also naturally integrate care with other tropical infections and can promote a shift from vertical to integrated programming. Future challenges involve building surveillance data on HIV case notification and covering the spectrum of engagement in care, including adherence to treatment and follow-up loss.

Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species / Marcadores moleculares para estudo da diversidade genética, fluxo génico e estrutura genética de populações de espécies de mexilhões de água doce

Freshwater mussel species are in global decline. Anthropogenic changes of river channels and the decrease of autochthonous fish population, the natural hosts of mussels larval stages (glochidia), are the main causes. Therefore, the conservation of mussel species depends not only on habitat conservation, but also on the availability of the fish host. In Portugal, information concerning most of the mussel species is remarkably scarce. One of the most known species, Unio pictorum is also in decline however, in the basins of the rivers Tua and Sabor (Northeast of Portugal), there is some indication of relatively large populations. The aforementioned rivers can be extremely important for this species conservation not only in Portugal, but also in the remaining Iberian Peninsula. Thus, it is important to obtain data concerning Unio pictorum bioecology (distribution, habitat requirements, population structure, genetic variability, reproductive cycle and recruitment rates), as well as the genetic variability and structure of the population. Concomitantly, information concerning fish population structure, the importance of the different fish species as “glochidia” hosts and their appropriate density to allow effective mussel recruitment, will also be assessed. The achieved data is crucial to obtain information to develop effective management measures in order to promote the conservation of this bivalve species, the conservation of autochthonous fish populations, and consequently the integrity of the river habitats.

As espécies de mexilhões de água doce estão em declínio global. Mudanças antropogénicas do canal dos rios e diminuição das populações de peixes autóctones, os hospedeiros naturais do mexilhão nos estágios larvais (glochidia), são as principais causas. Portanto, a conservação de espécies de mexilhão depende não só da conservação dos habitats, mas também da disponibilidade do hospedeiro peixe. Em Portugal, a informação relativa à maioria das espécies de mexilhão é extremamente escassa. Uma das espécies mais conhecidas, Unio pictorum também está em declínio, no entanto, nas bacias dos rios Tua e Sabor (Nordeste de Portugal), existe indicação de populações relativamente grandes. Os rios acima mencionados podem ser extremamente importantes para a conservação das espécies, não só em Portugal, mas também na restante Península Ibérica. Assim, é importante obter dados relativos à bioecologia do Unio pictorum (distribuição, requisitos de habitat, estrutura populacional, variabilidade genética, ciclo reprodutivo e as taxas de recrutamento), bem como a variabilidade e estrutura genética da população. Concomitantemente, informações sobre a estrutura da população de peixes, a importância das diferentes espécies de peixes como hospedeiros e sua densidade adequada para permitir o recrutamento eficaz do mexilhão, também será avaliada. Os resultados obtidos serão cruciais para obter informações que permitam o desenvolvimento de medidas de gestão eficazes, a fim de promover a conservação destas espécies de bivalves, a conservação das populações de peixes autóctones e, consequentemente, a integridade dos habitats fluviais.

Genetic architectures of ADME genes in five Eurasian admixed populations and implications for drug safety and efficacy.

BACKGROUND: Drug absorption, distribution, metabolism and excretion (ADME) contribute to the high heterogeneity of drug responses in humans. However, the same standard for drug dosage has been applied to all populations in China although genetic differences in ADME genes are expected to exist in different ethnic groups. In particular, the ethnic minorities in northwestern China with substantial ancestry contribution from Western Eurasian people might violate such a single unified standard. METHODS: In this study, we used Affymetrix SNP Array 6.0 to investigate the genetic diversity of 282 ADME genes in five northwestern Chinese minority populations, namely, Tajik, Uyghur, Kazakh, Kirgiz and Hui, and attempted to identify the highly differential SNPs and haplotypes and further explore their clinical implications. RESULTS: We found that genetic diversity of many ADME genes in the five minority groups was substantially different from those in the Han Chinese population. For instance, we identified 10 functional SNPs with substantial allele frequency differences, 14 functional SNPs with highly different heterozygous states and eight genes with significant haplotype differences between these admixed minority populations and the Han Chinese population. We further confirmed that these differences mainly resulted from the European gene flow, that is, this gene flow increased the genetic diversity in the admixed populations. CONCLUSIONS: These results suggest that the ADME genes vary substantially among different Chinese ethnic groups. We suggest it could cause potential clinical risk if the same dosage of substances (eg, antitumour drugs) is used without considering population stratification.

Divergence with gene flow within the recent chipmunk radiation (Tamias).

Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para- and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection.

Migration patterns of hepatitis C virus in China characterized for five major subtypes based on samples from 411 volunteer blood donors from 17 provinces and municipalities.

UNLABELLED: We investigated the migration patterns of hepatitis C virus (HCV) in China. Partial E1 and/or NS5B sequences from 411 volunteer blood donors sampled in 17 provinces and municipalities located in five large regions, the north-northeast, northwest, southwest, central south, and southeast, were characterized. The sequences were classified into eight subtypes (1a, n = 3; 1b, n = 183; 2a, n = 83; 3a, n = 30; 3b, n = 44; 6a, n = 55; 6n, n = 10; 6v, n = 1) and a new subtype candidate. Bayesian evolutionary analysis by sampling trees of the E1 sequences of the five major subtypes revealed distinct migration patterns. Subtype 1b showed four groups: one is prevalent nationwide with possible origins in the north-northeast; two are locally epidemic in the central south and northwest, respectively, and have spread sporadically to other regions; and the fourth one is likely linked to the long-distance dispersion among intravenous drug users from the northwest. Subtype 2a showed two groups: the larger one was mainly restricted to the northwest and seemed to show a trend toward migration via the Silk Road; the smaller one was geographically mixed and may represent descendants of those that spread widely during the contaminated plasma campaign in the 1990s. Subtype 3a exhibited three well-separated geographic groups that may be epidemically unrelated: one showed origins in the northwest, one showed origins in the southwest, and the other showed origins in the central south. In contrast, subtype 3b had a mixture of geographic origins, suggesting migrations from the southwest to the northwest and sporadically to other regions. Structurally resembling the tree for subtype 3a, the tree for subtype 6a showed four groups that may indicate migrations from the central south to southeast, southwest, and northwest. Strikingly, no subtype 6a strain was identified in the north-northeast. IMPORTANCE: With a population of greater than 1.3 billion and a territory of >9.6 million square kilometers, China has a total of 34 provinces and municipalities. In such a vast country, the epidemic history and migration trends of HCV are thought to be unique and complex but variable among regions and are unlikely to be represented by those observed in only one or at best a few provinces and municipalities. However, due to the difficulties in recruiting patients, all previous studies for this purpose have been based only on data from limited regions, and therefore, geographical biases were unavoidable. In this study, such biases were greatly reduced because we utilized samples collected from volunteer blood donors in 17 provinces and municipalities. To our knowledge, this is the first study in which the HCV isolates represented such a large portion of the country, and thus, the results should shed light on the current understanding of HCV molecular epidemiology.

Polyploidy in Indian paintbrush (Castilleja; Orobanchaceae) species shapes but does not prevent gene flow across species boundaries.

PREMISE OF STUDY: A difference in chromosome numbers (ploidy variation) between species is usually considered a major barrier to gene flow. Therefore, it is surprising that little is known about whether ploidy variation, both within and among species, influences spatial patterns of interspecific hybridization. The role that polyploidy plays in structuring gene flow patterns between three co-occurring Indian paintbrush (Castilleja) species is investigated. • METHODS: Reciprocal hand pollinations were performed in populations where the three species co-occur with and without variable plants (previous data tested the ancestral "hybrid" history of these variable plants). I measured fruit set, seed production, seed germination, and the DNA content of parent plants and 26 synthesized F(1) hybrids. Data were combined with pollinator fidelity data to estimate the contribution of individual barriers to reproductive isolation. • KEY RESULTS: Interspecific gene flow could occur in all directions, but barriers were weaker for conspecific vs. heterospecific crosses. Species were nearly fixed for different ploidy levels, but some deviations occurred, primarily in populations with variable plants. Interspecific gene flow could occur across ploidy levels, but it was more likely when species had the same number of chromosomes or when resulting F(1) hybrids had even numbers of chromosomes. Postzygotic reproductive barriers were generally weaker than pollinator fidelity. • CONCLUSIONS: Polyploidy likely plays a large role in shaping contemporary and historical patterns of gene flow among these species. This study suggests that differences in chromosome numbers among closely related, compatible species might help structure spatial patterns of hybridization.

Diversifying selection underlies the origin of allozyme polymorphism at the phosphoglucose isomerase locus in Tigriopus californicus.

The marine copepod Tigriopus californicus lives in intertidal rock pools along the Pacific coast, where it exhibits strong, temporally stable population genetic structure. Previous allozyme surveys have found high frequency private alleles among neighboring subpopulations, indicating that there is limited genetic exchange between populations. Here we evaluate the factors responsible for the diversification and maintenance of alleles at the phosphoglucose isomerase (Pgi) locus by evaluating patterns of nucleotide variation underlying previously identified allozyme polymorphism. Copepods were sampled from eleven sites throughout California and Baja California, revealing deep genetic structure among populations as well as genetic variability within populations. Evidence of recombination is limited to the sample from Pescadero and there is no support for linkage disequilibrium across the Pgi locus. Neutrality tests and codon-based models of substitution suggest the action of natural selection due to elevated non-synonymous substitutions at a small number of sites in Pgi. Two sites are identified as the charge-changing residues underlying allozyme polymorphisms in T. californicus. A reanalysis of allozyme variation at several focal populations, spanning a period of 26 years and over 200 generations, shows that Pgi alleles are maintained without notable frequency changes. Our data suggest that diversifying selection accounted for the origin of Pgi allozymes, while McDonald-Kreitman tests and the temporal stability of private allozyme alleles suggests that balancing selection may be involved in the maintenance of amino acid polymorphisms within populations.

Control of pollen-mediated gene flow in transgenic trees.

Pollen elimination provides an effective containment method to reduce direct gene flow from transgenic trees to their wild relatives. Until now, only limited success has been achieved in controlling pollen production in trees. A pine (Pinus radiata) male cone-specific promoter, PrMC2, was used to drive modified barnase coding sequences (barnaseH102E, barnaseK27A, and barnaseE73G) in order to determine their effectiveness in pollen ablation. The expression cassette PrMC2-barnaseH102E was found to efficiently ablate pollen in tobacco (Nicotiana tabacum), pine, and Eucalyptus (spp.). Large-scale and multiple-year field tests demonstrated that complete prevention of pollen production was achieved in greater than 95% of independently transformed lines of pine and Eucalyptus (spp.) that contained the PrMC2-barnaseH102E expression cassette. A complete pollen control phenotype was achieved in transgenic lines and expressed stably over multiple years, multiple test locations, and when the PrMC2-barnaseH102E cassette was flanked by different genes. The PrMC2-barnaseH102E transgenic pine and Eucalyptus (spp.) trees grew similarly to control trees in all observed attributes except the pollenless phenotype. The ability to achieve the complete control of pollen production in field-grown trees is likely the result of a unique combination of three factors: the male cone/anther specificity of the PrMC2 promoter, the reduced RNase activity of barnaseH102E, and unique features associated with a polyploid tapetum. The field performance of the PrMC2-barnaseH102E in representative angiosperm and gymnosperm trees indicates that this gene can be used to mitigate pollen-mediated gene flow associated with large-scale deployment of transgenic trees.

Diverse spore rains and limited local exchange shape fern genetic diversity in a recently created habitat colonized by long-distance dispersal.

BACKGROUND AND AIMS: Populations established by long-distance colonization are expected to show low levels of genetic variation per population, but strong genetic differentiation among populations. Whether isolated populations indeed show this genetic signature of isolation depends on the amount and diversity of diaspores arriving by long-distance dispersal, and time since colonization. For ferns, however, reliable estimates of long-distance dispersal rates remain largely unknown, and previous studies on fern population genetics often sampled older or non-isolated populations. Young populations in recent, disjunct habitats form a useful study system to improve our understanding of the genetic impact of long-distance dispersal. METHODS: Microsatellite markers were used to analyse the amount and distribution of genetic diversity in young populations of four widespread calcicole ferns (Asplenium scolopendrium, diploid; Asplenium trichomanes subsp. quadrivalens, tetraploid; Polystichum setiferum, diploid; and Polystichum aculeatum, tetraploid), which are rare in The Netherlands but established multiple populations in a forest (the Kuinderbos) on recently reclaimed Dutch polder land following long-distance dispersal. Reference samples from populations throughout Europe were used to assess how much of the existing variation was already present in the Kuinderbos. KEY RESULTS: A large part of the Dutch and European genetic diversity in all four species was already found in the Kuinderbos. This diversity was strongly partitioned among populations. Most populations showed low genetic variation and high inbreeding coefficients, and were assigned to single, unique gene pools in cluster analyses. Evidence for interpopulational gene flow was low, except for the most abundant species. CONCLUSIONS: The results show that all four species, diploids as well as polyploids, were capable of frequent long-distance colonization via single-spore establishment. This indicates that even isolated habitats receive dense and diverse spore rains, including genotypes capable of self-fertilization. Limited gene flow may conserve the genetic signature of multiple long-distance colonization events for several decades.

Complex patterns of autopolyploid evolution in alfalfa and allies (Medicago sativa; Leguminosae).

PREMISE OF THE STUDY: Although there is growing evidence that autopolyploidy is a widespread and important evolutionary phenomenon, it has received less attention than allopolyploidy. Medicago sativa comprises several diploid and autopolyploid taxa, including autotetraploid cultivated alfalfa, and affords an opportunity to elucidate the evolutionary history of a morphologically and genetically complex autopolyploid system. METHODS: Phylogenies and haplotype networks were constructed from two chloroplast noncoding regions (rpl20-rps12 and trnS-trnG spacers) across seven diploid and polyploid infraspecific taxa of M. sativa and five additional closely related Medicago species, and genetic differentiation was estimated. KEY RESULTS: The two most prominent M. sativa autopolyploids have contrasting evolutionary histories. Chloroplast data support a simple autopolyploid origin of subsp. sativa (alfalfa) from diploid subsp. caerulea, from which it is distinguishable in several quantitative characters. In contrast, morphologically identical diploid and autopolyploid cytotypes of subsp. falcata were found to possess very different chloroplast haplotypes, suggesting past introgression from M. prostrata into the polyploid. Despite the presence of hybrids between tetraploid subspecies falcata and sativa, there was little evidence of introgression of chloroplast genomes from either subspecies into the other. CONCLUSIONS: Autopolyploid evolution in M. sativa is complicated and has followed very different paths in different subspecific taxa. The potential exists for gene flow in virtually all combinations of subspecies both within and between ploidies, yet despite the existence of hybrids, morphologically and genetically distinctive subspecies persist.

The influence of historical geneflow, bathymetry and distribution patterns on the population genetics of morphologically diverse Galápagos' Opuntia echios.

Throughout history, remote archipelagos have repeatedly been designated natural laboratories to study evolutionary processes. The extensive, geographically structured, morphological variation within Galápagos' Opuntia cacti has been presumed to be another example of how such processes shape diversity. However, recent genetic studies on speciation and potential effects of plasticity within this system failed to confirm earlier classification and hypothesized radiation on both global and single island levels. Detailed population genetic information, however, is crucial in conserving these semi-arid ecosystem keystone species. In this article, we re-evaluate the genetics of Opuntia echios inhabiting one of the most taxon rich places on the archipelago: Santa Cruz and its surrounding satellite islands, using microsatellite data. Our analysis revealed high genetic variability within all sampled locations, providing little support for the hypothesis of clonal reproduction. Inter-island gene flow patterns appear to be largely influenced by bathymetry and sea levels during last ice ages. Although O. echios from Seymour Norte are morphologically recognized as being a separate taxon, Daphné Major's cacti are the most differentiated. In addition, we found a potential barrier for gene flow along the ring-like distribution of Opuntias at the western side of Santa Cruz, suggesting potential links with geology.

Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture.

• Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification. • Flow cytometry analyses detected ploidy polymorphisms of 2× and 4× in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species/subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles. • Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection. • High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis.

How can tsetse population genetics contribute to African trypanosomiasis control?

In sub-Saharan Africa, tsetse transmitted Trypanosomiases have an enormous impact on human health and economic development. Both the World Health Organisation and African countries through the Pan African Tsetse and Trypanosomiasis Eradication Campaign (PATTEC) have recently asserted their determination to rid the sub-continent of these diseases, and it is increasingly recognised that vector control should play an important role. This review mainly focuses on population genetics of tsetse of the palpalis group, the main vectors of sleeping sickness, and reports recent results on tsetse population structure and on measures of gene flow between populations. Implications of these studies for large-scale tsetse control programmes being undertaken in West Africa are important, particularly regarding control strategies (suppression or eradication).

Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma.

Despite highly active antiretroviral therapy (HAART), AIDS related lymphoma (ARL) occurs at a significantly higher rate in patients infected with the Human Immunodeficiency Virus (HIV) than in the general population. HIV-infected macrophages are a known viral reservoir and have been shown to have lymphomagenic potential in SCID mice; therefore, there is an interest in determining if a viral component to lymphomagenesis also exists. We sequenced HIV-1 envelope gp120 clones obtained post mortem from several tumor and non-tumor tissues of two patients who died with AIDS-related Non-Hodgkin's lymphoma (ARL-NH). Similar results were found in both patients: 1) high-resolution phylogenetic analysis showed a significant degree of compartmentalization between lymphoma and non-lymphoma viral sub-populations while viral sub-populations from lymph nodes appeared to be intermixed within sequences from tumor and non-tumor tissues, 2) a 100-fold increase in the effective HIV population size in tumor versus non-tumor tissues was associated with the emergence of lymphadenopathy and aggressive metastatic ARL, and 3) HIV gene flow among lymph nodes, normal and metastatic tissues was non-random. The different population dynamics between the viruses found in tumors versus the non-tumor associated viruses suggest that there is a significant relationship between HIV evolution and lymphoma pathogenesis. Moreover, the study indicates that HIV could be used as an effective marker to study the origin and dissemination of lymphomas in vivo.

Ocean barriers and glaciation: evidence for explosive radiation of mitochondrial lineages in the Antarctic sea slug Doris kerguelenensis (Mollusca, Nudibranchia).

Strong currents and deep passages of water can be barriers for larval dispersal of continental marine animals, but potential effects on direct developers are under-investigated. We examined the genetic structure of Doris kerguelenensis, a directly developing sea slug that occurs across the Drake Passage, the body of water separating Antarctica from South America. We found deep mitochondrial divergences within populations on both sides of the Drake Passage, and South American animals formed multiple sister-group relationships with Antarctic animals. A generalised molecular clock suggested these trans-Drake pairs diverged during the Pliocene­Pleistocene, after the formation of the Drake Passage. Statistical parsimony methods recovered 29 separate haplotype networks (many sympatric) that likely correlate with allopatric events caused by repeated glacial cycles. Data from 16S were congruent but more conserved than COI, and the estimated ancestral 16S haplotype was widespread. The marked difference in the substitution rates between these two mitochondrial genes results in different estimates of connectivity. Demographic analyses on networks revealed some evidence for selection and expanding populations. Contrasting with the Northern Hemisphere, glaciation in Antarctica appears to have increased rather than reduced genetic diversity. This suggests orbitally forced range dynamics based on Northern Hemisphere phylogeography do not hold for Antarctica. The diverse lineages found in D. kerguelenensis point towards a recent, explosive radiation, likely reflecting multiple refuges during glaciation events, combined with limited subsequent dispersal. Whether recognised as cryptic species or not, genetic diversity in Antarctic marine invertebrates appears higher than expected from morphological analyses, and supports the Antarctic biodiversity pump phenomenon.

Variación genética y flujo de genes entre poblaciones de Crocodylus acutus (Crocodylia: Crocodylidae) en tres ríos del Pacífico Central, Costa Rica

The crocodylid Crocodylus acutus is found in the Central Pacific of Costa Rica only in small populations, and the species is protected by law. RAPD was used to analyze 70 DNA samples of Crocodylus acutus from the rivers Jesus Maria, Tarcoles and Tusubres in the Central Pacific of Costa Rica in order to estimate genetic diversity, differentiation among populations, gene flow and genetic distance between them. Genetic diversity was low in the three rivers, H = 0.2201 in the Jesus Maria river, 0.2358 in the Tarcoles river and 0.2589 in the Tusubres river. Among the three populations there is a metapopulational dynamic (GST = 0.0367), mainly between the populations of the Jesus Maria and Tarcoles rivers. The value of gene flow (Nm = 13.1361) and the number of individuals reported for each river in 2004 suggests that the population of the Tarcoles river is the source and those from Jesus Maria and Tusubres are the drains. There was a direct relationship between the genetic distance and the geographical distance (z =1.1449, r =0.9731, p< 0.0010). A conservation strategy for these crocodiles must consider the existence of the metapopulation between the three rivers and the importance of studying the genetics of the American Crocodile in the rest of the Pacific coast of Costa Rica, as well as over the entire distribution range of this species. Rev. Biol. Trop. 56 (3): 1471-1480. Epub 2008 September 30.

Se utilizó la técnica de ADN Polimórfico Amplificado al Azar (RAPD) para analizar muestras de ADN de 70 individuos de C. acutus provenientes de los ríos Jesús María, Tárcoles y Tusubres en el Pacífico Central de Costa Rica para estimar la diversidad genética, la diferenciación entre poblaciones, el flujo genético y la distancia genética. La diversidad genética fue baja en los tres ríos H = 0.2201 en el río Jesús María, 0.2358 en el río Tárcoles y 0.2589 en el río Tusubres. La diversidad genética para el total de los individuos también fue baja, H = 0.2452. Entre las tres poblaciones hay una dinámica metapoblacional (G ST = 0.0367) principalmente en las poblaciones de los ríos Jesús María y Tárcoles. El valor de flujo genético (Nm = 13.1361) y el número de individuos registrado para cada río por Porras (2004) sugieren que la población del río Tárcoles está cumpliendo el papel de fuente y las de Jesús María y Tusubres constituyen los sumideros. Hubo relación directa entre la distancia genética y la distancia geográfica (z = 1.1449, r = 0.9731, p< 0.0010). Estos resultados indican la necesidad de diseñar una estrategia para la conservación de estos cocodrilos que considere la existencia de la metapoblación entre los tres ríos y también es importante realizar un estudio genético en el resto de la costa Pacífica del Costa Rica y en todo el ámbito de distribución de esta especie.

Fine scale gene flow and individual movements among subpopulations of Centrolene prosoblepon (Anura: Centrolenidae)

Dispersal capabilities determine and maintain local gene flow, and this has implications for population persistence and/or recolonization following environmental perturbations (natural or anthropogenic), disease outbreaks, or other demographic collapses. To predict recolonization and understand dispersal capacity in a stream-breeding frog, we examined individual movement patterns and gene flow among four subpopulations of the Neotropical glassfrog, Centrolene prosoblepon, at a mid-elevation cloud forest site at El Copé, Panama. We measured male movement directly during a two year mark-recapture study, and indirectly with gene flow estimates from mitochondrial DNA sequences (mtDNA). Individuals of this species showed strong site fidelity: over two years, male frogs in all four headwater streams moved very little (mean = 2.33 m; mode = 0 m). Nine individuals changed streams within one or two years, moving 675-1,108 m. For those males moving more than 10 m, movement was biased upstream (p < 0.001). Using mtDNA ND1 gene sequences, we quantified gene flow within and among headwater streams at two spatial scales: among headwater streams within two adjacent watersheds (2.5 km2) and among streams within a longitudinal gradient covering 5.0 km2. We found high gene flow among headwater streams (phi(ST) = 0.007, p = 0.325) but gene flow was more limited across greater distances (phi(CT) = 0.322, p = 0.065), even within the same drainage network. Lowland populations of C. prosoblepon potentially act as an important source of colonists for upland populations in this watershed.

La capacidad de dispersión determina y mantiene el flujo genético local, y esto tiene implicaciones para la persistencia poblacional y/o la recolonización que sigue a perturbaciones ambientales. Examinamos patrones individuales de movimiento y flujo genético entre subpoblaciones de Centrolene prosoblepon (Anura: Centrolenidae) en un sitio de elevación media en El Copé, Panamá. Medimos directamente el movimiento de los machos durante un estudio de marcado-recaptura, e indirectamente con estimaciones de flujo genético a partir de secuencias de ADN mitocondrial (mtDNA). Los individuos mostraron fuerte fidelidad a su lugar: por más de dos años, las ranas macho de los cuatro arroyos al inicio del río se movieron muy poco (promedio = 2.33 m; moda = 0 m). Nueve individuos cambiaron de corriente de agua en uno o dos años, moviéndose 675-1 108 m. Usando la secuencia genética ND1 del ADN mitocondrial, medimos el flujo genético en dos escalas espaciales: entre arroyos que originan el río (2.5 km2) y entre arroyos con un gradiente longitudinal en 5.0 km2. Encontramos un flujo genético alto entre los arroyos al inicio del río (f = 0.007, p = 0.325 y otro más limitado en distancias mayores (f = 0.322, p = 0.065).