The life-history basis of latitudinal diversity gradients: how do species traits vary from the poles to the equator.

1. Latitudinal variation among species in life-history traits is often suggested to contribute to high tropical species richness. However, traditional methods of analysing such variation rarely control for phylogeny and latitudinal range overlap between species, potentially giving misleading results. 2. Using a method of pairwise independent contrasts which overcomes these problems, I tested for latitudinal variation among bird species in a number of traits which have been linked, theoretically or empirically, with both latitude and species richness. 3. This method indicates strong support for Rapoport's Rule and decreasing clutch size towards the equator in both hemispheres, but only partial support for decreasing body size and ecological generalism towards the equator. 4. Indirect measures of sexual selection (sexual dichromatism and size dimorphism) show no variation with latitude; an apparent increase in dichromatism towards the equator is shown to be an artefact of phylogeny. 5. Many of the associations between life history and latitude were not detected by traditional cross-species analyses, highlighting the importance of incorporating phylogeny and overlap in studies of geographical life-history variation. Establishing associations between life-history traits and latitude does not prove, but is a necessary prerequisite for., a link between these traits and latitudinal diversity gradients.

Molecular clocks in reptiles: Life history influences rate of molecular evolution

Life history has been implicated as a determinant of variation in rate of molecular evolution amongst vertebrate species because of a negative correlation between bode size and substitution rate for many Molecular data sets. Both the generality and the cause of the negative bode size trend have been debated, and the validity of key studies has been questioned (particularly concerning the failure to account for phylogenetic bias). In this study, a comparative method has been used to test for an association between a range of life-history variables-such as body size age at maturity, and clutch size-and DNA substitution rate for three genes (NADH4, cytochrome b, and c-mos). A negative relationship between body size and rate of molecular evolution was found for phylogenetically independent pairs of reptile species spanning turtles. lizards. snakes, crocodile, and tuatara. Although this Study was limited by the number of comparisons for which both sequence and lite-history data were available, the results, suggest that a negative bode size trend in rate of molecular evloution may be a general feature of reptile molecular evolution. consistent with similar studies of mammals and birds. This observation has important implications for uncovering the mechanisms of molecular evolution and warns against assuming that related lineages will share the same substitution rate (a local molecular clock) in order to date evolutionary divergences from DNA sequences.

Combining the analyses of introgressive hybridisation and linkage mapping to investigate the genetic architecture of population divergence in the lake whitefish (Coregonus clupeaformis, Mitchill)

Adaptation and reproductive isolation, the engines of biological diversity, are still elusive when discussing the genetic bases of speciation. Namely, the number of genes and magnitude of selection acting positively or negatively on genomic traits implicated in speciation is contentious. Here, we describe the first steps of an ongoing research program aimed at understanding the genetic bases of population divergence and reproductive isolation in the lake whitefish (Coregonus clupeaformis). A preliminary linkage map originating from a hybrid cross between dwarf and normal ecotypes is presented, whereby some of the segregating AFLP markers were found to be conserved among natural populations. Maximum-likelihood was used to estimate hybrid indices from non-diagnostic markers at 998 AFLP loci. This allowed identification of the most likely candidate loci that have been under the influence of selection during the natural hybridisation of whitefish originating from different glacial races. As some of these loci could be identified on the linkage map, the possibility that selection of traits in natural populations may eventually be correlated to specific chromosomal regions was demonstrated. The future prospects and potential of these approaches to elucidate the genetic bases of adaptation and reproductive isolation among sympatric ecotypes of lake whitefish is discussed.

Social structure in migrating humpback whales (Megaptera novaeangliae)

Although largely solitary, humpback whales exhibit a number of behaviours where individuals co-operate with one another, for example during bubble net feeding. Such cases could be due to reciprocal altruism brought on by exceptional circumstances, for example the presence of abundant shoaling fish. An alternative explanation is that these behaviours have evolved through kin selection. With little restriction to either communication or movement, diffuse groups of relatives could maintain some form of social organization without the need to travel in tight-nit units. To try to distinguish between these hypotheses, we took advantage of the fact that migrating humpback whales often swim together in small groups. If kin selection is important in humpback whale biology, these groups should be enriched for relatives. Consequently, we analysed biopsy samples from 57 groups of humpback whales migrating off Eastern Australia in 1992. A total of 142 whales were screened for eight microsatellite markers. Mitochondrial DNA sequences (371 bp) were also used to verify and assist kinship identification. Our data add support to the notion that mothers travel with their offspring for the first year of the calf's life. However, beyond the presence of mother-calf/yearling pairs, no obvious relatedness pattern was found among whales sampled either in the same pod or on the same day. Levels of relatedness did not vary between migratory phases (towards or away from the breeding ground), nor between the two sexes considered either overall or in the north or south migrations separately. These findings suggest that, if any social organization does exist, it is formed transiently when needed rather than being a constant feature of the population, and hence is more likely based on reciprocal altruism than kin selection.

Complete mitochondrial genomes confirm the distinctiveness of the horse-dog and sheep-dog strains of Echinococcus granulosus

Unlike other members of the genus, Echinococcus granulosus is known to exhibit considerable levels of variation in biology, physiology and molecular genetics. Indeed, some of the taxa regarded as 'genotypes' within E. granulosus might be sufficiently distinct as to merit specific status. Here, complete mitochondrial genomes are presented of 2 genotypes of E. granulosus (G1-sheep-dog strain: G4-horse-dog strain) and of another taeniid cestode, Taenia crassiceps. These genomes are characterized and compared with those of Echinococcus multilocularis and Hymenolepis diminuta. Genomes of all the species are very similar in structure, length and base-composition. Pairwise comparisons of concatenated protein-coding genes indicate that the G1 and G4 genotypes of E. granulosus are almost as distant from each other as each is from a distinct species, E. multilocularis. Sequences for the variable genes atp6 and nad3 were obtained from additional genotypes of E. granulosus, from E. vogeli and E. oligarthrus. Again, pairwise comparisons showed the distinctiveness of the G1 and G4 genotypes. Phylogenetic analyses of concatenated atp6, nad1 (partial) and cox1 (partial) genes from E. multilocularis, E. vogeli, E. oligarthrus, 5 genotypes of E. granulosus, and using T. crassiceps as an outgroup, yielded the same results. We conclude that the sheep-dog and horse-dog strains of E. granulosus should be regarded as distinct at the specific level.

Isolation and characterization of nine microsatellite loci from the Hawaiian grouper Epinephelus quernus (Serranidae) for population genetic analyses

The availability of variable genetic markers for groupers (Serranidae) has generally been limited to mitochondrial DNA. For studies of population genetic structure, more loci are usually required; particularly useful are those that are nuclear in origin such as microsatellites. Here, we isolated and characterized 9 microsatellite loci from the endemic Hawaiian grouper Epinephelus quernus using a biotin-labeled oligonucleotide-streptavidin-coated magnetic bead approach. Of the 20 repeat-containing fragments isolated, 15 had sufficient flanking region in which to design primers. Among these, 9 produced consistent polymerase chain reaction product, and 6 were highly variable. These 6 loci were all composed of dinucleotide repeats, with the number of alleles ranging from 6 to 18, and heterozygosities from 33.3% to 91.7%. The high levels of variability observed should make these markers useful for population genetic studies of E. quernus, and potentially other epinephelines.

Doenças mitocondriais: síndrome da depleção do mtDNA

As citopatias mitocondriais constituem um importante grupo de doenças metabólicas de expressão clínica heterogénea, para as quais não existe uma terapia eficaz. A maioria destas doenças é causada por uma disfunção ao nível da fosforilação oxidativa (OXPHOS), originando consequentemente uma deficiente produção de energia. O correto funcionamento da OXPHOS resulta de uma interação coordenada entre o genoma nuclear e mitocondrial. Assim, as doenças mitocondriais podem ser causadas por defeitos moleculares no genoma mitocondrial, no nuclear, ou em ambos, originando as doenças da comunicação intergenómica, que resultam na perda ou na instabilidade do DNA mitocondrial (mtDNA), e podem causar quer deleções múltiplas, quer depleção do genoma mitocondrial. A síndrome da depleção do mtDNA constitui um grupo de doenças raras, autossómicas recessivas, que se manifestam maioritariamente após o nascimento, causando a morte de muitos doentes durante a infância ou início da adolescência devido a uma redução acentuada do número de cópias do mtDNA. Trata-se de uma síndrome fenotipicamente heterogénea, apresentando-se sob três apresentações clínicas: hepatocerebral, miopática e encefalomiopática. A caracterização molecular destes doentes é importante não só para permitir a realização de aconselhamento genético e diagnóstico pré-natal adequados, mas também para melhorar a compreensão da fisiopatologia da doença e as opções terapêuticas.

New mitochondrial and nuclear evidences support recent demographic expansion and an atypical phylogeographic pattern in the Spittlebug Philaenus spumarius (Hemiptera, Aphrophoridae)

Copyright: © 2014 Rodrigues et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Mutation accumulation in Tetrahymena

Background - The rate and fitness effects of mutations are key in understanding the evolution of every species. Traditionally, these parameters are estimated in mutation accumulation experiments where replicate lines are propagated in conditions that allow mutations to randomly accumulate without the purging effect of natural selection. These experiments have been performed with many model organisms but we still lack empirical estimates of the rate and effects of mutation in the protists. Results - We performed a mutation accumulation (MA) experiment in Tetrahymena thermophila, a species that can reproduce sexually and asexually in nature, and measured both the mean decline and variance increase in fitness of 20 lines. The results obtained with T. thermophila were compared with T. pyriformis that is an obligate asexual species. We show that MA lines of T. thermophila go to extinction at a rate of 1.25 clonal extinctions per bottleneck. In contrast, populations of T. pyriformis show a much higher resistance to extinction. Variation in gene copy number is likely to be a key factor in explaining these results, and indeed we show that T. pyriformis has a higher mean copy number per cell than T. thermophila. From fitness measurements during the MA experiment, we infer a rate of mutation to copy number variation of 0.0333 per haploid MAC genome of T. thermophila and a mean effect against copy number variation of 0.16. A strong effect of population size in the rate of fitness decline was also found, consistent with the increased power of natural selection. Conclusions - The rate of clonal extinction measured for T. thermophila is characteristic of a mutational degradation and suggests that this species must undergo sexual reproduction to avoid the deleterious effects detected in the laboratory experiments. We also suggest that an increase in chromosomal copy number associated with the phenotypic assortment of amitotic divisions can provide an alternative mechanism to escape the deleterious effect of random chromosomal copy number variation in species like T. pyriformis that lack the resetting mechanism of sexual reproduction. Our results are relevant to the understanding of cell line longevity and senescence in ciliates.

Selenium role in an human biomonitoring study applied to occupational health

Selenium functions as a co-factor for the reduction of antioxidant enzymes and is an important component of antioxidant enzymes. Dietary selenium significantly inhibits the induction of skin, liver, colon, and mammary tumours in experimental animals by a number of different carcinogens, as well as the induction of mammary tumours by viruses. Selenium shows a “U” shaped curve for functionality, whereby too little is as damaging as too much. At optimal levels, selenium may protect against the formation of DNA adducts, DNA or chromosome breakage, chromosome gain or loss, mitochondrial DNA, and telomere length and function. Aim of study: Investigate the relation between selenium and genotoxic effects in a human biomonitoring study applied to occupational health.

Identificação de biomarcadores de prognóstico e marcadores preditivos de resposta à terapia no cancro do cólon e recto

Mais de 50% dos novos casos de cancro do cólon e recto (CCR) diagnosticados desenvolvem metástases, as quais apresentam uma elevada resistência às terapias convencionais, tornando o CCR uma das principais causas de morte por cancro. Por estas razões, é necessário identificar biomarcadores moleculares de prognóstico e preditivos da resposta ao tratamento. A maioria dos tumores colorectais apresentam mutações em genes que codificam para componentes da via de sinalização WNT. O presente trabalho teve como objectivo estudar o papel de mutações específicas no gene TCF7L2, um importante factor de transcrição desta via, como potenciais factores de prognóstico no cancro do cólon e recto e avaliar a presença de alterações (epi)genéticas e a sua relação com a resposta à quimioradioterapia pré-operatória no cancro do recto, de modo a identificar marcadores preditivos de resposta ao tratamento. Foi efectuada a análise de mutações em exões específicos do TCF7L2 em 68 amostras de CCR, por DGGE, Genescan e sequenciação automática. Foi realizada a análise de perda de heterozigotia por Genescan e de copy-number e metilação por MS-MLPA, para o mesmo gene, em 16 tumores do recto. Foram confirmados alguns destes resultados, ao nível do DNA e RNA, por qPCR. Foram detectadas mutações no gene TCF7L2 em 7/68 (10%) CCR, as quais foram menos frequentes em tumores sem instabilidade de microssatélites (MSS) do que em tumores instáveis (5/56, 11% vs 8/12, 67%). Na maioria dos tumores do recto resistentes à terapia foram detectados ganhos da região upstream e 5´do gene, os quais foram mais frequentes do que em tumores sensíveis (4/6 vs 1/8, p=0,063). Os tumores do recto que responderam melhor à quimioradioterapia apresentaram mais frequentemente ganhos na região 3’ do gene. Em conclusão, as mutações no gene TCF7L2 são pouco frequentes em tumores estáveis, sendo necessário mais estudos para avaliar relação com o prognóstico. As alterações de copy number poderão ser potenciais marcadores de resposta à quimioradioterapia pré-operatória no recto, no entanto os resultados ainda são preliminares, sendo necessária a análise de um maior número de casos.

Estudo de mutações germinais em genes de suscetibilidade para o cancro do colón e reto familiar do tipo X

O cancro do cólon e reto familiar do tipo X (FCCTX) é um síndrome que define as famílias que preenchem os critérios de Amesterdão, mas cujos tumores não apresentam instabilidade de microssatélites e também nas quais não é identificada mutação germinal nos genes de reparação de erros de DNA do tipo mismatch (MMR). A sua causa molecular permanece desconhecida. O presente trabalho teve como objetivo avaliar o envolvimento de genes localizados numa região de suscetibilidade previamente identificada para o FCCTX (13q32-33), assim como de mutações identificadas previamente numa família FCCTX, através da análise do exoma por sequenciação de nova geração (NGS). Pretendeuse ainda melhorar a caracterização molecular de tumores FCCTX. Foi efetuada análise de mutações germinais nos genes KDELC1 e ERCC5 em 15 indivíduos índex de famílias FCCTX e 2 familiares de uma dessas famílias. No caso do gene TPP2, foi avaliado o envolvimento de um transcrito expresso alternativamente, previamente identificado, através de análise mutacional e da quantificação da expressão diferencial dos transcritos por real-time PCR. Foi ainda efetuada a análise de segregação com a doença na família, de 5 mutações em genes distintos, selecionadas a partir dos resultados da análise do exoma. Foi efetuada a análise de alterações de copy-number e de metilação nos genes MMR, MGMT e APC em 22 tumores FCCTX por MS-MLPA. Não foram identificadas mutações potencialmente patogénicas nos genes KDELC1 e ERCC5. No entanto, foram identificadas 2 mutações, uma no ERCC5 (c.2636 A>G) e outra no KDELC1 (c.455A>T) em relação às quais não se pode excluir a sua patogenicidade. Não foi detetada qualquer mutação no TPP2 associada à expressão diferencial dos transcritos, no entanto verificou-se que a expressão difere entre tecidos (sangue e cólon). A análise de segregação das mutações selecionadas a partir da análise do exoma, revelou que apenas para um dos genes a alteração poderá ser patogénica. Foram identificados ganhos frequentes, assim como metilação, nos genes MMR e MGMT, nos tumores FCCTX, sendo significativamente mais frequentes num subgrupo destes tumores que apresenta perdas em genes supressores de tumor (TSG+), em relação ao grupo que não apresenta estas alterações. A metilação no APC também apresentou padrões distintos entre os dois subgrupos de tumores FCCTX. Em conclusão, as variantes observadas nos genes KDELC1, ERCC5 e TPP2, assim como a alteração identificada no âmbito da análise do exoma não devem ser excluídas, podendo ser possível a sua contribuição para a suscetibilidade para o FCCTX. O padrão de alterações de copy-number e de metilação nos tumores FCCTX reforça a existência de pelo menos duas entidades moleculares distintas no FCCTX e sugere mecanismos de tumorigénese específicos para a iniciação tumoral neste síndrome.

Molecular characterization of Mycobacterium tuberculosis isolates from Tehran, Iran by restriction fragment length polymorphism analysis and spoligotyping

Abstract: INTRODUCTION Characterization of Mycobacterium tuberculosis (MTB) isolates by DNA fingerprinting has contributed to tuberculosis (TB) control. The aim of this study was to determine the genetic diversity of MTB isolates from Tehran province in Iran. METHODS MTB isolates from 60 Iranian and 10 Afghan TB patients were fingerprinted by standard IS6110-restriction fragment length polymorphism (RFLP) analysis and spoligotyping. RESULTS The copy number of IS6110 ranged from 10-24 per isolate. The isolates were classified into 22 clusters showing ≥ 80% similarity by RFLP analysis. Fourteen multidrug-resistant (MDR) isolates were grouped into 4 IS6110-RFLP clusters, with 10 isolates [71% (95% CI: 45-89%)] in 1 cluster, suggesting a possible epidemiological linkage. Eighteen Iranian isolates showed ≥ 80% similarity with Afghan isolates. There were no strains with identical fingerprints. Spoligotyping of 70 isolates produced 23 distinct patterns. Sixty (85.7%) isolates were grouped into 13 clusters, while the remaining 10 isolates (14.2%) were not clustered. Ural (formerly Haarlem4) (n = 22, 31.4%) was the most common family followed by Central Asian strain (CAS) (n = 18, 25.7%) and T (n = 9, 12.8%) families. Only 1strain was characterized as having the Beijing genotype. Among 60 Iranian and 10 Afghan MTB isolates, 25% (95% CI: 16-37) and 70% (95% CI: 39-89) were categorized as Ural lineage, respectively. CONCLUSIONS A higher prevalence of Ural family MTB isolates among Afghan patients than among Iranian patients suggests the possible transmission of this lineage following the immigration of Afghans to Iran.

Mosaic maternal ancestry in the Great Lakes region of East Africa

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.

60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2

Mitochondrial DNA (mtDNA) haplogroup L2 originated in Western Africa but is nowadays spread across the entire continent. L2 movements were previously postulated to be related to the Bantu expansion, but L2 expansions eastwards probably occurred much earlier. By reconstructing the phylogeny of L2 (44 new complete sequences) we provide insights on the complex net of within-African migrations in the last 60 thousand years (ka). Results show that lineages in Southern Africa cluster with Western/Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: (1) one migration at 70-50 ka into Eastern or Southern Africa, (2) postglacial movements (15-10 ka) into Eastern Africa; and (3) the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations.