In two waters: contemporary evolution of lagoonal and marine white seabream (Diplodus sargus) populations

Brackish water ecosystems are often exposed to wide variations in environmental variables, including temperature and salinity, which may cause strong selective pressures on organisms modifying the genetic patterns of species. The aim of this work was to test whether there is a ‘divergence-with-gene flow’ in coastal lagoon populations of white seabream (Diplodus sargus) (Ria Formosa, S Portugal and Mar Menor, SE Spain) respect to four marine populations, by using partial sequences of cyt b mitochondrial gene and information from nine microsatellite loci. Genetic diversity was highest in both coastal lagoons (Mar Menor and Ria Formosa) considering mitochondrial and nuclear markers. Although some of FST population pairwise comparisons were not significant, analyses of molecular variance (AMOVAs) detected differences between groups (coastal lagoon and marine) close to significance. Also, only two haplotypes (Cytb-17 and Cytb-18) were detected in both coastal lagoon sampling sites and these localities (Mar Menor and Ria Formosa) showed the highest number of singletons, some of them with a high number of mutations, as has been already described for other Mar Menor populations (Pomatochistus marmoratus and Holothuria polii). Also, several tests detected significant positive and balancing selection considering mtDNA and microsatellite data. These data support the hypothesis of selection as one of the drivers of the genetic differences found between coastal lagoon and marine populations. The life strategy adopted by Diplodus sargus in coastal lagoons allows it to decrease its mortality rate and improve the heritability of its genes. Also, the increase time spent in coastal lagoons with different temperatures and salinities favours the fitness selection and the maintenance of exclusive haplotypes and genotypes in coastal lagoon inhabitants favouring the ‘divergence-with-gene-flow’.

Phylogeography of the Atlanto-Mediterranean sea cucumber Holothuria (Holothuria) mammata: the combined effects of historical processes and current oceanographical pattern

We assessed the genetic structure of populations of the widely distributed sea cucumber Holothuria (Holothuria) mammata Grube, 1840, and investigated the effects of marine barriers to gene flow and historical processes. Several potential genetic breaks were considered, which would separate the Atlantic and Mediterranean basins, the isolated Macaronesian Islands from the other locations analysed, and the Western Mediterranean and Aegean Sea (Eastern Mediterranean). We analysed mitochondrial 16S and COI gene sequences from 177 individuals from four Atlantic locations and four Mediterranean locations. Haplotype diversity was high (H = 0.9307 for 16S and 0.9203 for COI), and the haplotypes were closely related (p = 0.0058 for 16S and 0.0071 for COI). The lowest genetic diversities were found in the Aegean Sea population. Our results showed that the COI gene was more variable and more useful for the detection of population structure than the 16S gene. The distribution of mtDNA haplotypes, the pairwise FST values and the results of exact tests and AMOVA revealed: (i) a significant genetic break between the population in the Aegean Sea and those in the other locations, as supported by both mitochondrial genes, and (ii) weak differentiation of the Canary and Azores Islands from the other populations; however, the populations from the Macaronesian Islands, Algarve and West Mediterranean could be considered to be a panmictic metapopulation. Isolation by distance was not identified in H. (H.) mammata. Historical events behind the observed findings, together with the current oceanographic patterns, were proposed and discussed as the main factors that determine the population structure and genetic signature of H. (H.) mammata

Population genetics of Cerastoderma edule in Ria Formosa (southern Portugal): the challenge of understanding an intraspecific hotspot of genetic diversity

Coastal lagoons are highly variable environments that may act as hotspots of genetic diversity as a consequence of their ecological role as nursery habitats of marine species with both ecological and fisheries importance. The edible cockle (Cerastoderma edule) is a commercially important shellfish resource inhabiting coastal lagoons in Europe and their fisheries management urgently needs genetic studies to design appropriate strategies to promote the recovery of exploited populations. The aim of this study was to assess the C. edule genetic diversity and population structure at a small geographic scale, inside Ria Formosa coastal lagoon (southern Portugal) using mitochondrial cytochrome oxidase I sequences in six locations. Outcomes pointed to a common pattern of high haplotype diversity and non-significant genetic structuring inside the Ria Formosa lagoon. A high level of gene flow was detected between all localities and the presence of a single stock from a genetic point of view may be considered for fisheries management purposes. The existence of a high number of haplotypes and high values of haplotype diversity of C. edule in Ria Formosa lagoon could be consistent with the hypothesis that higher genetic diversity is expected in populations occurring in coastal lagoons, suggesting that lagoons could increase standing genetic variation and an adaptive potential of lagoon populations as an ecological response to a highly variable environment.

Genetic diversity across geographical scales in marine coastal ecosystems: Holothuria arguinensis a model species

Coastal lagoons are considered one of the most productive areas of our planet harboring a large variety of habitats. Their transitional character, between terrestrial and marine environments, creates a very particular ecosystem with important variations of its environmental conditions. The organisms that are able to survive on these ecosystems frequently experience strong selective pressures and constrictions to gene flowwith marine populations, which could contribute to genetic divergence among populations inhabiting coastal lagoon and marine environments. Therefore, the main aims of this study are to asses the genetic diversity and population structure of Holothuria arguinensis across geographical ranges, to test the hypothesis of coastal lagoons as hotspots of genetic diversity in the Ria Formosa lagoon, and to determine the role of exporting standing genetic variation from the lagoon to open sea and their implications to recent geographical expansion events. To reach these objectives, we investigate the genetic structure of H. arguinensis using two mitochondrial DNA markers (COI and 16S) at different spatial scales: i) small, inside Ria Formosa coastal lagoon, South Portugal; 2) large, including most of the geographical distribution of this species (South and Western Portuguese coast and Canary islands); these results will allow us to compare the genetic diversity of lagoonal and marine populations of H. arguinensis. On this framework, its recent geographical expansion events, recorded by Rodrigues (2012) and González-Wangüemert and Borrero-Pérez (2012), will be analyzed considering the potential contribution from lagoonal genetic pool. Non-significant genetic structure and high haplotypic diversity were found inside the Ria Formosa coastal lagoon. Both genes were unable to detect significant genetic differentiation among lagoonal and marine localities, suggesting a high rate of gene flow. The results supported our hypotheses that coastal lagoons are not only acting as hotspots of genetic diversity, but also contributing for the genetic variability of the species, working as a source of new haplotypes and enhancing adaptation to the high variable conditions. Different genetic patterns of colonization were found on H. arguinensis, but they must be studied more deeply.

The history of the introduction of the giant river prawn, Macrobrachium cf. rosenbergii (Decapoda, Palaemonidae), in Brazil: new insights from molecular data

The giant river prawn, Macrobrachium cf. rosenbergii, is one of the most cultivated freshwater prawns in the world and has been introduced into more than 40 countries. In some countries, this prawn is considered an invasive species that requires close monitoring. Recent changes in the taxonomy of this species (separation of M. rosenbergii and M. dacqueti) require a re-evaluation of introduced taxa. In this work, molecular analyses were used to determine which of these two species was introduced into Brazil and to establish the geographic origin of the introduced populations that have invaded Amazonian coastal waters. The species introduced into Brazil was M. dacqueti through two introduction events involving prawns originating from Vietnam and either Bangladesh or Thailand. These origins differ from historical reports of the introductions and underline the need to confirm the origin of other exotic populations around the world. The invading populations in Amazonia require monitoring not only because the biodiversity of this region may be affected by the introduction, but also because admixture of different native haplotypes can increase the genetic variability and the likelihood of persistence of the invading species in new habitats.

Reassessing the Evolutionary History of the 17q21 Inversion Polymorphism

A polymorphic inversion that lies on chromosome 17q21 comprises two major haplotype families (H1 and H2) that not only differ in orientation but also in copy-number. Although the processes driving the spread of the inversion-associated lineage (H2) in humans remain unclear, a selective advantage has been proposed for one of its subtypes. Here, we genotyped a large panel of individuals from previously overlooked populations using a custom array with a unique panel of H2-specific single nucleotide polymorphisms and found a patchy distribution of H2 haplotypes in Africa, with North Africans displaying a higher frequency of inverted subtypes, when compared with Sub-Saharan groups. Interestingly, North African H2s were found to be closer to "non-African" chromosomes further supporting that these populations may have diverged more recently from groups outside Africa. Our results uncovered higher diversity within the H2 family than previously described, weakening the hypothesis of a strong selective sweep on all inverted chromosomes and suggesting a rather complex evolutionary history at this locus.

A single panmictic population of endemic red crabs, Gecarcoidea natalis, on Christmas Island with high levels of genetic diversity

The red crab, Gecarcoidea natalis, is endemic to Christmas Island in the Indian Ocean and largely responsible for shaping the unique ecosystem found throughout the island's rainforests. However, the introduction and establishment of supercolonies of the highly invasive yellow crazy ant, Anoplolepis gracilipes, has decimated red crab numbers over the last several decades. This poses a significant risk to the future conservation of G. natalis and consequently threatens the integrity of the unique island ecosystem. Here we undertook a population genetic analysis of G. natalis using a combination of 11 microsatellite markers and sequencing of the mitochondrial cytochrome oxidase subunit I gene from samples collected on Christmas Island as well as a single location from North Keeling Island (located approximately 900 km west of Christmas Island). The genetic results indicate that G. natalis is a single panmictic population on Christmas Island, with no spatial genetic structure or restricted gene flow apparent between sampled locations. Further, G. natalis from North Keeling Island are not genetically distinct and are recent immigrants from Christmas Island. The effective population size of G. natalis has likely remained large and stable on Christmas Island throughout its evolutionary history with relatively moderate to high levels of genetic diversity in microsatellite loci and mitochondrial haplotypes assessed in this study. For management purposes G. natalis can be considered a single panmictic population, which should simplify conservation efforts for the genetic management of this iconic island species. © 2014 Springer Science+Business Media Dordrecht.

Species delimitation in sharpnose sharks (genus Rhizoprionodon) in the western Atlantic Ocean using mitochondrial DNA

Despite Springer’s (1964) revision of the sharpnose sharks (genus Rhizoprionodon), the taxonomic definition and ranges of Rhizoprionodon in the western Atlantic Ocean remains problematic. In particular, the distinction between Rhizoprionodon terraenovae and R. porosus, and the occurrence of R. terraenovae in South American waters are unresolved issues involving common and ecologically important species in need of fishery management in Caribbean and southwest Atlantic waters. In recent years, molecular markers have been used as efficient tools for the detection of cryptic species and to address controversial taxonomic issues. In this study 415 samples of the genus Rhizoprionodon captured in the western Atlantic Ocean from Florida to southern Brazil were examined for sequences of the COI gene and the D-loop and evaluated for nucleotide differences. The results on nucleotide composition, AMOVA tests, and relationship distances using Bayesian-likelihood method and haplotypes network, corroborates Springer’s (1964) morphometric and meristic finding and provide strong evidence that supports consideration of R. terraenovae and R. porosus as distinct species.

The impact and control of malignant catarrhal fever in Tanzania

Malignant Catarrhal Fever (MCF), an often-lethal infectious disease, presents as a variable complex of lesions in susceptible ungulate species. The disease is caused by a -herpesvirus following transmission from an inapparent carrier host. Two major epidemiological forms exist: wildebeest-associated MCF (WA-MCF), in which the virus is transmitted to susceptible species by wildebeest calves less than approximately four months of age, and sheepassociated MCF (SA-MCF) in which the virus is spread by sheep (primarily adolescents). Due to the lack of an in-vitro propagation system for the causative agent of the more economically significant SA-MCF, and with the expectation that cross-protective immunity may be provided, vaccine development has focused on the more easily propagated alcelaphine herpesvirus-1 (AlHV-1) that causes WA-MCF. In 2008 a direct viral challenge trial showed that a novel vaccine, employing an attenuated AlHV-1 (atAlHV-1) `C5000 virus strain, protected British Friesian-Holstein (FH) cattle against an intranasal challenge with virulent AlHV-1 `C5000 virus. For cattle keeping people living near wildebeest calving areas in sub-Saharan Africa an effective vaccine would have value as it would release them from the costly annual disease avoidance strategy of having to move their herds away from the oncoming wildebeest. On the other hand, an effective vaccine will release herd owners from the need to avoid MCF, allowing them to graze their cattle alongside wildebeest on the highly nutritious pastures of the calving areas. As such conservationists have raised concerns that the development of a vaccine might lead to detrimental grazing competition. The principle objective of this study was to test the novel vaccine on Tanzanian shorthorn zebu cross cattle (SZC).We did this firstly using a natural challenge field trial (Chapter Two) which demonstrated that immunisation with the atAlHV-1 vaccine was well tolerated and induced an oro-nasopharyngeal AlHV-1-specific and -neutralising antibody response. This resulted in an immunity in SZC cattle that was partially protective and reduced naturally transmitted infection by 56%. We also demonstrated that non-fatal infections occurred with a much higher frequency than previously thought. Because the calculated efficacy of the vaccine was less than that seen in British FH cattle we wanted to determine whether host factors, particular to SZC cattle, had impacted the outcomes of the field trial. To do this we repeated the 2008 direct viral challenge trial using SZC cattle (Chapter Four). During this trial we also investigated whether the recombinant bacterial flagellin monomer (FliC), when used as an adjuvant, might improve the vaccine’s efficacy. The findings from this trial indicated that direct challenge with pathogenic AlHV-1 is effective at inducing MCF in SZC cattle and that FliC is not an appropriate adjuvant for this vaccine. Furthermore, with less control group cattle dying of MCF than expected we speculate that SZC cattle may have a degree of resistance to MCF that affords them protection from infection and developing fatal disease. In Chapter Three we investigated aspects of the epidemiology of MCF, specifically whether wildebeest placenta, long implicated by Maasai cattle owners as a source of MCF, might play a role in viral transmission. Additionally, through comparative sequence analysis, at two specific genes (A9.5 and ORF50) of wild-type and atAlHV-1, we investigated whether the `C5000 strain, the source of which was taken from Africa more than 40 years ago, was appropriate for vaccine development. The detection of AlHV-1 virus in approximately 50% of placentae indicated that infection can occur in-utero and that this tissue might play a role in disease transmission. And, despite describing three new alleles of the A9.5 gene (supporting previous evidence that this gene is polymorphic and encodes a secretory protein with interleukin-4 as the major homologue), the observation that the most frequently detected haplotypes, in both wild-type and attenuated AlHV-1, were identical suggests that AlHV-1 has a slow molecular clock and that the attenuated strain was appropriate for vaccine development. In Chapter Five we present the first quantitative assessment of the annual MCF avoidance costs that Maasai pastoralists incur. In particular we estimated that as a result of MCF avoidance 64% of the total daily milk yield during the MCF season was not available to be used by the 81% of the family unit remaining at the permanent boma. This represents an upper-bound loss of approximately 8% of a household0s annual income. Despite these considerable losses we concluded that, given an incidence of fatal MCF in cattle living in wildebeest calving areas of 5% to 10%, if herd owners were to stop trying to avoid MCF by allowing their cattle to graze alongside wildebeest, any gains made through increased availability of milk, improved body condition and reduced energy demands would be offset by an increase in MCF-incidence. With the development of an effective vaccine, however, this alternative strategy might become optimal. The overall conclusion we draw therefore is that, despite the substantial costs incurred each year avoiding MCF, the partial protection afforded by the novel vaccine strategy is not sufficient to warrant a wholesale change in disease avoidance strategy. Nonetheless, even the partial protection provided by this vaccine could be of value to protect animals that cannot be moved, for example where some of the herd remain at the boma to provide milk or where land-use changes make traditional disease avoidance difficult. Furthermore, the vaccine may offer a feasible solution to some of the current land-use challenges and conflicts, providing a degree of protection to valuable livestock where avoidance strategies are not possible, but with less risk of precipitating the potentially damaging environmental consequences, such as overgrazing of highly nutritious seasonal pastures, that might result if herd owners decide they no longer need to avoid wildebeest.

Infección por virus sincitial respiratorio y su relación con valores de IGG en niños críticos

Antecedente: La infección por el virus sincitial respiratorio (VSR) representa una elevada morbimortalidad, y en algunos casos necesidad de manejo en unidades de cuidado intensivo pediátrico (UCIP). La respuesta inmunológica influye de manera directa en la expresión de la severidad y pronóstico de los pacientes con infección respiratoria. Metodología: Estudio de una cohorte retrospectiva de pacientes con infección respiratoria grave secundaria a VSR, sin historia de inmunodeficiencia, atendidos en la UCIP del Hospital Universitario Clínica San Rafael. Se realizó análisis descriptivoglobaly de acuerdo a la categorización de las prueba de IgG. Resultados: De 188 pacientes que ingresaron a la UCIP, 13% presentaron infección por VSR (24), con una edad promedio de 7,3 (DE=3,6) meses. Pertenecían al sexo masculino79,83%. Se encontró que 12,5% tenían un valor de IgGbajo para su edad, 58,33% tenían valores en límite inferior y el 29,17% dentro de rangos normales para su edad. En los pacientes con IgG baja, fue mayor la presentación de choque séptico que no responde a líquidos (100 vs 92 vs 86%), la mediana de días de ventilación mecánica fue mayor (8 vs 6 vs 5 respectivamente), así como la mortalidad (67 vs 7,1 vs 0%). Conclusión: Nuestra serie encontró que aquellos pacientes con niveles bajos o valores en el límite inferior de IgG sérica tuvieron mayor compromiso sistémico, mayor duración de ventilación mecánica y mayor mortalidad. Se necesitan estudios prospectivos que relaciones niveles bajos de IgG con severidad y pronostico en estos pacientes con infección grave por VSR.

Genotypic profile of Pantanal creole sheep regarding susceptibility or resistance to scrapie.

The objective of this work was to determine the genotypic profile specific to scrapie in codons 136, 154, and 171 of the PRNP gene of the Pantanal creole sheep. Genomic DNA was extracted from blood samples collected from 66 sheep, and the regions of interest on the DNA strand were amplified by PCR. Five haplotypes were identified: ARR, alanine, arginine, arginine; ARQ, alanine, arginine, glutamine; AHQ, alanine, histidine, glutamine; ARH, alanine, arginine, histidine; and VRQ, valine, arginine, glutamine. The most common genotypes were ARQ/ARQ (27%) and ARR/ARQ (24%). The genotypic profile of the Pantanal creole sheep shows low to moderate susceptibility.

Association analyses pointed the TIPARP as a potential candidate gene influencing residual feed intake variation in Nelore cattle.

2016