Lack of geographic variation in anonymous nuclear polymorphisms in the American oyster, Crassostrea virginica

Comparing geographic variation of noncoding nuclear DNA polymorphisms, which presumably are neutral to natural selection, with geographic variation of allozymes is potentially a good way to detect the effects of selection on allozyme polymorphisms. A previous study of four anonymous nuclear markers in the American oyster, Crassostrea virginica, found dramatic differences in allele frequency between the Gulf of Mexico and the Atlantic Ocean. In contrast, 14 allozyme polymorphisms were fairly uniform in frequency between the two areas. This led to the conclusion that all of the allozyme polymorphisms were kept uniform in frequency by balancing selection. To test the robustness of this pattern, six additional anonymous nuclear DNA polymorphisms were surveyed in oysters from Panacea, Fla, and Charleston, S.C. on the Gulf and Atlantic coasts, respectively. Unlike the previously studied DNA markers, the six DNA polymorphisms examined here show geographic variation that is not significantly greater than that of allozymes. The reason for the discrepancy between the two sets of DNA polymorphisms is unclear.      

The mitogenome of Onchocerca volvulus from the Brazilian Amazonia focus

We report here the first complete mitochondria genome of Onchocerca volvulus from a focus outside of Africa. An O. volvulus mitogenome from the Brazilian Amazonia focus was obtained using a combination of high-throughput and Sanger sequencing technologies. Comparisons made between this mitochondrial genome and publicly available mitochondrial sequences identified 46 variant nucleotide positions and suggested that our Brazilian mitogenome is more closely related to Cameroon-origin mitochondria than West African-origin mitochondria. As well as providing insights into the origins of Latin American onchocerciasis, the Brazilian Amazonia focus mitogenome may also have value as an epidemiological resource.     

Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin

Understanding how natural selection generates and maintains adaptive genetic diversity in heterogeneous environments is key to predicting the evolutionary response of populations to rapid environmental change. Detecting selection in complex spatial environments remains challenging, especially for threatened species where the effects of strong genetic drift may overwhelm signatures of selection. We carried out a basinwide riverscape genomic analysis in the threatened southern pygmy perch (Nannoperca australis), an ecological specialist with low dispersal potential. High‐resolution environmental data and 5162 high‐quality filtered SNPs were used to clarify spatial population structure and to assess footprints of selection associated with a steep hydroclimatic gradient and with human disturbance across the naturally and anthropogenically fragmented Murray–Darling Basin (Australia). Our approach included F_ST outlier tests to define neutral loci, and a combination of spatially explicit genotype–environment association analyses to identify candidate adaptive loci while controlling for the effects of landscape structure and shared population history. We found low levels of genetic diversity and strong neutral population structure consistent with expectations based on spatial stream hierarchy and life history. In contrast, variables related to precipitation and temperature appeared as the most important environmental surrogates for putatively adaptive genetic variation at both regional and local scales. Human disturbance also influenced the variation in candidate loci for adaptation, but only at a local scale. Our study contributes to understanding of adaptive evolution along naturally and anthropogenically fragmented ecosystems. It also offers a tangible example of the potential contributions of landscape genomics for informing in situ and ex situ conservation management of biodiversity.     

Long-term landscape changes in vegetation structure: fire management in the wetlands of KwaMbonambi,South Africa

In wetlands the effects of fire on vegetation dynamics are somewhat uncertain. A change detection analysis in the herbaceous wetlands of KwaMbonambi, South Africa, which were subject to frequent fires, revealed that in 1937 the study area comprised grassland (69%), herbaceous wetland (25%), indigenous swamp forest (4%) and tree plantations (1%). However, by 1970, tree plantations occupied 78% of the landscape and grasslands and herbaceous wetlands had declined to 9% and 6%, respectively, whereas indigenous swamp forest had increased to 6%. By 2009 tree plantations had been removed from the wetland areas. Despite this opportunity for herbaceous wetlands to recover their historical extent, they decreased to only 2%, mostly changing to indigenous swamp forest or to an herbaceous/fern (Stenochlaena tenuifolia)/woodland mosaic. Fire records showed suppression of fire to be an important contributing factor, particularly in wetlands that had been disturbed by tree plantations, although subsequently removed. A pilot burning experiment revealed that S. tenuifolia did not inhibit fire. It is therefore practicable to increase fire frequency to prevent the mosaic developing into forest. A conceptual model of the influence of fire regime on wetland vegetation type is presented and priorities for further research on wetlands and fire are recommended.     

Male reproductive success increases with alliance size in Indo-Pacific bottlenose dolphins (Tursiops aduncus)

1. Determining the extent of variation in male mating strategies and reproductive success is necessary to understand the fitness benefits of social and cooperative behaviour. 2. This study assesses the reproductive success of male Indo-Pacific bottlenose dolphins in a small embayment population where different behavioural strategies of males have previously been identified. Parentage for 44 sampled calves was examined using 23 microsatellite loci and one mitochondrial DNA marker. Our candidate parent pool of 70 males and 64 females contained individuals sampled from both the embayment and adjacent coastal populations. 3. A moderate level of polygyny was detected in our sample. We assigned paternity of 23 calves to 12 males at the strict 95% confidence level and an additional nine calves to two males at the 80% confidence level. The majority (92%) of successful males were identified as residents to the embayment, and 46% of offspring were located within the same social group or community as their father. 4. Our results suggest that the size of alliances was the best predictor of reproductive success for males in this population, while the strength of association among allied males, alliance stability and male ranging patterns had little influence. In line with predictions for male alliances formed between unrelated individuals, we found that reproductive skew within alliances was not large. 5. Together, our genetic and behavioural analyses demonstrate that alliance formation between male dolphins is a successful strategy to enhance reproductive output.     

Genetic diversity and structure of blue whales (Balaenoptera musculus) in Australian feeding aggregations

The worldwide distribution of blue whales (Balaenoptera musculus) has not prevented this species from becoming endangered due to twentieth century whaling. In Australia there are two known feeding aggregations of blue whales, which most likely are the pygmy subspecies (B. m. brevicauda). It is unknown whether individuals from these feeding aggregations belong to one breeding stock, or multiple breeding stocks that either share or occupy separate feeding grounds. This was investigated using ten microsatellite loci and mitochondrial DNA control region sequences (N = 110). Both sets of markers revealed no significant genetic structure, suggesting that these whales are likely to belong to the same breeding stock.     

Genetic divergence, phylogeography and conservation units of giant tortoises from Santa Cruz and Pinzón, Galápagos Islands

Island radiations can offer challenging systemsfor the implementation of conservation policiesbecause descendent populations may exhibitdifferent levels of adaptive divergence,reproductive isolation, and phylogeneticdistinctiveness. This seems particularly truefor the endangered Galápagos gianttortoises (Geochelone nigra), whichcomprise a lineage that radiated rapidly andconcomitantly with the evolution of thearchipelago. We used mitochondrial DNAsequences and microsatellite markers toinvestigate the genetic structure, and toreconstruct genealogical relationships and thehistory of population colonization of gianttortoises from the Islands of Santa Cruz andPinzón, including samples of a basal taxonfrom the Island of San Cristóbal.Populations displayed marked geneticdivergence, contrasting demographic histories,and deep phylogeographic structure. The patternof diversification among populations wasconsistent with geological and biogeographichistory, and to some extent, with adaptive andmorphological divergence. Results stronglyindicate the presence of a minimum of fourconservation units with long-standingevolutionary separation: two in Santa Cruz, onein Pinzón, and one in San Cristóbal. Wepropose that these findings be effectivelyintegrated with other existing data by theappropriate environmental agencies to evaluatecurrent conservation efforts and implement newstrategies aimed at protecting the integrityand diversity of giant tortoise populations.     

Population history of the Amazonian one-lined pencilfish based on intron DNA data

The evolutionary history of Amazonian organisms is generally poorly understood. This is particularly true for small floodplain fish species that show reduced dispersal capabilities. The one-lined pencilfish Nannostomus unifasciatus (family Lebiasinidae) is a small fish found in flooded forests of the Rio Negro Floodplain (RNF) in central Amazonia, Brazil. We used a large number of samples collected throughout the species distribution in the RNF and in its headwaters and DNA data from the second intron of the S7 ribosomal protein to reconstruct the phylogeography of N. unifasciatus . Two markedly distinct phylogroups of N. unifasciatus were detected in the RNF. Although these lineages are largely allopatric, they remain reproductively isolated in regions where they overlap, suggesting cryptic speciation in this group in the Rio Negro basin. Coalescent-based statistical methods suggest that the history of these populations was dominated by a Miocene fragmentation of the species in the headwaters of the basin that originated the two phylogroups, followed by recent events of demographic and range expansions in the floodplain. This pattern is discussed within the context of the geomorphologic history of the region, especially geotectonics, and of marine incursions. Our results match the predictions of the palaeogeography hypothesis of speciation and outline the usefulness of an intron DNA marker to reconstruct population history of a central Amazonian fish. Because N. unifasciatus is harvested commercially in the ornamental fishery of the RNF, the two species and limited dispersal capacity between nearby populations identified here are also important to develop sound management decisions in the region.