Phylogeographic structure of Octopus vulgaris in South Africa revisited: identification of a second lineage near Durban harbor

In a previous study that investigated genetic structure of Octopus vulgaris along the South African coast by sequencing the mitochondrial cytochrome oxidase III gene (COIII), all sequences generated were identical. Such a finding is unusual, because mitochondrial DNA mutates quickly, and several marine invertebrates present in southern Africa show considerable genetic variation and structure. We reanalysed the samples using two different mitochondrial markers, namely cytochrome oxidase I (COI) and the large ribosomal subunit (16S rRNA). Sequences of both these markers showed variation. The conclusion of the previous study, that South Africa’s O. vulgaris population is characterised by a lack of genetic structure along the coast, is rejected. Some specimens from Durban (southeast Africa) were genetically more different from those found in the remainder of the country than were specimens from other regions (Tristan da Cunha and Senegal). We suggest that the lineage in Durban may have been recently introduced

A Comparison of Spectroscopic versus Imaging Techniques for Detecting Close Companions to Kepler Objects of Interest

(Abbreviated) Kepler planet candidates require both spectroscopic and imaging follow-up observations to rule out false positives and detect blended stars. [...] In this paper, we examine a sample of 11 Kepler host stars with companions detected by two techniques -- near-infrared adaptive optics and/or optical speckle interferometry imaging, and a new spectroscopic deblending method. We compare the companion Teff and flux ratios (F_B/F_A, where A is the primary and B is the companion) derived from each technique, and find no cases where both companion parameters agree within 1sigma errors. In 3/11 cases the companion Teff values agree within 1sigma errors, and in 2/11 cases the companion F_B/F_A values agree within 1sigma errors. Examining each Kepler system individually considering multiple avenues (isochrone mapping, contrast curves, probability of being bound), we suggest two cases for which the techniques most likely agree in their companion detections (detect the same companion star). Overall, our results support the advantage the spectroscopic deblending technique has for finding very close-in companions ($\theta \lesssim$0.02-0.05") that are not easily detectable with imaging. However, we also specifically show how high-contrast AO and speckle imaging observations detect companions at larger separations ($\theta \geq$0.02-0.05") that are missed by the spectroscopic technique, provide additional information for characterizing the companion and its potential contamination (e.g., PA, separation, $\Delta$m), and cover a wider range of primary star effective temperatures. The investigation presented here illustrates the utility of combining the two techniques to reveal higher-order multiples in known planet-hosting systems.Comment: Accepted to AJ. 40 pages, 12 figure

Mitochondrial DNA paradox: sex-specific genetic structure in a marine mussel despite maternal inheritance and passive dispersal

Background: When genetic structure is identified using mitochondrial DNA (mtDNA), but no structure is identified using biparentally-inherited nuclear DNA, the discordance is often attributed to differences in dispersal potential between the sexes. Results: We sampled the intertidal rocky shore mussel Perna perna in a South African bay and along the nearby open coast, and sequenced maternally-inherited mtDNA (there is no evidence for paternally-inherited mtDNA in this species) and a biparentally-inherited marker. By treating males and females as different populations, we identified significant genetic structure on the basis of mtDNA data in the females only. Conclusions: This is the first study to report sex-specific differences in genetic structure based on matrilineally-inherited mtDNA in a passively dispersing species that lacks social structure or sexual dimorphism. The observed pattern most likely stems from females being more vulnerable to selection in habitats from which they did not originate, which also manifests itself in a male-biased sex ratio. Our results have three important implications for the interpretation of population genetic data. First, even when mtDNA is inherited exclusively in the female line, it also contains information about males. For that reason, using it to identify sex-specific differences in genetic structure by contrasting it with biparentally-inherited markers is problematic. Second, the fact that sex-specific differences were found in a passively dispersing species in which sex-biased dispersal is unlikely highlights the fact that significant genetic structure is not necessarily a function of low dispersal potential or physical barriers. Third, even though mtDNA is typically used to study historical demographic processes, it also contains information about contemporary processes. Higher survival rates of males in non-native habitats can erase the genetic structure present in their mothers within a single generation

Signatures of seaway closures and founder dispersal in the phylogeny of a circumglobally distributed seahorse lineage

<p>Abstract</p> <p>Background</p> <p>The importance of vicariance events on the establishment of phylogeographic patterns in the marine environment is well documented, and generally accepted as an important cause of cladogenesis. Founder dispersal (i.e. long-distance dispersal followed by founder effect speciation) is also frequently invoked as a cause of genetic divergence among lineages, but its role has long been challenged by vicariance biogeographers. Founder dispersal is likely to be common in species that colonize remote habitats by means of rafting (e.g. seahorses), as long-distance dispersal events are likely to be rare and subsequent additional recruitment from the source habitat is unlikely. In the present study, the relative importance of vicariance and founder dispersal as causes of cladogenesis in a circumglobally distributed seahorse lineage was investigated using molecular dating. A phylogeny was reconstructed using sequence data from mitochondrial and nuclear markers, and the well-documented closure of the Central American seaway was used as a primary calibration point to test whether other bifurcations in the phylogeny could also have been the result of vicariance events. The feasibility of three other vicariance events was explored: a) the closure of the Indonesian Seaway, resulting in sister lineages associated with the Indian Ocean and West Pacific, respectively; b) the closure of the Tethyan Seaway, resulting in sister lineages associated with the Indo-Pacific and Atlantic Ocean, respectively, and c) continental break-up during the Mesozoic followed by spreading of the Atlantic Ocean, resulting in pairs of lineages with amphi-Atlantic distribution patterns.</p> <p>Results</p> <p>Comparisons of pairwise genetic distances among the seahorse species hypothesized to have diverged as a result of the closure of the Central American Seaway with those of published teleost sequences having the same distribution patterns show that the seahorses were among the last to diverge. This suggests that their cladogenesis was associated with the final closure of this seaway. Although two other divergence events in the phylogeny could potentially have arisen as a result of the closures of the Indonesian and Tethyan seaways, respectively, the timing of the majority of bifurcations in the phylogeny differed significantly from the dates of vicariance events suggested in the literature. Moreover, several divergence events that resulted in the same distribution patterns of lineages at different positions in the phylogeny did not occur contemporaneously. For that reason, they cannot be the result of the same vicariance events, a result that is independent of molecular dating.</p> <p>Conclusion</p> <p>Interpretations of the cladogenetic events in the seahorse phylogeny based purely on vicariance biogeographic hypotheses are problematic. We conclude that the evolution of the circumglobally distributed seahorse lineage was strongly influenced by founder dispersal, and suggest that this mode of speciation may be particularly important in marine organisms that lack a pelagic dispersal phase and instead disperse by means of rafting.</p

Climate change, genetics or human choice: why were the shells of mankind’s earliest ornament larger in the Pleistocene than in the Holocene?

The southern African tick shell, Nassarius kraussianus (Dunker, 1846), has been identified as being the earliest known ornamental object used by human beings. Shell beads dated from ~75,000 years ago (Pleistocene era) were found in a cave located on South Africa's south coast. Beads made from N. kraussianus shells have also been found in deposits in this region dating from the beginning of the Holocene era (<10,000 years ago). These younger shells were significantly smaller, a phenomenon that has been attributed to a change in human preference. We investigated two alternative hypotheses explaining the difference in shell size: a) N. kraussianus comprises at least two genetic lineages that differ in size; b) the difference in shell size is due to phenotypic plasticity and is a function of environmental conditions. To test these hypotheses, we first reconstructed the species' phylogeographic history, and second, we measured the shell sizes of extant individuals throughout South Africa. Although two genetic lineages were identified, the sharing of haplotypes between these suggests that there is no genetic basis for the size differences. Extant individuals from the cool temperate west coast had significantly larger shells than populations in the remainder of the country, suggesting that N. kraussianus grows to a larger size in colder water. The decrease in fossil shell size from Pleistocene to Holocene was likely due to increased temperatures as a result of climate change at the beginning of the present interglacial period. We hypothesise that the sizes of N. kraussianus fossil shells can therefore serve as indicators of the climatic conditions that were prevalent in a particular region at the time when they were deposited. Moreover, N. kraussianus could serve as a biomonitor to study the impacts of future climate change on coastal biota in southern Africa

Observations of Binary Stars with the Differential Speckle Survey Instrument. V. Toward an Empirical Metal-Poor Mass-Luminosity Relation

In an effort to better understand the details of the stellar structure and evolution of metal poor stars, the Gemini North telescope was used on two occasions to take speckle imaging data of a sample of known spectroscopic binary stars and other nearby stars in order to search for and resolve close companions. The observations were obtained using the Differential Speckle Survey Instrument, which takes data in two filters simultaneously. The results presented here are of 90 observations of 23 systems in which one or more companions was detected, and 6 stars where no companion was detected to the limit of the camera capabilities at Gemini. In the case of the binary and multiple stars, these results are then further analyzed to make first orbit determinations in five cases, and orbit refinements in four other cases. Mass information is derived, and since the systems span a range in metallicity, a study is presented that compares our results with the expected trend in total mass as derived from the most recent Yale isochrones as a function of metal abundance. These data suggest that metal-poor main-sequence stars are less massive at a given color than their solar-metallicity analogues in a manner consistent with that predicted from the theory

Assessing the Effect of Stellar Companions from High-Resolution Imaging of Kepler Objects of Interest

We report on 176 close (<2") stellar companions detected with high-resolution imaging near 170 hosts of Kepler Objects of Interest. These Kepler targets were prioritized for imaging follow-up based on the presence of small planets, so most of the KOIs in these systems (176 out of 204) have nominal radii <6 R_E . Each KOI in our sample was observed in at least 2 filters with adaptive optics, speckle imaging, lucky imaging, or HST. Multi-filter photometry provides color information on the companions, allowing us to constrain their stellar properties and assess the probability that the companions are physically bound. We find that 60 -- 80% of companions within 1" are bound, and the bound fraction is >90% for companions within 0.5"; the bound fraction decreases with increasing angular separation. This picture is consistent with simulations of the binary and background stellar populations in the Kepler field. We also reassess the planet radii in these systems, converting the observed differential magnitudes to a contamination in the Kepler bandpass and calculating the planet radius correction factor, $X_R = R_p (true) / R_p (single)$. Under the assumption that planets in bound binaries are equally likely to orbit the primary or secondary, we find a mean radius correction factor for planets in stellar multiples of $X_R = 1.65$. If stellar multiplicity in the Kepler field is similar to the solar neighborhood, then nearly half of all Kepler planets may have radii underestimated by an average of 65%, unless vetted using high resolution imaging or spectroscopy.Comment: 23 pages, 12 figures. Accepted for publication in The Astronomical Journa

Halobaculum gomorrense gen. nov., sp. nov., a Novel Extremely Halophilic Archaeon from the Dead Sea

A novel extremely halophilic archaeon was isolated from the Dead Sea, This isolate is rod shaped and, like Halobacterium sodomense, requires a relatively low level of sodium ions for growth and a very high level of magnesium; optimal growth occurs in the presence of 0.6 to 1.0 M Mg2+, The new strain resembles members of the Halobacterium saccharovorum-Halobacterium sodomense-Halobacterium trapanicum group in many physiological properties, However, the polar lipid composition of this organism is characteristic of representatives of the genus Haloferax; a sulfated diglycosyl diether is present, and the glycerol diether analog of phosphatidylglycerosulfate is absent, The G+C content of the DNA is 70 mol%. We found that on the basis of 16S rRNA sequence data our new isolate occupies a position intermediate between the position of the Halobacterium saccharovorum group and the position of the genus Haloferax and is sufficiently different from the previously described members of the Halobacteriaceae to justify classification in a new species and a new genus, We propose the name Halobaculum gomorrense gen. nov., sp, nov, for this organism; the type strain is strain DSM 9297

Gene flow and population structure of a solitary top carnivore in a human-dominated landscape

While African leopard populations are considered to be continuous as demonstrated by their high genetic variation, the southernmost leopard population exists in the Eastern and Western Cape, South Africa, where anthropogenic activities may be affecting this population's structure. Little is known about the elusive, last free-roaming top predator in the region and this study is the first to report on leopard population structuring using nuclear DNA. By analyzing 14 microsatellite markers from 40 leopard tissue samples, we aimed to understand the populations' structure, genetic distance, and gene flow (Nm). Our results, based on spatially explicit analysis with Bayesian methods, indicate that leopards in the region exist in a fragmented population structure with lower than expected genetic diversity. Three population groups were identified, between which low to moderate levels of gene flow were observed (Nm 0.5 to 3.6). One subpopulation exhibited low genetic differentiation, suggesting a continuous population structure, while the remaining two appear to be less connected, with low emigration and immigration between these populations. Therefore, genetic barriers are present between the subpopulations, and while leopards in the study region may function as a metapopulation, anthropogenic activities threaten to decrease habitat and movement further. Our results indicate that the leopard population may become isolated within a few generations and suggest that management actions should aim to increase habitat connectivity and reduce human-carnivore conflict. Understanding genetic diversity and connectivity of populations has important conservation implications that can highlight management of priority populations to reverse the effects of human-caused extinctions.Carnegie Corporation of New York to the Global Change and Sustainability Research Institute at the University of the Witwatersrand. ABAX Foundation, Henry and Iris Englund Foundation, National Lotteries Distribution Trust Fund, Mones Michaels Trust, Arne Hanson, and Deutsche Bank South Africa Foundation.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)2045-7758hb201

Connectivity between marine reserves and exploited areas in the philopatric reef fish Chrysoblephus laticeps (Teleostei: Sparidae)

"No-take‟ Marine Protected Areas (MPAs) are successful in protecting populations of many exploited fish species, but it is often unclear whether networks of MPAs are adequately spaced to ensure connectivity among reserves, and whether spillover occurs into adjacent exploited areas. Such issues are particularly important in species with low dispersal potential, many of which exist as genetically distinct regional stocks.The roman, Chrysoblephus laticeps, is an overexploited, commercially important fishery species endemic to South Africa. Post-recruits display resident behavior and occupy small home ranges, making C. laticeps a suitable model species to investigate connectivity in marine teleosts with potentially low dispersal ability. We used multilocus data from two types of highly variable genetic markers (mitochondrial DNA control region and microsatellites) to clarify patterns of genetic connectivity and population structure in C. laticeps using samples from two MPAs and several moderately or severely exploited regions. Despite using analytical tools that are sensitive to detect even subtle genetic structure, we found that this species exists as a single, well-mixed stock throughout its core distribution. This finding lends supports to the status of MPAs as an adequate tool for managing overexploited marine teleosts. Even though adult dispersal out of MPAs is limited, the fact that the large adults in these reserves produce exponentially more offspring than their smaller counterparts in exploited areas makes MPAs a rich source of recruits. We nonetheless caution against concluding that the lack of structure identified in C. laticeps and several other southern African teleosts can be considered to be representative of marine teleosts in this region in general. Many such species are represented in more than one marine biogeographic province and may be comprised of regionally-adapted stocks that need to be managed individually