Inter-island local adaptation in the Galápagos Archipelago: genomics of the Galápagos blue-banded goby, Lythrypnus gilberti

The Galápagos Archipelago is a place where terrestrial adaptive radiations of finches, mockingbirds, and tortoises have been studied extensively. In contrast, little is known about the potential for marine species to diverge among islands. The overall degradation of coral reefs in the Galápagos makes understanding the mechanisms and factors of speciation, the engine of biodiversity, important, and timely. While speciation in marine archipelagos has been described in the past, such as for cone snails in Cabo Verde Archipelago and limpets in Hawaii, adaptive radiations in the marine environment are still rare and poorly understood. In this study, we focused on the Galápagos blue-banded goby, Lythrypnus gilberti, a small endemic fish that is found in shallow subtidal rocky habitats. Using RAD sequencing, we analyzed 19,504 loci that were either neutral, or potentially under directional selection. As expected, considering the small geographic range, population structure based on neutral markers was weak. For loci under directional selection, however, marked differences between islands suggested potential for local adaptation. Our data suggest that for marine species, where dispersal barriers are less apparent, mechanisms of local adaptation may also be at play in the Galápagos Archipelago.

Translanguaging patterns in everyday urban conversations in Cameroon

This study analyses the translanguaging patterns of urban Cameroonians’ linguistic choices (e.g. lexical or phonological) in everyday conversations in Cameroon. Using observation and audio-recordings of 20 naturally occurring conversations as data, a descriptive corpus-based methodology was adopted for analysis. The quantitative approach utilises AntConc (Version 3.5.8) with descriptive analytical tools to identify the speakers’ idiolectal choices in meaning-making translanguaging patterns. The results revealed salient patterns of the speakers’ deployed lexical, grammatical, morphological, phonological and syntactical forms as an integrated system of language. It revealed the speakers preference for polysemous words (e.g. repe) over less polysemous words (e.g. father); choice for shorter lexical words (e.g. man) over longer words (e.g. manpikin); a preference for specialised gender-neutral markers (e.g. ih, which refers to both male and female) over gender-specific forms (e.g. he/she); a preference for voiceless interdental fricatives (e.g. dem, dey) over voiced interdental fricatives (e.g. them, they) and where the choice of inflectional morpheme expressing tense (e.g. ed) is one that can either be omitted or added to a word, the presence of this inflectional morpheme is sometimes fairly used. Such results have practical implications for understanding peoples’ language use as a translanguaging act in bi/multilingual contexts.

Population genetic structure of a major reef-building coral species Acropora downingi in northeastern Arabian Peninsula

Current seawater temperatures around the northeastern Arabian Peninsula resemble future global forecasts as temperatures > 35 °C are commonly observed in summer. To provide a more fundamental aim of understanding the structure of wild populations in extreme environmental conditions, we conducted a population genetic study of a widespread, regional endemic table coral species, Acropora downingi, across the northeastern Arabian Peninsula. A total of 63 samples were collected in the southern Arabian/Persian Gulf (Abu Dhabi and Qatar) and the Sea of Oman (northeastern Oman). Using RAD-seq techniques, we described the population structure of A. downingi across the study area. Pairwise G’st and distance-based analyses using neutral markers displayed two distinct genetic clusters: one represented by Arabian/Persian Gulf individuals, and the other by Sea of Oman individuals. Nevertheless, a model-based method applied to the genetic data suggested a panmictic population encompassing both seas. Hypotheses to explain the distinctiveness of phylogeographic subregions in the northeastern Arabian Peninsula rely on either (1) bottleneck events due to successive mass coral bleaching, (2) recent founder effect, (3) ecological speciation due to the large spatial gradients in physical conditions, or (4) the combination of seascape features, ocean circulation and larval traits. Neutral markers indicated a slightly structured population of A. downingi, which exclude the ecological speciation hypothesis. Future studies across a broader range of organisms are required to furnish evidence for existing hypotheses explaining a population structure observed in the study area. Though this is the most thermally tolerant acroporid species worldwide, A. downingi corals in the Arabian/Persian Gulf have undergone major mortality events over the past three decades. Therefore, the present genetic study has important implications for understanding patterns and processes of differentiation in this group, whose populations may be pushed to extinction as the Arabian/Persian Gulf warms.

Comparative analysis of genomic- and EST-SSRs in European plum (Prunus domestica L.): implications for the diversity analysis of polyploids

Simple sequence repeats (SSRs) are among the most useful DNA markers in plant science. The aim of this study was to compare the features and usefulness of genomic SSR (gSSR) and EST-SSRs in European plum (Prunus domestica L.), an economically important, hexaploid stone fruit crop globally cultivated to produce fleshy fruits and derived foodstuff. The analysis of an ample set of morphologically diverse varieties indicated that gSSRs and EST-SSRs provide different estimates of some of the locus-based indicators of diversity. Moreover, the two classes of SSRs gave different, weakly correlated, estimations of distance-based parameters with gSSRs being more powerful for discriminating purposes. The two SSR classes provide complementary information in European plum, making the contribution of EST-SSRs useful not only as non-neutral markers. The differences between SSR classes are discussed considering the neutral and non-neutral evolution, and the polyploidy and asexual propagation of the cultivated tree varieties.

An Integrated Biomarker Approach Using Flounder to Improve Chemical Risk Assessments in the Heavily Polluted Seine Estuary

The objective of this study was to develop an integrative approach in ecotoxicology (from biomarkers to population genetics) to assess the ecological status of fish populations. Flounders (Platichthys flesus) collected after the spawning season in the heavily polluted Seine estuary were compared with the moderately polluted Bay of Douarnenez. The muscle energetic reserves were highly depleted in Seine vs. Douarnenez fish. The Seine fish displaying a reduced capacity to manage the oxidative stress and a higher energetic metabolism. An increase in the content of muscle membrane phospholipids (sphingomyelin, phosphatidylserine, free sterols) was detected in the Seine vs. Douarnenez fish. The data integration allowed to hypothesize relationships between membrane phospholipids, xenobiotic metabolism, bioenergetics, and antioxidant defence. The genetic diversity considering neutral markers was maintained in the heavily polluted Seine population compared with the Douarnenez population. Finally, we suggest that the high physiological cost of tolerance to toxicants in the Seine flounder population could compromise its capacity to respond in the future to an additional stressor like warming waters in shallow depth. Thus, this population could be submitted to an ecological risk.

Highly replicated evolution of parapatric ecotypes

Parallel evolution of ecotypes occurs when selection independently drives the evolution of similar traits across similar environments. The multiple origin of ecotypes is often inferred on the basis of a phylogeny which clusters populations according to geographic location and not by the environment they occupy. However, the use of phylogenies to infer parallel evolution in closely related populations is problematic due to the potential for gene flow and incomplete lineage sorting to uncouple the genetic structure at neutral markers from the colonization history of populations. Here, we demonstrate multiple origins within ecotypes of an Australian wildflower, Senecio lautus. We observed strong genetic structure as well as phylogenetic clustering by geography, and show this is unlikely due to gene flow between parapatric ecotypes, which is surprisingly low. We further confirm this analytically by demonstrating that phylogenetic distortion due to gene flow often requires higher levels of migration than those observed in S. lautus. Our results imply that selection can repeatedly create similar phenotypes despite the perceived homogenizing effects of gene flow.

Stable word-combinations with a verbal component as the expressive means of subjective modality in german publicistic writing: the pragmatic aspect

The paper is devoted to the study of stable word-combinations with a verbal component, which are seen in the context as the expressive means of subjective modality. German online texts on political, social and sports topics were analyzed in this research. In this paper the functional approach is applied to the study of the above-mentioned linguistic phenomenon. It was proved that stable word-combinations with a verbal component indicate features of phraseological unities and phraseological combinations and are quite common in German publicistic texts. The word-combinations are identified differently: the expression of subjective modality as subjective modality has different markers, splitting into deontic (markers: necessary, possibly, accidently), epistemic (markers: proved, disproved, not resolved), aletic (markers: obligatory, prohibited, allowed), axiological (markers: good, bad, neutral). In the texts under consideration, stable word-combinations with a verbal component can be seen as lexical-syntactic units that enhance the expression of axiological modality as all analyzed examples have good, bad, and neutral markers in the context. Stable word-combinations with a verbal component are linguistic expressions of the force of figurative thinking (German Bildkraft), which has two components: visibility (German Bildhaftigkeit) and imagery / colourfulness (German Bildlichkeit). Visibility, to which stable word-combinations with a verbal component apply, is related to the direct meaning of all semantically relevant words and collocations. Therefore, the wider the semantic space of such words and collocations is, the higher degree of visibility and depth of meaning of such lexical and lexical-stylistic units can be observed, because each individual meaning element defines our understanding of the topic that is described, makes this description more detailed and complements our imagination. Stable word-combinations with a verbal component constitute a complementary element expressing subjective modality that reinforces the influence on the addressee. As the means of expressing subjective modality, these lexical-syntactic units can only be considered together with other lexical units in a context.

Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow?

Ecological speciation can proceed despite genetic interchange when selection counteracts the homogenizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, 2 parapatric Andean hummingbirds with marked plumage divergence. We sequenced putatively neutral markers (mitochondrial DNA [mtDNA] and nuclear ultraconserved elements [UCEs]) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Gloger’s rule that darker forms occur in more humid environments, and examined morphological variation to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was low in both ND2 and UCEs. Coalescent estimates of migration were consistent with divergence with gene flow, but we cannot reject incomplete lineage sorting reflecting recent speciation as an explanation for patterns of genetic variation. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in morphology. Although we reject adaptation to variation in macroclimatic conditions as a cause of divergence, speciation may have occurred in the face of gene flow driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.

Rapid isolation and characterization of microsatellites in the critically endangered Mountain Bongo (Tragelaphus eurycerus isaaci)

High-throughput sequencing tools promise to revolutionize many aspects of genetics research, e.g. by allowing the identification of functional adaptive genetic variation. However, the expense and expertise required to apply these tools to basic conservation questions is a challenge for applications outside academia, resulting in a so-called “conservation genomics gap” (Shafer et al. 2015). The conservation genetics paradigm is that basic information about inbreeding and gene flow are often critical to inform conservation management of small populations (Ouborg et al. 2010). This information is often needed quickly and ideally should be accessible to workers without special expertise in genomics (DeSalle & Amato 2004). While the inferential power of high-throughput sequencing to interrogate the genome is profound, the cost for population analysis is higher (though decreasing) than for traditional neutral markers. Thus, the use of neutral markers is still relevant in conservation applications. However, this assumes that neutral markers have been discovered and characterized for a given species of conservation concern, which is often untrue for non-model organisms. Here, we use a fast, cost-efficient, high-throughput sequencing method (Illumina MiSeq) to rapidly identify and characterize microsatellites in the mountain bongo (Tragelaphus eurycerus isaaci, hereafter bongo), which has a clear and timely conservation imperative but lacks any described neutral markers.