The burden of anthropogenic changes and mutation load in a critically endangered harrier from the Reunion biodiversity hotspot, Circus maillardi.

Anthropogenic impact is causing the decline of a large proportion of species worldwide and reduces their genetic diversity. Island species typically have smaller ranges than continental species. As a consequence, island species are particularly liable to undergo population bottlenecks, giving rise to conservation challenges such as inbreeding and unmasking of deleterious genetic load. Such challenges call for more detailed assessments of the genetic make-up of threatened island populations. The Mascarene islands (Indian Ocean) present many prime examples, being unusual in having been pristine until first human arrival ~400 years ago, following which anthropogenic pressure was unusually intense. A threatened harrier (Circus maillardi) endemic to the westernmost island of the archipelago is a good example of the challenges faced by species that have declined to small population size following intense anthropogenic pressure. In this study, we use an extensive set of population genomic tools to quantify variation at near-neutral and coding loci, in order to test the historical impact of human activity on this species, and evaluate the species' (mal)adaptive potential. We observed low but significant genetic differentiation between populations on the West and North-East sides of the island, echoing observations in other endemic species. Inbreeding was significant, with a substantial fraction of samples being first or second-degree relatives. Historical effective population sizes have declined from ~3000 to 300 individuals in the past 1000 years, with a more recent drop ~100 years ago consistent with human activity. Based on our simulations and comparisons with a close relative (Circus melanoleucos), this demographic history may have allowed purging of the most deleterious variants but is unlikely to have allowed the purging of mildly deleterious variants. Our study shows how using relatively affordable methods can reveal the massive impact that human activity may have on the genetic diversity and adaptive potential of island populations, and calls for urgent action to closely monitor the reproductive success of such endemic populations, in association with genetic studies.

Effects of age and noise on tympanal displacement in the Desert Locust.

Insect cuticle is an evolutionary-malleable exoskeleton that has specialised for various functions. Insects that detect the pressure component of sound bear specialised sound-capturing tympani evolved from cuticular thinning. Whilst the outer layer of insect cuticle is composed of non-living chitin, its mechanical properties change during development and aging. Here, we measured the displacements of the tympanum of the desert Locust, Schistocerca gregaria, to understand biomechanical changes as a function of age and noise-exposure. We found that the stiffness of the tympanum decreases within 12 h of noise-exposure and increases as a function of age, independent of noise-exposure. Noise-induced changes were dynamic with an increased tympanum displacement to sound within 12 h post noise-exposure. Within 24 h, however, the tone-evoked displacement of the tympanum decreased below that of control Locusts. After 48 h, the tone-evoked displacement of the tympanum was not significantly different to Locusts not exposed to noise. Tympanal displacements reduced predictably with age and repeatably noise-exposed Locusts (every three days) did not differ from their non-noise-exposed counterparts. Changes in the biomechanics of the tympanum may explain an age-dependent decrease in auditory detection in tympanal insects.

What can insects teach us about hearing loss?

Over the last three decades, insects have been utilized to provide a deep and fundamental understanding of many human diseases and disorders. Here, we present arguments for insects as models to understand general principles underlying hearing loss. Despite ∼600 million years since the last common ancestor of vertebrates and invertebrates, we share an overwhelming degree of genetic homology particularly with respect to auditory organ development and maintenance. Despite the anatomical differences between human and insect auditory organs, both share physiological principles of operation. We explain why these observations are expected and highlight areas in hearing loss research in which insects can provide insight. We start by briefly introducing the evolutionary journey of auditory organs, the reasons for using insect auditory organs for hearing loss research, and the tools and approaches available in insects. Then, the first half of the review focuses on auditory development and auditory disorders with a genetic cause. The second half analyses the physiological and genetic consequences of ageing and short- and long-term changes as a result of noise exposure. We finish with complex age and noise interactions in auditory systems. In this review, we present some of the evidence and arguments to support the use of insects to study mechanisms and potential treatments for hearing loss in humans. Obviously, insects cannot fully substitute for all aspects of human auditory function and loss of function, although there are many important questions that can be addressed in an animal model for which there are important ethical, practical and experimental advantages.

Auditory robustness and resilience in the aging auditory system of the desert locust.

After overexposure to loud music, we experience a decrease in our ability to hear (robustness), which usually recovers (resilience). Here, we exploited the amenable auditory system of the desert locust, Schistocerca gregaria, to measure how robustness and resilience depend on age. We found that gene expression changes are dominated by age as opposed to noise exposure. We measured sound-evoked nerve activity for young and aged locusts directly, after 24 hours and 48 hours after noise exposure. We found that both young and aged locusts recovered their auditory nerve function over 48 hours. We also measured the sound-evoked transduction current in individual auditory neurons, and although the transduction current magnitude recovered in the young locusts after noise exposure, it failed to recover in the aged locusts. A plastic mechanism compensates for the decreased transduction current in aged locusts. We suggest key genes upregulated in young noise-exposed locusts that mediate robustness to noise exposure and find potential candidates responsible for compensatory mechanisms in the auditory neurons of aged noise-exposed locusts.

Metabolic decline in an insect ear: correlative or causative for age-related auditory decline?

One leading hypothesis for why we lose our hearing as we age is a decrease in ear metabolism. However, direct measurements of metabolism across a lifespan in any auditory system are lacking. Even if metabolism does decrease with age, a question remains: is a metabolic decrease a cause of age-related auditory decline or simply correlative? We use an insect, the desert locust Schistocerca gregaria, as a physiologically versatile model to understand how cellular metabolism correlates with age and impacts on age-related auditory decline. We found that auditory organ metabolism decreases with age as measured fluorometrically. Next, we measured the individual auditory organ's metabolic rate and its sound-evoked nerve activity and found no correlation. We found no age-related change in auditory nerve activity, using hook electrode recordings, and in the electrophysiological properties of auditory neurons, using patch-clamp electrophysiology, but transduction channel activity decreased. To further test for a causative role of the metabolic rate in auditory decline, we manipulated metabolism of the auditory organ through diet and cold-rearing but found no difference in sound-evoked nerve activity. We found that although metabolism correlates with age-related auditory decline, it is not causative. Finally, we performed RNA-Seq on the auditory organs of young and old locusts, and whilst we found enrichment for Gene Ontology terms associated with metabolism, we also found enrichment for a number of additional aging GO terms. We hypothesize that age-related hearing loss is dominated by accumulative damage in multiple cell types and multiple processes which outweighs its metabolic decline.

Physiological changes throughout an insect ear due to age and noise - A longitudinal study.

Hearing loss is not unique to humans and is experienced by all animals in the face of wild and eclectic differences in ear morphology. Here, we exploited the high throughput and accessible tympanal ear of the desert locust, Schistocerca gregaria to rigorously quantify changes in the auditory system due to noise exposure and age. In this exploratory study, we analyzed tympanal displacements, morphology of the auditory Müller's organ and measured activity of the auditory nerve, the transduction current, and electrophysiological properties of individual auditory receptors. This work shows that hearing loss manifests as a complex disorder due to differential effects of age and noise on several processes and cell types within the ear. The "middle-aged deafness" pattern of hearing loss found in locusts mirrors that found for humans exposed to noise early in their life suggesting a fundamental interaction of the use of an auditory system (noise) and its aging.

The Phalangopsidae crickets (Orthoptera, Grylloidea) of the Seychelles Archipelago: Taxonomy of an ecological radiation.

The Phalangopsidae crickets (Grylloidea) of the Seychelles are examined following extensive field sampling on several main islands of the archipelago (Mah, Silhouette, Praslin, La Digue). Despite the small area of these islands, six genera (12 species) are documented, including one new genus and five new species. The type species of the genus Seychellesia Bolivar, 1912 is transferred to the genus Paragryllodes Karny, 1909 as Paragryllodes nitidula (Bolivar, 1912) n. comb. The other species described in Seychellesia are transferred to the genus Seselia Hugel Desutter-Grandcolas, n. gen., as Seselia longicercata (Bolivar, 1912) n. comb. and Seselia patellifera (Bolivar, 1912) n. comb. Two new species are also described in the genus Seselia Hugel Desutter-Grandcolas, n. gen., Seselia coccofessei Hugel Desutter-Grandcolas, n. gen., n. sp. (type species of the genus) and Seselia matyoti Hugel Desutter-Grandcolas, n. gen., n. sp. The genera Phaeogryllus Bolivar, 1912 and Phalangacris Bolivar, 1895 are redescribed, including Phalangacris ferlegro Hugel Desutter-Grandcolas, n. sp. and Phalangacris sotsote Hugel Desutter-Grandcolas, n. sp. that are new to science. The genus Gryllapterus Bolivar, 1912 is redescribed and transferred from the Landrevinae (Gryllidae) to the Cachoplistinae (Phalangopsidae). New tribes are defined for the genus Paragryllodes (Paragryllodini Hugel Desutter-Grandcolas, n. tribe) on the one hand, and for Seselia Hugel Desutter-Grandcolas, n. gen., Phalangacris, Phaeogryllus and Gryllapterus (Seselini Hugel Desutter-Grandcolas, n. tribe) on the other, using morphological characters and the results of molecular phylogenetic studies (Warren et al. 2019). Phaloria (Papuloria) insularis (Bolivar, 1912) (Phaloriinae) is redescribed and restricted to Mah, and its calling song is documented for the first time, while Phaloria (Papuloria) bolivari Hugel Desutter-Grandcolas, n. sp. is newly described from Silhouette. Identification keys are proposed for the genera of Seselini Hugel Desutter-Grandcolas, n. tribe, and for the species of Seselia Hugel Desutter-Grandcolas, n. gen. and Phalangacris. The confusion between the Mogoplistidae Ornebius succineus Bolivar, 1912 and the Phalangopsidae Heterotrypus succineus Bolivar, 1910 is discussed, and the name Subtiloria succineus (Bolivar, 1912) considered a nomen nudum.

Peridermal fruit skin formation in Actinidia sp. (kiwifruit) is associated with genetic loci controlling russeting and cuticle formation.

BACKGROUND: The skin (exocarp) of fleshy fruit is hugely diverse across species. Most fruit types have a live epidermal skin covered by a layer of cuticle made up of cutin while a few create an outermost layer of dead cells (peridermal layer). RESULTS: In this study we undertook crosses between epidermal and peridermal skinned kiwifruit, and showed that epidermal skin is a semi-dominant trait. Furthermore, backcrossing these epidermal skinned hybrids to a peridermal skinned fruit created a diverse range of phenotypes ranging from epidermal skinned fruit, through fruit with varying degrees of patches of periderm (russeting), to fruit with a complete periderm. Quantitative trait locus (QTL) analysis of this population suggested that periderm formation was associated with four loci. These QTLs were aligned either to ones associated with russet formation on chromosome 19 and 24, or cuticle integrity and coverage located on chromosomes 3, 11 and 24. CONCLUSION: From the segregation of skin type and QTL analysis, it appears that skin development in kiwifruit is controlled by two competing factors, cuticle strength and propensity to russet. A strong cuticle will inhibit russeting while a strong propensity to russet can create a continuous dead skinned periderm.

Gene transcription changes in a locust model of noise-induced deafness.

Locusts have auditory structures called Müller's organs attached to tympanic membranes on either side of the abdomen. We measured the normalized abundances of 500 different mRNA transcripts in 320 Müller's organs obtained from 160 locusts (Schistocerca gregaria) that had been subjected to a loud continuous 3-kHz tone for 24 h. Abundance ratios were then measured relative to transcripts from 360 control organs. A histogram of the number of observed transcripts versus their abundance ratios (noise exposed/control) was well fitted by a Cauchy distribution with median value near one. Transcripts below 5% and above 95% of the cumulative distribution function of the fitted Cauchy distribution were selected as putatively different from the expected values of an untreated preparation. This yielded eight transcripts with ratios increased by noise exposure (ratios 1.689-3.038) and 18 transcripts with reduced ratios (0.069-0.457). Most of the transcripts with increased abundance represented genes responsible for cuticular construction, suggesting extensive remodeling of some or all the cuticular components of the auditory structure, whereas the reduced abundance transcripts were mostly involved in lipid and protein storage and metabolism, suggesting a profound reduction in metabolic activity in response to the overstimulation.NEW & NOTEWORTHY Locust ears have functional and genetic similarities to human ears, including loss of hearing from age or noise exposure. We measured transcript abundances in transcriptomes of noise-exposed and control locust ears. The data indicate remodeling of the ear tympanum and profound reductions in metabolism that may explain reduced sound transduction. These findings advance our understanding of this useful model and suggest further experiments to elucidate mechanisms that ears use to cope with excessive stimulation.

An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes.

Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.

Mapping CRISPR-Cas9 public and commercial innovation using The Lens institutional toolkit.

CRISPR-Cas9 is a revolutionary technology because it is precise, fast and easy to implement, cheap and components are readily accessible. This versatility means that the technology can deliver a timely end product and can be used by many stakeholders. In plant cells, the technology can be applied to knockout genes by using CRISPR-Cas nucleases that can alter coding gene regions or regulatory elements, alter precisely a genome by base editing to delete or regulate gene expression, edit precisely a genome by homology-directed repair mechanism (cellular DNA), or regulate transcriptional machinery by using dead Cas proteins to recruit regulators to the promoter region of a gene. All these applications can be for: 1) Research use (Non commercial), 2) Uses related product components for the technology itself (reagents, equipment, toolkits, vectors etc), and 3) Uses related to the development and sale of derived end products based on this technology. In this contribution, we present a prototype report that can engage the community in open, inclusive and collaborative innovation mapping. Using the open data at the Lens.org platform and other relevant sources, we tracked, analyzed, organized, and assembled contextual and bridged patent and scholarly knowledge about CRISPR-Cas9 and with the assistance of a new Lens institutional capability, The Lens Report Builder, currently in beta release, mapped the public and commercial innovation pathways of the technology. When scaled, this capability will also enable coordinated editing and curation by credentialed experts to inform policy makers, businesses and private or public investment.

A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors.

BACKGROUND: Transcriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. RESULTS: Sixty-one samples covering diverse tissues at different developmental time points were selected for RNA-seq analysis and an eFP browser was generated to visualise this dataset. 2839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three "hub" genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF. CONCLUSIONS: This study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The Actinidia eFP browser is provided in an accessible format that allows researchers to download and work internally.

Correction: Rapid loss of flight in the Aldabra white-throated rail.

[This corrects the article DOI: 10.1371/journal.pone.0226064.].

Physiological Basis of Noise-Induced Hearing Loss in a Tympanal Ear.

Acoustic overexposure, such as listening to loud music too often, results in noise-induced hearing loss. The pathologies of this prevalent sensory disorder begin within the ear at synapses of the primary auditory receptors, their postsynaptic partners and their supporting cells. The extent of noise-induced damage, however, is determined by overstimulation of primary auditory receptors, upstream of where the pathologies manifest. A systematic characterization of the electrophysiological function of the upstream primary auditory receptors is warranted to understand how noise exposure impacts on downstream targets, where the pathologies of hearing loss begin. Here, we used the experimentally-accessible locust ear (male, Schistocerca gregaria) to characterize a decrease in the auditory receptor's ability to respond to sound after noise exposure. Surprisingly, after noise exposure, the electrophysiological properties of the auditory receptors remain unchanged, despite a decrease in the ability to transduce sound. This auditory deficit stems from changes in a specialized receptor lymph that bathes the auditory receptors, revealing striking parallels with the mammalian auditory system.SIGNIFICANCE STATEMENT Noise exposure is the largest preventable cause of hearing loss. It is the auditory receptors that bear the initial brunt of excessive acoustic stimulation, because they must convert excessive sound-induced movements into electrical signals, but remain functional afterward. Here we use the accessible ear of an invertebrate to, for the first time in any animal, characterize changes in auditory receptors after noise overexposure. We find that their decreased ability to transduce sound into electrical signals is, most probably, due to changes in supporting (scolopale) cells that maintain the ionic composition of the ear. An emerging doctrine in hearing research is that vertebrate primary auditory receptors are surprisingly robust, something that we show rings true for invertebrate ears too.

A simple dynamic model explains the diversity of island birds worldwide.

Colonization, speciation and extinction are dynamic processes that influence global patterns of species richness1-6. Island biogeography theory predicts that the contribution of these processes to the accumulation of species diversity depends on the area and isolation of the island7,8. Notably, there has been no robust global test of this prediction for islands where speciation cannot be ignored9, because neither the appropriate data nor the analytical tools have been available. Here we address both deficiencies to reveal, for island birds, the empirical shape of the general relationships that determine how colonization, extinction and speciation rates co-vary with the area and isolation of islands. We compiled a global molecular phylogenetic dataset of birds on islands, based on the terrestrial avifaunas of 41 oceanic archipelagos worldwide (including 596 avian taxa), and applied a new analysis method to estimate the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation). Our model predicts-with high explanatory power-several global relationships. We found a decline in colonization with isolation, a decline in extinction with area and an increase in speciation with area and isolation. Combining the theoretical foundations of island biogeography7,8 with the temporal information contained in molecular phylogenies10 proves a powerful approach to reveal the fundamental relationships that govern variation in biodiversity across the planet.

Geo-Climatic Changes and Apomixis as Major Drivers of Diversification in the Mediterranean Sea Lavenders (Limonium Mill.).

The Mediterranean realm, comprising the Mediterranean and Macaronesian regions, has long been recognized as one of the world's biodiversity hotspots, owing to its remarkable species richness and endemism. Several hypotheses on biotic and abiotic drivers of species diversification in the region have been often proposed but rarely tested in an explicit phylogenetic framework. Here, we investigate the impact of both species-intrinsic and -extrinsic factors on diversification in the species-rich, cosmopolitan Limonium, an angiosperm genus with center of diversity in the Mediterranean. First, we infer and time-calibrate the largest Limonium phylogeny to date. We then estimate ancestral ranges and diversification dynamics at both global and regional scales. At the global scale, we test whether the identified shifts in diversification rates are linked to specific geological and/or climatic events in the Mediterranean area and/or asexual reproduction (apomixis). Our results support a late Paleogene origin in the proto-Mediterranean area for Limonium, followed by extensive in situ diversification in the Mediterranean region during the late Miocene, Pliocene, and Pleistocene. We found significant increases of diversification rates in the "Mediterranean lineage" associated with the Messinian Salinity Crisis, onset of Mediterranean climate, Plio-Pleistocene sea-level fluctuations, and apomixis. Additionally, the Euro-Mediterranean area acted as the major source of species dispersals to the surrounding areas. At the regional scale, we infer the biogeographic origins of insular endemics in the oceanic archipelagos of Macaronesia, and test whether woodiness in the Canarian Nobiles clade is a derived trait linked to insular life and a biotic driver of diversification. We find that Limonium species diversity on the Canary Islands and Cape Verde archipelagos is the product of multiple colonization events followed by in situ diversification, and that woodiness of the Canarian endemics is indeed a derived trait but is not associated with a significant shift to higher diversification rates. Our study expands knowledge on how the interaction between abiotic and biotic drivers shape the uneven distribution of species diversity across taxonomic and geographical scales.

Rapid loss of flight in the Aldabra white-throated rail.

Flight loss has evolved independently in numerous island bird lineages worldwide, and particularly in rails (Rallidae). The Aldabra white-throated rail (Dryolimnas [cuvieri] aldabranus) is the last surviving flightless bird in the western Indian Ocean, and the only living flightless subspecies within Dryolimnas cuvieri, which is otherwise volant across its extant range. Such a difference in flight capacity among populations of a single species is unusual, and could be due to rapid evolution of flight loss, or greater evolutionary divergence than can readily be detected by traditional taxonomic approaches. Here we used genetic and morphological analyses to investigate evolutionary trajectories of living and extinct Dryolimnas cuvieri subspecies. Our data places D. [c.] aldabranus among the most rapid documented avian flight loss cases (within an estimated maximum of 80,000-130,000 years). However, the unusual intraspecific variability in flight capacity within D. cuvieri is best explained by levels of genetic divergence, which exceed those documented between other volant taxa versus flightless close relatives, all of which have full species status. Our results also support consideration of Dryolimnas [cuvieri] aldabranus as sufficiently evolutionary distinct from D. c. cuvieri to warrant management as an evolutionary significant unit. Trait variability among closely related lineages should be considered when assessing conservation status, particularly for traits known to influence vulnerability to extinction (e.g. flightlessness).

MYBA From Blueberry (Vaccinium Section Cyanococcus) Is a Subgroup 6 Type R2R3MYB Transcription Factor That Activates Anthocyanin Production.

The Vaccinium genus in the family Ericaceae comprises many species, including the fruit-bearing blueberry, bilberry, cranberry, huckleberry, and lingonberry. Commercially, the most important are the blueberries (Vaccinium section Cyanococcus), such as Vaccinium corymbosum (northern highbush blueberry), Vaccinium virgatum (rabbiteye blueberry), and Vaccinium angustifolium (lowbush blueberry). The rising popularity of blueberries can partly be attributed to their "superfood" status, with an increasing body of evidence around human health benefits resulting from the fruit metabolites, particularly products of the phenylpropanoid pathway such as anthocyanins. Activation of anthocyanin production by R2R3-MYB transcription factors (TFs) has been characterized in many species, but despite recent studies on blueberry, cranberry, and bilberry, no MYB anthocyanin regulators have been reported for Vaccinium. Indeed, there has been conjecture that at least in bilberry, MYB TFs divergent to the usual type are involved. We report identification of MYBA from blueberry, and show through sequence analysis and functional studies that it is homologous to known anthocyanin-promoting R2R3-MYBs of subgroup 6 of the MYB superfamily. In transient assays, MYBA complemented an anthocyanin MYB mutant of Antirrhinum majus and, together with a heterologous bHLH anthocyanin regulator, activated anthocyanin production in Nicotiana benthamiana. Furthermore anthocyanin accumulation and anthocyanin structural gene expression (assayed by qPCR and RNA-seq analyses) correlated with MYBA expression, and MYBA was able to transactivate the DFR promoter from blueberry and other species. The RNA-seq data also revealed a range of other candidate genes involved in the regulation of anthocyanin production in blueberry fruit. The identification of MYBA will help to resolve the regulatory mechanism for anthocyanin pigmentation in the Vaccinium genus. The sequence information should also prove useful in developing tools for the accelerated breeding of new Vaccinium cultivars.