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.

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.

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.

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

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

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).

Evaluating alternative explanations for an association of extinction risk and evolutionary uniqueness in multiple insular lineages.

Studies in insular environments have often documented a positive association of extinction risk and evolutionary uniqueness (i.e., how distant a species is from its closest living relative). However, the cause of this association is unclear. One explanation is that species threatened with extinction are evolutionarily unique because they are old, implying that extinction risk increases with time since speciation (age-dependent extinction). An alternative explanation is that such threatened species are last survivors of clades that have undergone an elevated extinction rate, and that their uniqueness results from the extinction of their close relatives. Distinguishing between these explanations is difficult but important, since they imply different biological processes determining extinction patterns. Here, we designed a simulation approach to distinguish between these alternatives using living species, and applied it to 12 insular radiations that show a positive association between extinction risk and evolutionary uniqueness. We also tested the sensitivity of results to underlying assumptions and variable extinction rates. Despite differences among the radiations considered, age-dependent extinction was supported as best explaining the majority of the empirical cases. Biological processes driving characteristic changes in abundance with species duration (age-dependency) may merit further investigation.

An expanded molecular phylogeny of Plumbaginaceae, with emphasis on Limonium (sea lavenders): Taxonomic implications and biogeographic considerations.

Plumbaginaceae is characterized by a history of multiple taxonomic rearrangements and lacks a broad molecular phylogenetic framework. Limonium is the most species-rich genus of the family with ca. 600 species and cosmopolitan distribution. Its center of diversity is the Mediterranean region, where ca. 70% of all Limonium species are endemic. In this study, we sample 201 Limonium species covering all described infrageneric entities and spanning its wide geographic range, along with 64 species of other Plumbaginaceae genera, representing 23 out of 29 genera of the family. Additionally, 20 species of the sister family Polygonaceae were used as outgroup. Sequences of three chloroplast (trnL-F, matK, and rbcL) and one nuclear (ITS) loci were used to infer the molecular phylogeny employing maximum likelihood and Bayesian analyses. According to our results, within Plumbaginoideae, Plumbago forms a non-monophyletic assemblage, with Plumbago europaea sister to Plumbagella, while the other Plumbago species form a clade sister to Dyerophytum. Within Limonioideae, Ikonnikovia is nested in Goniolimon, rejecting its former segregation as genus distinct from Goniolimon. Limonium is divided into two major clades: Limonium subg. Pteroclados s.l., including L. sect. Pteroclados and L. anthericoides, and L. subg. Limonium. The latter is divided into three well-supported subclades: the monospecific L. sect. Limoniodendron sister to a clade comprising a mostly non-Mediterranean subclade and a Mediterranean subclade. Our results set the foundation for taxonomic proposals on sections and subsections of Limonium, namely: (a) the newly described L. sect. Tenuiramosum, created to assign L. anthericoides at the sectional rank; (b) the more restricted circumscriptions of L. sect. Limonium (= L. sect. Limonium subsect. Genuinae) and L. sect. Sarcophyllum (for the Sudano-Zambezian/Saharo-Arabian clade); (c) the more expanded circumscription of L. sect. Nephrophyllum (including species of the L. bellidifolium complex); and (d) the new combinations for L. sect. Pruinosum and L. sect. Pteroclados subsect. Odontolepideae and subsect. Nobiles.

3-D imaging reveals four extraordinary cases of convergent evolution of acoustic communication in crickets and allies (Insecta).

When the same complex trait is exhibited by closely related species, a single evolutionary origin is frequently invoked. The complex stridulatory apparatus present in the forewings of extant crickets, mole crickets, katydids, and prophalangopsids, is currently interpreted as sharing a single common origin due to their similarity and unique function. An alternative hypothesis of convergent evolution in these ensiferan groups has challenged this common view, but remained controversial because of competing interpretations of wing venation. Here we propose another hypothesis for the widely and long debated homology of ensiferan stridulatory apparatus, performing the first 3D reconstruction of hidden structures at the wing bases. This approach allowed defining the homology of each vein from its very origin rather than after its more distal characteristics, which may be subjected to environmental pressure of selection. The stridulatory apparatus involves different veins in these four singing clades. In light of the most recent phylogenetic evidence, this apparatus developed four times in Ensifera, illustrating extraordinary convergent evolutions between closely related clades, by far exceeding the number of evolutionary steps ever proposed for calling ability in this group.