Biogeography and diversification of Rhegmatorhina (Aves: Thamnophilidae): Implications for the evolution of Amazonian landscapes during the Quaternary

© 2018 John Wiley & Sons Ltd Aim: To test the importance of alternative diversification drivers and biogeographical processes for the evolution of Amazonian upland forest birds through a densely sampled analysis of diversification of the endemic Amazonian genus Rhegmatorhina at multiple taxonomic and temporal scales. Location: Amazonia. Taxon: Antbirds (Thamnophilidae). Methods: We sequenced four mtDNA and nuclear gene regions of 120 individuals from 50 localities representing all recognized species and subspecies of the genus. We performed molecular phylogenetic analyses using both gene tree and species tree methods, molecular dating analysis and estimated population demographic history and gene flow. Results: Dense sampling throughout the distribution of Rhegmatorhina revealed that the main Amazonian rivers delimit the geographic distribution of taxa as inferred from mtDNA lineages. Molecular phylogenetic analyses resulted in a strongly supported phylogenetic hypothesis for the genus, with two main clades currently separated by the Madeira River. Molecular dating analysis indicated diversification during the Quaternary. Reconstruction of recent demographic history of populations revealed a trend for population expansion in eastern Amazonia and stability in the west. Estimates of gene flow corroborate the possibility that migration after divergence had some influence on the current patterns of diversity. Main Conclusions: Based on broad-scale sampling, a clarification of taxonomic boundaries, and strongly supported phylogenetic relationships, we confirm that, first, mitochondrial lineages within this upland forest Amazonian bird genus agree with spatial patterns known for decades based on phenotypes, and second, that most lineages are geographically delimited by the large Amazonian rivers. The association between past demographic changes related to palaeoclimatic cycles and the historically varying strength and size of rivers as barriers to dispersal may be the path to the answer to the long-standing question of identifying the main drivers of Amazonian diversification

Non-native fish species in the North Aegean Sea: a review of their distributions integrating unpublished fisheries data

Fisheries-dependent data and information gathered through fisheries-related scientific surveys can significantly contribute to research on the patterns and processes underlying marine biological invasions and their interactions with fisheries. This study presents an overview of the presence of non-native fish species in the North Aegean Sea, offering insights into their distributions and impact on fisheries. The findings are based on a comprehensive compilation of commercial fisheries-dependent and scientific survey data collected in Greece from 2016 to 2023, along with a systematic review of the international scientific literature. The study resulted in the documentation of the presence of 37 non-native fish species, including several recorded for the first time in the area. The results suggest that non-native fish species invasions in the North Aegean Sea are dynamic. Although most species were classified as casual, and the frequencies of occurrence as well as the quantities in commercial fisheries catches of established species are smaller than in the South Aegean Sea, species introductions and the extent of occurrence and area of occupancy of several species have been increasing since the 2000s. The significance of non-native fish species is becoming increasingly relevant to commercial fisheries in the study area. This is particularly evident in the Northeastern Aegean Sea, where catches of non-native species are on the rise, and new species with potential commercial value have emerged in recent years

Development of a quantitative colorimetric LAMP assay for fast and targeted molecular detection of the invasive lionfish Pterois miles from environmental DNA

The Mediterranean basin has faced an increased influx of invasive species since the Suez Canal expansion in 2015. The invasive lionfish species, Pterois miles, has rapidly established new populations in the Eastern Mediterranean Sea, impacting local fish biodiversity. Here, we have developed a new, fast (< 35 min) molecular approach to detect and quantify P. miles environmental DNA (eDNA) in combination with a portable device for field-based analysis. Using a species-specific real-time colorimetric loop-mediated isothermal amplification (qcLAMP) for the cytochrome oxidase subunit 1 (COI) gene, we demonstrate a high sensitivity with a limit of detection of 0.002 ng DNA per reaction, equivalent to only 50 copies of the COI gene. The assay is specific to the target in the presence of closely related and co-occurring species, and it is quantitative over five orders of magnitude. We validated the assay using aquarium water samples and further demonstrated its utility on natural eDNA samples collected from locations around the island of Crete where P. miles had been sighted. P. miles was indeed detected in three out of nine locations, two nature reserves and a closed bay. Lack of detection in the remaining locations suggests that populations are still at a low density. We also demonstrate the feasibility of P. miles eDNA qualitative detection directly from the filter used to collect eDNA-containing particles, completely omitting DNA extraction. Overall, we present a new approach for fast and targeted eDNA quantification. The developed LAMP assay together, with the quantitative real-time colorimetric detection approach, open new possibilities for monitoring invasive P. miles in the field

First record of the marbled ray, Dasyatis marmorata (Elasmobranchii: Dasyatidae), from Greece (central Aegean Sea)

Currently, seven dasyatid species have been described in the Mediterranean Sea: Bathytoshia lata, Dasyatis marmorata, Dasyatis pastinaca, Dasyatis tortonesei, Himantura uarnak, Pteroplatytrygon violacea and Taeniura grabata. Papaconstantinou (2014) listed four species of Dasyatidae occurring in Greece (P. violacea, D. pastinaca, D. tortonesei and D. centroura; the latter was a case of misidentification and it is currently identified as B. lata, according to genetic analysis). However, the marbled stingray (D. marmorata) was not amongst them. Here, the presence of D. marmorata was examined for the first time in Greece.The present study provides updated information on the geographical distribution of D. marmorata in the Eastern Mediterranean Sea. A juvenile male stingray was captured in February 2019, during an onshore survey in Maliakos Gulf, located in the central Aegean Sea, Greece. The ray was examined at the Fisheries laboratory of the Hellenic Centre for Marine Research (HCMR) in Athens and was identified as D. marmorata. Morphological characters were recorded and DNA barcoding was applied to confirm the species identification. The combination of the two methods verified the occurrence of the marbled ray in the Greek waters. This is the first record of D. marmorata from the Aegean Sea

Lionfish Diet Composition at Three Study Sites in the Aegean Sea: An Invasive Generalist?

The diet of the lionfish (Pterois miles), an invasive species in the Aegean Sea, was examined by collecting stomach content data from fish collected in three study sites in the Aegean Sea (southern Crete, Kastellorizo, and Nysiros islands). Prey composition in terms of numerical abundance and frequency of occurrence was used to compare lionfish’s diet between these sites. Lionfish largely preyed upon teleosts (4% to 83% numerical abundance and 16% to 58% frequency of occurrence, depending on the site) and decapods (12% to 95% numerical abundance and 11% to 81% frequency of occurrence). The most important teleost families in lionfish’s diet were Gobiidae, Labridae, and Scorpaenidae, while decapods and especially the family Scyllaridae and the genus Plesionika were the dominant decapod prey items. The lionfish was found to be an especially successful generalist across the study sites, an opportunistic, predatory species overall, and at the same time, at a local level, it seems to be an equally successful specialist that could increase the predation mortality of already stressed prey populations and can be a serious threat to endemic, critically endangered, and/or commercially important species

Biodiversity of dogfishes (genus Squalus) in the eastern Atlantic and Mediterranean Sea - a molecular perspective

V Jornadas Ibéricas de Ictiología SIBIC, Conhecer para preservar, 24-27 June 2014, Lisboa .-- 1 pageThe genus Squalus, or dogfishes, includes many coastal shark species commonly caught in commercial fisheries around the world. Despite their abundance, species diversity within Squalus is still poorly understood. In fact, recent studies on the Indo-Pacific region have described several new species, highlighting the need for revisionary taxonomic work clarifying and discriminating the different taxa. Less attention has been paid to the diversity of Squalus in the Atlantic Ocean sensu lato, where only five species have been reported out of the 27 species currently accepted for the genus, namely S. acanthias, S. blainville, S. megalops, S. mitsukurii, and S. cubensis. Notwithstanding, species identification across the region appears to be very inconsistent and there is great taxonomic uncertainty among some of the Atlantic Squalus, particularly concerning the status of S. megalops and S. blainville. This situation has contributed to the present confusion in terms of the actual species composition in the region, thus compromising the effectiveness and adequacy of any management and conservation efforts. In an initial effort to contribute to a comprehensive and clear alpha taxonomy of this highly diverse worldwidedistributed genus, we applied molecular genetic markers (mitochondrial cytochrome oxidase I and NADHdehydrogenase 2) aiming to evaluate the number of discrete genetic lineages within Squalus in the eastern Atlantic and Mediterranean Sea. Furthermore, we compared this regional lineage diversity to that found worldwide, using publicly available data. Our results confirm the inconsistencies in species identification in the eastern Atlantic and Mediterranean. For instance, putative S. blainville and S. megalops sampled across the Mediterranean and along the eastern Atlantic from Portugal to South Africa clustered together in a single clade, sister to the clade of the Australian S. megalops (i.e. from the type location). Our data also indicate the presence of three highly divergent genetic lineages of Squalus in the Mediterranean Sea, comprising three distinct species. Furthermore, we found evidence of the presence of the S. cubensis lineage (currently described only for the western Atlantic) in the equatorial eastern AtlanticPeer Reviewe

Isolation and characterization of seventeen polymorphic microsatellite DNA markers from Elaenia ruficeps (Aves: Tyrannidae)

Seventeen new polymorphic microsatellites were isolated and characterized for the South American Rufous-crowned Elaenia, (Elaenia ruficeps). E. ruficeps is a bird commonly found in white sand vegetation, a naturally fragmented and threatened Amazonian habitat. The number of alleles per locus ranged from 2 to 20, whilst the observed and expected heterozygosities varied from 0.074 to 0.967 and from 0.173 to 0.919, respectively. Seven loci significantly deviated from Hardy–Weinberg equilibrium. Eleven microsatellite loci were cross-amplified in at least one additional Tyrannidae species. These microsatellite markers will be useful tools for further studies of avian population structure and genetic variability in this unique habitat. © 2014, Springer Science+Business Media Dordrecht

Phylogeography and population dynamics of Antbirds (Thamnophilidae) from Amazonian fluvial islands

Aim: To investigate the evolution of the avifauna associated to Amazonian fluvial islands, focusing on the Negro River archipelagos. Locations: Fluvial islands in the Amazon Basin. Methods: One generalist floodplain species (Hypocnemoides melanopogon) and three river island specialists (Myrmotherula assimilis, Myrmoborus lugubris and Thamnophilus nigrocinereus) were studied (Thamnophilidae). We sequenced two mitochondrial genes and genotyped eight microsatellite loci. Phylogenetic relationships among intraspecific lineages and divergence times were estimated using Bayesian Inference. Haplotype networks, AMOVA (analysis of molecular variance) and Mantel tests were used to verify the spatial organization of genetic diversity. Gene flow and population structure were evaluated using a dissimilarity index, Bayesian inference and allele frequencies. Historical demography was inferred through neutrality tests and Extended Bayesian skyline plots (EBSP). Results: River island specialists have evolved distinct lineages in different Amazonian tributaries, but exhibit very weak population structure within the Negro river basin. The generalist floodplain species had no population structure along the Amazon basin or within the Negro river basin. Signals of weak and recent (Pleistocene) population expansion were recovered for all species. Main conclusions: River islands specialists show stronger population structure within Amazonia than floodplain generalists. They show a common spatial and temporal pattern of divergence between populations from the Negro islands and western Amazonia (upper and middle Solimões), which may be related to Amazonian drainage evolution. Island specialists had low genetic diversity within the Negro basin, while the higher and unstructured diversity pattern found in the floodplain generalist species may be a consequence of higher dispersal caused by the seasonal flooding pulse. River islands populations have a recent and dynamic history of contact and isolation, with small historical fluctuations of population sizes, which is in sharp contrast with the patterns found in upland forest birds. © 2017 John Wiley & Sons Lt

Mucus : aiding elasmobranch conservation through non-invasive genetic sampling

Acknowledgements. The fieldwork for this study in Ireland was funded by a Heritage Council Wildlife Grant (Grant Reference 16759). This work received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. Thanks to Margaret Wallace for technical support, and Michaél Cottrell, Darren Craig, Laura Kavanagh, Lucy Hunt, Nick Massett and Ian O’Connor for help with fieldwork and sample collection.Peer reviewedPublisher PD

Species diversity in the cryptic abyssal holothurian Psychropotes longicauda (Echinodermata)

Despite the plethora of studies on swallow-water invertebrates, almost nothing is known about the evolution and population structure of deep-sea species at the global scale. The aim of this study was to assess phylogeographic patterns of a common and cosmopolitan, predominantly abyssal sea cucumber, Psychropotes longicauda, based on samples from the Atlantic, Southern, Indian and Pacific oceans. Sequences of the mitochondrial COI and 16S genes were analysed for 128 specimens of P. longicauda. In addition, temporal genetic variation was investigated at one site, the Porcupine Abyssal Plain, NE Atlantic Ocean over a period of 34 years. Two distinct lineages within the global distribution were identified. The sister clades probably could be classified as separate species based on the observed genetic divergence (>5.0%) and phylogenetic reconstruction with indications of a Southern Hemisphere origin. Moreover, significant population differentiation was detected between the North Atlantic and localities in both the Pacific and Indian oceans. No bathymetric structuring was detected among lineages. Temporal genetic shifts were detected in a time series of samples from 1977 to 2011. Our data confirm the previously suspected cryptic species diversity throughout the wide distributional range previously attributed to the single species P. longicauda. The presence of sympatric species in the North Pacific and Indian Oceans has been underestimated by previous morphological analyses. The differentiation at the population level detected in the main lineages among the four oceans could suggest restricted gene flow despite wide-scale dispersal potential of the species