scholarly journals Challenges in building barcode reference libraries for marine invertebrates exemplified by the genus Prionospio (Annelida: Spionidae)

2021 ◽  
Vol 4 ◽  
Author(s):  
Martin Hektoen ◽  
Torbjørn Ekrem ◽  
Torkild Bakken
Keyword(s):  
Sanger Sequencing ◽  
Marine Invertebrates ◽  
Limiting Factor ◽  
Success Rates ◽  
Molecular Tools ◽  
Bioindicator Species ◽  
North East ◽  
The North ◽  
Amplification Rate ◽  
Substantial Bias

The completeness of reference libraries is often a limiting factor in the effectiveness of biomonitoring using molecular tools. The fact that these libraries are often built upon Sanger sequencing can create a substantial bias due to poor primer fits and unoptimized lab protocols. Some taxa of marine macroinvertebrates are known to be notoriously difficult to sequence using traditional, PCR-based means, and only about 15% of the known bioindicator species world-wide have publicly available sequences for any genetic marker (Aylagas et al. 2014). The Barcode of Life Data System (BOLD) indicates an amplification rate between 46% and 85% of the barcode region of COI for the most commonly used marine invertebrates that indicate pollution in the North East Atlantic (Capitellidae, Cirratulidae, Dorvilleidae, Spionidae and Tubificidae within Annelida, and Thyasiridae within Mollusca). A currently on-going integrative taxonomic study on Prionospio Malmgren, 1867 (Spionidae, Annelida) exemplifies the extensive issues of utilizing Sanger sequencing on marine invertebrates. The barcode region of COI was attempted amplified using five primer pairs: three designed to be universal for marine invertebrates (Folmer et al. 1994, Geller et al. 2013, Lobo et al. 2013), one specialized on polychaetes (Carr et al. 2011) and one self-designed. In addition, two DNA polymerases were tested (TaKaRa Ex Taq HS and Qiagen HotStarTaq) and three annealing temperatures. Only five sequences of COI were obtained from a total of 255 PCR reactions (2% success rate). Other genetic markers showed better amplification rates: 58% for 16S rDNA, and more than 90% success rates for 28S rDNA and Histone H3. This illustrates the importance of having more than one marker in mind when seeking to complete reference libraries, and the potential effectiveness of a multi-marker approach in molecular biomonitoring surveys. As sequencing costs decrease, utilizing shallow shotgun-based sequencing (genome skimming) on problematic groups such as Prionospio to bypass issues regarding unfit primers is also becoming a viable option.

scholarly journals Aedes species (Diptera: Culicidae) ecological and host feeding patterns in the north-eastern parts of South Africa, 2014–2018

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
M. M. Guarido ◽  
M. A. Riddin ◽  
T. Johnson ◽  
L. E. O. Braack ◽  
M. Schrama ◽  
...  
Keyword(s):  
South Africa ◽  
Limiting Factor ◽  
Sequence Information ◽  
Host Feeding ◽  
Entomological Surveillance ◽  
North East ◽  
The North ◽  
North Eastern ◽  
Control And Prevention ◽  
The Impact

Abstract Background There is a paucity of recent data and knowledge on mosquito diversity and potential vectors of arboviruses in South Africa, with most of the available data dating back to the 1950s–1970s. Aedes and Culex species are the major vectors of some of the principal arboviruses which have emerged and re-emerged in the past few decades. Methods In this study we used entomological surveillance in selected areas in the north-eastern parts of South Africa from 2014 to 2018 to assess mosquito diversity, with special emphasis on the Aedes species. The impact of trap types and environmental conditions was also investigated. Identification of the blood meal sources of engorged females collected during the study period was carried out, and DNA barcodes were generated for selected species. Results Overall, 18.5% of the total Culicidae mosquitoes collected belonged to the genus Aedes, with 14 species recognised or suspected vectors of arboviruses. Species belonging to the Neomelaniconion subgenus were commonly collected in the Bushveld savanna at conservation areas, especially Aedes mcintoshi and Aedes circumluteolus. Aedes aegypti was present in all sites, albeit in low numbers. Temperature was a limiting factor for the Aedes population, and they were almost exclusively collected at temperatures between 18 °C and 27 °C. The cytochrome oxidase subunit I (COI) barcode fragment was amplified for 21 Aedes species, and for nine of these species it was the first sequence information uploaded on GenBank. Conclusion This study provides a better understanding of the diversity and relative abundance of Aedes species in the north-east of South Africa. The information provided here will contribute to future arboviral research and implementation of efficient vector control and prevention strategies. Graphical abstract

scholarly journals Spatio-Temporal Variability of Harbor Porpoise Life History Parameters in the North-East Atlantic

2020 ◽  
Vol 7 ◽  
Author(s):  
Sinéad Murphy ◽  
Marie A. C. Petitguyot ◽  
Paul D. Jepson ◽  
Rob Deaville ◽  
Christina Lockyer ◽  
...  
Keyword(s):  
Life History ◽  
Average Length ◽  
Mortality Data ◽  
Limiting Factor ◽  
Harbor Porpoise ◽  
East Atlantic ◽  
Extrinsic Factors ◽  
Early Maturation ◽  
North East ◽  
The North

Harbor porpoises exhibit early maturation, relatively short gestation/lactation periods and a faster rate of reproduction as compared to other cetacean species. Intrinsic and extrinsic factors can influence both population vital rates and population structure, which ultimately cause changes in dynamics within and between populations. Here, we undertook a retrospective analysis of mortality data collected over a 24-year period for assessing life history traits of the North-east Atlantic harbor porpoise population. We use time-period specific models for key life history relationships that considered cause of death of individuals (as a proxy for health status), sex and management unit (MU). Sexual variation in asymptotic length, asymptotic age, average length at 50% maturity (L50) and average age at 50% maturity (A50) were observed, with females attaining a larger asymptotic length, larger L50, and delaying attainment of both sexual and physical maturity, compared to males. While females are constrained in their minimum body size due to giving birth to proportionally larger offspring, males exhibited more plasticity in size at sexual maturity, enabling re-allocation of available energy resources toward reproduction. Data were then used to compare biological parameters among two porpoise MUs in United Kingdom waters, both of which in the current study exhibited reduced reproductive rates compared to other geographic regions. In both MUs, females significantly increased their A50 and males significantly declined in their L50. An increase in the age at asymptotic length was also observed in both sexes, along with a significant decline in the Gompertz growth rate parameter that was more apparent in the female data. While availability of suitable prey resources may be a limiting factor, a combination of other factors cannot be ruled out. Porpoises in the Celtic and Irish Seas MU were significantly larger in their maximum length, asymptotic length and L50 compared to porpoises in the North Sea MU throughout the study period, suggesting limited gene flow between these two MUs. These results justify the maintenance of these harbor porpoise MUs or assessment units, as two separate units, within the range of the North-east Atlantic population, and for indicator assessments under the EU’s Marine Strategy Framework Directive.

Candidate cases of poecilogony in Neogastropoda: implications for the systematics of the genus Raphitoma Bellardi, 1847

2020 ◽  
Author(s):  
Valeria Russini ◽  
Riccardo Giannuzzi-Savelli ◽  
Francesco Pusateri ◽  
Jakov Prkic ◽  
Giulia Fassio ◽  
...  
Keyword(s):  
Larval Development ◽  
Intraspecific Variation ◽  
Sibling Species ◽  
Marine Invertebrates ◽  
Ancestral State ◽  
Reciprocal Monophyly ◽  
Evolutionary Transitions ◽  
North East ◽  
The North ◽  
Evolutionary Aspects

Poecilogony is the intraspecific variation in developmental mode, with larvae of different types produced by the same individual, population or species. It is very rare among marine invertebrates, and in gastropods has long been described only in a few opisthobranchs. The physiological and regulatory mechanisms underlying larval evolutionary transitions, such as loss of planktotrophy that occurred repeatedly in many caenogastropod lineages, are still largely unknown. We have studied the inter- v. intraspecific variation in larval development in the north-east Atlantic neogastropod genus Raphitoma Bellardi, 1847, starting with an iterative taxonomy approach: 17 morphology-based Preliminary Species Hypotheses were tested against a COI molecular-distance-based method (ABGD), and the retained species hypotheses were eventually inspected for reciprocal monophyly on a multilocus dataset. We subsequently performed an ancestral state reconstruction on an ultrametric tree of the 10 Final Species Hypotheses, time-calibrated by fossils, revealing that the interspecific changes were planktotrophy > lecithotrophy, and all have occurred in the Pleistocene, after 2.5 million years ago. This is suggestive of a major role played by Pleistocene Mediterranean oceanographic conditions – enhanced oligotrophy, unpredictable availability of water column resources – likely to favour loss of planktotrophy. Within this group of species, which has diversified after the Miocene, we identified one pair of sibling species differing in their larval development, Raphitoma cordieri (Payraudeau, 1826) and R. horrida (Monterosato, 1884). However, we also identified two Final Species Hypotheses, each comprising individuals with both larval developmental types. Our working hypothesis is that they correspond to one or two poecilogonous species. If confirmed by other nuclear markers, this would be the first documentation of poecilogony in the Neogastropoda, and the second in the whole Caenogastropoda. Although sibling species with different developmental strategies may offer good models to study some evolutionary aspects, poecilogonous taxa are optimally suited for identifying regulatory and developmental mechanisms underlying evolutionary transitions.

scholarly journals Trends in the numbers of red kangaroos and emus on either side of the South Australian dingo fence: evidence for predator regulation?

2000 ◽  
Vol 27 (3) ◽  
pp. 269 ◽  
Author(s):  
A. R. Pople ◽  
G. C. Grigg ◽  
S. C. Cairns ◽  
L. A. Beard ◽  
P. Alexander
Keyword(s):  
Canis Lupus ◽  
Predation Rate ◽  
Aerial Survey ◽  
Limiting Factor ◽  
The South ◽  
North East ◽  
The North ◽  
Red Kangaroo ◽  
Dromaius Novaehollandiae ◽  
Over Time

Most of Australia’s sheep rangelands are enclosed by a dingo-proof fence. Within these rangelands, where dingoes (Canis lupus dingo) are rare, red kangaroos (Macropus rufus) are considered to be food limited because their numbers respond to fluctuations in pasture biomass that are driven by highly variable rainfall. Outside this region, where dingoes are common, kangaroo densities are generally substantially lower, suggesting that dingoes are an important limiting factor. However, it is unclear whether dingoes can regulate kangaroo populations. In this study, red kangaroo and emu (Dromaius novaehollandiae) numbers were monitored for varying periods during 1978–92 by aerial survey on both sides of the dingo fence in three areas in the north of the South Australian pastoral zone. Densities of red kangaroos and emus were lower outside the fence, although the disparity varied between areas and over time. The similarity in the environments on both sides of the fence and the marked step in kangaroo density at the fence are consistent with dingoes strongly limiting these prey populations. In the north-east of the pastoral zone, where kangaroo and emu densities are greatest, the contrast in density across the fence was most pronounced. Furthermore, the trends in density over time differed across the fence. Outside the fence, red kangaroos and emus remained at low densities following drought as dingo numbers increased. Inside the fence, red kangaroo and emu populations showed a ‘typical’ post-drought recovery. The data therefore suggest that, in some situations, dingoes may not simply limit red kangaroo and emu populations, but also regulate them. For this to occur, predation rate would need to be density dependent at low prey densities. The availability of alternative prey, and the reduction in the numbers of all prey during drought may provide the mechanism.

Ras al Khaimah: further archaeological discoveries

Antiquity ◽  
1976 ◽  
Vol 50 (200) ◽  
pp. 216-222
Author(s):  
Beatrice De Cardi
Keyword(s):  
United Arab Emirates ◽  
The State ◽  
Focused Attention ◽  
North East ◽  
The North ◽  
History Of ◽  
The City

Ras a1 Khaimah is the most northerly of the seven states comprising the United Arab Emirates and its Ruler, H. H. Sheikh Saqr bin Mohammad al-Qasimi, is keenly interested in the history of the state and its people. Survey carried out there jointly with Dr D. B. Doe in 1968 had focused attention on the site of JuIfar which lies just north of the present town of Ras a1 Khaimah (de Cardi, 1971, 230-2). Julfar was in existence in Abbasid times and its importance as an entrep6t during the sixteenth and seventeenth centuries-the Portuguese Period-is reflected by the quantity and variety of imported wares to be found among the ruins of the city. Most of the sites discovered during the survey dated from that period but a group of cairns near Ghalilah and some long gabled graves in the Shimal area to the north-east of the date-groves behind Ras a1 Khaimah (map, FIG. I) clearly represented a more distant past.

Lichens in the North-East regions of Cyprus

1999 ◽  
Vol 110 (5-6) ◽  
pp. 455-463 ◽  
Author(s):  
S. Güvenç ◽  
Ş Öztürk
Keyword(s):  
North East ◽  
The North

TBE in Italy

2019 ◽  
Author(s):  
Valentina Tagliapietra ◽  
Flavia Riccardo ◽  
Giovanni Rezza
Keyword(s):  
Case Series ◽  
East Part ◽  
Mountainous Regions ◽  
North East ◽  
The North ◽  
Tick Borne Encephalitis ◽  
Low Incidence

Italy is considered a low incidence country for tick-borne encephalitis (TBE) in Europe. Areas at higher risk for TBE in Italy are geographically clustered in the forested and mountainous regions and provinces in the north east part of the country, as suggested by TBE case series published over the last decade.

TBE in Italy

2020 ◽  
Keyword(s):  
Surveillance System ◽  
Ad Hoc ◽  
National Level ◽  
Case Series ◽  
Incidence Rates ◽  
Mountainous Regions ◽  
North East ◽  
The North ◽  
Tick Borne Encephalitis ◽  
Low Incidence

Italy is considered a low-incidence country for tick-borne encephalitis (TBE) in Europe.1 Areas at higher risk for TBE in Italy are geographically clustered in the forested and mountainous regions and provinces in the north east part of the country, as suggested by TBE case series published over the last decade.2-5 A national enhanced surveillance system for TBE has been established since 2017.6 Before this, information on the occurrence of TBE cases at the national level in Italy was lacking. Both incidence rates and the geographical distribution of the disease were mostly inferred from endemic areas where surveillance was already in place, ad hoc studies and international literature.1

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