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Despite the fact that almost all historians today make use of such online tools as Google Books and digitised primary source archives, it is still considered unusual to make computer software a core part of one's methodology for learning about the past. This paper makes the case for the use of digital mapping as a tool which allows and encourages us to ask new questions of long-studied areas of history, and to pass knowledge on to others in new ways. It addresses and answers some criticisms that are commonly presented against digital mapping as a methodology, as well as exploring the benefits of the use of digital maps through the discussion of a previous project carried out by the author, in which a map was made and analysed showing popular political activity in Manchester and its surrounding areas in the 1790s.

Este artículo contiene 16 páginas, 5 figuras. ; DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines. ; This research was funded by the projects PopCOmics (CTM2017-88080, MCIN/AEI/10.13039/ 501100011033 and ``ERDF A way of making Europe'', EU), MARGECH (PID2020- 118550RB, MCIN/AEI/10.13039/501100011033), and BigPark (OAPN, 2462/2017) from the Spanish Government. The publication charges for this article have been funded by a grant from the publication fund of UiT The Arctic University of Norway. ; Peer reviewed

Este artículo contiene 24 páginas, 7 figuras, 1 tabla. ; Background: The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. Results: Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in different orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little influence on the final outcome. Conclusions: We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies. ; This study has been funded by Project PopCOmics (CTM2017-88080, MCIU/AEI/FEDER/UE) and project BigPark (Autonomous Organism of National Parks, OAPN 2462/2017) from the Spanish Government. ; Peer reviewed

Este artículo contiene 13 páginas, 9 figuras, 3 tablas. ; We analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds. ; This research was funded by projects Metabarpark and CORCLIM from the Spanish National Parks Autonomous Agency (OAPN 1036/ 2013 and 766S/2012), and ChallenGen CTM2013-48163 and ANIMA CGL2016-76341-R projects from the Spanish Government. OSW is currently funded by project SeaDNA, NE/N005759/1 grant from the Natural Environment Research Council (NERC). ; Peer reviewed

Este artículo contiene 30 páginas, 9 figuras, 2 tablas. ; Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present.Wedeveloped aDNAmetabarcoding protocol for biodiversity characterization of structurally complex natural marine hardbottom communities. We used two molecular markers: the ``Leray fragment'' of mitochondrial cytochrome c oxidase (COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans. The 18S marker lacks species-level resolution and thus cannot be recommended to assess the detailed taxonomic composition of these communities. Our new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities. ; This work was funded by projects Metabarpark from the Spanish National Parks Autonomous Agency (OAPN project 1036-2013) and ChallenGen CTM2013-48163 and PopComics CTM2017-88080 from the Spanish Government. ; Peer reviewed

12 páginas, 5 figuras, 3 tablas. ; We studied the reproductive cycle of the sea urchin Arbacia lixula in a subtidal population from northeast Spain over four years using a gonadosomatic index (GSI) and gonad histology. Our results show that the GSI of A. lixula follows a seasonal cycle which peaks in May– July and attains its lowest values in October–November every year. The time course of the GSI matched closely the photoperiod cycle. We also found a remarkable interannual variability in the maximum value of GSI, which correlated with mean water temperature during the gonad growth period (winter and spring). Gonad histology was also in agreement with a single gametogenic cycle per year in this species. We explored the application of circular statistics to present and analyse gonadal development data, which allowed us to adequately handle the high intraindividual variability detected, with several developmental stages commonly found within the same gonad. The picture that emerged is one of a gametogenic timing driven by photoperiod, while the amount of reproductive output is determined by temperature. This is coherent with the tropical origin of the species and lends support to recent warnings about an increase in the abundance of this species in the Mediterranean as a result of global warming, with associated increased impact potential in sublittoral communities. ; This work was funded by projects CTM2010-22218 from the Spanish Government, 2009SGR-484 from the Catalan Government, BIOCON 08-187/09 from BBVA Foundation and 287844 (COCONET) of the European Community's Seventh Framework Programme (FP7/2007–2013). ; Peer reviewed

We analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds ; This research was funded by projects Metabarpark and CORCLIM from the Spanish National Parks Autonomous Agency (OAPN 1036/2013 and 766S/2012), and ChallenGen CTM2013-48163 and ANIMA CGL2016-76341-R projects from the Spanish Government. OSW is currently funded by project SeaDNA, NE/N005759/1 grant from the Natural Environment Research Council (NERC)

8 páginas, 7 figuras, 5 tablas. ; We studied the effects of temperature and pH on larval development, settlement and juvenile survival of a Mediterranean population of the sea urchin Arbacia lixula. Three temperatures (16, 17.5 and 19 °C) were tested at present pH conditions (pHT 8.1). At 19 °C, two pH levels were compared to reflect present average (pHT 8.1) and near-future average conditions (pHT 7.7, expected by 2100). Larvae were reared for 52-days to achieve the full larval development and complete the metamorphosis to the settler stage. We analyzed larval survival, growth, morphology and settlement success. We also tested the carry-over effect of acidification on juvenile survival after 3 days. Our results showed that larval survival and size significantly increased with temperature. Acidification resulted in higher survival rates and developmental delay. Larval morphology was significantly altered by low temperatures, which led to narrower larvae with relatively shorter skeletal rods, but larval morphology was only marginally affected by acidification. No carry-over effects between larvae and juveniles were detected in early settler survival, though settlers from larvae reared at pH 7.7 were significantly smaller than their counterparts developed at pH 8.1. These results suggest an overall positive effect of environmental parameters related to global change on the reproduction of A. lixula, and reinforce the concerns about the increasing negative impact on shallow Mediterranean ecosystems of this post-glacial colonizer. ; This work was funded by projects CTM2010- 22218 from the Spanish Government, BIOCON 08-187/09 from BBVA Foundation, EPOCA (European Project on Ocean Acidification) N211384 from the European Community's Seventh Framework Programme (FP7/2007-2013) and grants from ASSEMBLE (Association of European Marine Biology Laboratories) and KVA (The Royal Swedish Academy of Sciences). OSW was funded by a grant from AGAUR BE-DGR 2012 (Generalitat de Catalunya). SD is funded by the CeMEB and supported by a Linnaeus-grant from the Swedish Research Councils VR and Formas ; Peer reviewed