identifier	taxonID	type	CVterm	format	language	title	description	additionalInformationURL	UsageTerms	rights	Owner	contributor	creator	bibliographicCitation
240787B5FF9CFFC6AA4EFC0D0EECFCD3.text	240787B5FF9CFFC6AA4EFC0D0EECFCD3.taxon	http://purl.org/dc/dcmitype/Text	http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription	text/html	en	Daphnia	<div><p>ALPINE DAPHNIA</p> <p>Firstly, COI sequences of melanic individuals were compared using the Basic Local Alignment Search Tool (BLAST, http://blast.ncbi.nlm.nih.gov/Blast.cgi, Altschul et al., 1997) with all homologous sequences available in GenBank (http://www.ncbi.nlm.nih.gov/GenBank/) using the nucleotide blast (nblast) with default parameters. Sequences were also compared with the Barcoding of Life Database (BOLD, http://www.barcodinglife.com/index.php/databases, Ratnasingham &amp; Hebert, 2007), using the engine BOLD-IDS for identification and checking the ‘All Barcode Records on BOLD’ option. Genetic distances amongst different COI haplotypes were estimated using a standard DNA barcoding method (i.e. Kimura’s two-parameter model correction, K2P, Kimura, 1980).</p> <p>Phylogenetic relationships of the newly discovered pigmented populations were inferred both by maximum likelihood (ML) criterion and posterior probability statistic based on Bayesian inference (BI). We based our analyses only on the ND5 fragment (540 bp) because no COI sequences were available for the distinct geographical EuPC lineages and haplogroups. Homologous sequences were retrieved from GenBank, including 139 samples representative of all EuPC populations analysed so far (Marková et al., 2007, 2013; Vergilino et al., 2009, 2011; Dufresne et al., 2011). Available sequences from the eight high-mountain populations sampled on the Alps (N = 14, see Table 1 and Fig. 3 for geographical distribution of samples) were used as a comparison to infer phylogenetic relationships of melanic individuals, together with 17 and 28 sequences belonging to the PYR and the HTM haplogroups, respectively (Table 1). In order to validate morphological taxonomy, we also selected four sequences of D. middendorffiana (MIDD) and 15 sequences of Nearctic D. pulicaria (NAPC), including haplotypes previously found in European pigmented populations (see Table 1 for accession numbers). Two sequences of European D. pulex Leydig, 1860 (EuPX) were considered as the outgroup, and the final alignment was performed using the CLUSTALW module of BIOEDIT 7.1 (Hall, 1999).</p> <p>The best-fit model Hasegawa-Kishino-Yano (Hasegawa, Kishino &amp; Yano, 1985) with gamma substitution parameter (+ G, α = 0.5490) was selected amongst 88 possible models of evolution according to the corrected Akaike information criterion (AICc; Hurvich &amp; Tsai, 1989) implemented in jMODELTEST 0.1.1 (Guindon &amp; Gascuel, 2003; Posada, 2008). ML was performed using the BEST approach implement- ed in PhyML 3.0 (Guindon et al., 2010), which combines the nearest-neighbour interchanges with the subtree pruning and regrafting algorithms to maximize tree likelihood. Statistical support for nodes was quantified by a nonparametric bootstrap test using 1000 replicates (Felsenstein, 1985) and estimating Shimodaira-Hasegawa (hereafter SH)-like approximate likelihood ratio probabilities. BI was performed using MrBayes 3.2 (Ronquist et al., 2012), which calculates posterior probabilities using a Markov chain Monte Carlo sampling approach (Huelsenbeck et al., 2001; Altekar et al., 2004). Two independent runs implementing four chains were carried out starting from random trees and with a total length of 10 × 106 generations for each one. Trees were sampled every 100th generations and the earliest 20% of the data sampled were discarded as burn-in after checking tracer plots in TRACER 1.5 (Rambaut &amp; Drummond, 2007). Convergence of chains upon a stationary distribution was also checked by monitoring the standard deviation of split frequencies (= 0.0034) and the potential scale reduction factor (= 1.000). Average genetic sequence divergences (and relative standard errors, SE) between distinct lineages and haplogroups found in European mountain regions were calculated by uncorrected pairwise genetic distance estimations (p -distance) using MEGA 5 and setting 1000 bootstrap replicates (Tamura et al., 2011).</p> <p>Finally, intraspecific relationships amongst highmountain populations sampled in the Alps (including pigmented Daphnia specifically sampled for this study) were visualized by haplotype network analysis using TCS 1.21 (Clement, Posada &amp; Crandall, 2000) after collapsing individual sequences into haplotypes using the online web tool DnaCollapser 1.0 available on the FaBox site (http://users-birc.au.dk/biopv/php/fabox/). A parsimony criterion following the algorithm by Templeton, Crandall &amp; Sign (1992) was used to estimate the number of mutational steps by which pairwise haplotypes differ, assessing also the minimum number of connections required to join together all the haplotypes in a single gene network.</p> </div>	https://treatment.plazi.org/id/240787B5FF9CFFC6AA4EFC0D0EECFCD3	Public Domain	No known copyright restrictions apply. See Agosti, D., Egloff, W., 2009. Taxonomic information exchange and copyright: the Plazi approach. BMC Research Notes 2009, 2:53 for further explanation.		Plazi	Bellati, Adriana;Tiberti, Rocco;Cocca, Walter;Galimberti, Andrea;Casiraghi, Maurizio;Bogliani, Giuseppe;Galeotti, Paolo	Bellati, Adriana, Tiberti, Rocco, Cocca, Walter, Galimberti, Andrea, Casiraghi, Maurizio, Bogliani, Giuseppe, Galeotti, Paolo (2014): A dark shell hiding great variability: a molecular insight into the evolution and conservation of melanic Daphnia populations in the Alps. Zoological Journal of the Linnean Society 171 (4): 697-715, DOI: 10.1111/zoj.12151, URL: http://dx.doi.org/10.1111/zoj.12151
240787B5FF97FFC3A8ABFAE40CD4FA6C.text	240787B5FF97FFC3A8ABFAE40CD4FA6C.taxon	http://purl.org/dc/dcmitype/Text	http://rs.tdwg.org/ontology/voc/SPMInfoItems#GeneralDescription	text/html	en	Daphnia pulicaria	<div><p>DAPHNIA PULICARIA IN THE ALPS</p> <p>As already observed for other EuPC populations inhabiting remote freshwater ecosystems of western and eastern European mountains, the alpine haplotypes are extremely diversified and show genetic uniqueness compared with all of the other lineages. Indeed, both phylogenetic inference and haplotype network analyses suggest they are actually endemic to this mountain region, none of them occurring in any other European population considered (Figs 2–4). The main outcome of our molecular analysis was however the discovery that our melanic populations belong to two deeply differentiated phylogeographical lineages (ALPS-1 and ALPS- 2, Fig. 2), which probably underwent alternative colonization patterns in this region after the start of the deglaciation of the Alps cirque lakes (fewer than 10 000 years ago). Indeed, despite the short geographical distances between our studied populations (5 km on average), the genetic differentiation amongst COI sequences found between melanic populations assigned to distinct lineages (2.4%) was at least twice as high as the estimated divergence between alpine and lowland haplotypes (1%).</p> <p>Noteworthily, the analysis of the four melanic populations recently discovered within the GPNP, in the Western Italian Alps, allows us to draw wider conclusions concerning the previously hidden evolutionary history of rare alpine the D. pulex group populations. Indeed, melanic forms inhabiting the three alpine lakes located in the valley of the Dora di Savarenche river (Fig. 1) show high genetic relatedness with circumpolar populations (all together constituting a clade that we tentatively named the ‘Boreal’ clade), whereas the only melanic populations located in the catchment of the river Orco (Lillet, Fig. 1) falls into a deeply differentiated ‘Alpine’ clade with more southern genetic affinities. This ancient alpine lineage probably diverged in a glacial refugium located in the same mountainous area, but at lower altitudes than the present distribution, as already suggested for the other ancient EuPC lineage inhabiting western European mountains (i.e. the PYR haplogroup). By contrast, alpine representatives of the ‘Boreal’ clade should derive from a northern ancestor, which spread southwards from the Arctic and then persisted only in relict populations in the Alps. So far, the closest extant populations of this boreal lineage (ALPS-1) are known from circumpolar islands (Iceland and Svalbard), located over 2500 and 4000 km away from the European Alps, respectively (Marková et al., 2013).</p> <p>The occurrence of boreal haplotypes in southern European alpine lakes is remarkable as to date this has never been reported by previous authors. Nevertheless, the persistence of boreal elements resulting from ancient postglacial colonizations of European mountain lakes has been already reported for members of the D. longispina group, particularly Daphnia lacustris Sars, 1862, from the High Tatra Mountains (Petrusek et al., 2007) and the persistence of arctic-boreal elements is also well documented in both alpine flora and fauna (e.g. Mani, 1968). Alpine representatives of the ‘Boreal’ clade may derive from a rare case of a recent long-range dispersal of circumpolar EuPC individuals from their current distributional range, or (in a more fascinating scenario) from much earlier postglacial colonization patterns. Interestingly, the area surrounding the three lakes Nivolet and Trebecchi Superiore/ Inferiore is renowned for being regularly frequented by waders such as the Eurasian dotterel (Charadrius morinellus Linnaeus, 1758) during the postbreeding migration towards their winter quarters in northern Africa (Gruppo Piemontese Studi Ornitologici, 2013). As the breeding distribution of this arctic species reaches the northernmost part of Scandinavia (i.e. the Varanger peninsula, Norway; Lüker, Kraatz &amp; Kraaz, 2011), we can speculate that at the end of glaciations migratory birds visiting alpine regions in southern Europe allowed the colonization of newly deglaciated lakes by arctic EuPC ancestors.</p> <p>The substantial genetic variation observed within the ALPS haplogroup (i.e. also including populations considered in previous studies) can be explained by local postglacial diversification and suggests that lakes of the alpine region were colonized from genetically divergent source populations. The genetic distinctiveness of the lakes further suggests that ancient genotypes might have quickly monopolized local resources, generating a priority effect against subsequent colonists (De Meester, 1996; De Meester et al., 2002). After ancestor populations were established, subsequent founder effects may have been major determinants of the present-day diversity, following a long-lasting expansion model of dispersal-by-colonization (Orsini et al., 2013). According to this pattern of expansion, private haplotypes should occur in the majority of the ponds, although gene flow may also rarely occur at small spatial scales (e.g. amongst the three lakes in the Dora di Savaranche river catchment, Fig. 3). Although we have not measured the genetic variation within populations to assess the extent of gene flow amongst lakes, differences in morphological characteristics of various populations (i.e. occurrence of melanic phenotypes), coupled with the genetic distinction of mitochondrial haplotypes, suggest that founder effects and subsequent local adaptation have played an important role in shaping the present genetic structure of EuPC alpine populations (De Meester et al., 2002; Ishida &amp; Taylor, 2007). The proposed scenario of alternative colonization events could be further supported, at least for our melanic populations, by considering present zooplankton communities inhabiting distinct alpine lakes. Lake Lillet is indeed the only one in which pigmented individuals do not live in sympatry with the D. longispina group, but instead with a well-diversified zooplankton community (Tiberti, 2011), whereas the others show very similar zooplankton communities (Tiberti et al., 2013).</p> </div>	https://treatment.plazi.org/id/240787B5FF97FFC3A8ABFAE40CD4FA6C	Public Domain	No known copyright restrictions apply. See Agosti, D., Egloff, W., 2009. Taxonomic information exchange and copyright: the Plazi approach. BMC Research Notes 2009, 2:53 for further explanation.		Plazi	Bellati, Adriana;Tiberti, Rocco;Cocca, Walter;Galimberti, Andrea;Casiraghi, Maurizio;Bogliani, Giuseppe;Galeotti, Paolo	Bellati, Adriana, Tiberti, Rocco, Cocca, Walter, Galimberti, Andrea, Casiraghi, Maurizio, Bogliani, Giuseppe, Galeotti, Paolo (2014): A dark shell hiding great variability: a molecular insight into the evolution and conservation of melanic Daphnia populations in the Alps. Zoological Journal of the Linnean Society 171 (4): 697-715, DOI: 10.1111/zoj.12151, URL: http://dx.doi.org/10.1111/zoj.12151
