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Environmental DNA reveals fine-scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft and hard-bottom habitats
<p>Accurate knowledge on spatiotemporal distributions of marine species and their association with surrounding habitats is crucial to inform adaptive management actions responding to coastal degradation across the globe. Here, we investigate the potential use of environmental DNA (eDNA) to detect species-habitat associations in a patchy coastal area of the Baltic Sea. We directly compare species-specific qPCR analysis of eDNA with baited remote underwater video systems (BRUVS), two non-invasive methods widely used to monitor marine habitats. Four focal species (cod Gadus morhua, flounder Platichthys flesus, plaice Pleuronectes platessa and goldsinny wrasse Ctenolabrus rupestris) were selected based on contrasting habitat associations (reef- vs. sand-associated species), as well as differential levels of mobility and residency, to investigate whether these factors affected the detection of species-habitat associations from eDNA. To this end, a species-specific qPCR assay for goldsinny wrasse is developed and made available herein. In addition, potential correlations between eDNA signals and abundance counts (MaxN) from videos were assessed. Results from Bayesian multi-level models revealed strong evidence for a sand association for sedentary flounder (98% posterior probability) and a reef association for highly resident wrasse (99% posterior probability) using eDNA, in agreement with BRUVS. However, contrary to BRUVS, eDNA sampling did not detect habitat associations for cod or plaice. We found a positive correlation between eDNA detection and MaxN for wrasse (posterior probability 95%), but not for the remaining species and explanatory power of all relationships was generally limited. Our results indicate that eDNA sampling can detect species-habitat associations on a fine spatial scale, yet this ability likely depends on the mobility and residency of the target organism, with associations for sedentary or resident species most likely to be detected. Combined sampling with conventional non-invasive methods is advised to improve detection of habitat associations for mobile and transient species, or for species with low eDNA concentrations. </p>
Рис. 3. Фотографии Laternula elliptica, сделанные около cтанции «Прогресс», ВосточнаЯ Антарктида. L. elliptica на морском дне с медкими камнЯми или гравием, глубина 27 м (А); несколько сифональных отверстий L. elliptica над поверхностью мЯгких осадков вокруг голотурии Staurocucumis turqueti, глубина 27 м (В); раковина L. elliptica (длина около 110 мм) на снегу около майны сраЗу после иЗвлечениЯ иЗ воды (С); пустые раковины L. elliptica на морском дне, глубина 56 м (D); раковина L. elliptica (вид с дорсального краЯ) на мЯгких осадках с камнЯми, покрытыми иЗвестковыми водорослЯми, глубина 30 м (Е); пара сифональных отверстий L. elliptica на поверхности мЯгких осадков, глубина 27 м (F). Фотографии О. Савинкина (A, B, D–F) и В. Потина (С). Fig. 3. Photographs of Laternula elliptica taken near «Progress» Research Station (East Antarctica). Softshelled clam L. elliptica on sea bottom with small stowns or gravel, depth 27 m (A); several open siphons of L. elliptica above soft bottom sediments around holothurian Staurocucumis turqueti, depth 27 m (B); a shell of L. elliptica (length about 110 mm) on snow near a dive hole just after dragging out of water (C); empty shells of L. elliptica on seafloor, depth 56 m (D); a shell of Laternula elliptica (dorsal view) on soft deposits among stones, covering by Lithothamnion, depth 30 m (E); pair of siphonal opening of L. elliptica on surface of soft sediments, depth 27 m (F). Photographs are taken by O. Savinkin (A, B, D–F) and V. Potin (C). in Species of warm-water origin Laternula elliptica (King, 1832) (Mollusca: Bivalvia: Laternulidae), a widespread mollusk in recent Antarctica
Рис. 3. Фотографии Laternula elliptica, сделанные около cтанции «Прогресс», ВосточнаЯ Антарктида. L. elliptica на морском дне с медкими камнЯми или гравием, глубина 27 м (А); несколько сифональных отверстий L. elliptica над поверхностью мЯгких осадков вокруг голотурии Staurocucumis turqueti, глубина 27 м (В); раковина L. elliptica (длина около 110 мм) на снегу около майны сраЗу после иЗвлечениЯ иЗ воды (С); пустые раковины L. elliptica на морском дне, глубина 56 м (D); раковина L. elliptica (вид с дорсального краЯ) на мЯгких осадках с камнЯми, покрытыми иЗвестковыми водорослЯми, глубина 30 м (Е); пара сифональных отверстий L. elliptica на поверхности мЯгких осадков, глубина 27 м (F). Фотографии О. Савинкина (A, B, D–F) и В. Потина (С). Fig. 3. Photographs of Laternula elliptica taken near «Progress» Research Station (East Antarctica). Softshelled clam L. elliptica on sea bottom with small stowns or gravel, depth 27 m (A); several open siphons of L. elliptica above soft bottom sediments around holothurian Staurocucumis turqueti, depth 27 m (B); a shell of L. elliptica (length about 110 mm) on snow near a dive hole just after dragging out of water (C); empty shells of L. elliptica on seafloor, depth 56 m (D); a shell of Laternula elliptica (dorsal view) on soft deposits among stones, covering by Lithothamnion, depth 30 m (E); pair of siphonal opening of L. elliptica on surface of soft sediments, depth 27 m (F). Photographs are taken by O. Savinkin (A, B, D–F) and V. Potin (C).
Figure 3 in Depth-related gradient of soft-bottom crustacean distribution along the Cilician shelf*
Figure 3. Spatiotemporal (depths and months) and annual (average) changes of crustacean faunistic parameters on the Cilician shelf for number of crustacean species (S), density (N), biomass, species richness (d), evenness (J'), and Shannon–Wiener diversity (H') indexes. Each point represents the value obtained from averaging values of each parameter across all replicates at each depth (n = 9).
Figure 5 in Depth-related gradient of soft-bottom crustacean distribution along the Cilician shelf*
Figure 5. CCA ordination of species (based on abundance data) with superimposed symbols representing bottom depth (see Figure 4), sedimentary parameters, and sea surface temperature of the sampling locations in February (F), May (M), August (A), and November (N). Symbol size is proportional to value of each variable, i.e. the largest symbol corresponds to the maximum value.
Figure 4 in Spatial and temporal variations of soft bottom polychaetes of Sinop Peninsula (southern Black Sea) with new records
Figure 4. Biplot of CCA performed on the total abundance of species and environmental variables recorded in the study area (DO: dissolved oxygen, OM: organic matter, TDS: total dissolved solids, WC: water content, Si: silicate, VFP: very fine pebbles, CS: coarse sand, MS: medium sand, FS: fine sand, VFS: very fine sand, VCS: very coarse silt).
Fig. 4 in New record and new species of Laubierpholoe Pettibone, 1992 (Annelida, Sigalionidae) from the soft bottom of submarine caves near Marseille (Mediterranean Sea) with discussion on phylogeny and ecology of the genus
Fig. 4. Laubierpholoe massiliana Zhadan sp. nov., SEM. A. ZMMSU WS16511, ventral view. B. ZMMSU WS16511, pharynx, dorso-anterior view. C. ZMMSU WS14001, parapodia of segments I-V, dorso-anterior view. D. Same, parapodia of segment III, anterior view. E. ZMMSU WS13977, bidentate neurochaetae. F–G. ZMMSU WS12292, tips of bidentate neurochaetae. Abbreviations: ne = neuropodium; no = notopodium; pa = palp; vbc = ventral buccal cirrus; vc = ventral cirrus. Arrows indicate papillae.
Fig. 2 in New record and new species of Laubierpholoe Pettibone, 1992 (Annelida, Sigalionidae) from the soft bottom of submarine caves near Marseille (Mediterranean Sea) with discussion on phylogeny and ecology of the genus
Fig. 2. Laubierpholoe massiliana Zhadan sp. nov., light microscopy. A–B. Living specimens from different samples. C. ZMMSU WS12418, paratype, general view with proboscis everted. D. ZMMSU WS16462, holotype, general view, proboscis everted. E. ZMMSU WS14001, paratype, general view. F–H. ZMMSU WS14001, paratype, compound microscope. F. General view. G. Anterior part, dark field. H. Right jaws.
Fig. 5 in New record and new species of Laubierpholoe Pettibone, 1992 (Annelida, Sigalionidae) from the soft bottom of submarine caves near Marseille (Mediterranean Sea) with discussion on phylogeny and ecology of the genus
Fig. 5. Laubierpholoe massiliana Zhadan sp. nov., line drawings. A. Anterior end, dorso-anterior view. B. Notochaeta and bidentate neurochaeta. C. Parapodium, anterior view. D. Jaw. Abbreviations: ah = anterior horns; dtc = dorsal tentacular cirrus; ma = median antenna; ne = neuropodium; no = notopodium; p = prostomium; pa = palp; vbc = ventral buccal cirrus; vc = ventral cirrus; vtc = ventral tentacular cirrus. Arrows indicate papillae.
Fig. 6. Bayesian phylogenetic tree obtained with the 18S rRNA and 28S in New record and new species of Laubierpholoe Pettibone, 1992 (Annelida, Sigalionidae) from the soft bottom of submarine caves near Marseille (Mediterranean Sea) with discussion on phylogeny and ecology of the genus
Fig. 6. Bayesian phylogenetic tree obtained with the 18S rRNA and 28S rRNA concatenated dataset showing position of Laubierpholoe massiliana Zhadan sp. nov. within Sigalionidae Kinberg, 1856. Posterior probabilities and bootstrap values are shown for each medium supported node.
Fig. 3 in New record and new species of Laubierpholoe Pettibone, 1992 (Annelida, Sigalionidae) from the soft bottom of submarine caves near Marseille (Mediterranean Sea) with discussion on phylogeny and ecology of the genus
Fig. 3. Laubierpholoe massiliana Zhadan sp. nov., SEM. A. ZMMSU WS12292, general view. B. ZMMSU WS14001, general view, elytra omitted. C. ZMMSU WS13977, elytra. D. ZMMSU WS14001, anterior end, dorsal view. E. Same, dorso-anterior view. F. ZMMSU WS16511, anterior end, dorso-anterior view, median antenna broken. G. ZMMSU WS16511, dorso-anterior view. Abbreviations: ah = anterior horns; dtc = dorsal tentacular cirrus; e = elytrophores; ma = median antenna; ne = neuropodium; no = notopodium; p = prostomium; pa = palp; ph = pharynx; vbc = ventral buccal cirrus; vtc = ventral tentacular cirrus. Arrows indicate papillae.
Environmental DNA reveals fine-scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft and hard-bottom habitats
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Figure 2 in Spatial and temporal variations of soft bottom polychaetes of Sinop Peninsula (southern Black Sea) with new records
Figure 2. Dendrogram of the sampling stations (A: autumn, W: winter, Sp: spring, S: summer).
Figure 1 in Spatial and temporal variations of soft bottom polychaetes of Sinop Peninsula (southern Black Sea) with new records
Figure 1. Map of the sampling stations.
Drilling predation on Early Jurassic bivalves and behavioral patterns of the presumed gastropod predator — evidence from Pliensbachian soft bottom deposits of northern Germany
<p><span>Drilling predation is a common reason for mortality of benthic molluscs but did not become common until the late Mesozoic. </span><span>The scarcity of drill holes in the early Mesozoic fossil record limits our </span><span>understanding of the evolution of drilling behavior and its role on shaping early Mesozoic marine communities. Here</span><span>,</span><span> we </span><span>use</span> <span>drill</span><span>ing trace</span><span>s on several bivalve taxa from the Lower Jurassic (Pliensbachian) marine soft bottom deposits in northern Germany</span> <span>to </span><span>explore</span><span> behavior</span><span>al patterns of the predator</span> <span>(e.g.,</span> <span>site selectivity</span><span>, change in site-selective behaviour with age)</span><span>. Although none of the known drilling gastropod groups existed in the Pliensbachian, including the studied localities, the drill hole morphology suggests that the predator was probably a gastropod. The </span><span>ecology and identity of the </span><span>target prey change from a diverse array of epifaunal to infaunal taxa in older deposits to focus on a single large deep infaunal taxon, <em>Gresslya</em> <em>intermedia</em>, in younger deposits, suggesting a potential trend in prey selectivity over time. Spatial point pattern analysis of traces (SPPAT) reveals an </span><span>aggregated pattern of drill holes </span><span>on <em>Gresslya</em>, suggesting strong selectivity in drill hole location. Drilling on a single large infaunal taxon and site selectivity are common patterns also inferred previously from the drilled deep infaunal Eothyasira from the Pliensbachian of southern Germany. In addition to the scarcity of predators, the highly specialized behavior of the early drilling predators, including strong prey selectivity in terms of prey identity and life habit, can partly explain the rarity of the early Mesozoic drill holes.</span></p>
Drilling predation on Early Jurassic bivalves and behavioral patterns of the presumed gastropod predator — evidence from Pliensbachian soft bottom deposits of northern Germany
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FIGURE 4. A in Soft-bottom sipunculans in Izmir Bay (Aegean Sea, eastern Mediterranean)
FIGURE 4. A, Golfingia (G.) vulgaris vulgaris, introvert hook. B, Thysanocardia procera, tentacles surrounding bilobed nuchal organ. C, D, Phascolion (P.) strombus strombus, holdfast papillae (C) and introvert hook (D). E, Onchnesoma steenstrupii steenstrupii, egg in coelomic cavity. F, Aspidosiphon (A.) mexicanus, intestinal coils and spindle muscle. G, Aspidosiphon (A.) muelleri, anal shield. Scale bars: A, 15 µm; B, 0.3 mm; C, 40 µm; D, 20 µm; E, 20 µm; F, 1 mm; G, 0.5 mm.
FIGURE 8 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 8. Consumption of local baited fish (vertebral columns of Trachurus trachurus (Linnaeus, 1758) and skin of undetermined deep-sea shark) by benthic scavengers (mainly Politolana sanchezi sp. nov.) during a 12h TFS night trophic experiment on the bottom of the Cantabrian continental slope (15–16/04/2004, 602 m depth). (Photo: F. Sánchez).
FIGURE 4 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 4. Politolana sanchezi sp. nov., (A–G) paratype male (MNCN 20.04/8351); posterior face of left pereopods: (A) pereopod 1, (B) pereopod 2, (C) pereopod 3, (D) pereopod 4, (E) pereopod 5, (F) pereopod 6, (G) pereopod 7. Scale bar: 1 mm.
FIGURE 3 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 3. Politolana sanchezi sp. nov., (A) holotype male (MNCN 20.04/8350); (B–G) paratype male (MNCN 20.04/ 8351); (A) frontal lamina, clypeus and labrum, (B) antennule, (C) antenna, (D) dorsal view of left mandible, (E) dorsal view of left maxillule, (F) dorsal view of left maxilla, (G) dorsal view of left maxilliped. Scale bars: 1 mm.
FIGURE 2 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 2. Politolana sanchezi sp. nov., (A) lateral and (B) dorsal views of holotype male (MNCN 20.04/8350); (C) pleotelson apex of paratype male (MNCN 20.04/8351) in dorsal view. Scale bars: A–B = 5 mm, C = 0.1 mm.
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