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211 results for “tropical fishes”
Data from: Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar
Taxonomic identification of archaeological fish bones provides important insights into the subsistence practices of ancient coastal peoples. However, it can be difficult to execute robust morphological identification of fish bones from species-rich fossil assemblages, especially from post-cranial material with few distinguishing features. Fragmentation, weathering and burning further impede taxonomic identification, resulting in large numbers of unidentifiable bones from archaeological sites. This limitation can be somewhat mitigated by taking an ancient DNA (aDNA) bulk-bone metabarcoding (BBM) approach to faunal identification, where DNA from non-diagnostic bone fragments is extracted and sequenced in parallel. However, a large proportion of fishing communities (both past and present) live in tropical regions that have sub-optimal conditions for long-term aDNA preservation. To date, the BBM method has never been applied to fish bones before, or to fossils excavated from an exposed context within a tropical climate. Here, we demonstrate that morphologically indistinct bulk fish bone from the tropics can be identified by sequencing aDNA extracted from 100 to 300 ya archaeological midden material in southwest Madagascar. Despite the biases of the approach, we rapidly obtained family, genus, and species-level assemblage information, and used this to describe a subset of the ichthyofauna exploited by an 18th century fishing community. We identified 23 families of fish, including benthic, pelagic, and coral-dwelling fishes, suggesting a reliance on a variety of marine and brackish habitats. When possible, BBM should be used alongside osteological approaches to address the limitations of both; however, this study highlights how genetic methods can nevertheless be a valuable tool for helping resolve faunal assemblages when morphological identification is hindered by taphonomic processes, lack of adequate comparative collections, and time constraints, and can provide a temporal perspective on fish biodiversity in the context of accelerated exploitation of the marine environment.
Supporting tables and figures for Cancel Villamil JJ, Locke SA (2022) - Fish assemblage response to removal of a low‐head dam in the lower reach of a tropical island river, Freshwater Biology
<p>Table S1 summarizes studies of the effects of dams on freshwater fish assemblages</p> <p>Table S2 provides results of fishing in 39 samples in three rivers in Puerto Rico in 2017-2019. See 2, below. </p> <p>Figure S1 shows the relationship between fish species richness and time spent electrofishing in these samples.</p> <p>Abstract of article:</p> <p>1. Dams are often removed from rivers to restore habitat connectivity for biota such as fish. Removal of inland dams is well studied in temperate mainland rivers but this approach has been little studied in fish assemblages in islands, tropic systems, or for dams near the mouth of the river. In Puerto Rico, one of the most intensively dammed territories in the world, all native river fishes migrate between fresh water and the sea, and previous work shows these movements are impeded or blocked by dams.</p> <p>2. Fish assemblages were compared before and after removal of the Cambalache dam, a porous, low-head structure near the mouth of the Río Grande de Arecibo, as well as in two other rivers in Western Puerto Rico, one with a similarly sized and positioned dam, and one reference river without artificial barriers. Fish were sampled using backpack electrofishing on 39 occasions during 2017-2019, including seven samples collected after removal of the Cambalache dam, at between four and six sites per river.</p> <p>3. Fish assemblages upstream from dams were poorer in species, and species richness showed a marginal tendency (P=0.0515) to increase upstream of the Cambalache dam three months after its removal. The two small lowland dams studied herein limited the upstream extent of marine species, which recolonized upstream sites of the Río Grande de Arecibo after removal of the Cambalache dam. An estimate of relative density (catch per unit effort) of common native freshwater species was higher above these two dams, and decreased at upstream sites after removal of the Cambalache dam. The estimated relative density of a native freshwater species that is of conservation concern, the American eel (Anguilla rostrata), was reduced above dams, and increased upstream of the former Cambalache dam after its removal. </p> <p>4. In extensive surveys conducted previously in Puerto Rico, sampling was concentrated higher in the watershed, and native fishes were more common and abundant below than above dams. The present work was conducted near the river mouth, and opposite results were observed. These contrasting results suggest that the effects of dams (or dam removal) on fish assemblages vary along the river gradient, although data from other systems are needed to confirm this.</p> <p>5. The present results suggest low-head dam removal to be a viable method of restoring connectivity in fish assemblages in lower reaches of rivers in Puerto Rico and, potentially, other tropical islands. Removal of dams near the mouth of the river appears to be of particular benefit to marine fish species that use lower river reaches.</p>
Neutral processes and taxonomic scale drive beta species-genetic diversity correlations in a submesophotic tropical reef fish
<p>This dataset is associated to the following publication:</p> <p>Vilcot M, Faure N, Andrews KR, Bowen BW, Leprieur F, Manel S. (2024) <strong>Neutral processes and taxonomic scale drive beta species-genetic diversity correlations in a submesophotic tropical reef fish</strong>. <em>Molecular Ecology</em> <strong>33</strong>, e17423. (doi:<a href="https://doi.org/10.1111/mec.17423">10.1111/mec.17423</a>)</p> <p> </p> <h2><strong>Data: </strong></h2> <ul> <li> <p>"Report_DEtel22-6705_SNP_2_ordered_Bowen.csv": SNP data from Dart Sequencing on <em>Etelis coruscans</em>, from Andrews et al. (2020) samples</p> </li> <li>"PA_Mat_GaspObis.RDS": fish species presence data, gathered from an updated version of Albouy et al. (2019)</li> <li> <p>"metadata_samples_full.csv": all <em>Etelis coruscans</em> sample information, from Andrews et al. (2020) and the SEAMOUNTS project</p> </li> <li> <p>"metadata_samples.csv": <em>Etelis coruscans</em> sample information, only for samples that have passed the genetic filtering and were used for subsequent analyses </p> </li> <li> <p>"metadata_stations.csv": sampling station information</p> </li> <li> <p>"Taxonomy_Fishbase.csv": species taxonomic information, downloaded with rfishbase::load_taxa() </p> </li> <li> <p>"traits_Luiz_et_al_2013.csv": species trait information from Luiz et al. (2013) </p> </li> </ul> <h2><strong>Related dataset</strong><strong>: </strong></h2> <p><em>Etelis coruscans </em>SNP data on samples from the SEAMOUNTS project are available at <a href="https://doi.org/10.5281/zenodo.11201065">https://doi.org/10.5281/zenodo.11201065</a></p> <h2><strong>Scripts: </strong></h2> <p>Scripts used to reproduce the analyses and figures of the final article are available at <a href="https://github.com/mvilcot/etelis_SGDCs">https://github.com/mvilcot/etelis_SGDCs</a> </p> <p> </p> <h2><strong>References: </strong></h2> <p>Albouy, C., Archambault, P., Appeltans, W., Araújo, M. B., Beauchesne, D., Cazelles, K., Cirtwill, A. R., Fortin, M.-J., Galiana, N., Leroux, S. J., Pellissier, L., Poisot, T., Stouffer, D. B., Wood, S. A., & Gravel, D. (2019). The marine fish food web is globally connected. Nature Ecology & Evolution, 3(8), Article 8. <a href="https://doi.org/10.1038/s41559-019-0950-y" target="_blank" rel="noopener">https://doi.org/10.1038/s41559-019-0950-y</a> </p> <p>Andrews, K. R., Copus, J. M., Wilcox, C., Williams, A. J., Newman, S. J., Wakefield, C. B., & Bowen, B. W. (2020). Range-Wide population structure of 3 deepwater Eteline snappers across the Indo-Pacific Basin. Journal of Heredity, 111(5), 471‑485. <a href="https://doi.org/10.1093/jhered/esaa029" target="_blank" rel="noopener">https://doi.org/10.1093/jhered/esaa029</a> </p> <p>Luiz, O. J., Allen, A. P., Robertson, D. R., Floeter, S. R., Kulbicki, M., Vigliola, L., Becheler, R., & Madin, J. S. (2013). Adult and larval traits as determinants of geographic range size among tropical reef fishes. Proceedings of the National Academy of Sciences, 110(41), 16498‑16502. <a href="https://doi.org/10.1073/pnas.1304074110" target="_blank" rel="noopener">https://doi.org/10.1073/pnas.1304074110</a> </p> <p>Boettiger, C., Lang, D. T., & Wainwright, P. C. (2012). rfishbase: Exploring, manipulating and visualizing FishBase data from R. Journal of Fish Biology, 81(6), 2030‑2039. <a href="https://doi.org/10.1111/j.1095-8649.2012.03464.x" target="_blank" rel="noopener">https://doi.org/10.1111/j.1095-8649.2012.03464.x</a></p> <p> </p>
Supplementary material 1 from: Souza CD, Batista VS, Fabré NN (2018) What are the main local drivers determining richness and fishery yields in tropical coastal fish assemblages? Zoologia 35: 1-12. https://doi.org/10.3897/zoologia.35.e12898
Taxonomic list of fish species in phylogenetic order (Nelson 2006), captured from October 2010 to August 2011 on the coast of Alagoas. : Data type: species data
Supplementary material 1 from: Souza CD, Batista VS, Fabré NN (2018) What are the main local drivers determining richness and fishery yields in tropical coastal fish assemblages? Zoologia 35: 1-12. https://doi.org/10.3897/zoologia.35.e12898
Taxonomic list of fish species in phylogenetic order (Nelson 2006), captured from October 2010 to August 2011 on the coast of Alagoas. : Data type: species data
Smithsonian Tropical Research Instiitute: STRI Neotropical Fishes
<p></p>https://stri.si.edu/research-computing/databases
FIGURE 60 in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURE 60. Host distribution of Cardicola chaetodontis Yamaguti, 1970 mapped on the phylogeny of the Chaetodontidae (modified from that proposed by Littlewood, et al. (2004)). Boxed species are infected. Chaetodon fremblii was not included in the modified phylogeny because there is a lack of convincing evidence as to its relationships with other Chaetodontidae.
FIGURE 59. ITS2 sequence alignment for putative species sequenced here. Where identical ITS2 in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURE 59. ITS2 sequence alignment for putative species sequenced here. Where identical ITS2 sequences were obtained from sanguinicolids of different host/location combinations (not differentiated by morphological comparisons) only one representative sequence has been included here. Gaps of five spaces delineate the 5' and 3' ends of ITS2 (and subsequent 3' end of 5.8S and the 5' end of 28S).
FIGURES 56–58. Braya jexi n in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURES 56–58. Braya jexi n. sp. 56. Anterior region, ventral view, showing vestigial oral sucker delimited by fine membrane. Although spines seen on sucker exact number of concentric rows not clear, spines illustrated to show their presence only. 57. Male terminal genitalia. A. Ventral view. B. Lateral view. Sperm has moved away from the wall of the seminal vesicle to give the appearance of a double wall (and thus illustrate a cirrussac); this is not the case. The male terminal genitalia of Braya n. gen. species consists of a seminal vesicle only. 58. Female terminal genitalia. A. Ventral view. Vitelline duct and vitelline reservoir omitted from figure as they obscure the path of the oviducal seminal receptacle and uterus as they pass posteriorly. B. Lateral view; ovary, oviducal seminal receptacle, and oötype figured only. Scalebars: 200 m.
FIGURE 55. Braya jexi n in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURE 55. Braya jexi n. sp. from the atrium (heart) of Scarus frenatus off Heron Island. Adult, whole mount. A. Lateral view. B. Dorsoventral view. Scalebars: 250 m.
FIGURES 51–54. Braya yantschi n in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURES 51–54. Braya yantschi n. sp. from the atrium (heart) of Chlorurus microrhinos off Heron Island. 51. Adult, whole mount, ventral view. Specimen rolled ventrally sinistrally, anteriorly and posteriorly. Although broken anterior to intestinal bifurcation major morphological components undamaged. 52. Anterior region, ventral view, showing vestigial oral sucker delimited by fine membrane. Although spines seen on sucker exact number of concentric rows not clear, spines illustrated to show their presence only. 53. Male terminal genitalia, ventral view. Posterior margin of worm rolled ventrally. 54. Female terminal genitalia, ventral view. Vitelline duct and vitelline reservoir omitted from figure as they obscure the path of the oviducal seminal receptacle and uterus as they pass posteriorly. Scalebars: 51, 250 m; 52–54, 200 m.
FIGURES 48–50. Braya psittacus n. g., n in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURES 48–50. Braya psittacus n. g., n. sp. 48. A,B. Anterior region, ventral view. Arrow indicates thin septum separating the vestigial oral sucker from body proper. Spines not seen on specimens due to small size of vestigial oral sucker. 49. A,B. Male terminal genitalia, ventral view. Seminal vesicle extends from arrow "a" to arrow "b". 50. Female terminal genitalia, ventral view. Vitelline duct and vitelline reservoir omitted from figure as they obscure the path of the oviducal seminal receptacle and uterus as they pass posteriorly. Scalebars: 48A, 49A, 50, 200 m; 48B, 49B, 100 m.
FIGURE 47. Braya psittacus n. g., n in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURE 47. Braya psittacus n. g., n. sp. from the atrium (heart) of Scarus ghobban off Heron Island. Adult, whole mount, ventral view. Scalebar: 250 m.
FIGURES 44–46. Cardicola chaetodontis Yamaguti, 1970. 44. A,B in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURES 44–46. Cardicola chaetodontis Yamaguti, 1970. 44. A,B. Anterior region, ventral view, showing vestigial oral sucker delimited by fine membrane. Arrow indicates thin septum separating the vestigial oral sucker from body proper. Given the size of the vestigial oral sucker it is not clear if concentric rows of fine spines are present. Tegumental spines not clear on this specimen. 45. Male terminal genitalia, ventral view. Seminal vesicle appearing as small terminal expansion of vas deferens, laterally directed. 46. Female terminal genitalia, ventral view. Oviducal seminal receptacle present, not appearing as conspicuous expansion of oviduct as in other Cardicola species. Vitelline duct and vitelline reservoir omitted from figure as they obscure the path of the uterus as they pass posteriorly. Scalebars: 100 m.
FIGURE 43. Cardicola chaetodontis Yamaguti, 1970 in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURE 43. Cardicola chaetodontis Yamaguti, 1970 from the blood vessels of the intestine of Chaetodon reticulatus off Moorea. Adult, whole mount, ventral view. Scalebar: 250 m.
FIGURE 1 in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURE 1. Phylogram of relationships between host/parasite/location combinations sequenced here; inferred by distance analysis (HKY85 (Hasegawa et al. 1985)) of complete ITS2 rDNA sequence data from species of Cardicola and Braya n. gen. Figures in parentheses indicate the number of replicates sequences obtained for each combination. Phylogram midpoint rooted as Cardicola forsteri Cribb, Daintith & Munday, 2000 (from Thunnus maccoyii (Castelnau)), the intended taxa for outgroup comparisons, was embedded with sanguinicolids from other Scombridae. Nodal support based on bootstrapping (percentage for 1000 replicates). Legend: (A). Cardicola coeptus n. sp.; (B). C. covacinae n. sp.; (C). C. bartolii n. sp.; (D). C. watsonensis n. sp.; (E). C. lafii n. sp.; (F). C. parilus n. sp.; (G). Cardicola sp. 1; (H). C. tantabiddii n. sp.; (I). Cardicola sp. 2; (J). C. milleri n. sp.; (K). C. chaetodontis Yamaguti, 1970; (L). C. forsteri Cribb, Daintith & Munday, 2000; (M). Cardicola sp. 3; (N). Cardicola sp. 4; (O). Braya psittacus n. g., n. sp.; (P). Braya sp. 2; (Q). B. yantschi n. sp.; (R). Braya sp. 1; (S). B. jexi n. sp.
FIGURES 19–22. Cardicola covacinae. n in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURES 19–22. Cardicola covacinae. n. sp. from the bulbus arteriosus (heart) of Siganus punctatus off Heron Island. 19. Adult, whole mount, ventral view. Mehlis' gland not seen in this specimen. 20. Anterior region, ventral view, showing vestigial oral sucker delimited by fine membrane. No spines seen on sucker due to very small size of specimen. 21. Male terminal genitalia, ventral view. 22. Female terminal genitalia, ventral view. Vitelline duct omitted from figure as it obscures the path of the uterus as it passes posteriorly. Scalebars: 19, 250 m; 20, 200
FIGURES 35–38. Cardicola parilus n in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURES 35–38. Cardicola parilus n. sp. from the atrium and ventricle (heart) of Siganus fuscescens of Ningaloo Reef, Western Australia. 35. Adult, whole mount, ventral view. 36. Anterior region, ventral view, showing vestigial oral sucker delimited by fine membrane. 37. Male terminal genitalia, ventral view. Ejaculatory duct directed dorsally. 38. Female terminal genitalia, ventral view. Vitelline duct and vitelline reservoir omitted from figure as they obscure the path of the oviducal seminal receptacle and uterus as they pass posteriorly. Scalebars: 35, 100 m; 36–38, 100
FIGURES 15–18. Cardicola coeptus n in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURES 15–18. Cardicola coeptus n. sp. from the atrium and ventricle (heart), and the gills of Siganus punctatus off Heron Island. 15. Adult, whole mount, ventral view. Mehlis' gland not seen in this specimen. 16. Anterior region, ventral view, showing vestigial oral sucker delimited by fine membrane. Although spines seen on sucker exact number of concentric rows not clear, spines illustrated to show their presence only. 17. Male terminal genitalia, dorsal view. 18. Female terminal genitalia, dorsal view. Vitelline duct omitted from figure as it obscures the path of the uterus as it passes posteriorly. Scalebars: 15, 250 m; 16–18, 100 m.
FIGURES 39–42. Cardicola tantabiddii n in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURES 39–42. Cardicola tantabiddii n. sp. from the atrium and ventricle (heart) of Siganus fuscescens of Ningaloo Reef, Western Australia. 39. Adult, whole mount, ventral view. Oesophagus obscured medially by gland cells. Posterior caecal outline not seen, assumed convoluted by coloration of intestinal contents. 40. Anterior region, ventral view, showing vestigial oral sucker delimited by fine membrane. 41. Male terminal genitalia, ventral view. Seminal vesicle tubular, thin. 42. Female terminal genitalia, ventral view. Vitelline duct and vitelline reservoir omitted from figure as they obscure the path of the oviduct, oviducal seminal receptacle and uterus as they pass posteriorly. Scalebars: 39,41,42, 250 m; 40, 100 m.
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