4  Level 2 : advanced classification

This advanced classification is based on the general level 3 classification proposed in this guide. Some knowledge of biology is required to effectively classify vignettes into the … groups proposed.

4.1 Plankton_crustacea

vigns <- fs::dir_ls(
  here::here(training_dir, "Plankton_crustacea"), 
  type = "file", glob = "*.png", recurse = TRUE)

The group plankton_crustacea includes the crustaceans. Typical organisms in this group are copepods, krill, crabs, shrimps, gammarids

Within the plankton_crustacea group, it is possible to differentiate between gymnoplea, podoplea, branchiopoda and malacostraca.

4.1.1 Gymnoplea

Gymnoplea are copepods, which are a well-studied class of crustaceans. These copepods have antennules longer than the cephalosome and the urosome smaller than the prosoma. The calanoida below shows these morphological features (Figure 4.1).

Figure 4.1: Vignette of gymnoplea (Calanoida)

Figure 4.2 shows a set of individuals in this group.

plot_vignettes(vigns, group = "Gymnoplea", nx = 5, ny = 5)

Figure 4.2: Vignettes of Gymnoplea

More details on this suborder of copepods can be found in the Section 5.1.1.

4.1.2 Podoplea

Podoplea is composed by the order of cyclopoida and the order of Harpacticoida. These organisms have a great morphological diversity. The antennules are not longer than the prosome and urosome. The urosome is as long as the prosome or not clearly distinguished from the prosome. A copepod that does not look like a gymnoplea belongs to the podoplea.

plot_vignettes(vigns, group = "Podoplea", nx = 5, ny = 5)

Figure 4.3: Vignettes of Podoplea

More details on this suborder of copepods can be found in the Section 5.1.2.

4.1.3 Branchiopoda

Among the branchiopoda are the Evadne (Section 5.2.1.1.1) and podon (Section 5.2.1.1.2). These small crustaceans have a very clear shells on the vignettes

plot_vignettes(vigns, group = "Branchiopoda", nx = 4, ny = 3)

Figure 4.4: Vignettes of Branchiopoda

4.1.4 Malacostraca

Among the malacostraca are the decapods (crabs, lobsters, shrimps,…), the euphausiids (krill), the amphipods (gammarids), the isopods and the stomatopods (the mantis shrimps). This group of crustaceans corresponds to the main idea that novices have of crustaceans (Figure 4.5).

plot_vignettes(vigns, group = "Malacostraca", nx = 5, ny = 5)

Figure 4.5: Vignettes of malacostraca

More details on class of Malacostraca can be found in the Section 5.2.2.

4.2 Plankton_dark

The plankton_dark group includes darkened organisms in the vignettes. This group consists of molluscs (bivalves and gastropods), annelids and actinopterygians (fish larvae).

vigns <- fs::dir_ls(
  here::here(training_dir, "Plankton_dark"), 
  type = "file", glob = "*.png", recurse = TRUE)

4.2.1 Mollusca

This group includes the bivalvia and gastropoda. All the organisms studied have shells ( Figure 4.6 ).

Cavoliniidae and creseis are easily recognisable individuals among molluscs

plot_vignettes(vigns, group = "Mollusca", nx = 4, ny = 4)

Figure 4.6: Vignettes of Mollusca

More details on this phylum of mollusca can be found in the Section 6.1.

4.2.2 Annelida

This group includes worms. Annelida are vermiform and metamerised body in several segments along a longitudinal axis ( Figure 4.7 ). Polychaetes are mainly found in the marine environment

plot_vignettes(vigns, group = "Annelida", nx = 3, ny = 3)

Figure 4.7: Vignettes of Annelida

More details on this phylum of annelida can be found in the Section 6.2.

4.2.3 Actinopterygii (fish larvae)

This group includes fish larvae. These vertebrates are easily identifiable. This group includes fish larvae. These vertebrates are easily identifiable. The most detailed level of the proposed classification allows differentiation between the different developmental stages of the organisms.

plot_vignettes(vigns, group = "Actinopterygii", nx = 4, ny = 5
)

Figure 4.8: Vignettes of Actinopterygii

More details on this class of Actinopterygii can be found in the Section 6.3.1.1.

4.3 Plankton_gelatinous

The plankton_gelatinous group includes organisms that are clear in the vignettes. These organisms have a gelatinous body like jellyfish for example. These organisms are quite fragile and are broken during collection. This can make identification more complex.

vigns <- fs::dir_ls(
  here::here(training_dir, "Plankton_gelatinous"), 
  type = "file", glob = "*.png", recurse = TRUE)

4.3.1 Thaliacea

These organisms are transparent, which is indicated by the very light yellow on the vignettes (Figure 4.9). The band of muscle present in the Doliolida (Section 7.1.1.3) is not present. There is, however, the presence of muscle (Section 7.1.1.1).

plot_vignettes(vigns, group = "Thaliacea", nx = 4, ny = 4)

Figure 4.9: Vignettes of Thaliacea

4.3.2 Appendicularia

The appendicularia are vermiform. There are two distinct parts: the head (darker) and the tail (longer and lighter) (Figure 4.10). Despite their vermiform appearance, they are quite different from annelida.

plot_vignettes(vigns, group = "Appendicularia", nx = 5, ny = 5)

Figure 4.10: Vignettes of Appendicularia

4.3.3 Chaetognatha

Chaetognatha are also wormlike. These predators have the particularity of having hooks on the front of their head (Figure 4.11). After observing a head of these organisms. It is no longer possible to get the wrong group.

plot_vignettes(vigns, group = "Chaetognatha", nx = 3, ny = 3)

Figure 4.11: Vignettes of Chaetognatha

4.3.4 Cnidaria

Cnidarians include corals, anemones and medusas. Only individuals living in the water body are considered in this study. Gelatinous organisms are lightly coloured in the vignettes. These are mainly jellyfish ( Figure 4.12 ).

library(flow)
vigns %>.%
  stringr::str_subset(., "Siphonophorae", negate = TRUE) %>.%
  plot_vignettes(., group = "Cnidaria", nx = 5, ny = 5)

Figure 4.12: Vignettes of Cnidaria

Figure 4.13

plot_vignettes(vigns, group = "Siphonophorae", nx = 5, ny = 5)

Figure 4.13: Vignettes of Siphonophorae