Indicator: Pathways associated with alien species introductions

This document describes how to build indicators based on checklist data. In particular, this document focuses on pathways of introduction.

1 Setup

Load libraries:

library(tidyverse) # To do datascience
library(magrittr) # To use extract2 function
library(tidylog) # To provide feedback on dplyr functions
library(here) # To find files
library(trias) # To use functions developed for TrIAS
library(kableExtra) # To customize tables
library(INBOtheme)  # INBO graph style

2 Get data

data_file <- here::here(
  "data",
  "interim",
  "data_input_checklist_indicators.tsv"
)
data <- read_tsv(data_file,
  na = "",
  guess_max = 5000
)

3 Pathway indicators

3.1 Find categories

We divide the species in categories. Each kingdom, except Animalia, is a category. If animal species are present, they are separated in two categories: vertebrates (phylum Chordata) and invertebrates (phylum other than Chordata, defined as Not Chordata).

Categories present in our checklist data:

3.2 Pathway analysis level 1

Total number of taxa introduced for each pathway level 1:

data %>% 
  visualize_pathways_level1() %>% 
  extract2("plot")

Per category:

map(categories$category, function(x) {
  data %>% 
    visualize_pathways_level1(
      category = x,
      title = x) %>%
  extract2("plot")
})

3.3 Pathways analysis level 2

Total number of taxa introduced for pathways level 2:

pathways_level1 <- 
  data %>%
  tidylog::distinct(pathway_level1) %>%
  tidylog::filter(pathway_level1 != "unknown") %>%
  pull()
map(pathways_level1,
    function(x) {
      data %>%
        visualize_pathways_level2(chosen_pathway_level1 = x,
                                  title = x) %>% 
        extract2("plot")
    }
)

Per category:

categories_path_lev1 <- expand_grid(categories, pathways_level1)
map2(categories_path_lev1$category,
     categories_path_lev1$pathways_level1,
     function(x, y) {
       data %>%
         visualize_pathways_level2(chosen_pathway_level1 = y,
                                   category = x,
                                   title = paste(x, y, collapse = ": ")) %>% 
         extract2("plot")}
)

3.4 Pathways level 1 evolution

We show the evolution in time of the pathways level 1.

First, considering all taxa:

data %>%
  visualize_pathways_year_level1() %>%
  extract2("plot")

and now splitting them by category:

map(categories$category, function(x) {
  data %>%
    visualize_pathways_year_level1(category = x, title = x) %>%
    extract2("plot")}
)

3.5 Pathways analysis: tables

We also summarize pathway information in one table per category. Number of species for each pathway level 2 and some species as example are provided.

Number of species returned in table as examples of the group:

n_species <- 5

We limit to pathways of taxa introduced from 2000.

start_year <- 2000

Create tables:

tables <- map(categories$category, ~
get_table_pathways(data,
  category = .,
  from = start_year,
  n_species = n_species
))
names(tables) <- categories$category

3.5.1 Pathways per category

Intentionality of introduction is mapped by cell color background: white for intentional introduction (pathway value: release), light orange for unintentional introduction.

3.5.1.1 Plantae

Pathways associated to plants (category Plantae):

pathway_level1	pathway_level2	n	examples
contaminant	habitat_material	28	Erigeron sumatrensis, Centranthus calcitrapae, Oenothera moravica, Epilobium brachycarpum, Cheilanthes viridis macrophylla
contaminant	nursery	6	Phyllanthus tenellus, Cardamine corymbosa, Cardamine graeca, Acalypha indica, Cardamine occulta
contaminant	on_animals	17	Amaranthus viridis, Amaranthus thunbergii, Calibrachoa parviflora, Eragrostis pilosa, Malva parviflora
contaminant	seed	87	Cichorium calvum, Notobasis syriaca, Tripleurospermum decipiens, Melilotus elegans, Corispermum tylocarpum
contaminant	timber	4	Carex loliacea, Euphorbia vermiculata, Symphyotrichum lateriflorum, Melampyrum nemorosum
contaminant	unknown	1	Campylopus introflexus
corridor	unknown	6	Crassula helmsii, Cortaderia selloana, Rosa rugosa, Campylopus introflexus, Pontederia crassipes
escape	agriculture	6	Daucus carota sativus, Allium ampeloprasum, Triticum aestivum, Salvia officinalis, Valerianella locusta locusta
escape	food_bait	9	Persea americana, Cucumis sativus, Cucurbita maxima, Actinidia deliciosa, Jaltomata procumbens
escape	horticulture	563	Asclepias syriaca, Ageratina altissima, Nemophila maculata, Acer tataricum ginnala, Corylus maxima
escape	unknown	2	Cortaderia selloana, Elodea densa
release	unknown	8	Pontederia crassipes, Phytolacca americana, Rosa rugosa, Elodea densa, Akebia quinata
stowaway	people_luggage	7	Parentucellia latifolia, Trifolium nigrescens, Spergularia bocconei, Trifolium suffocatum, Poa infirma
stowaway	unknown	6	Urtica membranacea, Polypogon viridis, Euphorbia prostrata, Campylopus introflexus, Chondrilla juncea
unaided	natural_dispersal	6	Pontederia crassipes, Crassula helmsii, Cortaderia selloana, Campylopus introflexus, Rosa rugosa
unknown	unknown	430	Chamaecytisus elongatus, Festuca ambigua, Sassafras albidum, Osmanthus heterophyllus, Paspalum saurae

3.5.1.2 Vertebrates

Pathways associated to vertebrates (category Chordata):

pathway_level1	pathway_level2	n	examples
contaminant	nursery	1	Ambystoma macrodactylum
contaminant	timber	2	Naja melanoleuca, Natrix maura
contaminant	unknown	2	Rattus norvegicus, Ambystoma macrodactylum
corridor	unknown	2	Procyon lotor, Oxyura jamaicensis
escape	farm	1	Dromaius novaehollandiae
escape	pet	69	Acridotheres cristatellus, Triturus marmoratus, Testudo hermanni, Misgurnus anguillicaudatus, Mephitis mephitis
escape	research	1	Xenopus laevis
escape	unknown	33	Psittacula alexandri, Psittacula eupatria, Poicephalus cryptoxanthus, Rattus norvegicus, Psittacula derbiana
escape	zoo	4	Callosciurus erythraeus, Tamias sibiricus, Oxyura jamaicensis, Himantopus mexicanus
release	hunting	1	Muntiacus reevesi
release	landscape_improvement	2	Pleurodeles waltl, Triturus marmoratus
release	other	58	Apalone ferox, Trachemys scripta, Caiman crocodilus, Graptemys ouachitensis, Pogona
release	unknown	4	Procyon lotor, Oxyura jamaicensis, Rattus norvegicus, Tamias sibiricus
stowaway	ballast_water	1	Gobiosoma bosc
stowaway	container	8	Boaedon, Lacerta strigata, Boa constrictor, Chrysopelea ornata, Dryophytes japonicus
stowaway	other	4	Vipera aspis, Siren intermedia, Pelophylax ridibundus, Podarcis muralis
stowaway	unknown	1	Rattus norvegicus
unaided	natural_dispersal	2	Oxyura jamaicensis, Procyon lotor
unknown	unknown	291	Caracara plancus, Zamenis situla, Plectropterus gambensis, Chloephaga picta, Mauremys

3.5.1.3 Invertebrates

Pathways associated to invertebrates (category Not Chordata):

pathway_level1	pathway_level2	n	examples
contaminant	animal_parasite	3	Mastophorus, Enderleinellus kumadai, Hoplopleura erismata
contaminant	food	1	Chaetopelma olivaceum
contaminant	habitat_material	14	Eumodicogryllus bordigalensis, Caenoplana variegata, Boettgerilla pallens, Hawaiia minuscula, Paralaoma servilis
contaminant	nursery	2	Obama nungara, Caenoplana coerulea
contaminant	on_animals	1	Sinanodonta woodiana
contaminant	on_plants	27	Gittenbergia sororcula, Cacyreus marshalli, Tandonia budapestensis, Triaeris stenaspis, Branchiodrilus hortensis
contaminant	timber	2	Camponotus vagus, Xylocopa virginica
contaminant	unknown	11	Arion vulgaris, Drosophila suzukii, Corbicula fluminalis, Corbicula fluminea, Dreissena polymorpha
corridor	unknown	3	Arion vulgaris, Dreissena polymorpha, Dreissena bugensis
corridor	water	12	Potamothrix vejdovskyi, Corbicula fluminalis, Limnomysis benedeni, Jaera istri, Chaetogammarus trichiatus
escape	aquaculture	9	Neomysis americana, Sinanodonta woodiana, Pontastacus leptodactylus, Hemigrapsus takanoi, Faxonius limosus
escape	pet	7	Faxonius limosus, Lissachatina fulica, Branchiodrilus hortensis, Pontastacus leptodactylus, Eobania vermiculata
escape	research	1	Eobania vermiculata
release	biological_control	5	Cryptolaemus montrouzieri, Harmonia axyridis, Rhyzobius forestieri, Hippodamia convergens, Rhyzobius lophanthae
release	fishery	2	Hemigrapsus sanguineus, Hemigrapsus takanoi
release	other	2	Cernuella virgata, Theba pisana
release	unknown	1	Deroceras invadens
stowaway	ballast_water	19	Hemigrapsus takanoi, Rangia cuneata, Psammoryctides moravicus, Tasserkidrilus americanus, Branchiodrilus hortensis
stowaway	container	10	Callobius nomeus, Plexippus paykulli, Latrodectus geometricus, Latrodectus hesperus, Grammostola rosea
stowaway	hull_fouling	3	Crangonyx pseudogracilis, Hypania invalida, Potamopyrgus antipodarum
stowaway	organic_packing	1	Anoplophora glabripennis
stowaway	other	7	Girardia tigrina, Physella acuta, Aedes japonicus, Potamopyrgus antipodarum, Aedes koreicus
stowaway	people_luggage	6	Cernuella aginnica, Cochlicella barbara, Coccinella miranda, Xeroplexa intersecta, Cernuella neglecta
stowaway	ship	3	Telmatogeton japonicus, Eobania vermiculata, Marenzelleria neglecta
stowaway	unknown	16	Cochlicella barbara, Sinanodonta woodiana, Corbicula fluminea, Corbicula fluminalis, Dreissena bugensis
stowaway	vehicles	8	Cernuella aginnica, Xeroplexa intersecta, Meconema meridionale, Cernuella virgata, Eupholidoptera chabrieri
unaided	natural_dispersal	11	Boettgerilla pallens, Ambigolimax valentianus, Xeroplexa intersecta, Dreissena polymorpha, Theba pisana
unknown	unknown	331	Trichopsocus clarus, Amphitomeus attemsi, Uloborus plumipes, Sinelobus vanhaareni, Tricellaria inopinata

3.5.1.4 Fungi

Pathways associated to fungi (category Fungi):

pathway_level1	pathway_level2	n	examples
escape	agriculture	1	Volvariella volvacea
unknown	unknown	15	Batrachochytrium dendrobatidis, Phragmidium mexicanum, Amanita inopinata, Entyloma eschscholziae, Seifertia azaleae

Note: add sections for other kingdoms if needed in the future.

3.6 Table of pathways related to EU policy relevant species

It is important to focus our attention also to a intercategory group of species which is of particular policy importance: the List of Invasive Alien Species of Union concern (see more info about here).

We import this list of species:

eu_concern_file <- here::here("data", "input", "eu_concern_species.tsv")
eu_concern_species <- read_tsv(eu_concern_file)

Check which species from this subgroup are not present in data:

eu_concern_species %>%
  tidylog::filter(!backbone_taxonKey %in% data$nubKey)

Categories present in this subgroup:

As done before, we limit to pathways of taxa introduced from 2000.

Create tables:

tables_eu_concern <- map(categories_eu_concern$category, ~
get_table_pathways(data %>%
  tidylog::filter(nubKey %in% eu_concern_species$backbone_taxonKey),
category = .,
from = start_year,
n_species = n_species
))
names(tables_eu_concern) <- categories_eu_concern$category

3.6.1 Plantae

Pathways associated to plants (category Plantae):

pathway_level1	pathway_level2	n	examples
escape	horticulture	2	Asclepias syriaca, Celastrus orbiculatus
unknown	unknown	5	Ludwigia grandiflora, Lysichiton americanus, Pistia stratiotes, Ludwigia peploides, Gunnera tinctoria

3.6.2 Chordata

Pathways associated to vertebrates (category Chordata):

pathway_level1	pathway_level2	n	examples
corridor	unknown	2	Oxyura jamaicensis, Procyon lotor
escape	pet	7	Procyon lotor, Acridotheres tristis, Callosciurus erythraeus, Trachemys scripta, Tamias sibiricus
escape	research	1	Xenopus laevis
escape	unknown	4	Callosciurus erythraeus, Oxyura jamaicensis, Tamias sibiricus, Procyon lotor
escape	zoo	3	Tamias sibiricus, Oxyura jamaicensis, Callosciurus erythraeus
release	hunting	1	Muntiacus reevesi
release	other	2	Trachemys scripta, Xenopus laevis
release	unknown	3	Oxyura jamaicensis, Tamias sibiricus, Procyon lotor
unaided	natural_dispersal	2	Procyon lotor, Oxyura jamaicensis
unknown	unknown	9	Callosciurus finlaysonii, Pycnonotus cafer, Sciurus niger, Lepomis gibbosus, Sciurus carolinensis

3.6.3 Not Chordata

Pathways associated to invertebrates (category Not Chordata):

pathway_level1	pathway_level2	n	examples
escape	aquaculture	3	Faxonius limosus, Pacifastacus leniusculus, Procambarus clarkii
escape	pet	2	Procambarus clarkii, Faxonius limosus
stowaway	ballast_water	1	Eriocheir sinensis