Syntopy in North American Passerines

Analysis of BBS Data with R

NoteMaterials and Methods

The study will use data from the North American Breeding Bird Survey (BBS), a long-term, standardised monitoring programme that records bird assemblages across approximately 2,900 routes annually. Each route includes 50 point counts spaced at 0.5-mile intervals. I will analyse patterns of syntopy at two spatial resolutions:

1. Point scale (individual stops) and

2. Transect scale (combined stops along each route).

To infer drivers of syntopy, I will replicate the analytical framework of Remeš & Harmáčková (2023), which uses cooccurrence analyses and species trait data to identify ecological predictors of coexistence. A novel feature of this thesis will be analysing syntopy at two spatial resolutions (see above).

Remeš, V. and Harmáčková, L. (2023), Resource use divergence facilitates the evolution of secondary syntopy in a continental radiation of songbirds (Meliphagoidea): insights from unbiased co-occurrence analyses. Ecography, 2023: e06268. https://doi.org/10.1111/ecog.06268

1 Data Preparation

1.1 Sister Pairs Extraction

In this code I will select sister species pairs of North American passerines for the subsequent analysis of syntopy using these packages:

clootl, diverge, tidyverse and ape.

Firstly we are going to select the phylogeny of wood-warblers to try the workflow. We can get the acces to eBird taxonomy files using taxonomyGet(), than we select the family of wood-warblers (Parulidae).

taxonomy <- taxonomyGet(taxonomy_year = 2021)
warblers <- taxonomy |> 
  filter(FAMILY == "Parulidae (New World Warblers)")
head(warblers, 3)

TAXON_ORDER	SPECIES_CODE	TAXON_CONCEPT_ID	PRIMARY_COM_NAME	SCI_NAME	ORDER1	FAMILY	ott_id	ott_name	ott_tax_sources	ott_match_type	H_M_name	H_M_match_type	Birdlife_name	Birdlife_match_type	IOC_name	IOC_match_type	underscores
32843	ovenbi1	avibase-CEA5B6AA	Ovenbird	Seiurus aurocapilla	Passeriformes	Parulidae (New World Warblers)	285207	Seiurus aurocapilla	ncbi:182946,worms:422653,gbif:2489590,irmng:11346310,irmng:11704550	canonical_match	Seiurus aurocapilla	concepts_match	Seiurus aurocapilla	concepts_match	Seiurus aurocapilla	concepts_match	Seiurus_aurocapilla
32847	woewar1	avibase-295C4CD6	Worm-eating Warbler	Helmitheros vermivorum	Passeriformes	Parulidae (New World Warblers)	860003	Helmitheros vermivorum	ncbi:182932,worms:422651,gbif:2489603,irmng:11833136,irmng:10856823	canonical_match	Helmitheros vermivorum	concepts_match	Helmitheros vermivorum	concepts_match	Helmitheros vermivorum	concepts_match	Helmitheros_vermivorum
32849	louwat	avibase-7AB0F3A4	Louisiana Waterthrush	Parkesia motacilla	Passeriformes	Parulidae (New World Warblers)	660355	Parkesia motacilla	ncbi:231571,worms:567886,gbif:6093862,irmng:10452680,irmng:11797571	canonical_match	Parkesia motacilla	concepts_match	Parkesia motacilla	concepts_match	Parkesia motacilla	concepts_match	Parkesia_motacilla

We need to select the species names vector for the tree extraction:

warb_names_vec <- warblers |> 
  select(SCI_NAME) |> 
  pull(SCI_NAME)
glimpse(warb_names_vec)

 chr [1:111] "Seiurus aurocapilla" "Helmitheros vermivorum" ...

We can extract the tree using extractTree() function from clootl package:

tree <- extractTree(species = warb_names_vec, taxonomy_year = 2021)
tree

Phylogenetic tree with 111 tips and 110 internal nodes.

Tip labels:
  Setophaga_chrysoparia, Setophaga_virens, Setophaga_occidentalis, Setophaga_townsendi, Setophaga_graciae, Setophaga_nigrescens, ...
Node labels:
  mrcaott5620ott285207, mrcaott5620ott860003, mrcaott5620ott285210, mrcaott5620ott85249, mrcaott5620ott63581, mrcaott5620ott757859, ...

Rooted; includes branch length(s).

We can plot it using ape package.

plot(tree, type = "fan", cex = 1.5, tip.color = "darkblue")

Now it’s time to extract species pairs using function extract_sisters() from diverge package:

sister_pairs <- extract_sisters(tree)
glimpse(sister_pairs)

Rows: 38
Columns: 2
$ sp1 <chr> "Setophaga_chrysoparia", "Setophaga_occidentalis", "Setophaga_grac…
$ sp2 <chr> "Setophaga_virens", "Setophaga_townsendi", "Setophaga_nigrescens",…