DOI: 10.5061/dryad.3n5tb2rwp
title: Data from: Corridors and reservoirs: An analysis of inter-Andean historical biogeography

description: The Andes are a global biodiversity hotspot, and the formation of this
 mountain range has been linked to the rapid diversification of numerous
 lineages across the Tree of Life. In addition to generating high species
 richness, the Andes may have functioned as a reservoir from which lineages
 dispersed across South America. Recent syntheses of Andean geological
 history, together with the growing number of phylogenetic studies across
 diverse Andean clades, provide an opportunity to integrate current
 knowledge of the historical biogeography of the Andean biota. Here, we
 present a meta-analysis of phylogenetic studies in which we scored
 disjunction events within and out of the Andes based on published
 biogeographic reconstructions. Across clades and through time, dispersal
 events within the Andes were approximately as frequent as those out of the
 Andes. The highest number of extra-Andean disjunctions originated in the
 northern Andes, despite this region being the most recently uplifted. Our
 results also indicate sustained bidirectional dispersal within the Andes
 over the past 50 million years, with northward dispersals occurring at a
 slightly but significantly higher rate than southward movements.
 Furthermore, crown clades of Andean plants tend to be older than those of
 animals, the latter largely originating within the past 30 million years.
 Overall, these findings demonstrate that the Andes have functioned both as
 a reservoir and as a corridor of biodiversity across clades with widely
 differing dispersal strategies.
description: # Data from: Corridors and reservoirs: An analysis of inter-Andean
 historical biogeography Dataset DOI:
 [10.5061/dryad.3n5tb2rwp](10.5061/dryad.3n5tb2rwp) ## Description of the
 data and file structure Using a Python script, we performed three rounds
 of web scraping of Google Scholar search results for the keyword “Andes.”
 Each web scraping round targeted publications that cite a specific major
 historical biogeographic reconstruction methodology. The first round
 scraped all the publications from 2014 to 2024 that cited the R package
 BioGeoBEARS (Matzke 2014) and returned 304 results. The second round
 scraped all publications from 2016 to 2024 that cited RevBayes (Höhna et
 al. 2016), returning 62 results. The last round scraped all publications
 from 2013 to 2024 that cited LagRange (Matzke 2013), returning 178
 results. Among the scrape results, we excluded publications that did not
 perform ancestral reconstructions on a time-calibrated phylogeny, lacked
 at least one dispersal either out of or within the Andes, treated the
 entire Andes as one region in the phylo-biogeography analysis, or were not
 published in a peer-reviewed journal (e.g., a thesis). Finally, we
 excluded duplicates across scrape rounds. For our scoring, we identified
 three regions in the Andes: northern, central, and southern. This is
 consistent with the regions used in the majority of biogeographical
 studies of the Andes and corresponds to major geologic and climatic
 barriers across the Andean range (Boschman, 2021; Luebert & Weigend,
 2014; Pérez-Escobar et al., 2022). We only scored papers that included at
 least two of the three regions so that we could infer directionality of
 movement within the Andes. In total, we retained 52 studies out of 544
 identified from our scraping process (see Appendix S1 in Supporting
 Information). For each paper, we recorded the major taxonomic group, clade
 name, areas represented (of northern Andes, central Andes, southern Andes,
 and outside of the Andes), and the crown age of the most inclusive clade
 with Andean origin. If multiple Andean clades with non-Andean common
 ancestry were present, we treated each clade separately. Within the target
 clade, we recorded each disjunction event separately, including the
 origin, destination, and age of movement. For reconstructions with
 weighted probabilities, we required &gt;50% to assign to a region. We
 biased our estimated ages of disjunction toward minimum ages by assigning
 the age of disjunction to the crown clade rather than the stem. Shifts
 occurring between the most recent node and the tip were recorded as “0.00
 Ma.” We only scored inferred dispersals out of the Andes and not back in,
 as these were not relevant to our questions, and did not record range
 contractions (e.g., an inferred movement from northern Andes + central
 Andes to only northern Andes). ### Files and variables #### File:
 scoring_clean.csv **Description:**  ##### Variables * paper_ID: assigned
 ID number * doi: doi of paper scored * scorer: person who did the scoring
 * taxonomy: taxonomic group ofa  clade of study * areas: areas of the
 Andes defined and included in the historical biogeography analysis *
 clade: name assigned to the Andean clade * crown_age: crown age of the
 Andean clade * region_shift: includes origin and destination of movement *
 origin: inferred movement origin * destination: inferred movement
 destination  * dispersal_age: inferred age of movement * direction:
 inferred directionality of movement * notes: notes #### File:
 scraped_papers.xlsx **Description:** This is the document containing
 sheets with all scraped papers, sorted by citation. It was not used for
 downstream analyses, but rather to keep track of manual scoring of all
 papers and elimination of non-relevant papers.   ##### Variables *
 Tabs/sheets: citation of scraped papers * Duplicate: whether or not the
 paper appears more than once across all sheets * Title: title of paper *
 Authors: authors of the paper * Date: publication date * Publisher:
 publisher * Person: initials of the person who scored the paper *
 Relevant: whether or not the paper was included in our study * If no, why
 excluded: reason for excluding * Done: whether scored or not  #### File:
 scraped_papers.csv **Description:** the same as above, but in csv format,
 collapsed into a single sheet without formatting.