DOI: 10.5061/dryad.9s4mw6mfs
title: Characterizing the spatio-temporal threats, conservation hotspots and conservation gaps for the most extinction-prone bird family (Aves: Rallidae)

description: Here we worked on the rails (bird family Rallidae), looking at whether the
 current threats are consistent with those that led to recent extinctions,
 and ultimately, what conservation actions might be necessary to mitigate
 further losses. We undertook a global synthesis of the temporal and
 spatial threat patterns for Rallidae and determined conservation
 priorities and gaps.
description: <b>Database
 compilation</b> We compiled a database for all
 144 species of extant rails (including 42 island endemic species and 33
 threatened species) and 24 extinct rails using the 2019 version of the
 International Union for Conservation of Nature (IUCN) Red List (IUCN,
 2019) and the ‘Guide to the Rails, Crakes, Gallinules and Coots of the
 world’ (Taylor & van Perlo, 1998). We used the taxonomic
 classification followed by the IUCN which included the rallid family of
 Sarothruridae (some authors consider it separate from the Rallidae family,
 see (Garcia-R.<i> et al.</i>, 2014; Garcia-R<i> et
 al.</i>, 2020)). The Sarothruridae family contains 15 species,
 including two threatened species, and is mostly present in the
 Afrotropics. In preliminary analyses, we evaluated the effect of excluding
 this group, finding no major effect on results or their interpretations
 (except a minor effect of Threat rank of countries, see Table S1) and,
 thus, elected to retain the Sarothruridae in the Rallidae family. We
 considered island endemic species as those restricted to one or a group of
 adjacent islands. Species considered ‘Data deficient’ were excluded from
 the analysis (Table S2). Similarly, the New Caledonian rail
 (<i>Gallirallus lafresnayanus</i>) and the Samoan moorhen
 (<i>Pareudiastes pacificus</i>) are two ‘Critically
 endangered’ rail species that have not been seen with certainty since the
 19<sup>th</sup> century and are suspected to be extinct (IUCN,
 2019), so they were considered ‘extinct’ in this study (Table
 S2). <b>Spatial and temporal patterns of threats
 </b> We
 compiled the contemporary threats for all extant rails and historical
 causes of extinction for all extinct rails, available from the online IUCN
 database for each species (http://iucnredlist.org). The IUCN’s threats classification organises threats in a hierarchy (https://www.iucnredlist.org/resources/threat-classification-scheme). <i>2.1 Spatial threats patterns of extinct and threatened rails</i> First, we compared the historical causes of extinction (extinct rails) to the contemporary threats (threatened rails) to assess temporal changes in the threat pattern and changes in the spatial distribution of threatened and extinct species. Then, we described the number of threats impacting threatened and extinct species for different spatial scales (globally, on continents, on islands, between bioregions). For this analysis of threat diversity, we used the threats’ first sub-category as the level of threat (e.g., a rail being impacted by sub-categories ‘5.1. Hunting & collecting terrestrial animals’ and ‘5.3. Logging & wood harvesting’ within the threat ‘5. Biological resource use’ was considered as threatened by two threats). A total of 45 threats were considered, but only 28 were relevant to rails. <i>2.2 Spatial threats patterns of all extant rails</i> We assessed the spatial pattern of contemporary threats for all extant rails (whether or not they were considered threatened by the IUCN) by descriptively comparing the type of threats and their impact: i) globally, ii) on islands, iii) on continents, and iv) by bioregions (biogeographic realms, hereafter ‘bioregions’: Australasia, Oceania, Nearctic, Neotropics, Palearctic, Afrotropics, Indomalaya; defined following (Olson<i> et al.</i>, 2001)). Oceania was grouped with the Australasia bioregion because of its few extant species (five, including three present across the two bioregions). We calculated each threat’s impact score using the <i>Threat Impact Scoring System</i> (<i>IUCN - CMP Unified Classification of Direct Threats</i>, version 3.2) proposed by the IUCN (2019) that defines an overall impact based on scope, severity and timing, and ranges within ‘Negligible’, ‘Low’, ‘Medium’, and ‘High’ impact (https://www.iucnredlist.org/resources/threat-classification-scheme; Fig. S1). If a threat had a different impact in two sub-categories, we used the higher impact for the classification. We included ‘Past’ and ‘Ongoing’ impact to illustrate the temporal evolution of threats (‘Future’ was not considered). For this analysis, we used the first category as the level of threat (e.g., 1. ‘Residential & commercial development’ and 2. ‘Agriculture’) to be more informative. We split the threat ‘5. Biological resource use’ in two categories: ‘Hunting & collecting terrestrial animals’ (5.1.) and ‘Logging & indirect effects’ (regrouping ‘5.2. Gathering terrestrial plants’, ‘5.3 Logging & wood harvesting’, and ‘5.4. Fishing & harvesting aquatic resources’) to provide relevant conservation policy. The sub-category ‘10. Geological events’ was not included because it was not listed for any species. <b>Conservation status and gaps </b> To identify gaps in conservation efforts for rails, we summarised the IUCN’s <i>Conservation actions classification scheme</i> version 2.0 (https://www.iucnredlist.org/resources/conservation-actions-classification-scheme)<i> </i>and <i>Research needed classification scheme</i> version 2.0 (https://www.iucnredlist.org/resources/research-needed-classification-scheme): i) globally, ii) per country, and iii) per bioregion, following Olah <i>et al.</i> (2016). Countries and overseas territories were grouped together for country-level analysis (Table S3). These schemes specify the conservation actions and research needed for each species and were available on the online IUCN database (http://iucnredlist.org). We gathered the possible classifications in five categories: (i) ‘Research & Monitoring’, (ii) ‘Ecosystem Protection & Management’, (iii) ‘Species Management’, (iv) ‘Education & Awareness’, and (v) ‘Law & Policy’ (i.e., legislative protection). (i) ‘Research & Monitoring’ category was formed by grouping all categories in the <i>Research Needed Classification Scheme</i>: ‘1. Research’, ‘2. Conservation Planning’, ‘3. Monitoring’, and ‘4. Other’. (ii) ‘Ecosystem Protection & Management’ category was formed by grouping the first two categories, ‘1. Land/water protection’ and ‘2. Land/water management’, in the <i>Conservation Actions Classification Scheme</i>. (iii) ‘Species Management’, (iv) ‘Education & Awareness’, and (v) ‘Law & Policy’ corresponded directly to each remaining category in the <i>Conservation Actions Classification Scheme</i>. Furthermore, category ‘6. Livelihood, economic & other incentives’ of the <i>Conservation Actions Classification Scheme</i> was not represented as it did not appear in any of the studied species. To assess whether conservation status had improved or deteriorated over time, we characterised changes in species’ IUCN conservation status since 1988 (first IUCN Red List assessment) through to 2019 (IUCN, 2019). Changes in conservation status could happen any year between 1988 and 2019. In cases where status changed more than once, we only used the most recent change. We considered ‘Unknown (LR/LC)’ as Least Concern and ‘Unknown (LR/NT)’ as Near Threatened when they were the assessments preceding a new status. However, we ignored it when included between two assessments. For example, if a species conservation status’ history was: 1996: Vulnerable (VU); 2000: Unknown (LR/NT); 2004: Near threatened (NT), we considered that the species improved from Vulnerable to Near threatened. <b>Rails ‘conservation hotspots’ and priority rankings</b> Rallidae combine species with unique evolutionary traits (e.g., flightlessness and endemism) and species with elevated vulnerability (24% of the species are threatened); however to date, there is no framework that accounts for these important aspects in terms of conservation priority. To identify areas with high conservation interest and/or those that deserve improvements in their protection, we conceived a ranking system to classify both world bioregions and countries of high conservation priority for rails (‘conservation hotspots’). Analysis at the country-level grouped countries and their overseas territories together (Table S3). We created two categories that we deemed useful to reflect important rail conservation: ‘Heritage’ and ‘Threat’. The ‘Heritage’ category aimed to account for species with high conservation value, using endemism and unique evolutionary trait (flightlessness). It was calculated by ranking the number of rail species being either flightless (firstly), island endemic (secondly), or country endemic (thirdly). When relevant, species were classified by one of the above attributes, in this hierarchical order. For instance, a flightless rail that is also endemic to an island, would only be classified as ‘flightless’, and an island endemic rail that is also endemic to one country, would only be classified as ‘island endemic’. The ‘Threat’ category was calculated by ranking the number of threatened species (firstly), and the number of species with a worsened IUCN status since their last change in status (secondly). In cases where ranks were equal, they were split using the country/bioregion’s richness in rail species as the tie breaker (i.e., higher richness would get the higher rank of conservation importance). In this rank system, rank one represents the highest rank for conservation priority. The rank classifications were not made to adequately differentiate between two entities as close scores would not illustrate true difference in conservation priority. We recommend identifying entities with the highest conservation priority as the ones present in both top classifications for the two ranks, or as parts of a top 5, top 10, or top 20. <b>REFERENCES</b> Garcia-R, J.C., Lemmon, E.M., Lemmon, A.R. & French, N. (2020) Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution. <i>Diversity</i>, <b>12</b>, 70. https://doi.org/10.3390/d12020070 Garcia-R., J.C., Gibb, G.C. & Trewick, S.A. (2014) Deep global evolutionary radiation in birds: diversification and trait evolution in the cosmopolitan bird family Rallidae. <i>Molecular Phylogenetics and Evolution</i>, <b>81</b>, 96-108. https://doi.org/10.1016/j.ympev.2014.09.008 IUCN (2019) <i>The IUCN Red List of Threatened Species. Version 2019-3.</i> Available at:  http://www.iucnredlist.org (accessed 12 December 2019) Olah, G., Butchart, S.H.M., Symes, A., Guzmán, I.M., Cunningham, R., Brightsmith, D.J. & Heinsohn, R. (2016) Ecological and socio-economic factors affecting extinction risk in parrots. <i>Biodiversity and Conservation</i>, <b>25</b>, 205-223. https://doi.org/10.1007/s10531-015-1036-z Olson, D.M., Dinerstein, E., Wikramanayake, E.D., Burgess, N.D., Powell, G.V., Underwood, E.C., D'amico, J.A., Itoua, I., Strand, H.E. & Morrison, J.C. (2001) Terrestrial Ecoregions of the World: A New Map of Life on Earth. A new global map of terrestrial ecoregions provides an innovative tool for conserving biodiversity. <i>BioScience</i>, <b>51</b>, 933-938. https://doi.org/10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2 Taylor, B. & van Perlo, B. (1998) <i>Rails: a guide to rails, crakes, gallinules and coots of the world</i>. Pica Press, Mountfield, U.K.
description: Date of data collection: 2017-2020 Date file
 was written: 2021/02/01 For more information on
 methods, please refer to publication preprint
 (https://doi.org/10.1101/2021.01.20.427508). All
 modelling is done in R software. The dataset is
 separated into two parts: 1. THREAT PATTERN: look at
 characterising how threats are distributed at different scales
 (bioregions, global and islands), the threat diversity per species, and
 compare their intensity spatially. We also looked at the causes of
 extinctions in extinct rails from the 16th century onwards to compare with
 modern threat pattern. Variables in code are:
 1.1. THREAT DIVERSITY (R.file 'Leveque et al. threat
 diversity') -iucn: iucn conservation status: T=
 threatened (include 'vulnerable', 'endangered',
 'critically endangered'); NoT= not threatened ('not
 concerned', 'near threatened')
 -common.name: vernacular name of the species
 -island.ende: whether the species is island endemic (value:
 "yes" or "no") -flightless:
 whether  the species is flightless (value: "flightless" or
 "flying") -threatdiv: how many threats each
 species is suffering from -scale: the spatial scale
 considered (value: 'gl.combined': global scale (both continental
 and island species, including threatened ('T') and
 non-threatened ('NoT') species; 'global': both
 continental and island species; 'continent': continental species
 only; 'island': island endemic species only)
 -type: the spatial scale with the threatened status of a species
 (value: 'combined': threatened and non-threatened species
 together; 'globalT': global scale for threatened species only;
 'globalNoT': global scale for non-threatened species only;
 'continent-T': continental species that are threatened only;
 'continent-NoT': continental species that are non-threatenend
 only; 'island-T': island endemic species that are threatened
 only; 'island-NoT': island endemic species that are
 non-threatened only) 1.2. THREAT PATTERNS (R.files
 'Leveque et al. threats_global and island' and 'Leveque et
 al. threats_regions') -threat: threats impacting
 species (value according to the ICUN: "Residential &
 commercial development"; "Agriculture"; "Energy
 production and mining"; "Transportation & service
 corridors"; "Hunting & collecting animals";
 "Logging & wood harvesting"; "Human intrusions
 & disturbance"; "Natural system modifications";
 "Invasive & problematic species"; "Pollution";
 "Climate change & severe weather";
 "Other") -impact: the strength of the threat
 impact, according to the IUCN (value: "Low Impact", "Medium
 Impact", "Unknown", "Past Impact")
 -percentage: percentage of species impacted by the threat at this
 scale -nb. sp: the number of species impacted by the
 threat at this scale -scale: scale considered (value:
 "Gb": global; "Is": island endemic species;
 "Ct": continental species) REGIONS
 -region: bioregion a species is found in (value: Afrotropic;
 Australasia/Oceania; Indomalaya; Nearctic; Neotropic ;Other; Palearctic.
 Other refers to remote islands in the Atlantic ocean that were hardly
 associable with a bioregion. (note: the same species can be present in
 different bioregions) -iucn: iucn conservation status:
 'VU' (vulnerable); EN (endangered); CR (critically endangered);
 LC (least concerned), NT (near threatened) 2. RANKINGS
 AND GAPS: Look at describing what conservation gaps are missing per rail
 species (based on the IUCN database, available on their website
 online).<br> Secondly, we created a ranking system to find what
 countries and what bioregions are in priority for conservation (the ones
 that need to organise conservation efforts the most). The ranking system
 is based on the degree of threat and threatening clues (having a degraded
 IUCN status; 'Threat rank'). The other ranking system is based
 on the uniqueness of species (flightless, island endemic or country
 endemic) for their cultural value ('Heritage' rank) that
 therefore should have inforced conservation efforts. The two ranks are
 analysed separately, but in the case of countries present in two ranks,
 these are of the highest priority for conservation actions.
 R.files are: 'Leveque et al. 2021 -
 ranking_gaps_countries' and 'Leveque et al. 2021 -
 ranking_gaps_regions_2020')<br> Variables in R code
 are: -iucn: iucn conservation status: T= threatened
 (include 'vulnerable', 'endangered', 'critically
 endangered'); NoT= not threatened ('least concerned',
 'near threatened'). -country: country name
 where rail species are present (note: the same species can be present in
 different countries) -n: number of countries
 -bioregion: bioregion a species is found in (value: Afrotropic;
 Australasia/Oceania; Indomalaya; Nearctic; Neotropic ;Other; Palearctic.
 Other refers to remote islands in the Atlantic ocean that were hardly
 associable with a bioregion. (note: the same species can be present in
 different bioregions) -research: gap in ‘Research,
 Monitoring and Planning’(value: 'needed' (later '1')
 and 'no (later '0')) -habitat.prot: gap
 in ‘Ecosystem Protection and Management’(value: 'needed' (later
 '1') and 'no (later '0'))
 -management: gap in ‘Species Management’ (value:
 'needed' (later '1') and 'no (later
 '0')) -education : gap in ‘Education
 & Awareness’ (value: 'needed' (later '1') and
 'no (later '0')) -law : gap in ‘Law
 & Policy’ (i.e., legislative protection) (value:
 'needed' (later '1') and 'no (later
 '0')) -lack: average number of conservation
 gaps per threatened sp. -degraded.status: if the iucn
 conservation status has deteriorated (value: 'improved'  or
 'yes') -richness: countries sp richness
 (rails) (value: number of rails species) -island.ende:
 whether the species is island endemic (value: "yes" or
 "no" -flightless: whether  the species is
 flightless (value: "flightless" or "flying")
 -country.end: whether  the species is endemic to a (value:
 "yes" or "no")