jhpoelen/bat-taxonomic-alignment

prototype focused on bat names

bat-taxonomic-alignment's Issues

suggest to put a static "pretty" colorized version of bta sheet (aka ForPub) on the website https://..../bat-taxonomic-alignment

order BTA by interesting-ness - order by (un-harmonized taxonomic names) level of disagreements

when using BTA, I'd like to understand which taxonomic concepts are "interesting", where an interesting taxonomic concept is one in which interpretation varies across taxonomic authorities.

E.g.,

taxonomicId	name	authority
BTA:895@eb557c6d	Neoromicia - see robertsi	name_HMW
BTA:895@eb557c6d	Laephotis - see capensis	name_batnames
BTA:895@eb557c6d	**	name_ALC
BTA:895@eb557c6d	**	name_GBIF
BTA:895@eb557c6d	Laephotis - see capensis	name MDD
BTA:895@eb557c6d	Neoromicia melckorum	name_MSW4

For this example, we see that only MSW and IUCN agree.

We'd like to quantify this degree of agreeness.

Aja's idea is to list all permutations of authority pairs (e.g., MSW vs IUCN, MSW vs HMW) and score them with a 0 if they agree, and 1 if they disagree.

Now, a agreement index can be generated by:

agreeness index = sum (disagreements ) / total comparison

Absolute difference in interpretation across all different authorities.

In our example above, the score / distance (need to find a corresponding existing measure name) would be:

comparison table:

name_HMW vs

in pairwise comparison table 1. display disagreements and total amount of overlap for pair only

color blind sensitive palette like viridis.

Suggest to color codes to help guide.

include split annotations provided by @n8upham

"previously included P. fuscus, P. mesoamericanus, P. mexicanus, P. portoricensis, P. pusillus, and P. rubiginosus" ==
Pteronotus parnellii	Pteronotus fuscus			(note geolocation)
Pteronotus parnellii	Pteronotus mesoamericanus	(note geolocation)
Pteronotus parnellii	Pteronotus mexicanus		(note geolocation)
Pteronotus parnellii	Pteronotus portoricensis	(note geolocation)
Pteronotus parnellii	Pteronotus pusillus			(note geolocation)
Pteronotus parnellii	Pteronotus rubiginosus		(note geolocation)
Pteronotus parnellii	Pteronotus paraguanensis	(note geolocation)
Pteronotus parnellii	Pteronotus parnellii		Cuba and Jamaica

with connecting verb being "was split into" or "split"

e.g.,

According to Nathan Upham, the text fragment previously included P. fuscus, P. mesoamericanus, P. mexicanus, P. portoricensis, P. pusillus, and P. rubiginosus extracted from (note content citation) claims that Pteronotus parnellii was split into Pteronotus fuscus with distribution range (note geolocation) .

see attached screenshot

develop method to automatically add a taxonomic checklist (e.g., study, taxonomic authority) to the BTA as an authority

currently, we have some authorities: MSW3, HMW2019, etc.

We'd like to develop a method to (semi-) automatically add other authorities to into the BTA.

For instance, we'd want to add the ITIS taxonomy including all taxonomic notes, references, and add this the to the appropriate treatment/taxonomic concept in the BTA datasets.

add agreementindex on family level to help guide taxonomist to bat families in need

As suggested by @ajacsherman

most agreements between batnames 2023, MDD, HMW2019 on the family level.

Guiding question - which bat families have the least agreement and need attention of taxonomist?

suggest to add Catalogue of Life as a taxonomic authority

Group the heat map squares by genus and/or family

HQ HR
DR DU

https://jhpoelen.nl/bat-taxonomic-alignment/#map

add addition column "treatmentId" to names.tsv to capture the name relations

instead of:

id	scientificName
name_batnames	Rhinolophus sinicus
name_GBIF	Rhinolophus sinicus
name_HMW	Rhinolophus - see sinicus septentrionalis
name_HMW	Rhinolophus sinicus
name MDD	Rhinolophus - see sinicus
name MDD	Rhinolophus sinicus
name_MSW4	Rhinolophus sinicus

we'd like to have,

id	taxonomicId	scientificName
name_batnames	BTA_v2.1:1318	Rhinolophus sinicus
name_GBIF	BTA_v2.1:1318	Rhinolophus sinicus
name_HMW	BTA_v2.1:1317	Rhinolophus - see sinicus septentrionalis
name_HMW	BTA_v2.1:1318	Rhinolophus sinicus
name MDD	BTA_v2.1:1317	Rhinolophus - see sinicus
name MDD	BTA_v2.1:1318	Rhinolophus sinicus
name_MSW4	BTA_v2.1:1318	Rhinolophus sinicus

where BTA_v2.1 refers to a specific version of the Bat Taxonomic Alignment . Note that the taxonomicIds may change across versions for now. Because the taxonomicIds are derived from the row number that the name come from.

carriage returns in BTA tsv export causing misalignment of data when importing into speadsheets

to reproduce:

download a BTA version using

curl "https://linker.bio/hash://sha256/981b8f9ece76eb4418fe82e8dfa077165943fe1d63103fa4a25f21a2d7881e75"\
 > bta.tsv

open the bta.tsv into a spreadsheet program like LibreOffice Calc.

Expected to see well-aligned data.

Actual notice apparent truncated lines causing incomplete rows (see screenshot).

Root cause appears to be carriage returns embedded in the tsv file. In vi these carriage returns are encoded as ^M .

cat bta.tsv\
 | grep -n "bunkeri"\
  | head -n1 > aline.tsv

with

cat aline.tsv | wc -l yielding "1", indicated that only a single new line exists (\n). However, when opening the aline.tsv in LibreOffice Calc, multiple lines are observed, apparently caused by occurrences of carriage returns (\r or ^M).

@n8upham

create a flow diagram and description of the process of name alignment

to help document the process of name alignment

use case: when "Thomas's fruit-eating bats" align with BTA_55@26d368c7 aka "Dermanura watsoni" by MDD

Note that BTA_55@25d368c7 can be expressed as

curl 'https://linker.bio/line:hash://sha256/26d368c772f240d65645248caa56dabae5cb2414ac57e8f0438d4c3dcf62e377!/L2,L55.tsv'\
 | mlr --itsvlite --oxtab cat

results in:

Name_MSW3                                    Artibeus watsoni
Name_HMW                                     Artibeus watsoni
Name_BatNames                                Dermanura watsoni
Name_MDD                                     Dermanura watsoni
Name_IUCN                                    Dermanura watsoni
Name_BatNames_2023                           Dermanura watsoni
                                             
name_MSW3                                    Artibeus incomitatus
name_HMW2019                                 Artibeus watsoni
name_batnames                                Dermanura watsoni
name_MDD                                     Dermanura watsoni
taxonomic_notes_concatenated                 HMW: Artibeus watson: Thomas, 1901 , “Bogava [= Bugaba,] Chiriqui , Panama . Altitude 250 m .” Artibeus watsoni is placed in Dermanura by some authors, but it was reassigned to Artibeus (subgenus Dermanura ) after reinterpretation of molecular results. Dermanura jucundum Elliot 1906 from Veracruz (S Mexico ) has been considered a synonym; A. incomitatus described by E. K. V. Kalko and C. O. Handley, Jr., 1994 from Isla Escudo ( Panama ) is molecularly the same as A. watson . Other authors also listed A. rosenbergi from north-western Ecuador as a synonym, but it is a distinct species based on molecular and morphological analyses. Monotypic. BatNames: Subgenus Dermanura . Distinct from glaucus ; see Handley (1987). Includes incomitata; see Solari et al(2008). MDD: includes incomitatus; moved to Dermanura from Artibeus, although some recent publications do not agree with this split, there seems to be more publications using this revised taxonomy rather than leaving all species under Artibeus IUCN: <p>Subgenus<span class="apple-converted-space">&#160; Dermanura . This subgenus has been recognized as a separate genus on molecular grounds, but there are no diagnostic morphological differences from<span class="apple-converted-space">&#160; Artibeus <span class="apple-converted-space"> &#160; (Lim<span class="apple-converted-space">&#160; et al .&#160;2004).</span></span></p> msw3: Subgenus Dermanura. Distinct from glaucus; see Handley (1987). See also Kalko and Handley (1994).
_2                                           
MDD_v1.10_in_review                          
_3                                           
no_match_MSW_HMW                             0
no_match_MSW_batnames                        1
no_match_MSW_MDD                             1
no_match_MSW_IUCN                            1
no_match_MSW_batnames2023                    1
no_match_HMW_batnames                        1
no_match_HMW_MDD                             1
no_match_HMW_IUCN                            1
no_match_HMW_batnames2023                    1
no_match_batnames_MDD                        0
no_match_batnames_IUCN                       0
no_match_batnames_batnames2023               0
no_match_MDD_IUCN                            0
no_match_MDD_batnames2023                    0
no_match_IUCN_batnames2023                   0
spelling                                     
_4                                           
Subspecies_MSW_interpreted                   
Synonym_MSW_interpreted                      jucundum
subspecies_HMW_interpreted                   
synonym_HMW_interpreted                      rosenbergi?, jucundum, incomitatus
subspecies_batnames_interpreted              
synonym_batnames_interpreted                 jucundum, incomitatus
synonym_MDD_interpreted                      watsoni, jucundum, incomitatus
_5                                           
name_GBIF                                    Artibeus watsoni
status_GBIF                                  ACCEPTED
rank_GBIF                                    SPECIES
_6                                           
docId                                        03A687BCFFEDFFEC168CF3F2FD87FB81
docOrigin                                    Handbook of the Mammals of the World – Volume 9 Bats, Barcelona: Lynx Edicions
docISBN                                      978-84-16728-19-0
docName                                      hbmw_9_Phyllostomidae_444.pdf.imf
docMasterId                                  hash://md5/ff9fffc4ffb1ffb1133cffbaffe0f244
docPageNumber                                576
derivedFrom                                  zip:hash://sha256/ec5fd314a06aba1a7b0b72f23e54ac625ae272bd98f82f1d01f4c09627d9e8e0!/treatments-xml-main/data/03/A6/87/03A687BCFFEDFFEC168CF3F2FD87FB81.xml
name_HMW                                     Artibeus watsoni
family_HMW                                   Phyllostomidae
interpretedGenus                             Artibeus
interpretedSpecies                           watsoni
interpretedAuthorityName                     Thomas
interpretedAuthorityYear                     1901
commonNames                                  Dermanure de Watson @fr | Thomas-Fruchtvampir @de | Artibeo de Watson @es | Watson's Fruit-eating Bat @en
taxonomy                                     Artibeus watson: Thomas, 1901 , “Bogava [= Bugaba,] Chiriqui , Panama . Altitude 250 m .” Artibeus watsoni is placed in Dermanura by some authors, but it was reassigned to Artibeus (subgenus Dermanura ) after reinterpretation of molecular results. Dermanura jucundum Elliot 1906 from Veracruz (S Mexico ) has been considered a synonym; A. incomitatus described by E. K. V. Kalko and C. O. Handley, Jr., 1994 from Isla Escudo ( Panama ) is molecularly the same as A. watson . Other authors also listed A. rosenbergi from north-western Ecuador as a synonym, but it is a distinct species based on molecular and morphological analyses. Monotypic.
subspeciesAndDistribution                    From S Mexico ( Veracruz ) through Central America (mainly in the Caribbean lowlands of Costa Rica ) to SE Panama . Records from NW South America would represent A. rosenbergi , which was thought to be part of this taxon.
descriptiveNotes                             Head-body 50-58 mm (tailless), ear 14-17 mm, hindfoot 8-12 mm, forearm 35-41 mm; weight 9-15-6 g. Thomas’s Fruit-eating Bat is small, with facial stripes and short broad rostrum. Dorsalfur is gray-brown or tan, long (6-7 mm), fluffy, and faintly tricolored. Rostrum has two well-marked white facial stripes, but supraocular is more evident than subocular. Ventralfur is slightly paler than dorsum. Ears and noseleaf are pale brown, and bases of ears are sometimes edged in white, cream, or rarely yellow. Horseshow of noseleafis free. Fur covers more than one-half of each forearm. Wing membranes are brownish, except for second interdigital membrane that lacks pigmentation. Tail membrane is pale brown, moderated in size (10-12 mm), U-shaped, and almost completely naked. Dental formulais12/2,C1/1,P2/2,M 2/3 ( x2 ) = 30. Skull has inflated frontal and supraorbital areas. Hypocone (talon) on M' is narrow, and M, is small, but it does not have defined cusps.
habitat                                      Common to abundant in semideciduous and evergreen lowlands forests, second growth, and fruit groves and also upland and swamp forests on islands from lowlands to elevations of ¢. 1500 m (usually below 800 m ). Thomas’s Fruit-eating Bat favors taller and more humid forests than the Pygmy Fruit-eating Bat (A. phaeotis ).
foodAndFeeding                               Thomas’s Fruit-eating Bat is mainly frugivorous and includes fruits of Ficus spp. ( Moraceae ), Cecropia spp. ( Urticaceae ), and Piper spp. ( Piperaceae ) in its diet.
breeding                                     Breeding pattern of Thomas's Fruit-eating Bat has been characterized as a bimodal polyestry. Most reproductive females were found in February and June but records include February-April,July-August, and November. Without exception, each gravid female had one embryo.
activityPatterns                             Thomas’s Fruit-eating Bats is nocturnal. It seems to be active at the first hour after sunset and again in early morning hours. It appears to be an obligate tent-maker because it has not been found roosting in other situations. For tents,it modifies leaves of Heliconia ( Heliconiaceae ), banana ( Musaceae ), bifid and palmate palm ( Anthurium , Araceae ), and species of Cyclanthaceae . Leaves are cut in a variety of styles, depending on shape and size. Individuals (usually males) occupying a tent roost make distinctive multiharmonic social call. These calls could help females find available roosts, or indicate presence of a male in the tent to other males.
movementsHomeRangeAndSocialOrganization      Thomas’s Fruit-eating Bat roost alone or form small groups. Variation in roost fidelity among males and females, and among individuals under different breeding conditions, depended on relative roost availability. In a fragmented landscape in Panama , home ranges of radio-tracked individuals varied widely from 1-8 ha to 17-9 ha (mean c.9 ha).
statusAndConservation                        Classified as Least Concern on The IUCN Red List (as Dermanura watsoni ). Thomas's Fruit-eating Bat has a wide distribution, is locally common, occurs in protected areas, and is tolerant of some degree of habitat modification, suggesting population stability.
bibliography                                 Albrecht et al. (2007) | Andersen (1908c) | Chaverri et al. (2007) | Davis (1970a) | Gillam et al. (2013) | Kalko & Handley (1994) | LaVal & Rodriguez-Herrera (2002) | Reid (2009) | Rodriguez-Herrera et al. (2007) | Stoner (2001) | Thomas (1897a, 1901a) | Timm (1987)
distributionImageURL                         https://zenodo.org/record/6458995/files/figure.png
verbatimText                                 200. Thomas's Fruit-eating Bat Artibeus watsoni French: Dermanure de Watson / German: Thomas-Fruchtvampir / Spanish: Artibeo de Watson Other common names: Watson's Fruit-eating Bat Taxonomy. Artibeus watson: Thomas, 1901 , “Bogava [= Bugaba,] Chiriqui , Panama . Altitude 250 m .” Artibeus watsoni is placed in Dermanura by some authors, but it was reassigned to Artibeus (subgenus Dermanura ) after reinterpretation of molecular results. Dermanura jucundum Elliot 1906 from Veracruz (S Mexico ) has been considered a synonym; A. incomitatus described by E. K. V. Kalko and C. O. Handley, Jr., 1994 from Isla Escudo ( Panama ) is molecularly the same as A. watson . Other authors also listed A. rosenbergi from north-western Ecuador as a synonym, but it is a distinct species based on molecular and morphological analyses. Monotypic. Distribution. From S Mexico ( Veracruz ) through Central America (mainly in the Caribbean lowlands of Costa Rica ) to SE Panama . Records from NW South America would represent A. rosenbergi , which was thought to be part of this taxon. Descriptive notes. Head-body 50-58 mm (tailless), ear 14-17 mm, hindfoot 8-12 mm, forearm 35-41 mm; weight 9-15-6 g. Thomas’s Fruit-eating Bat is small, with facial stripes and short broad rostrum. Dorsalfur is gray-brown or tan, long (6-7 mm), fluffy, and faintly tricolored. Rostrum has two well-marked white facial stripes, but supraocular is more evident than subocular. Ventralfur is slightly paler than dorsum. Ears and noseleaf are pale brown, and bases of ears are sometimes edged in white, cream, or rarely yellow. Horseshow of noseleafis free. Fur covers more than one-half of each forearm. Wing membranes are brownish, except for second interdigital membrane that lacks pigmentation. Tail membrane is pale brown, moderated in size (10-12 mm), U-shaped, and almost completely naked. Dental formulais12/2,C1/1,P2/2,M 2/3 ( x2 ) = 30. Skull has inflated frontal and supraorbital areas. Hypocone (talon) on M' is narrow, and M, is small, but it does not have defined cusps. Habitat. Common to abundant in semideciduous and evergreen lowlands forests, second growth, and fruit groves and also upland and swamp forests on islands from lowlands to elevations of ¢. 1500 m (usually below 800 m ). Thomas’s Fruit-eating Bat favors taller and more humid forests than the Pygmy Fruit-eating Bat (A. phaeotis ). Food and Feeding. Thomas’s Fruit-eating Bat is mainly frugivorous and includes fruits of Ficus spp. ( Moraceae ), Cecropia spp. ( Urticaceae ), and Piper spp. ( Piperaceae ) in its diet. Breeding. Breeding pattern of Thomas's Fruit-eating Bat has been characterized as a bimodal polyestry. Most reproductive females were found in February and June but records include February-April,July-August, and November. Without exception, each gravid female had one embryo. Activity patterns. Thomas’s Fruit-eating Bats is nocturnal. It seems to be active at the first hour after sunset and again in early morning hours. It appears to be an obligate tent-maker because it has not been found roosting in other situations. For tents,it modifies leaves of Heliconia ( Heliconiaceae ), banana ( Musaceae ), bifid and palmate palm ( Anthurium , Araceae ), and species of Cyclanthaceae . Leaves are cut in a variety of styles, depending on shape and size. Individuals (usually males) occupying a tent roost make distinctive multiharmonic social call. These calls could help females find available roosts, or indicate presence of a male in the tent to other males. Movements, Home range and Social organization. Thomas’s Fruit-eating Bat roost alone or form small groups. Variation in roost fidelity among males and females, and among individuals under different breeding conditions, depended on relative roost availability. In a fragmented landscape in Panama , home ranges of radio-tracked individuals varied widely from 1-8 ha to 17-9 ha (mean c.9 ha). Status and Conservation. Classified as Least Concern on The IUCN Red List (as Dermanura watsoni ). Thomas's Fruit-eating Bat has a wide distribution, is locally common, occurs in protected areas, and is tolerant of some degree of habitat modification, suggesting population stability. Bibliography. Albrecht et al. (2007), Andersen (1908c), Chaverri et al. (2007), Davis (1970a), Gillam et al. (2013), Kalko & Handley (1994), LaVal & Rodriguez-Herrera (2002), Reid (2009), Rodriguez-Herrera et al. (2007), Stoner (2001), Thomas (1897a, 1901a), Timm (1987).
docOrigin_2                                  Simmons, N.B. and A.L. Cirranello. 2022B. Bat Species of the World: A taxonomic and geographic database. Accessed on 10/11/2022.
family_batnames                              Phyllostomidae
name_batnames_2                              Dermanura watsoni
Genus                                        Dermanura
Subgenus                                     
Species                                      watsoni
Author                                       Thomas
Date                                         1901
Parentheses (1=author & date in parentheses) 1
Citation                                     Ann. Mag. Nat. Hist.
Pages                                        ser. 7, 7: 542
Common Name                                  Thomas' Fruit-eating Bat
Synonyms                                     <i>jucundum</i> Elliot, 1906; <i>incomitatus</i> Kalko and Handley 1994.
Type Locality                                Panama, Chiriquí, Bogava [Bugaba], 250 m.
Distribution                                 S Mexico to SW Colombia.
CITES                                        Not listed.
IUCN                                         Least Concern
Comments                                     Subgenus <i>Dermanura</i>.<i> </i>Distinct from <i>glaucus</i>; see Handley (1987). Includes <i>incomitata;</i> see Solari et al(2008).
source                                       GBIF Secretariat (2021). GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via GBIF.org on 2022-09-16.
verbatimScientificName                       Artibeus watsoni
sciname_GBIF                                 Artibeus watsoni Thomas, 1901
name_GBIF_2                                  Artibeus watsoni
key                                          4.00E+06
matchType                                    EXACT
confidence                                   99
status                                       ACCEPTED
rank                                         SPECIES
kingdom                                      Animalia
phylum                                       Chordata
class                                        Mammalia
order                                        Chiroptera
family_GBIF                                  Phyllostomidae
genus                                        Artibeus
species                                      Artibeus watsoni
canonicalName                                Artibeus watsoni
authorship                                   Thomas, 1901
docOrigin_3                                  Mammal Diversity Database. (2022). Mammal Diversity Database (Version 1.9.1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4139818
name_MDD_2                                   Dermanura watsoni
id                                           1.00E+06
phylosort                                    2.30E+01
mainCommonName                               Thomas's Fruit-eating Bat
otherCommonNames                             Watson's Fruit-eating Bat
subclass                                     Theria
infraclass                                   Placentalia
magnorder                                    Boreoeutheria
superorder                                   Laurasiatheria
order_2                                      CHIROPTERA
suborder                                     VESPERTILIONIFORMES
infraorder                                   NA
parvorder                                    NA
superfamily                                  NOCTILIONOIDEA
family_MDD                                   PHYLLOSTOMIDAE
subfamily                                    STENODERMATINAE
tribe                                        STENODERMATINI
genus_2                                      Dermanura
subgenus                                     NA
specificEpithet                              watsoni
authoritySpeciesAuthor                       O. Thomas
authoritySpeciesYear                         1901
authorityParentheses                         1
originalNameCombination                      Artibeus_Watsoni
authoritySpeciesCitation                     Thomas, O. (1901). New Myotis, Artibeus, Sylvilagus, and Metachirus from Central and South America. Annals and Magazine of Natural History, Ser. 7, 7, 542.
authoritySpeciesLink                         https://www.biodiversitylibrary.org/item/78511#page/572/mode/1up
holotypeVoucher                              BM 1900.7.11.19
holotypeVoucherURIs                          
typeLocality                                 "Bogava [= Bugaba,] Chiriqui, Panama. Altitude 250 m."
typeLocalityLatitude                         
typeLocalityLongitude                        
nominalNames                                 watsoni (O. Thomas, 1901)|jucundum D. G. Elliot, 1906|incomitatus (Kalko & Handley, 1994)
taxonomyNotes                                includes incomitatus; moved to Dermanura from Artibeus, although some recent publications do not agree with this split, there seems to be more publications using this revised taxonomy rather than leaving all species under Artibeus
taxonomyNotesCitation                        Hoofer, S. R., Solari, S., Larsen, P. A., Bradley, R. D., & Baker, R. J. (2008). Phylogenetics of the fruit-eating bats (Phyllostomidae: Artibeina) inferred from mitochondrial DNA sequences. Occasional Papers of the Museum of Texas Tech University, 277, 1-15.|Wilson D.E. & Mittermeier R.A. 2019. Handbook of the mammals of the world. Vol. 9. Bats. Lynx Edicions, Barcelona.|York, H. A., Rodríguez-Herrera, B., Laval, R. K., Timm, R. M., & Lindsay, K. E. (2019). Field key to the bats of Costa Rica and Nicaragua. Journal of Mammalogy, 100(6), 1726-1749.|Turcios-Casco, M. A., �vila-Palma, H. D., LaVal, R. К., Stevens, R. D., Ordoñez-Trejo, E. J., Soler-Orellana, J. A., & Ordoñez-Mazier, D. I. (2020). A systematic revision of the bats (Chiroptera) of Honduras: an updated checklist with corroboration of historical specimens and new records. Zoosystematics and Evolution, 96, 411.|
countryDistribution                          Mexico|Guatemala|Belize|Honduras|Nicaragua|Costa Rica|Panama
continentDistribution                        North America
biogeographicRealm                           Nearctic|Neotropic
iucnStatus                                   LC
extinct                                      0
domestic                                     0
flagged                                      0
CMW_sciName                                  Artibeus_watsoni
diffSinceCMW                                 0
MSW3_matchtype                               oldname match
MSW3_sciName                                 Artibeus_watsoni
diffSinceMSW3                                0
docOrigin_4                                  IUCN. 2022. The IUCN Red List of Threatened Species. Version 2022-1. https://www.iucnredlist.org. Accessed on [28 September, 2022].
internalTaxonId                              1.00E+08
NAME_IUCN                                    Dermanura watsoni
kingdomName                                  ANIMALIA
phylumName                                   CHORDATA
className                                    MAMMALIA
orderName                                    CHIROPTERA
family_IUCN                                  PHYLLOSTOMIDAE
genusName                                    Dermanura
speciesName                                  watsoni
infraType                                    
infraName                                    
infraAuthority                               
subpopulationName                            
authority                                    (Thomas, 1901)
taxonomicNotes                               <p>Subgenus<span class="apple-converted-space">&#160;Dermanura</em>. This subgenus has been recognized as a separate genus on molecular grounds, but there are no diagnostic morphological differences from<span class="apple-converted-space">&#160;Artibeus</em><span class="apple-converted-space">&#160;</em>(Lim<span class="apple-converted-space">&#160;et al</em>.&#160;2004).</span></span></p>
assessmentId                                 2.00E+07
internalTaxonId_2                            1.00E+08
scientificName                               Dermanura watsoni
redlistCategory                              Least Concern
redlistCriteria                              
yearPublished                                2016
assessmentDate                               2016-07-05 00:00:00 UTC
criteriaVersion                              3.1
language                                     English
rationale                                    This species is listed as Least Concern in because of its wide distribution, presumed large population, occurrence in a number of protected areas, tolerance to some degree of habitat modification, and because it is unlikely to be declining at nearly the rate required to qualify for listing in a threatened category.
habitat_2                                    This bat is usually found below 800 m above sea level, in evergreen and semi-deciduous lowland forests, tolerates second growth and disturbed habitats. According to&#160;Kalko&#160;et al.</em>&#160;(1996) this small bat could be characterized as belonging to the&#160;Highly Cluttered Space/Gleaning Frugivores. Feeds on small figs, Cecropia </em>fruits, etc. Roosts in small colonies in leaf tents (LaVal and Rodriguez H. 2002). Reproduction seems to involve bimodal polyestry. <br/>It feeds primarily on fruits, although to a lesser extent may consume insects and pollen (LaVal and Rodrıguez-H. 2002).
threats                                      There are no threats for this species.
population                                   This species is common and abundant.
populationTrend                              Stable
range                                        This bat species is found from southern Mexico to southeastern Panama (Simmons 2005, Solari et al</em>. 2009). There are no verified record for El Salvador or Colombia (Owen and Giron 2012, Solari et al</em>. 2013).
useTrade                                     
systems                                      Terrestrial
conservationActions                          It is found in protected areas. In Mexico is listed as subject to special protection under NOM - 059 - SEMARNAT - 2001 (Arroyo-Cabrales pers. comm.).
realm                                        Neotropical
yearLastSeen                                 
possiblyExtinct                              FALSE
possiblyExtinctInTheWild                     FALSE
scopes                                       Global
docOrigin_5                                  Don E. Wilson & DeeAnn M. Reeder (editors). 2005. Mammal Species of the World. A Taxonomic and Geographic Reference (3rd ed), Johns Hopkins University Press, 2,142 pp. (Available from Johns Hopkins University Press, 1-800-537-5487 or [phone], or at http://www.press.jhu.edu).
ORDER                                        CHIROPTERA
SUBORDER                                     
INFRAORDER                                   
SUPERFAMILY                                  
family_MSW3                                  Phyllostomidae
SUBFAMILY                                    Stenodermatinae
TRIBE                                        Stenodermatini
name_msw3                                    Artibeus watsoni
GENUS                                        Artibeus
SUBGENUS                                     Dermanura
SPECIES                                      watsoni
SUBSPECIES                                   
TAXON LEVEL                                  SPECIES
ORIGINAL NAME                                
VALID NAME (YES OR NO)                       YES
AUTHOR                                       Thomas
( )?                                         
DATE                                         1901
ACTUAL DATE?                                 
CITATION                                     Ann. Mag. Nat. Hist., ser. 7
VOLUME                                       7
ISSUE                                        
PAGES                                        542
CITATION TYPE                                
TYPE SPECIES                                 
COMMON NAME                                  Thomas's Fruit-eating Bat
TYPE LOCALITY                                Panama, Chiriquí, Bogava [Bugaba], 250 m.
DISTRIBUTION                                 S Mexico to SW Colombia.
STATUS                                       IUCN 2003 – Not listed (lapsus); IUCN/SSC Action Plan (2001) – Lower Risk (lc).
SYNONYMS                                     jucundum Elliot, 1906.
COMMENTS                                     Subgenus Dermanura. Distinct from glaucus; see Handley (1987). See also Kalko and Handley (1994).
family_batnames2023                          Phyllostomidae
GENUS_2                                      Dermanura
SUBGENUS_2                                   
SPECIES_2                                    watsoni
AUTHOR_2                                     Thomas
DATE_2                                       1901
PARENTHESES (1=AUTHOR & DATE IN PARENTHESES) 1
CITATION_2                                   Ann. Mag. Nat. Hist.
PAGES_2                                      ser. 7, 7: 542
COMMON NAME_2                                Thomas' Fruit-eating Bat
SYNONYMS_2                                   <i>jucundum</i> Elliot, 1906; <i>incomitatus</i> Kalko and Handley 1994.
TYPE LOCALITY_2                              Panama, Chiriquí, Bogava [Bugaba], 250 m.
DISTRIBUTION_2                               S Mexico to SW Colombia.
CITES_2                                      Not listed.
IUCN_2                                       Least Concern
COMMENTS                                     Subgenus <i>Dermanura</i>.<i> </i>Distinct from <i>glaucus</i>; see Handley (1987). Includes <i>incomitata;</i> see Solari et al(2008). 

publish a version of BTA on Zenodo

version on Zenodo would include:

1. machine readable files (e.g., Preston, provenance stuff)
2. human readable files including: bta.tsv bta.csv bta.xlsx bta.json
3. description (suggest to include description as a separate text file included in the publication README README.pdf)
4. title
5. author list
6. keywords
7. license
8. add links to related items like HWM, MSW, and associate manuscript (this can be added later)

use case: saw [Tadarida pumila] referenced in publication from the 80s, what is the current accepted name?

excerpt from email received by Nancy Simmons June 29, 2023, Liam McGuire

---

Taxonomy question for you…or I suppose more about paper trail or other resources. I’ve got a paper from the 80s that refers to Tadarida pumila. I gather the name has changed and I’m trying to track it down. I suspect it went on to be known as Chaerephon pumilus, and now Mops pumilus.

Looking at batnames.org there are no pumila species, but there are several pumilus species and Mops pumilus is the only Molossid on that list. In the species account for M. pumilus there are notes about the history of classification of Mops, Chaerephon, and Tadarida at the genus level. If I go to the Mammalian Species account for C. pumilus, there is a note about C. pumilus being split into four species of Tadarida, including Tadarida pumila.

So I’m feeling pretty good that the T. pumila bat that I’m reading about is now known as M. pumilus. But I’m wondering- is there a more efficient way to go about this sleuthing? Is there a record somewhere that I should be checking? Or is my approach about the right way to go?
Taxonomy question for you…or I suppose more about paper trail or other resources. I’ve got a paper from the 80s that refers to Tadarida pumila. I gather the name has changed and I’m trying to track it down. I suspect it went on to be known as Chaerephon pumilus, and now Mops pumilus.

Looking at batnames.org there are no pumila species, but there are several pumilus species and Mops pumilus is the only Molossid on that list. In the species account for M. pumilus there are notes about the history of classification of Mops, Chaerephon, and Tadarida at the genus level. If I go to the Mammalian Species account for C. pumilus, there is a note about C. pumilus being split into four species of Tadarida, including Tadarida pumila.

So I’m feeling pretty good that the T. pumila bat that I’m reading about is now known as M. pumilus. But I’m wondering- is there a more efficient way to go about this sleuthing? Is there a record somewhere that I should be checking? Or is my approach about the right way to go?

---

suggest to add wikidata as a taxonomic authority

@ajacsherman @Daniel-Mietchen

need to account for splits and merges in BTA

@n8upham

For instance Pteronotus parnellii currently has an agreement index of 1.0, which does not account the splits.

Pteronotus parnellii was split into 8 species (e.g., mesoamericanus . . . )

Solution is to put the name Pteronotus parnellii in MSW3 column of the Pteronotus mesoamericanus row.

See attached screenshot.

Then we should be albe to update the agreement index to reflect what we know about this Pteronotus parnellii name in that was split and is therefore problematic when encourered in old literature / observations.

move bat-taxonomic-alignment from https://jhpoelen.nl/bat-taxonomic-alignment to https://batbase.org/bat-taxonomic-alignment/

as suggested by @ajacsherman

give some example of taxonomic splits and review the related "taxonomicIds"

as suggested by @n8upham

add MDD names

@n8upham noted that the names.csv doesn't appear to include the MDD names yet.

Suggest to investigate why the MDD names didn't make it through.

suggest add alignment with a mammal phylogeny

as suggested by @arw36 and @n8upham -

Suggest add alignment with a mammal phylogeny. Please add Upham et al. 2019 Mammal Tree Paper. Plos Biology.

When searching for a valid species name, I need a list of all the different combinations of names associated with the epithet I am searching for

'https://docs.google.com/spreadsheets/d/...edit#gid=1542784635&range=7:7'

When searching for a valid species name for Acerodon floresianus according to MDD, a search should bring me to row 7 of the BTA; valid name Acerodon mackloti.
In order to search for synonyms, nomen dubia, subspecies, etc. we need a list of all the different combinations of names associated with each alignment. To produce this list, we need a formula to concatenate the full row of name combinations, but also need to establish that bolded names are subspecies, italisized names are synonyms, and if there is a subspecies followed by "-" and more names separated by commas, then these are synonyms of that subspecies.

add a "getting started" task as part of the documentation