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Moscow Digital Herbarium, an online open access contribution to the flora of Turkey, with a special reference to the type specimens

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Abstract

Massive imaging of herbarium collections is performed only in a few countries, leading to disproportions in geographical coverage of the world’s flora across virtual herbaria. The Moscow University Herbarium (MW) digitised all Asian collections in 2016–2017 and published them online at https://plant.depo.msu.ru/, including 3283 specimens from Turkey. These collections include important historical gatherings by P.E. Boissier, C. Haussknecht, and T. Kotschy and recent collections by the Moscow University staff members. Currently, MW holds 331 type specimens of 285 taxa described from Anatolia—19 holotypes, 47 isotypes, 48 isolectotypes, and 203 syntypes.
801
http://journals.tubitak.gov.tr/botany/
Turkish Journal of Botany
Turk J Bot
(2018) 42: 801-805
© TÜBİTAK
doi:10.3906/bot-1802-9
Moscow Digital Herbarium, an online open access contribution to the ora of Turkey,
with a special reference to the type specimens
Alexey P. SEREGIN1,*, Dmitry F. LYSKOV2, Ksenia V. DUDOVA1
1Herbarium, Department of Geobotany, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
2Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
* Correspondence: botanik.seregin@gmail.com
1. Introduction
Massive imaging of herbarium collections has changed
their accessibility for researchers and wider audience
throughout the world. Successful eorts on rapid scanning
of more than one million specimens have been undertaken
in Paris (P) (Le Bras et al., 2017), Leiden (L) (Heerlien et
al., 2015), Beijing (PE) (Ma and Xu, 2014), New York (NY)
(iers et al., 2016), Mexico (MEXU) (Gerenandt et al.,
2014), Washington (US) (Orrell and Hollowell, 2018),
and Meise (Engledow et al., 2017). is list should be
supplemented with ve herbaria from China, three from
Europe, and two from the Americas with 0.5M+ scanned
holdings as of early 2018 (original data). erefore, only
nine countries are currently involved into the large-scale
imaging of terrically important dry plant collections,
leading to great disproportions in geographical coverage
of the world’s ora across virtual herbaria.
Unfortunately, plants from Turkey are not widely
represented in open access digital herbaria in the form
of scanned herbarium specimens. e highest number
of published images from Turkey can be found at
Edinburgh (E), P, Kew, Geneva, Bratislava, and British
Museum herbaria as well as the JACQ-aggregator based
in Vienna. Scanned holdings are largely represented by
type specimens that are usually old, except those from E.
We have detected only one Turkish herbarium, namely
e Virtual Herbarium of Lake Van Basin, created at the
Faculty of Education of Yüzüncü Yıl University (VANF
herbarium) with 9000 scanned specimens (no label data
available).
For a long time, plant collections from Asia Minor were
among the most wanted materials for Russian systematic
botanists. Old Russian herbaria like the Komarov Institute
in St. Petersburg and Moscow University Herbarium
have accumulated large holdings of plant specimens from
northeast provinces of modern Turkey (Artvin, Erzurum,
Kars, etc.). Hundreds of new species were discovered by
Russian collectors in this area. Later on, these collections
were intensively studied and fully covered by the standard
Flora Kavkaza (Grossheim, 1934).
e Moscow University Herbarium (MW) includes
1,030,000 specimens with 40% of collections gathered
beyond the modern borders of Russia. Fiy-one out of 63
species of vascular plants described by Moscow University
sta members in 2013–2017 were collected outside Russia.
erefore, research, documentation, and nal delivering
of plant diversity data in a modern electronic form to a
wider international community is an important mission of
M W.
Since the 1990s, MW has received fully or partly
recent collections by A.P. Khokhryakov, M.G. Pimenov,
E.V. Kljuykov, and D.F. Lyskov that have supplemented
complementary important classical collections of the 19th
century by E. Boissier, C. Haussknecht, T. Kotschy, W.
Abstract: Massive imaging of herbarium collections is performed only in a few countries, leading to disproportions in geographical
coverage of the world’s ora across virtual herbaria. e Moscow University Herbarium (MW) digitised all Asian collections in
2016–2017 and published them online at https://plant.depo.msu.ru/, including 3283 specimens from Turkey. ese collections include
important historical gatherings by P.E. Boissier, C. Haussknecht, and T. Kotschy and recent collections by the Moscow University sta
members. Currently, MW holds 331 type specimens of 285 taxa described from Anatolia—19 holotypes, 47 isotypes, 48 isolectotypes,
and 203 syntypes.
Key words: Asia Minor, authentic collections, historical collections, vascular plants
Research Note
is work is licensed under a Creative Commons Attribution 4.0 International License.
Received: 07.02.2018 Accepted/Published Online: 02.08.2018 Final Version: 22.11.2018
SEREGIN et al. / Turk J Bot
802
Siehe, and P. Sintenis and early 20th century collections
by G. Woronow, B. Shishkin, D. Sosnowsky, and others. A
list of MW collectors with years of activity and sources of
acquisition was published by Balandin (2006).
In late 2014, MW received direct investment for
digitisation within the grant l4-50-00029 from the Russian
Science Foundation (Seregin, 2016). is helped us to scan
89% of herbarium specimens within the Moscow Digital
Herbarium initiative in 2015–2017. Fast digitisation of all
incoming accessions made the herbarium an attractive
place for duplicate deposition and made an exceptional
contribution of 22K new specimens in 2016 and 19.5K
in 2017. Now all these holdings are fully available online,
including interesting collections from Turkey.
2. Materials and methods
2.1. Curation of physical collections
Due to the long tradition of oristic research, MW consists
of 11 regional collections of vascular plants curated as
independent units: Eastern Europe (E), Asian Russia
(S), Caucasus (K), Crimea (KRYM), Middle Asia (M),
Mongolia (MONG), Western Europe (WEU), South Asia
(ASIA), Africa (AFR), America (AMER), and Australia &
Oceania (AUS). Type specimens are preserved separately.
erefore, physical collections from Turkey are splitted
between four (!) units—(1) NE Turkey being part of the
Caucasian herbarium and treated as K7 area, (2) the rest
of Asia Minor stored among South Asian without further
geographical indexation, (3) Turkey-in-Europe being
part of WEU branch, and (4) type collections. e only
possibility to study all Turkish material as a single unit in
this sophisticated scheme was digitisation of all specimens
with further retrieving of images in search results. e
same is true for any requests that involve studying of
plant specimens from various regions used for curation of
physical collections.
2.2. Brief description of the dataset before imaging
Before imaging and further geographical indexation, we
did not have any reliable gures or even estimates on
how many herbarium specimens from Turkey we have
(except for types). Gubanov et al. (in Balandin, 2006) gave
a geographical overview of a catalogue of type collections
preserved in MW, stating that types of at least 215 taxa
described from Turkey were preserved at that time in MW.
irty taxa were described since 1993 from Turkey upon
recent collections by Moscow University sta members—
mainly from Apiaceae (Khokhrjakov, 1993; Pimenov et
al., 1998, 2005, 2011; Akalın and Pimenov, 2004; Pimenov
and Kljuykov, 2010, 2011, 2013a; Bani et al., 2012; Lyskov
et al., 2017), but also from Boraginaceae, Brassicaceae,
Lamiaceae, Fabaceae, and other families (Khokhrjakov,
1993, 1995, 1997a, 1997b; Podlech and Sytin, 2002). Some
of these protologues were published in serials that are
not available on the web or with short Latin descriptions
inserted into the Russian text just to validate new taxa.
Frequent requests for the specimens of these newly
described taxa made us sure that published descriptions are
not enough for correct interpretation of the names.
Comprehensive lists of MW collectors with years of
activity and sources of acquisition were published by
Shvedchikova (in Balandin, 2006) for NE provinces of
Turkey intensively studied by Russian researchers and by
Seregin (in Balandin, 2006) for the rest of the country. All
together these lists named 37 persons who contributed to
MW with specimens from Turkey, but we did not have at
the time any knowledge on how large their collections were.
2.3. Technical issues of digitisation
Getting a stable budget for the next four years, we scheduled
to scan 1M specimens at 300 dpi (TIFF + JPG) in 2015–
2018, to image 4.6K type specimens at 600 dpi, to scan 78K
labels from bryophyte capsules, and nally to database
and georeference label data from as many specimens as
possible until complete exhaustion of the budget (Seregin,
2016). In 2015–2017, we compiled specication and
protocols for scanning of specimens following the world’s
best practices, selected a commercial partner, restructured
old xls-database for further production of image metadata,
barcoded and prepared for digitisation 953K specimens,
transferred to the scanning area and led back 911K
specimens, conducted quality control of images and
metadata, and nally transferred back to the scanning area
27K specimens for rescans.
2.4. Online publication
We did our best to facilitate free full online access to all
imaged specimens from MW. Currently, all 910,817
images are fully available through the general Google
Search and four dierent web addresses: Moscow Digital
Herbarium (https://plant.depo.msu.ru/), Open version
(https://plant.depo.msu.ru/open/), Global Biodiversity
Information Facility (https://www.gbif.org/), and Yandex.
Images (https://yandex.ru/images/). Each point of access
has a number of tools and services for eective interaction
between a researcher and content.
An operational version (https://plant.depo.msu.ru/) is
the dataset homepage with a number of search tools like
label search, geosearch, search on taxonomic tree, and
search by Latin and vernacular names. Data administrators
are managing here the content and editing the data through
their accounts. IT sta are incorporating here new datasets
like tables with labels, georeferences, and taxonomic
treatments. Users can download xlsx-les with general
metadata. Basic statistics of the Moscow Digital Herbarium
are available here. Currently, it is the sixth largest imaged
herbarium in the world fully available on the web aer
P (5.4M), L (4.6M), NY (1.7M), PE (1.7M), and MEXU
(1.2M).
SEREGIN et al. / Turk J Bot
803
Taxonomy in the Moscow Digital Herbarium fully
reects names used in the collection. To make the names
permanently updated we cross-linked them automatically
with the Catalogue of Life (http://www.catalogueoife.
org/col/). We extracted from this source higher hierarchy
(familial and suprafamilial names), currently accepted
names, and complete synonymy.
3. Results
3.1. Library of images
In 2016, we imaged 22,649 specimens from South Asia,
378 specimens from NE Turkey, and 4640 type specimens.
Western European holdings were not imaged, but there
are no specimens from Turkey-in-Europe in MW at all
(Balandin, 2006). Aer country tagging of the Asian and
type collections performed in early 2017 and imaging
of new accessions in late 2017, we nally got a precise
number of specimens from Turkey as well as for other
Asian countries.
e trickiest challenge was to perform correct country
assignment of Haussknecht’s 992 specimens collected
during his two expeditions known as Iter Orientale
(1865 and 1866–1869). It was not an easy job to interpret
his handwriting, but using his itineraries (see map on
http://www.spezbot.uni-jena.de/herbarium/sammlung/
haussknechts-travel-diaries/) and collection dates 468
specimens were nally country tagged as originating from
modern Turkey. Other specimens come from Iraq, Iran,
and Syria. We also hold some collections by Haussknecht
from Georgia and Azerbaijan, but they were curated as
part of the well-managed Caucasian collections. Eighteen
specimens from his collections were not assigned to
any country. Baytop (2008) assumed that Haussknecht’s
Anatolian collections might comprise up to 2000 specimens
and so MW holds roughly a quarter of his gatherings.
As of January 2018, the Turkish collections in MW
include 3283 vascular plant specimens. ey are all fully
available in the Moscow Digital Herbarium, making it
the seventh largest hub of digitised herbarium specimens
from Turkey available online (Table). Our collectors M.G.
Pimenov, E.V. K ljuykov, and D.F. Lyskov are still identifying
and transferring their collections, and therefore Moscow
University’s position in the ranking will surely have strong
positive dynamics in the next few years.
3.2. Taxonomic coverage
Beside some infraspecic taxa, our Turkish dataset includes
1872 species (i.e. names accepted in the collection).
Some names traditionally used for curation are currently
treated as synonyms. Crosslinking of the dataset with
the Catalogue of Life gave a slightly lower gure of 1709
species from 617 genera and 103 families. Meanwhile,
263 specimens are still not identied up to species level or
bearing never-published names, and so the actual number
of species is ca. 10% higher.
e most peculiar feature of our Turkish collection is
a high proportion of Apiaceae specimens (Table). Moscow
University is a distinguished centre of Apiaceae research
in Asia. Large collections by Pimenov and Kljuykov’s
team from all over Asia form the core of our carrot-
family holdings and served as a basis for the description
of hundreds of new species, dozens of molecular revisions,
and several monographs.
3.3. Type specimens
As of January 2018, MW holds 331 type specimens collected
in Turkey—19 holotypes, 47 isotypes, 48 isolectotypes, and
203 syntypes of early authors (Appendix). We consider them
to be types of 285 taxa (species, subspecies, and varieties).
e names in the list below are given as published with no
references on the current taxonomic status of the names.
Tab le . Top-10 families and genera of the imaged Turkish collections from the Moscow University
Herbarium.
Rank Top-10 families Number of specimens Rank Top-10 genera Number of specimens
1 Apiaceae 697 1 Salvia 72
2 Asteraceae 308 2 Bupleurum 66
3 Fabaceae 305 3 Astragalus 65
4 Lamiaceae 302 4 Galium 57
5 Caryophyllaceae 183 5–6 Ferulago 40
6 Poaceae 139 5–6 Quercus 40
7 Brassicaceae 105 7 Silene 39
8 Rubiaceae 101 8 Campanula 38
9 Boraginaceae 79 9 Euphorbia 34
10 Rosaceae 70 10 Vero n ica 34
SEREGIN et al. / Turk J Bot
804
eir modern status could be traced easily from revisions,
oras, and online resources like http://www.theplantlist.
org/, http://bizimbitkiler.org.tr/v3/demo/, and https://
plant.depo.msu.ru/. e type statuses of some specimens
of older authors are dierent from those indicated in
the standard Flora of Turkey. Current regulations of type
statuses led to mere absence of holotypes and isotypes in
older herbaria. Types with duplicate specimens collected
in the 19th century are usually regarded as syntypes, from
which lectotypes are designated (Phillips et al., 1992).
Old collections from Turkey especially by Boissier and
Haussknecht surely include more type specimens of
various rank, but they are still not traced and need further
study. Any contributions are warmly welcome.
4. Discussion
e main theme of this paper is the feeling that the
international community contributes more to the
digitisation of natural history collections from Turkey
than the country of origin itself. It is done in a paradigm
of “virtual repatriation of material to countries of origin”
widely disputed and generally supported (Vollmar et al.,
2010). e only imaged collection physically located in
Turkey and available on the web is e Virtual Herbarium
of Lake Van Basin created in VANF. It comprises ca. 9000
images of scanned specimens (and some living plants as
well) in a gallery form, but no label details are presented.
Nonetheless, it is a wonderful contribution that makes the
Turkish ora more visible. Unluckily, the widely advertised
project Turkey Plant Bank (Duzenli and Karaomerlioglu,
2012) is currently inaccessible.
e Global Biodiversity Information Facility (GBIF),
available at https://www.gbif.org/, is the most successful
global attempt to present in a standard manner diverse
electronic resources on life on Earth. As of 28 January 2018,
966,686,831 occurrences of living beings are available via
GBIF, including 1,168,052 records from Turkey (0.12%).
e Moscow University Herbarium provides access to
1.2% of vascular plants occurrences from Turkey available
in GBIF (273,733 in total) and for 2.2% vascular plants
occurrences based upon specimens (150,039). Currently,
there are no occurrence records in GBIF published by
Turkish institutions.
Following P and E herbaria practices, MW imaged and
published all specimens without prior databasing. We have
done that in the belief that researchers will transcribe the
label details themselves from a screen. In fact, we need
to do label capturing as soon as possible, because year
by year general skills to read older handwritten texts are
disappearing.
In August 2017, we started publication of label details
captured from scans or uploaded directly from the
databases that are based on our specimens. As of May 2018,
labels of 108,819 specimens are completely databased,
including 22,423 from the Crimea, 9987 from Middle
Russia (excluding Moscow area), 6647 from NW Russia,
6414 from Central Siberia (mainly Taimyr Peninsula),
5777 from the central part of the Northern Caucasus, 4276
from Krasnodar Krai and Adygeya, 2900 from Azerbaijan,
2764 from the Black Sea coast of the Russian Caucasus,
2419 from the Moscow area, 2358 from Armenia, etc. We
focused on label capturing on the Cyrillic labels, which
are almost unreadable for the international community.
Using typed transcriptions one could at least use online
translation services to read labels.
Simultaneously, we started georeferencing of
collections sites. As of May 2018, 137,467 specimens
received georeferences. Russia, Caucasus, Mediterranean,
and Ethiopia were selected as the top priorities in
geocoding. We launched the Intellectual System of
Toponymic Reading and Attribution (ISTRA) for machine
georeferencing of specimens grouped against captured
labels. Two algorithms of further specimen grouping were
programmed—(1) by matching of the collector/date pair;
and (2) by matching of textual description of the collection
site. Coordinates for 9.3K specimens (22%) were identied
automatically by ISTRA.
Label capturing and georeferencing of the Moscow
University collections from Turkey are in progress now.
As a general conclusion, we do consider further
digitisation eorts (and especially imaging of plant
specimens) on oristically diverse regions of Turkey
to be one of the most desirable activities in Eastern
Mediterranean biodiversity projects focused on plants.
Online publication of images of all Turkish plant specimens
from the Moscow University Herbarium in 2017 is one
of the milestones on this road. We also published scans
of all collections from the Crimea, Caucasus, Iran, Syria,
Israel, and Cyprus to contribute plant research of Eastern
Mediterranean plants on a wider ground.
e year 2017 was exceptional in understanding of the
value of digitised herbarium collections. A few studies were
published discovering new horizons of deep learning and
neural networks in machine identication of herbarium
specimens (Carranza-Rojas et al., 2017; Schuettpelz et al.,
2017). Plants from P and US herbaria were used in these
challenging studies. Undoubtedly, computers will help us
in the near future to check massively misnamed specimens
or even to point out undescribed species preserved in
world herbaria. It’s awesome, isn’t it?
Acknowledgment
Moscow University Herbarium digitisation in 2015–2018
is supported by the grant l4-50-00029 from the Russian
Science Foundation (RNF).
SEREGIN et al. / Turk J Bot
805
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Appendix. List of the type specimens stored at MW.
Amaranthaceae
Noaea tournefortii var. leptoclados Woron.: Isotypus
(MW0592050).
Amaryllidaceae
Allium myrianthum Boiss.: Syntypus (MW0591676). –
Allium tauricola Boiss.: Isolectotypus (MW0591703).
Apiaceae
Anthriscus anatolica Boiss.: Isolectotypus (MW0593738).
Bunium pinnatifolium Kljuykov: Holotypus (MW0593825);
Isotypus (MW0593822); Isotypus (MW0593823); Isotypus
(MW0593824); Paratypus (MW0593817); Paratypus
(MW0593818); Paratypus (MW0593819); Paratypus
(MW0593820); Paratypus (MW0593821). – Bupleurum
andronakii Woronow: Isotypus (MW0593785). – Bupleurum
schistosum Woronow: Isotypus (MW0593800). – Bupleurum
terminum A.P.Khokhr.: Holotypus (MW0593801). – Carum
microcarpum Boiss.: Isotypus (MW0593810). – Dichoropetalum
anatolicum Pimenov & Kljuykov: Holotypus (MW0593942);
Isotypus (MW0593943); Isotypus (MW0593944); Isotypus
(MW0593945); Paratypus (MW0593946); Paratypus
(MW0593947); Paratypus (MW0593948). – Echinophora radians
Boiss.: Syntypus (MW0593733). – Eryngium kotschyi Boiss.:
Isotypus (MW0593730). – Ferula divaricata Pimenov & Kljuykov:
Holotypus (MW0593993); Isotypus (MW0593994); Isotypus
(MW0593995); Isotypus (MW0593996). – Ferulago asparagifolia
Boiss.: Isolectotypus (MW0594047). – Ferulago aucherii Boiss.:
Syntypus (MW0594048). – Ferulago humilis Boiss.: Isolectotypus
(MW0594053). – Ferulago trojana Akalın & Pimenov: Isotypus
(MW0594055); Paratypus (MW0594054). – Oenanthe cyclocarpa
Pimenov & Kljuykov: Holotypus (MW0593892); Isotypus
(MW0593893); Isotypus (MW0593894). – Polylophium
petrophilum Boiss.: Isolectotypus (MW0594094). – Prangos
ilanae Pimenov, Akalın & Kljuykov: Isotypus (MW0593782);
Isotypus (MW0593783). – Rhabdosciadium anatolyi Lyskov
& Kljuykov: Holotypus (MW0595616). – Seseli marashicum
E.Doğan & H.Duman: Paratypus (MW0595662). – Seseli
paphlagonicum Pimenov & Kljuykov: Holotypus (MW0593871);
Isotypus (MW0593872). – Seseli phrygium Pimenov & Kljuykov:
Holotypus (MW0593874); Isotypus (MW0593875). – Seseli
serpentinum B.L.Burtt ex H.Duman & E.Doğan: Paratypus
(MW0595661). – Tordylium macropetalum Boiss.: Isotypus
(MW0594092). – Torilis grandiora Boiss.: Isolectotypus
(MW0593741).
Apocynaceae
Vincetoxicum tmoleum Boiss.: Syntypus (MW0594262);
Syntypus (MW0594263).
Asparagaceae
Chionodoxa luciliae Boiss.: Syntypus (MW0591726). –
Ornithogalum nivale Boiss.: Syntypus (MW0591725). – Scilla
nivalis Boiss.: Syntypus (MW0591723).
Aspleniaceae
Asplenium haussknechtii Godet & Reuter: Syntypus
(MW0591008); Syntypus (MW0591009).
Asteraceae
Achillea armenorum Boiss. & Hausskn.: Isolectotypus
(MW0595018). – Anthemis absinthifolia Boiss. & Spruner:
Isolectotypus (MW0595008). – Anthemis albida Boiss.:
Sy
ntypus (MW0595009). – Anthemis auriculata Boiss.:
Syntypus (MW0595010). – Anthemis leucanthemoides Boiss.:
Isolectotypus (MW0595012). – Anthemis reuteriana Boiss.:
Syntypus (MW0595015). – Anthemis smyrnaea Boiss.:
Syntypus (MW0595017). – Centaurea cadmea Boiss.: Syntypus
(MW0595215). – Centaurea calolepis Boiss.: Syntypus
(MW0595216). – Centaurea goniocaula Boiss.: Isolectotypus
(MW0595217). – Centaurea hierapolitana Boiss.: Syntypus
(MW0595221). – Centaurea lydia Boiss.: Syntypus (MW0595225).
Centaurea matthiolifolia Boiss.: Isolectotypus (MW0595226).
Centaurea pinardii Boiss.: Syntypus (MW0595227). – Crepis
dioritica Schott & Kotschy ex Boiss.: Isolectotypus (MW0595345).
Gnaphalium leucopilinum Schott & Kotschy ex Boiss.: Syntypus
(MW0594994). – Helichrysum anatolicum Boiss.: Syntypus
(MW0594996). – Hieracium macrotrichum Boiss.: Syntypus
(MW0595442). – Inula acaulis Schott & Kotschy ex Boiss.:
Syntypus (MW0595000). – Inula multicaulis Boiss.: Syntypus
(MW0595001); Syntypus (MW0595002). – Jurinea anatolica
Boiss.: Syntypus (MW0595175). – Jurinea cataonica Boiss. &
Hausskn.: Syntypus (MW0595177). – Jurinea ramulosa Boiss. &
Hausskn.: Isolectotypus (MW0595185). – Lactuca intricata Boiss.:
Syntypus (MW0595342). – Lapsana adenophora Boiss.: Syntypus
(MW0595244). – Phaeopappus cataonicus Boiss. & Hausskn.
ex Boiss.: Isolectotypus (MW0595233). – Pyrethrum cadmeum
Boiss.: Syntypus (MW0595035). – Senecio hypochionaeus Boiss.:
Syntypus (MW0595122). – Senecio olympicus Boiss.: Isolectotypus
(MW0595128).
Betulaceae
Betula transcaucasica V.N.Vassil.: Isotypus (MW0591848).
Boraginaceae
Alkanna areolata Boiss.: Syntypus (MW0594362). –
Alkanna tubulosa Boiss.: Syntypus (MW0594363). – Moltkia
anatolica Boiss.: Syntypus (MW0594397). – Moltkia aurea
Boiss.: Syntypus (MW0594398). – Myosotis gueneri A.P.Khokhr.:
Holotypus (MW0594367). – Myosotis olympica Boiss.: Syntypus
(MW0594374). – Omphalodes cariensis Boiss.: Syntypus
(MW0594299). – Omphalodes luciliae Boiss.: Syntypus
(MW0594300); Syntypus (MW0595602). – Onosma mirabilis
A.P.K hokhr.: Holotypus (MW0594404); Paratypus (MW0594405).
Onosma pallidum Boiss.: Syntypus (MW0594406). – Paracaryum
reuteri Boiss. & Hausskn. ex Boiss.: Isolectotypus (MW0594304). –
Rochelia karsensis Popov: Isotypus (MW0594410). – Symphytum
anatolicum Boiss.: Syntypus (MW0594332).
Brassicaceae
Aethionema rubescens Boiss.: Syntypus (MW0592541). –
Alyssum eriophyllum Boiss. & Hausskn.: Syntypus (MW0592649).
Alyssum haussknechtii Boiss.: Isolectotypus (MW0592661). –
Alyssum minutiorum Boiss.: Syntypus (MW0592666). – Arabis
drabiformis Boiss.: Syntypus (MW0592617). – Aubrieta pinardii
Boiss.: Syntypus (MW0592615). – Barbamine procumbens
A.P.Khokhr.: Isotypus (MW0595584); Isotypus (MW0595585).
Camelina anomala Boiss. & Hausskn.: Isolectotypus
(MW0592592). – Erysimum laciniatum Boiss.: Syntypus
(MW0592633). – Heldreichia bupleurifolia var. subtriloba
Boiss.: Syntypus (MW0592550). – Hesperis armena Boiss.:
Syntypus (MW0592687). – Hesperis violacea Boiss.: Syntypus
(MW0592683). – Isatis tinctoria subsp. parchalensis A.P.Khokhr.:
Isotypus (MW0595565); Isotypus (MW0595566).
SEREGIN et al. / Turk J Bot
2
Campanulaceae
Campanula olympica Boiss.: Syntypus (MW0594921).
Campanula raveyi Boiss.: Isolectotypus (MW0594924).
Campanula telephioides Boiss. & Hausskn.: Isolectotypus
(MW0594932). – Podanthum scoparium Boiss. & Hausskn.:
Syntypus (MW0594939).
Caryophyllaceae
Alsine leucocephala Boiss.: Syntypus (MW0592093). – Alsine
pulvinaris Boiss.: Syntypus (MW0592094). – Arenaria balansae
Boiss.: Syntypus (MW0592103). – Arenaria tmolea Boiss.: Syntypus
(MW0592121). – Bufonia virgata Boiss.: Syntypus (MW0592086).
Cerastium coeruleum Boiss.: Syntypus (MW0592073). –
Cerastium frag illimum Boiss: Syntypus (MW0592075). – Cerastium
macrocarpum Boiss. & Hausskn: Isolectotypus (MW0592077).
Dianthus anatolicus Boiss.: Isolectotypus (MW0592269).
Dianthus erinaceus Boiss.: Isolectotypus (MW0592275). –
Dianthus lydus Boiss.: Syntypus (MW0592278). – Gypsophila
frankenioides Boiss.: Syntypus (MW0592257). – Holosteum
tenerrimum: Syntypus (MW0592085). – Saponaria mesogitana
Boiss.: Syntypus (MW0592287). – Saponaria pumilio Boiss.:
Syntypus (MW0592288). – Silene brevicaulis var. latifolia Boiss.:
Isolectotypus (MW0592131). – Silene cariensis Boiss.: Syntypus
(MW0592132). – Silene ispirensis A.P.Khokhr.: Holotypus
(MW0592144). – Silene olympica Boiss.: Syntypus (MW0592155).
Silene squamigera Boiss.: Syntypus (MW0592165). – Silene
swertiifolia var. stenophylla Boiss.: Isolectotypus (MW0592167).
Convolvulaceae
Convolvulus compactus Boiss.: Syntypus (MW0594276).
Crassulaceae
Sedum bithynicum Boiss.: Isotypus (MW0738883). – Sedum
lydium Boiss.: Syntypus (MW0592716). – Sedum olympicum
Boiss.: Syntypus (MW0592717). – Umbilicus haussknechtii Boiss.
& Reut. ex Boiss.: Isolectotypus (MW0592720). – Umbilicus
pallidus Schott & Kotschy: Isotypus (MW0738886). – Umbilicus
pestalozzae Boiss.: Syntypus (MW0592721).
Cyperaceae
Blysmus compressus subsp. subulifolius A.P.Khokhr.: Holotypus
(MW0591513).
Dipsacaceae
Knautia bidens Boiss.: Syntypus (MW0594897). – Scabiosa
cosmoides Boiss.: Syntypus (MW0594904). – Scabiosa hispidula
Boiss.: Syntypus (MW0594905). – Scabiosa reuteriana Boiss.:
Isolectotypus (MW0594908).
Euphorbiaceae
Euphorbia altissima Boiss.: Syntypus (MW0593503). –
Euphorbia ana campseros Boiss.: Syntypus (MW0593504); Syntypus
(MW0593505). – Euphorbia schottiana Boiss.: Isolectotypus
(MW0593527).
Fabaceae
Adenocarpus villosus Boiss.: Isotypus (MW0592996). – Alhagi
maurorum var. karduchorum Boiss.: Syntypus (MW0593381).
Astragalus anatolicus Boiss.: Syntypus (MW0593079). –
Astragalus cadmicus Boiss.: Syntypus (MW0593095). – Astragalus
avescens Boiss.: Syntypus (MW0593115). – Astragalus gladiatus
Boiss.: Isolectotypus (MW0593119). – Astragalus khokhrjakovii
Sytin & Podlech: Holotypus (MW0593143). – Astragalus lydius
Boiss.: Syntypus (MW0593157). – Astragalus mesogitanus
Boiss.: Syntypus (MW0593158). – Astragalus pennatus
Bunge: Isotypus (MW0593173). – Astragalus sibthorpianus
Boiss.: Syntypus (MW0593214). – Cytisus chrysotrichus
Boiss.: Syntypus (MW0592998). – Cytisus eriocarpus Boiss.:
Syntypus (MW0592999). – Cytisus smyrnaeus Boiss.: Syntypus
(MW0593002). – Ebenus barbigera Boiss.: Syntypus (MW0593380).
Genista anatolica Boiss.: Syntypus (MW0592988). – Genista
liparioides Boiss.: Syntypus (MW0592989). – Genista lydia
Boiss.: Syntypus (MW0592992). – Hedysarum callichroum Boiss.:
Syntypus (MW0593348). – Hedysarum erythroleucum Schott
& Kotschy ex Boiss.: Syntypus (MW0593354). – Hedysarum
lydium Boiss.: Syntypus (MW0593357). – Hedysarum sipyleum
Boiss.: Isolectotypus (MW0593364). – Lathyrus pseudoaphaca
Boiss.: Syntypus (MW0593400). – Lotus sulphureus Boiss.:
Syntypus (MW0593057). – Onobrychis cadmea Boiss.:
Syntypus (MW0593371). – Onobrychis hypargyrea Boiss.:
Syntypus (MW0593375). – Onobrychis lasiostachya Boiss.:
Syntypus (MW0593378). – Ononis adenotricha Boiss.:
Syntypus (MW0593003). – Oxytropis dioritica Boiss.: Syntypus
(MW0593282). – Trifolium anatolicum Boiss.: Syntypus
(MW0593014). – Trifolium glanduliferum Boiss.: Syntypus
(MW0593016). – Trifolium mesogitanum Boiss.: Syntypus
(MW0593022). – Trifolium pilulare Boiss.: Syntypus (MW0593023).
Trifolium setiferum Boiss.: Syntypus (MW0593025). – Trifolium
smyrnaeum Boiss.: Syntypus (MW0593026). – Trigonella
aurantiaca Boiss.: Syntypus (MW0593006). – Trigonella capitata
Boiss.: Syntypus (MW0593007). – Trigonella crassipes Boiss.:
Syntypus (MW0593008). – Trigonella spruneriana Boiss.:
Syntypus (MW0593010). – Trigonella velutina Boiss.: Syntypus
(MW0593012). – Vicia cuspidata Boiss.: Syntypus (MW0593388).
Vicia noeana Boiss.: Syntypus (MW0593394); Syntypus
(MW0595595). – Vicia sericocarpa var. microphylla Boiss.:
Syntypus (MW0593396).
Fagaceae
Quercus cedrorum Kotschy: Syntypus (MW0591850); Syntypus
(MW0591851). – Quercus haas Kotschy: Syntypus (MW0591854).
Gentianaceae
Gentiana boissieri Schott & Kotschy ex Boiss.: Syntypus
(MW0594209).
Geraniaceae
Erodium leucanthum Boiss.: Syntypus (MW0593413).
Erodium sibthorpianum Boiss.: Syntypus (MW0593418). –
Geranium macrostylum Boiss.: Syntypus (MW0593403).
Hypericaceae
Hypericum crenulatum Boiss.: Syntypus (MW0593608).
Hypericum kotschyanum Boiss.: Syntypus (MW0593609). –
Hypericum leprosum Boiss.: Syntypus (MW0593610). – Hypericum
lydium Boiss.: Syntypus (MW0593611).
Lamiaceae
Ajuga mesogitana Boiss.: Syntypus (MW0594423).
Calamintha orida Boiss.: Syntypus (MW0594598). –
Lamium demirizii A.P.Khokhr.: Holotypus (MW0594524).
Lamium microphyllum Boiss.: Isotypus (MW0594531);
Isotypus (MW0594532). – Lamium tschorochense A.P.Khokhr.:
Holotypus (MW0594544); Isotypus (MW0594545); Paratypus
(MW0594546). – Lamium violaceovelutinum A.P.Khokhr.:
Holotypus (MW0594547). – Lamium vreemanii A.P.Khokhr.:
Holotypus (MW0594548); Isotypus (MW0594549). – Marrubium
lutescens Boiss. & Heldr.: Syntypus (MW0594453). – Micromeria
congesta Boiss. & Hausskn. ex Boiss.: Isolectotypus (MW0594599).
Nepeta tmolea Boiss.: Isolectotypus (MW0594462). – Phlomis
SEREGIN et al. / Turk J Bot
3
oppositiora Boiss. & Hausskn.: Isolectotypus (MW0594504).
Salvia cadmica Boiss.: Syntypus (MW0594572); Syntypus
(MW0594573). – Salvia cedronella Boiss.: Syntypus (MW0594574).
Salvia chionantha Boiss.: Syntypus (MW0594575). – Salvia
frigida Boiss.: Syntypus (MW0594578). – Salvia macrochlamys
Boiss. & Kotschy: Isolectotypus (MW0594580). – Salvia
smyrnaea Boiss.: Syntypus (MW0594584). – Salvia tmolea
Boiss.: Isolectotypus (MW0594585). – Scutellaria uzunderensis
A.P.Khokhr.: Holotypus (MW0594448). – Sideritis sipylea Boiss.:
Isolectotypus (MW0594456). – Stachys bithynica Boiss.: Syntypus
(MW0594567). – Stachys tmolea Boiss.: Syntypus (MW0594571).
Teucrium ozturkii A.P.Khokhr.: Isotypus (MW0595568). –
ymus sipyleus Boiss.: Syntypus (MW0594629).
Liliaceae
Gagea cespitosa Hausskn. ex Boiss.: Syntypus (MW0591647).
Tulipa aleppensis Boiss. ex Regel: Syntypus (MW0591711). –
Tulipa undulatifolia Boiss.: Syntypus (MW0591720).
Linaceae
Linum anatolicum Boiss.: Syntypus (MW0593422). – Linum
aretioides Boiss.: Isolectotypus (MW0593423). – Linum hirsutum
var. alpinum Boiss.: Syntypus (MW0593426). – Linum olympicum
Boiss.: Syntypus (MW0593430).
Orobanchaceae
Pedicularis cadmea Boiss.: Syntypus (MW0594740). –
Pedicularis sibthorpii Boiss.: Syntypus (MW0594761).
Oxalidaceae
Oxalis violacella A.P.Khokhr.: Isotypus (MW0595561).
Plantaginaceae
Linaria pterospora Boiss.: Syntypus (MW0594662);
Syntypus (MW0594663). – Veronica caespitosa Boiss.:
Syntypus (MW0594683). – Veronica cariensis Boiss.: Syntypus
(MW0594684). – Veronica kotschyana Benth.: Syntypus
(MW0594692).
Plumbaginaceae
Acantholimon breviscapum Boiss. & Hausskn. ex Boiss.:
Syntypus (MW0594159); Syntypus (MW0594160). –
Acantholimon phrygium Boiss.: Syntypus (MW0594165); Syntypus
(MW0594166).
Poaceae
Agrostis karsensis Litv.: Isotypus (MW0591245); Isotypus
(MW0591246). – Catabrosa variegata Boiss.: Isotypus
(MW0591323). – Hordeum lycium Boiss.: Isotypus (MW0591482).
Melica cappadocica Boiss.: Syntypus (MW0591325). –
Nephelochloa orientalis Boiss.: Syntypus (MW0591326). – Stipa
pontica P.A.Smirn.: Paratypus (MW0591222). – Stipa sibthorpii
Roem. & Schult.: Syntypus (MW0591226). – Triticum thaoudar
Reut. ex Boiss. nom. inval.: Syntypus (MW0591481).
Polygalaceae
Polygala pruinosa Boiss.: Syntypus (MW0593466).
Primulaceae
Androsace olympica Boiss.: Syntypus (MW0594155).
Ranunculaceae
Delphinium cinereum Boiss.: Isotypus (MW0592320).
Delphinium oliganthum Boiss.: Syntypus (MW0592332). –
Delphinium raveyi Boiss.: Syntypus (MW0592333). – Delphinium
sulphureum Boiss. & Hausskn.: Isolectotypus (MW0592334).
Nigella elata Boiss.: Syntypus (MW0592294). – Ranunculus
cadmicus Boiss.: Syntypus (MW0592416). – Ranunculus isthmicus
Boiss.: Isolectotypus (MW0592419). – Ranunculus reuterianus
Boiss.: Syntypus (MW0592436). – Ranunculus vermirrhizus
A.P.Khokhr.: Holotypus (MW0592445); Isotypus (MW0592446);
Isotypus (MW0592447).
Rosaceae
Amelanchier parviora Boiss.: Syntypus (MW0592219).
Cerasus tortuosa Boiss. & Hausskn. ex Boiss.: Syntypus
(MW0592973). – Cotoneaster peduncularis Boiss.: Syntypus
(MW0592211).
Rubiaceae
Asperula brunnea Boiss.: Syntypus (MW0594820). –
Asperula mutica Boiss.: Syntypus (MW0594824). – Asperula
nitida var. puberula Boiss.: Syntypus (MW0594825). – Asperula
stricta var. scabrida Boiss.: Syntypus (MW0594826). –
Asperula tenuifolia Boiss.: Syntypus (MW0594828). – Galium
aretioides Boiss.: Syntypus (MW0594829). – Galium aureum
var. scabrifolium Boiss.: Syntypus (MW0594830). – Galium
bornmuelleri Hausskn. ex Bornm.: Syntypus (MW0594831). –
Galium caudatum Boiss.: Syntypus (MW0594832). – Galium
concinnum Boiss.: Syntypus (MW0594833). – Galium coronatum
var. lasiocarpum Boiss. ex Pojark.: Syntypus (MW0594834). –
Galium dumosum Boiss.: Syntypus (MW0594836). – Galium
eusum Boiss.: Syntypus (MW0594837). – Galium musciforme
Boiss.: Syntypus (MW0594839). – Galium nebulosum Boiss.:
Syntypus (MW0594840). – Galium olympicum Boiss.: Syntypus
(MW0594842). – Galium orientale var. alpinum Boiss.: Syntypus
(MW0594843). – Galium penduliorum Boiss.: Syntypus
(MW0594844). – Galium peplidifolium Boiss.: Syntypus
(MW0594845).
Rutaceae
Haplophyllum pumilum Boiss.: Syntypus (MW0593442).
Salicaceae
Salix pseudodepressa A.K.Skvortsov: Isotypus (MW0591818).
Santalaceae
esium graecum Boiss. & Sprun.: Syntypus (MW0591926). –
esium tauricolum Boiss. & Hausskn.: Syntypus (MW0591929).
Saxifragaceae
Saxifraga corymbosa Boiss.: Syntypus (MW0592727).
Saxifraga olympica Boiss.: Isolectotypus (MW0592175). –
Saxifraga scotophila Boiss.: Syntypus (MW0592179).
Scrophulariaceae
Celsia luciliae Boiss.: Isolectotypus (MW0594653);
Isolectotypus (MW0594654). – Scrophularia depauperata
Boiss.: Syntypus (MW0594665). – Scrophularia olympica
Boiss.: Syntypus (MW0594670). – Scrophularia pinardi Boiss.:
Syntypus (MW0594671). – Scrophularia smyrnaea Boiss.:
Isolectotypus (MW0594673). – Scrophularia tmolea Boiss.:
Syntypus (MW0594674). – Scrophularia xylorrhiza Boiss. &
Hausskn.: Syntypus (MW0594676). – Verbascum cheiranthifolium
Boiss.: Syntypus (MW0594642). – Verbascum glomeratum
Boiss.: Syntypus (MW0594644). – Verbascum indelium Boiss.
& Hausskn.: Isolectotypus (MW0594645). – Verbascum lydium
Boiss.: Isolectotypus (MW0594646). – Verbascum napifolium
Boiss.: Isolectotypus (MW0594647). – Verbascum salviifolium
Boiss.: Syntypus (MW0594649). – Verbascum smyrnaeum Boiss.:
Isolectotypus (MW0594650); Isolectotypus (MW0594651). –
Verbascum taraxacifolium Lam.: Syntypus (MW0594652).
Violaceae
Viola yuzufelensis A.P.Khokhr.: Isotypus (MW0595567).
... Herbarium specimen have been preserved for several years which is important for regions such as tropics were the amount of these specimen samples are limited [7], [8], [9]. Technological advancement has enabled digitization of these specimens as a way to preserve and make it more accessible to other researchers [10], [11]. These collections become valuable assets especially in tropical regions which are normally characterized with both high diversity and extinction risks [12]. ...
... Eighteen studies involved identification of plant species at different taxonomic levels [5], 5 studies have focused on digitization workflow [35] while the remaining studies have focused on studying the interaction between plants and insects [36], reconstruction of damaged herbarium leaves [37], proposing various automation tools, data augmentation technique and the study of reverse senescence for digitization herbarium specimen [38]. 11 ...
Preprint
Full-text available
Herbarium contains treasures of millions of specimens which have been preserved for several years for scientific studies. To speed up more scientific discoveries, a digitization of these specimens is currently on going to facilitate easy access and sharing of its data to a wider scientific community. Online digital repositories such as IDigBio and GBIF have already accumulated millions of specimen images yet to be explored. This presents a perfect time to automate and speed up more novel discoveries using machine learning and computer vision. In this study, a thorough analysis and comparison of more than 50 peer-reviewed studies which focus on application of computer vision and machine learning techniques to digitized herbarium specimen have been examined. The study categorizes different techniques and applications which have been commonly used and it also highlights existing challenges together with their possible solutions. It is our hope that the outcome of this study will serve as a strong foundation for beginners of the relevant field and will also shed more light for both computer science and ecology experts.
... The idea of the virtual herbarium was initially advanced in the U.S.A. in the 1990s, and since then individual herbaria and a consortium of multiple herbaria have led to the creation of virtual herbaria that serve as additional portals for botanical research and education. Virtual herbaria are now commonly available in most major herbaria in many regions, i.e., North America, Europe, and Australia (Schmull et al., 2005;Thiers et al., 2016;Seregin et al., 2018;. This system has recently been implemented in many institutes in eastern Asiatic countries as well. ...
Article
Full-text available
Daphne kiusiana is an evergreen shrub with dense head-like umbels of white flowers distributed in southern Korea, Japan, China, and Taiwan. Plants in China and Taiwan are recognized as var. atrocaulis by having a dark purple stem, elliptic leaves, and persistent bracts. Recently, plants on Jejudo Island were segregated as a separate species, D. jejudoensis, given their elliptic leaves with an acuminate apex, a long hypanthium and sepals, and a glabrous hypanthium. Morphological variations of three closely related taxa, the D. kiusiana complex, were investigated across the distributional range to clarify the taxonomic delimitation of members of the complex. Twelve characters of the leaf and flower were measured from digitized herbarium specimens using the image analysis program ImageJ and were included in a morphometric analysis, the results of which indicate that the level of variation in the characters is very high. The results of a principal component analysis weakly separated D. jejudoensis from D. kiusiana according to their floral characteristics, such as a longer, glabrous hypanthium, and larger sepals. However, some individuals of D. kiusiana, particularly those from Bigeumdo Island, were included in D. jejudoensis. Recognition of D. kiusiana var. atrocaulis based on the leaf shape was not supported in the analysis, and D. jejudoensis may be recognized as a variety of D. kiusiana. Our morphometric analysis shows that digitized images of herbarium specimens could be useful and an additional method by which to investigate more diverse specimens.
... Technological advancement has enabled the digitization of these specimens to preserve and make them more accessible to other researchers (Nelson and Ellis, 2019;Seregin et al., 2018). These collections have become valuable assets, especially in tropical regions, which are typically characterized both by high species diversity and by high extinction risk (Lughadha et al., 2019). ...
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Herbaria contain the treasure of millions of specimens that have been preserved for several years for scientific studies. To increase the rate of scientific discoveries, digitization of these specimens is currently ongoing to facilitate the easy access and sharing of data to a wider scientific community. Online digital repositories such as Integrated Digitized Biocollection and the Global Biodiversity Information Facility have already accumulated millions of specimen images yet to be explored. This presents the perfect time to take advantage of the opportunity to automate the identification process and increase the rate of novel discoveries using computer vision (CV) and machine learning (ML) techniques. In this study, a systematic literature review of more than 70 peer-reviewed publications was conducted focusing on the application of computer vision and machine learning techniques to digitized herbarium specimens. The study categorizes the different techniques and applications that are commonly used for digitized herbarium specimens and highlights existing challenges together with their potential solutions. We hope this study will serve as a firm foundation for new researchers in the relevant disciplines and will also be enlightening to both computer science and ecology experts.
... Specimens were collected from the Anamur district (around Çukurabanoz village), Mersin province in the south of Turkey by Ömer ÇEÇEN (Figure 1, 2). The specimens were identified using the relevant literature (Ekim, 1982;Duman, 2000;Dirmenci, 2012;Seregin et al., 2018;Özhatay et al., 2019Özhatay et al., , Aksoy et al., 2020 and compared with materials stored in herbaria ANK, B, BM, E, EGE, GAZI, HUB, ISTE, ISTO, K, LE, MA, W, and WU (see http://sweetgum.nybg.org/science/ih/ for the indicated acronmys), as well as with our own herbarium specimens. ...
... The relevant literature was used for typification (Ali, 1972;Turland and Jarvis, 1997;Seregin et al., 2018). ...
... Specimens were collected from the Seydikemer district (Pinara Ancient City), Muğla province in southwestern Turkey (Figure 2, Appendix). The collected specimens were identified using the relevant literature (Ekim, 1982;Duman, 2000;Dirmenci, 2012;Seregin et al., 2018;Özhatay et al., 2019) and compared with materials stored in herbaria which the acronyms are indicated as ANK, B, BM, E, EGE, GAZI, HUB, ISTE, ISTO, K, LE, MA, W, and WU, as well as with our own herbarium specimens in the Balıkesir University Herbarium (see Appendix). ...
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