Malagasy frogs of the subgenus Brygoomantis in the
mantellid frog genus Mantidactylus currently comprise 14
described species of mostly brown, riparian frogs. Data from
DNA barcoding suggested that the diversity of this subgenus
is dramatically underestimated by current taxonomy. We
here provide a comprehensive revision of this subgenus. We
use hybrid-enrichment based DNA barcode fishing to obtain
mitochondrial DNA fragments from the name-bearing type
material of 16 of the 20 available names for members of this
subgenus, and integrate these into a genetic dataset consisting
of 1305 individuals sampled across Madagascar. By thus
assigning the nomina to genetic lineages, we can confidently
establish synonyms, revalidate old names, and describe the
remaining diversity. We take an integrative approach to our
descriptions, drawing together genetics, morphometrics
and morphology, and bioacoustics for assignment. We also
provide a robust phylogenomic hypothesis for the subgenus,
based on 12,818 nuclear-encoded markers (almost 10 million
base pairs) for 58 representative samples, sequenced using a
hybrid-enrichment bait set for amphibians. Those data suggest
a division of the subgenus into eight major clades and show
that morphological species complexes are often paraphyletic
or polyphyletic. Lectotypes are designated for Rana
betsileana Boulenger, 1882; Rana biporus Boulenger, 1889;
Rana curta Boulenger, 1882; Mantidactylus ambohimitombi
Boulenger, 1918; Mantidactylus tripunctatus Angel, 1930;
and Rana inaudax Peracca, 1893. For several other nomina,
previous authors had considered a certain syntype as holotype;
this has been seen as lectotype designation by implication,
which, however, is ambiguous according to the provisions of
the International Code of Zoological Nomenclature. Hence,
we validate a previous lectotype designation by implication
for Limnodytes ulcerosus Boettger, 1880 by explicitly
designating the same individual as lectotype. In one other
such case, that of Mantidactylus brauni Ahl, 1929, we deviate
from previous authors and designate a different specimen
as lectotype. We revalidate Rana inaudax Peracca, 1893 as
Mantidactylus inaudax (Peracca, 1893) bona species, and
Mantidactylus tripunctatus Angel, 1930 bona species. The
identities of three further species (M. ambohimitombi, M.
biporus, M. tricinctus) are largely redefined based on new
genetic data. By designating the lectotype of Rana aluta
(MZUT An725.1) as the neotype of Mantidactylus laevis
Angel, 1929 we also stabilize the latter nomen (as junior
synonym of M. alutus) whose original type material is lost.
Based on DNA sequences of its lectotype, we consider
Mantidactylus brauni Ahl, 1929 as junior synonym of M.
ulcerosus (rather than M. biporus). We formally name 20
new species and four new subspecies: M. ambohimitombi
marefo ssp. nov., M. ambohimitombi miloko ssp. nov., M.
mahery sp. nov., M. steinfartzi sp. nov., M. incognitus sp.
nov., M. jonasi sp. nov., M. katae sp. nov., M. kortei sp.
nov., M. riparius sp. nov., M. fergusoni sp. nov., M. georgei
sp. nov., M. jahnarum sp. nov., M. marintsoai sp. nov., M.
grubenmanni sp. nov., M. gudrunae sp. nov., M. augustini
sp. nov., M. bletzae sp. nov., M. brevirostris sp. nov., M.
eulenbergeri sp. nov., M. glosi sp. nov., M. stelliger sp. nov.,
M. manerana sp. nov., M. manerana fotaka ssp. nov., and
M. manerana antsanga ssp. nov. This leaves Mantidactylus
subgenus Brygoomantis with 35 described species and six
subspecies (including nominate subspecies). Based on
our taxonomic revision, we discuss (i) the importance of
definitive assignment of historical names via archival DNA
analysis; (ii) the relevance of the subspecies category to
name geographic variation within species; (iii) the value
of molecular characters in formal species diagnoses in
taxa with substantial individual variation of morphology;
(iv) the use of phylogenomic approaches for taxonomy, by
confirming that some morphologically similar taxa are not
each other’s closest relatives, and in several cases belong to
entirely different major subclades within Brygoomantis, thus
facilitating lineage diagnosis; and (v) the need to interpret
genetic distances in a probabilistic framework rather than
using fixed thresholds, where higher distances confer a
higher likelihood of genetic incompatibilities across the
genome and thus completion of speciation.