Article

A New, Morphologically Cryptic Species of Adenomera Closely Related to Adenomera araucaria from the Atlantic Forest of Southern Brazil (Anura, Leptodactylidae)

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Abstract

ABSTRACT.—We describe a new species of Adenomera from the Brazilian Atlantic Forest corresponding to one of the candidate species indicated in the published phylogeny of the genus (‘‘sp. R’’). The new species differs from all 18 congeners by the combination of small size, absence of toe discs, and the advertisement call composed of a single nonpulsed note with pronounced frequency upsweep. From the closest related and morphologically cryptic Adenomera araucaria, the new species is distinguished only by its nonpulsed advertisement call (multipulsed call in A. araucaria). The new species is distributed in the Serra do Tabuleiro mountain range and the Santa Catarina Island, as well as localities in between them in the eastern portion of the state Santa Catarina. This is the second Adenomera species endemic to the Atlantic Forest of eastern Santa Catarina in southern Brazil, sympatric to Adenomera engelsi and allopatric to the sibling A. araucaria.

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... From the other seven species of its own clade (i.e., the Atlantic Forest endemic A. marmorata clade), A. cantitata is distinguished from A. bokermanni (21.2 to 24.3 mm, n ¼ 18; specimens listed in Appendix I) and A. engelsi (20.9 to 22.7 mm; n ¼ 12; Kwet et al. 2009) by having small adult males (SVL ¼ 16.4 to 19.5 mm; n ¼ 22). The new species is also distinguished by having toe tips expanded into discs, whereas they are unexpanded or slightly expanded in A. araucaria, A. bokermanni, A. engelsi, and A. kweti (Carvalho et al. 2019d (Almeida and Angulo 2006). From the two species of the A. lutzi clade, A. cantitata is distinguished by having a single-note call, in comparison with the multinote call of A. glauciae (Carvalho et al. 2020b). ...
... From the other species of the Adenomera marmorata clade, A. cantitata is distinguished by a nonpulsed call (pulsed call in A. araucaria; Kwet and Angulo 2002) and the dominant frequency coinciding with the fundamental harmonic (coincident with the second harmonic in A. bokermanni, A. engelsi, A. kweti, and A. nana;Kwet 2007;Kwet et al. 2009;Carvalho et al. 2019d). The high acoustic variation within A. marmorata contains that of the allopatric A. cantitata (Cassini et al. 2020, their table 3), but these two species do not share an immediate common ancestor, with A. cantitata being the sister taxon to A. ajurauna (Fig. 1). ...
... Our phylogenetic analyses recovered Adenomera ajurauna and A. cantitata as sister species, in agreement with previous studies (e.g., Fouquet et al. 2014;Carvalho et al. 2019d;Cassini et al. 2020). These species display remarkable divergence in mtDNA and acoustic traits. ...
Article
The Atlantic Forest is recognized as a biodiversity hotspot because of the high species richness and the remaining natural areas comprising less than 30% relative to its primary vegetation. Even though many anuran species from this biome are ecologically restricted to pristine ecosystems, there are some examples of new species discovered from anthropized areas. Adenomera represents a widespread and abundant frog genus in Atlantic Forest ecosystems, with species occurring in areas with varying degrees of human disturbance. In this paper, we name and describe a new species of Adenomera endemic to the Atlantic Forest typically found in human-altered ecosystems, such as urban and rural sites. The new species was recovered as belonging to the Adenomera marmorata clade, and sister to A. ajurauna. These two species have allopatric distributions in southeastern and southern Brazil, with a single known sympatric occurrence. They display different calls and occupy distinct habitats. The newly described species of Adenomera is an additional case of new species discovered from urban sites in the Atlantic Forest hotspot.
... Toe tip development (character states A-D) was assessed according to Heyer (1973), modified by Carvalho et al. (2019d). U n l e s s o t h e r w i s e s t a t e d , c o m p a r i s o n s o f morphological and chromatic characters among species of Adenomera throughout the taxonomic accounts were based primarily on specimens examined and measured for this study (Table 2; Supporting Information, Appendix S1) and the following studies [when applicable, taxonomic authorities in square brackets]: Adenomera ajurauna [Berneck, Costa & Garcia, 2008] (Berneck et al., 2008), Adenomera andreae [Müller, 1923] (Carvalho et al., 2019d), Adenomera araucaria Kwet & Angulo, 2002(Carvalho et al., 2019b, Adenomera bokermanni [Heyer, 1973] (Carvalho et al., 2019b), Adenomera chicomendesi Carvalho, Angulo, Kokubum, Barrera, Souza, Haddad & Giaretta, 2019(Carvalho et al., 2019a, Adenomera coca [Angulo & Reichle, 2008] (Angulo & Reichle, 2008, Adenomera cotuba (Carvalho & Giaretta, 2013a), Adenomera diptyx [Boettger, 1885] (Carvalho & Giaretta, 2013b), Adenomera engelsi Kwet, Steiner & Zillikens, 2009(Carvalho et al., 2019a, A. heyeri (Boistel et al., 2006), Adenomera hylaedactyla [Cope, 1868] (Carvalho et al., 2019d), Adenomera juikitam (Carvalho & Giaretta, 2013a), Adenomera kweti Carvalho, Cassini, Taucce & Haddad, 2019(Carvalho et al., 2019b, Adenomera lutzi Heyer, 1975(Kok et al., 2007, Adenomera marmorata Steindachner, 1867(Cassini et al., 2020, Adenomera martinezi [Bokermann, 1956] (Carvalho & Giaretta, 2013b), Adenomera nana [Müller, 1922] (Carvalho et al., 2019b), Adenomera phonotriccus (Carvalho et al., 2019c), Adenomera saci Carvalho & Giaretta, 2013(Carvalho & Giaretta, 2013b ...
... Toe tip development (character states A-D) was assessed according to Heyer (1973), modified by Carvalho et al. (2019d). U n l e s s o t h e r w i s e s t a t e d , c o m p a r i s o n s o f morphological and chromatic characters among species of Adenomera throughout the taxonomic accounts were based primarily on specimens examined and measured for this study (Table 2; Supporting Information, Appendix S1) and the following studies [when applicable, taxonomic authorities in square brackets]: Adenomera ajurauna [Berneck, Costa & Garcia, 2008] (Berneck et al., 2008), Adenomera andreae [Müller, 1923] (Carvalho et al., 2019d), Adenomera araucaria Kwet & Angulo, 2002(Carvalho et al., 2019b, Adenomera bokermanni [Heyer, 1973] (Carvalho et al., 2019b), Adenomera chicomendesi Carvalho, Angulo, Kokubum, Barrera, Souza, Haddad & Giaretta, 2019(Carvalho et al., 2019a, Adenomera coca [Angulo & Reichle, 2008] (Angulo & Reichle, 2008, Adenomera cotuba (Carvalho & Giaretta, 2013a), Adenomera diptyx [Boettger, 1885] (Carvalho & Giaretta, 2013b), Adenomera engelsi Kwet, Steiner & Zillikens, 2009(Carvalho et al., 2019a, A. heyeri (Boistel et al., 2006), Adenomera hylaedactyla [Cope, 1868] (Carvalho et al., 2019d), Adenomera juikitam (Carvalho & Giaretta, 2013a), Adenomera kweti Carvalho, Cassini, Taucce & Haddad, 2019(Carvalho et al., 2019b, Adenomera lutzi Heyer, 1975(Kok et al., 2007, Adenomera marmorata Steindachner, 1867(Cassini et al., 2020, Adenomera martinezi [Bokermann, 1956] (Carvalho & Giaretta, 2013b), Adenomera nana [Müller, 1922] (Carvalho et al., 2019b), Adenomera phonotriccus (Carvalho et al., 2019c), Adenomera saci Carvalho & Giaretta, 2013(Carvalho & Giaretta, 2013b ...
... Toe tip development (character states A-D) was assessed according to Heyer (1973), modified by Carvalho et al. (2019d). U n l e s s o t h e r w i s e s t a t e d , c o m p a r i s o n s o f morphological and chromatic characters among species of Adenomera throughout the taxonomic accounts were based primarily on specimens examined and measured for this study (Table 2; Supporting Information, Appendix S1) and the following studies [when applicable, taxonomic authorities in square brackets]: Adenomera ajurauna [Berneck, Costa & Garcia, 2008] (Berneck et al., 2008), Adenomera andreae [Müller, 1923] (Carvalho et al., 2019d), Adenomera araucaria Kwet & Angulo, 2002(Carvalho et al., 2019b, Adenomera bokermanni [Heyer, 1973] (Carvalho et al., 2019b), Adenomera chicomendesi Carvalho, Angulo, Kokubum, Barrera, Souza, Haddad & Giaretta, 2019(Carvalho et al., 2019a, Adenomera coca [Angulo & Reichle, 2008] (Angulo & Reichle, 2008, Adenomera cotuba (Carvalho & Giaretta, 2013a), Adenomera diptyx [Boettger, 1885] (Carvalho & Giaretta, 2013b), Adenomera engelsi Kwet, Steiner & Zillikens, 2009(Carvalho et al., 2019a, A. heyeri (Boistel et al., 2006), Adenomera hylaedactyla [Cope, 1868] (Carvalho et al., 2019d), Adenomera juikitam (Carvalho & Giaretta, 2013a), Adenomera kweti Carvalho, Cassini, Taucce & Haddad, 2019(Carvalho et al., 2019b, Adenomera lutzi Heyer, 1975(Kok et al., 2007, Adenomera marmorata Steindachner, 1867(Cassini et al., 2020, Adenomera martinezi [Bokermann, 1956] (Carvalho & Giaretta, 2013b), Adenomera nana [Müller, 1922] (Carvalho et al., 2019b), Adenomera phonotriccus (Carvalho et al., 2019c), Adenomera saci Carvalho & Giaretta, 2013(Carvalho & Giaretta, 2013b ...
Article
A large proportion of the biodiversity of Amazonia, one of the most diverse rainforest areas in the world, is yet to be formally described. One such case is the Neotropical frog genus Adenomera. We here evaluate the species richness and historical biogeography of the Adenomera heyeri clade by integrating molecular phylogenetic and species delimitation analyses with morphological and acoustic data. Our results uncovered ten new candidate species with interfluve-associated distributions across Amazonia. In this study, six of these are formally named and described. The new species partly correspond to previously identified candidate lineages ‘sp. F’ and ‘sp. G’ and also to previously unreported lineages. Because of their rarity and unequal sampling effort of the A. heyeri clade across Amazonia, conservation assessments for the six newly described species are still premature. Regarding the biogeography of the A. heyeri clade, our data support a northern Amazonian origin with two independent dispersals into the South American Dry Diagonal. Although riverine barriers have a relevant role as environmental filters by isolating lineages in interfluves, dispersal rather than vicariance must have played a central role in the diversification of this frog clade.
... The phylogenetic and lineage delimitation analyses uncovered 31 confirmed candidate species. Some of these genetic lineages were subsequently named and described as new species of Adenomera in a series of taxonomic contributions to the genus (Carvalho et al. 2019b(Carvalho et al. , 2019c(Carvalho et al. , 2019d(Carvalho et al. , 2020a, including lineages that had not been sampled previously (see Carvalho et al. 2020cCarvalho et al. , 2021 ...
... The toe tip development (character states A-D) was assessed according to Heyer (1973) and modified by Carvalho et al. (2019a). Morphological comparisons were based on original species descriptions, redescriptions, and taxonomic reviews of species of Adenomera (Heyer 1973(Heyer , 1975Kwet & Angulo 2002;Almeida & Angulo 2006;Kok et al. 2007;Kwet 2007;Angulo & Reiche 2008;Berneck et al. 2008;Kwet et al. 2009;Angulo & Icochea 2010;Carvalho & Giaretta 2013a, 2013bCarvalho et al. 2019aCarvalho et al. , 2019bCarvalho et al. , 2019cCarvalho et al. , 2019dCarvalho et al. , 2020aCarvalho et al. , 2020cCarvalho et al. , 2021Cassini et al. 2020), as well as specimens morphologically examined by us (see Appendix 1). ...
Article
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Adenomera is a genus of Neotropical leaf-litter frogs widely distributed in South America and regarded taxonomic-wise challenging. One of these is the open-habitat Adenomera diptyx from Paraguay, which may correspond to a species complex. An integrative analysis of morphological variation, in combination with acoustic and molecular data of several populations from Argentina, Paraguay, and Brazil resulted in the recharacterization of nominal A. diptyx and the description of a new, closely related species. Adenomera diptyx is recognized by its advertisement call given at a high repetition rate (176–299 per minute), and the dorsal color pattern consisting of a light mid-dorsal line and a dark brown interorbital bar with irregular black edges. In comparison with A. diptyx, the new species, Adenomera guarani sp. nov., produces its advertisement call at a lower repetition rate (73–147 per minute), and the dorsal color pattern consists of a light, broad, mid-dorsal stripe and a mask-like patch in the interorbital region. The redefinition of A. diptyx will contribute to future studies focusing on the taxonomic status of other genetic lineages tentatively assigned to this species complex, which could represent additional unnamed species in the open-habitat Adenomera clade.
... Additionally, many authors have consistently stressed that the species richness in Adenomera is underestimated as a consequence of high levels of cryptic diversity (Angulo et al., 2003;Angulo and Reichle, 2008;Carvalho et al., 2013a). As such, specieslevel systematics of Adenomera has recently benefited from the incorporation of acoustic and molecular data (e.g., Carvalho et al., 2019bCarvalho et al., , 2019cCarvalho et al., , 2019dCassini et al., 2020). ...
... Absence of toe discs distinguishes the new species from A. ajurauna, A. andreae, A. chicomendesi, A. lutzi, A. marmorata, A. nana, and A. simonstuarti (Angulo et al., 2003;Kok et al., 2007;Kwet, 2007;Berneck et al., 2008;Angulo and Icochea, 2010;Carvalho et al., 2019aCarvalho et al., , 2019dCassini et al., 2020). Adenomera glauciae differs from A. araucaria, A. bokermanni, A. heyeri, A. kweti, A. lutzi, and A. nana by having creamcolored belly in life (yellow or at least with yellowish tints in the other species; Boistel et al., 2006;Kok et al., 2007;Carvalho et al., 2019b). From the closely related A. lutzi, A. glauciae is further distinguished by lacking bright coloration (yellow to red tints in life) on hidden surfaces of thigh (Kok et al., 2007). ...
Article
We describe a new species of the South American frog genus Adenomera, based on external morphology, color patterns, advertisement call, and mtDNA sequences. The new species was collected from the Japurá River basin in northwestern Brazilian Amazonia and is distinguished from all congeners by the combination of large snout–vent length (SVL), toe tips unexpanded, presence of antebrachial tubercle on underside of forearm, and by a multi-note advertisement call composed of non-pulsed notes. This new species is part of the A. lutzi clade together with a candidate new species known as Adenomera sp. P and A. lutzi. The three species have the largest SVL in the genus. The presence of toe tips fully expanded and a single-note advertisement call distinguish A. lutzi from the new species. Acoustic and morphological data are still required to assess the taxonomic identity of Adenomera sp. P. Our new species of Adenomera is the third anuran species described from the Solimões-Japurá interfluve. This flags this poorly known region of lowland forests as an important area of species richness in northwestern Amazonia.
... Interspecific comparisons. Adenomera albarena differs from all congeners, except A. simonstuarti by having a nearly solid dark-coloured stripe on the underside of the forearm (Heyer 1973(Heyer , 1975Kwet and Angulo 2002;Almeida and Angulo 2006;Kok et al. 2007;Kwet 2007;Angulo and Reichle 2008;Berneck et al. 2008;Kwet et al. 2009;Angulo and Icochea 2010;Giaretta 2013a, 2013b;Carvalho et al. 2019aCarvalho et al. , 2019bCarvalho et al. , 2019cCarvalho et al. , 2019dCarvalho et al. , 2020aCarvalho et al. , 2020cCarvalho et al. , 2021Cassini et al. 2020;Zaracho et al. 2023). ...
Article
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By using integrative taxonomy, we describe a new species of terrestrial foam-nesting frog of the genus Adenomera from white-sand forests of the Rio Negro Sustainable Development Reserve, Central Amazonia, Brazil. Within the A. andreae clade, the new species belongs to the A. simonstuarti complex where it is sister to the lineage from the lower Juruá River. The new species is assigned to the genus Adenomera by having adult SVL smaller than 34.1 mm, by its lack of fringing and webbing between toes and by the absence of spines on the thumb of adult males. It differs from other Adenomera by the following combination of characters: antebrachial tubercle absent; toe tips flattened or slightly flattened, with visible expansions; nearly solid, dark-coloured stripe on underside of forearm; single-note advertisement call; notes formed by 11–21 incomplete pulses; call duration varying between 100 and 199 ms; fundamental frequency 1,765–2,239 Hz; dominant frequency 3,448–4,349 Hz; and endotrophic tadpoles with spiracle present and labial teeth absent. Over the last decade, we have inventoried many permanent sampling modules in ombrophilous forests in the Manaus Region and in the Purus-Madeira interfluve, but the new species was found only in the white-sand forest from West Negro-Solimões Interfluve. Adenomera sp. nov. may be endemic to, or at least a specialist in, this environment.
... New species of amphibians have been frequently described in recent years from areas .1000 m above sea level (m a.s.l.) in the AF (Taucce et al. 2018;de Carvalho et al. 2019;Cruz et al. 2019;Nunes et al. 2021). Because of the increase in deforestation in this ecoregion (Mittermeier et al. 2004), most of these endemic and rare species are threatened or, due to the lack of studies, do not have enough data to be assigned a conservation status (Neves et al. 2018), which draws attention to these amphibians. ...
Article
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We described a new species of Dendrophryniscus from the Mantiqueira Mountains, a mountain range in the Atlantic Forest in the state of Minas Gerais, Brazil. Dendrophryniscus cuca sp. nov. is known only from its type locality, the private Protected Area Chapada͂o da Serra Negra, municipality of Santa Bárbara do Monte Verde. The new species is morphologically distinguished from its congeners mainly by the combination of the following characters: medium size for the genus, longitudinal set of granules posterior to the corner of mouth, fingers neither fringed nor webbed, and presence of nuptial pads in males. Molecular analysis of the 16S mitochondrial DNA indicates a genetic distance range from 2.39% (D. brevipollicatus) to 17.92% (D. carvalhoi). Individuals were found in bromeliads, and we described a male–male amplexus with the presence of release vibrations, but calling activity was not observed. This is the fourth endemic anuran species of the Serra Negra da Mantiqueira, part of the Mantiqueira mountain range (Serra Negra da Mantiqueira), highlighting the importance of the region for the Neotropical herpetofauna.
... New species of amphibians have been frequently described in recent years from areas .1000 m above sea level (m a.s.l.) in the AF (Taucce et al. 2018;de Carvalho et al. 2019;Cruz et al. 2019;Nunes et al. 2021). Because of the increase in deforestation in this ecoregion (Mittermeier et al. 2004), most of these endemic and rare species are threatened or, due to the lack of studies, do not have enough data to be assigned a conservation status (Neves et al. 2018), which draws attention to these amphibians. ...
Article
Full-text available
We described a new species of Dendrophryniscus from the Mantiqueira Mountains, a mountain range in the Atlantic Forest in the state of Minas Gerais, Brazil. Dendrophryniscus cuca sp. nov. is known only from its type locality, the private Protected Area Chapadão da Serra Negra, municipality of Santa Bárbara do Monte Verde. The new species is morphologically distinguished from its congeners mainly by the combination of the following characters: medium size for the genus, longitudinal set of granules posterior to the corner of mouth, fingers neither fringed nor webbed, and presence of nuptial pads in males. Molecular analysis of the 16S mitochondrial DNA indicates a genetic distance range from 2.39% (D. brevipollicatus) to 17.92% (D. carvalhoi). Individuals were found in bromeliads, and we described a male-male amplexus with the presence of release vibrations, but calling activity was not observed. This is the fourth endemic anuran species of the Serra Negra da Mantiqueira, part of the Mantiqueira mountain range (Serra Negra da Mantiqueira), highlighting the importance of the region for the Neotropical herpetofauna.
... Na lista de anfíbios, por exemplo, pelo menos nove espécies não ocorrem em São Francisco do Sul com base em trabalhos de taxonomia: Adenomera engelsi, Cycloramphus asper, C. duseni, Dendrophryniscus brevipollicatus, Ischnocnema guentheri, I. manezinho, Scinax perpusillus, Physalaemus maculiventris, Physalaemus spiniger (e. g. Canedo & Haddad, 2012, Lourenço et al., 2015, Carvalho et al., 2019, Cruz et al., 2019, de Sá et al., 2019. A confirmação do registro de espécies pode causar confusão na literatura, principalmente em se tratando de espécies com distribuição restrita, como é o caso de Cycloramphus asper, C. duseni e I. manezinho e pode prejudicar estratégias de conservação. ...
Article
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O conhecimento sobre a fauna local fornece subsídios chave para a elaboração de estratégias e implementação de práticas de conservação. O Ecossistema Babitonga (EB), no nordeste do estado de Santa Catarina, abriga uma importante diversidade biológica, ao mes-mo tempo em que sua economia crescente tem acelerado o uso dos recursos naturais da re-gião. O presente trabalho teve como objetivo fazer uma revisão do conhecimento existente sobre a herpetofauna não marinha desta região sobre a qual existem grandes lacunas de in-formação. Foi realizada uma revisão da literatura que reuniu 69 trabalhos a fim de listar as espécies com ocorrência comprovada ou provável ocorrência no EB. Foram identificadas 128 espécies da herpetofauna, quatro estão ameaçadas de extinção em Santa Catarina, sendo que 56 espécies de anfíbios e 31 espécies de répteis são endêmicas do Bioma Mata Atlântica e a espécie Brachycephalus actaeus é endêmica do EB. Esperamos que este trabalho sinalize a importância da região para a conservação da herpetofauna em Santa Catarina e incentive futuros trabalhos que contribuam para uma gestão sustentável de seu ecossistema.
... Adenomera guarayo is distinguished from A. simonstuarti by lacking a nearly solid dark-colored bar along the underside of forearm (see fig. 6 of Angulo and Icochea 2010). Adenomera guarayo is distinguished in life colors from the yellow-bellied A. araucaria, A. heyeri, A. kweti, and A. lutzi (Boistel et al. 2006;Kok et al. 2007;Carvalho et al. 2019b) by having a cream-colored belly (Fig. 2D). Adenomera guarayo cannot be distinguished unambiguously from most congeners also possessing toe tips expanded into discs (morphological distinction in relation to A. lutzi and A. simonstuarti; see previous paragraph). ...
Article
We describe a new species of Adenomera from southwestern Amazonia. The new species corresponds to one of the acoustic patterns and morphotypes from Tambopata National Reserve (Adenomera ‘‘Forest Call II’’), which was associated with the candidate species identified via molecular data as Adenomera sp. C in the phylogeny of the genus. The new species is distinguished from all congeners, except A. phonotriccus, by a unique advertisement call: calls are composed of complete pulses, i.e., separated by silent gaps, whereas those of remaining Adenomera species are composed of incomplete pulses (partly fused) or nonpulsed calls. The new species occurs in southeastern Peru and north central Bolivia, with two sympatric records with A. chicomendesi. The taxonomic status of two candidate species (sp. D and sp. T) of the A. andreae clade in southwestern Amazonia still needs to be addressed by the acquisition of additional phenotypic and molecular data.
... A striking example of a Neotropical frog group with predominance of cryptic species is the genus Adenomera Steindachner, 1867 (e.g., Angulo & Reichle 2008;Carvalho & Giaretta 2013a;Carvalho et al. 2019aCarvalho et al. , 2019b. These small-sized leptodactylids (snout-vent length up to 34 mm; Kok et al. 2007) are widely distributed in South America east of the Andes, currently comprising 21 described species (Carvalho et al. 2019b). ...
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Adenomera simonstuarti is a poorly known species complex inhabiting western Amazonia. Here we reevaluate the species diversity within this complex based on previously documented and newly acquired molecular and phenotypic data. We also redescribe the calling pattern of the nominal species based on the original recording (Peru) and a new recording (Brazil). Our results indicate eight geographically structured genetic lineages and the nominal species with a multi-note call pattern. This is the fi rst association of calls and DNA sequence from a voucher specimen, thereby enabling the assignment of A. simonstuarti to one specifi c lineage within the complex. The multi-note call was not previously reported and represents an important additional diagnostic character within Adenomera. The geographic distribution of A. simonstuarti is substantially narrowed down to the southwestern portion of the entire geographic range recognized for the complex. The lack of taxonomic resolution in the complex is a major conservation concern by preventing us from evaluating the potential threats and extinction risks of each of the lineages. Future research should follow the protocol of combining calls and DNA sequences associated with voucher specimens as a means to address the taxonomic status of genetic lineages within the A. simonstuarti complex.
... Given these inconsistencies and the need to elucidate the acoustic parameters of S. squalirostris, we redescribe its advertisement call based on a new sample of topotypes. It is likely that S. squalirostris may comprise a species complex across its presumptive range (Pombal et al. 2011, Faria et al. 2013; thus, it is important to redescribe and authenticate its advertisement call, because vocalizations can be a key to the identification of cryptic diversity among frogs (e.g., Nunes et al. 2012, Caminer and Ron 2014, Ron et al. 2018, Carvalho et al. 2019. To determine if there is inter-populational variation in advertisement calls, we report call data of a population from the Poços de Caldas Plateau in the Mantiqueira Range in the state of Minas Gerais (MG). ...
Article
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Scinax squalirostris (Lutz, 1925) is thought to occur along a broad range in South America. The values reported for calls of topotypes differ substantially among studies. Because vocalizations often play a key role in uncovering cryptic diversity, the call of S. squalirostris is herein redescribed based on a new sample of topotypes. The call of a population from Poços de Caldas, Minas Gerais state, is also described. Topotypic advertisement calls have a dominant frequency between 3970 and 4125 Hz; 13-15 notes emitted at a rate of 24-27/s; call rate of 67/min and duration of 0.52-0.61 s; mid-call notes having 6 or 7 well-defined pulses, and an intra-note pulse rate of 223-266/s. Calls of the Poços de Caldas population have dominant frequency between 4083 and 4358 Hz; 15-18 notes emitted at a rate of 32-34/s; call rate of 64/min and duration of 0.46-0.56 s; mid-call notes having 6 or 8 well-defined pulses, and an intra-note pulse rate of 252-312/s. The advertisement calls of these populations have some differences with each other, and are promptly distinguished from calls of morphologically similar species. Our data to topotypes are inconsistent with some previously reported. A more detailed study of the population from Poços de Caldas is required, and more marked differences may be found in populations more distant from type locality of S. squalirostris.
... This high richness and endemism within the Atlantic Forest might be due to the wide latitudinal range, variable climatic gradient, presence of distinct ecoregions, high topographical complexity, and intense sampling effort (Vasconcelos et al. 2014;Rodríguez et al. 2015;Oliveira et al. 2016). Even with high sampling efforts along the Atlantic Forest, several new species of anurans are still described every year (e.g., Bornschein et al. 2015;Forlani et al. 2017;Taucce et al. 2018;Carvalho et al. 2019). Factors such as the many remote and still-unsampled areas, limited geographical range, and low abundance of some species, cryptic habits, and the difficulty to differentiate some species from related congeners can explain the high rate of new descriptions (Pimm et al. 2014;Costello et al. 2015). ...
Article
Crossodactylodes is a poorly known genus of small-sized bromeligenous frogs, endemic to Brazil. They have a patchy distribution across the mountains of the Atlantic Forest and the ‘‘campo rupestre’’ ecosystem. To better resolve their evolutionary relationships, we performed phylogenetic analyses using a multigene DNA matrix and representative sampling within the genus. We then evaluated the evolution of phenotypical and natural history traits with the inferred phylogeny. We recovered Crossodactylodes as monophyletic, diagnosed by seven putative synapomorphies in morphological and natural history characters. Evidence supports some morphological synapomorphies as adaptations to the bromeligenous habit. We found high genetic distances among closely distributed lineages within C. bokermanni and C. izecksohni. Some of these lineages might represent undescribed cryptic species. We provide detailed accounts for each species including data on their geographic range, conservation, and natural history. All species of Crossodactylodes occur in highly threatened environments, are restricted to very small geographic ranges, and probably have limited dispersal capacity due to their small body size and dependence on bromeliads. These factors emphasize the need for habitat protection to safeguard species viability.
... Notwithstanding, taxonomical contributions for the genus Adenomera within this domain are seldom published. Before the recent description of A. kweti [15], the most recent taxonomical contribution for the genus in the Atlantic Forest domain was published a decade ago [16]. ...
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Taxonomists always have had intense discussions about how species should be delimited and recently many studies have used integrative approaches by combining molecular, morphological, and bioacoustic data. Although these studies are paramount for understanding species diversity, few of them actually formalize species delimitations to the final step of nomenclatural acts. Historically, the Neotropical frog genus Adenomera has been considered as a difficult taxonomic group because it comprises many morphologically similar species exhibiting high levels of intraspecific polymorphism. A recent work using molecular data shed light on the phylogenetic relationships within the genus and identified several lineages that may correspond to undescribed species but did not delimit species boundaries. In the Atlantic Forest, a clade formed by A. marmorata and two putative species (Adenomera sp. J and Adenomera sp. K) were identified. In this paper, we combine morphological, acoustic, and molecular data in order to evaluate species limits within this Atlantic Forest Adenomera clade. We provide a redescription of A. marmorata and restrict its type locality to the Tijuca Massif, in the Municipality of Rio de Janeiro, Brazil. Our results do not support A. marmorata and the two candidate species as diagnosable distinct species. Therefore A. marmorata corresponds to a species with pronounced morphological and acoustic variation in the genus and a complex phylogeographic structure.
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The following list includes all recognized species of amphibians, known by vouchers or published information to occur within the political borders of Brazil (as of April 2021). Supra-generic taxonomy follows Frost (2021), as do most generic and species names. Other taxonomic decisions and species exclusions are explained below. All inclusions relative to the previous list (Segalla et al. 2019) are informed in the status column. The known amphibian fauna of Brazil comprises 1188 species, an increase of 95 species compared to the previous list. The vast majority of species are anurans, including 1144 species (two exotic and invasive species) representing 20 families and 107 genera, followed by caecilians, with 39 species in 4 families and 13 genera, and salamanders, with 5 species in a single family and genus. Registation in Zoobank: urn:lsid:zoobank.org:pub:D19AF1F3-AEF4-40BD-91E-6-43AA8313E2D2
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We present the latest version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, MEGA has been optimized for use on 64-bit computing systems for analyzing bigger datasets. Researchers can now explore and analyze tens of thousands of sequences in MEGA. The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit MEGA is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OSX. The command line MEGA is available as native applications for Windows, Linux, and Mac OSX. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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A new species of Leptodactylus from Bertioga municipality, São Paulo State, Brazil is described. Leptodactylus ajurauna sp. nov. differs from others species in the L. marmoratus group by its dark brown throat and the advertisement call. The taxonomy of other species in the group and the status of the population of Leptodactylus marmoratus sympatric with the new species are discussed. The advertisement call is also described.
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Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1 we were able to recover COI sequences for 100% of the species analyzed (N=161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species. This article is protected by copyright. All rights reserved.
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PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder The source code is available at https://github.com/brettc/partitionfinder.
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Standardization and repeatability is at the heart of all scientific research, yet very little literature exists to standardize morphometric measurements within vertebrate groups. This is particularly true for amphibians. Our study attempts to rectify this lack of methodological standardization for the measurement of morphological characters in anurans through an extensive literature survey of 136 species descriptions representing 45 currently recognized families of frogs. The survey revealed 42 morphological measurements represented in five percent or more of the literature reviewed. All measurements are listed by most commonly used name, acronym, and most precise definition, and we provide statistics summarizing the variation in measurement use and description from the surveyed literature. Of these 42 measurements, a subset of 16 were found in the top 75% of all surveyed descriptions and identified as a focal set of recommended measurements in an effort to standardize the morphometric measurements that describe anuran species diversity. Illustrations of these 16 measurements are provided as a visual reference for standardizing their measurement.
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We review Seewave, new software for analysing and synthesizing sounds. Seewave is free and works on a wide variety of operating systems as an extension of the R operating environment. Its current 67 functions allow the user to achieve time, amplitude and frequency analyses, to estimate quantitative differences between sounds, and to generate new sounds for playback experiments. Thanks to its implementation in the R environment, Seewave is fully modular. All functions can be combined for complex data acquisition and graphical output, they can be part of important scripts for batch processing and they can be modified ad libitum. New functions can also be written, making Seewave a truly open-source tool.
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Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available. The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Alexandros.Stamatakis@h-its.org.
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AimFor many taxa, inaccuracy of species boundaries and distributions hampers inferences about diversity and evolution. This is particularly true in the Neotropics where prevalence of cryptic species has often been demonstrated. The frog genus Adenomera is suspected to harbour many more species than the 16 currently recognized. These small terrestrial species occur in Amazonia, Atlantic Forest (AF), and in the open formations of the Dry Diagonal (DD: Chaco, Cerrado and Caatinga). This widespread and taxonomically complex taxon provides a good opportunity to (1) test species boundaries, and (2) investigate historical connectivity between Amazonia and the AF and associated patterns of diversification. LocationTropical South America east of the Andes. Methods We used molecular data (four loci) to estimate phylogenetic relationships among 320 Adenomera samples. These results were integrated with other lines of evidence to propose a conservative species delineation. We subsequently used an extended dataset (seven loci) and investigated ancestral area distributions, dispersal–vicariance events, and the temporal pattern of diversification within Adenomera. ResultsOur conservative delineation identified 31 Confirmed Candidate Species (four remaining unconfirmed) representing a 94% increase in species richness. The biogeographical analysis suggested an Amazonian origin of Adenomera with as many as three dispersals to the DD and one to the AF during the Miocene. These dispersals were associated with habitat shifts from forest towards open habitats. Main conclusionsThe DD played a major role in the history of Adenomera in limiting dispersal and favouring diversification of open-habitat lineages. Moreover, a forest bridge during the Miocene Climatic Optimum may have permitted dispersal from Amazonia towards the AF and subsequent diversification. Uncovering species boundaries and distributions might drastically change inferences based on currently perceived distribution patterns.
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A new species of Leptodactylus from Bertioga municipality, São Paulo State, Brazil is described. Leptodactylus ajurauna sp. nov. differs from others species in the L. marmoratus group by its dark brown throat and the advertisement call. The taxonomy of other species in the group and the status of the population of Leptodactylus marmoratus sympatric with the new species are discussed. The advertisement call is also described
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As part of the remarkable biodiversity of anurans in the southern range of the Brazilian Mata Atlântica, Adenomera engelsi sp. nov. is described here as a new taxon occurring on the island of Santa Catarina and adjacent coastal mainland. This litter-inhabiting frog is restricted to the Atlantic rain forest biome, living in primary and secondary woods and semi-open areas from sea level to about 900 m a.s.l., partly in sympatry with its congener A. araucaria. Both species are also referred to the Leptodactylus marmoratus group. Adenomera engelsi sp. nov. is a medium-sized member of the genus (snout–vent length 20.9–22.7 mm in males), characterized by a brown dorsal coloration with a maculated pattern of variable dark spots and blotches and a unique advertisement call, consisting of single, unpulsed notes with duration of 95–160 ms, dominant frequency between 3500 and 4300 Hz, and note repetition rates of 10–24 notes/min.Está descrita, como parte da enorme biodiversidade de anuros na região sul da Mata Atlântica brasileira, Adenomera engelsi sp. nov. que ocorre na Ilha de Santa Catarina e no litoral adjacente. A espécie está restrita ao bioma da Mata Atlântica, onde vive no folhiço em mata primária, secundária e áreas semi-abertas, desde o nível do mar até 900 m, parcialmente em simpatria com A. araucaria. Ambas as espécies também são atribuidas ao grupo Leptodactylus marmoratus. Adenomera engelsi sp. nov., de tamanho medio dentro do gênero (SVL 20.9–22.7 mm em machos), é caraterizada pela coloração dorsal marrom, com manchas escuras de tamanho e forma variável e um canto de anúncio distinto, que consiste de notas únicas e sem pulsos de 95–160 ms com frequência dominante entre 3500–4300 Hz e taxa de repetição de 10–24 notas por minuto.
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The genus Adenomera has been a difficult group for systematic studies because the species are similar and geographically variable. Two species have been reported from the Peruvian Amazon Basin: Adenomera andreae and Adenomera hylaedactyla. However, acoustic recordings from the Tambopata National Reserve in southeastern Peru reveal four sympatric advertisement call types that are distinctive in acoustic parameters and to the human ear. Some subtle morphological differences are also present. We conclude that there are at least four sympatric species at Tambopata and that Adenomera has a greater species diversity than currently acknowledged.
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We describe a new species of the genus Adenomera from French Guiana. Collecting conditions, details about the localities and microhabitats are given. The advertisement call was recorded and is herein analyzed and described. Morphologi - cal and bioacoustic comparisons are drawn with other species of the genus. The new species is readily distinguished from other taxa by its distinctive coloration pattern, the occurrence of dorsolateral ridges and inguinal glands, and by the longer duration of the notes of its advertisement call. The taxonomy of Adenomera is evaluated with regard to current available knowledge.
Article
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Bioacoustic variation recorded from different Adenomera populations in southern Brazil is presented and discussed. Recent recordings of advertisement calls from different localities in the states of Santa Catarina and southern Paraná are compared with calls of closely related A. araucaria and A. marmorata from adjacent regions in the Atlantic Rain Forest domain. Acoustic data allow for the differentiation of at least five different species of Adenomera occurring in southern Brazil. None of these seem to be conspecific with nominal A. marmorata. Based on bioacoustic data, Adenomera nana (Müller, 1922) is revalidated in this study. In addition to A. nana and A. araucaria, whose distribution range is extended about 200 km to the north, three as yet undescribed species of Adenomera are involved. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
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Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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Prior to this study, Leptodactylus lutzi was known only from three localities in west-central Guyana. We refer here to a series of 60 additional specimens of L. lutzi collected in Kaieteur National Park, Mount Ayanganna, Mount Wokomung and the Merume Mountains in the Pakaraima Mountains region, substantially extending the knowndistribution of the species. We provide a revised diagnosis and an expanded description of L. lutzi discussing the extent of color-pattern variation in the species. Additionally, we describe its advertisement call and provide data on its reproductive biology.
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Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. Availability: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
Article
Adults and tadpoles of a new species of the genus Leptodactylus are described from southeastern Brazil. Leptodactylus thomei sp.nov. can be found amidst the leaf litter within cocoa plantations along the northern coastal region of the state of Espírito Santo. It can be distinguished from other species of the Leptodactylus marmoratus group by its advertisement call, which is described, together with agonistic calls, and compared to advertisement calls of other species of the group that occur in southern and southeastern Brazil. The systematics of associated populations is discussed.
Article
In this paper, we provide a taxonomic circumscription of Adenomera martinezi from its type locality (Cachimbo, southwestern State of Pará) since its description (57 years ago) based on a newly collected series of eleven adult topotypes, and through a bioacoustic approach, recognize an undescribed cryptic taxon under this nominal species, which is widely distributed in central and northern Brazil. Adenomera martinezi and Adenomera saci sp. nov. can be diagnosed from all con-geners by their distinctive 4–6 symmetrically arranged rows of longitudinal dark-colored spots on dorsum. They differ from each other through advertisement call structure, pulsed in Adenomera martinezi (audibly pulsed to the human ear), and non-pulsed in Adenomera saci sp. nov. (a whistle to the human ear). The recognition of Adenomera saci sp. nov. has conservation implications. Based on our assumed distribution of A. martinezi and Adenomera saci sp. nov., the IUCN conservation status of A. martinezi requires a reassessment, inasmuch as we herein reconsider this species, as far as we know, as endemic to Cachimbo, southwestern State of Pará, Brazil. The 2004 extinction risk assessment included both A. mar-tinezi and Adenomera saci sp. nov., and the conservation status category of 'Least Concern' might only be applied to Ad-enomera saci sp. nov., a widely distributed and abundant species in central and northern Brazil.
Article
In this paper, we describe two syntopic species of Adenomera from the Chapada dos Veadeiros microregion, northern State of Goiás, central Brazil, recognized based on morphology, color patterns, and bioacoustics. Specimens and calls were obtained in the Municipality of Teresina de Goiás, central Brazil. Adenomera cotuba sp. nov. is diagnosed from the other 16 congeneric species by its 1) small size (adult male SVL 18.6-20.5 mm) and very robust body; 2) dorsum glandular/granular with no distinctive dorsal granular rows or dorsolateral folds; 3) black or very dark dorsal coloration with no distinctive color patterns (e.g., dorsolateral or vertebral stripes); 4) toe tips not developed into flattened disks; 5) presence of antebrachial tubercle; and 6) advertisement call consisting of a well-defined series of pulsed calls (7-32 calls/series) with progressive increment in amplitude in the first third of each call series when it reaches a sustained plateau. Adenomera juikitam sp. nov. is diagnosed from the other 16 congeneric species by its 1) dorsum profusely glandular/granular with no distinctive dorsal granular rows or dorsolateral folds; 2) dorsum with a marble-like and red coloration with no distinctive color patterns (e.g., dorsolateral or vertebral stripes); 3) toe tips not developed into flattened disks; 4) small size (adult male SVL 19.1-19.5 mm) and very robust body; and 5) long (148-202 ms) advertisement call composed of 16-21pulses. Both new taxa occur in syntopy, and our data allow us to differentiate them both in temporal (pulses/call) and spectral (frequency peaks) traits of their advertisement calls. Besides, dorsal coloration is distinctive, Adenomera cotuba sp. nov. has a black or very dark-colored dorsum, whereas Adenomera juikitam sp. nov. has a marble-like and red-colored dorsum, in addition to the presence (A. cotuba sp. nov.) or absence (A. juikitam sp. nov.) of antebrachial tubercle.
Article
The advertisement calls of 23 Bolivian anuran species in the family Leptodactylidae are described including information on calling behaviour. For each species, a characteristic audiospectrogram and oscillogram are presented. Numerical information about the spectral and temporal features of the calls is provided and, when available, the results are compared with any previous description of the calls. A phenogram based on holistic comparisons of the mating calls (audiospectrogram correlation) is presented for the genera Eleutheroduciylus, Leptoducrylus. and Plzysalaemus. The intrageneric variability of four basic call parameters is compared. The results suggest that fundamental and dominant frequency (and possibly duration for the genus Physalaemus) are the most likely variables to play a role in isolation of congeneric species.
Article
Morphologically cryptic species act as a wild card when it comes to biodiversity assessments and conservation, with the capacity to dramatically alter our understanding of the biological landscape at the taxonomic, ecological, biogeographic, evolutionary, and conservation levels. We discuss the potential effects that cryptic species may have on biodiversity assessments and conservation, as well as some of the current issues involving the treatment of cryptic species both at taxonomic and conservation levels. In addition, using a combination of advertisement call and morphological data, we describe a new species of the Leptodactylus marmoratus group from the upper Amazon basin, and we assess how cryptic species can affect conservation assessments of species in the Leptodactylus marmoratus group by examining how recent findings affect our understanding of the distribution of what is assumed to be a widespread Amazonian species, Leptodactylus andreae.
Article
Spider: SPecies IDentity and Evolution in R is a new R package implementing a number of useful analyses for DNA barcoding studies and associated research into species delimitation and speciation. Included are functions essential for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, and for testing and optimizing divergence threshold limits. In terms of investigating evolutionary and taxonomic questions, techniques for assessing diagnostic nucleotides and probability of reciprocal monophyly are also provided. Additionally, a sliding window function offers opportunities to analyse information across a gene, essential for marker design in degraded DNA studies. Spider capitalizes on R’s extensible ethos and offers an integrated platform ideal for the analysis of both nucleotide and morphological data. The program can be obtained from the comprehensive R archive network (CRAN, http://cran.r-project.org) and from the R-Forge package development site (http://spider.r-forge.r-project.org/).
Article
Overall morphological similarity and intrapopulation variation of morphological features make species identification in cryptic species complexes challenging. In such cases, additional features, such as acoustic and/or genetic characters, are being used to aid species identification. The use of acoustic signals as a suite of diagnostic features can be especially rewarding in certain taxonomic groups that rely on acoustic communication. Such is the case of the Neotropical leaf litter frogs of the Leptodactylus marmoratus group (formerly Adenomera). Recent studies using different suites of features for field identification have revealed a previously undetected species richness for this group. It is in the light of acoustic signals that we identify a new species for this group, and describe it herein. We also discuss the systematics of populations associated with the Amazonian realm. We further explore the use of acoustic signals in species identification and diagnosis in anurans and other taxa that communicate acoustically (e.g. lacewings, orthopterans, and birds), and the relevance and importance of the use of species concepts in species diagnosis and descriptions. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 152, 59–77.
Article
This study produces a nearly comprehensive phylogeny for the marine gastropod group Cypraeidae (cowries) and uses this topology to examine diversification patterns in the tropics. The dataset is based on molecular sequence data from two mitochondrial genes and includes 210 evolutionary significant units (ESUs) from 170 recognized species (>80%). Systematics for the group is revised based on well-supported clades, and tree topology is generally consistent with previously proposed classification schemes. Three new genera are introduced (Cryptocypraea gen. nov, Palmulacypraea gen. nov, and Contradusta gen. nov) and two previous genera are resurrected (Perisserosa and Eclogavena). One new tribe is proposed (Bistolidini). Topologies produced by a range of transition:transversion (Ti:Tv) weighting schemes in parsimony are pooled and evaluated using maximum likelihood criteria. Extensive geographical coverage shows persistent, large-scale geographical structure in sister-groups. Genetic divergence between subspecies is often equivalent or even greater than that between recognized species. Using ESUs as a metric, diversity throughout the Indo-West Pacific (IWP) increases by 38%. Intra- and inter-regional diversification patterns show that the IWP is the centre for speciation in cowries. The other major tropical regions of the world are inhabited by a predominantly relictual fauna; from a cowrie's eye-view. Good dispersal ability begets larger ranges, increased extinction resistance and morphological stasis; whereas shorter larval duration results in smaller ranges, higher speciation rates, but also higher turnover. Larval duration and dispersal ability appear correlated with ocean productivity as taxa with longer-lived larvae are associated with oligotrophic conditions; whereas taxa with shorter larval durations are associated with eutrophic, continental conditions. This tendency is carried to the extreme in temperate or upwelling regions where a planktonic phase is completely lost and crawl-away larvae evolve multiple times. A strong phylogenetic trend supports these observations as lineages leading up to and including the derived Indo-West Pacific Erroneinae clade contain taxa predominantly restricted to continental habitats and have undergone the greatest evolutionary radiations in their respective regions. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 79, 401– 459.
Article
A bias correction to the Akaike information criterion, AIC, is derived for regression and autoregressive time series models. The correction is of particular use when the sample size is small, or when the number of fitted parameters is a moderate to large fraction of the sample size. The corrected method, called AICC, is asymptotically efficient if the true model is infinite dimensional. Furthermore, when the true model is of finite dimension, AICC is found to provide better model order choices than any other asymptotically efficient method. Applications to nonstationary autoregressive and mixed autoregressive moving average time series models are also discussed.
Article
The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.
Article
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log‐expectation score, and refinement using tree‐dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T‐Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T‐Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
Table 1) Adenomera araucaria (Kwet, 2007: in part
  • Kwet
Adenomera kweti sp. nov. (Figs. 2A,B, 3, 5, Table 1) Adenomera araucaria (Kwet, 2007: in part; Kwet et al., 2009:99, specimens on the left of fig. 4A,B,G,H; Conte et al., 2010:203, fig. 1H);
Indaial: PARNA da Serra do Itajaí (CFBH 43208)
  • Santa Catarina
SANTA CATARINA: Ilhota: Morro do Báu (MCP 1346-52); Indaial: PARNA da Serra do Itajaí (CFBH 43208); Jaraguá do Sul (CFBH 39262);
RORAIMA: Upper Máu River (INPA-H 6247)
  • Adenomera
  • Brazil
Adenomera lutzi-BRAZIL: RORAIMA: Upper Máu River (INPA-H 6247); GUYANA: Potaro-Siparuni (MZUSP 150799-804).
  • A Angulo
  • R B Cocroft
ANGULO, A., R. B. COCROFT, AND S. REICHLE. 2003. Species identity in the genus Adenomera (Anura: Leptodactylidae) in southeastern Peru. Herpetologica 59:490-504.
Audacity(R): Free Audio Editor and Recorder, version 2.2.1
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AUDACITY TEAM. 2017. Audacity(R): Free Audio Editor and Recorder, version 2.2.1. Available at https://www.audacityteam.org. Archived by WebCite at http://www.webcitation.org/732btrNLV on 9 October 2018.
Novos registros na distribuição geográfica de anuros na floresta com araucária e considerações sobre suas vocalizações
  • C E Conte
  • F Nomura
  • R A Machado
CONTE, C. E., F. NOMURA, R. A. MACHADO, A. KWET, R. LINGNAU, AND D. C. ROSSA-FERES. 2010. Novos registros na distribui¸c˜ao geogr´afica de anuros na floresta com arauc´aria e considera¸c˜oes sobre suas vocaliza¸c˜oes. Biota Neotropica 10:201-224.
Soundruler: acoustic analysis for research and teaching
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GRIDI-PAPP, M. 2007. Soundruler: acoustic analysis for research and teaching. Available at http://soundruler.sourceforge.net. Archived by WebCite at http://www.webcitation.org/732cA62V3 on 9 October 2018.
A new species of Adenomera (Anura, Leptodactylidae) from the Araucaria forest of Rio Grande do Sul (Brazil), with comments on the systematic status of southern populations of the genus
  • A Kwet
  • A Angulo
KWET, A., AND A. ANGULO. 2002. A new species of Adenomera (Anura, Leptodactylidae) from the Araucaria forest of Rio Grande do Sul (Brazil), with comments on the systematic status of southern populations of the genus. Alytes 20:28-43.
tuneR: analysis of music and speech
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  • S Krey
  • O Mersmann
LIGGES U., S. KREY, O. MERSMANN, AND S. SCHNACKENBERG. 2017. tuneR: analysis of music and speech. Available at https://CRAN.R-project. org/package=tuneR. Archived by WebCite at http://www. webcitation.org/74jswKLGU on 17 December 2018.
The language of technical computing, version 6.5.2. The MathWorks Inc
  • Matlab
MATLAB. 2004. The language of technical computing, version 6.5.2. The MathWorks Inc., USA.
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
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  • Huelsenbeck
RONQUIST F., M. TESLENKO, P. VAN DER MARK, D. L. AYRES, A. DARLING, S. HÖ HNA, B. LARGET, L. LIU, M. A. SUCHARD, AND J. P. HUELSENBECK. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61:539-542.
Standard symbolic codes for institutional resource collections in herpetology and ichthyology: an online reference (v6.5)
  • M H Sabaj
SABAJ, M. H. 2016. Standard symbolic codes for institutional resource collections in herpetology and ichthyology: an online reference (v6.5). Available at http://www.asih.org/sites/default/files/ documents/symbolic_codes_for_collections_v6.5_2016.pdf. Archived by WebCite at http://www.webcitation.org/74ilEB3Nr on 16 December 2018.
Ilhota: Morro do Ba´u (MCP 1346-52); Indaial: PARNA da Serra do Itajaí (CFBH 43208)
  • Santa Catarina
SANTA CATARINA: Ilhota: Morro do Ba´u (MCP 1346-52); Indaial: PARNA da Serra do Itajaí (CFBH 43208); Jaraguá do Sul (CFBH 39262);
RORAIMA: Upper Ma´u River (INPA-H 6247)
  • Brazil
Adenomera lutzi-BRAZIL: RORAIMA: Upper Ma´u River (INPA-H 6247); GUYANA: Potaro-Siparuni (MZUSP 150799-804).
PARÁ: Novo Progresso: Cachimbo (holotype: MZUSP 73695; allotype: MZUSP 73684
  • Brazil
Adenomera martinezi-BRAZIL: PARÁ: Novo Progresso: Cachimbo (holotype: MZUSP 73695; allotype: MZUSP 73684; topotypes: AAG-UFU 1515-25).
Arquivos de Zoologia
  • W R Heyer
  • A S Rand
  • C A G Cruz