Outstanding diversity and microendemism in a clade of rare Atlantic Forest montane frogs.

Distributed across topographically complex landscapes that vary from lowland to high elevation, the Atlantic Forest harbors one of the richest biotas worldwide. Atlantic Forest amphibians are particularly speciose, taxonomic accounts are rising and the group is used as model for biogeographic inference. Past climate-related habitat fragmentation is often invoked to explain diversification, with montane taxa expected to become more widespread during glacial times and restrained at interglacials. In this study we investigate diversification in Ischnocnema lactea and I. holti (Anura: Brachycephalidae), two rare frog species inhabiting Atlantic Forest montane regions in Southeastern Brazil. Previous phylogenetic accounts have suggested uncertain limits between these two sister species. We assembled a multilocus DNA dataset, delimited lineages in this clade, and used ecological niche modeling to explore past and future putative ranges. Assignment analyses and traditional and coalescent phylogenetic methods confirmed the existence of a species complex of Miocene origin comprising nine lineages, most of which show very narrow ranges. Lineages were fully supported as species based in coalescent species delimitation, but the phylogenetic relationships among lineages in higher elevation were unresolved. Models of past ranges suggest extensive suitable areas at the last glacial maximum which, along with phylogenetic uncertainty, are consistent with a hypothesis that climate driven vicariance at higher elevation areas resulted in hard polytomies. Species distribution models under future climates suggest narrower ranges of the lineages relative to now, but no species are currently considered endangered. Overall, our results argue in favor for the reassessment of the taxonomic and conservation status of the I. holti - I. lactea species complex.

Cryptic diversity and ancient diversification in the northern Atlantic Forest Pristimantis (Amphibia, Anura, Craugastoridae).

The Neotropical region is known both for its megadiverse fauna and for the significant deficiency of our knowledge on species limits. The Amazon and Atlantic Forest are the two most diverse and large rainforests in South America, and they harbor many groups of sister species and sister genera. The frog genus Pristimantis is the most speciose genus of terrestrial vertebrates with 546 species, but only three of them occur in the Atlantic forest. Herein, we investigate the diversification history and phylogenetic relationship among the Atlantic Forest Pristimantis lineages in a spatial-temporal framework, using mitochondrial and nuclear genes. Our results reveal a remarkable hidden diversity, with nine highly structure lineages that may correspond to undescribed species, with many cases of sympatry among these divergent lineages. Atlantic forest Pristimantis form a monophyletic group that started to diversify over 40 million years ago. This ancient group shows diversification events that remount the early bursts of the Atlantic Forest diversification history, as well as lineage diversification likely resulting from recent Pleistocene climatic fluctuations. Future work must concentrate in comparing these lineages under an integrative framework including morphology, advertisement calls and other ecology traits to confidently delimit species of Pristimantis in the Atlantic Forest.

Molecular phylogeny of Ischnocnema (Anura: Brachycephalidae) with the redefinition of its series and the description of two new species.

We present a new phylogenetic hypothesis for Ischnocnema, a Neotropical brachycephaloid genus of ground-dwelling direct-developing frogs. We performed Bayesian inference, maximum likelihood, and maximum parsimony analyses using two nuclear (RAG1 and Tyr) and three mitochondrial genes (12S rRNA, tRNA-Val, and 16S rRNA) in a matrix comprising more than 80% of the described species. We recover Ischnocnema nanahallux outside the Ischnocnema parva series, and it is now unassigned to any species series, nor are Ischnocnema manezinho and Ischnocnema sambaqui. We propose the Ischnocnema venancioi species series to comprise Ischnocnema venancioi, Ischnocnema hoehnei, and two new species described herein (Ischnocnema parnaso sp. nov. and Ischnocnema colibri sp. nov.). Furthermore, we designate a lectotype for I. venancioi. The nuptial pad present in males is an important character in the genus, and having a large, conspicuous, and glandular-appearing nuptial pad seems to be a synapomorphy for the clade composed of the I. parva, Ischnocnema guentheri, and the newly proposed I. venancioi series.

A molecular phylogeny recovers Strabomantis aramunha Cassimiro, Verdade and Rodrigues, 2008 and Haddadus binotatus (Spix, 1824) (Anura: Terrarana) as sister taxa.

The taxonomic and biogeographic affinities of Strabomantis aramunha from the Campos Rupestres of Brazil are intriguing. A unique skull morphology of females suggest affinities with the broad-headed eleutherodactylines of Northwestern South America in the genus Strabomantis. Male and juvenile morphology nonetheless suggest S. aramunha could be related to members of the recently described genus Haddadus from eastern Brazil. We assess the affinities of S. aramunha using molecular phylogenetic analyses of mitochondrial (12S, tRNAval, 16S, cyt b) and nuclear sequences (RAG-1and rhodopsin). Bayesian inference, likelihood, and parsimony analysis recover a highly supported clade with S. aramunha and H. binotatus as sister taxa. Accordingly, we transfer S. aramunha to Haddadus, and provide a new generic definition of the later. The distribution of species in Haddadus (highlands of the Espinhaço mountain Range and coastal eastern Brazil) is now concordant with the general pattern observed for other species in the area.

Phylogenetic relationships within anuran clade Terrarana, with emphasis on the placement of Brazilian Atlantic rainforest frogs genus Ischnocnema (Anura: Brachycephalidae).

We present a phylogenetic hypothesis of the anuran clade Terrarana based on partial sequences of nuclear (Tyr and RAG1) and mitochondrial (12S, tRNA-Val, and 16S) genes, testing the monophyly of Ischnocnema and its species series. We performed maximum parsimony, maximum likelihood, and Bayesian inference analyses on 364 terminals: 11 outgroup terminals and 353 ingroup Terrarana terminals, including 139 Ischnocnema terminals (accounting for 29 of the 35 named Ischnocnema species) and 214 other Terrarana terminals within the families Brachycephalidae, Ceuthomantidae, Craugastoridae, and Eleutherodactylidae. Different optimality criteria produced similar results and mostly recovered the currently accepted families and genera. According to these topologies, Ischnocnema is not a monophyletic group. We propose new combinations for three species, relocating them to Pristimantis, and render Eleutherodactylus bilineatus Bokermann, 1975 incertae sedis status within Holoadeninae. The rearrangements in Ischnocnema place it outside the northernmost Brazilian Atlantic rainforest, where the fauna of Terrarana comprises typical Amazonian genera.

How long does it take to know a species? Redescription, vocalization, and chigger mites infestation pattern in the centenary emBrachycephalus/em emgarbeanus/em (Anura: Brachycephalidae).

Although we celebrate the centennial of Brachycephalus garbeanus' discovery, little progress has been done on understanding this species' biology apart from a few morphological and ecological studies, which includes its redescription based on three specimens from the type-series, microhabitat use, sexual dimorphism in body size, and feeding habits. This species is endemic to the Serra dos Órgãos Mountain range, in the state of Rio de Janeiro, southeastern Brazil. Here we redescribe B. garbeanus based on a wide sampling, including its advertisement and aggressive calls, and also the chigger mites infestation pattern. The advertisement call is longer than 25.8 s with pulsed notes series emitted at an average rate of 2.3 notes/s and 14.1 pulses/s; long inter-note interval with 320 ms; notes with distinctly short pulses (1 to 16 ms); low dominant frequency for this genus (3.0-5.4 kHz) and presence of four harmonics. This species is often parasitized by chigger mites of Hannemania, with a prevalence of infection of 67%, mainly affecting the ventral body surface. Females had a higher prevalence of parasites than males and there was no correlation found between the size of specimens and the number of parasites. Our study, provides an important and overdue taxonomical contribution, including a large amount of novel information for B. garbeanus.

The tadpole of Hylodes caete (Anura: Hylodidae), an endemic Atlantic rainforest Torrent frog of Brazil.

The genus Hylodes Fitzinger currently comprises 26 species of Torrent frogs, organized into four morphological taxonomic groups (Heyer 1982; Frost 2020): Hylodes glaber, H. lateristrigatus, H. mertensi, and H. nasus groups. Hylodes lateristrigatus is the most speciose group, comprising today 20 known species (Frost 2020). Nested in this group, a clade has been recovered based on molecular evidence, gathering the only four Hylodes species that are known to have males with nuptial thumb tubercles (de Sá et al. 2015; Malagoli et al. 2017). This well-supported clade includes H. phyllodes Heyer Cocroft, Hylodes fredi Canedo Pombal, H. pipilans Canedo Pombal, and H. caete Malagoli, de Sá, Canedo Haddad. Among these four Torrent frogs, tadpoles are unknown only for the most recently described H. caete (see tadpole descriptions in Heyer et al. 1990; Laia et al. 2010; Nogueira-Costa et al. 2019). With important taxonomic and conservation implications for the family Hylodidae (Laia Rocha 2012), we describe here the tadpole of Hylodes caete, a species endemic to the crests and slopes of Serra do Mar, State of São Paulo, southeastern Brazil (Malagoli et al. 2017). The present description is particularly important because, in its type-locality, H. caete occurs in sympatry and syntopy with H. phyllodes (Malagoli et al. 2017).

The mitochondrial genomes of five frog species of the Neotropical genus Ischnocnema (Anura: Brachycephaloidea: Brachycephalidae).

We report the mitogenomes for five species of the Ischnocnema guentheri series, being the first described for this genus of brachycephalid frogs. We assembled mitogenomes from anchored hybrid enrichment data and recovered the 13 protein-coding genes, 22 tRNA genes, and two rRNA genes for all species. The general structure agrees with most previously sequenced neobatrachians, with two exceptions: the origin of replication of L-strand (OL) was found between tRNA-A and tRNA-N, and the position of tRNA-L and tRNA-T, which are dispersed in the control region. We provide a phylogenetic tree with outgroups, which is consistent with previous phylogenetic hypotheses.

Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest.

We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population's distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow.