Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae)

Boana, the third largest genus of Hylinae, has cryptic morphological species. The potential applicability of b-fibrinogen intron 7 – FGBI7 is explored to propose a robust phylogeny of Boana. The phylogenetic potential of FGBI7 was evaluated using maximum parsimony, MrBayes, and maximum likelihood analysis. Comparison of polymorphic sites and topologies obtained with concatenated analysis of FGBI7 and other nuclear genes (CXCR4, CXCR4, RHO, SIAH1, TYR, and 28S) allowed evaluation of the phylogenetic signal of FGBI7. Mean evolutionary rates were calculated using the sequences of the mitochondrial genes ND1 and CYTB available for Boana in GenBank. Dating of Boana and some of its groups was performed using the RelTime method with secondary calibration. FGBI7 analysis revealed high values at informative sites for parsimony. The absolute values of the mean evolutionary rate were higher for mitochondrial genes than for FGBI7. Dating of congruent Boana groups for ND1, CYTB, and FGBI7 revealed closer values between mitochondrial genes and slightly different values from those of FGBI7. Divergence times of basal groups tended to be overestimated when mtDNA was used and were more accurate when nDNA was used. Although there is evidence of phylogenetic potential arising from concatenation of specific genes, FGBI7 provides well-resolved independent gene trees. These results lead to a paradigm for linking data in phylogenomics that focuses on the uniqueness of species histories and ignores the multiplicities of individual gene histories.

Prepollex diversity and evolution in Cophomantini (Anura: Hylidae: Hylinae)

Several species of Cophomantini are known to have an enlarged prepollex, commonly modified as an osseous spine. We surveyed the osteology and myology of the prepollex and associated elements of 94 of the 190 species of Cophomantini, sampling all genera, except Nesorohyla. Two distinct prepollex morphologies were found: a blade-shaped and a spine-shaped morphology. We described the observed variation in 17 discrete characters to study their evolution in the most inclusive phylogenetic hypothesis for Cophomantini. Both morphologies evolved multiple times during the evolutionary history of this clade, but the origin of the spine-shaped distal prepollex in Boana and Bokermannohyla is ambiguous. The articulation of metacarpal II with the prepollex through a medial expansion of the metacarpal proximal epiphysis is a synapomorphy for Boana. The shape of the curve of the spine, and a large post-articular process of the distal prepollex, are synapomorphies for the Boana pulchella group, the latter being homoplastic in the Bokermannohyla martinsi group. Muscle character states associated with the spine-shaped prepollex are plesiomorphic for Cophomantini. We discuss evolution, function, behaviour and sexual dimorphism related to the prepollical elements. A bony spine is associated with fights between males, but forearm hypertrophy could be more related with habitat than with territorial combat.

Phylogenetic relationships of the Boana pulchella Group (Anura: Hylidae)

In this paper we present a phylogenetic analysis of the treefrogs of the Boana pulchella Group with the goals of (1) providing a rigorous test of its monophyly; (2) providing a test of relationships supported in previous studies; and (3) exploring the relationships of the several species not included in previous analyses. The analyses included>300 specimens of 37 of the 38 species currently included in the group, plus 36 outgroups, exemplars of the diversity of Boana and the other genera of the hylid tribe Cophomantini. The dataset included eight mitochondrial genes (12S, 16S, CytB, COI, ND1, tRNA^Ile, tRNA^Leu, and tRNA^Val) and five nuclear genes (RHO, TYR, RAG-1, CXCR4, SIAH1). The phylogenetic analyses recover the monophyly of the B. pulchella Group with lower support than previous studies, as a result of the inclusion of the B. claresignata Group, which is recovered as its sister taxon. Within the B. pulchella Group, the inclusion of almost all species of the group had little impact on previous notions of its phylogeny, except for the rejection of the hypothesized B. polytaenia Clade (B. goiana and B. phaeopleura are nested in the clade here called the B. prasina Clade), which is redefined. Phylogenetic support is strong for five major clades, which collectively include all but three of the species sampled: the B. balzani Clade (B. aguilari, B. balzani, B. gladiator, B. melanopleura, B. palaestes), the redefined B. polytaenia Clade (B. botumirim, B. buriti, B. cipoensis, B. jaguariaivensis, B. leptolineata, B. polytaenia, B. stenocephala, and two undescribed species), the B. prasina Clade (B. bischoffi, B. caingua, B. cordobae, B. goiana, B. guentheri, B. marginata, B. phaeopleura, B. prasina, B. pulchella, and one undescribed species), the B. riojana Clade (B. callipleura, B. marianitae, B. riojana), and the B. semiguttata Clade (B. caipora, B. curupi, B. joaquini, B. poaju, B. semiguttata, B. stellae, and two undescribed species). The monophyly of the B. prasina + B. riojana Clades, and that of the B. polytaenia + B. semiguttata Clades are well-supported. The relationships among these two clades, the B. balzani Clade, B. ericae + B. freicanecae, and B. cambui (representing the deepest phylogenetic splits within the B. pulchella Group) are recovered with weak support. We discuss the phenotypic evidence supporting the monophyly of the B. pulchella Group, and the taxonomy of several species, identifying three new synonyms of Boana polytaenia, one new synonym of Boana goiana, and one new synonym of B. riojana.

High-throughput DNA sequencing of museum specimens sheds light on the long-missing species of the Bokermannohyla claresignata group (Anura: Hylidae: Cophomantini)

The two species of the Bokermannohyla claresignata species group (Anura: Hylidae) have not been collected for the last four decades. It is the only species group of the hyline tribe Cophomantini that has not yet been analysed genetically. Its phylogenetic position is thus uncertain, and it has a combination of adult and larval character states that make this group a crucial missing piece that hinders our understanding of Cophomantini phylogenetics and character evolution. We obtained DNA sequences from a museum larval specimen of Bok. claresignata, using specialized extraction methods and high-throughput DNA sequencing, and combined the molecular phylogenetic results with available phenotypic information to provide new insights into the taxonomy and phylogenetic relationships of its species group. Our phylogenetic results place Bok. claresignata as sister to the Boana pulchella group, supporting its inclusion in Boana, together with Bokermannohyla clepsydra. In light of this new finding, we recognize a newly defined Boana claresignata group to accommodate these species, thus resolving both the polyphyly of Bokermannohyla and the paraphyly of Boana. Considering the phylogenetic relationships of the Boana claresignata group, we also discuss the evolution of suctorial tadpoles and mature oocyte/egg pigmentation in Cophomantini.

Systematics of the Boana semilineata species group (Anura: Hylidae), with a description of two new species from Amazonian Ecuador

The combination of genetic and phenotypic characters for species delimitation has allowed the discovery of many undescribed species of Neotropical amphibians. In this study, we used DNA sequences (genes 12S, 16S, ND1 and COI) and morphologic, bioacoustic and environmental characters of the Boana semilineata group to evaluate their phylogenetic relationships and assess their species limits. In addition, we included DNA sequences of several species of Boana to explore cryptic diversity in other groups. We found three Confirmed Candidate Species (CCS) within the B. semilineata group. Holotype examination of Hyla appendiculata shows that it is a valid species that corresponds to one of the CCS, which is here transferred to Boana. We describe the two remaining CCS. Our phylogeny highlights a number of secondary but meaningful observations that deserve further investigation: (1) populations of B. pellucens from northern Ecuador are more closely related to B. rufitela from Panama than to other Ecuadorian populations of B. pellucens; (2) we report, for the first time, the phylogenetic relationships of B. rubracyla showing that it is closely related to B. rufitela and B. pellucens; and (3) B. cinerascens and B. punctata form two species complexes consisting of several unnamed highly divergent lineages. Each of these lineages likely represents an undescribed species.

Richness, diversity patterns, and taxonomic notes of amphibians from the Tocantins state

Abstract: Herein, we provide the first comprehensive amphibian checklist for the State of Tocantins, North of Brazil, based on field sampling, literature data, and specimens deposited in zoological collections. We performed field surveys from 2012 to 2019 in 12 Tocantins municipalities, totaling 376 days of sampling effort. We analyzed 25 papers from the literature and examined 1311 specimens from collections and collected 750 during field surveys. We recorded 90 amphibian species distributed in 12 anurans and two caecilians families. At least seven undescribed species along the state were recorded. We also present new records for 20 species for the state, nine of them corresponding to Amazonian species, four Cerrado endemic, one Caatinga species, and the widely distributed treefrog Boana crepitans; the others five new records comprise undescribed species. Our data also suggest that the Tocantins amphibian composition is not geographically structured in relation to the biomes, since Amazonian, Caatinga, and Cerrado amphibian lineages have their distribution nearly completely overlapped in the state. We propose that this absence of spatial structuration may be a result of two factors (synergetic or not). First, the events of expansion and retraction of the biomes caused by the Quaternary climatic cycles, which may have mixed the populations of species from different biomes causing the notable pattern of overlapped distribution observed here. Second, the forest environments (e.g. gallery and riparian forests) associated to the Araguaia-Tocantins River basins may have acted as historical dispersal corridors for the Amazonian amphibian lineages into the Cerrado of the Tocantins. Despite the sampling effort of the present study, we stress that gaps of information still remain and further field sampling efforts should be performed along the state. Lastly, taxonomic appraisals involving the species with problematic taxonomic status recorded here should be based on multiples lines of evidences (acoustic, molecular, and morphological data), which will render a more accurate view on the Tocantins amphibian diversity. Such data are extremely necessary under the current high rate of habitat loss across the state, since they can be used to guide public policies of conservation.