Journal of Threatened Taxa | www.threatenedtaxa.org | 26 April 2024 | 16(4): 25040–25048

 

ISSN 0974-7907 (Online) | ISSN 0974-7893 (Print) 

https://doi.org/10.11609/jott.8694.16.4.25040-25048

#8694 | Received 14 August 2023 | Final received 27 January 2024 | Finally accepted 09 April 2024

 

 

DNA barcoding reveals a new population of the threatened Atlantic Forest frog Sphaenorhynchus canga

 

Diego J. Santana 1 , André Yves 2, Elvis A. Pereira 3, Priscila S. Carvalho 4, Lucio M.C. Lima 5, Henrique C. Costa 6  & Donald B. Shepard 7

 

1 Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Av. Costa e Silva, s/n, 79070-900, Cidade Universitária, Campo Grande, Mato Grosso do Sul, Brazil.

2 Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo 2936, 69060-001, Petrópolis, Manaus, Amazonas, Brazil.

3 Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil.

4 Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Av. Costa e Silva, s/n, 79070-900, Cidade Universitária, Campo Grande, Mato Grosso do Sul, Brazil.

5 Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer S/n, 36036-330, Campus Universitário, Juiz de Fora, Minas Gerais, Brazil.

6 Departamento de Zoologia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer S/n, 36036-330, Campus Universitário, Juiz de Fora, Minas Gerais,Brazil.

7 Department of Biological Sciences, University of Arkansas, 601 Science Engineering Hall, Fayetteville, Arkansas, 72701, USA.

1 jose.santana@ufms.br (corresponding author), 2 andreyves7@gmail.com, 3 elvisaps21@gmail.com, 4 pricarvalho.bio@gmail.com, 5 luciobiolima@yahoo.com.br, 6 ccostah@gmail.com, 7 dshep@uark.edu

 

 

Abstract: Species identification plays a significant role in biodiversity conservation. As many species remain unrecognized, particularly in neotropical hotspots like the Brazilian Atlantic Forest (AF), novel molecular techniques are being widely employed to bridge this gap. In this study, we used DNA barcoding and phylogenetic tools to identify a new population of Sphaenorynchus canga in the central region of the Brazilian AF. Our results extend the species’ known distribution by approximately 200 km to the south, encompassing a different mountain range than its type locality (Serra do Espinhaço). This disjunct distribution, while not uncommon among amphibians, suggests a historical connection between these two mountain complexes as a biogeographic explanation. Despite the discovery of a new S. canga population, the species continues to face numerous anthropogenic threats such as mining, land use, and cattle ranching. Urgent conservation and research efforts are warranted to ensure the survival of S. canga populations across these habitats.

 

Keywords: 16S mtDNA, Hylidae, Mantiqueira mountain range, Minas Gerais, species identification.

 

Abbreviations: ASAP – Assemble Species by Automatic Partitioning | CAUFJF – Coleção de Anfíbios da Universidade Federal de Juiz de Fora | ICMBIO – Instituto Chico Mendes de Conservação da Biodiversidade | IUCN ---– International Union for Conservation of Nature | MCMC – Markov chain Monte Carlo | ML – Maximum Likelihood | mtDNA – mitochondrial DNA | PCR – Polymerase chain reaction | SISBio – Sistema de Autorização e Informação em Biodiversidade | ZUFMS-AMP – Coleção Zoológica da Universidade Federal de Mato Grosso do Sul.

 

Editor: S.R. Ganesh, Kalinga Foundation, Shivamogga, India.         Date of publication: 26 April 2024 (online & print)

 

Citation: Santana, D.J., A. Yves, E.A. Pereira, P.S. Carvalho, L.M.C. Lima, H.C. Costa & D.B. Shepard (2024). DNA barcoding reveals a new population of the threatened Atlantic Forest frog Sphaenorhynchus canga. Journal of Threatened Taxa 16(4): 25040–25048. https://doi.org/10.11609/jott.8694.16.4.25040-25048

  

Copyright: © Santana et al. 2024. Creative Commons Attribution 4.0 International License.  JoTT allows unrestricted use, reproduction, and distribution of this article in any medium by providing adequate credit to the author(s) and the source of publication.

 

Funding: Fieldwork was partially funded by Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG, project APQ-02302-21).

 

Competing interests: The authors declare no competing interests.

 

Author details: DJS is a professor in the Zoology Laboratory at the Federal University of Mato Grosso do Sul (UFMS). He is  a zoologist with emphasis in herpetology, working with frogs and reptiles, focusing on topics such as natural history, phylogenetics, phylogeography, and biogeography. AY is currently a PhD student at the Universidade Federal do Paraná. He is an ecologist working on neotropical reptiles and amphibians, with focus on subjects such as adaptive evolution, landscape genetics and natural history. EAP is a postdoctoral researcher in the Laboratory of Natural History of Brazilian Amphibians at the State University of Campinas (UNICAMP). He is a zoologist with an emphasis on herpetology, working with amphibians, focusing on topics such as systematics, phylogenetics, phylogeography, biogeography and conservation. PSC is a postdoctoral researcher in the Mapinguari Lab at Federal University of Mato Grosso do Sul (UFMS). She is a zoologist with an emphasis on reptiles, working with systematics, phylogenetics, phylogeography, biogeography and conservation. LMCL is a zoologist who has worked on natural history and distribution of reptiles and amphibians in Brazil. Currently, he directs a private protection area, supporting initiatives of research, conservation and sustainable tourism. HCC is a professor at Universidade Federal de Juiz de Fora, Brazil, researching biogeography, natural history, and taxonomy of amphibians and reptiles. DBS is a Teaching Associate Professor in the Department of Biological Sciences at the University of Arkansas, Fayetteville, Arkansas, USA. His research employs molecular methods and geospatial tools to examine patterns of genetic variation, identify cryptic diversity, and understand the processes that drive diversification of amphibians and reptiles.

 

Author contributions: Field work: AY, DJS, EAP, HCC, LMCL, PSC; data analysis: DJS, SBS, PSC; writing: all authors; revisions: all authors.

 

Acknowledgments: We thank Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG process APQ-02302-21) and the Institutional Program of Internationalization sponsored by Coordination for the Improvement of Higher Education Personnel (Capes-PrInt 41/2017 – Process 88881.311897/2018–01) for financial support. DJS thanks CNPq for his research fellowships (CNPq 309420/2020-2; CNPq 402012/2022-4). Lab work and DNA sequencing were supported by Dr. Johnny Armstrong and the Louisiana Tech University School of Biological Sciences. Collections were authorized by the System of Authorization and Information in Biodiversity, Ministry of the Environment (license SISBIO 45889).

 

 

Species identification is a crucial component of biodiversity research and conservation (Delić et al. 2017; Lyra et al. 2017; Sheth & Thaker 2017). To this end, DNA barcoding has become a widely used molecular technique for identifying species. This approach relies on sequencing a standardized fragment of DNA that can be compared to reference databases to accurately identify species (Gehara et al. 2013; Koroiva & Santana 2022). DNA barcoding has also proven to be effective in delimiting species, and it has been applied across a wide range of taxa, including amphibians (Jansen et al. 2011; Koroiva et al. 2020; Koroiva & Santana 2022).

Delimitation and identification of amphibians using robust methods is paramount, given that they are the most threatened group of terrestrial vertebrates worldwide (Howard & Bickford 2014; Cox et al. 2022; Toledo et al. 2023). Many species of amphibians are being classified under the IUCN Red List categories at the same time they are being formally named (Brasileiro et al. 2007; Caramaschi & Cruz 2011; Assis et al. 2013). Atlantic Forest, a biodiversity hotspot (Myers et al. 2000; Ribeiro et al. 2011; Zachos & Habel 2011), harbors more than 625 amphibian species, 77% of them endemic, and many with very narrow distributions (Rossa-Feres et al. 2017). Since the arrival of the first European colonizers in the early 16th century, the Atlantic Forest has lost most of its original cover, and the remaining is heavily fragmented (Ribeiro et al. 2009, 2011). In Brazil, habitat loss is the main threat to amphibians living in this rainforest (ICMBio 2018); 41 species are in peril, and two are already declared extinct (Ministério do Meio Ambiente 2022). The Atlantic Forest is also the region with the highest amphibian population declines reported worldwide (Toledo et al. 2023). Therefore, identifying and describing the amphibian diversity of the Atlantic Forest is crucial for its  conservation and for developing targeted conservation strategies.

The landscape of the southeastern portion of the Atlantic Forest includes many mountain ranges that are considered cradles of amphibian diversity (Leite et al. 2008; Neves et al. 2018; Silva et al. 2018). These mountain chains harbor most of the endemic amphibian species from the Atlantic Forest (Guedes et al. 2020), and many are threatened (Pontes & Guidorizzi 2023). One such species is the Hatchet-faced Canga Lime Treefrog, Sphaenorhynchus canga, first described in 2015 (Araujo-Vieira et al. 2015) and  known only from a small area in the southern portion of the Espinhaço Mountain range in Minas Gerais (Silveira et al. 2020). The species is classified by the Brazilian Ministry of Environment as Critically Endangered (Ministério do Meio Ambiente 2022; Pontes & Guidorizzi 2023).

During field expeditions in the northern portion of the Mantiqueira Mountain range in southern Minas Gerais in December 2015, January 2020, and November 2021, a series of specimens of Sphaenorhynchus were collected. We collected five adult male specimens during visual and acoustic searches in one pond in the countryside of Bom Jardim de Minas, Minas Gerais (-22.004, -44.180; 1,210 m; datum = SAD69).  Specimens were euthanized in a 2% lidocaine chlorhydrate solution (MCTIC 2018), fixed in 10% formalin, and preserved in 70% alcohol. Prior to fixation, we collected tissue samples (muscle and liver) and stored them in cryotubes filled with 100% ethanol. Voucher specimens and tissues were deposited in the Coleção de Anfíbios da Universidade Federal de Juiz de Fora (CAUFJF), Juiz de Fora municipality, Minas Gerais, and in the Coleção Zoológica da Universidade Federal de Mato Grosso do Sul (ZUFMS-AMP), Campo Grande municipality, Mato Grosso do Sul, Brazil. Collection permits for this study were issued by ICMBIO (SISBio 73975-1 and 72874-1).

 DNA was extracted using the QIAGEN DNeasy Blood and Tissue Kit (Valencia, California, USA) following the manufacturer’s protocol. Next, a fragment of the mitochondrial 16S gene was amplified using primers 16Sar and 16Sbr (Palumbi et al. 2002). The PCR protocol was configured with one initial phase of 94°C for 3 min, followed by 35 cycles of 94°C for 20s, 50°C for 20s, 72°C for 60s, and a final extension phase of 72°C for 5 min. Purification of PCR products and sequencing were performed by Eurofins Genomics Inc. (Louisville, Kentucky, USA). Comparable 16S sequences of Sphaenorhynchus from GenBank and one sequence of Scinax fuscovarius to use as an outgroup were  downloaded (Supplementary Table 1). All 16S mtDNA gene fragments were aligned using the MAFFT algorithm (Katoh & Toh 2008) in Geneious v9.0.5 with default settings. The final dataset comprised 53 sequences of a 515 base-pair (bp) fragment of the 16S gene. A maximum likelihood tree was inferred in RAxML (Stamatakis 2014) via raxmlGUI 2.0 (Edler et al. 2021). The analysis was conducted using a ML + rapid bootstrap setting with a GTR+I+G substitution model and 1,000 bootstrap replicates. The appropriate substitution model was confirmed with Modeltest (Darriba et al. 2020) in raxmlGUI 2.0. Additionally, PTP and bPTP species delimitation analyses were conducted (Zhang et al. 2013) using the ML Tree. Calculations were performed on PTP webserver (http: //species.h-its.org/ptp/) with 500,000 MCMC generations, thinning set at 100, and burn-in at 10%. In addition, we performed the delimitation method Assemble Species by Automatic Partitioning (ASAP) on the online server (https://bioinfo.mnhn.fr/abi/public/asap/asapweb.html) using a simple distance model to compute distances between samples and default parameters (Puillandre et al. 2021). To explore relationships among mtDNA haplotypes, we estimated a 16S haplotype network among species closely related to S. cangaS. botocudo, S. cammaeus, S. caramaschii, S. platycephalus, and S. surdus (Pereira et al. 2022)—in POPART (Leigh & Bryant 2015) using the median-joining network method. We depict each species using different colors in the haplotype network. Lastly, we calculated sequence divergence (uncorrected p-distance) among species/individuals using MEGA v10.1.1 (Kumar et al. 2018).

We identified the Sphaenorhynchus from Bom Jardim de Minas as Sphaenorhynchus canga (Image 1). Our maximum likelihood tree (Figure 1) of the mitochondrial 16S gene confidently (bootstrap = 0.98) placed the sequenced specimens with Sphaenorhynchus canga, sister to a clade formed by S. botocudo and S. surdus. The three species delimitation methods we used yielded the same results, recovering one evolutionary entity for each known species (Figure 1). All three analyses confidently recovered all populations of Sphaenorhynchus canga as a single evolutionary lineage. Our haplotype network (Figure 2) shows a clear separation between all species of Sphaenorhynchus. The genetic distance between S. canga from Bom Jardim de Minas and S. canga from the type locality was 0.4% (Supplementary Table 2). Overall, the morphology of S. canga from Bom Jardim de Minas also have the standard diagnosis of the species presented in its original description, such as the lack of tympanic membrane, the snout protruding in profile, the presence of a canthal white line, a dorsolateral white line from the eye to sacral region, and a dorsolateral black line from the tip of snout extending beyond the eye and disappearing up to the flanks (Araujo-Vieira et al. 2015). The newly discovered population of S. canga in Bom Jardim de Minas extends the distribution of the species by about 200 km southward to a different mountain range, Serra da Mantiqueira (Image 2).

The distribution of S. canga in both the southern Espinhaço and the northern Mantiqueira mountain ranges is a pattern observed in other anuran species as well, including Bokermannohyla feioi, Pithecopus ayeaye, Physalaemus maximus, and Scinax tripui (Baêta et al. 2007; Magalhães et al. 2017; Silveira et al. 2019; Brunes et al. 2023). This shared distribution pattern has led biogeographers to hypothesize a historical connection between the Espinhaço and Mantiqueira mountain ranges (Magalhães et al. 2017; Neves et al. 2018; Brunes et al. 2023). The discovery of S. canga in the Mantiqueira Mountains adds additional support for a historical connection between these mountain ranges and increases the potential area where this species could occur, particularly in protected areas in the northern portion of Serra da Mantiqueira.

While the International Union for Conservation of Nature (IUCN) Red List of Threatened Species classifies this species as of Least Concern (IUCN & Boitatá 2023), the latest update of the Brazilian Red List, which is based on IUCN criteria, classifies Sphaenorhynchus canga as Critically Endangered (Pontes & Guidorizzi 2023) due to its limited geographic distribution and restriction to ponds in ironstone outcrops, a habitat severely impacted by mining (Bastos et al. 2022). The IUCN assessment states that ‘there are no ongoing major threats, the species is a habitat generalist occurring even in modified areas, and it is presumed to have a large and stable population’ (IUCN & Boitatá 2023). However, mining activity poses a significant threat to S. canga. Five out of six ponds where the type series was collected are influenced by mining activities (Pena et al. 2017). Mining activity has resulted in a continuous decline in both the area and quality of S. canga’s habitat due to the suppression of ironstone outcrops and vegetation (Bastos et al. 2022). Recent surveys have had some success in finding the species in additional localities and habitats, including perennial small dams and anthropogenic swamps inside or on the edge of semi-deciduous seasonal forests, suggesting that it may have some degree of ecological plasticity; nonetheless, the species’ spatial extent has only slightly increased because of these discoveries (Silveira et al. 2020). The discovery of S. canga in Bom Jardim de Minas is an important contribution to the conservation of this species, as research on its geographic distribution is among the main priorities (Bastos et al. 2022). Although our discovery has increased the species’ distribution by more than 200 km (straight-line distance), it is important to note that is still restricted to high-elevation areas, reproducing in ponds (Araujo-Vieira et al. 2015; Silveira et al. 2020). Furthermore, no known populations of the species occur in protected areas (Bastos et al. 2022; this study).

While this discovery provides a glimmer of hope for the species, it is essential to note that the new population was found adjacent to a dirt road and in areas designated for cattle ranching, where vegetation around marshes is typically burned annually by local farmers. Moreover, the region is experiencing an increase in real estate speculation for allotments, and a proposal is currently under consideration for the installation of a hydroelectric power plant at the Pacau waterfall (Cachoeira do Pacau), just 5 km from the discovered population. Therefore, future visits to the locality are of utmost importance to monitor this population and to search for additional areas where the species may be present. A reevaluation of the conservation status of S. canga based on this discovery is beyond the scope of this work. Nonetheless, it is evident that this finding underscores the urgent need for further research, conservation measures, and advocacy efforts to ensure the survival of this critically endangered species.

 

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Supplementary Table 1. GenBank accession numbers for mitochondrial 16S gene sequences of specimens of Sphaenorhynchini (Sphaenorhynchus and Gabohyla) and the outgroup Scinax fuscovarius included in the molecular analyses.

Species

Genbank accession number

Reference

S. botocudo

KY418014

Roberto et al. (2017)

S. botocudo

MK266722

Araujo-Vieira et al. (2019)

S. botocudo

MK266723

Araujo-Vieira et al. (2019)

S. botocudo

MK266724

Araujo-Vieira et al. (2019)

S. botocudo

MK266725

Araujo-Vieira et al. (2019)

S. cammaeus

KY418013

Roberto et al. (2017)

S. cammaeus

MK266726

Araujo-Vieira et al. (2019)

S. cammaeus

MK266727

Araujo-Vieira et al. (2019)

S. canga

KY418015

Roberto et al. (2017)

S. canga

HCC193

Present Work

S. canga

HCC194

Present Work

S. canga

MAP6807

Present Work

S. canga

MK266728

Araujo-Vieira et al. (2019)

S. caramaschii

KP096219

Araujo-Vieira et al. (2015)

S. caramaschii

KP096220

Araujo-Vieira et al. (2015)

S. caramaschii

MK266729

Araujo-Vieira et al. (2019)

S. caramaschii

MK266730

Araujo-Vieira et al. (2019)

S. caramaschii

MK266731

Araujo-Vieira et al. (2019)

S. caramaschii

MK266732

Araujo-Vieira et al. (2019)

S. caramaschii

MK266733

Araujo-Vieira et al. (2019)

S. caramaschii

MK266734

Araujo-Vieira et al. (2019)

S. caramaschii

MK266735

Araujo-Vieira et al. (2019)

S. caramaschii

MK266736

Araujo-Vieira et al. (2019)

S. caramaschii

MK266737

Araujo-Vieira et al. (2019)

S. caramaschii

MK266738

Araujo-Vieira et al. (2019)

S. caramaschii

MK266739

Araujo-Vieira et al. (2019)

S. carneus

MK266740

Araujo-Vieira et al. (2019)

S. carneus

MK266741

Araujo-Vieira et al. (2019)

S. dorisae

AY843766

Faivovich et al. (2005)

S. dorisae

MK266742

Araujo-Vieira et al. (2019)

S. lacteus

AY549367

Faivovich et al. (2004)

S. lacteus

JF790143

Jansen et al. (2011)

S. lacteus

JF790144

Jansen et al. (2011)

S. lacteus

MK266743

Araujo-Vieira et al. (2019)

S. lacteus

MK266744

Araujo-Vieira et al. (2019)

S. mirim

MK266745

Araujo-Vieira et al. (2019)

G. pauloalvini

MK266747

Araujo-Vieira et al. (2019)

G. pauloalvini

MK266748

Araujo-Vieira et al. (2019)

G. pauloalvini

MK266749

Araujo-Vieira et al. (2019)

G. pauloalvini

MK266750

Araujo-Vieira et al. (2019)

G. pauloalvini

MT503969

Orrico et al. (2021)

S. planicola

MK266751

Araujo-Vieira et al. (2019)

S. platycephalus

KY418016

Roberto et al. (2017)

S. platycephalus

MK266746

Araujo-Vieira et al. (2019)

S. prasinus

MK266752

Araujo-Vieira et al. (2019)

S. prasinus

MK266753

Araujo-Vieira et al. (2019)

S. prasinus

MK266754

Araujo-Vieira et al. (2019)

S. surdus

KY418017

Roberto et al. (2017)

S. surdus

MK266755

Araujo-Vieira et al. (2019)

S. surdus

MK266756

Araujo-Vieira et al. (2019)

S. surdus

MK266757

Araujo-Vieira et al. (2019)

S. surdus

MK266758

Araujo-Vieira et al. (2019)

Scinax fuscovarius

MK266760

Araujo-Vieira et al. (2019)

 

 

Supplementary Table 2. Average uncorrected (p-distance) sequence divergence between different species of Sphaenorhynchus. Values in bold along the diagonal are intraspecific divergences. n/c= not calculated.

 

 

1

2

3

4

5

6

7

8

9

10

11

12

13

1

S. botocudo

0.004

 

 

 

 

 

 

 

 

 

 

 

 

2

S. cammaeus

0.067

0.000

 

 

 

 

 

 

 

 

 

 

 

3

S. canga

0.039

0.055

0.004

 

 

 

 

 

 

 

 

 

 

4

S. caramaschi

0.073

0.073

0.059

0.006

 

 

 

 

 

 

 

 

 

5

S. carneus

0.151

0.140

0.143

0.137

0.004

 

 

 

 

 

 

 

 

6

S. dorisae

0.133

0.140

0.121

0.137

0.167

0.002

 

 

 

 

 

 

 

7

S. lacteus

0.107

0.102

0.106

0.099

0.137

0.090

0.005

 

 

 

 

 

 

8

S. mirim

0.166

0.157

0.149

0.156

0.183

0.126

0.127

n/c

 

 

 

 

 

9

S. platycephalus

0.053

0.054

0.032

0.060

0.140

0.132

0.102

0.135

0.000

 

 

 

 

10

S. pauloalvini

0.114

0.092

0.107

0.097

0.130

0.128

0.107

0.149

0.096

0.006

 

 

 

11

S. planicola

0.147

0.139

0.127

0.135

0.162

0.131

0.122

0.065

0.112

0.132

n/c

 

 

12

S. prasinus

0.110

0.089

0.087

0.090

0.137

0.125

0.091

0.142

0.090

0.096

0.144

0.007

 

13

S. surdus

0.032

0.045

0.023

0.060

0.140

0.135

0.107

0.157

0.028

0.105

0.139

0.092

0.000