A Pan-Amazonian species delimitation: high species diversity within the genus<i>Amazophrynella</i>(Anura: Bufonidae)

Rojas, Rommel R.; Fouquet, Antoine; Ron, Santiago R.; Hernández-Ruz, Emil José; Melo-Sampaio, Paulo Roberto; Chaparro, Juan C.; Vogt, Richard C.; Carvalho, Vinícius Tadeu de; Pinheiro, Leandra Cardoso; Ávila, Róbson Waldemar; Farias, Izeni Pires; Gordo, Marcelo; Hrbek, Tomas

doi:10.7717/peerj.4941

Cited by 38 publications

(70 citation statements)

References 78 publications

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“…In our phylogenetic analyses we recovered the same three main clades observed by Rojas et al (2018a). However, we found three previously recognized lineages (A. teko, A. aff.…”

Section: Discussionsupporting

confidence: 79%

“…In addition to the A. teko paraphyletic in relation to Amazophrynella sp.1., we found 1.2% of 16S p-distances between these two lineages (1% in Kaefer et al, 2019, and3% in Rojas et al, 2018a;Rojas et al, 2018b), which might indicate that they represent the same species. The difference between the topologies from Rojas et al (2018a) and in the present work can be due to the different methods used in each study (concatenated vs concatenated with partition finder). We also recovered A. bilinguis as sister taxa of A. sp.2, A. sp.3, and A. xinguensis, different from the topology found by Kaefer et al (2019), where A. bilinguis was recovered within a clade formed by A.…”

Section: Discussionmentioning

confidence: 84%

“…Nowadays, the genus contains 12 described species, of which 10 have been described in the last six years, all recovered as genetically distinct lineages (see Kaefer et al, 2019). Despite the high number of descriptions, recent studies have shown that species richness of this genus is underestimated, and several undescribed species likely exist (Fouquet et al, 2012a;Rojas et al, 2016;Rojas et al, 2018a;Vacher et al, 2020). Emphasizing the existence of many species still unknown for the genus, we collected a series of small-sized bufonid specimens in Óbidos municipality, Pará State, Brazil, that represents a genetically structured lineage within the genus Amazophrynella, which we describe as a new species.…”

Section: Introductionmentioning

confidence: 99%

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A new tiny toad species ofAmazophrynella(Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil

Mângia

Koroiva

Santana

2020

PeerJ

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The combination of different approaches has successfully delimited new species within many Neotropical species complexes traditionally classified as a single nominal organism. Recent studies have shown that the Amazonian endemic genus Amazophrynella, currently composed of 12 small-sized species, could harbor several additional species. Based on morphology and molecular data, we describe a new species of Amazophrynella from east of the Guiana Shield, in Pará state, Brazil. The new species is characterized by having one of the biggest size of the genus (SVL of males 16.0–17.8 mm and females 22.9–24.4 mm), presence of a large palmar tubercle (occupying 2/4 of the palmar surface), 5.6–8.1% uncorrected p-distance from its sister clade (including A. teko, A. sp.1, and A. manaos) for the 16S mitochondrial gene, and 8.8% for the COI. The new species described here represents a newly discovered lineage. Of the 12 Amazophrynella species currently recognized, two were describe in the last century (A. bokermanni and A. minuta) and the remaining species were recently discovered and described (in the last six years), which underscores the degree to which species richness of Amazophrynella is underestimated.

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“…In our phylogenetic analyses we recovered the same three main clades observed by Rojas et al (2018a). However, we found three previously recognized lineages (A. teko, A. aff.…”

Section: Discussionsupporting

confidence: 79%

Section: Discussionmentioning

confidence: 84%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A new tiny toad species ofAmazophrynella(Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil

Mângia

Koroiva

Santana

2020

PeerJ

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“…However, interest in species description has dwindled over the years, along with the number of students of taxonomy (Hopkins & Freckleton 2002). To complicate matters further, growing evidence for an ongoing biodiversity crisis has accumulated, and it is considered virtually impossible for biologists to describe all unknown species at the current pace of biodiversity loss (Kim & Byrne 2006, Carrete et al 2009, Joppa et al 2011, Pimm et al 2014, Rojas et al 2018.…”

Section: Introductionmentioning

confidence: 99%

Employing statistical learning to derive species‐level genetic diversity for mammalian species

Schrago

Mello

2020

Mammal Review

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1. The patterns of genetic diversity in several genomic regions have been used in mammalian systematics for decades. For instance, when studying closely related species, it is generally assumed that the mitochondrial cytochrome b gene (cytb) exhibits significant information that can be used for differentiation between intraspecies and interspecies variation in mammals. Because of sampling limitations, early analyses of this proposition were conducted mainly on rodents and bats. 2. Currently, more than 57000 cytb sequences are available covering all major lineages of mammals, and sequencing of several individuals per species is common practice in molecular systematics. We were thus prompted to carry out a large-scale analysis of the utility of cytb genetic variation as a predictor of whether a pair of sequences came from within-species or between-species comparisons. 3. Using predetermined species-level assignments, we employed standard methods from statistical learning to calculate the cutoff values able to classify genetic distances in either intraspecies or interspecies categories; we then measured the performance of such statistical classifiers to predict the species-level taxonomic rank as defined by experts. 4. Depending on the classifier, our results showed that when adopting cytb distance cutoff values of 7.3% and 5.5% for small mammals (Metatheria, Rodentia, Chiroptera, and Eulipotyphla) and 4.3% and 3% for medium-sized to large mammals (Primates, Carnivora, and Artiodactyla), the frequency of incorrect assignment of within-species divergences to the between-species category (type I error) varied from 7 to 11%. 5. In order to avoid over-splitting by future researchers, we calculated cutoff values using a more conservative evaluation and provided a list of mammalian species that are likely to consist of complexes of cryptic species. We show that our supervised method can provide practical guidelines to improve the performance of unsupervised algorithms for species delimitation. Finally, we discuss limitations of large-scale approaches (e.g. effects of misclassification in databases and the need for case-by-case evaluation of cryptic species complexes) and their consequences for conservation policies. SUPPORTING INFORMATION Additional supporting information may be found in the online version of this article at the publisher's web-site. Appendix S1. Empirically estimated density distributions for within-and between-species genetic distances.

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“…Other leaf-litter vertebrates are remarkably similar to it -especially regarding levels of genetic structure and spatial organization of lineages (e.g. Fouquet et al, 2014;Geurgas & Rodrigues, 2010;Nunes et al, 2012;Rojas et al, 2018). However, not all Amazonian reptiles share the same pattern: natural history traits appear to influence genetic structure since traits determine long-term dispersal capacity of species, and hence impact gene flow and admixture (Paz, Ibáñez, Lips, & Crawford, 2015;Zamudio, Bell, & Mason, 2016 Pinto et al, 2019;Prates et al, 2016).…”

Section: Rivers Refuges and Natural History Traitsmentioning

confidence: 99%

Hidden in the DNA: How multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf‐litter lizardLoxopholis osvaldoi(Squamata: Gymnophthalmidae)

Marques‐Souza

Pellegrino

Brunes

et al. 2019

Journal of Biogeography

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Aim To investigate the cryptic diversity and diversification timing in the putatively low‐dispersal Amazonian leaf‐litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location Central Amazonia, Brazil. Taxon Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with *BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographical distance among localities, the environment and the position of localities in relation to main rivers were tested by redundancy analysis (RDA). Results We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE or historical factors. Main Conclusions Our results strongly suggest that L. osvaldoi is a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history of L. osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that nonlinear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.

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A Pan-Amazonian species delimitation: high species diversity within the genusAmazophrynella(Anura: Bufonidae)

Cited by 38 publications

References 78 publications

A new tiny toad species ofAmazophrynella(Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil

A new tiny toad species ofAmazophrynella(Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil

Employing statistical learning to derive species‐level genetic diversity for mammalian species

Hidden in the DNA: How multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf‐litter lizardLoxopholis osvaldoi(Squamata: Gymnophthalmidae)

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