Mapping the hidden diversity of the Geophagus sensu stricto species group (Cichlidae: Geophagini) from the Amazon basin

Abstract

South American freshwater ichthyofauna is taxonomically the most diverse on the planet, yet its diversity is still vastly underestimated. The Amazon basin alone holds more than half of this diversity. The evidence of this underestimation comes from the backlog of morphologically distinct, yet undescribed forms deposited in museum collections, and from DNA-based inventories which consistently identify large numbers of divergent lineages within even well-studied species groups. In the present study, we investigated lineage diversity within the Geophagus sensu stricto species group. To achieve these objectives, we analyzed 337 individuals sampled from 77 locations within and outside the Amazon basin representing 10 nominal and six morphologically distinct but undescribed species. We sequenced the mitochondrial cytochrome c oxidase subunit I (COI) and delimited lineages using four different single-locus species discovery methods (mPTP-15 lineages; LocMin-14 lineages; bGMYC-18 lineages; and GMYC-30 lineages). The six morphologically distinct but undescribed species were also delimited by the majority of the species discovery methods. Five of these lineages are restricted to a single collection site or a watershed and their habitats are threatened by human activities such as deforestation, agricultural activities and construction of hydroelectric plants. Our results also highlight the importance of combining DNA and morphological data in biodiversity assessment studies especially in taxonomically diverse tropical biotas.

Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding

“…The literature reports deep genetic divergence, cryptic speciation, a species complex, recent description of new species, or population structuring in 13 (76.47%) of the 17 genera shown in quadrant II of Figure 2: Bivibranchia (Nogueira et al, 2021), Bryconops (Silva‐Oliveira et al, 2021), Colomesus (Amaral et al, 2013), Geophagus (Ximenes et al, 2021), Hemigrammus (Albornoz‐Garzón et al, 2019; Marinho et al, 2014), Hoplias (Guimarães et al, 2022; Pires et al, 2021), Leporinus (Nascimento et al, 2023; Silva‐Santos et al, 2018), Moenkhausia (Benine et al, 2009; De Carvalho et al, 2011; Pereira et al, 2013), Mugil (Hasan et al, 2021), Nannostomus (Benzaquem et al, 2015), Pimelodella (Pugedo et al, 2016), Potamotrygon (Renza‐Millán et al, 2019), and Trachelyopterus (Dos Santos et al, 2021; Haerter et al, 2023).…”

“…The inclusion of molecular approaches has the potential to provide more robustness in the process of identification of species, as the use of this type of approach is able to reveal and assist in solving problems in identification of fish by indicating high rates of cryptic diversity (Benzaquem et al, 2015; Ramirez et al, 2017; Ximenes et al, 2021). In addition, such molecular approaches are able to reveal substantially underestimated diversity (Machado et al, 2018) and cases in which unique evolutionary lineages are evidenced and commonly already threatened by dam construction, habitat degradation, and invasive species (Souza et al, 2018).…”

Molecular evidence about ancestral origin, colonization patterns, and phylogenetic diversity of Coffea arabica, with insights in Latin America

“…Likely, the explication of the contradiction of these results might be explained by four principal hypotheses: (i) the implementation of the SLSD method, which has already permitted the estimation of cryptic diversity in several taxa using phylogenetic information (Machado et al 2018;Carvalho et al 2019;Ximenes et al 2021) revealing cryptic diversity. This differs from other studies that commonly use algorithms based on allelic frequencies; which require more demanding conditions to detect population differences, structure or existence of genetic clusters: being in Hardy-Weinberg equilibrium, having samples of robust size for the calculation of frequencies, as well as homogeneity of sample sizes between populations (Pritchard et al 2000; Puechmaille 2016) (ii) The utilization of more variable and informative molecular markers such as the ITS gene has been reported to allow the analysis of intraspeci c variation in some taxa and to determine relationships between closely related congeners and genera (Hao et 2020), like the humidity, altitude and pest resistance.…”

Multilocus approach reveals distinct evolutionary units of the South American apapa Pellona flavipinnis (Valenciennes, 1837) (Clupeiformes, Pristigasteridae)

“…South American ichthyofauna is the most diverse on the planet, although its diversity is underestimated, with about 42% of Neotropical freshwater fish species still to be formally described (Reis et al ., 2016). Recent molecular studies have revealed a large number of previously unknown evolutionary lineages in Neotropical fishes, suggesting that cryptic diversity is common (Arruda et al ., 2019; Collins et al ., 2018; Machado et al ., 2018; Ximenes et al ., 2021). Despite advances in studies of the Amazon ichthyofauna, the number of fish species remains uncertain.…”