Taxonomic diversity of Cebuella in the western Amazon: Molecular, morphological and pelage diversity of museum and free‐ranging specimens

Abstract

Objectives We investigated the diversity of the pygmy marmoset, Cebuella pygmaea, by comparing genetic, morphological and pelage traits of animals from Peru and Ecuador. Materials and Methods We extracted DNA from museum specimen osteocrusts and from fecal samples collected from free‐ranging individuals. We sequenced the mtDNA cytochrome b gene and the control region from samples collected at 13 different sites and used Bayesian inference and Maximum Likelihood to identify distinct clades. We took measurements of the crania of a subset of these specimens (n = 26) and ran a logistic regression to determine if any of the cranial measurements (n = 22) could predict a specimen's clade. In addition, we examined the pelage patterns of the museum specimens and photographs taken of free‐ranging individuals and divided them into pelage types based on coloration of the underbelly. Results We identified two divergent clades, and two distinct groups with clear geographic boundaries within one of those clades. Two measurements of the zygomatic bone perfectly predicted a given individual's mtDNA clade. We found four distinct pelage patterns in our samples, but these patterns are variable within clades and among individuals within the same population. Conclusion These analyses indicate that the two recognized subspecies of pygmy marmoset should be elevated to the species level (C. pygmaea and C. niveiventris) based on molecular and cranial differences but not on pelage patterns. We provide evidence on the geographic limits of the two clades and identify regions where additional sampling is required to better define the geographic distribution of the two clades.

Ancient DNA of the pygmy marmoset type specimen <i>Cebuella pygmaea</i> (Spix, 1823) resolves a taxonomic conundrum

“…By placing these data in the context of available cyt b mitochondrial barcode gene sequences from pygmy marmosets across their distribution, we provide the first range-wide phylogenetic analysis of this taxon and confirm the correct naming of the two species of Cebuella , thereby resolving the present taxonomic uncertainty. We also re-evaluate the current geographical distribution hypothesis for the two Cebuella species ( Mittermeier et al, 2013 ) based on our results and those of Porter et al ( 2021 ).…”

“…The morphological analyses of Garbino et al ( 2019 ) and Porter et al ( 2021 ) identified the Napo River as the southern range limit of C. pygmaea in Peru and Ecuador. Previously, it had been thought that the divide was marked by the Amazonas-Marañón rivers, extending west to the left bank of the Pastaza River ( Mittermeier et al, 2013 ; van Roosmalen & van Roosmalen, 1997 ).…”

“…Based on their phylogenetic analysis using newly generated genomic data for a relatively large sample of individuals, Boubli et al ( 2018 ) proposed the division of pygmy marmosets into two species of Cebuella (see Boubli et al, 2018 ; Garbino et al, 2019 ; see also Porter et al, 2021 ) separated by the Solimões-Amazonas River. However, as pointed out by these authors, confirming the names to be attributed to these two newly identified clades was hindered by the uncertainty of the type locality of Spix’s Cebuella pygmaea ( Lönnberg, 1940 ; see Boubli et al, 2018 ; Garbino et al, 2019 ).…”

“…We supplemented the newly sequenced mitochondrial data with cyt b sequencing data from previous publications ( Boubli et al, 2018 ; Porter et al, 2021 ), as well as mitogenomes available in GenBank. Our final dataset consisted of cyt b sequences from 65 individuals and full mitogenomes from 15 individuals.…”

“…A recent molecular genetic study ( Boubli et al, 2018 ) tested the validity of separating this taxon into two subspecies, namely, Cebuella pygmaea pygmaea (Spix, 1823) and Cebuella pygmaea niveiventris ( Lönnberg, 1940 ), which have been recognized in various studies, including da Cruz Lima ( 1945 ), Napier ( 1976 ), van Roosmalen & van Roosmalen ( 1997 ), and Groves ( 2001 , 2005 ). Using the mitochondrial cytochrome b (cyt b ) gene and ddRAD nuclear genome sequences from geographically representative samples from both sides of the Solimões River (upper Amazon), Boubli et al ( 2018 ) recovered two highly supported clades that diverged 2.25 million years ago (Ma), leading the authors to suggest the existence of two species of Cebuella ; one comprising pygmy marmosets sampled on the northern side (left bank) of the Solimões and the other comprising samples collected on the southern side (right bank) (see also Porter et al, 2021 ). Reconciling the results of these molecular and morphological analyses with the current Cebuella taxonomy was confusing, however, due to the uncertainty of the provenance of Spix’s holotype of Iacchus pygmaeus ( Boubli et al, 2018 ; Rylands et al, 2009 ).…”