Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world's most threatened primates

The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world's most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.

The source-filter theory of whistle-like calls in marmosets: Acoustic analysis and simulation of helium-modulated voices

Whistle-like high-pitched "phee" calls are often used as long-distance vocal advertisements by small-bodied marmosets and tamarins in the dense forests of South America. While the source-filter theory proposes that vibration of the vocal fold is modified independently from the resonance of the supralaryngeal vocal tract (SVT) in human speech, a source-filter coupling that constrains the vibration frequency to SVT resonance effectively produces loud tonal sounds in some musical instruments. Here, a combined approach of acoustic analyses and simulation with helium-modulated voices was used to show that phee calls are produced principally with the same mechanism as in human speech. The animal keeps the fundamental frequency (f0) close to the first formant (F1) of the SVT, to amplify f0. Although f0 and F1 are primarily independent, the degree of their tuning can be strengthened further by a flexible source-filter interaction, the variable strength of which depends upon the cross-sectional area of the laryngeal cavity. The results highlight the evolutionary antiquity and universality of the source-filter model in primates, but the study can also explore the diversification of vocal physiology, including source-filter interaction and its anatomical basis in non-human primates.

Systematics and evolution of the Jacchus group of marmosets (Platyrrhini)

Interspecific differentiation and geographic variation patterns in 39 skull traits of eastern Brazilian marmosets are analyzed. Eastern Callithrix taxa are distinct morphologically, and no evidence of intergradation among taxa is observed. Instead, there are sharp, stepped morphological boundaries among taxa, consistent with species-level distinction. The morphological similarity cluster diagram obtained from Mahalanobis distances is different from available molecular trees, and the general picture emerging is that the eastern Callithrix taxa should be considered as good species arising recently in South American history. In particular, C. kuhlii is morphologically distinct from other marmoset taxa, including C. geoffroyi and C. penicillata, which were previously hypothesized to be the parental populations that formed C. kuhlii by hybridization. Furthermore, C. kuhlii populations from southeastern Bahia do not overlap morphologically with any C. penicillata population, including the upper São Francisco River populations that display skin colors and pelage patterns to some extent similar to true Kuhli's marmosets. There is a negative, though insignificant, correlation between the morphological distance matrix and a Mahalanobis distance matrix estimated from nine climatic variables, a pattern opposite to that expected under a parapatric speciation model. This result, together with the lack of clinal variation in skull traits, suggests that an allopatric model of speciation might best explain eastern marmoset diversification.

The concept of species and the foundations of biology, a case study: the Callithrix jacchus group (Primates-Platyrrhini)

The axiomatic theory presented in Galleni and Forti [1999], being part of the foundational programme of Ennio De Giorgi, is based on the fundamental notions of quality, relation, operation and collection, and provides a very general axiomatization of the biological notions of living object, generation, species and speciation. Within this theoretical framework we consider here a difficult case of classification of species: the Callithrix jacchus group of the New World monkeys. Although the morphological analysis strongly suggests the individuation of six different species, nevertheless several experiments of crossing give evidence to fertility of hybrids. Since both the morphological and the hybridological criteria have shown to be of enormous importance in actual classification of species, this apparent contradiction seems very disappointing. Our axiomatization of speciation processes as operations acting in special time intervals permits to avoid the contradiction by allowing for individuals which, during such special periods, may belong to more than one species. Therefore we assume that one or more speciation processes are developing, starting from a unique protospecies and differentiating in six new ones. In order to obtain more evidence of these processes, new observations and suitable experiments are needed.

Comparative chromosomal study of five taxa of genus Callithrix, group jacchus (Platyrrhini, Primates)

The karyotypes of four marmoset species of the Callithrix jacchus group (C. aurita, C. kuhlii, C. geoffroyi, and C. penicillata) were investigated. The patterns of G-, C-, and NOR-bands of these karyotypes were compared with those of C. jacchus, previously described, in order to clarify the taxonomic relationships of this species group. All species present 2n = 46, 14 uni- and 30 biarmed autosomes, a median size submetacentric X chromosome, and the same NOR-band patterns. No rearrangement or constitutive heterochromatic variation differentiate these species, which differ only in the morphology of the Y chromosome. The data obtained indicate that, from the chromosomal point stand, the marmoset species of C. jacchus group constitute a homogeneous clade.

Phylogenetic relationships of the Callitrichinae (Platyrrhini, primates) based on beta2-microglobulin DNA sequences

The phylogenetic relationships of callitrichine primates have been determined by DNA sequence analyses of exons 1, 2, and 3 of the beta2-microglobulin gene. Parsimony, distance, and maximum likelihood analyses of ca. 900 base pairs of 21 taxa, representing all callitrichine genera, indicated that Saguinus was the most basal offshoot. Within Saguinus, S. fuscicollis appeared as the first divergent lineage followed by an unresolved trichotomy formed by S. mystax/S. imperator, S. midas/S. bicolor, and S. oedipus. A second callitrichine lineage was formed by Leontopithecus; each of the three species studied showed identical nucleotide sequences. Callimico appeared as the sister taxon of Callithrix/Cebuella. Genetic distances within this latter group were very small, although a stronger association between Cebuella and species of the Callithrix argentata group was observed. The inclusion of Cebuella in the genus Callithrix is suggested. These studies indicated that tamarins are more plesiomorphic than marmosets in agreement with the phyletic dwarfism hypothesis.

Comparative karyology and evolution of the Amazonian Callithrix (Platyrrhini, Primates)

Chromosomal studies in three species of Amazonian Callithrix (2n=44) and data in the literature show that this group is karyomonotypic. Moreover, it is characterized by the presence of abundant heterochromatic regions, unlike the situation in congeneric forms of Callithrix of the Atlantic coast with 2n=46, and by the presence of a highly repetitive, exclusive DNA component, with a basic repeat motif of 1528bp. Karyotypic comparisons with other Callitrichids and an outgroup species showed that Callitrichids are karyologically conserved and explained several rearrangements that had presumably occurred during their phyletic radiation. Analyses of karyologic data enabled the construction of two alternative phylogenetic topologies. The lack of derived homoeologies, common to all members of the genus Callithrix grouped at present, and the fact that Amazonian species were more similar to Cebuella pygmaea (2n=44) than to their congeneric forms with 2n=46 suggested that species at present included in the Amazonian Callithrix should be grouped with C. pygmaea.

Analysis of constitutive heterochromatin by fluorochromes and in situ digestion with restriction enzymes in species of the group Callithrix argentata (Callitrichidae, Primates)

The karyotypes of the species belonging to the group Callithrix argentata (Callitrichidae, Platyrrhini) are characterized by large amounts of distal constitutive heterocharomatin (CH). The CH of the species C. argentata, C. humeralifera and C. emiliae was analyzed by banding with the restriction enzymes HinfI, MboI, aluI, RsaI, DdeI, HaeIII and MspI, as well as the fluorochromes CMA3 and DAPI. The results obtained permitted us to classify the CH of these species into three distinct types: 1) distal CH with a homogeneous response to enzymatic action, which was unchanged (HinfI, MboI, AluI, HaeIII), partially digested (DdeI) or fully digested (RsaI), being CMA3+, DAPI-; 2) centromeric CH, generally presenting a reduced band size. The varying extent of reduction, ranging from none to total, and also the variation of fluorochrome staining indicates that there is heterogeneity in this type of CH; 3) CH of the distal portion of the X chromosome of C. argentata and of the Y chromosome was CMA3- and unchanged by the enzymes, except for RsaI, which caused a reduction in size. MspI was the only enzyme unable to induce bands. Sequential C-banding permitted us to perceive banding variations that could not be observed simply by RE banding.

Chromosomal relationships and phylogenetic and clustering analyses on genes Callithrix group argentata (Callitrichidae, Primates)

The karyotypes of three species of marmosets of the Callithrix argentata group (C. argentata, C. humeralifera and C. chrysoleuca) were studied. Comparisons were made among species and with the previously described karyotypes of C. emiliae, C. mauesi (argentata group) and C. jacchus (jacchus group). Two chromosomes rearrangements differentiate the argentata (2n=44) and jacchus (2n=46) groups: fusion or fission and a paracentric invasion. The argentata group is also characterized by the addition of large amounts of distal constitutive heterochromatin (CH) in some chromosomes, while the jacchus group shows mainly centromeric heterochromatin. The five species of the argentata group differ in the amount or location of the distal CH. Interspecific differences were converted to a Basic Data Matrix (BDM), that was submitted to phenetic and cladistic analyses. For cladistic analyses C. jacchus was the outgroup. The results agree with morphological and geographical data.