Phylogenetic woods and divergence times during the Callithrix mitochondrial clades

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February 8, 2022
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Phylogenetic woods and divergence times during the Callithrix mitochondrial clades

To build upon the above past Callithrix reports, there is executed the greatest to-date geographical sample of Callithrix mitogenomes across Brazil (Fig. 1) making use of the after objectives: (1) develop quality of phylogenetic relations and divergence days quotes between Callithrix mtDNA haplotypes; (2) decide which Callithrix mtDNA lineages is autochthonous across Callithrix range; and (3) diagnose allochthonous Callithrix mtDNA lineages within the southeastern Atlantic Forest as well as their feasible biogeographic roots. We sequenced, the very first time, the complete mitogenome of C. aurita, as well as in full received 49 newer mitogenome sequences from four species (C. aurita, C. geoffroyi, C. jacchus, C. penicillata), and four hybrid type (C. aurita x Callithrix sp., C. penicillata x C.jacchus, Callithrix sp. x Callithrix sp., C. penicillata x C. geoffroyi) for those analyses.

Success

Making use of Illumina complete genome sequencing (WGS) and Sanger sequencing approaches, we sequenced total mitogenomes from 49 Callithrix (Fig. 1, dining table 1, and Table S1). We combined these new mitogenomes with earlier published primate mitogenome sequences for downstream analyses (placed in Table S1). The size of the ensuing sequence alignment after mixing many of these mitogenomes is 17,132 angles. Sampled individuals who https://datingranking.net/recon-review/ had similar mtDNA haplotypes were placed in dining table S2. The organization in the C. aurita mitogenome had been in line with previously published Callithrix mitogenomes from . This mitogenome consists of 12 protein-coding genes, two rRNAs, and 14 tRNAs about heavy string and one protein-coding gene and eight tRNAs throughout the light string, plus the regulation part (desk S3). The duration of the C. aurita mitogenome introduced in desk S3 had been 16,471 angles.

Maximum-likelihood (ML) and Bayesian inference made well-supported phylogenetic woods that show primarily congruent phylogenetic relationships involving the aurita and jacchus groups (Fig. 2, Figures S1-S3). The key difference between the topology of the ML and Bayesian trees was in grouping habits of some haplotypes within C. jacchus clade described below. Many nodes inside ML tree held 100% bootstrap service but most experienced bootstrap many > 70% (Figure S1). More nodes inside Bayesian woods got rear probabilities of 1 (Fig. 2, Figures S2-S3). Major node labels and divergence period within and outside the Callithrix clade were revealed in Fig. 2, Figure S3, dining table 2, and Table S4.

Phylogenetic affairs and divergence many years in million ages (Ma) among Callithrix haplotypes as computed from total mitogenomes (comprehensive tree with outgroups try presented in Figure S3)

Biggest nodes tend to be determined by money characters, and blue taverns at nodes show 95% highest rear densities (HPD) of divergence occasions. Node support was found for biggest nodes in which either posterior probability was< 1 in the BEAST tree, posterior probability was < 1 in the MRBAYES tree, or bootstrap support < 70% in the ML tree. Haplotype colors at tips correspond to the aˆ?Species and Hybrid Phenotypes' legend, and indicate phenotypes associated with each given haplotype

Callithrix diverged from Cebuella about 6.83 Ma (Fig. 2 node E) and preliminary separate within Callithrix, isolating C. aurita together with jacchus cluster, taken place roughly 3.54 Ma (Fig. 2 node D) (Table 2). Hence, C. aurita developed the Callithrix basal clade, and C. geoffroyi established more basal clade inside the jacchus class by arising 1.18 Ma (node C). Callithrix penicillata haplotypes grouped into three polyphyletic clades that corresponded to 3 various biome parts, an Atlantic Forest-Cerrado change area, Cerrado, and Caatinga. The very first of the C. penicillata clades to diverge after C. geoffroyi got the Atlantic Forest-Cerrado changeover clade at 0.92 Ma. Afterwards, the C. penicillata Cerrado clade showed up at 0.87 Ma, with the C. kuhlii clade at 0.82 Ma (Fig. 2 node B). The C. penicillata Caatinga clade together with C. jacchus clades portray both youngest clades inside the phylogeny, splitting about 0.51 Ma (Fig. 2 node A). Since the C. jacchus clade showed certain shallowest part strategies among Callithrix haplotypes and poor phylogenetic solution, a ParsimonySplits community had been constructed for haplotypes inside this clade (Fig. 3).

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