Mitogenomic Phylogeny ofCallithrixwith Special Focus on Human Transferred Taxa

Abstract

Background Callithrix marmosets are a relatively young non-human primate radiation, whose phylogeny is not yet fulllly resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed in this study to reconstruct a robust Callithrix phylogeny and divergence time estimates, as well as identify autochthonous and allochthonous Callithrix mitogenome lineages across Brazil. We sequenced 49 mitogenomes from four species (C. aurita, C. geoffroyi, C. jacchus, C. penicillata) and anthropogenic hybrids (C. aurita x Callithrix sp., C. penicillata x C. jacchus, Callithrix sp. x Callithrix sp., C. penicillata x C. geoffroyi) via Sanger and whole genome sequencing. We combined these data with previously published Callithrix mtDNA genomes to analyze five Callithrix species in total. Results We report the complete sequence and organization of the C. aurita mtDNA genome. Phylogenetic analyses showed that C. aurita was the first to diverge within Callithrix 3.54 million years ago (MYA), while C. jacchus and C. penicillata lineages diverged most recently 0.5 MYA as sister clades. MtDNA clades of C. aurita, C. geoffroyi, and C. penicillata show intraspecific geographic structure, but C. penicillata clades appear polyphyletic. Hybrids, which were identified by phenotype, possessed mainly C. penicillata or C. jacchus mtDNA plotypes. The geographic origins of mtDNA haplotypes from hybrid and allochthonous Callithrix were broadly distributed across natural Callithrix ranges. Our phylogenetic results also evidence introgression of C. jacchus mtDNA into C. aurita. Conclusion Our robust Callithrix mitogenome phylogeny shows C. aurita lineages as basal and C. jacchus lineages among the most recent within Callithrix. We provide the first evidence that parental mtDNA lineages of anthropogenic hybrid and allochtonous marmosets are broadly distributed inside and outside of the Atlantic Forest. We also show evidence of cryptic hybridization between allochthonous Callithrix and autochthonous C. aurita. Our results encouragingly show that further development of genomic resources will allow to more clearly elucidate Callithrix evolutionary relationships and understand the dynamics.

Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

“…We aligned mitochondrial genomes newly assembled with mitofinder ( n = 205), as well as complete mitochondrial genomes from 32 additional platyrrhines and six primate outgroups (Table ) available in ncbi 's RefSeq database from previous phylogenomic studies (Arnason et al, 2000, 2002; Babb et al, 2011; Chan et al, 2010; Chiou et al, 2011; de Freitas et al, 2018; Finstermeier et al, 2013; Hao & Yi, 2019; Hodgson et al, 2009; Horai et al,1995; Malukiewicz et al, 2017, 2021; Matsui et al, 2009; Menezes et al, 2013; Raaum et al, 2005; Wang et al, 2016; Zhang et al, 2016). To facilitate the alignment of circular genomes, we first shifted the genome start for all sequences to begin with the gene cytochrome B, using the fasta_shift tool (https://github.com/b-brankovics/fasta_tools).…”

“…Mitochondrial markers and genomes are especially useful for species identification and delimitation (Reese et al, 2020), for assessing population structure (Flores‐Manzanero et al, 2022; Gagneux et al, 1999; Phukuntsi et al, 2021; Serrao et al, 2018; Skovrind et al, 2021), for assessing introgression and admixture (Makhov et al, 2021; Malukiewicz et al, 2021), for monitoring of species assemblages using environmental DNA (Barnes & Turner, 2016; Thomsen & Willerslev, 2015), and for identifying the origin of animals found in wild meat markets and the illegal pet trade (Cardeñosa et al, 2021; Maligana et al, 2020; Russello et al, 2008). However, many of these methods are reliant on databases from which sequences can be integrated and against which results can be compared, and which are often incomplete (Curry et al, 2018).…”