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Background: The Callithrix geoffroyi are increasingly present in Brazilian urban areas, where they are vulnerable to health problems. The purpose of this study was a description of hematology and nine blood chemistry parameters of free‐ranging C. geoffroyi. Methods: Thirty individuals were captured in urban‐forested settings. The marmosets were anesthetized, venopunctioned, and released shortly after recovery. The analysis was carried on in a veterinary laboratory, using automatic cells counter, staining methods, and an automatic biochemical analyzer. Results and Conclusions: Male and female free‐ranging C. geoffroyi have similar hematological and blood chemistry values. The adults presented higher concentrations of erythrocytes (P <.02) and hemoglobin (P <.02) than young marmosets. The platelet concentration was lower (P <.05) in adults comparing to young marmosets. There were not statistically significant differences between young and adult blood chemistry concentrations. This is the first time that are presented hematology and blood biochemistry data on free‐ranging C. geoffroyi. [ABSTRACT FROM AUTHOR]

During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex‐differences in behavior, Haldane's rule and the large X‐effect, and transgressive phenotypic variation. [ABSTRACT FROM AUTHOR]

An understanding of current Callithrix distributions is important for species management and conservation in the wild because of widespread deforestation and the introduction, and spread, of marmosets outside their natural ranges. Here we report on a survey of the natural and introduced Callithrix distributions in five mesoregions of the southeastern Brazilian state of Minas Gerais: Metropolitana de Belo Horizonte, Sul/Sudoeste de Minas, Zona da Mata, Campo das Vertentes and Vale do Rio Doce. Our study was based on on- and off-line literature searches, e-mail questionnaires, photographic records, and field observations. The collected data were superimposed on geopolitical and vegetation maps and compared to the historical records available in mammal collections from national museums and the currently recognized natural ranges of Callithrix species. Callithrix geoffroyi and C. penicillata were widely distributed in our study area, particularly in regions and biomes where they do not occur naturally. Callithrix penicillata has apparently expanded its range into the Atlantic Forest from its native Cerrado in Central Brazil. Although not native to Minas Gerais, C. jacchus was reported at several locations in our study area. These three species were reported even in the areas of natural occurrence of C. aurita and C. flaviceps. We detected the presence of five species of Callithrix (C. aurita, C. flaviceps, C. geoffroyi, C. penicillata, and C. jacchus) in some locations of the Zona da Mata. Marmoset groups are present in some urban areas, in close contact with human populations. Marmosets are found in artificial sympatry due to the introduction of species outside their native areas of distribution. Such introductions, together with the destruction of native marmoset habitats, are a threat due to ongoing hybridization. [ABSTRACT FROM AUTHOR]

Callithrix jacchus and C. penicillata are among the smallest anthropoid primates, are highly specialized tree gougers, and largely occupy Brazil's most extreme, semi-arid biomes. However, the underlying genomic factors that underpin the evolution of these species and their unique traits are under-investigated. Additionally, exotic populations of these two species are widely established throughout Brazil and hybridize with threatened native congers. Thus, both genomic and conservation factors call for a better understanding of C. jacchus and C. penicillata evolution. Here, we applied PE-RADseq to characterize genomic variation in these two species, using six C. jacchus and seven C. penicillata individuals. We identified an average of 7,463 and 5,180 SNPs/individual in C. penicillata and C. jacchus, respectively, and also found 1,395 variable sites that were represented in both species. C. penicillata showed overall higher levels of genetic diversity than C. jacchus at the variable sites present in both species. Additionally, among these variable sites, 106 showed relative interspecific divergence levels that were significantly higher than the genome-wide average. We further compared relative and absolute divergence for C. penicillata and C. jacchus between RAD loci associated with the 106 significantly diverged variable sites and all other RAD loci present in both species. The former RAD loci set showed significantly elevated relative and absolute divergence measures in comparison to the latter set. This convergence suggests that C. jacchus and C. penicillata may have diverged under a scenario of gene flow under secondary contact. Here, we demonstrate that RADseq is an efficient method to simultaneously discover and genotype a large number of markers and validate the utility of RADseq for examining Callithrix evolution. [ABSTRACT FROM AUTHOR]

Objectives Two subgroups make up the marmoset genus Callithrix. The ' aurita' group is composed of two species, whereas evolutionary relationships among the four species of the ' jacchus' group remain unclear. To uncover these relationships, we first sequenced mitochondrial genomes for C. kuhlii and C. penicillata to complement data available for congeners. We then constructed a phylogenetic tree based on mtDNA heavy chain protein coding genes from several primates to untangle species relationships and estimate divergence times of the jacchus group. Materials and Methods MtDNA genomes of C. kuhlii and C. penicillata were Sanger sequenced. These Callithrix mitogenomes were combined with other publically available primate mtDNA genomes. Phylogenies were produced using maximum likelihood and Bayesian inference. Finally, divergence times within the jacchus group of marmosets were estimated with Bayesian inference. Results In our phylogenetic tree, C. geoffroyi was the sister to all other jacchus group species, followed by C. kuhlii, while C. jacchus and C. penicillata diverged most recently. Bayesian inference showed that C. jacchus and C. penicillata diverged approximately 0.70 MYA and that the jacchus group radiated approximately 1.30 MYA. Discussion Callithrix nuclear and mtDNA phylogenies frequently result in polytomies and paraphyly. Here, we present a well-supported phylogenetic tree based on mitochondrial genome sequences, which facilitates the understanding of the divergence of the jacchus marmosets. Our results demonstrate how mitochondrial genomes can enrich Callithrix phylogenetic studies by alleviating some of the difficulties faced by previous mtDNA studies and allow formulation of hypotheses to test further under larger genomic-scale analyses. [ABSTRACT FROM AUTHOR]

Zoonotic pathogens that cause leprosy (Mycobacterium leprae) and tuberculosis (Mycobacterium tuberculosis complex, MTBC) continue to impact modern human populations. Therefore, methods able to survey mycobacterial infection in potential animal hosts are necessary for proper evaluation of human exposure threats. Here we tested for mycobacterial-specific single- and multi-copy loci using qPCR. In a trial study in which armadillos were artificially infected with M. leprae, these techniques were specific and sensitive to pathogen detection, while more traditional ELISAs were only specific. These assays were then employed in a case study to detect M. leprae as well as MTBC in wild marmosets. All marmosets were negative for M. leprae DNA, but 14 were positive for the mycobacterial rpoB gene assay. Targeted capture and sequencing of rpoB and other MTBC genes validated the presence of mycobacterial DNA in these samples and revealed that qPCR is useful for identifying mycobacterial-infected animal hosts. [ABSTRACT FROM AUTHOR]

Animal hybridization is well documented, but evolutionary outcomes and conservation priorities often differ for natural and anthropogenic hybrids. Among primates, an order with many endangered species, the two contexts can be hard to disentangle from one another, which carries important conservation implications. Callithrix marmosets give us a unique glimpse of genetic hybridization effects under distinct natural and human-induced contexts. Here, we use a 44 autosomal microsatellite marker panel to examine genome-wide admixture levels and introgression at a natural C. jacchus and C. penicillata species border along the São Francisco River in NE Brazil and in an area of Rio de Janeiro state where humans introduced these species exotically. Additionally, we describe for the first time autosomal genetic diversity in wild C. penicillata and expand previous C. jacchus genetic data. We characterize admixture within the natural zone as bimodal where hybrid ancestry is biased toward one parental species or the other. We also show evidence that São Francisco River islands are gateways for bidirectional gene flow across the species border. In the anthropogenic zone, marmosets essentially form a hybrid swarm with intermediate levels of admixture, likely from the absence of strong physical barriers to interspecific breeding. Our data show that while hybridization can occur naturally, the presence of physical, even if leaky, barriers to hybridization is important for maintaining species genetic integrity. Thus, we suggest further study of hybridization under different contexts to set well informed conservation guidelines for hybrid populations that often fit somewhere between “natural” and “man-made.” [ABSTRACT FROM AUTHOR]

ABSTRACT Hybridization is continually documented in primates, but effects of natural and anthropogenic hybridization on biodiversity are still unclear and differentiating between these contexts remains challenging in regards to primate evolution and conservation. Here, we examine hybridization effects on the mitochondrial DNA (mtDNA) control region of Callithrix marmosets, which provide a unique glimpse into interspecific mating under distinct anthropogenic and natural conditions. DNA was sampled from 40 marmosets along a 50-km transect from a previously uncharacterized hybrid zone in NE Brazil between the ranges of Callithrix jacchus and Callithrix penicillata. DNA was also collected from 46 marmosets along a 30-km transect in a hybrid zone in Rio de Janeiro state, Brazil, where exotic marmosets appeared in the 1980s. Combining Callithrix DNA sampled inside and outside of these hybrid zones, phylogenetic and network analyses show C. jacchus and C. penicillata being parental species to sampled hybrids. We expand limited Callithrix population genetics work by describing mtDNA diversity and demographic history of these parental species. We show ancient population expansion in C. jacchus and historically constant population size in C. penicillata, with the latter being more genetically diverse than the former. The natural hybrid zone contained higher genetic diversity relative to the anthropogenic zone. While our data suggest hybrid swarm formation within the anthropogenic zone due to removed physical reproductive barriers, this pattern is not seen in the natural hybrid zone. These results suggest different genetic dynamics within natural and anthropogenic hybridization contexts that carry important implications for primate evolution and conservation. Am J Phys Anthropol 155:522-536, 2014. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across three primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral "copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs that were processed pseudogenes and some of which were expressed. Furthermore, there were copy number-different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA. [ABSTRACT FROM AUTHOR]

A correction to the article "Validation of qPCR Methods for the Detection of Mycobacterium in New World Animal Reservoirs" published in a previous issue is presented.

Genomics provides effective tools to characterize biodiversity, but the full implementation of genomic techniques in practical conservation is still limited. We review some of the main approaches in biodiversity genomics available to conservationists and genomicists. High-quality, long-read sequencing and bioinformatic technologies facilitate genome sequencing and assembly for any species. We summarize how reference genomes, in conjunction with population genomic data, can contribute to biodiversity monitoring, conservation, and restoration efforts. Over the past decade, many initiatives to generate reference genomes spanning the tree of life have emerged worldwide. We call for increased integration of reference genomes and population genomics data into interdisciplinary conservation efforts to fully unlock the potential of genomics in safeguarding global biodiversity. The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics. [ABSTRACT FROM AUTHOR]

We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives., Competing Interests: COMPETING INTERESTS E.E.E. is a scientific advisory board (SAB) member of Variant Bio, Inc. C.T.W. is a co-founder/CSO of Clareo Biosciences, Inc. W.L. is a co-founder/CIO of Clareo Biosciences, Inc. The other authors declare no competing interests.

We provide here a current overview of marmoset (Callithrix) evolution, hybridization, species biology, basic/biomedical research, and conservation initiatives. Composed of 2 subgroups, the aurita group (C aurita and C flaviceps) and the jacchus group (C geoffroyi, C jacchus, C kuhlii, and C penicillata), this relatively young primate radiation is endemic to the Brazilian Cerrado, Caatinga, and Atlantic Forest biomes. Significant impacts on Callithrix within these biomes resulting from anthropogenic activity include (1) population declines, particularly for the aurita group; (2) widespread geographic displacement, biological invasions, and range expansions of C jacchus and C penicillata; (3) anthropogenic hybridization; and (4) epizootic Yellow Fever and Zika viral outbreaks. A number of Brazilian legal and conservation initiatives are now in place to protect the threatened aurita group and increase research about them. Due to their small size and rapid life history, marmosets are prized biomedical models. As a result, there are increasingly sophisticated genomic Callithrix resources available and burgeoning marmoset functional, immuno-, and epigenomic research. In both the laboratory and the wild, marmosets have given us insight into cognition, social group dynamics, human disease, and pregnancy. Callithrix jacchus and C penicillata are emerging neotropical primate models for arbovirus disease, including Dengue and Zika. Wild marmoset populations are helping us understand sylvatic transmission and human spillover of Zika and Yellow Fever viruses. All of these factors are positioning marmosets as preeminent models to facilitate understanding of facets of evolution, hybridization, conservation, human disease, and emerging infectious diseases., (© The Author(s) 2021. Published by Oxford University Press on behalf of the National Academies of Sciences, Engineering, and Medicine 2021. All rights reserved. For permissions, please email: journals.permissions@oup.com.)