1
|
Tang-Wing C, Mohanty I, Bryant M, Makowski K, Melendez D, Dorrestein PC, Knight R, Caraballo-Rodríguez AM, Allaband C, Jenné K. Impact of diet change on the gut microbiome of common marmosets ( Callithrix jacchus). mSystems 2024; 9:e0010824. [PMID: 38975760 PMCID: PMC11334461 DOI: 10.1128/msystems.00108-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/01/2024] [Indexed: 07/09/2024] Open
Abstract
Gastrointestinal diseases are the most frequently reported clinical problems in captive common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal and ultimately their use as a research subject. The microbiome has been shown to be intimately connected to diet and gastrointestinal health. Here, we use shotgun metagenomics and untargeted metabolomics in fecal samples of common marmosets collected before, during, and after a dietary transition from a biscuit to a gel diet. The overall health of marmosets, measured as weight recovery and reproductive outcome, improved after the diet transition. Moreover, each marmoset pair had significant shifts in the microbiome and metabolome after the diet transition. In general, we saw a decrease in Escherichia coli and Prevotella species and an increase in Bifidobacterium species. Untargeted metabolic profiles indicated that polyamine levels, specifically cadaverine and putrescine, were high after diet transition, suggesting either an increase in excretion or a decrease in intestinal reabsorption at the intestinal level. In conclusion, our data suggest that Bifidobacterium species could potentially be useful as probiotic supplements to the laboratory marmoset diet. Future studies with a larger sample size will be beneficial to show that this is consistent with the diet change. IMPORTANCE Appropriate diet and health of the common marmoset in captivity are essential both for the welfare of the animal and to improve experimental outcomes. Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, is linked to increases in Bifidobacterium species, and increases the removal of molecules associated with disease. The diet transition had an influence on the molecular changes at both the pair and time point group levels, but only at the pair level for the microbial changes. It appears to be more important which genes and functions present changed rather than specific microbes. Further studies are needed to identify specific components that should be considered when choosing an appropriate diet and additional supplementary foods, as well as to validate the benefits of providing probiotics. Probiotics containing Bifidobacterium species appear to be useful as probiotic supplements to the laboratory marmoset diet, but additional work is needed to validate these findings.
Collapse
Affiliation(s)
- Cassandra Tang-Wing
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| | - Ipsita Mohanty
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Katherine Makowski
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| | - Daira Melendez
- Bioinformatics Graduate Program, University of California, San Diego, La Jolla, California, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA
| | | | - Celeste Allaband
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Keith Jenné
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| |
Collapse
|
2
|
Garcez FS, Tchaicka L, Lemos FG, Kasper CB, Dalponte JC, Eizirik E. Phylogeographic analyses of an endemic Neotropical fox (Lycalopex vetulus) reveal evidence of hybridization with a different canid species (L. gymnocercus). J Hered 2024; 115:399-410. [PMID: 38412545 DOI: 10.1093/jhered/esae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 02/29/2024] Open
Abstract
The hoary fox (Lycalopex vetulus) is the only species of the Canidae (Mammalia: Carnivora) endemic to Brazil, and so far has been the target of few genetic studies. Using microsatellites and mtDNA markers, we investigated its present genetic diversity and population structure. We also tested the hypothesis that this species currently hybridizes with the pampas fox (L. gymnocercus), as suggested by previous mtDNA data from two individuals. We collected tissue and blood samples from animals representing most of the two species' distributions in Brazil (n = 87), including their recently discovered geographic contact zone in São Paulo state. We observed that the hoary fox exhibits high levels of genetic diversity and low levels of population structure. We identified six individuals from São Paulo state with clear evidence of hybridization based on introgressed pampas fox mitochondrial DNA and/or admixed microsatellite genotypes (three individuals bore both types of evidence). These results demonstrate the existence of admixed individuals between hoary and pampas foxes in southeastern Brazil, representing the first identified case of interspecies admixture between native South American canids. We discuss our findings in the context of the evolutionary history of these foxes and address potential conservation implications of this interspecies hybridization process.
Collapse
Affiliation(s)
- Fabricio Silva Garcez
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Ligia Tchaicka
- Departamento de Química e Biologia, Centro de Educação, Ciências Exatas e Naturais (CECEN), Universidade Estadual do Maranhão (UEMA), São Luís, MA, Brazil
| | - Frederico Gemesio Lemos
- Departamento de Ciências Biológicas, Universidade Federal de Catalão (UFCAT), Programa de Conservação de Mamíferos do Cerrado (PCMC), Catalão, GO, Brazil
| | - Carlos Benhur Kasper
- Laboratório de Biologia de Mamíferos e Aves (LABIMAVE), Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, Brazil
| | - Júlio Cesar Dalponte
- Instituto para a Conservação dos Carnívoros Neotropicais (Pró-Carnívoros), Atibaia, SP, Brazil
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Instituto para a Conservação dos Carnívoros Neotropicais (Pró-Carnívoros), Atibaia, SP, Brazil
| |
Collapse
|
3
|
Ito T, Kimura R, Wakamori H, Tanaka M, Tezuka A, Nagano AJ, Hamada Y, Kawamoto Y. Hybridization and its impact on the ontogenetic allometry of skulls in macaques. Evolution 2024; 78:284-299. [PMID: 37952211 DOI: 10.1093/evolut/qpad206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
The role of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite the accumulated knowledge on adult hybrid variation, how hybridization affects ontogenetic allometry is less well understood. Here, we investigated the effects of hybridization on postnatal ontogenetic allometry in the skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (Macaca fuscata). Genomic analyses indicated that the population consisted of individuals with varying degrees of admixture, formed by male migration from Japanese to Taiwanese macaques. For overall skull shape, ontogenetic trajectories were shifted by hybridization in a nearly additive manner, with moderate transgressive variation observed throughout development. In contrast, for the maxillary sinus (hollow space in the face), hybrids grew as fast as Taiwanese macaques, diverging from Japanese macaques, which showed slow growth. Consequently, adult hybrids showed a mosaic pattern, that is, the maxillary sinus is as large as that of Taiwanese macaques, while the overall skull shape is intermediate. Our findings suggest that the transgressive variation can be caused by prenatal shape modification and nonadditive inheritance on regional growth rates, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.
Collapse
Affiliation(s)
- Tsuyoshi Ito
- The Kyoto University Museum, Kyoto University, Sakyo, Kyoto, Japan
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Hikaru Wakamori
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Mikiko Tanaka
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Ayumi Tezuka
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | - Atsushi J Nagano
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Yuzuru Hamada
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yoshi Kawamoto
- School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
- Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| |
Collapse
|
4
|
Furusato IN, Figueiredo KB, de Carvalho ACSR, da Silva Ferreira CS, Takahashi JPF, Kimura LM, Aleixo CS, de Brito OP, Luchs A, Cunha MS, de Azevedo Fernandes NCC, de Araújo LJT, Catão-Dias JL, Guerra JM. Detection of herpesviruses in neotropical primates from São Paulo, Brazil. Braz J Microbiol 2023; 54:3201-3209. [PMID: 37688686 PMCID: PMC10689701 DOI: 10.1007/s42770-023-01105-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/14/2023] [Indexed: 09/11/2023] Open
Abstract
Transmission of herpesvirus between humans and non-human primates represents a serious potential threat to human health and endangered species conservation. This study aimed to identify herpesvirus genomes in samples of neotropical primates (NTPs) in the state of São Paulo, Brazil. A total of 242 NTPs, including Callithrix sp., Alouatta sp., Sapajus sp., and Callicebus sp., were evaluated by pan-herpesvirus polymerase chain reaction (PCR) and sequencing. Sixty-two (25.6%) samples containing genome segments representative of members of the family Herpesviridae, including 16.1% for Callitrichine gammaherpesvirus 3, 6.1% for Human alphaherpesvirus 1, 2.1% for Alouatta macconnelli cytomegalovirus, and 0.83% for Cebus albifrons lymphocryptovirus 1. No co-infections were detected. The detection of herpesvirus genomes was significantly higher among adult animals (p = 0.033) and those kept under human care (p = 0.008671). These findings confirm the importance of monitoring the occurrence of herpesviruses in NTP populations in epizootic events.
Collapse
Affiliation(s)
- Isabella Naomi Furusato
- Centro de Patologia, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 351, Pacaembú, São Paulo, SP, 01246000, Brazil
| | | | | | | | - Juliana Possatto Fernandes Takahashi
- Centro de Patologia, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 351, Pacaembú, São Paulo, SP, 01246000, Brazil
- Programa de Pós-Graduação Em Doenças Infecciosas E Parasitárias - Faculdade de Medicina, Universidade Federal de Mato Grosso Do Sul, Bairro Universitário, Av. Costa E Silva, S/nº, Campo Grande, MS, 79070900, Brazil
| | - Lidia Midori Kimura
- Centro de Patologia, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 351, Pacaembú, São Paulo, SP, 01246000, Brazil
| | - Camila Siqueira Aleixo
- Centro de Patologia, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 351, Pacaembú, São Paulo, SP, 01246000, Brazil
| | - Odília Pereira de Brito
- Centro de Patologia, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 351, Pacaembú, São Paulo, SP, 01246000, Brazil
| | - Adriana Luchs
- Centro de Virologia, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 351, Pacaembú, São Paulo, SP, 01246000, Brazil
| | - Mariana Sequetin Cunha
- Centro de Virologia, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 351, Pacaembú, São Paulo, SP, 01246000, Brazil
| | | | | | - José Luiz Catão-Dias
- Laboratório de Patologia Comparada (LAPCOM), Departamento de Patologia, Faculdade de Veterinária E Zootecnia, Universidade de São Paulo, Avenida Professor Orlando Marques de Paiva, 70, São Paulo, SP, 05508270, Brazil
| | - Juliana Mariotti Guerra
- Centro de Patologia, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 351, Pacaembú, São Paulo, SP, 01246000, Brazil.
- Laboratório de Patologia Comparada (LAPCOM), Departamento de Patologia, Faculdade de Veterinária E Zootecnia, Universidade de São Paulo, Avenida Professor Orlando Marques de Paiva, 70, São Paulo, SP, 05508270, Brazil.
| |
Collapse
|
5
|
Malukiewicz J, D'arc M, Dias CA, Cartwright RA, Grativol AD, Moreira SB, Souza AR, Tavares MCH, Pissinatti A, Ruiz-Miranda CR, Santos AFA. Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools. Sci Rep 2023; 13:15679. [PMID: 37735195 PMCID: PMC10514281 DOI: 10.1038/s41598-023-42059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.
Collapse
Affiliation(s)
- Joanna Malukiewicz
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, 37077, Germany.
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, SP, 05403-000, Brazil.
| | - Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Cecilia A Dias
- Centro de Primatologia, Universidade de Brasília, Brasília, Brazil
| | - Reed A Cartwright
- School of Life Sciences and the Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | | | - Silvia Bahadian Moreira
- Centro de Primatologia do Rio de Janeiro, Instituto Estadual do Ambiente, Rio de Janeiro, Brazil
| | | | | | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro, Instituto Estadual do Ambiente, Rio de Janeiro, Brazil
| | - Carlos R Ruiz-Miranda
- Laboratorio das Ciencias Ambientais, Centro de Biociencias e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - André F A Santos
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
6
|
Harvati K, Ackermann RR. Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins. Nat Ecol Evol 2022; 6:1573-1585. [PMID: 36064759 DOI: 10.1038/s41559-022-01875-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.
Collapse
Affiliation(s)
- K Harvati
- Paleoanthropology section, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - R R Ackermann
- Human Evolution Research Institute, University of Cape Town, Cape Town, South Africa.
- Department of Archaeology, University of Cape Town, Cape Town, South Africa.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
| |
Collapse
|
7
|
Malukiewicz J, Cartwright RA, Dergam JA, Igayara CS, Nicola PA, Pereira LMC, Ruiz-Miranda CR, Stone AC, Silva DL, Silva FDFRD, Varsani A, Walter L, Wilson MA, Zinner D, Roos C. Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world's most threatened primates. Sci Rep 2021; 11:17279. [PMID: 34446741 PMCID: PMC8390465 DOI: 10.1038/s41598-021-96404-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/10/2021] [Indexed: 12/28/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Joanna Malukiewicz
- German Primate Center, Leibniz Institute for Primate Research, Primate Genetics Laboratory, Göttingen, 37077, Germany.
- Universidade de São Paulo, Faculdade de Medicina, São Paulo, São Paulo, 05403-000, Brazil.
| | - Reed A Cartwright
- School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Jorge A Dergam
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | | | - Patricia A Nicola
- Centro de Conservação e Manejo de Fauna da Caatinga, Universidade Federal do Vale do São Francisco, Petrolina, PE, 56300-000, Brazil
| | - Luiz M C Pereira
- Centro de Conservação e Manejo de Fauna da Caatinga, Universidade Federal do Vale do São Francisco, Petrolina, PE, 56300-000, Brazil
| | - Carlos R Ruiz-Miranda
- Laboratório das Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Arizona State University, Institute of Human Origins, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Daniel L Silva
- Núcleo de Pesquisas em Ciências Biológicas - NUPEB, Federal University of Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Lutz Walter
- German Primate Center, Leibniz Institute for Primate Research, Primate Genetics Laboratory, Göttingen, 37077, Germany
| | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Dietmar Zinner
- German Primate Center, Leibniz Institute for Primate Research, Cognitive Ethology Laboratory, Göttingen, 37077, Germany
- Leibniz ScienceCampus Primate Cognition, Göttingen, 37077, Germany
- Department of Primate Cognition, Georg-August-University, Göttingen, 37077, Germany
| | - Christian Roos
- German Primate Center, Leibniz Institute for Primate Research, Primate Genetics Laboratory, Göttingen, 37077, Germany
- German Primate Center, Leibniz Institute for Primate Research, Gene Bank of Primates, Göttingen, 37077, Germany
| |
Collapse
|
8
|
Mitogenomic phylogeny of Callithrix with special focus on human transferred taxa. BMC Genomics 2021; 22:239. [PMID: 33823806 PMCID: PMC8025498 DOI: 10.1186/s12864-021-07533-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/15/2021] [Indexed: 12/04/2022] Open
Abstract
Background Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully 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 here to reconstruct a robust Callithrix phylogeny and divergence time estimates, and identify the biogeographic origins of autochthonous and allochthonous Callithrix mitogenome lineages. 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 mitogenomes to analyze five Callithrix species in total. Results We report the complete sequence and organization of the C. aurita mitogenome. Phylogenetic analyses showed that C. aurita was the first to diverge within Callithrix 3.54 million years ago (Ma), while C. jacchus and C. penicillata lineages diverged most recently 0.5 Ma 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 haplotypes. The biogeographic 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 allochthonous 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 of Callithrix anthropogenic introductions into the Brazilian Atlantic Forest. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07533-1.
Collapse
|
9
|
Shivambu N, Shivambu TC, Downs CT. Assessing the potential impacts of non-native small mammals in the South African pet trade. NEOBIOTA 2020. [DOI: 10.3897/neobiota.60.52871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The pet trade is one of the most important pathways by which small mammals are introduced to non-native areas. To prevent the introduction and invasion of non-native pets, an impact assessment protocol is useful in understanding which pets might have potential negative impacts should they escape or be released from captivity. In this study, we used the Generic Impact Scoring System (GISS) to assess the potential effects associated with 24 non-native small mammal species sold in the South African pet trade. European rabbits Oryctolagus cuniculus, house mice Mus musculus, Norwegian rats Rattus norvegicus and eastern grey squirrels Sciurus carolinensis had the highest potential impacts for both socio-economic and environmental categories. We found no statistically significant difference between the overall environmental and socio-economic impact scores. Impacts on agricultural and animal production (livestock) were the main mechanisms in the socio-economic category, while the impacts on animals (predation), competition and hybridisation prevailed for environmental impacts. The non-native mammal pet species with high impacts should be strictly regulated to prevent the potential impacts and establishment of feral populations in South Africa.
Collapse
|
10
|
Species assignment in forensics and the challenge of hybrids. Forensic Sci Int Genet 2020; 48:102333. [PMID: 32615399 DOI: 10.1016/j.fsigen.2020.102333] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 01/04/2023]
Abstract
Forensic identification of species is in growing demand, particularly from law enforcement authorities in the areas of wildlife, fisheries and hunting as well as food authentication. Within the non-human forensic genetics expanding applications' field, the major current difficulties result from the lack of standards and genetic databases as well as the poor or absent taxonomic definition of several groups. Here we focus on a forensically important and overlooked problem in species identification: the exclusive use of uniparental markers, a common practice in current genetic barcoding methodologies, may lead to incorrect or impossible assignment whenever hybrids can occur (frequently, not only in domesticates, but also in the wild). For example, if one of these cases involves a mammal, and mitochondrial DNA alone is used (which in instances may be the only type of DNA sequence available in databases), the sample will be wrongfully assigned to the female parental species, completely missing the detection of a possible hybrid animal. The importance of this issue in the forensic contributions to food authentication, wildlife and conservation genetics is analyzed. We present a cautionary guidance on the forensic reporting of results avoiding this error.
Collapse
|
11
|
Moraes AM, Vancine MH, Moraes AM, de Oliveira Cordeiro CL, Pinto MP, Lima AA, Culot L, Silva TSF, Collevatti RG, Ribeiro MC, Sobral-Souza T. Predicting the potential hybridization zones between native and invasive marmosets within Neotropical biodiversity hotspots. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
12
|
Cortés-Ortiz L, Baiz MD, Hermida-Lagunes J, García-Orduña F, Rangel-Negrín A, Kitchen DM, Bergman TJ, Dias PAD, Canales-Espinosa D. Reduced Introgression of Sex Chromosome Markers in the Mexican Howler Monkey ( Alouatta palliata × A. pigra) Hybrid Zone. INT J PRIMATOL 2019; 40:114-131. [PMID: 30880850 PMCID: PMC6394575 DOI: 10.1007/s10764-018-0056-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 06/07/2018] [Indexed: 01/12/2023]
Abstract
Interspecific hybridization allows the introgression or movement of alleles from one genome to another. While some genomic regions freely exchange alleles during hybridization, loci associated with reproductive isolation do not intermix. In many model organisms, the X chromosome displays limited introgression compared to autosomes owing to the presence of multiple loci associated with hybrid sterility or inviability (the "large X-effect"). Similarly, if hybrids are produced, the heterogametic sex is usually inviable or sterile, a pattern known as Haldane's rule. We analyzed the patterns of introgression of genetic markers located in the mitochondrial (control region) and nuclear (autosomal microsatellites and sex chromosome genes) genomes of two howler monkey species (Alouatta palliata and A. pigra) that form a natural hybrid zone in southern Mexico, to evaluate whether the large X-effect and Haldane's rule affect the outcomes of hybridization between these sister species. To identify the level of admixture of each individual in the hybrid zone (N = 254) we analyzed individuals sampled outside the hybrid zone (109 A. pigra and 39 A. palliata) to determine allele frequencies of parental species and estimated a hybrid index based on nuclear markers. We then performed a cline analysis using individuals in the hybrid zone to determine patterns of introgression for each locus. Our analyses show that although the hybrid zone is bimodal (with no known F1 s and few recent generation hybrids) and quite narrow, there has been extensive introgression in both directions, and there is a large array of admixed individuals in the hybrid zone. Mitochondrial and most autosomal markers showed bidirectional introgression, but some had biased introgression toward one species or the other. All markers on the sex chromosomes and a few autosomal markers showed highly restricted introgression. This pattern is consistent with the hypothesis that the sex chromosomes make a disproportionate contribution to reproductive isolation, and our results broaden the taxonomic representation of these patterns across animal taxa.
Collapse
Affiliation(s)
- Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA
| | - Marcella D Baiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA
| | | | | | | | - Dawn M Kitchen
- Department of Anthropology, The Ohio State University, Columbus, OH 43210 USA
| | - Thore J Bergman
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA.,Department of Psychology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Pedro A D Dias
- Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | | | | |
Collapse
|
13
|
Malukiewicz J. A Review of Experimental, Natural, and Anthropogenic Hybridization in Callithrix Marmosets. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0068-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
14
|
Mekonnen A, Rueness EK, Stenseth NC, Fashing PJ, Bekele A, Hernandez-Aguilar RA, Missbach R, Haus T, Zinner D, Roos C. Population genetic structure and evolutionary history of Bale monkeys (Chlorocebus djamdjamensis) in the southern Ethiopian Highlands. BMC Evol Biol 2018; 18:106. [PMID: 29986642 PMCID: PMC6038355 DOI: 10.1186/s12862-018-1217-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
Background Species with a restricted geographic distribution, and highly specialized habitat and dietary requirements, are particularly vulnerable to extinction. The Bale monkey (Chlorocebus djamdjamensis) is a little-known arboreal, bamboo-specialist primate endemic to the southern Ethiopian Highlands. While most Bale monkeys inhabit montane forests dominated by bamboo, some occupy forest fragments where bamboo is much less abundant. We used mitochondrial DNA (mtDNA) sequences to analyse the genetic structure and evolutionary history of Bale monkeys covering the majority of their remaining distribution range. We analysed 119 faecal samples from their two main habitats, continuous forest (CF) and fragmented forests (FF), and sequenced 735 bp of the hypervariable region I (HVI) of the control region. We added 12 orthologous sequences from congeneric vervets (C. pygerythrus) and grivets (C. aethiops) as well as animals identified as hybrids, previously collected in southern Ethiopia. Results We found strong genetic differentiation (with no shared mtDNA haplotypes) between Bale monkey populations from CF and FF. Phylogenetic analyses revealed two distinct and highly diverged clades: a Bale monkey clade containing only Bale monkeys from CF and a green monkey clade where Bale monkeys from FF cluster with grivets and vervets. Analyses of demographic history revealed that Bale monkey populations (CF and FF) have had stable population sizes over an extended period, but have all recently experienced population declines. Conclusions The pronounced genetic structure and deep mtDNA divergence between Bale monkey populations inhabiting CF and FF are likely to be the results of hybridization and introgression of the FF population with parapatric Chlorocebus species, in contrast to the CF population, which was most likely not impacted by hybridization. Hybridization in the FF population was probably enhanced by an alteration of the bamboo forest habitat towards a more open woodland habitat, which enabled the parapatric Chlorocebus species to invade the Bale monkey's range and introgress the FF population. We therefore propose that the CF and FF Bale monkey populations should be managed as separate units when developing conservation strategies for this threatened species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1217-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Addisu Mekonnen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway. .,Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia.
| | - Eli K Rueness
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.,Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia
| | - Peter J Fashing
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.,Department of Anthropology and Environmental Studies Program, California State University Fullerton, Fullerton, CA, 92834, USA
| | - Afework Bekele
- Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia
| | - R Adriana Hernandez-Aguilar
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Rose Missbach
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tanja Haus
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| |
Collapse
|
15
|
Detwiler KM. Mitochondrial DNA Analyses of Cercopithecus Monkeys Reveal a Localized Hybrid Origin for C. mitis doggetti in Gombe National Park, Tanzania. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0029-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
16
|
Warren KA, Ritzman TB, Humphreys RA, Percival CJ, Hallgrímsson B, Ackermann RR. Craniomandibular form and body size variation of first generation mouse hybrids: A model for hominin hybridization. J Hum Evol 2018; 116:57-74. [PMID: 29477182 PMCID: PMC6699179 DOI: 10.1016/j.jhevol.2017.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/04/2017] [Accepted: 12/12/2017] [Indexed: 12/27/2022]
Abstract
Hybridization occurs in a number of mammalian lineages, including among primate taxa. Analyses of ancient genomes have shown that hybridization between our lineage and other archaic hominins in Eurasia occurred numerous times in the past. However, we still have limited empirical data on what a hybrid skeleton looks like, or how to spot patterns of hybridization among fossils for which there are no genetic data. Here we use experimental mouse models to supplement previous studies of primates. We characterize size and shape variation in the cranium and mandible of three wild-derived inbred mouse strains and their first generation (F1) hybrids. The three parent taxa in our analysis represent lineages that diverged over approximately the same period as the human/Neanderthal/Denisovan lineages and their hybrids are variably successful in the wild. Comparisons of body size, as quantified by long bone measurements, are also presented to determine whether the identified phenotypic effects of hybridization are localized to the cranium or represent overall body size changes. The results indicate that hybrid cranial and mandibular sizes, as well as limb length, exceed that of the parent taxa in all cases. All three F1 hybrid crosses display similar patterns of size and form variation. These results are generally consistent with earlier studies on primates and other mammals, suggesting that the effects of hybridization may be similar across very different scenarios of hybridization, including different levels of hybrid fitness. This paper serves to supplement previous studies aimed at identifying F1 hybrids in the fossil record and to introduce further research that will explore hybrid morphologies using mice as a proxy for better understanding hybridization in the hominin fossil record.
Collapse
Affiliation(s)
- Kerryn A Warren
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Terrence B Ritzman
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa; Department of Neuroscience, Washington University School of Medicine, USA; School of Human Evolution and Social Change, Arizona State University, USA
| | - Robyn A Humphreys
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Christopher J Percival
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, Alberta Children's Hospital Research Institute, University of Calgary, Canada; The Alberta Children's Hospital Research Institute, University of Calgary, Canada; The McCaig Institute for Bone and Joint Health, University of Calgary, Canada; Department of Anthropology, Stony Brook, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, Alberta Children's Hospital Research Institute, University of Calgary, Canada; The Alberta Children's Hospital Research Institute, University of Calgary, Canada; The McCaig Institute for Bone and Joint Health, University of Calgary, Canada
| | - Rebecca Rogers Ackermann
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa.
| |
Collapse
|
17
|
Detogne N, Ferreguetti ÁC, Mello JHF, Santana MC, da Conceição Dias A, da Mota NCJ, Esteves da Cruz Gonçalves A, de Souza CP, Bergallo HG. Spatial distribution of buffy-tufted-ear (Callithrix aurita) and invasive marmosets (Callithrix spp.) in a tropical rainforest reserve in southeastern Brazil. Am J Primatol 2017; 79. [PMID: 29072335 DOI: 10.1002/ajp.22718] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 11/08/2022]
Abstract
We investigated the spatial distribution of native and invasive marmoset species (Callithrix), as well as their hybrids, in the Serra dos Órgãos National Park (PARNASO) and surrounding area in Rio de Janeiro state, Brazil. To estimate occupancy and the detection probability, we surveyed 56 sites within the park and 52 sites outside its limits using vocal playbacks, as well as by interviewing local residents in the surrounding area. We estimated the occupancy and detection probability of Callithrix aurita and the observed groups composed of Callithrix jacchus, Callithrix penicillata, and their hybrids. We also recorded the presence or absence of mixed groups of native and exotic species, and their hybrids. We recorded similar occupancy rates and detection probabilities for both native and invasive species within the national park. C. aurita was found more often within the areas of the park located furthest from access roads and with the least human interference, while invasive species were more likely to be found along the edge of the park and in areas with greater human interference. In the area surrounding the park, invasive marmosets were recorded at seven sites, and a mixed group of native and invasive marmosets was observed at one site, but non-hybrid C. aurita groups were not recorded. The occupancy probability of C. aurita in the study area is relatively low, which may indicate a low population density, with groups restricted to a small region within the PARNASO in the proximity of groups of invasive marmosets.
Collapse
Affiliation(s)
- Nathalia Detogne
- Department of Ecology, Institute of Biology, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Átilla C Ferreguetti
- Department of Ecology, Institute of Biology, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - José Henrique F Mello
- Department of Ecology, Institute of Biology, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Marcelo C Santana
- Department of Ecology, Institute of Biology, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Aline da Conceição Dias
- Department of Ecology, Institute of Biology, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Natalia C J da Mota
- Department of Ecology, Institute of Biology, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | | | - Cristiane P de Souza
- Department of Ecology, Institute of Biology, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Helena G Bergallo
- Department of Ecology, Institute of Biology, Rio de Janeiro State University, Rio de Janeiro, Brazil
| |
Collapse
|
18
|
Cezar AM, Pessoa LM, Bonvicino CR. Morphological and genetic diversity in Callithrix hybrids in an anthropogenic area in southeastern Brazil (Primates: Cebidae: Callitrichinae). ZOOLOGIA 2017. [DOI: 10.3897/zoologia.34.e14881] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Two species of Callithrix, C. jacchus (Linnaeus, 1758) and C. penicillata (É. Geoffroy, 1812), are considered invasive in Rio de Janeiro. This study determined the genetic and morphological diversity and verified the species involved in the hybridization of 10 individuals from the municipalities of Silva Jardim (N = 9) and Rio das Ostras (N = 1). We compared the external morphology and skull of C. jacchus (N = 15) and C. penicillata (N = 14) specimens deposited in the collection of the National Museum of Rio de Janeiro (MN- UFRJ). Phylogenetic (maximum likelihood and Bayesian inference) and phylogeographical analyses (network analysis) were performed based on cytochrome b sequences. These analyses included hybrids from the metropolitan region of Rio de Janeiro (N = 3), C. penicillata (N = 2), C. jacchus (N = 2), C. geoffroyi (N = 2), C. kuhlii (N = 2), C. aurita (N = 1), and as outgroups, Mico emiliae (N = 1) and Saguinus mystax (N = 1). The pelage and skull characters of most hybrids were more closely related to C. jacchus. Skull morphometric analysis revealed an intermediate state for the hybrids. Phylogenetic analyses revealed a high similarity between the hybrids and C. penicillata. Six haplotypes of hybrids were identified. Network analysis including them and C. penicillata recovered the topology generated by phylogenetic analysis. The results corroborate that C. jacchus and C. penicillata participate in the hybridization process. There was no geographic structure between hybrids from the coastal lowlands and from the metropolitan region of Rio de Janeiro.
Collapse
|
19
|
van Wyk AM, Dalton DL, Hoban S, Bruford MW, Russo IRM, Birss C, Grobler P, van Vuuren BJ, Kotzé A. Quantitative evaluation of hybridization and the impact on biodiversity conservation. Ecol Evol 2016; 7:320-330. [PMID: 28070295 PMCID: PMC5214875 DOI: 10.1002/ece3.2595] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/04/2016] [Accepted: 10/19/2016] [Indexed: 11/26/2022] Open
Abstract
Anthropogenic hybridization is an increasing conservation threat worldwide. In South Africa, recent hybridization is threatening numerous ungulate taxa. For example, the genetic integrity of the near‐threatened bontebok (Damaliscus pygargus pygargus) is threatened by hybridization with the more common blesbok (D. p. phillipsi). Identifying nonadmixed parental and admixed individuals is challenging based on the morphological traits alone; however, molecular analyses may allow for accurate detection. Once hybrids are identified, population simulation software may assist in determining the optimal conservation management strategy, although quantitative evaluation of hybrid management is rarely performed. In this study, our objectives were to describe species‐wide and localized rates of hybridization in nearly 3,000 individuals based on 12 microsatellite loci, quantify the accuracy of hybrid assignment software (STRUCTURE and NEWHYBRIDS), and determine an optimal threshold of bontebok ancestry for management purposes. According to multiple methods, we identified 2,051 bontebok, 657 hybrids, and 29 blesbok. More than two‐thirds of locations contained at least some hybrid individuals, with populations varying in the degree of introgression. HYBRIDLAB was used to simulate four generations of coexistence between bontebok and blesbok, and to optimize a threshold of ancestry, where most hybrids will be detected and removed, and the fewest nonadmixed bontebok individuals misclassified as hybrids. Overall, a threshold Q‐value (admixture coefficient) of 0.90 would remove 94% of hybrid animals, while a threshold of 0.95 would remove 98% of hybrid animals but also 8% of nonadmixed bontebok. To this end, a threshold of 0.90 was identified as optimal and has since been implemented in formal policy by a provincial nature conservation agency. Due to widespread hybridization, effective conservation plans should be established and enforced to conserve native populations that are genetically unique.
Collapse
Affiliation(s)
- Anna M van Wyk
- National Zoological Gardens of South Africa Pretoria South Africa; Genetics Department University of the Free State Bloemfontein South Africa
| | - Desiré L Dalton
- National Zoological Gardens of South Africa Pretoria South Africa; Genetics Department University of the Free State Bloemfontein South Africa
| | - Sean Hoban
- Department of Life Sciences and Biotechnology University of Ferrara Ferrara Italy; The Morton Arboretum Lisle IL USA; National Institute for Mathematical and Biological Synthesis (NIMBioS) University of Tennessee Knoxville TN USA
| | | | | | | | - Paul Grobler
- Genetics Department University of the Free State Bloemfontein South Africa
| | - Bettine Janse van Vuuren
- Molecular Zoology Laboratory Department of Zoology University of Johannesburg Auckland Park South Africa
| | - Antoinette Kotzé
- National Zoological Gardens of South Africa Pretoria South Africa; Genetics Department University of the Free State Bloemfontein South Africa
| |
Collapse
|
20
|
Malukiewicz J, Hepp CM, Guschanski K, Stone AC. Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 162:157-169. [PMID: 27762445 DOI: 10.1002/ajpa.23105] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/07/2016] [Accepted: 09/13/2016] [Indexed: 01/26/2023]
Abstract
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.
Collapse
Affiliation(s)
- Joanna Malukiewicz
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Crystal M Hepp
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Katerina Guschanski
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ 85287, USA
| |
Collapse
|
21
|
Malukiewicz J, Guschanski K, Grativol AD, Oliveira MAB, Ruiz-Miranda CR, Stone AC. Application of PE-RADSeq to the study of genomic diversity and divergence of two Brazilian marmoset species (Callithrix jacchusandC. penicillata). Am J Primatol 2016; 79:1-12. [DOI: 10.1002/ajp.22587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 07/03/2016] [Accepted: 07/10/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Joanna Malukiewicz
- Departamento de Bioquímica e Biologia Molecular; Universidade Federal de Viçosa; Viçosa MG Brazil
- School of Life Sciences; Arizona State University; Tempe Arizona
| | - Katerina Guschanski
- Department of Animal Ecology, Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Adriana D. Grativol
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes RJ Brazil
| | - Maria Adélia B. Oliveira
- Departamento de Morfologia e Fisiologia Animal; Universidade Federal Rural de Pernambuco; Recife PE Brazil
| | - Carlos R. Ruiz-Miranda
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes RJ Brazil
| | - Anne C. Stone
- School of Human Evolution and Social Change; Arizona State University; Tempe Arizona
| |
Collapse
|
22
|
Housman G, Malukiewicz J, Boere V, Grativol AD, Pereira LCM, Silva IDOE, Ruiz-Miranda CR, Truman R, Stone AC. Validation of qPCR Methods for the Detection of Mycobacterium in New World Animal Reservoirs. PLoS Negl Trop Dis 2015; 9:e0004198. [PMID: 26571269 PMCID: PMC4646627 DOI: 10.1371/journal.pntd.0004198] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 10/06/2015] [Indexed: 11/19/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
| | - Joanna Malukiewicz
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Vanner Boere
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Adriana D. Grativol
- Laboratório de Ciências Ambientias, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Luiz Cezar M. Pereira
- Centro de Conservação e Manejo de Fauna da Caatinga, Universidade Federal do Vale do São Francisco, Petrolina, Pernambuco, Brazil
| | - Ita de Oliveira e Silva
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Carlos R. Ruiz-Miranda
- Laboratório de Ciências Ambientias, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Richard Truman
- HHS\HRSA\HSB National Hansen's Disease Program-NIAID IAA-2646, Baton Rouge, Louisiana, United States of America
| | - Anne C. Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
| |
Collapse
|
23
|
Malukiewicz J, Boere V, Fuzessy LF, Grativol AD, de Oliveira e Silva I, Pereira LCM, Ruiz-Miranda CR, Valença YM, Stone AC. Natural and Anthropogenic Hybridization in Two Species of Eastern Brazilian Marmosets (Callithrix jacchus and C. penicillata). PLoS One 2015; 10:e0127268. [PMID: 26061111 PMCID: PMC4464756 DOI: 10.1371/journal.pone.0127268] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 04/14/2015] [Indexed: 11/29/2022] Open
Abstract
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."
Collapse
Affiliation(s)
- Joanna Malukiewicz
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa MG, Brazil
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, 85287, United States of America
| | - Vanner Boere
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa MG, Brazil
| | - Lisieux F. Fuzessy
- Department of Plant Biology, Universidade Federal de Minas Gerais, Belo Horizonte MG, Brazil
| | - Adriana D. Grativol
- Ciências Ambientias, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ, Brazil
| | | | - Luiz C. M. Pereira
- Centro de Conservação e Manejo de Fauna da Caatinga, Universidade Federal do Vale do São Francisco, Petrolina PE, Brazil
| | - Carlos R. Ruiz-Miranda
- Ciências Ambientias, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ, Brazil
| | - Yuri M. Valença
- Centro de Reabilitação de Animais Silvestres do Santuário dos Três Reinos, Recife PE, Brazil
| | - Anne C. Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, 85287, United States of America
| |
Collapse
|