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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Genet.</journal-id>
<journal-title>Frontiers in Genetics</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Genet.</abbrev-journal-title>
<issn pub-type="epub">1664-8021</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">742870</article-id>
<article-id pub-id-type="doi">10.3389/fgene.2021.742870</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Genetics</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Revalidation of <italic>Mazama rufa</italic> (Illiger 1815) (Artiodactyla: Cervidae) as a Distinct Species out of the Complex <italic>Mazama americana</italic> (Erxleben 1777)</article-title>
<alt-title alt-title-type="left-running-head">Peres et&#x20;al.</alt-title>
<alt-title alt-title-type="right-running-head">Revalidation of <italic>Mazama rufa</italic>
</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Peres</surname>
<given-names>Pedro H. F.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="corresp" rid="c001">&#x2a;</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1410456/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Luduv&#xe9;rio</surname>
<given-names>Douglas J.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Bernegossi</surname>
<given-names>Agda Maria</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1482272/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Galindo</surname>
<given-names>David J.</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1410565/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Nascimento</surname>
<given-names>Guilherme B.</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Oliveira</surname>
<given-names>M&#xe1;rcio L.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Sandoval</surname>
<given-names>Eluzai Dinai Pinto</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1410563/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Vozdova</surname>
<given-names>Miluse</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Kubickova</surname>
<given-names>Svatava</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1268203/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Cernohorska</surname>
<given-names>Halina</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Duarte</surname>
<given-names>Jos&#x00e9; Maur&#x00ed;cio Barbanti</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="corresp" rid="c001">&#x2a;</xref>
</contrib>
</contrib-group>
<aff id="aff1">
<label>
<sup>1</sup>
</label>Deer Research and Conservation Center (NUPECCE), S&#xe3;o Paulo State University (UNESP), <addr-line>Jaboticabal</addr-line>, <country>Brazil</country>
</aff>
<aff id="aff2">
<label>
<sup>2</sup>
</label>Faculty of Veterinary Medicine, National University of San Marcos (UNMSM), <addr-line>Lima</addr-line>, <country>Peru</country>
</aff>
<aff id="aff3">
<label>
<sup>3</sup>
</label>Medical School, University Center of Adamantina (UniFAI), <addr-line>Jaboticabal</addr-line>, <country>Brazil</country>
</aff>
<aff id="aff4">
<label>
<sup>4</sup>
</label>Veterinary Research Institute, <addr-line>Brno</addr-line>, <country>Czech Republic</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>
<bold>Edited by:</bold> <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/696685/overview">Fernando Marques Quintela</ext-link>, Taxa Mundi Institute, Brazil</p>
</fn>
<fn fn-type="edited-by">
<p>
<bold>Reviewed by:</bold> <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/715796/overview">Mara Cristina De Almeida</ext-link>, Universidade Estadual de Ponta Grossa, Brazil</p>
<p>
<ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/111166/overview">Matjaz Kuntner</ext-link>, National Institute of Biology (NIB), Slovenia</p>
</fn>
<corresp id="c001">&#x2a;Correspondence: Pedro H. Peres, <email>pedrof182@gmail.com</email>; Jos&#x00E9; Maur&#x00ED;cio Barbanti Duarte, <email>mauricio.barbanti@unesp.br</email>
</corresp>
<fn fn-type="other">
<p>This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Genetics</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>14</day>
<month>12</month>
<year>2021</year>
</pub-date>
<pub-date pub-type="collection">
<year>2021</year>
</pub-date>
<volume>12</volume>
<elocation-id>742870</elocation-id>
<history>
<date date-type="received">
<day>16</day>
<month>07</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>09</day>
<month>11</month>
<year>2021</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2021 Peres, Luduv&#xe9;rio, Bernegossi, Galindo, Nascimento, Oliveira, Sandoval, Vozdova, Kubickova, Cernohorska and Duarte.</copyright-statement>
<copyright-year>2021</copyright-year>
<copyright-holder>Peres, Luduv&#xe9;rio, Bernegossi, Galindo, Nascimento, Oliveira, Sandoval, Vozdova, Kubickova, Cernohorska and Duarte</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these&#x20;terms.</p>
</license>
</permissions>
<abstract>
<p>The red brocket deer <italic>Mazama americana</italic> Erxleben, 1777 is considered a polyphyletic complex of cryptic species with wide chromosomal divergence. Evidence indicates that the observed chromosomal divergences result in reproductive isolation. The description of a neotype for <italic>M. americana</italic> allowed its genetic characterization and represented a comparative basis to resolve the taxonomic uncertainties of the group. Thus, we designated a neotype for the synonym <italic>Mazama rufa</italic> Illiger, 1815 and tested its recognition as a distinct species from the <italic>M. americana</italic> complex with the analysis of morphological, cytogenetic and molecular data. We also evaluated its distribution by sampling fecal DNA in the wild. Morphological data from craniometry and body biometry indicated an overlap of quantitative measurements between <italic>M. rufa</italic> and the entire <italic>M.&#x20;americana</italic> complex. The phylogenetic hypothesis obtained through mtDNA confirmed the reciprocal monophyly relationship between <italic>M. americana</italic> and <italic>M. rufa</italic>, and both were identified as distinct molecular operational taxonomic units by the General Mixed Yule Coalescent species delimitation analysis. Finally, classic cytogenetic data and fluorescence in situ hybridization with whole chromosome painting probes showed <italic>M. rufa</italic> with a karyotype of 2n &#x3d; 52, FN &#x3d; 56. Comparative analysis indicate that at least fifteen rearrangements separate <italic>M. rufa</italic> and <italic>M. americana</italic> (<italic>sensu stricto</italic>) karyotypes, which confirmed their substantial chromosomal divergence. This divergence should represent an important reproductive barrier and allow its characterization as a distinct and valid species. Genetic analysis of fecal samples demonstrated a wide distribution of <italic>M. rufa</italic> in the South American continent through the Atlantic Forest, Cerrado and south region of Amazon. Thus, we conclude for the revalidation of <italic>M. rufa</italic> as a distinct species under the concept of biological isolation, with its karyotype as the main diagnostic character. The present work serves as a basis for the taxonomic review of the <italic>M. americana</italic> complex, which should be mainly based on cytogenetic characterization and directed towards a better sampling of the Amazon region, the evaluation of available names in the species synonymy and a multi-locus phylogenetic analysis.</p>
</abstract>
<kwd-group>
<kwd>Odocoileini</kwd>
<kwd>GMYC</kwd>
<kwd>bayesian phylogenetic inference</kwd>
<kwd>non-invasive sampling</kwd>
<kwd>scat detection dog</kwd>
<kwd>cytotaxonomy, molecular cytogenetics</kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="s1">
<title>Introduction</title>
<p>The genus <italic>Mazama</italic> <xref ref-type="bibr" rid="B108">Rafinesque, 1817</xref> is the most diversified of the tribe Odocoileini with nine species of medium-sized (10&#x2013;65&#xa0;kg), solitary forest deer with spiked antlers, and elusive behavior (<xref ref-type="bibr" rid="B98">Weber and Gonzalez, 2003</xref>; <xref ref-type="bibr" rid="B60">Merino and Rossi, 2010</xref>; <xref ref-type="bibr" rid="B35">Guti&#xe9;rrez et&#x20;al., 2015</xref>). The taxonomy within <italic>Mazama</italic> was historically based on morphological data and discordant arrangements, with 2&#x2013;11 species considered for the genus (<xref ref-type="bibr" rid="B2">Allen, 1915</xref>; <xref ref-type="bibr" rid="B4">Cabrera, 1960</xref>; <xref ref-type="bibr" rid="B11">Czernay, 1987</xref>). In this context, the red brocket deer <italic>Mazama americana</italic> (<xref ref-type="bibr" rid="B22">Erxleben, 1777</xref>), type species of the genus, had its delimitation varying depending on the study (<xref ref-type="bibr" rid="B2">Allen, 1915</xref>; <xref ref-type="bibr" rid="B4">Cabrera, 1960</xref>; <xref ref-type="bibr" rid="B11">Czernay, 1987</xref>) and there are currently 20 names considered synonymous (<xref ref-type="bibr" rid="B60">Merino and Rossi, 2010</xref>). Nevertheless, all taxonomic reviews were based on morphological data, and such characters are not informative in uncovering <italic>Mazama</italic> species diversity (<xref ref-type="bibr" rid="B16">Duarte et&#x20;al., 2008</xref>; <xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>; <xref ref-type="bibr" rid="B32">Gonz&#xe1;lez and Duarte, 2020</xref>). The retention of a morphological pattern among genetic lineages within the red brocket complex does not allow their differentiation and represents a challenge in the taxonomy of the group (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>).</p>
<p>The red brocket deer <italic>M. americana</italic> was identified as a complex of cryptic species because it does not represent a monophyletic group and presents great karyotypic diversity (<xref ref-type="bibr" rid="B16">Duarte et&#x20;al., 2008</xref>; <xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>; <xref ref-type="bibr" rid="B34">Guti&#xe9;rrez et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B40">Heckeberg, 2020</xref>). Two species previously classified as <italic>M. america</italic>na, <italic>Mazama temama</italic> (<xref ref-type="bibr" rid="B102">Kerr, 1972</xref>) and <italic>Mazama bororo</italic> (<xref ref-type="bibr" rid="B17">Duarte and Jorge, 1996</xref>), have already been recognized as distinct species based on their extreme chromosomal differences (<xref ref-type="bibr" rid="B47">Jorge and Benirsche, 1977</xref>; <xref ref-type="bibr" rid="B18">Duarte and Jorge, 2003</xref>). The cytogenetic evaluation carried out by <xref ref-type="bibr" rid="B17">Duarte and Jorge (1996)</xref> was the first study to reveal the cryptic diversity of <italic>M. americana</italic> when describing chromosomal variants in Brazil. After that two distinct chromosomal lineages were identified for the species and several cytotypes (geographically established karyotypes) were described (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>). One of these main lineages has a low chromosome number (2n &#x3d; 42&#x2013;45) and is located in the western Amazon. It is composed of cytotypes Rond&#xf4;nia (RO; 2n &#x3d; 42/43; FN &#x3d; 46) and Ju&#xed;na (JU; 2n &#x3d; 44/45; FN &#x3d; 48). The other main lineage presents a high chromosome number (2n &#x3d; 49&#x2013;53) and occurs in the eastern region of the Amazon and in the Atlantic Forest. This lineage is composed of the cytotypes Paran&#xe1; (PR; 2n &#x3d; 52/53; FN &#x3d; 56), Caraj&#xe1;s (CA; 2n &#x3d; 50/51; FN &#x3d; 54), Santar&#xe9;m (SA; 2n &#x3d; 50/51; FN &#x3d; 56) and Jari (JA; 2n &#x3d; 48/49; FN &#x3d; 56) (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>; <xref ref-type="fig" rid="F1">Figure&#x20;1</xref>).</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption>
<p>Distribution modelling (maximum entropy model, AUC &#x3d; 0.908, SD 0.018, <italic>p</italic>&#x20;&#x3c; 0.001) for the red brocket deer <italic>Mazama rufa</italic> (<xref ref-type="bibr" rid="B46">Illiger, 1815</xref>) compared to the IUCN geographic distribution of <italic>M. americana</italic> (<italic>sensu lato</italic>), cytotypes reference regions, type localities, and fecal sampling sites.</p>
</caption>
<graphic xlink:href="fgene-12-742870-g001.tif"/>
</fig>
<p>Captive breeding studies showed that hybrid progeny between animals with high chromosomal divergence showed total infertility, or a high degree of subfertility due to flaws in both male and female gametogenesis (<xref ref-type="bibr" rid="B10">Cursino et&#x20;al., 2014</xref>; <xref ref-type="bibr" rid="B82">Salviano et&#x20;al., 2017</xref>). Subfertility was also observed, to a lesser degree, among less divergent cytotypes (<xref ref-type="bibr" rid="B10">Cursino et&#x20;al., 2014</xref>; <xref ref-type="bibr" rid="B82">Salviano et&#x20;al., 2017</xref>). The reproductive fitness of these same hybrids, however, must be severely aggravated by the chromosomal imbalance observed in sperm (<xref ref-type="bibr" rid="B30">Galindo et&#x20;al., 2021</xref>). Thus, in a conservative taxonomic approach, the greatest chromosomal divergence among populations (&#x3e;3 chromosome pairs) represented a post-zygotic reproductive barrier. This indicates the presence of two species in the <italic>M. americana</italic> complex correspondent to the two described lineages (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>; <xref ref-type="bibr" rid="B10">Cursino et&#x20;al., 2014</xref>; <xref ref-type="bibr" rid="B82">Salviano et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B5">Carranza et&#x20;al., 2018</xref>). In a less conservative taxonomic approach, the subfertility observed among populations with a minor divergence (1 or 2 chromosome pairs) would already represent isolation, leading to the hypothesis that each cytotype could correspond to a distinct species (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>; <xref ref-type="bibr" rid="B10">Cursino et&#x20;al., 2014</xref>; <xref ref-type="bibr" rid="B82">Salviano et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B5">Carranza et&#x20;al., 2018</xref>; <xref ref-type="bibr" rid="B30">Galindo et&#x20;al., 2021</xref>).</p>
<p>Cytogenetic information is supported by molecular phylogeny data, indicating that the <italic>M. americana</italic> complex is not monophyletic (<xref ref-type="bibr" rid="B16">Duarte et&#x20;al., 2008</xref>; <xref ref-type="bibr" rid="B39">Heckeberg et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B34">Guti&#xe9;rrez et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>; <xref ref-type="bibr" rid="B40">Heckeberg, 2020</xref>). The two chromosomal lineages were recovered in distinct well-supported clades (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>), and clustered among other species (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>). The lineage with the higher diploid number was recovered in a proper clade and the one with the lower diploid number was also monophyletic and was recovered as a sister group of <italic>M. bororo</italic> (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>). Nevertheless, the reciprocal monophyly among less divergent cytotypes within each lineage (Paran&#xe1; x Caraj&#xe1;s and Ju&#xed;na x Rond&#xf4;nia) was not properly tested (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>; <xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>).</p>
<p>Given that no type specimen was never indicated for <italic>M. americana</italic> and the morphological information is not informative for the taxon, a neotype for the species was designated and cytogenetic analyses were conducted (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>). The animal presented a distinct karyotype (2n &#x3d; 45 and FN &#x3d; 50), divergent from all cytotypes known so far. This finding raised the need to review the taxonomic status of names currently considered synonymous of <italic>M. americana</italic> towards the different genetic lineages observed for the species (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>). The oldest available name in the timeline of the <italic>M. americana</italic> synonymy is <italic>Cervus rufus</italic> <xref ref-type="bibr" rid="B46">Illiger 1815</xref> (<xref ref-type="bibr" rid="B60">Merino and Rossi, 2010</xref>). This species was originally described by <xref ref-type="bibr" rid="B3">Azara (1801)</xref> in Paraguay as the <italic>guazupit&#xe1;</italic> deer and should correspond to the geographic occurrence of Paran&#xe1; cytotype in the south of <italic>M. americana</italic> distribution. Its formal description was made by <xref ref-type="bibr" rid="B46">Illiger (1815)</xref> based on the morphological description by <xref ref-type="bibr" rid="B3">Azara (1801)</xref>, and later transferred by <xref ref-type="bibr" rid="B55">Lydekker (1898)</xref> to the genus <italic>Mazama,</italic> which resulted in the binomial <italic>Mazama&#x20;rufa</italic>.</p>
<p>Most of the mammals described by F&#xe9;lix de Azara did not have a specimen sent to Europe, and from those who had, few survived to serve as type material (<xref ref-type="bibr" rid="B41">Hershkovitz, 1989</xref>; <xref ref-type="bibr" rid="B95">Voss et&#x20;al., 2009</xref>; <xref ref-type="bibr" rid="B70">Pereira, 2013</xref>). The designation of neotypes from species described from Azara&#x2019;s observations has been common in literature and were essential in the organization of taxonomic nomenclature of different taxa as the case of oryzomyine rodents (<xref ref-type="bibr" rid="B104">Musser et&#x20;al., 1998</xref>), opossums from the genus <italic>Thylamys</italic> (<xref ref-type="bibr" rid="B95">Voss et&#x20;al., 2009</xref>) and felids from the genus <italic>Leopardus</italic> (<xref ref-type="bibr" rid="B105">Nascimento et&#x20;al., 2020</xref>). Therefore, the indication of a neotype to anchor the name <italic>M. rufa</italic> is essential to clarify its taxonomic status concerning the <italic>M. americana</italic> complex. In particular, the taxonomic review of <italic>Mazama</italic> would be favored with the collection of present topotypes that provides living tissue for cytogenetic analysis. This would allow us to verify its correlation with the Paran&#xe1; cytotype, the neotype specimen and elucidate the species delimitation towards <italic>M. americana</italic> complex.</p>
<p>Thus, the present study sought to 1) collect a specimen to be indicated as a neotype of <italic>Mazama rufa</italic>; 2) perform a morphological and cytogenetic comparison between <italic>M. rufa</italic> and the newly described <italic>M. americana</italic> neotype; 3) elucidate <italic>M. rufa</italic> species delimitation towards a set of specimens from the <italic>M. americana</italic> complex (<italic>sensu lato</italic>) and other <italic>Mazama</italic> species; 4) Estimate the geographic distribution of <italic>M. rufa</italic> and its potential conservation status. These efforts were based on an integrative taxonomic approach that considered the general Lineage Species Concept (<xref ref-type="bibr" rid="B12">De Queiroz, 2007</xref>), and the operational biological (<xref ref-type="bibr" rid="B59">Mayr, 1942</xref>) and phylogenetic (<xref ref-type="bibr" rid="B9">Cracraft, 1983</xref>) concepts based on morphological, cytogenetic and molecular&#x20;data.</p>
</sec>
<sec sec-type="materials|methods" id="s2">
<title>Materials and Methods</title>
<sec id="s2-1">
<title>Samples</title>
<sec id="s2-1-1">
<title>Type Locality and Neotype Collection</title>
<p>The description of <italic>Mazama rufa</italic> (<xref ref-type="bibr" rid="B46">Illiger, 1815</xref>) did not indicate nor deposit a holotype and there were no details about the collection site (<xref ref-type="bibr" rid="B3">Azara, 1801</xref>). The studies of Azara took place in Paraguay, along the Paraguay River, located in the R&#xed;o La Plata Basin (<xref ref-type="bibr" rid="B70">Pereira, 2013</xref>). Two unsuccessful scientific expeditions were carried out in 2016 to collect the neotype in the region of Asunci&#xf3;n, urban reference on where the naturalist was based. This city is now the capital of Paraguay, a metropolis complex with more than 500,000 inhabitants with a surrounding region that is heavily altered by anthropogenic impacts. There were indications that hunting pressure in the region remains intense, both for cultural reasons and for obtaining animal protein. Several local actors (e.g., cowhands and indigenous people) have long reported the absence of the red brocket deer in the region. Thus, an alternative location was sought, as close as possible, with preserved forest habitat, evidence of the species&#x2019; presence, and no evident geographical barrier concerning the original type location.</p>
<p>The region of the Brazilian city of Foz do Igua&#xe7;u, on the Brazil-Paraguay border, 290&#xa0;km from Asunci&#xf3;n, was selected as the target location to collect a specimen. The region comprises the Igua&#xe7;u National Park, a continuous block of 185,000&#xa0;ha of preserved Atlantic Forest, on the banks of the Paran&#xe1; River, the main river of the R&#xed;o de La Plata Basin, with direct connection with Paraguay River. An adult female, run over on BR 469, a few meters from Igua&#xe7;u National Park, was indicated as a neotype in this&#x20;study.</p>
</sec>
<sec id="s2-1-2">
<title>Animal Samples</title>
<p>The present work had access to a set of individuals (<italic>n</italic>&#x20;&#x3d; 53) that allowed a broad analysis of brocket deer species of <italic>Mazama</italic>. The set consisted of samples from <italic>Mazama nana</italic> (<italic>n</italic>&#x20;&#x3d; 11); <italic>M. bororo</italic> (<italic>n</italic>&#x20;&#x3d; 9); <italic>M. temama</italic> (<italic>n</italic>&#x20;&#x3d; 4) and samples of various cytotypes within the <italic>M. americana</italic> complex (<italic>n</italic>&#x20;&#x3d; 29). All analyzed specimens are preserved in the Deer Research and Conservation Center (NUPECCE) Museum, Tissue and Cell Banking at S&#xe3;o Paulo State University, Jaboticabal city, Brazil. The samples and information came from animals collected directly from nature, injured animals received for treatment, or samples collected from animals in public and private breeding sites with wild origin (<xref ref-type="fig" rid="F1">Figure&#x20;1</xref>). The neotypes specimens were present in all datasets (morphology, cytogenetics, molecular), but not all samples were present in all datasets. The information of which sample composed each dataset is detailed in the table presented in&#x20;SM01.</p>
</sec>
<sec id="s2-1-3">
<title>Fecal Samples</title>
<p>Non-invasive genetic sampling was conducted with the collection of fecal samples, which focused on several forest habitats in the central region of South America, more specifically the Brazilian biomes of the Atlantic Forest, Cerrado, Pantanal and southern Amazon region. The collection was carried out in 20 locations and samples from 10 other locations used in previous studies were added (<xref ref-type="bibr" rid="B20">Duarte et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B67">Oliveira et&#x20;al., 2019</xref>, <xref ref-type="bibr" rid="B66">2020</xref>) (<xref ref-type="fig" rid="F1">Figure&#x20;1</xref>; SM-02). The collection of fecal samples was performed with the support of a detection dog trained to find feces from all deer in the study region. Altogether, 107&#xa0;days of field work were performed, with an average of 4&#xa0;h of daily effort. The samples were preserved in absolute ethanol at the ratio of 1 volume of feces to 4 volumes of ethanol (approximately 40&#xa0;ml) and all had their geographic coordinates&#x20;noted.</p>
</sec>
</sec>
<sec id="s2-2">
<title>Cytogenetic Data</title>
<sec id="s2-2-1">
<title>Sample Preparation and Analysis</title>
<p>For each animal accessed, either alive or recently slaughtered, a skin biopsy of the inguinal region was collected and frozen in liquid nitrogen as described for leucocytes by <xref ref-type="bibr" rid="B19">Duarte et&#x20;al. (1999)</xref> in order to obtain chromosomal preparations from fibroblast culture (<xref ref-type="bibr" rid="B93">Verma and Babu, 1995</xref>). Metaphasic chromosomes were subjected to conventional Giemsa staining, C-banding by barium hydroxide solution (<xref ref-type="bibr" rid="B87">Sumner, 1972</xref>), Ag-RON silver nitrate staining (<xref ref-type="bibr" rid="B44">Howell and Black, 1980</xref>) and G-banding using standard trypsin/Giemsa treatment (<xref ref-type="bibr" rid="B85">Seabright, 1971</xref>). We classified the chromosomes according to the ratio of arms as metacentric, submetacentric, or acrocentric (<xref ref-type="bibr" rid="B52">Levan et&#x20;al., 1969</xref>). Relative length (CR) was used to organize chromosome pairs into group A (large two-armed chromosomes, CR &#x2265; 6%), group C (small two-armed chromosomes, CR &#x3c; 6%), group D (large one-armed chromosomes, CR &#x2265; 5%), group E (small one-armed chromosomes, CR &#x3c; 5%), and group B (B chromosomes, CR &#x3c; 1.5%) (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#x00F3;n et al., 2020</xref>). We assembled the G and C-banding graphical representation with the Adobe Illustrator software.</p>
</sec>
<sec id="s2-2-2">
<title>Fluorescent <italic>in situ</italic> Hybridization</title>
<p>Fluorescent <italic>in situ</italic> hybridization (FISH) was performed using bovine whole chromosome painting (WCP) probes on karyotypes of the <italic>M. rufa</italic> and <italic>M. americana</italic> (<italic>sensu stricto</italic>) neotypes, in a male of the Paran&#xe1; cytotype (T308), and another male of the Caraj&#xe1;s cytotype (T166) of the <italic>M. americana</italic> complex (<italic>sensu lato</italic>). Painting probes derived from cattle were selected considering their proven efficiency in karyotypic studies of the family Cervidae (<xref ref-type="bibr" rid="B28">Frohlich et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B30">Galindo et&#x20;al., 2021</xref>). Whole chromosomes were isolated by microdissection in the PALM Microlaser system (Carl Zeiss MicroImaging GmbH, Munich, Germany) (<xref ref-type="bibr" rid="B51">Kubickova et&#x20;al., 2002</xref>) or by flow sorting using MoFlo XDP Cell Sorter (Beckman Coulter, Indianapolis, IN, United&#x20;States) (<xref ref-type="bibr" rid="B28">Frohlich et&#x20;al., 2017</xref>). For amplification and labeling of chromosomal DNA, a DOP-PCR (degenerate oligonucleotide primed polymerase chain reaction) reaction (<xref ref-type="bibr" rid="B90">Telenius et&#x20;al., 1992</xref>) was performed followed by a second PCR with Green-dUTP or Orange-dUTP (Abbott Park, IL, United&#x20;States) (<xref ref-type="bibr" rid="B51">Kubickova et&#x20;al., 2002</xref>). FISH was performed as presented in <xref ref-type="bibr" rid="B96">Vozdova et&#x20;al. (2019)</xref>. Hybridization signals were examined using Zeiss Axio Image Z2 fluorescent microscope (Carl Zeiss Microimaging GmbH, Jena, Germany), equipped with appropriate fluorescent filters, and images were captured using the Metafer Slide Scanning System (MetaSystems, Altlussheim, Germany). Images were analyzed using ISIS3 software (MetaSystems, Altlussheim, Germany).</p>
</sec>
</sec>
<sec id="s2-3">
<title>Morphological Data</title>
<sec id="s2-3-1">
<title>Neotype Morphology Description</title>
<p>The animal proposed as a neotype for <italic>Mazama rufa</italic> (<xref ref-type="bibr" rid="B46">Illiger, 1815</xref>) was identified as T385 and had its morphology described qualitatively and quantitatively. The specimen was photographed and 14 external body characters (body biometry) were measured using a pendular scale, measuring tape, and common caliper (0.1&#xa0;mm accuracy) (SM-03). After bone maceration, the skull was photographed at different angles and measured according to the standard of cervid cranial measurements proposed by <xref ref-type="bibr" rid="B77">Rees (1969)</xref> and <xref ref-type="bibr" rid="B15">Driesch (1976)</xref> with a digital caliper (precision 0.01&#xa0;mm) (SM-03). The entire skin was removed and treated with a tanning solution to desiccate the material. Aspects of general coat color, chromogenic fields of the body, pigment band patterns in hair from different regions of the body, hair length in different regions of the body, and the occurrence of anteverted hair bands and rounded hair tuft in the tarsal region were examined. The chromogenic fields of the head were also analyzed according to the pattern of <xref ref-type="bibr" rid="B42">Hershkovitz (1982)</xref>. This qualitative description performed for the <italic>M. rufa</italic> neotype (T385) was compared with the amended description of the <italic>M. americana</italic> neotype (T358) (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>).</p>
</sec>
<sec id="s2-3-2">
<title>Morphometric Analyses</title>
<p>External body and skull measurements formed two distinct datasets&#x2014;body biometry and craniometry. Regarding the 42 animals with morphometric data, 27 (64%) composed the body biometry dataset and 32 (76%) the craniometry dataset, with 17 superimposed in the two datasets (SM-03). To assess the similarity among individuals and a possible discrimination of species and cytotypes, a principal component analysis (PCA) based on the correlation matrix between the variables was performed. The first two eigenvectors with the highest percentage of accumulated variance were used to build the graphs. The size of the confidence ellipses indicates the degree of grouping of the evaluated groups based on a normal distribution considering a coefficient of 0.95. All analyzes were performed using Software R (<xref ref-type="bibr" rid="B75">R Core Team, 2020</xref>). In addition, we performed UPGMA cluster analysis with Euclidean distance and 1,000 bootstrap using the &#x201c;Paleontological Statistics&#x201d; PAST program (<xref ref-type="bibr" rid="B37">Hammer et&#x20;al., 2001</xref>).</p>
</sec>
</sec>
<sec id="s2-4">
<title>Molecular Data</title>
<sec id="s2-4-1">
<title>Tissue and Blood DNA Extraction, Amplification and Sequencing</title>
<p>We followed the phenol-chloroform purification protocol described in <xref ref-type="bibr" rid="B83">Sambrook et&#x20;al. (1989)</xref> for DNA extraction of tissue fragments (skin and spleen) and eventually leukocyte ring. Partial genes, Cytochrome-b (Cytb; 978 bp), NADH dehydrogenase subunit 5 (ND5; 1128&#xa0;bp), and control region (Dloop; 454&#xa0;bp) were amplified and sequenced using primers described in the literature that can be found together with detailed protocols in SM-04. All amplicons were purified using the Wizard<sup>&#xae;</sup> SV gel and PCR Clean-Up System kit (Promega) and sequenced in both directions in an ABI 3730XL automated sequencer. The forward and reverse sequences were exported to the BioEdit 7.2.6 program (<xref ref-type="bibr" rid="B36">Hall, 1999</xref>) and had their electropherograms visually reviewed for quality control and assembly of a consensus sequence of each sample. All sequences produced from tissue samples in this study were deposited in Genbank with accession number MZ488858 to MZ488910 (SM01).</p>
</sec>
<sec id="s2-4-2">
<title>Molecular Alignment, Composition, and Model Selection</title>
<p>The tissue dataset was composed by sequences from 38 animals from this study and additional sequences obtained from mitogenomes deposited in GenBank belonging to <italic>M. americana</italic> and <italic>Odocoileus virginianus</italic>. The species <italic>Rangifer tarandus</italic>, <italic>Alces alces</italic> and <italic>Capreolus pygargus</italic> were also obtained from GenBank and were used as outgroup in the phylogenetic analyses (SM01). The consensus sequences of each amplicon and the sequences obtained from GenBank were aligned on the Mafft online server (<xref ref-type="bibr" rid="B48">Katoh et&#x20;al., 2018</xref>), reviewed and trimmed using the Bioedit 7.2.6 software. The alignments from each region were then concatenated using the Mesquite 3.61 (<xref ref-type="bibr" rid="B56">Maddison and Maddison, 2019</xref>) resulting in a final alignment of 2560&#xa0;bp. Polymorphism and saturation were characterized using MEGA X and tests by <xref ref-type="bibr" rid="B100">Xia et&#x20;al. (2003)</xref> using the DAMBE 7.2 software (<xref ref-type="bibr" rid="B99">Xia, 2018</xref>). These are presented in SM-04. The selection of the best evolutionary model was determined by data partition analysis with the Partition Finder 2 software on the CIPRES Science Gateway online platform (<xref ref-type="bibr" rid="B62">Miller et&#x20;al., 2011</xref>). Data partitions were tested by mtDNA region and by the Cytb and ND5 codon position. The best scheme was selected among all possible combinations through the smallest Bayesian Inference Criterion (BIC) value. The selection of the best model for each subset of the scheme was also selected through the lowest BIC value among 40 possible evolutionary models in order to be applied into the BEAST package (SM-04).</p>
</sec>
<sec id="s2-4-3">
<title>Molecular Phylogenetic and Species Delimitation Analysis</title>
<p>The phylogenetic analysis was performed using the Bayesian Inference (BI) criterion in the BEAST 1.10.4 software package, running parameters implemented through BEAUti, and the analysis performed through the CIPRES Science Gateway online server. The Monte Carlo Markov Chains analysis included 10 million generations, sampled every 1,000 generations performed in three independent runs. Data were combined using the Log Combiner app, the best tree were summarized with a 30% burn-in, and the values of posterior probability (PP) node support were accessed with Tree Annotator. We verified the convergence of the analysis with Tracer v.1.7, considering satisfactory when it presented ESS (Estimated Sample Size) values greater than&#x20;200.</p>
<p>We used the General Mixed Yule Coalescent (GMYC) method to identify molecular operational taxonomic units (MOTUs) through the SPLITS software package (<xref ref-type="bibr" rid="B63">Monaghan et&#x20;al., 2009</xref>) in the R program. For this analysis, we used the phylogenetic hypothesis represented by the ultrametric BI-tree considering the ingroup. The GMYC model hypothesis was tested towards single and multiple thresholds. The hypothesis that the GMYC and null models were different was not rejected when presenting <italic>p</italic>&#x20;&#x3c;&#x20;0.05.</p>
</sec>
</sec>
<sec id="s2-5">
<title>Distribution Data</title>
<sec id="s2-5-1">
<title>Fecal DNA Analysis</title>
<p>Genetic species identification was necessary due to the presence of sympatric deer species in the fecal sampling sites (<italic>Mazama gouazoubira, Mazama nemorivaga, Ozotoceros bezoarticus</italic>) in which fecal morphological identification is not a valid option (<xref ref-type="bibr" rid="B8">Costa et&#x20;al., 2017</xref>). Furthermore, the differentiation between the <italic>M. americana</italic> complex and <italic>M. rufa</italic> was never tested and should also rely on genetic identification. Fecal DNA was extracted using the QIAmp Fast DNA Stool MiniKit (QIAGEN) kit and all lab procedures were made in an exclusive forensic DNA room encompassing blank controls for contamination detection. Species identification was conducted with a multiple small mtDNA fragment (&#x223c;250&#xa0;bp) amplification and sequencing strategy that included five regions, internal to the previously sequenced amplicons from the tissue dataset. The protocol proposed by <xref ref-type="bibr" rid="B33">Gonz&#xe1;lez et&#x20;al. (2009)</xref> was used to sort out <italic>M. americana</italic> complex samples from the other species. After that, we selected 2&#x2013;3&#x20;<italic>M. americana</italic> complex fecal samples per site to conduct <italic>M. rufa</italic> identification. In this step, the complete five mtDNA regions were sequenced and the final alignment (1103&#xa0;bp) was analyzed in a BI phylogeny using our tissue dataset as reference sequences. All sequences produced from fecal samples in this study were deposited in Genbank with accession number MZ521085 to MZ521234 (SM04).</p>
</sec>
<sec id="s2-5-2">
<title>Distribution Modeling</title>
<p>In order to generate distribution models, we used all fecal samples from sites where <italic>M. rufa</italic> was identified as the red brocket present to compose our occurrence records (<italic>n</italic>&#x20;&#x3d; 49; SM-02). We used six previously interpolated environmental variables at 30&#x20;arc-seconds (approx. 1&#xa0;km) resolution and clipped them to our modeling scope. Our modeling scope consisted of a 1000&#xa0;km buffer around our occurrence records and constrained by IUCN <italic>M. americana</italic> geographical distribution plus a 50&#xa0;km buffer. The variables we selected are recognized to be highly influential in neotropical forest deer distributions (<xref ref-type="bibr" rid="B20">Duarte et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B67">Oliveira et&#x20;al., 2019</xref>, <xref ref-type="bibr" rid="B66">2020</xref>), these were: percentage of tree cover (<xref ref-type="bibr" rid="B38">Hansen et&#x20;al., 2003</xref>), altitude (<xref ref-type="bibr" rid="B92">Valeriano, 2008</xref>), slope, temperature seasonality (BIO4), annual precipitation (BIO12) and precipitation of the driest month (BIO14) (<xref ref-type="bibr" rid="B43">Hijmans et&#x20;al., 2005</xref>). To ensure these variables are not correlated in our modeling scope we performed a Pearson&#x2019;s correlation test to confirm <italic>r</italic>&#x20;&#x3c;&#x20;0.8.</p>
<p>We performed the analysis using Maxent software version 3.4.1 (<xref ref-type="bibr" rid="B73">Phillips and Schapire, 2004</xref>; <xref ref-type="bibr" rid="B71">Phillips et&#x20;al., 2006</xref>). The model was &#x201c;trained&#x201d; using 70% of the occurrence records and tested with the remaining 30% of the records (<xref ref-type="bibr" rid="B69">Pearson, 2010</xref>). The occurrence records were sampled using the bootstrap method, with ten random partitions and substitutions. We assessed each species average model using the area under the curve (AUC), calculation of the omission error, and binomial test for comparison of two proportions (<xref ref-type="bibr" rid="B24">Fielding and Bell, 1997</xref>; <xref ref-type="bibr" rid="B21">Elith et&#x20;al., 2006</xref>; <xref ref-type="bibr" rid="B72">Phillips and Dud&#xed;k, 2008</xref>).</p>
</sec>
</sec>
</sec>
<sec sec-type="results" id="s3">
<title>Results</title>
<sec id="s3-1">
<title>Neotype Designation and Species Diagnosis</title>
<sec id="s3-1-1">
<title>Amended description of <italic>Mazama rufa</italic> (<xref ref-type="bibr" rid="B46">Illiger, 1815</xref>) (MAMMALIA, CERVIDAE):</title>
<p>Predominantly reddish-brown at laterals, with blackened areas in the head region, neck, thorax, distal regions of hind, and forelimbs. Lumbar line, darker than the predominant bright reddish coloration. Posterior region of the hips and tail dorsum with reddish-brown color. Whitish Inguinal region whitish as well as its inner thigh. Presence of a tarsal hair tuft. Whitish tail in ventral region, while reddish in dorsal region. Color of the lateral area of limbs well-defined, bright reddish in the proximal area and dark brown in the distal part, as well in the dorsal line and rostral area. White inner thigh and inguinal region. Proximal region of hind limbs reddish brown medially. Presence of tarsal hair tuft. Longer hair in the basal region of the ear. Anteverted hair band at the nape of the neck. Sides of the head with brown coloration. Small, inclined ears, white auricular border and blackened posterior auricular border. Whitish anterobasal auricular patch and brown reddish posterobasal auricular patch. Outer auricular surface blackish brown. Yellowish-red upper orbital band. Inferior orbital band with the same rostral coloration, over a yellow band. Absence of superciliary spot. Nasal patch present, followed by a dark lateral rostral band and pale lateral rostral band. Mental white patch. Reddish brown mandibular band. Buccal patch present. Presence of white gular patch. Light brown neck at the ventral region. Skull with shallow lacrimal fossa not deepened, two lacrimal foramina internally to the edge of the orbit, separated from each other. Vomerine septum typical of Capreolinae. Small tympanic bulla. Short inclined pedicles and rectangular pre-orbital region (<xref ref-type="fig" rid="F2">Figure&#x20;2</xref>).</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption>
<p>Images of the female specimen designated as the <italic>Mazama rufa</italic> neotype (T385) (<xref ref-type="bibr" rid="B46">Illiger, 1815</xref>) (Artiodactyla: Cervidae). <bold>(A)</bold> lateral view of the body; <bold>(B)</bold> detailed view of the head; <bold>(C)</bold> dorsal, ventral, left lateral, and right lateral view of the skull. Material deposited at the NUPECCE museum identified under voucher NPC118.</p>
</caption>
<graphic xlink:href="fgene-12-742870-g002.tif"/>
</fig>
<p>
<italic>Synonymy</italic>: <italic>Cervus gouazoupita</italic> G. <xref ref-type="bibr" rid="B25">Fischer, 1814</xref>:465<italic>.</italic> Type locality Paraguay; based on <xref ref-type="bibr" rid="B3">Azara (1801)</xref> <italic>Troisi&#xe8;me cerf ou Gouazoupita</italic>; <italic>Mazama pita</italic> <xref ref-type="bibr" rid="B108">Rafinesque, 1817</xref>:363. Type locality Paraguay; based on <xref ref-type="bibr" rid="B3">Azara (1801)</xref> <italic>Troisi&#xe8;me cerf ou Gouazoupita</italic>.</p>
<p>
<italic>Amended diagnosis.</italic>&#x2014;The amended diagnosis of <italic>Mazama rufa</italic> adds to the original description (<xref ref-type="bibr" rid="B3">Azara, 1801</xref>) other approaches different from morphology. Chromosomic diploid number ranging from 52 to 53, fundamental number of 56, one pair of submetacentric autosomes, 48 acrocentric autosomes and multiple sexual system XY1Y2 due to an X-autosomal fusion. Thus, differing from <italic>M. americana</italic> (<xref ref-type="bibr" rid="B22">Erxleben, 1777</xref>), type species of the genus <italic>Mazama</italic> that showed chromosomic diploid number of 45 and fundamental number&#x20;51.</p>
<p>
<italic>Neotype</italic> (<italic>T385</italic>)<italic>. &#x2014;</italic> Avenida das Cataratas, n&#xfa;mero 2,264. BR 469. Foz de Igua&#xe7;u, Paran&#xe1;, Brazil (25&#xba;36&#x2032;22&#x2033;S, 54&#xba;29&#x2032;54&#x2033;W; datum WGS84). Deposit number: NPC118; full skull, post skull, taxidermied skin; live cells and tissues. Karyotype: 2n &#x3d; 52, FN &#x3d; 56 (female). Mithocondrial DNA sequences deposited in GenBank under accession numbers: MZ488852; MZ488925; MZ488894. Specimen deposited in Museum, Tissue and Cell Bank of the Deer Research and Conservation Center (NUPECCE) of the Faculty of Agricultural and Veterinary Sciences of the S&#xe3;o Paulo State University (UNESP), Jaboticabal campus, Brazil.</p>
</sec>
</sec>
<sec id="s3-2">
<title>Cytogenetic Data</title>
<p>The <italic>M. rufa</italic> neotype presented a karyotype constitution of 2n &#x3d; 52 and FN &#x3d; 56. The chromosome measurement by relative length classified pair 1 belonging to Group A, pairs 2 to 4 to Group D, pairs 5 to 25 to Group E. The X chromosome was submetacentric (<xref ref-type="fig" rid="F3">Figure&#x20;3</xref>). Two to six supernumerary chromosomes (Bs) were observed at metaphases. This autosomal pattern observed for the neotype corresponds to the Paran&#xe1; cytotype of <italic>M. americana</italic> (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>), which from now on corresponds to the species <italic>M. rufa</italic>. Thus, the description of the sex chromosomes was also performed for a male specimen (T308). The sexual system was XY1Y2 due to an X-autosomal fusion. The male presented a karyotypic constitution of 2n &#x3d; 53, FN &#x3d; 56, Y1 was the smallest chromosome, and Y2 a medium acrocentric.</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption>
<p>
<italic>Mazama rufa</italic> neotype karyotype (2n &#x3d; 52 &#x2b; 2&#x2013;6&#xa0;B, FN &#x3d; 56). Conventional Giemsa staining, schematic representation of G and C banding, and homologies to <italic>Mazama americana</italic> (MAM) chromosomes are displayed in a left-to-right direction. The gray squares indicate the homologies with MAM chromosomes. The letters a, b, c, and d represent regions of the chromosome that were homologous to <italic>M. rufa</italic>. For the submetacentric pairs MAM1 and MAM2: a &#x3d; p arm, b &#x3d; proximal q arm, c &#x3d; medial q arm, and d &#x3d; terminal q arm. For acrocentric pair MAM3: a &#x3d; proximal region, b &#x3d; medial region, and c &#x3d; terminal region. MAM4 and MAMY2: a &#x3d; proximal and b &#x3d; terminal region. The red arrows indicate the position of the nucleolus organizer regions.</p>
</caption>
<graphic xlink:href="fgene-12-742870-g003.tif"/>
</fig>
<p>C-banding showed constitutive heterochromatin blocks in the centromeric region of all autosomal chromosomes, two interstitial bands in the q arm of pairs 1 and 3, and three discrete interstitial bands in pair 2. The sex chromosome X had a strong interstitial band in the proximal region of the q arm and a discrete interstitial band in the distal region of the same arm. Chromosome Y<sub>1</sub> is completely euchromatic and chromosome Y<sub>2</sub> has a discrete interstitial band in the medial region of its arm. The B chromosomes showed variation in their heterochromatin content. While some B were completely heterochromatic, others had only interstitials heterochromatin bands. The nucleolus organizer regions were localized in the distal region of the long arms of both chromosomes from pairs 5 and 6. <xref ref-type="fig" rid="F3">Figure&#x20;3</xref> shows the graphical representation of the G and C-banded <italic>M. rufa</italic> chromosomes, which is of considerable importance in comparative cytogenetics.</p>
<p>The comparative cytogenetics analysis with G-band and cattle (BTA) WCP probes (<xref ref-type="fig" rid="F4">Figure&#x20;4</xref>) showed that <italic>M. rufa</italic> (MRU) and <italic>M. americana</italic> (<italic>sensu stricto</italic>) (MAM, 2n &#x3d; 45, FN &#x3d; 51) accumulated different rearrangements during their karyotype evolution. The p arm of the submetacentric MRU1 is homologous to the proximal region of MAM4 (<xref ref-type="fig" rid="F3">Figure 3</xref>, 4a), and the q arm to the proximal region of MAM3 (<xref ref-type="fig" rid="F3">Figure 3</xref>, 3a) and to the MAM5 chromosome. The large acrocentric MRU2 showed homologies with the terminal region of MAM1 (<xref ref-type="fig" rid="F3">Figure 3</xref>, 1d) and the distal region of MAM4 (<xref ref-type="fig" rid="F3">Figure 3</xref>, 4b). The MRU3 pair corresponded to the distal regions of MAM1 (<xref ref-type="fig" rid="F3">Figure 3</xref>, 1c) and MAM2 (<xref ref-type="fig" rid="F3">Figure 3</xref>, 2d) and to the proximal region of MAM3 (<xref ref-type="fig" rid="F3">Figure 3</xref>, 3b). MRU4 and MRU12 are homologous to the proximal region of the MAM1 q arm (<xref ref-type="fig" rid="F3">Figure 3</xref>, 1b) and to the p arm (<xref ref-type="fig" rid="F3">Figure 3</xref>, 1a), respectively. MRU5 corresponded to the distal region of MAM3 (<xref ref-type="fig" rid="F3">Figure 3</xref>, 3c). MRU8 and MRU15 is homologous to the proximal region of the q arm of MAM2 (<xref ref-type="fig" rid="F3">Figure 3</xref>, 2b and 2c). Finally, acrocentric pairs MRU 6, 7, 9, 11, 13, 14 and MRU 16 to 25 were homologous to one MAM acrocentric chromosome.</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption>
<p>FISH results demonstrating some of chromosomal rearrangements differences between the species <italic>Mazama rufa</italic> (MRU) and <italic>Mazama americana</italic> (MAM) using cattle chromosome painting probes (indicated on the right). The dashed white lines indicate the position of centromeres.</p>
</caption>
<graphic xlink:href="fgene-12-742870-g004.tif"/>
</fig>
<p>The composition of sex chromosomes also differed between the two species. Both species have a multiple sex chromosome system XY<sub>1</sub>Y<sub>2</sub> formed by X-autosomal fusions during the divergence from a common ancestor. However, the distal parts of X and Y<sub>2</sub> were not homologous between the two species. In <italic>M. rufa</italic>, the distal regions of X and Y<sub>2</sub> correspond to the p arm of MAM2 (<xref ref-type="fig" rid="F3">Figures 3</xref>, 2a), while the distal part of X and Y<sub>2</sub> of <italic>M. americana</italic> corresponds to MRU10. The Y<sub>2</sub> chromosomes of these species were partially homologous, demonstrating that the first X-autosomal fusion probably occurred in an ancestral karyotype of the group and the second fusion was formed later in each species (<xref ref-type="fig" rid="F3">Figure&#x20;3</xref>). Thus, at least 15 rearrangements separate <italic>M. rufa</italic> and <italic>M. americana</italic> karyotypes.</p>
<p>Furthermore, the <italic>M. americana</italic> Caraj&#xe1;s cytotype (2n &#x3d; 50, FN &#x3d; 54) showed the fixation of a tandem fusion between two acrocentric chromosomes of <italic>Mazama rufa</italic>. This fusion occurred between MRU5 and MRU8, forming CA3, while the other chromosomes corresponded between these species. The location of the hybridization signals for each bovine probe used is specified in SM-05.</p>
</sec>
<sec id="s3-3">
<title>Morphological Data</title>
<p>In the body biometric dataset, none of the variables presented extreme outliers (&#x3e;3SD in relation to the mean) and the total proportion of lost data was 5.16%. In the craniometry dataset, only one variable for a single animal showed extreme outlier and was removed, and the total proportion of lost data was 4.08%. Descriptive analyses (mean, standard deviation, maximum and maximum) of both datasets are presented in SM-03.</p>
<p>The UPGMA distance tree from the two morphometry datasets subdivided the specimens into two groups (<xref ref-type="fig" rid="F5">Figure&#x20;5</xref>). The first group corresponds to the <italic>M. americana</italic> complex (<italic>sensu lato</italic>), including the neotype from French Guiana, the neotype proposed for <italic>M. rufa</italic> and specimens from Brazilian cytotypes. The second group was represented by the <italic>M. nana</italic> and <italic>M. temama</italic>. Finaly, <italic>M. bororo</italic> was subdivided with two individuals in each group. All specimens were positioned in a mixed manner within each main group where neither species nor cytotypes were grouped together (<xref ref-type="fig" rid="F5">Figure&#x20;5</xref>). In the PCA analysis, the two datasets presented similar results to those of the UPGMA with a high overlap among species and among cytotypes, but some distinctions were observed in the craniometry dataset (<xref ref-type="fig" rid="F6">Figure&#x20;6</xref>). It was possible to discriminate <italic>M. bororo</italic> from the other animals, characterizing the species as an intermediate morphological taxon between the <italic>M. americana</italic> complex, <italic>M. nana</italic> and <italic>M. temama</italic>. The <italic>M. americana</italic> complex, represented by the neotypes and by the Paran&#xe1; (<italic>M. rufa</italic>), Caraj&#xe1;s, Rond&#xf4;nia, and Ju&#xed;na cytotypes, presented the greatest overlap, reinforcing their cryptic complex aspect. In both datasets (body and skull) it is noteworthy that despite the large number of variables, all showed a high association with PCA1, which was able to concentrate respectively 76 and 64% of the data variation in each dataset.</p>
<fig id="F5" position="float">
<label>FIGURE 5</label>
<caption>
<p>Distance tree made with body biometrics <bold>(A)</bold> and craniometry <bold>(B)</bold> datasets using the UPGMA method for the species of the genus <italic>Mazama</italic> (<italic>Mna</italic>&#x2013;<italic>M. nana</italic>; <italic>Mbo</italic>&#x2013;<italic>M. bororo</italic>; <italic>Mte</italic>&#x2013;<italic>M. temama</italic>; <italic>Mam</italic>&#x2013;<italic>M. americana</italic>) and different <italic>Mazama americana</italic> cytotypes (RO&#x2013;Rond&#xf4;nia; JU&#x2013;Ju&#xed;na; CA&#x2014;Caraj&#xe1;s; PR&#x2014;Paran&#xe1;).</p>
</caption>
<graphic xlink:href="fgene-12-742870-g005.tif"/>
</fig>
<fig id="F6" position="float">
<label>FIGURE 6</label>
<caption>
<p>Morphology PCA results of body biometry <bold>(A)</bold> and craniometry <bold>(B)</bold> datasets represented by scatterplot of first and second principal components with 95% confidence ellipses clustered by the test groups <bold>(left)</bold> and loading plot of the environmental parameters <bold>(right)</bold>. The colored scale bar represents the correlation of each parameter to the first principal component.</p>
</caption>
<graphic xlink:href="fgene-12-742870-g006.tif"/>
</fig>
<p>The qualitative characteristics of coat color and hair length showed subtle differences between the amended description of the <italic>M. rufa</italic> (<xref ref-type="bibr" rid="B46">Illiger 1815</xref>) neotype and the <italic>M. americana</italic> (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>) neotype. The <italic>M. rufa</italic> species presented a reddish-brown color pattern in the anterobasal region of the ears and in the inner proximal region of the hind limbs, with the presence of long hairs in the basal ears regions and medial to hind limbs. This contrasts with the <italic>M. americana</italic> neotype, which showed a whiter pattern in each of these areas, and an absence of hair at the base of the ears, and the inner proximal region of both limbs (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>).</p>
</sec>
<sec id="s3-4">
<title>Molecular Data</title>
<p>The phylogenetic hypothesis obtained by BI in the tissue dataset presented most clades with good support (PP &#x3e; 0.95&#x20;<xref ref-type="fig" rid="F7">Figure&#x20;7A</xref>). Molecular species delimitation analysis showed the GMYC model significantly higher than the null model for the single threshold (p &#x3d; 0.0018), while the GMYC&#x20;model was not significantly higher for multiple thresholds (p &#x3d; 0.0959) (SM-04). Thus, the single threshold model identified nine MOTUs (<xref ref-type="fig" rid="F7">Figure&#x20;7D</xref>) that were compared with delimitations based on the current taxonomy of the analyzed species (<xref ref-type="bibr" rid="B60">Merino and Rossi, 2010</xref>; <xref ref-type="fig" rid="F7">Figure&#x20;7B</xref>) and on the cytotypes taxonomic hypothesis (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>; <xref ref-type="bibr" rid="B10">Cursino et&#x20;al., 2014</xref>; <xref ref-type="bibr" rid="B82">Salviano et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B30">Galindo et&#x20;al., 2021</xref>; <xref ref-type="fig" rid="F7">Figure&#x20;7C</xref>).</p>
<fig id="F7" position="float">
<label>FIGURE 7</label>
<caption>
<p>Summary of the phylogenetic inference results and molecular species delimitation for the <italic>Mazama americana</italic> complex (Artiodactyla: Cervidae). <bold>(A)</bold> Ultrametric tree representing the phylogenetic hypothesis generated by Bayesian Inference by the BEAST package. The support values of the clades are represented by the posterior probability (PP 0-1). Numbers I to VII identify clades highlighted in the text. <bold>(B)</bold> Present taxonomic hypothesis. <bold>(C)</bold> Cytotype taxonomic hypothesis. <bold>(D)</bold> Molecular taxonomic hypothesis represented by the Molecular Operational Taxonomic Units obtained by the single-threshold GMYC coalescence method (p &#x3d; 0.0018). Sequences identified with T&#x23;&#x23;&#x23; represent sampled animals and sequences identified by &#x23;&#x23;&#x23;&#x23; are those obtained from GenBank, &#x2a; indicates neotypes.</p>
</caption>
<graphic xlink:href="fgene-12-742870-g007.tif"/>
</fig>
<p>The phylogenetic hypothesis recovered the sampled <italic>Mazama</italic> species as a well-supported monophyletic group (clade I) in relation to genus <italic>Odocoileus</italic> (<xref ref-type="fig" rid="F7">Figure&#x20;7</xref>). <italic>Mazama temama</italic> was positioned as a basal species in the group and was recovered as a&#x20;monophyletic clade and single MOTU. The rest of the genus (clade II) was divided into two main clades, one with <italic>M.&#x20;americana</italic> Ju&#xed;na and Rond&#xf4;nia cytotypes, <italic>M. nana,</italic> and <italic>M. bororo</italic> (III), and another with only <italic>M. americana</italic> (<italic>sensu lato</italic>)&#x20;lineages (IV). In clade III, we observed a reciprocal monophyly relationship between <italic>M. nana</italic> and <italic>M. bororo</italic>, and each one was indicated as a distinct MOTU. Also in clade III, a sub-clade composed of the Ju&#xed;na and Rond&#xf4;nia <italic>M. americana</italic> (<italic>sensu lato</italic>) cytotypes was positioned as a sister group to <italic>M. nana</italic>-<italic>M. bororo</italic>. Those did not show reciprocal monophyly because one Rond&#xf4;nia sample (T269) was grouped in the Ju&#xed;na clade. However, the GMYC analysis indicated the clades of each cytotype as two distinct MOTUS and recognize this sample as belonging to a third potential species. In the other main clade (IV), only with <italic>M. americana</italic> (<italic>sensu lato</italic>) samples, two MOTUs were delimited, each one with a distinct neotype. The <italic>M. americana</italic> neotype (T358) was grouped with another sample from French Guiana and with animal T424 from the extreme north of Brazil, forming an exclusive clade (V) that represents <italic>M. americana</italic> (<italic>sensu stricto</italic>). This clade, in turn, was the sister group of the <italic>M. rufa</italic> neotype (T385) clade (VI), whose MOTU was composed of the Caraj&#xe1;s and Paran&#xe1; cytotypes. The animals of the Paran&#xe1; cytotype were recovered in a well-supported monophyletic clade, but nested to the two clades composed by the Caraj&#xe1;s cytotype animals (VII and VIII), with no reciprocal monophyletic relationship observed among the two cytotypes.</p>
</sec>
<sec id="s3-5">
<title>Distribution Data</title>
<p>Non-invasive sampling resulted in 241 fecal samples that, coupled with the previously red brocket samples collected, resulted in 15 sites with <italic>M. rufa</italic> confirmed presence (<xref ref-type="fig" rid="F1">Figure&#x20;1</xref>; SM-02). Our distribution model had a high AUC value (AUC &#x3d; 0.908, SD 0.018), low omission errors (0.05) for a fixed cumulative value 10 Logistic threshold and were significant (<italic>p</italic>&#x20;&#x3c; 0.05) for the binomial test. It indicated a potential distribution of <italic>M. rufa</italic> across southeast Brazil extending to eastern Paraguay and Argentina, northward to eastern Bolivia and southern Amazon (<xref ref-type="fig" rid="F1">Figure&#x20;1</xref>). The high suitability core areas were close to the neotype capture site encompassing forests fragments in the Misiones province in Argentina, and other fragmented areas in the border between Paraguay and Bolivia. This analysis also showed the habitat suitability connection between the neotype locality and the original type locality described by <xref ref-type="bibr" rid="B46">Illiger (1815)</xref> in the Asunci&#xf3;n city region.</p>
</sec>
</sec>
<sec sec-type="discussion" id="s4">
<title>Discussion</title>
<sec id="s4-1">
<title>Cytogenetics</title>
<p>The difference between <italic>M. americana</italic> (<italic>sensu stricto</italic>) and <italic>M. rufa</italic> (former Paran&#xe1; cytotype) was suggested to envolve two tandem fusions, two Robertsonian translocations and a pericentric inversion based on the hypothetical <italic>M. americana</italic> ancestral karyotype (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>; <xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>). However, the association of the G-Band with cattle WCP probes demonstrated that <italic>M. americana</italic> (<italic>sensu stricto</italic>) (2n &#x3d; 45, FN &#x3d; 51) and <italic>M. rufa</italic> (2n &#x3d; 52/53, FN &#x3d; 56) underwent surprisingly distinct chromosomal rearrangements during their karyotypic evolutions and diverge in at least 15 rearrangements. These findings support the hypothesis that <italic>M. rufa</italic> is a distinct species from <italic>M. americana</italic>, given that smaller karyotypic differences among other <italic>M. americana</italic> cytotypes resulted in complete sterility of their hybrids (<xref ref-type="bibr" rid="B10">Cursino et&#x20;al., 2014</xref>; <xref ref-type="bibr" rid="B82">Salviano et&#x20;al., 2017</xref>). Accumulation of chromosomal rearrangements leads to errors in meiosis and chromosome pairing, recombination suppression, errors in meiotic segregation, and subsequent germ cell or zygote death (<xref ref-type="bibr" rid="B80">Rieseberg, 2001</xref>; <xref ref-type="bibr" rid="B94">Villag&#xf3;mez and Pinton, 2008</xref>; <xref ref-type="bibr" rid="B13">Dobigny et&#x20;al., 2017</xref>).</p>
<p>On the other hand, the difference of one tandem fusion between <italic>M. rufa</italic> and the Caraj&#xe1;s cytotype (MRU 5/8, forming CA3) has been described (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>; <xref ref-type="bibr" rid="B30">Galindo et&#x20;al., 2021</xref>). The potential hybridization between both populations would lead to the formation of individuals carrying one tandem fusion in heterozygosis, considering the conservative observation of absence of a prezygotic barrier in captivity (<xref ref-type="bibr" rid="B5">Carranza et&#x20;al., 2018</xref>). Such rearrangement is considered deleterious and with a hypothetical 50% reduction in the production of balanced gamete (<xref ref-type="bibr" rid="B49">King, 1993</xref>), resulting in reduced fertility of the carrier (<xref ref-type="bibr" rid="B64">Moritz, 1986</xref>; <xref ref-type="bibr" rid="B74">Pillay et&#x20;al., 1995</xref>; <xref ref-type="bibr" rid="B53">Long, 1996</xref>; <xref ref-type="bibr" rid="B30">Galindo et&#x20;al., 2021</xref>). Nevertheless, spermiogram and testicular histology analysis failed to demonstrate a significant reduction in the reproductive fitness of hybrids carrying one tandem fusion in heterozygosis when compared to purebred animal. These were classified as sub-fertile, which would reduce the possibility of establishing a post-zygotic reproductive barrier between populations (<xref ref-type="bibr" rid="B82">Salviano et&#x20;al., 2017</xref>). In this context, a recent study evaluated the meiotic segregation of hybrids with one tandem fusion in heterozygosis in the <italic>M. americana</italic> complex, including a hybrid between the Caraj&#xe1;s and Paran&#xe1; (<italic>M. rufa</italic>) cytotypes, obtaining a rate of &#x223c;30% gametic unbalance (<xref ref-type="bibr" rid="B30">Galindo et&#x20;al., 2021</xref>). Considering the chance of successful reproduction in a backcross breeding with animals from the parent populations (&#x223c;35% with the presence or &#x223c;35% with the absence of tandem fusion in balanced gametes) this reduction in hybrid fertility might be even greater (&#x223c;65% of gametic unbalance). Thus, the difference of one tandem fusion among populations is suggested as an efficient post-zygotic reproductive barrier, similar to that observed for <italic>Otomys irroratus</italic> (<xref ref-type="bibr" rid="B74">Pillay et&#x20;al., 1995</xref>). Furthermore, it is important to indicate the apparent ongoing process of karyotypic evolution of the Caraj&#xe1;s cytotype, demonstrated by the presence of chromosomal polymorphisms such as centromeric fusion in heterozygosis and homozygosis (<xref ref-type="bibr" rid="B30">Galindo et&#x20;al., 2021</xref>). The possibility of crossing these latter cytogenetic variants with <italic>M. rufa</italic> could result in the production of hybrids carrying tandem fusion and centromeric fusion, both in heterozygosis. This interaction among different chromosomal rearrangements could result in increased rates of unbalanced gametes, as already observed in a hybrid of the <italic>M. americana</italic> complex carrying both rearrangements (43.05% of sperm with aneuploidy), with a subsequent gametic unbalance of &#x223c;70%, regarding any parent population (<xref ref-type="bibr" rid="B30">Galindo et&#x20;al., 2021</xref>). This evidence supports the hypothesis of considering <italic>M. rufa</italic> and the animals of the Caraj&#xe1;s cytotype as distinct species.</p>
</sec>
<sec id="s4-2">
<title>Morphology</title>
<p>The external morphological similarity (body biometry) among <italic>M. americana</italic> lineages and other <italic>Mazama</italic> species has been previously demonstrated (<xref ref-type="bibr" rid="B16">Duarte et&#x20;al., 2008</xref>). A similar result was also obtained in a craniometry analysis of <italic>M. americana</italic> lineages, but the comparison with other species of the genus was limited (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>). Our results showed a level of distinction among different species in the body biometric data, specifically between <italic>M. nana</italic>, <italic>M. temama</italic> and the other evaluated species. In the craniometry data, <italic>M. bororo</italic> was isolated, with only one specimen of <italic>M. americana</italic> overlapping it. Nevertheless, this distinction of <italic>M. bororo</italic> was not statistically supported in <xref ref-type="bibr" rid="B81">Rossi (2000)</xref> assessment, nor is it confirmed in the broad overlap of forest deer craniometry reported by <xref ref-type="bibr" rid="B6">Cassini and Toledo (2021)</xref>.</p>
<p>The positioning of the <italic>M. americana</italic> neotype was close to the <italic>M. rufa</italic> neotype and quite overlapping with other <italic>M. rufa</italic> specimens (Paran&#xe1; cytotype) and also Caraj&#xe1;s cytotype specimens in both datasets. Qualitative analysis, however, identified coat features that appreciably distinguish the neotypes of the two species. This represents a first step towards finding diagnostic morphological characters, which must be tested within a broader sample. The detailed analysis of deposited specimens using a <italic>post hoc</italic> approach to compare the&#x20;<italic>M. americana</italic> genetic lineages may contribute to the identification of diagnostic characters. This type of analysis is also called &#x201c;reverse taxonomy&#x201d; (<xref ref-type="bibr" rid="B58">Markmann and Tautz, 2005</xref>) and can be an interesting way to identify morphological differences, reinforce the delimitations observed by genetic data and organize scientific collections where a high primary identification error in their <italic>Mazama</italic> vouchers have been observed (<xref ref-type="bibr" rid="B61">Michaloudi et&#x20;al., 2018</xref>; <xref ref-type="bibr" rid="B57">Mantellatto et&#x20;al., 2020</xref>).</p>
</sec>
<sec id="s4-3">
<title>Mitochondrial DNA Phylogeny</title>
<p>Mitochondrial genes have been systematically used in several works that aimed to recover the phylogenetic relationships among species of the tribe Odocoileini in the last 2&#xa0;decades (<xref ref-type="bibr" rid="B31">Gilbert et&#x20;al., 2006</xref>; <xref ref-type="bibr" rid="B16">Duarte et&#x20;al., 2008</xref>; <xref ref-type="bibr" rid="B35">Guti&#xe9;rrez et&#x20;al., 2015</xref>, <xref ref-type="bibr" rid="B34">2017</xref>; <xref ref-type="bibr" rid="B23">Escobedo-Morales et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B39">Heckeberg et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>; <xref ref-type="bibr" rid="B40">Heckeberg, 2020</xref>). Some studies tested the use of nuclear regions (a-lactalbumin; protein kinase C iota; satellite DNA) but they were not informative in recovering phylogenetic relationships between recently divergent species (<xref ref-type="bibr" rid="B31">Gilbert et&#x20;al., 2006</xref>; <xref ref-type="bibr" rid="B40">Heckeberg, 2020</xref>; <xref ref-type="bibr" rid="B97">Vozdova et&#x20;al., 2021</xref>). Although the present work brought the widest sampling (number of vouchers and mitochondrial sequence size) in the <italic>M. americana</italic> complex, it still represents a single-locus analysis that limits interpretation of the results, given that mtDNA gene-tree may underestimate introgression and hybridization processes (<xref ref-type="bibr" rid="B86">Shaw, 2002</xref>). Given that results can diverge depending on the analyzed regions, a multi-loci analysis involving nuclear markers and species-trees would be a more precise approach to recover phylogenetic relationships, divergence times, and MOTU delimitation in an unbiased analysis (<xref ref-type="bibr" rid="B45">Igea et&#x20;al., 2015</xref>; <xref ref-type="bibr" rid="B14">Dool et&#x20;al., 2016</xref>).</p>
<p>The polyphyletic status of <italic>Mazama americana</italic> was revealed when the species was recovered into two clades that formed a polytomy with <italic>Odocoileus virginianus</italic> and were nested with <italic>M. nana</italic> and <italic>M. bororo</italic> (<xref ref-type="bibr" rid="B16">Duarte et&#x20;al., 2008</xref>). Different studies observed the same results in phylogenetic analyses involving more species from the tribe Odocoileini (<xref ref-type="bibr" rid="B23">Escobedo-Morales et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B39">Heckeberg et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B34">Guti&#xe9;rrez et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B40">Heckeberg, 2020</xref>). The problem is that studies restricted to Cytb gene did not present sufficient resolution, and recovered the specimens in a mixed form, without clades consistent with the region of origin, chromosomal lineage, or cytotype (<xref ref-type="bibr" rid="B16">Duarte et&#x20;al., 2008</xref>; <xref ref-type="bibr" rid="B34">Guti&#xe9;rrez et&#x20;al., 2017</xref>). On the other hand, more informative alignments recovered each chromosomal lineage in distinct and well-supported clades (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>). In these analyses, it was possible to observe the sister-group relationship between the <italic>M. americana</italic> lower diploid number lineage and <italic>M. bororo</italic>, and between the higher diploid number lineage and <italic>M. americana</italic> (<italic>sensu stricto</italic>) (<xref ref-type="bibr" rid="B7">Cifuentes-Rinc&#xf3;n et&#x20;al., 2020</xref>). Nevertheless, previous works have not actually tested reciprocal monophyly between closely related cytotypes, such as Rond&#xf4;nia x Juina (lower 2n) or Paran&#xe1; x Caraj&#xe1;s (higher 2n). Our results were consistent with previously phylogeny regarding chromosomal lineages and species, and for the first time tested the relationship between cytotypes of close divergence. The absence of reciprocal monophyly between both pairs of close cytotypes would invalidate the hypothesis that they represent distinct species, taking the strict phylogenetic species concept into account (<xref ref-type="bibr" rid="B9">Cracraft, 1983</xref>). However, this result should be evaluated with caution as it may be the result of insufficient polymorphism in the analyzed sequence or the bias from incomplete lineage sorting in an analysis restricted to a single&#x20;locus.</p>
</sec>
<sec id="s4-4">
<title>Revalidation and Delimitation of <italic>Mazama rufa</italic> (<xref ref-type="bibr" rid="B46">Illiger 1815</xref>)</title>
<p>Modern taxonomy proposes an integrative method in which different data sets could result in a greater accumulation of evidence to support taxonomic revisions (<xref ref-type="bibr" rid="B68">Padial et&#x20;al., 2010</xref>; <xref ref-type="bibr" rid="B29">Fujita et&#x20;al., 2012</xref>). More interesting than searching for consistency in the different sources of evidence it is necessary to search for the information that is biological meaningful for the taxon in question (<xref ref-type="bibr" rid="B68">Padial et&#x20;al., 2010</xref>). The definition of a taxonomic hypothesis in view of contrasting data can be equally relevant if well-grounded in the evolutionary processes that drive the speciation of the analyzed group (<xref ref-type="bibr" rid="B26">Fi&#x161;er et&#x20;al., 2018</xref>).</p>
<p>The incongruity between morphological and genetic data should not represent a problem given that morphological similarity in cryptic species is understood as a result of three possible evolutionary mechanisms: recent divergence, niche phylogenetic conservatism, or morphological convergence (<xref ref-type="bibr" rid="B26">Fi&#x161;er et&#x20;al., 2018</xref>). The niche phylogenetic conservatism hypothesis is interesting for the <italic>M. americana</italic> complex as it considers specialist species under strong selective pressure (<xref ref-type="bibr" rid="B26">Fi&#x161;er et&#x20;al., 2018</xref>). In this regard, brocket deer species are considered forest specialists (<xref ref-type="bibr" rid="B98">Weber and Gonzalez, 2003</xref>; <xref ref-type="bibr" rid="B20">Duarte et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B67">Oliveira et&#x20;al., 2019</xref>; <xref ref-type="bibr" rid="B32">Gonz&#xe1;lez and Duarte, 2020</xref>) and the selective pressure of this environment has already been identified as a determinant feature in the morphological convergence of different lineages of the genus <italic>Mazama</italic> and <italic>Pudu</italic> (<xref ref-type="bibr" rid="B31">Gilbert et&#x20;al., 2006</xref>; <xref ref-type="bibr" rid="B16">Duarte et&#x20;al., 2008</xref>; <xref ref-type="bibr" rid="B40">Heckeberg, 2020</xref>). In these taxa, for example, spiked antlers are understood as characters that emerged independently throughout the evolution of neotropical deer (<xref ref-type="bibr" rid="B31">Gilbert et&#x20;al., 2006</xref>; <xref ref-type="bibr" rid="B16">Duarte et&#x20;al., 2008</xref>; <xref ref-type="bibr" rid="B40">Heckeberg, 2020</xref>). In the case of the red brocket lineage (<italic>M. temama</italic>, <italic>M. nana</italic>, <italic>M. bororo</italic>, <italic>M. rufa</italic> and <italic>M. americana</italic> complex), a group of close-sister species, it would not be the case of convergence, but of morphological stasis resulting from the maintenance of the niche under similar environmental pressure of forests habitats. Thus, the absence of morphological differentiation does not necessarily represent persistence of gene flow among <italic>M. americana</italic> cytotypes and therefore does not invalidate the recognition of distict species such as the present description of <italic>M.&#x20;rufa</italic>.</p>
<p>Molecular data and cytogenetic data converged in indicating <italic>Mazama rufa</italic> (<xref ref-type="bibr" rid="B46">Illiger, 1815</xref>) as a distinct species in relation to <italic>Mazama americana</italic> (<xref ref-type="bibr" rid="B22">Erxleben, 1777</xref>). The role of chromosomal divergence is related to the gene flow reduction between divergent populations of mammals (<xref ref-type="bibr" rid="B80">Rieseberg, 2001</xref>), which can lead to a process of isolation and speciation as already discussed above. The operational biological species concept is the core of this hypothesis, in which reproductive isolation would unequivocally identify the existence of different species (<xref ref-type="bibr" rid="B59">Mayr, 1942</xref>). It is clear that both species represent independent evolutionary lineages within the ontological concept of Lineage Species Concept from <xref ref-type="bibr" rid="B12">De Queiroz (2007)</xref>. Cytogenetic data also provide strong evidence that <italic>Mazama rufa</italic> is composed only by the Paran&#xe1; cytotype, even considered the close divergence between the Paran&#xe1; and Caraj&#xe1;s cytotypes. They would be in isolation since the reproductive fitness of a potential hybrid could be greatly aggravated by chromosomal imbalance, and thus being practically sterile (<xref ref-type="bibr" rid="B30">Galindo et&#x20;al., 2021</xref>). This is observed in hybrids or populations with the presence of heterozygous tandem fusion, which are considered highly deleterious chromosomal rearrangements, rapidly removed or fixed at meiosis during speciation (<xref ref-type="bibr" rid="B49">King, 1993</xref>; <xref ref-type="bibr" rid="B101">Yang et&#x20;al., 1997</xref>; <xref ref-type="bibr" rid="B13">Dobigny et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B65">Mudd et&#x20;al., 2020</xref>). Although molecular data indicated the absence of reciprocal monophyly between Paran&#xe1; and Caraj&#xe1;s and suggested both as a single MOTU in the GMYC analyses, this needs to be further explored. The phylogenetic analysis and species delimitation presented here have important limitations, as they assessed only one locus, represented by part of the mitochondrial DNA. Additionally, literature strongly recommends that GMYC results should not be considered alone to guide taxonomic reviews, but should be discussed in the light of other evidences and biological information (<xref ref-type="bibr" rid="B88">Talavera et&#x20;al., 2013</xref>; <xref ref-type="bibr" rid="B89">Tang et&#x20;al., 2014</xref>).</p>
<p>The elucidation of the phylogenetic relationships and species delimitation in the <italic>M. americana</italic> complex depends not only of an advance in molecular analysis, but also an advance in Amazonian populations sampling, which are still underrepresented. Future analyses should include other chromosomal variants associated with the higher diploid number lineage described for this region (<xref ref-type="bibr" rid="B1">Abril et&#x20;al., 2010</xref>). Additionally, the evaluation and nominal description of new species related to the lower diploid number lineage (Ju&#xed;na and Rond&#xf4;nia) also depends on the evaluation of names in the synonymy of <italic>M. americana</italic> in neighboring Amazonian areas such as <italic>Mazama sarae</italic> (<xref ref-type="bibr" rid="B106">Thomas, 1925</xref>) described in Bolivia and <italic>Mazama whitelyi</italic> (<xref ref-type="bibr" rid="B103">Gray, 1873</xref>) described in&#x20;Peru.</p>
</sec>
<sec id="s4-5">
<title>Nomenclature Justification</title>
<p>The names and informal descriptions of brocket deer in South America by Azara in &#x201c;Apuntamientos Para La Historia Natural De Los Quadr&#xfa;pedos del Paraguay Y Rio De La Plata&#x201d; based <xref ref-type="bibr" rid="B46">Illiger (1815)</xref> formal description. He named the species &#x201c;Gouazoupit&#xe1;&#x201d; (red brocket deer) and gouazoubir&#xe1;&#x201d; (brown brocket deer) as <italic>Cervus rufus</italic> and <italic>Cervus simplicicornis,</italic> respectively. These descriptions, according to <xref ref-type="bibr" rid="B2">Allen (1915)</xref>, were the basis for the nomenclature of the species in the genus and represent a historical landmark. It is necessary, however, to mention that <xref ref-type="bibr" rid="B25">Fischer (1814)</xref> also formally described the Azara deer (<italic>Cervus gouazoupita</italic>, the red one and <italic>Cervus gouazoubira</italic>, the brown one). However, Fisher&#x2019;s work is summarily disregarded in relation to the red brocket deer forest species and the name <italic>Cervus gouazoupita</italic> <xref ref-type="bibr" rid="B25">Fischer, 1814</xref> disappears completely from the literature, never again being mentioned or listed as synonymous in taxonomic reviews of the genus <italic>Mazama</italic>. For example, publications that bring a broad taxonomic organization of the genus, such as that conducted by <xref ref-type="bibr" rid="B55">Lydekker (1898)</xref>, <xref ref-type="bibr" rid="B2">Allen (1915)</xref>, <xref ref-type="bibr" rid="B4">Cabrera (1960)</xref>, and more recently <xref ref-type="bibr" rid="B60">Merino and Rossi (2010)</xref>, do not even mention <italic>Cervus gouazoupita</italic> <xref ref-type="bibr" rid="B25">Fischer, 1814</xref> and always list <italic>Mazama rufa</italic> (<xref ref-type="bibr" rid="B46">Illiger, 1815</xref>) as the valid species. It is important to mention that Illiger makes his work public at the Berlin Academy of Sciences in 1811, the publication of 1815 makes it clear on its back cover that the works described there were presented between 1804 and 1811. Perhaps a previous reading is one of the reasons for his historical preference, given that Illiger&#x2019;s oral presentation is highlighted as a priority by <xref ref-type="bibr" rid="B2">Allen (1915)</xref>, and <xref ref-type="bibr" rid="B54">Lydekker (1915)</xref> mentions that separate copies were issued in&#x20;1811.</p>
<p>The International Code on Zoological Nomenclature is clear that any work published after 1757 [Art. 11.1] must comply with the requirements of providing a public and permanent scientific record and be easily obtainable soon after publication to be considered valid [Art. 8.1], it does not consider public speech or materials issued primarily to participants of scientific meetings [Art. 9.10]. In this regard, a historical recovery would be necessary to prioritize the name <italic>Mazama goazoupita</italic> (<xref ref-type="bibr" rid="B25">Fischer, 1814</xref>). However, the priority principle does not aim to change a name already widely used by introducing a new one that is an older synonym or homonym [Art. 23.2]. Given the frequent use and total dominance of the name <italic>Mazama rufa</italic> (<xref ref-type="bibr" rid="B46">Illiger, 1815</xref>) by the scientific community, to the detriment of <italic>Mazama gouazoupita</italic> (<xref ref-type="bibr" rid="B25">Fischer, 1814</xref>) in the last 200&#x20;years, we decided to maintain the use of the first for the sake of clarity and taxonomic stability in the specific case of the red brocket deer of Paraguay-Brazil.</p>
</sec>
<sec id="s4-6">
<title>Distribution and Conservation Aspects</title>
<p>The results indicate that the species is distributed over a wide area, from the south of the continent, in the Atlantic Forest; passing the dry diagonal through the Cerrado and to the southern limit of the Amazon. In addition to occurring in Brazil, it is likely to occur in the Atlantic Forest and Humid Chaco regions of Argentina and Paraguay, as well as possibly in the Dry Forest of Bolivia, on the western edge of the original distribution of <italic>M. americana</italic>. The eastern portion of the red brocket deer distribution, which extends to the coastal Atlantic Forest and the central Cerrado region, needs to be evaluated for the presence of any red brocket deer, whether <italic>M. americana</italic>, <italic>M. bororo</italic> or <italic>M.&#x20;rufa</italic>.</p>
<p>Despite the wide distribution, this species must be under severe anthropogenic pressure. The forest formations where it occurs in the Atlantic Forest (Araucaria and Interior formations) are the most devastated in the biome, characterized by intense fragmentation (<xref ref-type="bibr" rid="B79">Ribeiro et&#x20;al., 2009</xref>). The conversion of native vegetation and intense fragmentation also impact the Cerrado, which has lost more than 50% of its original cover (<xref ref-type="bibr" rid="B50">Klink and Machado, 2005</xref>; <xref ref-type="bibr" rid="B78">Reynolds et&#x20;al., 2016</xref>). The biome also lacks conservation units, with only 3% of its area under strict protection (<xref ref-type="bibr" rid="B27">Fran&#xe7;oso et&#x20;al., 2015</xref>). The species was only marginally detected in the Pantanal, an area that did not show suitable habitat. It is important to confirm this information as the presence of a red brocket deer species is known in the area and the region is a refuge for large populations of various mammals, especially deer (<xref ref-type="bibr" rid="B91">Tomas et&#x20;al., 2010</xref>). Finally, the local reality in the southern range of the Amazon where the species was found is of severe deforestation (<xref ref-type="bibr" rid="B84">Santos et&#x20;al., 2021</xref>) and is the most worrying region for <italic>M. rufa</italic> decline.</p>
</sec>
<sec id="s4-7">
<title>Conclusion and Future Directions</title>
<p>The present work demonstrated the revalidation of <italic>Mazama rufa</italic> (<xref ref-type="bibr" rid="B46">Illiger, 1815</xref>) as a distinct species, another cryptic species to be separated from the <italic>Mazama americana</italic> complex. It is composed by the former <italic>M. americana</italic> Paran&#xe1; cytotype and widely distributed throughout South America in the Atlantic Forest, Cerrado, and the south of Amazon. The information presented here should serve as a basis for a detailed assessment of the species extinction risk by the IUCN Red List since it occupies areas of high anthropogenic pressure.</p>
<p>The <italic>Mazama americana</italic> complex begin to be unraveled after a century of divergent taxonomic arrangements. The next steps in the group&#x2019;s taxonomic review should prioritize: 1) a comprehensive review of museum specimens, accompanied by molecular characterization, and including the analysis of holotypes; 2) sampling and collection of vouchers for cytogenetic characterization with live tissue, especially in the Amazon; 3) a multi-locus molecular analysis, with nuclear markers or population approaches, to better understand the historical and current isolation between close divergence cytotypes.</p>
</sec>
</sec>
</body>
<back>
<sec id="s5">
<title>Data Availability Statement</title>
<p>The datasets presented in this study can be found in GenBank. Sequences obtained from tissue samples were recorded with the accession numbers MZ488858 to MZ488910 and sequences obtained from fecal samples received the access numbers &#x201c;MZ521085&#x201d; to &#x201c;MZ521234&#x201d;.</p>
</sec>
<sec id="s6">
<title>Author Contributions</title>
<p>All authors contributed to the writing of the article. PP and DL organized the article design and were responsible for the molecular data and analysis; ES and GN were responsible for the morphology data and analyses; AB, DG, MV, SK, and HC were responsible for the cytogenetic data and analyses; MO was responsible for the distribution modeling analysis and maps; JD organized the research conception and the article design and conducted the final revision of the article.</p>
</sec>
<sec id="s7">
<title>Funding</title>
<p>This study and the authors were supported by the S&#xe3;o Paulo State Research Foundation (FAPESP, grants 2017/07014-8 and 2019/06940-1); the National Council for Scientific and Technological Development (CNPq; grant 302368/2018-3 and 406299/2013-7); the Coordena&#x00E7;&#x00E3;o de Aperfei&#x00E7;oamento de Pessoal de N&#x00ED;vel Superior - Brasil (CAPES) - Finance Code 001 and the Czech Science Foundation (GACR, grant 20&#x2013;22517J). PP was supported by FAPESP (Grant Contract N&#xb0; 2017/02200-8). AM was supported by FAPESP (Grant Contract N&#xb0; 2019/20810-3). DG was supported by the National Fund for Scientific, Technological Development and Technological Innovation (FONDECYT), the funding branch of the National Council for Science, Technology and Technological Innovation (CONCYTEC) Peru (Grant Contract N&#xb0;. 116-2017-FONDECYT).</p>
</sec>
<sec sec-type="COI-statement" id="s8">
<title>Conflict of Interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec sec-type="disclaimer" id="s9">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<ack>
<p>We would like to thank Nat&#x00E1;lia Aranha Azevedo for the brocket deer ilustration used in <xref ref-type="fig" rid="F7">Figure 7</xref>.</p>
</ack>
<sec id="s10">
<title>Supplementary Material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fgene.2021.742870/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fgene.2021.742870/full&#x23;supplementary-material</ext-link>
</p>
<supplementary-material>
<label>Supplementary Table S1</label>
<caption>
<p>Animals and Datasets.</p>
</caption>
</supplementary-material>
<supplementary-material>
<label>Supplementary Table S2</label>
<caption>
<p>Distribution and Fecal Sampling.</p>
</caption>
</supplementary-material>
<supplementary-material>
<label>Supplementary Table S3</label>
<caption>
<p>Morphological Data.</p>
</caption>
</supplementary-material>
<supplementary-material>
<label>Supplementary Table S4</label>
<caption>
<p>Molecular Data and Protocols.</p>
</caption>
</supplementary-material>
<supplementary-material>
<label>Supplementary Table S5</label>
<caption>
<p>Cytogenetic Data.</p>
</caption>
</supplementary-material>
<supplementary-material xlink:href="Table2.XLSX" id="SM1" mimetype="application/XLSX" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Table3.XLSX" id="SM2" mimetype="application/XLSX" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Table5.DOCX" id="SM3" mimetype="application/DOCX" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Table1.XLSX" id="SM4" mimetype="application/XLSX" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Table4.DOCX" id="SM5" mimetype="application/DOCX" xmlns:xlink="http://www.w3.org/1999/xlink"/>
</sec>
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