26
|
Costa-Araújo R, Silva-Jr JS, Boubli JP, Rossi RV, Canale GR, Melo FR, Bertuol F, Silva FE, Silva DA, Nash SD, Sampaio I, Farias IP, Hrbek T. An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico) from the arc of deforestation. Sci Rep 2021; 11:15665. [PMID: 34341361 PMCID: PMC8328995 DOI: 10.1038/s41598-021-93943-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/23/2021] [Indexed: 12/03/2022] Open
Abstract
Amazonia has the richest primate fauna in the world. Nonetheless, the diversity and distribution of Amazonian primates remain little known and the scarcity of baseline data challenges their conservation. These challenges are especially acute in the Amazonian arc of deforestation, the 2500 km long southern edge of the Amazonian biome that is rapidly being deforested and converted to agricultural and pastoral landscapes. Amazonian marmosets of the genus Mico are little known endemics of this region and therefore a priority for research and conservation efforts. However, even nascent conservation efforts are hampered by taxonomic uncertainties in this group, such as the existence of a potentially new species from the Juruena-Teles Pires interfluve hidden within the M. emiliae epithet. Here we test if these marmosets belong to a distinct species using new morphological, phylogenomic, and geographic distribution data analysed within an integrative taxonomic framework. We discovered a new, pseudo-cryptic Mico species hidden within the epithet M. emiliae, here described and named after Horacio Schneider, the pioneer of molecular phylogenetics of Neotropical primates. We also clarify the distribution, evolutionary and morphological relationships of four other Mico species, bridging Linnean, Wallacean, and Darwinian shortfalls in the conservation of primates in the Amazonian arc of deforestation.
Collapse
|
27
|
Fouquet A, Marinho P, Réjaud A, Carvalho TR, Caminer MA, Jansen M, Rainha RN, Rodrigues MT, Werneck FP, Lima AP, Hrbek T, Giaretta AA, Venegas PJ, Chávez G, Ron S. Systematics and biogeography of the Boana albopunctata species group (Anura, Hylidae), with the description of two new species from Amazonia. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1873869] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
28
|
DE Almeida AP, Moraes LJCL, Rojas RR, Roberto IJ, Carvalho VTDE, Ávila RW, Frazão L, Silva AAA, Menin M, Werneck FP, Hrbek T, Farias IP, Gordo M. Phylogenetic relationships of the poorly known treefrog Boana hobbsi (Cochran amp; Goin, 1970) (Anura: Hylidae), systematic implications and remarks on morphological variations and geographic distribution. Zootaxa 2021; 4933:zootaxa.4933.3.1. [PMID: 33756784 DOI: 10.11646/zootaxa.4933.3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Indexed: 11/04/2022]
Abstract
Boana hobbsi is a poorly known hylid frog currently placed within the Boana punctata group. Yet, morphological, ecological and bioacoustic traits do not support this placement, with no molecular data being available to date to test this hypothesis. Based on newly collected mitochondrial DNA sequences, morphological data review and field observations, we provide new insight into the phylogenetic relationships, morphological variations and geographic distribution of B. hobbsi. Our findings reveal that B. hobbsi is nested (with strong support) within the Boana benitezi group, recovering once more a polyphyletic Boana punctata group. Supported by this new genetic, morphological and ecological evidence, we propose a new taxonomic arrangement which includes B. hobbsi as a member of the Boana benitezi group. Furthermore, we emphasize the importance of conducting biological inventories in remote Amazonian areas, where many taxonomic and geographic knowledge gaps persist with regards to Amphibian diversity.
Collapse
|
29
|
Fouquet A, Leblanc K, Framit M, Réjaud A, Rodrigues MT, Castroviejo-Fisher S, Peloso PLV, Prates I, Manzi S, Suescun U, Baroni S, Moraes LJCL, Recoder R, de Souza SM, Dal Vecchio F, Camacho A, Ghellere JM, Rojas-Runjaic FJM, Gagliardi-Urrutia G, de Carvalho VT, Gordo M, Menin M, Kok PJR, Hrbek T, Werneck FP, Crawford AJ, Ron SR, Mueses-Cisneros JJ, Rojas Zamora RR, Pavan D, Ivo Simões P, Ernst R, Fabre AC. Species diversity and biogeography of an ancient frog clade from the Guiana Shield (Anura: Microhylidae: Adelastes, Otophryne, Synapturanus) exhibiting spectacular phenotypic diversification. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa204] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
The outstanding biodiversity of the Guiana Shield has raised many questions about its origins and evolution. Frogs of the genera Adelastes, Otophryne and Synapturanus form an ancient lineage distributed mostly across this region. These genera display strikingly disparate morphologies and life-history traits. Notably, Synapturanus is conspicuously adapted to fossoriality and is the only genus within this group to have dispersed further into Amazonia. Moreover, morphological differences among Synapturanus species suggest different degrees of fossoriality that might be linked to their biogeographical history. Through integrative analysis of genetic, morphometric and acoustic data, we delimited 25 species in this clade, representing a fourfold increase. We found that the entire clade started to diversify ~55 Mya and Synapturanus ~30 Mya. Members of this genus probably dispersed three times out of the Guiana Shield both before and after the Pebas system, a wetland ecosystem occupying most of Western Amazonia during the Miocene. Using a three-dimensional osteological dataset, we characterized a high morphological disparity across the three genera. Within Synapturanus, we further characterized distinct phenotypes that emerged concomitantly with dispersals during the Miocene and possibly represent adaptations to different habitats, such as soils with different physical properties.
Collapse
|
30
|
Buainain N, Canton R, Zuquim G, Tuomisto H, Hrbek T, Sato H, Ribas CC. Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus. Mol Ecol 2020; 29:2922-2939. [PMID: 32623766 DOI: 10.1111/mec.15534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 06/04/2020] [Accepted: 06/18/2020] [Indexed: 01/27/2023]
Abstract
Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally-dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modelling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380 to 166 kya, and expansion of the distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated with long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.
Collapse
|
31
|
Carneiro J, Sampaio I, Lima T, Silva-Júnior JDS, Farias I, Hrbek T, Valsecchi J, Boubli J, Schneider H. Phylogenetic relationships in the genus Cheracebus (Callicebinae, Pitheciidae). Am J Primatol 2020; 82:e23167. [PMID: 32652664 DOI: 10.1002/ajp.23167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/06/2020] [Accepted: 04/13/2020] [Indexed: 11/08/2022]
Abstract
Cheracebus is a new genus of New World primate of the family Pitheciidae, subfamily Callicebinae. Until recently, Cheracebus was classified as the torquatus species group of the genus Callicebus. The genus Cheracebus has six species: C. lucifer, C. lugens, C. regulus, C. medemi, C. torquatus, and C. purinus, which are all endemic to the Amazon biome. Before the present study, there had been no conclusive interpretation of the phylogenetic relationships among most of the Cheracebus species. The present study tests the monophyly of the genus and investigates the relationships among the different Cheracebus species, based on DNA sequencing of 16 mitochondrial and nuclear markers. The phylogenetic analyses were based on Maximum Likelihood, Bayesian Inference, and multispecies coalescent approaches. The divergence times and genetic distances between the Cheracebus taxa were also estimated. The analyses confirmed the monophyly of the genus and a well-supported topology, with the following arrangement: ((C. torquatus, C. lugens), (C. lucifer (C. purinus, C. regulus))). A well-differentiated clade was also identified within part of the geographic range of C. lugens, which warrants further investigation to confirm its taxonomic status.
Collapse
|
32
|
Roberto IJ, Bittencourt PS, Muniz FL, Hernández-Rangel SM, Nóbrega YC, Ávila RW, Souza BC, Alvarez G, Miranda-Chumacero G, Campos Z, Farias IP, Hrbek T. Unexpected but unsurprising lineage diversity within the most widespread Neotropical crocodilian genus Caiman (Crocodylia, Alligatoridae). SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1769222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
33
|
Vargas-Ramírez M, Caballero S, Morales-Betancourt MA, Lasso CA, Amaya L, Martínez JG, das Neves Silva Viana M, Vogt RC, Farias IP, Hrbek T, Campbell PD, Fritz U. Genomic analyses reveal two species of the matamata (Testudines: Chelidae: Chelus spp.) and clarify their phylogeography. Mol Phylogenet Evol 2020; 148:106823. [PMID: 32278863 DOI: 10.1016/j.ympev.2020.106823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 10/24/2022]
Abstract
The matamata is one of the most charismatic turtles on earth, widely distributed in northern South America. Debates have occurred over whether or not there should be two subspecies or species recognized due to its geographic variation in morphology. Even though the matamata is universally known, its natural history, conservation status and biogeography are largely unexplored. In this study we examined the phylogeographic differentiation of the matamata based on three mitochondrial DNA fragments (2168 bp of the control region, cytochrome oxidase subunit I, and the cytochrome b gene), one nuclear genomic DNA fragment (1068 bp of the R35 intron) and 1661 Single Nucleotide Polymorphisms (SNPs). Our molecular and morphological analyses revealed the existence of two distinct, genetically deeply divergent evolutionary lineages of matamatas that separated in the late Miocene (approximately 12.7 million years ago), corresponding well to the time when the Orinoco Basin was established. As a result of our analyses, we describe the genetically and morphologically highly distinct matamata from the Orinoco and Río Negro Basins and the Essequibo drainage as a species new to science (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto is distributed in the Amazon Basin and the Mahury drainage. Additionally, the analyses revealed that each species displays phylogeographic differentiation. For C. orinocensis, there is moderate mitochondrial differentiation between the Orinoco and the Río Negro. For C. fimbriata, there is more pronounced differentiation matching different river systems. One mitochondrial clade was identified from the Amazon, Ucayali, and Mahury Rivers, and another one from the Madeira and Jaci Paraná Rivers. The C. orinocensis in the Essequibo and Branco Rivers have haplotypes that constitute a third clade clustering with C. fimbriata. Phylogenetic analyses of the R35 intron and SNP data link the matamatas from the Essequibo and Branco with the new species, suggesting past gene flow and old mitochondrial introgression. Chelus orinocensis is collected for the pet trade in Colombia and Venezuela. However, neither the extent of the harvest nor its impact are known. Hence, it is crucial to gather more information and to assess its exploitation throughout its distribution range to obtain a better understanding of its conservation status and to design appropriate conservation and management procedures. RESUMEN: La matamata es una de las tortugas más carismáticas del mundo, ampliamente distribuida en el norte de Sudamérica. Debido a su variación morfológica geográfica, se debate sobre el reconocimiento de dos subespecies o especies. A pesar de que la matamata es universalmente conocida, su historia natural, estado de conservación y biogeografía han sido muy poco estudiados. En este estudio examinamos la diferenciación filogeográfica de las matamatas en base a tres fragmentos de ADN mitocondrial (2168 pb de la región de control, la subunidad I del citocromo oxidasa y el gen del citocromo b), un fragmento de ADN genómico nuclear (1068 pb del intrón R35) y 1661 polimorfismos de nucleótido único (SNPs). Nuestros análisis moleculares y morfológicos revelaron la existencia de dos linajes evolutivos distintos de matamatas, genéticamente divergentes que se separaron en el Mioceno tardio (hace aproximadamente 12.7 millones de años), correspondiendo al tiempo en que se estableció la cuenca del Orinoco. Como resultado de nuestros análisis, describimos las genéticamente y morfológicamente distintas matamatas de las cuencas del Orinoco, Río Negro y Essequibo como una especie nueva para la ciencia (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto se distribuye en la cuenca del Amazonas y en el drenaje del Mahury. Adicionalmente, los análisis revelaron que cada especie muestra diferenciación filogeográfica. Para C. orinocensis, hay una moderada diferenciación mitocondrial entre el Orinoco y el Río Negro. Para C. fimbriata, hay una diferenciación más pronunciada, concordando con los diferentes sistemas fluviales. Se identificó un clado de los ríos Amazonas, Ucayali y Mahury y otro de los ríos Madeira y Jaci Paraná. Las C. orinocensis de los ríos Essequibo y Branco tienen haplotipos que constituyen un tercer clado que se agrupa con C. fimbriata. Los análisis filogenéticos del intrón R35 y los datos de SNP asocian las matamatas de Essequibo y Branco con la nueva especie, sugiriendo flujo de genes pasado e introgresión mitocondrial antigua. Chelus orinocensis se colecta para el comercio de mascotas en Colombia y Venezuela. Sin embargo, ni se conoce el alcance de las colectas ni su impacto. Por lo tanto, es crucial recopilar más información y evaluar su explotación en todo su rango de distribución, comprender mejor su estado de conservación y para diseñar acciones apropiadas de conservación y manejo.
Collapse
|
34
|
Bittencourt PS, Machado VN, Marshall BG, Hrbek T, Farias IP. Phylogenetic relationships of the neon tetras Paracheirodon spp. (Characiformes: Characidae: Stethaprioninae), including comments on Petitella georgiae and Hemigrammus bleheri. NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2019-0109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT Neon tetras (Paracheirodon spp.) are three colorful characid species with a complicated taxonomic history, and relationships among the species are poorly known. Molecular data resolved the relationships among the three neon tetras, and strongly supported monophyly of the genus and its sister taxon relationship to Brittanichthys. Additionally, the sister-taxon relationship of the rummy-nose tetras Hemigrammus bleheri and Petitella georgiae was strongly supported by molecular and morphological data. Therefore, we propose to transfer the rummy-nose tetras H. bleheri and H. rhodostomus to the genus Petitella. Furthermore, Petitella georgiae is likely to be a species complex comprised of at least two species.
Collapse
|
35
|
Frazão L, Oliveira ME, Menin M, Campos J, Almeida A, Kaefer IL, Hrbek T. Species richness and composition of snake assemblages in poorly accessible areas in the Brazilian Amazonia. BIOTA NEOTROPICA 2020. [DOI: 10.1590/1676-0611-bn-2018-0661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract: Snakes are a diverse group of terrestrial vertebrates of the order Squamata. Despite that, in the Amazonian biome, information about distribution and identification of snakes is limited when compared to other groups. Additionally, in Amazonia there is a sampling bias towards areas geographically close to urban centers and more densely populated areas. This in turn leads to false distribution gaps in poorly accessible areas of Amazonia. In this article we report the composition of snake assemblages in six areas of the Brazilian Amazonia, based on field sampling conducted over four years using standardized methods. We sampled 70 species from eight families: Typhlopidae (n=1), Leptotyphlopidae (n=1), Anillidae (n=1), Boidae (n=5), Colubridae (n=15), Dipsadidae (n=35), Elapidae (n=7), and Viperidae (n=5). The largest number of species was recorded in the Trombetas River area and the lowest in the Jatapu River area. The total beta diversity was 0.40 and the snake assemblages were structured mainly by replacement (72.5%). The time-limited search was the method that recorded the greatest number of individuals in the studied areas (44.1%) and also the greatest number of species (n=40). However, some species were recorded only by other methods such as interception by pitfall traps with directional fences. Despite the large number of species sampled in the study, no particular area comprised more than 40% of species registered in all the areas, indicating that snakes are poorly detected even with large sampling effort across multiple areas of a species distribution.
Collapse
|
36
|
Ota RP, Machado VN, Andrade MC, Collins RA, Farias IP, Hrbek T. Integrative taxonomy reveals a new species of pacu (Characiformes: Serrasalmidae: Myloplus) from the Brazilian Amazon. NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-20190112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT Pacus of the genus Myloplus represent a formidable taxonomic challenge, and particularly so for the case of M. asterias and M. rubripinnis, two widespread and common species that harbor considerable morphological diversity. Here we apply DNA barcoding and multiple species discovery methods to find candidate species in this complex group. We report on one well-supported lineage that is also morphologically and ecologically distinct. This lineage represents a new species that can be distinguished from congeners by the presence of dark chromatophores on lateral-line scales, which gives the appearance of a black lateral line. It can be further diagnosed by having 25-29 branched dorsal-fin rays (vs. 18-24), 89-114 perforated scales from the supracleithrum to the end of hypural plate (vs. 56-89), and 98-120 total lateral line scales (vs. 59-97). The new species is widely distributed in the Amazon basin, but seems to have a preference for black- and clearwater habitats. This ecological preference and black lateral line color pattern bears a striking similarity to the recently described silver dollar Metynnis melanogrammus.
Collapse
|
37
|
Farias IP, Willis S, Leão A, Verba JT, Crossa M, Foresti F, Porto-Foresti F, Sampaio I, Hrbek T. The largest fish in the world's biggest river: Genetic connectivity and conservation of Arapaima gigas in the Amazon and Araguaia-Tocantins drainages. PLoS One 2019; 14:e0220882. [PMID: 31419237 PMCID: PMC6697350 DOI: 10.1371/journal.pone.0220882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 07/25/2019] [Indexed: 12/02/2022] Open
Abstract
Arapaima, pirarucu or paiche (Arapaima gigas) is one of the largest freshwater fish in the world, and has a long history of commercial exploitation in the Amazon region. To estimate levels of genetic variability and historical and recent connectivity in Arapaima, we examined variation in eleven microsatellite DNA markers in individuals from 22 localities in Brazil, Colombia, and Peru. The results of analysis of molecular variance, Bayesian clustering and discriminant analysis of principal components showed that Arapaima in our samples represents two major populations, one in the Amazonas and one in the Araguaia-Tocantins River basins. The Amazonas population is further structured by isolation-by-distance with the hydrologically largely unconnected Amapá locality representing the eastern-most extreme of this continuum; gene flow predominates at distances of less than 1500 km with localities separated by over 2000 km dominated by genetic drift and effectively forming different populations. We saw no evidence of multiple species of Arapaima in the Amazonas basin, and analysis of pairwise genetic divergence (FST) with Mantel tests and correlograms indicated that this largest population exhibits a large-scale pattern of isolation-by-distance, with which results from MIGRATE-N agreed. The degree and significance of genetic divergence indicates that most sampled localities represent demographically independent sub-populations, although we did identify several recent migration events between both proximal and more distant localities. The levels of genetic diversity were heterogeneous across sites, including low genetic diversity, effective population sizes, and evidence of genetic bottlenecks in several places. On average the levels of gene diversity and rarefied allelic richness were higher for localities along the Amazonas mainstem than in the tributaries, despite these being the areas of highest fishing pressure, while the lowest values were found in tributary headwaters, where landscape modification is a significant threat. We recommend that managers consider the regional and local threats to these populations and tailor strategies accordingly, strategies which should ensure the ability of young A. gigas to disperse through floodplain corridors to maintain genetic diversity among otherwise sedentary adult sub-populations.
Collapse
|
38
|
Escobar L MD, Ota RP, Machado-Allison A, Andrade-López J, Farias IP, Hrbek T. A new species of Piaractus (Characiformes: Serrasalmidae) from the Orinoco Basin with a redescription of Piaractus brachypomus. JOURNAL OF FISH BIOLOGY 2019; 95:411-427. [PMID: 31017302 DOI: 10.1111/jfb.13990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Piaractus orinoquensis, a new species of serrasalmid fish, is described from the Orinoco River basin. The new species differs from congeners by having a slenderer body, relatively smaller head and snout, more compressed mid-body, fewer scales above and below the lateral line and diagnostic molecular characters in the coI mitochondrial gene region. We also provide a re-description of Piaractus brachypomus, restricting its geographic distribution to the Amazon River basin. Both species are economically important in their respective basins and need to be independently managed as distinct species.
Collapse
|
39
|
Costa-Araújo R, de Melo FR, Canale GR, Hernández-Rangel SM, Messias MR, Rossi RV, Silva FE, da Silva MNF, Nash SD, Boubli JP, Farias IP, Hrbek T. The Munduruku marmoset: a new monkey species from southern Amazonia. PeerJ 2019; 7:e7019. [PMID: 31380146 PMCID: PMC6661146 DOI: 10.7717/peerj.7019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 04/25/2019] [Indexed: 11/22/2022] Open
Abstract
Although the Atlantic Forest marmosets (Callithrix spp.) are among the best studied Neotropical primates, the Amazonian marmosets (Callibella humilis, Cebuella spp. and Mico spp.) are much less well-known. Even species diversity and distributions are yet to be properly determined because field data and materials currently available in scientific collections do not allow comprehensive taxonomic studies of Amazonian marmosets. From 2015 to 2018, we conducted 10 expeditions in key-areas within southern Amazonia where little or no information on marmosets was available. In one such region-the Tapajós-Jamanxim interfluve-we recorded marmosets with a distinctive pelage pigmentation pattern suggesting they could represent a new species. We tested this hypothesis using an integrative taxonomic framework that included phylogenomic data (ddRAD sequences), pelage pigmentation characters, and distribution records. We found that the marmosets of the northern Tapajós-Jamanxim interfluve have unique states in pelage pigmentation characters, form a clade (100% support) in our Bayesian and Maximum-Likelihood phylogenies, and occur in an area isolated from other taxa by rivers. The integration of these lines of evidence leads us to describe a new marmoset species in the genus Mico, named after the Munduruku Amerindians of the Tapajós-Jamanxim interfluve, southwest of Pará State, Brazil.
Collapse
|
40
|
Gravena W, Hrbek T, da Silva VMF, Farias IP. Boto ( Inia geoffrensis-Cetacea: Iniidae) aggregations in two provisioning sites in the lower Negro River-Amazonas, Brazil: are they related? PeerJ 2019; 7:e6692. [PMID: 31024759 PMCID: PMC6475133 DOI: 10.7717/peerj.6692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 02/28/2019] [Indexed: 11/20/2022] Open
Abstract
The Negro River currently has seven floating houses where tourists can feed and interact with botos, each with its own history of how these aggregations were formed. Some keepers say these groups are familial, even reporting individuals being born into the group. However, behavioral studies have shown that botos are solitary, only forming groups at feeding areas and during the mating season. In the present study we used 12 microsatellite and molecular sex markers to characterize relationships within and between two boto aggregations (ten and seven botos each) in the lower Negro River. Molecular sexing revealed that all botos sampled from both aggregations were males. This may be explained by habitat preference, as male botos are primarily found in the main channels of large rivers, whereas females prefer more protected areas, such as flooded forests and its channels and lakes. Most of the animals were unrelated within each aggregation, demonstrating that these aggregations are not normally formed due to kinship bonds, but are exclusively for feeding, as botos learn that these places provide easy access to food. This study provides important information that helps us understand how human interaction is affecting the social structure and behavior of these animals.
Collapse
|
41
|
Bittencourt PS, Campos Z, Muniz FDL, Marioni B, Souza BC, Da Silveira R, de Thoisy B, Hrbek T, Farias IP. Evidence of cryptic lineages within a small South American crocodilian: the Schneider's dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae). PeerJ 2019; 7:e6580. [PMID: 30931177 PMCID: PMC6433001 DOI: 10.7717/peerj.6580] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 02/01/2019] [Indexed: 11/25/2022] Open
Abstract
Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.
Collapse
|
42
|
Muniz FL, Ximenes AM, Bittencourt PS, Hernández-Rangel SM, Campos Z, Hrbek T, Farias IP. Detecting population structure of Paleosuchus trigonatus (Alligatoridae: Caimaninae) through microsatellites markers developed by next generation sequencing. Mol Biol Rep 2019; 46:2473-2484. [DOI: 10.1007/s11033-019-04709-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/16/2019] [Indexed: 12/30/2022]
|
43
|
Collins RA, Hrbek T. An In Silico Comparison of Protocols for Dated Phylogenomics. Syst Biol 2018; 67:633-650. [PMID: 29319797 DOI: 10.1093/sysbio/syx089] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 10/24/2017] [Indexed: 01/02/2023] Open
Abstract
In the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics, viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here, we present a procedure to perform in silico extractions from genomes and create directly comparable data sets for each class of marker. We then compare these data sets in terms of both phylogenetic resolution and ability to consistently and precisely estimate clade ages using fossil-calibrated molecular-clock models. Furthermore, we were also able to directly compare these results to previously published data sets from Sanger-sequenced nuclear exons and mitochondrial genomes under the same analytical conditions. Our results show-although with the exception of the mitochondrial genome data set and the smallest ddRADseq data set-that for uncontroversial nodes all data classes performed equally well, that is they recovered the same well supported topology. However, for one difficult-to-resolve node comprising a rapid diversification, we report well supported but conflicting topologies among the marker classes consistent with the mismodeling of gene tree heterogeneity as demonstrated by species tree analyses of single nucleotide polymorphisms. Likewise, clade age estimates showed consistent discrepancies between data sets under strict and relaxed clock models; for recent nodes, clade ages estimated by nuclear exon data sets were younger than those of the UCE, RADseq and mitochondrial data, but vice versa for the deepest nodes in the primate phylogeny. This observation is explained by temporal differences in phylogenetic informativeness (PI), with the data sets with strong PI peaks toward the present underestimating the deepest node ages. Finally, we conclude by emphasizing that while huge numbers of loci are probably not required for uncontroversial phylogenetic questions-for which practical considerations such as ease of data generation, sharing, and aggregating, therefore become increasingly important-accurately modeling heterogeneous data remains as relevant as ever for the more recalcitrant problems.
Collapse
|
44
|
Rojas RR, Fouquet A, De Carvalho VT, Ron S, Chaparro JC, Vogt RC, Ávila RW, Farias IP, Gordo M, Hrbek T. Redescription of the Amazonian tiny tree toad Amazophrynella minuta (Melin, 1941) (Anura: Bufonidae) from its type locality. Zootaxa 2018; 4482:511-526. [PMID: 30313811 DOI: 10.11646/zootaxa.4482.3.4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Indexed: 11/04/2022]
Abstract
The description of Amazophrynella minuta was published in 1941 by the Swedish naturalist Douglas Melin based on material from Taracuá (Amazonas state, Brazil). This description was very brief and based on the morphology of few specimens with diagnostic characters and color variation not well defined. Moreover, the type series is currently in poor state of conservation. Consequently, taxonomic ambiguity surrounds the nominal taxon A. minuta, which hampers the description of many unnamed congeneric species. Herein, we redescribe A. minuta based on recently collected specimens from the type locality, designate a lectotype, formulate a new diagnosis, provide patterns of morphological variation, measurements and body proportions.
Collapse
|
45
|
Hrbek T, Meliciano NV, Zuanon J, Farias IP. Remarkable Geographic Structuring of Rheophilic Fishes of the Lower Araguaia River. Front Genet 2018; 9:295. [PMID: 30154824 PMCID: PMC6102472 DOI: 10.3389/fgene.2018.00295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 07/13/2018] [Indexed: 11/13/2022] Open
Abstract
Rapids and waterfalls, and their associated fauna and flora are in peril. With the construction of each new hydroelectric dam, more rapids and waterfalls are destroyed, leading to the disappearance of associated fauna and flora. Areas of rapids harbor distinct, highly endemic rheophilic fauna and flora adapted to an extreme environment. Rheophilic habitats also have disjunct distribution both within and across rivers. Rheophilic habitats thus represent islands of suitable habitat separated by stretches of unsuitable habitat. In this study, we investigated to what extent, if any, species of cichlid and anostomid fishes associated with rheophilic habitats were structured among the rapids of Araguaia River in the Brazilian Amazon. We tested both for population structuring as well as non-random distribution of lineages among rapids. Eight of the nine species had multiple lineages, five of these nine species were structured, and three of the eight species with multiple lineages showed non-random distribution of lineages among rapids. These results demonstrate that in addition to high levels of endemicism of rheophilic fishes, different rapids even within the same river are occupied by different lineages. Rheophilic species and communities occupying different rapids are, therefore, not interchangeable, and this realization must be taken into account when proposing mitigatory/compensatory measures in hydroelectric projects, and in conservation planning.
Collapse
|
46
|
Rojas RR, De Carvalho VT, Ávila RW, Kawashita-Ribeiro RA, Hrbek T, Gordo M. Description of the advertisement calls of four species of Amazophrynella (Anura:Bufonidae). Zootaxa 2018; 4459:193-196. [PMID: 30314140 DOI: 10.11646/zootaxa.4459.1.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Indexed: 11/04/2022]
Abstract
Amazophrynella comprises 11 small bufonid species with a pan-Amazonian distribution (Fouquet et al. 2012a, b; Rojas et al. 2016, Rojas et al. 2018). All species inhabit the forest leaf litter, breed in seasonal puddles and are diurnally and nocturnally active (Fouquet et al. 2012b; Rojas et al. 2014; 2015; 2016). Until now only one nominal species, A. javierbustamantei, and two putative lineages-A. moisesii (Rio Yuyapichis, Peru) and A. siona (Santa Cecilia, Ecuador)-had their advertisement calls formally described (Duellman 1978; Schlüter 1981; Rojas et al. 2016). Herein, we described for the first time the advertisement calls from additional four species of Amazophrynella.
Collapse
|
47
|
Santos MDCF, Hrbek T, Farias IP. A Multilocus Approach to Understanding Historical and Contemporary Demography of the Keystone Floodplain Species Colossoma macropomum (Teleostei: Characiformes). Front Genet 2018; 9:263. [PMID: 30154822 PMCID: PMC6102471 DOI: 10.3389/fgene.2018.00263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 06/28/2018] [Indexed: 11/19/2022] Open
Abstract
We studied the natural populations of a flagship fish species of the Amazon, Colossoma macropomum which in recent years has been suffering from severe exploitation. Our aim was to investigate the existence or not of genetic differentiation across the wide area of its distribution and to investigate changes in its effective population size throughout its evolutionary history. We sampled individuals from 21 locations distributed throughout the Amazon basin. We analyzed 539 individuals for mitochondrial genes (control region and ATPase gene 6/8), generating 1,561 base pairs, and genotyped 604 individuals for 13 microsatellite loci obtaining, on average, 21.4 alleles per locus. Mean HE was 0.78 suggesting moderate levels of genetic variability. AMOVA and other tests used to detect the population structure based on both markers indicate that C. macropomum comprises a single and large panmitic population in the main channel of the Solimões-Amazonas River basin, on the other hand localities in the headwaters of the tributaries Juruá, Purus, Madeira, Tapajós, and localities of black water, showed genetic structure. The greatest genetic differentiation was observed between the Brazilian Amazon basin and the Bolivian sub-basin with restricted genetic flow between the two basins. Demographic analyzes of mitochondrial genes indicated population expansion in the Brazilian and Bolivian Amazon basins during the Pleistocene, and microsatellite data indicated a population reduction during the Holocene. This shows that the historical demography of C. macropomum is highly dynamic. Conservation and management strategies should be designed to respect the existing population structure and minimize the effects of overfishing by limiting fisheries C. macropomum populations.
Collapse
|
48
|
Byrne H, Lynch Alfaro JW, Sampaio I, Farias I, Schneider H, Hrbek T, Boubli JP. Titi monkey biogeography: Parallel Pleistocene spread byPlecturocebusandCheracebusinto a post-Pebas Western Amazon. ZOOL SCR 2018. [DOI: 10.1111/zsc.12300] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
49
|
Rojas RR, Fouquet A, Ron SR, Hernández-Ruz EJ, Melo-Sampaio PR, Chaparro JC, Vogt RC, de Carvalho VT, Pinheiro LC, Avila RW, Farias IP, Gordo M, Hrbek T. A Pan-Amazonian species delimitation: high species diversity within the genus Amazophrynella (Anura: Bufonidae). PeerJ 2018; 6:e4941. [PMID: 30013824 PMCID: PMC6042491 DOI: 10.7717/peerj.4941] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/21/2018] [Indexed: 11/20/2022] Open
Abstract
Amphibians are probably the most vulnerable group to climate change and climate-change associate diseases. This ongoing biodiversity crisis makes it thus imperative to improve the taxonomy of anurans in biodiverse but understudied areas such as Amazonia. In this study, we applied robust integrative taxonomic methods combining genetic (mitochondrial 16S, 12S and COI genes), morphological and environmental data to delimit species of the genus Amazophrynella (Anura: Bufonidae) sampled from throughout their pan-Amazonian distribution. Our study confirms the hypothesis that the species diversity of the genus is grossly underestimated. Our analyses suggest the existence of eighteen linages of which seven are nominal species, three Deep Conspecific Lineages, one Unconfirmed Candidate Species, three Uncategorized Lineages, and four Confirmed Candidate Species and described herein. We also propose a phylogenetic hypothesis for the genus and discuss its implications for historical biogeography of this Amazonian group.
Collapse
|
50
|
Motta J, Menin M, Almeida AP, Hrbek T, Farias IP. When the unknown lives next door: a study of central Amazonian anurofauna. Zootaxa 2018; 4438:79-104. [PMID: 30313157 DOI: 10.11646/zootaxa.4438.1.3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Indexed: 11/04/2022]
Abstract
The number of species of anurans in the Amazon is highly underestimated with new studies reporting the discovery of a large number of species every year. This advance in the discovery of biodiversity is due to the use of molecular tools, especially 16S rRNA gene barcoding, which is used to identify species and discover cryptic lineages. Few anurans of the central Amazon have molecular sequence data available in public databases, which contrasts with the considerable species richness of this biome. The aim of the present study was to test for the presence of cryptic species using the mPTP delimitation algorism. We morphologically identified 26 species, of which 23 were confirmed molecularly with the remaining three species identified as other congeneric species, since sequences with the same epithet do not exist in GenBank. Of these 23 species, nine contained one lineage restricted to central Amazon. This represents an underestimate of 39% in the taxonomic diversity in our sample. This is particularly surprising given that our sampling sites are among the best-studied regions of the central Amazon.
Collapse
|