Browsing by Author "Vianna, Juliana A."

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    A noninvasive sampling method for genetic analysis of the West Indian manatee (Trichechus manatus)
    (2009) Muschett Rivera, Giselle Elena; Bonacic Salas, Cristián; Vianna, Juliana A.
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    Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors
    (2022) Fiddaman, Steven R.; Vinkler, Michal; Spiro, Simon G.; Levy, Hila; Emerling, Christopher A.; Boyd, Amy C.; Dimopoulos, Evangelos A.; Vianna, Juliana A.; Cole, Theresa L.; Pan, Hailin; Fang, Miaoquan; Zhang, Guojie; Hart, Tom; Frantz, Laurent A. F.; Smith, Adrian L.
    Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.
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    Are threatened seabird colonies of the pacific ocean genetically vulnerable? The case of the red-tailed tropicbird, Phaethon rubricauda, as a model species
    (2024) Varela, Andrea, I; Brokordt, Katherina; Vianna, Juliana A.; Frugone, Maria Jose; Ismar-Rebitz, Stefanie M. H.; Gaskin, Chris P.; Carlile, Nicholas; O'Dwyer, Terence; Adams, Josh; Vanderwerf, Eric A.; Luna-Jorquera, Guillermo
    Oceanic seabirds have suffered population declines and extirpations due to human disturbance and still face multiple threats. Here, we assessed the potential genetic vulnerability of the red-tailed tropicbird, Phaethon rubricauda, a seabird species threatened by human disturbance and listed as 'least concern' by the IUCN. Using Single Nucleotide Polymorphisms (SNPs) we evaluated the genetic population structure of the red-tailed tropicbird throughout the Pacific Ocean using samples from 132 individuals from six islands. We sampled individuals from islands without human-related disturbance (non-impacted islands) and with human-related disturbance (impacted islands). Results of genome-wide SNP analyses were consistent with previous results using mitochondrial DNA sequences analyses. Genetic diversity did not differ between impacted and non-impacted islands, and low inbreeding estimates were detected for all colonies. The SNPs analyses confirmed a pattern of isolation by distance and significant inter-regional (Chile, Australasia, and Hawai'i) genetic structure, but revealed greater differentiation of tropicbirds in Hawai'i compared with Chile and Australasia. Within regions, our results further indicated significant differentiation between Rapa Nui and Salas & G & oacute;mez Island (Chile), and between Meyer and Phillip islands (Australasia) that was not detected using mitochondrial DNA analyses. Within Hawai'i, we found a lack of significant genetic differentiation between O'ahu and Kaua'i, separated by 200 km. Our findings indicated that red-tailed tropicbird colonies are at genetic risk due to limited dispersal among colonies which may reduce the fitness of the species in the long-term. We suggest that red-tailed tropicbird colonies are vulnerable to future population declines because recovery through immigration from other islands may be limited by geographic distance. Conservation actions will help preserve genetic diversity and discrete populations for this native seabird at colonies throughout the Pacific.
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    Associations among MHC genes, latitude, and avian malaria infections in the rufous-collared sparrow (Zonotrichia capensis)
    (2024) de Aguilar, Juan Rivero; Barroso, Omar; Bonaccorso, Elisa; Cadena, Hector; Hussing, Lucas; Jorquera, Josefina; Martinez, Javier; Martinez-de la Puente, Josue; Marzal, Alfonso; Miranda, Fabiola Leon; Merino, Santiago; Matta, Nubia E.; Ramenofsky, Marilyn; Rozzi, Ricardo; Valeris-Chacin, Carlos E.; Vasquez, Rodrigo A.; Vianna, Juliana A.; Wingfield, John C.
    The major histocompatibility complex (MHC) is a genetic region in jawed vertebrates that contains key genes involved in the immune response. Associations between the MHC and avian malaria infections in wild birds have been observed and mainly explored in the Northern Hemisphere, while a general lack of information remains in the Southern Hemisphere. Here, we investigated the associations between the MHC genes and infections with Plasmodium and Haemoproteus blood parasites along a latitudinal gradient in South America. We sampled 93 rufous-collared sparrows (Zonotrichia capensis) individuals from four countries, Colombia, Ecuador, Peru, and Chile, and estimated MHC-I and MHC-II allele diversity. We detected between 1-4 (MHC-I) and 1-6 (MHC-II) amino acidic alleles per individual, with signs of positive selection. We obtained generalized additive mixed models to explore the associations between MHC-I and MHC-II diversity and latitude. We also explored the relationship between infection status and latitude/biome. We found a non-linear association between the MHC-II amino acidic allele diversity and latitude. Individuals from north Chile presented a lower MHC genetic diversity than those from other locations. We also found an association between deserts and xeric shrublands and a lower prevalence of Haemoproteus parasites. Our results support a lower MHC genetic in arid or semi-arid habitats in the region with the lower prevalence of Haemoproteus parasites.
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    Comparative Genomics Supports Ecologically Induced Selection as a Putative Driver of Banded Penguin Diversification
    (2024) Leon, Fabiola; Pizarro, Eduardo; Noll, Daly; Pertierra, Luis R.; Parker, Patricia; Espinaze, Marcela P. A.; Luna-Jorquera, Guillermo; Simeone, Alejandro; Frere, Esteban; Dantas, Gisele P. M.; Cristofari, Robin; Cornejo, Omar E.; Bowie, Rauri C. K.; Vianna, Juliana A.
    The relative importance of genetic drift and local adaptation in facilitating speciation remains unclear. This is particularly true for seabirds, which can disperse over large geographic distances, providing opportunities for intermittent gene flow among distant colonies that span the temperature and salinity gradients of the oceans. Here, we delve into the genomic basis of adaptation and speciation of banded penguins, Gal & aacute;pagos (Spheniscus mendiculus), Humboldt (Spheniscus humboldti), Magellanic (Spheniscus magellanicus), and African penguins (Spheniscus demersus), by analyzing 114 genomes from the main 16 breeding colonies. We aim to identify the molecular mechanism and genomic adaptive traits that have facilitated their diversifications. Through positive selection and gene family expansion analyses, we identified candidate genes that may be related to reproductive isolation processes mediated by ecological thermal niche divergence. We recover signals of positive selection on key loci associated with spermatogenesis, especially during the recent peripatric divergence of the Gal & aacute;pagos penguin from the Humboldt penguin. High temperatures in tropical habitats may have favored selection on loci associated with spermatogenesis to maintain sperm viability, leading to reproductive isolation among young species. Our results suggest that genome-wide selection on loci associated with molecular pathways that underpin thermoregulation, osmoregulation, hypoxia, and social behavior appears to have been crucial in local adaptation of banded penguins. Overall, these results contribute to our understanding of how the complexity of biotic, but especially abiotic, factors, along with the high dispersal capabilities of these marine species, may promote both neutral and adaptive lineage divergence even in the presence of gene flow.
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    Genetics, Morphometrics and Health Characterization of Green Turtle Foraging Grounds in Mainland and Insular Chile
    (2022) Alvarez-Varas, Rocio; Medrano, Carol; Benitez, Hugo A.; Guerrero, Felipe; Leon Miranda, Fabiola; Vianna, Juliana A.; Gonzalez, Camila; Veliz, David
    Simple Summary Chilean waters constitute a foraging habitat for the endangered green turtle. Information about this species in the country has increased in recent years; nevertheless, little is known of its ecology and health status. Additionally, some populations have drastically decreased, probably due to human factors. Here, we studied the proportion of sex, age, morphological variation, genetic characteristics, origin, and health status of green turtles in mainland and insular Chile. We found that turtles from both regions are morphologically and genetically different. Individuals from the mainland territory are juveniles and probably originated from Galapagos. In contrast, the insular territory hosts juveniles and adults that probably originated from Galapagos and French Polynesia. We also found that turtles from both regions are facing numerous anthropic threats that must be controlled. We suggest the creation of protected areas for mainland foraging grounds, and strengthen the administrative plan of the insular region to ensure sea turtle population health. Two divergent genetic lineages have been described for the endangered green turtle in the Pacific Ocean, occurring sympatrically in some foraging grounds. Chile has seven known green turtle foraging grounds, hosting mainly juveniles of different lineages. Unfortunately, anthropic factors have led to the decline or disappearance of most foraging aggregations. We investigated age-class/sex structure, morphological variation, genetic diversity and structure, and health status of turtles from two mainland (Bahia Salado and Playa Chinchorro) and one insular (Easter Island) Chilean foraging grounds. Bahia Salado is composed of juveniles, and with Playa Chinchorro, exclusively harbors individuals of the north-central/eastern Pacific lineage, with Galapagos as the major genetic contributor. Conversely, Easter Island hosts juveniles and adults from both the eastern Pacific and French Polynesia. Morphological variation was found between lineages and foraging grounds, suggesting an underlying genetic component but also an environmental influence. Turtles from Easter Island, unlike Bahia Salado, exhibited injuries/alterations probably related to anthropic threats. Our findings point to establishing legal protection for mainland Chile's foraging grounds, and to ensure that the administrative plan for Easter Island's marine protected area maintains ecosystem health, turtle population viability, and related cultural and touristic activities.
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    Have Historical Climate Changes Affected Gentoo Penguin (Pygoscelis papua) Populations in Antarctica?
    (2014) Pena M., Fabiola; Poulin, Elie; Dantas, Gisele P. M.; Gonzalez-Acuna, Daniel; Petry, Maria Virginia; Vianna, Juliana A.
    The West Antarctic Peninsula (WAP) has been suffering an increase in its atmospheric temperature during the last 50 years, mainly associated with global warming. This increment of temperature trend associated with changes in sea-ice dynamics has an impact on organisms, affecting their phenology, physiology and distribution range. For instance, rapid demographic changes in Pygoscelis penguins have been reported over the last 50 years in WAP, resulting in population expansion of sub-Antarctic Gentoo penguin (P. papua) and retreat of Antarctic Adelie penguin (P. adeliae). Current global warming has been mainly associated with human activities; however these climate trends are framed in a historical context of climate changes, particularly during the Pleistocene, characterized by an alternation between glacial and interglacial periods. During the last maximal glacial (LGM similar to 21,000 BP) the ice sheet cover reached its maximum extension on the West Antarctic Peninsula (WAP), causing local extinction of Antarctic taxa, migration to lower latitudes and/or survival in glacial refugia. We studied the HRVI of mtDNA and the nuclear intron beta fibint7 of 150 individuals of the WAP to understand the demographic history and population structure of P. papua. We found high genetic diversity, reduced population genetic structure and a signature of population expansion estimated around 13,000 BP, much before the first paleocolony fossil records (similar to 1,100 BP). Our results suggest that the species may have survived in peri-Antarctic refugia such as South Georgia and North Sandwich islands and recolonized the Antarctic Peninsula and South Shetland Islands after the ice sheet retreat.
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    History of Diversification and Adaptation from North to South Revealed by Genomic Data: Guanacos from the Desert to Sub-Antarctica
    (2024) Leon, Fabiola; Pizarro, Eduardo J.; Noll, Daly; Pertierra, Luis R.; Gonzalez, Benito A.; Johnson, Warren E.; Marin, Juan Carlos; Vianna, Juliana A.
    The increased availability of quality genomic data has greatly improved the scope and resolution of our understanding of the recent evolutionary history of wild species adapted to extreme environments and their susceptibility to anthropogenic impacts. The guanaco (Lama guanicoe), the largest wild ungulate in South America, is a good example. The guanaco is well adapted to a wide range of habitats, including the Sechura Desert, the high Andes Mountains to the north, and the extreme temperatures and conditions of Navarino Island to the south. Guanacos also have a long history of overexploitation by humans. To assess the evolutionary impact of these challenging habitats on the genomic diversity, we analyzed 38 genomes (similar to 10 to 16x) throughout their extensive latitudinal distribution from the Sechura and Atacama Desert to southward into Tierra del Fuego Island. These included analyses of patterns of unique differentiation in the north and geographic region further south with admixture among L. g. cacsilensis and L. g. guanicoe. Our findings provide new insights on the divergence of the subspecies similar to 800,000 yr BP and document two divergent demographic trajectories and to the initial expansion of guanaco into the more southern portions of the Atacama Desert. Patagonian guanacos have experienced contemporary reductions in effective population sizes, likely the consequence of anthropogenic impacts. The lowest levels of genetic diversity corresponded to their northern and western limits of distribution and some varying degrees of genetic differentiation. Adaptive genomic diversity was strongly linked with environmental variables and was linked with colonization toward the south followed by adaptation.
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    Integrating morphological and genetic data at different spatial scales in a cosmopolitan marine turtle species: challenges for management and conservation
    (2021) Alvarez-Varas, Rocio; Heidemeyer, Maike; Riginos, Cynthia; Benitez, Hugo A.; Resendiz, Eduardo; Lara-Uc, Monica; Godoy, Daniel A.; Pablo Munoz-Perez, Juan; Alarcon-Ruales, Daniela E.; Velez-Rubio, Gabriela M.; Fallabrino, Alejandro; Piovano, Susanna; Alfaro-Shigueto, Joanna; Ortiz-Alvarez, Clara; Mangel, Jeffrey C.; Esquerre, Damien; Zarate, Patricia; Medrano, Carol; Leon Miranda, Fabiola; Guerrero, Felipe; Vianna, Juliana A.; Veliz, David
    Patterns of genetic structure in highly mobile marine vertebrates may be accompanied by phenotypic variation. Most studies in marine turtles focused on population genetic structure have been performed at rookeries. We studied whether genetic and morphological variation of the endangered green turtle (Chelonia mydas) is consistent geographically, focusing on foraging grounds. An association between population genetic structure and body shape variation at broad (inter-lineage) and fine (foraging grounds) scales was predicted and analysed using mitochondrial DNA and geometric morphometrics. Although genetic and phenotypic differentiation patterns were congruent between lineages, no fine-scale association was found, suggesting adaptive divergence. Connectivity among Pacific foraging grounds found here suggests that temperatures of ocean surface currents may influence the genetic structure of C. mydas on a broad scale. Our results suggest that vicariance, dispersal, life-history traits and ecological conditions operating in foraging grounds have shaped the intraspecific morphology and genetic diversity of this species. Considering a range of geographic and temporal scales is useful when management strategies are required for cosmopolitan species. Integrating morphological and genetic tools at different spatial scales, conservation management is proposed based on protection of neutral and adaptive diversity. This approach opens new questions and challenges, especially regarding conservation genetics in cosmopolitan species.
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    Molecular divergence between insular and continental Pudu deer (Pudu puda) populations in the Chilean Patagonia
    (TAYLOR & FRANCIS LTD, 2011) Fuentes Hurtado, Marcelo; Marin, Juan C.; Gonzalez Acuna, Daniel; Verdugo, Claudio; Vidal, Fernando; Vianna, Juliana A.
    Island-continent isolation scenarios have played major roles in the understanding and development of evolutionary theories. During the last glacial maximum (LGM) in southern Chile, ice sheet advances and retreats formed the Patagonian archipelago along the southern Pacific Ocean. Chiloe Island is the largest island from the archipelago isolated from the continent by a narrow and shallow stretch of ocean. Pudu puda is a species endemic to Chile and part of Argentina, distributed along the Valdivian Temperate rainforest. We used mtDNA control region (654 bp) and cytochrome b (734 bp) sequences to understand the consequences in the evolutionary history and population structure of Pudu puda island-continent isolation. Bayesian and Maximum Likelihood phylogenetic analysis revealed two divergent clades corresponding to the continent and Chiloe Island. The Median Joining Network also supports these findings with an isolation of 10 mutational steps between Chiloe and the continent. We also found a significant high genetic structure (phi st = 0.75) and a sequence divergence percentage of 2.3% between the two clades. On the other hand, on the continent we found high haplotype genetic diversity (H = 0.9790 +/- 0.0103) but no clear geographical population structure or phylogenetic clades. Our results suggest that the southern Pudu deer populations were isolated since the interglacial period (less than 0.5 million years ago) from the continent leading to two reciprocally monophyletic clades. We propose two subspecies to be considered in the development of future conservation programs for the species.
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    Phylogenomics of the world's otters
    (2022) de Ferran, Vera; Figueiro, Henrique Vieira; Trindade, Fernanda de Jesus; Smith, Oliver; Sinding, Mikkel-Holger S.; Trinca, Cristine S.; Lazzari, Gabriele Zenato; Veron, Geraldine; Vianna, Juliana A.; Barbanera, Filippo; Kliver, Sergei; Serdyukova, Natalia; Bulyonkova, Tatiana; Ryder, Oliver A.; Gilbert, M. Thomas P.; Koepfli, Klaus-Peter; Eizirik, Eduardo
    Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,(1-5) a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.
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    Phylogeography and Demographic History of the Neotropical Otter (Lontra longicaudis)
    (OXFORD UNIV PRESS INC, 2012) Trinca, Cristine S.; de Thoisy, Benoit; Rosas, Fernando C. W.; Waldemarin, Helen F.; Koepfli, Klaus Peter; Vianna, Juliana A.; Eizirik, Eduardo
    The Neotropical otter (Lontra longicaudis) is a medium-sized semiaquatic carnivore with a broad distribution in the Neotropical region. Despite being apparently common in many areas, it is one of the least known otters, and genetic studies on this species are scarce. Here, we have investigated its genetic diversity, population structure, and demographic history across a large portion of its geographic range by analyzing 1471 base pairs (bp) of mitochondrial DNA from 52 individuals. Our results indicate that L. longicaudis presents high levels of genetic diversity and a consistent phylogeographic pattern, suggesting the existence of at least 4 distinct evolutionary lineages in South America. The observed phylogeographic partitions are partially congruent with the subspecies classification previously proposed for this species. Coalescence-based analyses indicate that Neotropical otter mitochondrial DNA lineages have shared a rather recent common ancestor, approximately 0.5 Ma, and have subsequently diversified into the observed phylogroups. A consistent scenario of recent population expansion was identified in Eastern South America based on several complementary analyses of historical demography. The results obtained here provide novel insights on the evolutionary history of this largely unknown Neotropical mustelid and should be useful to design conservation and management policies on behalf of this species and its habitats.
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    Phylogeography of the Marine Otter (Lontra felina): Historical and Contemporary Factors Determining Its Distribution
    (2010) Vianna, Juliana A.; Ayerdi, Paula; Medina-Vogel, Gonzalo; Mangel, Jeffrey C.; Zeballos, Horacio; Apaza, Manuel; Faugeron, Sylvain
    The evolutionary history of a species can be revealed by phylogeographical analysis; nevertheless, not only historical but also contemporary processes can imprint on the distribution of genetic diversity. We report on the phylogeny of Lontra ssp. in South America, and the role of spatial heterogeneity in shaping the distribution and population structure of the endangered marine otter, Lontra felina. Analyzing a total of 2261 bp of mitochondrial DNA (mtDNA) revealed the recent divergence of L. felina from L. provocax. A strong population structure (Phi(st) = 0.83, P < 0.0001) and a significant pattern of isolation by distance were described for L. felina (n = 168) across a wide geographical distribution (13 degrees 53'S to 43 degrees 36'S). Lontra felina mtDNA phylogeny is composed of 2 main clades: a clade from Peru and another composed of Chilean haplotypes. Northern populations show different divergent lineages and higher genetic diversity when compared with more recently colonized southern populations. Furthermore, long sandy beaches seem to act as barriers to dispersal, creating 2 evolutionary significant units in agreement with subspecies previous description, and at least 5 different management units (MUs). At a fine spatial scale, the size of rocky seashore patches, the distance between patches and anthropogenic factors also play important roles in species gene flow.
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    Phylogeography of the Patagonian otter Lontra provocax: adaptive divergence to marine habitat or signature of southern glacial refugia?
    (2011) Vianna, Juliana A.; Medina-Vogel, Gonzalo; Chehebar, Claudio; Sielfeld, Walter; Olavarria, Carlos; Faugeron, Sylvain
    Background: A number of studies have described the extension of ice cover in western Patagonia during the Last Glacial Maximum, providing evidence of a complete cover of terrestrial habitat from 41 degrees S to 56 degrees S and two main refugia, one in south-eastern Tierra del Fuego and the other north of the Chilo, Island. However, recent evidence of high genetic diversity in Patagonian river species suggests the existence of aquatic refugia in this region. Here, we further test this hypothesis based on phylogeographic inferences from a semi-aquatic species that is a top predator of river and marine fauna, the huillin or Southern river otter (Lontra provocax).
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    Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia
    (2024) Kasinsky, Tatiana; Rosciano, Natalia; Vianna, Juliana A.; Yorio, Pablo; Campagna, Leonardo
    The genetic identification of evolutionary significant units and information on their connectivity can be used to design effective management and conservation plans for species of concern. Despite having high dispersal capacity, several seabird species show population structure due to both abiotic and biotic barriers to gene flow. The Kelp Gull is the most abundant species of gull in the southern hemisphere. In Argentina it reproduces in both marine and freshwater environments, with more than 100,000 breeding pairs following a metapopulation dynamic across 140 colonies in the Atlantic coast of Patagonia. However, little is known about the demography and connectivity of inland populations. We aim to provide information on the connectivity of the largest freshwater colonies (those from Nahuel Huapi Lake) with the closest Pacific and Atlantic populations to evaluate if these freshwater colonies are receiving immigrants from the larger coastal populations. We sampled three geographic regions (Nahuel Huapi Lake and the Atlantic and Pacific coasts) and employed a reduced-representation genomic approach to genotype individuals for single-nucleotide polymorphisms (SNPs). Using clustering and phylogenetic analyses we found three genetic groups, each corresponding to one of our sampled regions. Individuals from marine environments are more closely related to each other than to those from Nahuel Huapi Lake, indicating that the latter population constitutes the first freshwater Kelp Gull colony to be identified as an evolutionary significant unit in Patagonia.
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    Species delimitation and intraspecific diversification in recently diverged South American foxes
    (2024) Pizarro, Eduardo J.; Julio-Kalajzic, Bernardita; Sallaberry-Pincheira, Nicole; Munoz, Valentina; Gonzalez-Acuna, Daniel; Cabello, Javier; Acosta-Jamett, Gerardo; Bonacic, Cristian; Iriarte, Agustin; Rodriguez, Alejandro; Travaini, Alejandro; Cevidanes, Aitor; Brito, Jose Luis; Millan, Javier; Marin, Juan Carlos; Vianna, Juliana A.
    The divergence between the Andean fox (Lycalopex culpaeus) and the South American gray fox (L. griseus) represents a recent speciation event in South America. These taxa are partially sympatric and share biological, morphological, and ecological traits. Previous studies failed to recover reciprocal monophyly, suggesting the occurrence of introgression or incomplete lineage sorting (ILS). Here, we obtained mitochondrial and nuclear markers for 140 L. culpaeus and 134 L. griseus from the Southern Cone of South America to assess their inter and intraspecific divergence. We recovered reciprocal monophyly of L. culpaeus and L. griseus, with mild signatures of introgression or ILS. Therefore, taxonomic misidentification and the use of a limited number of markers may be the main reason behind the past debate about the delimitation of both species. Two main divergent clades were found in L. culpaeus with a phylogeographical boundary in the High Plateau of northeastern Chile. The southern clade along with three northern sub-clades corresponded to four morphological subspecies. Less genetic differentiation was found in L. griseus with a spatial population structure that does not support the occurrence of distinct subspecies. The results found in this study suggest the extant evolutionary significant units that need to be considered for biological conservation management of these species.
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    The systematics of Tachymenini (Serpentes, Dipsadidae): An updated classification based on molecular and morphological evidence
    (2022) Trevine, Vivian C.; Grazziotin, Felipe G.; Giraudo, Alejandro; Sallesbery-Pinchera, Nicole; Vianna, Juliana A.; Zaher, Hussam
    Despite the recent advances in the systematics of snakes, the diversity of several Neotropical groups of species remains poorly understood. The lack of studies focused on the phylogenetic relationship within most of the 20 tribes of Dipsadidae precludes a better understanding of the evolution of this diverse family. Here, we present a comprehensive phylogenetic analysis of Tachymenini, a heterogeneous tribe that comprises 36 viviparous species of dipsadids, grouped in seven genera based on morphological similarities. The tribe is widely distributed throughout South America presenting very distinctive phenotypes, habitats, and behaviours. The phylogenetic relationship among tachymenins is a well-recognized challenge regarding the systematics of the South American dipsadids. The similar morphotype of some generalist species, combined with the very derived morphology of some strict specialists, creates a complexity of traits that has prevented the comprehension of the systematics of the group. To address such a challenge, we combine molecular (six loci) and morphological (70 characters) datasets in an integrative phylogenetic approach. The resultant phylogenetic trees indicate, with strong support, that three of the seven current recognized genera (Tachymenis, Tomodon, and Thamnodynastes) are non-monophyletic and, consequently, we propose a new systematic arrangement for Tachymenini. We revalidate two genera, Dryophylax and Mesotes, and we describe three additional monotypic genera, Apographon gen. n., Tachymenoides gen. n., and Zonateres gen. n. to accommodate Tomodon orestes, Tachymenis affinis, and Thamnodynastes lanei, respectively. We also include Tomodon ocellatus and Pseudotomodon trigonatus in Tachymenis and describe a new genus, Galvarinus gen. n., to accommodate the Tachymenis chilensis species group. Furthermore, we also provide an evolutionary scenario for the speciation events based on a time-calibrated tree, commenting on the diversification and origin of the tribe, and on the probable existence of undescribed species of Mesotes and Dryophylax.
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    Uncovering population structure in the Humboldt penguin (Spheniscus humboldti) along the Pacific coast at South America
    (2019) Dantas, Gisele P. M.; Oliveira, Larissa R.; Santos, Amanda M.; Flores, Mariana D.; de Melo, Daniella R.; Simeone, Alejandro; Gonzalez-Acuna, Daniel; Luna-Jorquera, Guillermo; Le Bohec, Celine; Valdes-Velasquez, Armando; Cardena, Marco; Morgante, Joao S.; Vianna, Juliana A.
    The upwelling hypothesis has been proposed to explain reduced or lack of population structure in seabird species specialized in food resources available at cold-water upwellings. However, population genetic structure may be challenging to detect in species with large population sizes, since variation in allele frequencies are more robust under genetic drift. High gene flow among populations, that can be constant or pulses of migration in a short period, may also decrease power of algorithms to detect genetic structure. Penguin species usually have large population sizes, high migratory ability but philopatric behavior, and recent investigations debate the existence of subtle population structure for some species not detected before. Previous study on Humboldt penguins found lack of population genetic structure for colonies of Punta San Juan and from South Chile. Here, we used mtDNA and nuclear markers (10 microsatellites and RAG1 intron) to evaluate population structure for 11 main breeding colonies of Humboldt penguins, covering the whole spatial distribution of this species. Although mtDNA failed to detect population structure, microsatellite loci and nuclear intron detected population structure along its latitudinal distribution. Microsatellite showed significant R-st values between most of pairwise locations (44 of 56 locations, R-st = 0.003 to 0.081) and 86% of individuals were assigned to their sampled colony, suggesting philopatry. STRUCTURE detected three main genetic clusters according to geographical locations: i) Peru; ii) North of Chile; and iii) Central-South of Chile. The Humboldt penguin shows signal population expansion after the Last Glacial Maximum (LGM), suggesting that the genetic structure of the species is a result of population dynamics and foraging colder water upwelling that favor gene flow and phylopatric rate. Our findings thus highlight that variable markers and wide sampling along the species distribution are crucial to better understand genetic population structure in animals with high dispersal ability.