Comparing alignment methods for inferring the history of the new world lizard genus Mabuya (Squamata

Abstract The rapid increase in the ability to generate molecular data, and the focus on model-based methods for tree reconstruction have greatly advanced the use of phylogenetics in many Welds. The recent Xurry of new analytical techniques has focused almost solely on tree reconstruction, whereas alignment issues have received far less attention. In this paper, we use a diverse sampling of gene regions from lizards of the genus Mabuya to compare the impact, on phylogeny estimation, of new maximum likelihood alignment algorithms with more widely used methods. Sequences aligned under diVerent optimality criteria are analyzed using partitioned Bayesian analysis with independent models and parameter settings for each gene region, and the most strongly supported phylogenetic hypothesis is then used to test the hypothesis of two colonizations of the New World by African scincid lizards. Our results show that the consistent use of model-based methods in both alignment and tree reconstruction leads to trees with more optimal likelihood scores than the use of independent criteria in alignment and tree reconstruction. We corroborate and extend earlier evidence for two independent colonizations of South America by scincid lizards. Relationships within South American Mabuya are found to be in need of taxonomic revision, speciWcally complexes under the names M. heathi, M. agilis, and M. bistriata (sensu, M.T. Rodrigues, Papeis Avulsos de Zoologia 41 (2000) 313)

Comparing alignment methods for inferring the history of the new world lizard genus Mabuya (Squamata

Abstract The rapid increase in the ability to generate molecular data, and the focus on model-based methods for tree reconstruction have greatly advanced the use of phylogenetics in many Welds. The recent Xurry of new analytical techniques has focused almost solely on tree reconstruction, whereas alignment issues have received far less attention. In this paper, we use a diverse sampling of gene regions from lizards of the genus Mabuya to compare the impact, on phylogeny estimation, of new maximum likelihood alignment algorithms with more widely used methods. Sequences aligned under diVerent optimality criteria are analyzed using partitioned Bayesian analysis with independent models and parameter settings for each gene region, and the most strongly supported phylogenetic hypothesis is then used to test the hypothesis of two colonizations of the New World by African scincid lizards. Our results show that the consistent use of model-based methods in both alignment and tree reconstruction leads to trees with more optimal likelihood scores than the use of independent criteria in alignment and tree reconstruction. We corroborate and extend earlier evidence for two independent colonizations of South America by scincid lizards. Relationships within South American Mabuya are found to be in need of taxonomic revision, speciWcally complexes under the names M. heathi, M. agilis, and M. bistriata (sensu, M.T. Rodrigues, Papeis Avulsos de Zoologia 41 (2000) 313)

Description and Phylogenetic Relationships of a New Genus and Species of Lizard (Squamata, Gymnophthalmidae) from the Amazonian Rainforest of Northern Brazil

Peloso, Pedro L.V., Pellegrino, Katia C. M., Rodrigues, Miguel T., Ávila-Pires, Teresa C.S. (2011): Description and Phylogenetic Relationships of a New Genus and Species of Lizard (Squamata, Gymnophthalmidae) from the Amazonian Rainforest of Northern Brazil. American Museum Novitates 2011 (3713): 1-24, DOI: 10.1206/3713.2, URL: http://www.bioone.org/doi/abs/10.1206/3713.

Description and Phylogenetic Relationships of a New Genus and Species of Lizard (Squamata, Gymnophthalmidae) from the Amazonian Rainforest of Northern Brazil

Marinussaurus curupira, a new genus and species of Gymnophthalmidae lizard is described from Iranduba, state of Amazonas, Brazil. The genus is characterized by an elongate body; short and stout pentadactyl limbs; all digits clawed; single frontonasal; two prefrontals; absence of frontoparietals; interparietal and parietals forming a straight posterior margin, with interparietal shorter than parietals; distinctive ear opening and eyelid; few temporals; three pairs of chin shields; nasal divided; a distinct collar; smooth, mainly hexagonal, dorsal scales; smooth quadrangular ventral scales; two precloacal and three femoral pores on each side in males; pores between three or four scales. Parsimony (PAR) and partitioned Bayesian (BA) phylogenetic analyses with morphological and molecular data recovered the new genus as a member of the Ecpleopodini radiation of the Cercosaurinae. A close relationship of the new genus with Arthrosaura is postulated.Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)[03/10335-8R]Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)Smithsonian InstitutionCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior / Fulbright Commission (CAPES/IIE)[BEX 2806/09-6]Richard Gilder Graduate School at the American Museum of Natural Histor

The first mitochondrial genome of a South America parthenogenetic lizard (Squamata: Gymnophthalmidae)

The mitogenome of the South American parthenogenetic lizard Loxopholis percarinatum Müller, 1923 (Squamata: Gymnophthalmidae), a uni-bisexual species complex, was recovered for three individuals from Rio Negro region, Amazonas, Brazil. The content and order of genes are typical for vertebrate mitochondrial genomes, and we recovered 13 protein-coding genes, 22 tRNA, and two rRNA (12S and 16S), in addition to partial fragments of the Control Region. A maximum likelihood phylogenetic analysis with mitogenomes of selected lizard families recovered L. percarinatum with Iphisa elegans Gray, 1851, the only other Gymnophthalmidae species available in GenBank

Karyotype characterization and nucleolar organizer regions of marsupial species (Didelphidae) from areas of Cerrado and Atlantic Forest in Brazil

The karyotypes of 23 specimens belonging to 16 species from nine genera of Brazilian marsupials (family Didelphidae) were studied. The animals were collected in eight localities of Cerrado or Atlantic Forest biomes in the states of Goiás, Tocantins and São Paulo. The karyotypes were analyzed after conventional Giemsa staining and silver staining of the nucleolus organizer regions (Ag-NORs). New karyotypic data were obtained for Gracilinanus microtarsus (2n = 14, FN = 24), Marmosops paulensis (2n = 14, FN = 24) , Micoreus paraguayanus (2n = 14, FN = 20) and Monodelphis rubida (2n = 18, FN = 32) and are discussed in detail. The karyotypes of G. microtarsus , M. paulensis and M. paraguayanus include three large pairs of submetacentrics (pairs 1, 2 and 3) and a medium-sized metacentric or submetacentric pair 4. Pairs 5 and 6 are small submetacentrics in G. microtarsus and M. paulensis and acrocentrics in M. paraguayanus . M. paulensis presented a single Ag-NOR in pair 6 (6p6p), while M. paraguayanus exhibited multiple Ag-NORs in pairs 5 and 6 (5pq5pq6p6p). There was variation in size and morphology of the sex chromosomes among these species. Monodelphis rubida presented a karyotype with 2n = 18 and FN = 32 composed of a large submetacentric pair 1, a medium-sized metacentric pair 2 and six pairs of submetacentrics (pairs 3 through 8). The X was a small acrocentric and the Y was dot-like. A single Ag-NOR bearing pair (5p5p) characterized M. rubida. Relevant karyotypic information was obtained for 19 specimens belonging to 12 species collected in areas sampled for the first time [ Caluromys lanatus and C. philander (2n = 14, FN = 20), Gracilinanus emiliae (2n = 14, FN = 24), Marmosa murina , Metachirus nudicaudatus and Micoureus demerarae (2n = 14, FN = 20), Monodelphis americana (2n = 18, FN = 32) and M. domestica (2n = 18, FN = 20), and Didelphis marsupialis, Philander frenata, P. opossum and P. sp (2n = 22, FN = 20)]. Although the karyotypes were relatively conserved with respect to the morphology of the autosomes among species with the same diploid number, some differences regarding FN, sex chromosomes morphology and Ag-NORs patterns were detected

Karyotypes of a Cryptic Diploid Form of the Unisexual Leposoma percarinatum (Squamata, Gymnophthalmidae) and the Bisexual Leposoma ferreirai from the Lower Rio Negro, Amazonian Brazil

Karyotypes of Leposoma show a clear differentiation between species of the scincoides group from Brazilian Atlantic Forest (2n = 52, without distinctive size groups of chromosomes) and those of the parietale group from the Amazon (2n = 44, with 20M + 24m). In a previous study, we found that in the parietale group the parthenoform Leposoma percarinatum from the state of Mato Grosso, Brazil, exhibited a triploid karyotype (3n = 66) with 30 macrochromosomes and 36 microchromosomes. It was suggested that this karyotype arose after hybridization between a bisexual species with N = 22 (10M + 12m) and a hypothetical unisexual cryptic diploid form of the L. percarinatum complex. Herein, we describe the karyotypes for two species of the parietale group occurring sympatrically in the Arquipelago das Anavilhanas, lower Rio Negro, in Amazonian Brazil. The first represents a distinctive diploid parthenogenetic clone of the L. percarinatum complex, and the other is the recently described Leposoma ferreirai. Both species have 44 biarmed chromosomes clearly represented by 20 macrochromosomes and 24 microchromosomes and present Ag-NORs in one pair of the smallest sized microchromosomes; heteromorphism of size for these regions was detected in L. percarinatum. C-banding revealed blocks of constitutive heterochromatin on the telomeric and pericentromeric regions of macrochromosomes and some microchromosomes. The description of a diploid karyotype (2n = 44, 20M + 24m) for the L. percarinatum complex and its sympatric congener L. ferreirai provides new insight for a better understanding of the origin of parthenogenesis in the L. percarinatum complex.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Sao Paulo, Inst Biociencias, Dept Genet & Biol Evolut, BR-05508090 Sao Paulo, BrazilUniv Sao Paulo, Inst Biociencias, Dept Zool, BR-05508090 Sao Paulo, BrazilMuseu Paraense Emilio Goeldi CZO, BR-66017970 Belem, Para, BrazilUniv Fed Sao Paulo, Dept Ciencias Biol, BR-09972270 Sao Paulo, BrazilUniv Fed Sao Paulo, Dept Ciencias Biol, BR-09972270 Sao Paulo, BrazilWeb of Scienc

Karyotypes of a Cryptic Diploid Form of the Unisexual Leposoma percarinatum (Squamata, Gymnophthalmidae) and the Bisexual Leposoma ferreirai from the Lower Rio Negro, Amazonian Brazil

Karyotypes of Leposoma show a clear differentiation between species of the scincoides group from Brazilian Atlantic Forest (2n = 52, without distinctive size groups of chromosomes) and those of the parietale group from the Amazon (2n = 44, with 20M + 24m). In a previous study, we found that in the parietale group the parthenoform Leposoma percarinatum from the state of Mato Grosso, Brazil, exhibited a triploid karyotype (3n = 66) with 30 macrochromosomes and 36 microchromosomes. It was suggested that this karyotype arose after hybridization between a bisexual species with N = 22 (10M + 12m) and a hypothetical unisexual cryptic diploid form of the L. percarinatum complex. Herein, we describe the karyotypes for two species of the parietale group occurring sympatrically in the Arquipelago das Anavilhanas, lower Rio Negro, in Amazonian Brazil. The first represents a distinctive diploid parthenogenetic clone of the L. percarinatum complex, and the other is the recently described Leposoma ferreirai. Both species have 44 biarmed chromosomes clearly represented by 20 macrochromosomes and 24 microchromosomes and present Ag-NORs in one pair of the smallest sized microchromosomes; heteromorphism of size for these regions was detected in L. percarinatum. C-banding revealed blocks of constitutive heterochromatin on the telomeric and pericentromeric regions of macrochromosomes and some microchromosomes. The description of a diploid karyotype (2n = 44, 20M + 24m) for the L. percarinatum complex and its sympatric congener L. ferreirai provides new insight for a better understanding of the origin of parthenogenesis in the L. percarinatum complex.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESP Fundacao de Amparo a Pesquisa do Estado de Sao PauloCNPq Conselho Nacional de Desenvolvimento Cientifico e TecnologicoConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes.

Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete mitochondrial genomes with high sequencing depth. Identification of dozens of microsatellite loci and assembly of complete mitogenomes is exemplified here using three species of Poospiza warbling finches from southern and southeastern Brazil. This strategy opens exciting opportunities to simultaneously analyze genome-wide nuclear datasets and traditionally used mtDNA and microsatellite markers in non-model amniotes at no additional cost