RESUMEN

The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world's most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.

Asunto(s)

Callithrix/genética , Especies en Peligro de Extinción , Genómica/métodos , Hibridación Genética/genética , Secuenciación de Nanoporos/métodos , Animales , Brasil , Callithrix/clasificación , ADN Mitocondrial/clasificación , ADN Mitocondrial/genética , Evolución Molecular , Genoma Mitocondrial/genética , Masculino , Fenotipo , Filogenia , Especificidad de la Especie

RESUMEN

The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.

Asunto(s)

ADN Mitocondrial/genética , Variación Genética , Genética de Población , Genoma Mitocondrial/genética , Migración Humana , Argentina , ADN Antiguo/análisis , ADN Mitocondrial/análisis , ADN Mitocondrial/clasificación , Geografía , Haplotipos , Humanos , Filogenia , Análisis de Secuencia de ADN , América del Sur , Factores de Tiempo

RESUMEN

Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700-2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200-1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.

Asunto(s)

ADN Antiguo/análisis , Fósiles , Flujo Génico , Genoma Humano/genética , Migración Humana , Arqueología/métodos , Argentina , Huesos/metabolismo , Chile , ADN Mitocondrial/clasificación , ADN Mitocondrial/genética , Variación Genética , Geografía , Humanos , Filogenia , Datación Radiométrica/métodos , Análisis de Secuencia de ADN/métodos , Diente/metabolismo

RESUMEN

OBJECTIVES: The aim of this work is to explore the maternal genetic diversity of hunter-gatherers of the southern Tierra del Fuego, specifically the north coast of Beagle Channel, the Península Mitre, and Isla de los Estados through ancient mitochondrial DNA analysis. MATERIALS AND METHODS: The hypervariable regions 1 and 2 of the mitochondrial genome of five individuals from the north coast of Beagle Channel, six individuals from Península Mitre, and one individual from Isla de los Estados were analyzed. Through diversity statistics, Analysis of Molecular Variance (AMOVA), and Median Joining networks analyses, maternal relationships in the region were evaluated and phylogenetic similarities between ancient and contemporary populations of Tierra del Fuego were determined. RESULTS: The mitochondrial DNA lineages from the ancient individuals analyzed reveals the presence of subclades C1b and D1g. Pattern of decreasing genetic diversity toward the South is observed. The AMOVAs performed found no statistically significant differences between individuals of the north coast of Beagle Channel and Península Mitre-Isla de los Estados, and modern Yámana populations. Median joining network of haplotypes of clades C1 and D1g, show the same results. DISCUSSION: Ethnohistoric and ethnographic records of Península Mitre show that this region was occupied during the 19th century by Haush or Manekenk populations, although their biological, cultural, and subsistence characterization is unclear. We explore their maternal lineages and encounter low levels of genetic diversity and the absence of population differentiation with modern Yámana groups. We suggest that Península Mitre-Isla de los Estado was part of the same hunting and gathering populations as those of the Beagle Channel.

Asunto(s)

ADN Mitocondrial , Indígenas Sudamericanos , Adulto , Argentina , ADN Mitocondrial/clasificación , ADN Mitocondrial/genética , Femenino , Variación Genética/genética , Genética de Población , Haplotipos/genética , Historia Antigua , Humanos , Indígenas Sudamericanos/clasificación , Indígenas Sudamericanos/genética , Indígenas Sudamericanos/historia , Masculino , Persona de Mediana Edad , Adulto Joven

RESUMEN

We infer phylogenetic relationships, divergence times, and the diversification history of the avian Neotropical antpitta genera Hylopezus and Myrmothera (Grallariidae), based on sequence data (3,139 base pairs) from two mitochondrial (ND2 and ND3) and three nuclear nuclear introns (TGFB2, MUSK and FGB-I5) from 142 individuals of the 12 currently recognized species in Hylopezus and Myrmothera and 5 outgroup species. Phylogenetic analyses recovered 19 lineages clustered into two major clades, both distributed in Central and South America. Hylopezus nattereri, previously considered a subspecies of H. ochroleucus, was consistently recovered as the most divergent lineage within the Grallaricula/Hylopezus/Myrmothera clade. Ancestral range estimation suggested that modern lowland antpittas probably originated in the Amazonian Sedimentary basin during the middle Miocene, and that most lineages within the Hylopezus/Myrmothera clade appeared in the Plio-Pleistocene. However, the rate of diversification in the Hylopezus/Myrmothera clade appeared to have remained constant through time, with no major shifts over the 20 million years. Although the timing when most modern lineages of the Hylopezus/Myrmothera clade coincides with a period of intense landscape changes in the Neotropics (Plio-Pleistocene), the absence of any significant shifts in diversification rates over the last 20 million years challenges the view that there is a strict causal relationship between intensification of landscape changes and cladogenesis. The relative old age of the Hylopezus/Myrmothera clade coupled with an important role ascribed to dispersal for its diversification, favor an alternative scenario whereby long-term persistence and dispersal across an ever-changing landscape might explain constant rates of cladogenesis through time.

Asunto(s)

Passeriformes/clasificación , Animales , Biodiversidad , ADN Mitocondrial/química , ADN Mitocondrial/clasificación , ADN Mitocondrial/genética , Variación Genética , Intrones , Passeriformes/genética , Filogenia , Filogeografía , Análisis de Secuencia de ADN , América del Sur , Factor de Crecimiento Transformador beta2/clasificación , Factor de Crecimiento Transformador beta2/genética , Factor de Crecimiento Transformador beta2/metabolismo

RESUMEN

 This study was realized to determine the genetic variation of Central Javanese duck based on the D-Loop mtDNA gene. D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method with ABI automatic sequencer. ClustalW from MEGA-6.06 software program was employed for multiple alignments of nucleotide sequences. Nucleotide sequences of D-loop gene of mtDMA from the Central Javanese duck were aligned together with other Anas isolates from Genbank using ClustalW of MEGA-6.06 program. The estimation of genetic distance and phylogenetic tree construction were analyzed by Neighbor-Joining method, whereas the calculation of distance matrix was performed using Kimura 2-parameter. Multiple alignments obtained were 720 nucleotides at position 56 to 779 at the 5 "end. The results of the polymorphism analysis on D-loop sequences produced 23 haplotypes. However, this haplotype information does not represent the relationship among the geographical origins of duck with the certain duck species name. Moreover, a total number of 32 variable sites were identified. Insertions were detected in four sequences (126, 155, 771 and 779 nucleotide number). In the phylogenetic analysis, it is safe to conclude that the Central Javanese duck is closely related to Anas platyrhynchos and Anas zonorynchos.(AU)

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Este estudo foi realizado para determinar a variação genética do pato de Java Central baseado no D-Loop mtDNA. A D-Loop foi amplificada utilizando a técnica de PCR com primer específico e sequenciado usando o método de terminação dideoxi com sequenciador ITB automático. ClustalW do programa software de MEGA-6.06 foi utilizado para alinhamentos de algumas sequências de nucleótidos. Sequências de nucleótidos de D-loop gene da mtDMA do pato de Java Central foram alinhados em conjunto com alguns isolados de Anas que foram obtidos de Genbank utilizando o programa ClustalW do programa MEGA-6.06. A estimativa da distância genética e a estrutura da árvore filogenética foram analisadas com o método Neighbor-Joining, enquanto que o cálculo da matriz de distância foi utilizado o parâmetro-2 Kimura. Os alinhamentos múltiplos obtidos foram 720 nucleótideos na posição 56 a 779 na extremidade 5. As análises do polimorfismo sequencial do D-loop resultaram em 23 haplótipos. No entanto, esta informação haplótipo não representa a relação entre a origem geográfica de pato com o nome de determinadas espécies do pato. Além disso, num total de 32 sites favoráveis foram identificados. As inserções foram detectadas em quatro sequências (126, 155, 771 e 779 números de nucleotídeos). Na análise filogenética é seguro concluir que o pato de Java Central está estreitamente relacionada com a Anas platyrhynchos e Anas zonorynchos.(AU)

Asunto(s)

Animales , Patos/genética , ADN Mitocondrial/análisis , ADN Mitocondrial/clasificación , ADN Mitocondrial/genética

RESUMEN

This study was realized to determine the genetic variation of Central Javanese duck based on the D-Loop mtDNA gene. D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method with ABI automatic sequencer. ClustalW from MEGA-6.06 software program was employed for multiple alignments of nucleotide sequences. Nucleotide sequences of D-loop gene of mtDMA from the Central Javanese duck were aligned together with other Anas isolates from Genbank using ClustalW of MEGA-6.06 program. The estimation of genetic distance and phylogenetic tree construction were analyzed by Neighbor-Joining method, whereas the calculation of distance matrix was performed using Kimura 2-parameter. Multiple alignments obtained were 720 nucleotides at position 56 to 779 at the 5 "end. The results of the polymorphism analysis on D-loop sequences produced 23 haplotypes. However, this haplotype information does not represent the relationship among the geographical origins of duck with the certain duck species name. Moreover, a total number of 32 variable sites were identified. Insertions were detected in four sequences (126, 155, 771 and 779 nucleotide number). In the phylogenetic analysis, it is safe to conclude that the Central Javanese duck is closely related to Anas platyrhynchos and Anas zonorynchos.

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Este estudo foi realizado para determinar a variação genética do pato de Java Central baseado no D-Loop mtDNA. A D-Loop foi amplificada utilizando a técnica de PCR com primer específico e sequenciado usando o método de terminação dideoxi com sequenciador ITB automático. ClustalW do programa software de MEGA-6.06 foi utilizado para alinhamentos de algumas sequências de nucleótidos. Sequências de nucleótidos de D-loop gene da mtDMA do pato de Java Central foram alinhados em conjunto com alguns isolados de Anas que foram obtidos de Genbank utilizando o programa ClustalW do programa MEGA-6.06. A estimativa da distância genética e a estrutura da árvore filogenética foram analisadas com o método Neighbor-Joining, enquanto que o cálculo da matriz de distância foi utilizado o parâmetro-2 Kimura. Os alinhamentos múltiplos obtidos foram 720 nucleótideos na posição 56 a 779 na extremidade 5’. As análises do polimorfismo sequencial do D-loop resultaram em 23 haplótipos. No entanto, esta informação haplótipo não representa a relação entre a origem geográfica de pato com o nome de determinadas espécies do pato. Além disso, num total de 32 sites favoráveis foram identificados. As inserções foram detectadas em quatro sequências (126, 155, 771 e 779 números de nucleotídeos). Na análise filogenética é seguro concluir que o pato de Java Central está estreitamente relacionada com a Anas platyrhynchos e Anas zonorynchos.

Asunto(s)

Animales , ADN Mitocondrial/análisis , ADN Mitocondrial/clasificación , ADN Mitocondrial/genética , Patos/genética

RESUMEN

The Basque Diaspora in Western USA and Argentina represents two populations which have maintained strong Basque cultural and social roots in a completely different geographic context. Hence, they provide an exceptional opportunity to study the maternal genetic legacy from the ancestral Basque population and assess the degree of genetic introgression from the host populations in two of the largest Basque communities outside the Basque Country. For this purpose, we analyzed the complete mitochondrial DNA control region of Basque descendants living in Western USA (n = 175) and in Argentina (n = 194). The Diaspora populations studied here displayed a genetic diversity in their European maternal input which was similar to that of the Basque source populations, indicating that not important founder effects would have occurred. Actually, the genetic legacy of the Basque population still prevailed in their present-day maternal pools, by means of a haplogroup distribution similar to the source population characterized by the presence of autochthonous Basque lineages, such as U5b1f1a and J1c5c1. However, introgression of non-Basque lineages, mostly Native American, has been observed in the Diaspora populations, particularly in Argentina, where the quick assimilation of the newcomers would have favored a wider admixture with host populations. In contrast, a longer isolation of the Diaspora groups in USA, because of language and cultural differences, would have limited the introgression of local lineages. This study reveals important differences in the maternal evolutionary histories of these Basque Diaspora populations, which have to be taken into consideration in forensic and medical genetic studies.

Asunto(s)

ADN Mitocondrial/química , Argentina , Evolución Biológica , ADN Mitocondrial/clasificación , Emigración e Inmigración , Ligamiento Genético , Variación Genética , Genética de Población , Haplotipos , Humanos , Mitocondrias/genética , Filogenia , Análisis de Secuencia de ADN , Estados Unidos , Población Blanca/genética

RESUMEN

In 1985, a frozen mummy was found in Cerro Aconcagua (Argentina). Archaeological studies identified the mummy as a seven-year-old Inca sacrifice victim who lived >500 years ago, at the time of the expansion of the Inca Empire towards the southern cone. The sequence of its entire mitogenome was obtained. After querying a large worldwide database of mitogenomes (>28,000) we found that the Inca haplotype belonged to a branch of haplogroup C1b (C1bi) that has not yet been identified in modern Native Americans. The expansion of C1b into the Americas, as estimated using 203 C1b mitogenomes, dates to the initial Paleoindian settlements (~18.3 thousand years ago [kya]); however, its internal variation differs between Mesoamerica and South America. By querying large databases of control region haplotypes (>150,000), we found only a few C1bi members in Peru and Bolivia (e.g. Aymaras), including one haplotype retrieved from ancient DNA of an individual belonging to the Wari Empire (Peruvian Andes). Overall, the results suggest that the profile of the mummy represents a very rare sub-clade that arose 14.3 (5-23.6) kya and could have been more frequent in the past. A Peruvian Inca origin for present-day C1bi haplotypes would satisfy both the genetic and paleo-anthropological findings.

Asunto(s)

ADN Mitocondrial/genética , Genoma Mitocondrial/genética , Indígenas Sudamericanos , Momias , Argentina , Niño , ADN Mitocondrial/química , ADN Mitocondrial/clasificación , Haplotipos , Humanos , Filogenia , Religión , Análisis de Secuencia de ADN

RESUMEN

Historical discourses about the Caribbean often chronicle West African and European influence to the general neglect of indigenous people's contributions to the contemporary region. Consequently, demographic histories of Caribbean people prior to and after European contact are not well understood. Although archeological evidence suggests that the Lesser Antilles were populated in a series of northward and eastern migratory waves, many questions remain regarding the relationship of the Caribbean migrants to other indigenous people of South and Central America and changes to the demography of indigenous communities post-European contact. To explore these issues, we analyzed mitochondrial DNA and Y-chromosome diversity in 12 unrelated individuals from the First Peoples Community in Arima, Trinidad, and 43 unrelated Garifuna individuals residing in St. Vincent. In this community-sanctioned research, we detected maternal indigenous ancestry in 42% of the participants, with the remainder having haplotypes indicative of African and South Asian maternal ancestry. Analysis of Y-chromosome variation revealed paternal indigenous American ancestry indicated by the presence of haplogroup Q-M3 in 28% of the male participants from both communities, with the remainder possessing either African or European haplogroups. This finding is the first report of indigenous American paternal ancestry among indigenous populations in this region of the Caribbean. Overall, this study illustrates the role of the region's first peoples in shaping the genetic diversity seen in contemporary Caribbean populations.

Asunto(s)

Cromosomas Humanos Y , ADN Mitocondrial/genética , Variación Genética , Pueblo Asiatico/genética , Población Negra/genética , Región del Caribe , Hibridación Genómica Comparativa , ADN Mitocondrial/análisis , ADN Mitocondrial/clasificación , Femenino , Genética de Población , Haplotipos , Humanos , Masculino , Filogenia , Polimorfismo de Nucleótido Simple , San Vicente y las Grenadinas , Trinidad y Tobago , Población Blanca/genética

RESUMEN

In the present study, the complete mitochondrial (mt) genome of Cyclemys dentata was determined using PCR reactions. The structural organization and gene order of C. dentata were equivalent to those of most other vertebrates. The mt genome was 16,489 bp in length, has rich A+T content, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). All protein-coding genes started with ATG, many genes have complete stop codons, except ND2, COX3, ND3, and cyt-b genes had incomplete stop codons of T. The light-strand replication origin (OL) of C. dentata might fold into a stable stem-loop secondary structure, and its loop had 2 nt less than that of the Cyclemys atripons OL sequence. The D-Loop of C. dentata contained a central domain (CD), 2 extended termination associated sequences (ETAS1, ETAS2) and 3 conserved sequence blocks (CSB1, CSB2, CSB3). The average length of 20 turtles' mt genomes was 16,692.5 bp, including 34.1% A, 27.0% T, 26.0% C and 12.9% G. The C. dentata mitochondrial genome could provide useful data for further studies on phylogenetics and conservation genetics of this species. The phylogenetic relationships of the family Geoemydidae were analyzed by maximum-likelihood (ML) and neighbor-joining (NJ) based on concatenated sequences of 13 protein-coding genes from 20 turtle species. The ML and NJ trees had homologous topologies. The results support the existing classification of the genera of Geoemydidae, that C. dentata was a sister species of C. atripons, Pyxidea nested in Cuora, and Chinemys was synonymous with Mauremys.

Asunto(s)

ADN Mitocondrial/genética , Genoma Mitocondrial/genética , Filogenia , Tortugas/genética , Animales , Secuencia de Bases , ADN Circular/química , ADN Circular/genética , ADN Mitocondrial/química , ADN Mitocondrial/clasificación , Orden Génico , Genes Mitocondriales/genética , Proteínas Mitocondriales/genética , Datos de Secuencia Molecular , Análisis de Secuencia de ADN , Tortugas/clasificación

RESUMEN

Population genetic structure and demographic history of the ground beetle Chlaenius costiger (Coleoptera: Carabidae) in the Tsinling-Dabashan Mountains of central China were estimated using mitochondrial DNA sequences (Cox1-tRNALeu-Cox2) of 144 individuals from 16 local populations. The high haplotype diversity was accompanied by low nucleotide diversity. Phylogenetic analysis (Bayesian inference) of the 43 haplotypes revealed no phylogeographic structure. Analysis of molecular variance suggested that most of the variation was attributed to within population variation (79.26%). Mantel test results showed a significant correlation between the genetic distance and geographical distance of the populations with a correlation coefficient equal to 0.216964 (P = 0.0471 < 0.05), indicating the presence of isolation by distance. Spatial AMOVA and PERMUT analyses showed no phylogeographic structure. Gene flow calculated through the number of migrants was high between many pairs of populations. The results of a neutrality test, mismatch distribution analyses, and Bayesian skyline plot analysis together showed a demographic expansion. The estimated expansion time of the whole sampled population was 0.125 million years. The complex topography in the Tsinling-Dabashan Mountains area led to the high level of genetic diversity, and migratory flight resulted in the high level of gene flow, leading to the lack of a phylogeographic structure.

Asunto(s)

Escarabajos/genética , ADN Mitocondrial/genética , Variación Genética , Haplotipos , Altitud , Análisis de Varianza , Migración Animal , Animales , Teorema de Bayes , China , ADN Mitocondrial/clasificación , Vuelo Animal , Flujo Génico , Genética de Población , Geografía , Filogenia , Filogeografía , Dinámica Poblacional

RESUMEN

BACKGROUND: Guatemala is a multiethnic and multilingual country located in Central America. The main population groups separate 'Ladinos' (mixed Native American-African-Spanish), and Native indigenous people of Maya descent. Among the present-day Guatemalan Maya, there are more than 20 different ethnic groups separated by different languages and cultures. Genetic variation of these communities still remains largely unexplored. The principal aim of this study is to explore the genetic variability of the Maya and 'Ladinos' from Guatemala by means of uniparental and ancestry informative markers (AIMs). RESULTS: Analyses of uniparental genetic markers indicate that Maya have a dominant Native American ancestry (mitochondrial DNA [mtDNA]: 100%; Y-chromosome: 94%). 'Ladino', however, show a clear gender-bias as indicated by the large European ancestry observed in the Y-chromosome (75%) compared to the mtDNA (0%). Autosomal polymorphisms (AIMS) also mirror this marked gender-bias: (i) Native American ancestry: 92% for the Maya vs. 55% for the 'Ladino', and (ii) European ancestry: 8% for the Maya vs. 41% for the 'Ladino'. In addition, the impact of the Trans-Atlantic slave trade on the present-day Guatemalan population is very low (and only occurs in the 'Ladino'; mtDNA: 9%; AIMS: 4%), in part mirroring the fact that Guatemala has a predominant orientation to the Pacific Ocean instead of a Caribbean one. Sequencing of entire Guatemalan mitogenomes has led to improved Native American phylogeny via the addition of new haplogroups that are mainly observed in Mesoamerica and/or the North of South America. CONCLUSIONS: The data reveal the existence of a fluid gene flow in the Mesoamerican area and a predominant unidirectional flow towards South America, most likely occurring during the Pre-Classic (1800 BC-200 AD) and the Classic (200-1000 AD) Eras of the Mesoamerican chronology, coinciding with development of the most distinctive and advanced Mesoamerican civilization, the Maya. Phylogenetic features of mtDNA data also suggest a demographic scenario that is compatible with moderate local endogamy and isolation in the Maya combined with episodes of gene exchange between ethnic groups, suggesting an ethno-genesis in the Guatemalan Maya that is recent and supported on a cultural rather than a biological basis.

Asunto(s)

Etnicidad/genética , Genoma Humano , Cromosomas Humanos Y/genética , ADN Mitocondrial/análisis , ADN Mitocondrial/clasificación , ADN Mitocondrial/genética , ADN Mitocondrial/aislamiento & purificación , Frecuencia de los Genes , Genética de Población , Guatemala , Haplotipos , Humanos , Filogenia , Polimorfismo de Nucleótido Simple , Análisis de Componente Principal , Análisis de Secuencia de ADN

RESUMEN

The edible Chilean red sea urchin, Loxechinus albus, is the only species of its genus and endemic to the Southeastern Pacific. In this study, we reconstructed the mitochondrial genome of L. albus by combining Sanger and pyrosequencing technologies. The mtDNA genome had a length of 15,737 bp and encoded the same 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes as other animal mtDNAs. The size of this mitogenome was similar to those of other Echinodermata species. Structural comparisons showed a highly conserved structure, composition, and gene order within Echinoidea and Holothuroidea, and nearly identical gene organization to that found in Asteroidea and Crinoidea, with the majority of differences explained by the inversions of some tRNA genes. Phylogenetic reconstruction supported the monophyly of Echinozoa and recovered the monophyletic relationship of Holothuroidea and Echinoidea. Within Holothuroidea, Bayesian and maximum likelihood analyses recovered a sister-group relationship between Dendrochirotacea and Aspidochirotida. Similarly within Echinoidea, these analyses revealed that L. albus was closely related to Paracentrotus lividus, both being part of a sister group to Strongylocentrotidae and Echinometridae. In addition, two major clades were found within Strongylocentrotidae. One of these clades comprised all of the representative species Strongylocentrotus and Hemicentrotus, whereas the other included species of Mesocentrotus and Pseudocentrotus.

Asunto(s)

Equinodermos/genética , Genoma Mitocondrial/genética , Genómica/métodos , Erizos de Mar/genética , Animales , ADN Mitocondrial/química , ADN Mitocondrial/clasificación , ADN Mitocondrial/genética , Equinodermos/clasificación , Orden Génico , Filogenia , Análisis de Secuencia de ADN , Especificidad de la Especie

RESUMEN

Xantusiidae (night lizards) is a clade of small-bodied, cryptic lizards endemic to the New World. The clade is characterized by several features that would benefit from interpretation in a phylogenetic context, including: (1) monophyletic status of extant taxa Cricosaura, Lepidophyma, and Xantusia; (2) a species endemic to Cuba (Cricosaura typica) of disputed age; (3) origins of the parthenogenetic species of Lepidophyma; (4) pronounced micro-habitat differences accompanied by distinct morphologies in both Xantusia and Lepidophyma; and (5) placement of Xantusia riversiana, the only vertebrate species endemic to the California Channel Islands, which is highly divergent from its mainland relatives. This study incorporates extensive new character data from multiple gene regions to investigate the phylogeny of Xantusiidae using the most comprehensive taxonomic sampling available to date. Parsimony and partitioned Bayesian analyses of more than 7 kb of mitochondrial and nuclear sequence data from 11 loci all confirm that Xantusiidae is monophyletic, and comprises three well-supported clades: Cricosaura, Xantusia, and Lepidophyma. The Cuban endemic Cricosaura typica is well supported as the sister to all other xantusiids. Estimates of divergence time indicate that Cricosaura diverged from the (Lepidophyma+Xantusia) clade ≈ 81 million years ago (Ma), a time frame consistent with the separation of the Antilles from North America. Our results also confirm and extend an earlier study suggesting that parthenogenesis has arisen at least twice within Lepidophyma without hybridization, that rock-crevice ecomorphs evolved numerous times (>9) within Xantusia and Lepidophyma, and that the large-bodied Channel Island endemic X. riversiana is a distinct, early lineage that may form the sister group to the small-bodied congeners of the mainland.

Asunto(s)

Núcleo Celular/genética , ADN Mitocondrial/clasificación , Especiación Genética , Lagartos/clasificación , Filogenia , Animales , Teorema de Bayes , Tamaño Corporal , California , Cuba , ADN Mitocondrial/genética , Variación Genética , Genética de Población , Lagartos/genética , Filogeografía , Dinámica Poblacional , Análisis de Secuencia de ADN , Factores de Tiempo

Asunto(s)

Población Negra , ADN Bacteriano/genética , ADN Mitocondrial/genética , Mycobacterium tuberculosis/genética , Tuberculosis/microbiología , Adolescente , Adulto , Secuencia de Bases , Brasil/epidemiología , ADN Bacteriano/clasificación , ADN Bacteriano/aislamiento & purificación , ADN Mitocondrial/clasificación , ADN Mitocondrial/aislamiento & purificación , Antropología Forense , Haplotipos , Historia del Siglo XVIII , Historia del Siglo XIX , Humanos , Masculino , Datos de Secuencia Molecular , Mycobacterium tuberculosis/clasificación , Mycobacterium tuberculosis/aislamiento & purificación , Paleopatología , Problemas Sociales , Tuberculosis/etnología , Tuberculosis/historia

RESUMEN

Morphological convergence is a frequently observed pattern that occurs in species with similar environments, trophic niches, and/or life history strategies. In particular, adaptive morphological convergence is common in small, highly diverse invertebrate taxa sharing similar life history strategies such as parasitoidism. The genus Notiospathius is a braconid parasitoid wasp group with a vast, undetermined number of species distributed throughout the Neotropics. Members of this genus possess a considerably elongated, petiolate first metasomal tergite. This structure, however, also occurs in species of other doryctine genera, both closely and distantly related, probably due to adaptation for attacking wood and bark boring coleopteran larvae. Here we investigated the phylogenetic relationships among 117 species assigned to Notiospathius, including species of its closely related genera Masonius and Tarasco, as well as members of a number of other doryctine genera in order to test its monophyly. Separate and concatenated Bayesian partitioned analyses were carried out using two mitochondrial and three nuclear gene markers. The influence of each gene on the overall topology was verified using a cross-validation analysis for each marker with a "leave-one-out" approach. Moreover, the historical biogeography of Notiospathius was assessed calculating divergence time estimates of clades with BEAST and performing ancestral area reconstruction analyses both with RASP (Bayesian and S-DIVA) and Lagrange (DEC). All analyses recovered a polyphyletic Notiospathius consisting of three separate clades that were more related to other doryctine genera than to each other. The relationships reconstructed could not be used to confidently establish the limits of Notiospathius with respect to its closely related genera Tarasco and Masonius, and thus the generic status of the latter two taxa is maintained. Our divergence time estimates and ancestral area reconstructions indicate that the most recent common ancestor of Notiospathius sensu stricto originated in the Caribbean subregion during the Oligocene-Miocene boundary, and subsequently diversified during the mid- to late Miocene, radiating throughout the Neotropics.

Asunto(s)

Núcleo Celular/genética , ADN Mitocondrial/clasificación , Especiación Genética , Filogenia , Avispas/clasificación , Adaptación Biológica , Estructuras Animales/anatomía & histología , Estructuras Animales/fisiología , Animales , Teorema de Bayes , Región del Caribe , América Central , ADN Mitocondrial/genética , Variación Genética , Modelos Genéticos , Filogeografía , Análisis de Secuencia de ADN , América del Sur , Factores de Tiempo , Avispas/genética

RESUMEN

The echinoderm species richness of the Aerolito de Paraiso anchialine cave, on Cozumel Island, in the Mexican Caribbean, is assessed on the basis of morphological and DNA barcoding data. We included specimens from this cave system and from different open sea areas, and employed two different approaches for species delineation based on DNA barcoding data: a 2% cox1 divergence and the general mixed Yule-coalescent (GMYC) approaches. We subsequently compared the results derived from these approaches with our morphospecies discrimination. A total of 188 cox1 sequences belonging to specimens of four echinoderm classes were examined. The 2% cox1 divergence and GMYC approaches recovered 78 and 70 putative species, respectively, 24 and 22 of which corresponded to specimens from the anchialine system. Of 26 echinoderm species identified in the cave system, seven appear to be endemic to it. Among these are Copidaster carvenicola Solís-Marín & Laguarda-Figueras, 2010, two morphologically distinctive, undescribed species belonging to Asterinides and Ophionereis and four probably cryptic undescribed species originally assigned to Amphipholis squamata (Delle Chiaje, 1839), Astropecten duplicatus Gray, 1840, Copidaster lymani (AH Clark, 1948) and Ophiothrix angulata (Say, 1825). Further research and protection of this particularly fragile ecosystem becomes urgent because construction of tourism developments is planned nearby.

Asunto(s)

Biodiversidad , Código de Barras del ADN Taxonómico , Equinodermos/genética , Animales , ADN Mitocondrial/química , ADN Mitocondrial/clasificación , Equinodermos/clasificación , México , Datos de Secuencia Molecular

RESUMEN

Characidae is the most species-rich family of freshwater fishes in the order Characiformes, with more than 1000 valid species that correspond to approximately 55% of the order. Few hypotheses about the composition and internal relationships within this family are available and most fail to reach an agreement. Among Characidae, Cheirodontinae is an emblematic group that includes 18 genera (1 fossil) and approximately 60 described species distributed throughout the Neotropical region. The taxonomic and systematic history of Cheirodontinae is complex, and only two hypotheses about the internal relationships in this subfamily have been reported to date. In the present study, we test the composition and relationships of fishes assigned to Cheirodontinae based on a broad taxonomic sample that also includes some characid incertae sedis taxa that were previously considered to be part of Cheirodontinae. We present phylogenetic analyses of a large molecular dataset of mitochondrial and nuclear DNA sequences. Our results reject the monophyly of Cheirodontinae as previously conceived, as well as the tribes Cheirodontini and Compsurini, and the genera Cheirodon, Compsura, Leptagoniates, Macropsobrycon, Odontostilbe, and Serrapinnus. On the basis of these results we propose: (1) the exclusion of Amazonspinther and Spintherobolus from the subfamily Cheirodontinae since they are the sister-group of all remaining Characidae; (2) the removal of Macropsobrycon xinguensis of the genus Macropsobrycon; (3) the removal of Leptagoniates pi of the genus Leptagoniates; (4) the inclusion of Leptagoniates pi in the subfamily Cheirodontinae; (5) the removal of Cheirodon stenodon of the genus Cheirodon and its inclusion in the subfamily Cheirodontinae under a new genus name; (6) the need to revise the polyphyletic genera Compsura, Odontostilbe, and Serrapinnus; and (7) the division of Cheirodontinae in three newly defined monophyletic tribes: Cheirodontini, Compsurini, and Pseudocheirodontini. Our results suggest that our knowledge about the largest Neotropical fish family, Characidae, still is incipient.

Asunto(s)

Núcleo Celular/genética , Characidae/clasificación , ADN Mitocondrial/clasificación , Mitocondrias/genética , Filogenia , ARN Ribosómico 16S/clasificación , Animales , Núcleo Celular/química , Characidae/genética , Citocromos b/clasificación , Citocromos b/genética , ADN Mitocondrial/genética , Proteínas de Unión al ADN/clasificación , Proteínas de Unión al ADN/genética , Agua Dulce , Especiación Genética , Proteínas de Homeodominio/clasificación , Proteínas de Homeodominio/genética , Mitocondrias/química , Cadenas Pesadas de Miosina/clasificación , Cadenas Pesadas de Miosina/genética , ARN Ribosómico 16S/genética

RESUMEN

Amphibians constitute a diverse yet still incompletely characterized clade of vertebrates, in which new species are still being discovered and described at a high rate. Amphibians are also increasingly endangered, due in part to disease-driven threats of extinctions. As an emergency response, conservationists have begun ex situ assurance colonies for priority species. The abundance of cryptic amphibian diversity, however, may cause problems for ex situ conservation. In this study we used a DNA barcoding approach to survey mitochondrial DNA (mtDNA) variation in captive populations of 10 species of Neotropical amphibians maintained in an ex situ assurance programme at El Valle Amphibian Conservation Center (EVACC) in the Republic of Panama. We combined these mtDNA sequences with genetic data from presumably conspecific wild populations sampled from across Panama, and applied genetic distance-based and character-based analyses to identify cryptic lineages. We found that three of ten species harboured substantial cryptic genetic diversity within EVACC, and an additional three species harboured cryptic diversity among wild populations, but not in captivity. Ex situ conservation efforts focused on amphibians are therefore vulnerable to an incomplete taxonomy leading to misidentification among cryptic species. DNA barcoding may therefore provide a simple, standardized protocol to identify cryptic diversity readily applicable to any amphibian community.

Asunto(s)

Anfibios/clasificación , Conservación de los Recursos Naturales , Código de Barras del ADN Taxonómico , Anfibios/genética , Animales , ADN Mitocondrial/química , ADN Mitocondrial/clasificación , Especies en Peligro de Extinción , Variación Genética , Funciones de Verosimilitud , Panamá , Filogenia , Especificidad de la Especie