scholarly journals Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog (Sarcohyla; Hylidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6045 ◽  
Author(s):  
Eugenia Zarza ◽  
Elizabeth M. Connors ◽  
James M. Maley ◽  
Whitney L.E. Tsai ◽  
Peter Heimes ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Closely Related Species ◽  
Ultraconserved Elements ◽  
Species Discovery ◽  
The North ◽  
Geographic Feature ◽  
Genomic Marker ◽  
History Of ◽  
Dispersal Corridor ◽  
Lineage Diversity

Molecular studies have uncovered significant diversity in the Mexican Highlands, leading to the description of many new endemic species. DNA approaches to this kind of species discovery have included both mitochondrial DNA (mtDNA) sequencing and multilocus genomic methods. While these marker types have often been pitted against one another, there are benefits to deploying them together, as linked mtDNA data can provide the bridge between uncovering lineages through rigorous multilocus genomic analysis and identifying lineages through comparison to existing mtDNA databases. Here, we apply one class of multilocus genomic marker, ultraconserved elements (UCEs), and linked mtDNA data to a species complex of frogs (Sarcohyla bistincta, Hylidae) found in the Mexican Highlands. We generated data from 1,891 UCEs, which contained 1,742 informative SNPs for S. bistincta and closely related species and captured mitochondrial genomes for most samples. Genetic analyses based on both whole loci and SNPs agree there are six to seven distinct lineages within what is currently described as S. bistincta. Phylogenies from UCEs and mtDNA mostly agreed in their topologies, and the few differences suggested a more complex evolutionary history of the mtDNA marker. Our study demonstrates that the Mexican Highlands still hold substantial undescribed diversity, making their conservation a particularly urgent goal. The Trans-Mexican Volcanic Range stands out as a significant geographic feature in Sarcohyla and may have acted as a dispersal corridor for S. bistincta to spread to the north. Combining multilocus genomic data with linked mtDNA data is a useful approach for identifying potential new species and associating them with already described taxa, which will be especially important in groups with undescribed subadult phenotypes and cryptic species.

scholarly journals Combining next-generation sequencing and mtDNA data to uncover cryptic lineages of Mexican highland frogs

2017 ◽  
Author(s):  
Eugenia Zarza ◽  
Elizabeth M. Connors ◽  
James M. Maley ◽  
Whitney L.E. Tsai ◽  
Peter Heimes ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genomic Analysis ◽  
Mitochondrial Genomes ◽  
Diversity Combining ◽  
Species Status ◽  
Closely Related Species ◽  
Geographic Ranges ◽  
Species Discovery ◽  
Genomic Marker ◽  
Generation Sequencing

AbstractRecently, molecular studies have uncovered significant cryptic diversity in the Mexican Highlands, leading to the description of many new endemic species. DNA approaches to this kind of species discovery have included both mitochondrial DNA (mtDNA) sequencing and multilocus genomic methods. While these marker types have often been pitted against one another, there are benefits to deploying them together, as linked mtDNA data can provide the bridge between uncovering lineages through rigorous multilocus genomic analysis and identifying lineages through comparison to existing mtDNA databases. Here, we apply one class of multilocus genomic marker, ultraconserved elements (UCEs), and linked mtDNA data to a species complex of frogs (Sarcohyla bistincta) found in the Mexican Highlands. We generated data from 1,891 UCEs, which contained 1,742 informative SNPs for S. bistincta and closely related species and captured mitochondrial genomes for most samples. Genetic analyses based on both whole loci and SNPs agree there are numerous distinct and divergent lineages within S. bistincta. The SNP-based species tree provides the most conservative estimate of 8 well-supported lineages in three major clades. Having linked mtDNA data allowed us to tap into the large number of mtDNA sequences available on GenBank and identify one of these lineages as an already-described species, S. pentheter. One identified clade (containing 2 of the 8 lineages) was 10% divergent in mtDNA and paraphyletic with other S. bistincta, making this clade a clear candidate for species status. Phylogenies from UCEs and mtDNA mostly agreed in their topologies, but differed in that mtDNA suggested a more complex evolutionary history perhaps influenced by gene flow between some neighboring lineages. Our study demonstrates that the Mexican Highlands still hold substantial undescribed diversity. Combining multilocus genomic data with linked mtDNA data is a useful approach for identifying potential new species and associating them with already described taxa, which is especially important in groups with undescribed subadult phenotypes, where geographic ranges are unclear, or where phenotypes are conserved.

Ras al Khaimah: further archaeological discoveries

Antiquity ◽  
1976 ◽  
Vol 50 (200) ◽  
pp. 216-222
Author(s):  
Beatrice De Cardi
Keyword(s):  
United Arab Emirates ◽  
The State ◽  
Focused Attention ◽  
North East ◽  
The North ◽  
History Of ◽  
The City

Ras a1 Khaimah is the most northerly of the seven states comprising the United Arab Emirates and its Ruler, H. H. Sheikh Saqr bin Mohammad al-Qasimi, is keenly interested in the history of the state and its people. Survey carried out there jointly with Dr D. B. Doe in 1968 had focused attention on the site of JuIfar which lies just north of the present town of Ras a1 Khaimah (de Cardi, 1971, 230-2). Julfar was in existence in Abbasid times and its importance as an entrep6t during the sixteenth and seventeenth centuries-the Portuguese Period-is reflected by the quantity and variety of imported wares to be found among the ruins of the city. Most of the sites discovered during the survey dated from that period but a group of cairns near Ghalilah and some long gabled graves in the Shimal area to the north-east of the date-groves behind Ras a1 Khaimah (map, FIG. I) clearly represented a more distant past.

Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

2020 ◽  
pp. 37-40
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Breast Cancer Patients ◽  
The North ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

North American Association for the Study of Religion (NAASR)

2015 ◽  
Vol 44 (2) ◽  
pp. 29-30
Author(s):  
Matt Sheedy
Keyword(s):  
North American ◽  
American Association ◽  
The North ◽  
History Of

I interviewed Russell McCutcheon back in March 2015, about his new role as president of the North American Association for the Study of Religion (NAASR), asking him about the history of the organization, goals for his tenure, and developments for NAASR’s upcoming conference in Atlanta in November 2015.

UNRAVELING THE HISTORY OF COMPLEX ZONED GARNETS IN RETROGRADE ECLOGITES: INSIGHTS FROM THE NORTH MOTAGUA MÉLANGE IN CENTRAL GUATEMALA

2017 ◽  
Author(s):  
Celine Martin ◽  
◽  
Guillaume Bonnet ◽  
Guillaume Bonnet ◽  
Kennet E. Flores ◽  
...  
Keyword(s):  
The North ◽  
History Of
Sign in / Sign up

Export Citation Format

Share Document