scholarly journals Mitochondrial genomes and phylogenetic analysis of Central American weakly-electric fishes: Apteronotus rostratus, Brachyhypopomus occidentalis and Sternopygus dariensis

2018 ◽  
Author(s):  
Celestino Aguilar ◽  
Matthew J. Miller ◽  
Jose R. Loaiza ◽  
Rüdiger Krahe ◽  
Luis F. De León
Keyword(s):  
Phylogenetic Analyses ◽  
Electric Organ ◽  
Sequence Divergence ◽  
Central American ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
South American ◽  
South American Species ◽  
Neotropical Fishes ◽  
Electric Fishes

AbstractElectric fishes are a diverse group of freshwater organisms with the ability to generate electric organ discharges (EODs) that are used for communication and electrolocation. Over 200 species have originated in South America, but of these, only a few have managed to colonize the Central American Isthmus. Here, we assembled two complete and one nearly complete mitochondrial genomes (mitogenomes) for three Central American Gymnotiformes: Sternopygus dariensis, Brachyhypopomus occidentalis and Apteronotus rostratus. We then explored the three species’ phylogenetic position in the context of South American electric fishes. Mitogenomes were organized in the standard fish mitogenome order, and presented sizes of 16,600, 16,540 and 15,940 base pairs (bp) (nearly complete) for S. dariensis, B. occidentalis and A. rostratus, respectively. We uncovered a novel 60 bp intergenic spacer (IGS) located between the COII and tRNALys genes, which appears to be unique to the Apteronotidae. Furthermore, phylogenetic relationships supported the traditional monophyly of Gymnotiformes, with the three species positioned within their respective family. In addition, the genus Apteronotus was placed as the basal taxon of the order. Finally, we found high sequence divergence (13.3%) between our B. occidentalis specimen and a sequence previously reported in GenBank, suggesting that the prior mitogenome of B. occidentalis represents a different South American species that was misidentified. Indeed, phylogenetic analyses using Cytochrome b gene across the genus placed the previously reported individual within B. bennetti. Our study provides novel mitogenome resources that will advance our understanding of the diversity and phylogenetic history of Neotropical fishes.

scholarly journals “Ancient DNA” reveals that the scientific name for an extinct tortoise from Cape Verde refers to an extant South American species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Kehlmaier ◽  
Luis F. López-Jurado ◽  
Nayra Hernández-Acosta ◽  
Antonio Mateo-Miras ◽  
Uwe Fritz
Keyword(s):  
Phylogenetic Analyses ◽  
Cape Verde ◽  
Type Material ◽  
Mitochondrial Genomes ◽  
South American ◽  
Type Specimens ◽  
South American Species ◽  
Ams Radiocarbon Dating ◽  
Species Groups ◽  
Scientific Name

AbstractWe examined the type material of the extinct tortoise species Geochelone atlantica López-Jurado, Mateo and García-Márquez, 1998 from Sal Island, Cape Verde, using aDNA approaches and AMS radiocarbon dating. High-quality mitochondrial genomes obtained from the three type specimens support that all type material belongs to the same individual. In phylogenetic analyses using mitochondrial genomes of all species groups and genera of extant and some recently extinct tortoises, the type material clusters within the extant South American red-footed tortoise Chelonoidis carbonarius (Spix, 1824). Our radiocarbon date indicates that the tortoise from which the type series of G. atlantica originates was still alive during 1962 and 1974. These results provide firm evidence that the type material of G. atlantica does not belong to the Quaternary tortoise bones excavated on Sal Island in the 1930s, as originally thought. Thus, the extinct tortoise species remains unstudied and lacks a scientific name, and the name G. atlantica has to be relegated into the synonymy of C. carbonarius. The circumstances that led to this confusion currently cannot be disentangled.

scholarly journals First record of Gymnotus henni (Albert, Crampton and Maldonado, 2003) in Panama: phylogenetic position and electric signal characterization

Check List ◽  
2013 ◽  
Vol 9 (3) ◽  
pp. 655 ◽  
Author(s):  
Fernando Alda ◽  
Sophie Picq ◽  
Luis Fernando De León ◽  
Rigoberto González ◽  
Henriette Walz ◽  
...  
Keyword(s):  
Electric Organ Discharge ◽  
Electric Organ ◽  
First Record ◽  
Central American ◽  
Weakly Electric Fish ◽  
Electric Signal ◽  
Phylogenetic Position ◽  
South American ◽  
The Pacific ◽  
Weakly Electric

We present the first record of the weakly electric fish Gymnotus henni in Panama, which also represents the first record of Gymnotus in the Pacific slope of the country. One specimen was collected in a tributary of the Chucunaque River in the Tuira basin. The species showed a monophasic electric organ discharge. Molecular analyses indicated that G. henni from Panama and Colombia are closely related and represent an independent and basal lineage to the Central American G. cylindricus and South American G. carapo groups. Evolutionary and biogeographic implications are discussed.

Cnidochloa: A New Genus of Grasses from Brazil (Poaceae: Panicoideae: Paniceae)

2020 ◽  
Vol 105 (2) ◽  
pp. 183-194
Author(s):  
Fernando O. Zuloaga ◽  
Sandra S. Aliscioni ◽  
M. Amalia Scataglini
Keyword(s):  
New Genus ◽  
Phylogenetic Position ◽  
South American ◽  
The South ◽  
South American Species ◽  
Molecular Characters

Generic boundaries of the South American species Panicum longipedicellatum Swallen are explored and compared with allied genera of the tribe Paniceae. On the basis of morphological, anatomical, and molecular characters a new genus, Cnidochloa Zuloaga, is proposed. The phylogenetic position of the new genus within the Paniceae is evaluated.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

scholarly journals Arganiella Giusti & Pezzoli, 1980 (Caenogastropoda: Truncatelloidea: Hydrobiidae): a widespread genus or several narrow-range endemic genera?

2021 ◽  
Vol 750 ◽  
Author(s):  
Diana Delicado ◽  
Vladimir Pešić ◽  
Marian A. Ramos
Keyword(s):  
Narrow Range ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Taxonomic Status ◽  
Phylogenetic Position ◽  
The Balkans ◽  
Endemic Genera ◽  
Taxonomic Evaluation ◽  
Molecular Framework

Most valvatiform genera of the gastropod family Hydrobiidae are narrow-range taxa. One exception is the genus Arganiella, which is comprised of three congeners: the type species A. pescei from the Apennine Peninsula, A. wolfi from the Iberian Peninsula and A. tabanensis from the Balkans. The genus assignment of the latter two species was based on morphological similarities with A. pescei in the shell, operculum, radula and genitalia. Given that the morphology of hydrobiids is sometimes susceptible to convergence, this study re-evaluates the taxonomic status of species of Arganiella by analysing mitochondrial (mtCOI) and nuclear (18S rRNA) sequences of topotypes or near topotypes to infer their phylogenetic position. Our phylogenetic analyses depicted Arganiella as a non-monophyletic group within Hydrobiidae, and sequence divergence among the three species ranged from 14.5 to 16.7% for mtCOI and 2.0 to 3.8% for 18S. We also re-examined the extent of morphological variation among species of Arganiella and found a few differences among them and other valvatiform genera. Consequently, we propose two new genera for A. wolfi and A. tabanensis. Our results conflict with the classification of valvatiform hydrobiid species solely based on traditional phenotypical methods and suggest further taxonomic evaluation within a molecular framework.

Cheilanthes ecuadorensis: A New Species of Cheilanthes s. s. (Pteridaceae) from Northern South America

2021 ◽  
Vol 46 (2) ◽  
pp. 249-259
Author(s):  
Karla Sosa ◽  
Kathleen M. Pryer ◽  
Layne Huiet ◽  
George Yatskievych ◽  
Michael D. Windham
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
South American ◽  
South American Species ◽  
Ongoing Research ◽  
Species Discovery ◽  
Molecular Phylogenetic ◽  
Poorly Differentiated ◽  
Northern South America ◽  
A New Species

Abstract— Ongoing research on the taxonomically complex genus Cheilanthes (Pteridaceae; Cheilanthoideae) has resulted in the identification of a new species from Loja Province in Ecuador, Cheilanthes ecuadorensis, described and illustrated herein. Originally collected in 1988 and identified as C. cf. rufopunctata, C. ecuadorensis is clearly distinct from that species in having pubescent adaxial blade surfaces and narrow, poorly-differentiated false indusia (rather than the glabrous adaxial surfaces and wide false indusia of C. rufopunctata). Among the South American species currently included in Cheilanthes, C. ecuadorensis is superficially most similar to C. pilosa. However, our molecular phylogenetic analyses indicate that C. ecuadorensis is sister to C. micropteris, the morphologically disparate generitype of Cheilanthes. Here we examine the phylogenetic relationships, morphology, cytogenetics, and geography of these four South American Cheilanthes species in a study that, once again, highlights the importance of herbaria in the process of new species discovery.

Phylogenetic relationships among southern South American species of Camptosema, Galactia and Collaea (Diocleinae: Papilionoideae: Leguminosae) on the basis of molecular and morphological data

2009 ◽  
Vol 57 (1) ◽  
pp. 76 ◽  
Author(s):  
Silvana M. Sede ◽  
Daniela Tosto ◽  
Paola Talia ◽  
Melissa Luckow ◽  
Lidia Poggio ◽  
...  
Keyword(s):  
South America ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Morphological Data ◽  
South American ◽  
South American Species ◽  
Aflp Data ◽  
Southern South America ◽  
Good Support

The neotropical genus Camptosema in its southern distribution is represented by the following four species: Ca. paraguariense, Ca. praeandinum, Ca. rubicundum and Ca. scarlatinum. Ca. rubicundum is the only species with all the diagnostic characters of the genus, i.e. tubular calyx. The other three taxa are related morphologically and cytologically to Galactia and Collaea, two closely allied genera in the subtribe Diocleinae. Individual and combined phylogenetic analyses of morphology, ITS and trnL-F were conducted to examine the position of these species as well as to explore their relationship with Galactia and Collaea species in southern South America. In none of the analyses does Camptosema species form a monophyletic group. Instead, they are scattered in different groups. These results together with cytological, morphological and AFLP data provide good support for re-evaluating the taxonomic position of these species within Camptosema.

Genomic in situ hybridization reveals both auto- and allopolyploid origins of different North and Central American hexaploid potato (Solanum sect. Petota) species

Genome ◽  
2012 ◽  
Vol 55 (6) ◽  
pp. 407-415 ◽  
Author(s):  
Galina Pendinen ◽  
David M. Spooner ◽  
Jiming Jiang ◽  
Tatjana Gavrilenko
Keyword(s):  
In Situ Hybridization ◽  
Genomic In Situ Hybridization ◽  
Central American ◽  
South American ◽  
South American Species ◽  
A Genome ◽  
Solanum Sect ◽  
In Series ◽  
Mexican Species

Wild potato ( Solanum L. sect. Petota Dumort.) species contain diploids (2n = 2x = 24) to hexaploids (2n = 6x = 72). J.G. Hawkes classified all hexaploid Mexican species in series Demissa Bukasov and, according to a classic five-genome hypothesis of M. Matsubayashi in 1991, all members of series Demissa are allopolyploids. We investigated the genome composition of members of Hawkes’s series Demissa with genomic in situ hybridization (GISH), using labeled DNA of their putative progenitors having diploid AA, BB, or PP genome species or with DNA of tetraploid species having AABB or AAAaAa genomes. GISH analyses support S. hougasii Correll as an allopolyploid with one AA component genome and another BB component genome. Our results also indicate that the third genome of S. hougasii is more closely related to P or a P genome-related species. Solanum demissum Lindl., in contrast, has all three chromosome sets related to the basic A genome, similar to the GISH results of polyploid species of series Acaulia Juz. Our results support a more recent taxonomic division of the Mexican hexaploid species into two groups: the allopolyploid Iopetala group containing S. hougasii, and an autopolyploid Acaulia group containing S. demissum with South American species S. acaule Bitter and S. albicans (Ochoa) Ochoa.

scholarly journals Insights into genomic evolution from the chromosomal and mitochondrial genomes of Ustilaginoidea virens

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Kang Zhang ◽  
Zaixu Zhao ◽  
Ziding Zhang ◽  
Yuejiao Li ◽  
Shaojie Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Phylogenetic Analyses ◽  
Homing Endonuclease ◽  
Rapid Evolution ◽  
Sequence Divergence ◽  
Mitochondrial Genomes ◽  
Structural Variations ◽  
High Quality ◽  
Ustilaginoidea Virens ◽  
Gain Loss

AbstractUstilaginoidea virens, the causal agent of rice false smut, is an economically important filamentous fungal pathogen. A high-quality reference genome of U. virens promotes understanding of molecular mechanisms underlying its virulence and pathogenicity. Here, we report the first chromosome-level assembly of U. virens genome consisting of seven chromosomes ranging from 2.4 to 7.5 Mb. The assembly has dramatic improvements over previous assemblies, including considerably longer contigs, higher proportion of repetitive elements and more functionally annotated genes. Phylogenetic analyses revealed an extremely low intraspecific sequence divergence in U. virens. By contrast, intraspecific genome comparisons uncovered dynamic genomic alterations including massive structural variations and widespread lineage-specific regions (LSRs) among U. virens strains, which were mainly generated by recent burst of retrotransposons. Genomic plasticity created by structural variations and LSRs might drive rapid evolution of U. virens. High-quality mitochondrial genomes of eight U. virens strains exhibit size variations from 94 to 102 kb. Consistently, U. virens contains conserved lengths of exons and highly dynamic mobile introns, which contribute to intraspecific size variations due to gain/loss of homing endonuclease genes. This study highlights unique characteristics in nuclear and mitochondrial genomic divergence and provides new insights into genomic and mitochondrial evolution of U. virens.

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