Relationships of scincid lizards (Mabuya spp.) from the islands of the Gulf of Guinea based on mtDNA sequence data

AbstractRelationships of Mabuya lizards from the islands of the Gulf of Guinea where estimated using partial 12S rRNA, 16S rRNA and cytochrome b mitochondrial gene sequences. Mabuya maculilabris from São Tomé and Principe are discreet monophyletic units, highly divergent from each other and from mainland populations, indicating M. maculilabris may be a species complex. Mabuya affinis from Principe is similarly distinct from mainland populations of this species. The relationships of Mabuya ozorii from Annobon are unclear, but the three species in the Gulf of Guinea islands are not closely related, indicating multiple independent colonization events. The recent proposal to partition Mabuya into four genera is premature, since at least five distinct genetic lineages can be identified.

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Phylogenetics and phylogeography of a long-legged harvestman (Arachnida : Opiliones) in the Brazilian Atlantic Rain Forest reveals poor dispersal, low diversity and extensive mitochondrial introgression

Invertebrate Systematics ◽

10.1071/is15009 ◽

2015 ◽

Vol 29 (4) ◽

pp. 386 ◽

Cited By ~ 15

Author(s):

Cibele Bragagnolo ◽

Ricardo Pinto-da-Rocha ◽

Manuel Antunes ◽

Ronald M. Clouse

Keyword(s):

Rain Forest ◽

Species Complex ◽

Sequence Data ◽

Historical Event ◽

12S Rrna ◽

Atlantic Rain Forest ◽

Effective Population ◽

Narrow Region ◽

Low Genetic Diversity ◽

Mitochondrial Introgression

We used DNA sequence data to test the morphology-based taxonomy and examine the biogeography of the Brazilian Atlantic Rain Forest genus Promitobates. Most species are well differentiated morphologically, and a previous morphological phylogeny recovered the genus as monophyletic. However, some of these species have overlapping geographical distributions and considerable intraspecific variation, perhaps representing a species complex. Mitochondrial (12S rRNA and COI) and nuclear (ITS2 and 28S) genes were sequenced from 132 specimens collected from 27 localities. The results are consistent with significant mitochondrial introgression among the species P. ornatus, P. hatschbachi, P. lager, P. bellus and P. intermedius (the ‘P. ornatus species complex’), with one specimen identified as a hybrid between P. nigripes and this complex. A phylogeographic study of the complex was conducted using mitochondrial haplotypes. This revealed remarkably poor dispersal among populations, with only one case of a shared haplotype, and very low genetic diversity. The phylogeny showed a clear break between populations on either side of a narrow region of forest, suggesting an important historical event separated these lineages in the genus. The analyses also pointed to population breaks that date back several millions of years or extremely small effective population sizes, depending on the mutation rate.

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Hidden in the highlands: the description and phylogenetic position of a novel endemic freshwater crab species (Potamonautidae : Potamonautes) from Zimbabwe

Invertebrate Systematics ◽

10.1071/is13012 ◽

2013 ◽

Vol 27 (5) ◽

pp. 530 ◽

Cited By ~ 17

Author(s):

Ethel E. Phiri ◽

Savel R. Daniels

Keyword(s):

Southern Africa ◽

Sequence Data ◽

Phylogenetic Position ◽

12S Rrna ◽

Mountain Range ◽

Freshwater Crab ◽

Crab Species ◽

Mountainous Regions ◽

Freshwater Crabs ◽

Mtdna Sequence

A recent sampling endeavour of freshwater crabs along the high-lying streams of the Nyanga mountain range in Mutare (Eastern Highlands, Zimbabwe) yielded a morphologically distinct, as yet undescribed species. The novel Zimbabwean species is compared to the 16 described species from southern Africa based on mtDNA sequence data derived from three partial gene sequences (12S rRNA, 16S rRNA and COI). The new Zimbabwean species was found to be a sister taxon to Potamonautes mulanjeensis. These two species are morphologically and genetically easily differentiated. The new species is described as Potamonautes mutareensis, sp. nov. and is compared morphologically to the known freshwater crab species of southern Africa. A dichotomous key to the four described freshwater crab species that occur in Zimbabwe is also provided. Our results suggest that species diversity and endemism of freshwater decapods and other habitat specialists is likely to be high in unsampled mountainous regions.

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Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽

10.12688/f1000research.23635.2 ◽

2020 ◽

Vol 9 ◽

pp. 339 ◽

Cited By ~ 1

Author(s):

Tshifhiwa G. Matumba ◽

Jody Oliver ◽

Nigel P. Barker ◽

Christopher D. McQuaid ◽

Peter R. Teske

Keyword(s):

Dna Barcoding ◽

Dna Sequences ◽

Sequence Data ◽

Mitochondrial Gene ◽

Population Expansion ◽

Species Level ◽

Molecular Dating ◽

Coi Gene ◽

28S Rrna ◽

Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics. Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

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Albumin and mitochondrial DNA evolution: Phylogenetic implications for colubrine snakes (Colubridae: Colubrinae)

Amphibia-Reptilia ◽

10.1163/156853896x00423 ◽

1996 ◽

Vol 17 (3) ◽

pp. 247-259 ◽

Cited By ~ 3

Author(s):

T.J. Lopez ◽

L.R. Maxson

Keyword(s):

16S Rrna ◽

Cytochrome B ◽

Sequence Data ◽

Phylogenetic Signal ◽

Mitochondrial Gene ◽

Mitochondrial Cytochrome B ◽

Nucleotide Sequence Variation ◽

Phylogenetic Implications ◽

Rrna Sequences ◽

16S Rrna Sequences

AbstractPrevious molecular analyses of colubrine snake relationships have been based on estimates of amino acid sequence differences in the nuclear-encoded protein, serum albumin. Phylogenetic hypotheses based on albumin data are compared to new trees derived from nucleotide sequence variation in a 307-base pair (bp) region of the mitochondrial cytochrome b gene and a 384-bp region of the mitochondrial gene encoding the 16S ribosomal RNA (rRNA) subunit. There are so many multiple substitutions at degenerate sites in the cytochrome b sequences that little phylogenetic signal remains, leaving major conclusions based on the more informative 16S rRNA sequences. Analyses of the sequence data using both parsimony and genetic distance algorithms are largely congruent with earlier conclusions based on albumin, and corroborate (1) the monophyly of the ratsnakes, (2) the derivation of the ratsnake clade from within the racer lineage, and (3) the monophyly of the Nearctic racer clade (Coluber + Masticophis). The 16S rRNA data provide greater resolution of relationships within the racer lineage than either the cytochrome b or albumin data. The trees based on cytochrome b and 16S rRNA sequences do not support monophyly of the racers, in contrast to the albumin data.

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Genome-wide and cuticular hydrocarbon evidence shed light on potential drivers of speciation in a Neotropical ant species complex

10.22541/au.163421334.49704543/v1 ◽

2021 ◽

Author(s):

Rubi Meza-Lázaro ◽

Kenzy Peña-Carrillo ◽

Chantal Poteaux ◽

Maria Lorenzi ◽

James Wetterer ◽

...

Keyword(s):

Species Complex ◽

Sequence Data ◽

Cuticular Hydrocarbon ◽

Distinct Species ◽

Species Limits ◽

Geographic Barriers ◽

Genome Wide ◽

Mtdna Sequence ◽

Mating Signal ◽

Southeast Mexico

Reproductive isolation between geographically separated populations is generally considered the most common form of speciation. However, speciation may also occur in the absence of geographic barriers due phenotypic and genotypic factors such as chemical cue divergence, mating signal divergence and mitonuclear conflict. Here we performed an integrative study based on two genome-wide techniques, 3RAD and ultraconserved elements, coupled with cuticular hydrocarbon and mtDNA sequence data, to assess the species limits within the E. ruidum species-complex, a widespread and conspicuous group of Neotropical ants for which heteroplasmy has been recently discovered in some populations from southeast Mexico. Our analyses indicate the existence of at least five distinct species in this complex, two widely distributed along the Neotropics and three that are restricted to southeast Mexico and that apparently have high levels of heteroplasmy. We found that species boundaries in the complex did not coincide with geographic barriers. We therefore consider possible roles of alternative drivers that may have promoted the observed patterns of speciation, including mitonuclear incompatibility, cuticular hydrocarbon differentiation, and colony structure. Our study highlights the importance of simultaneously assessing different sources of evidence to disentangle the species limits of taxa with complicated evolutionary histories.

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Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽

10.12688/f1000research.23635.1 ◽

2020 ◽

Vol 9 ◽

pp. 339 ◽

Cited By ~ 1

Author(s):

Tshifhiwa G. Matumba ◽

Jody Oliver ◽

Nigel P. Barker ◽

Christopher D. McQuaid ◽

Peter R. Teske

Keyword(s):

Dna Barcoding ◽

Dna Sequences ◽

Sequence Data ◽

Mitochondrial Gene ◽

Population Expansion ◽

Species Level ◽

Molecular Dating ◽

Coi Gene ◽

28S Rrna ◽

Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. To our knowledge, this is the first study to use nuclear rRNA at this taxonomic level, presumably because this marker is assumed to evolve so slowly that it is only suitable for phylogenetics. Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolves effectively clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

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An assessment of Raphitoma and allied genera (Neogastropoda: Raphitomidae)

Journal of Molluscan Studies ◽

10.1093/mollus/eyz022 ◽

2019 ◽

Cited By ~ 2

Author(s):

Giulia Fassio ◽

Valeria Russini ◽

Francesco Pusateri ◽

Riccardo Giannuzzi-Savelli ◽

Tore Høisæter ◽

...

Keyword(s):

16S Rrna ◽

Sequence Data ◽

Genetic Distances ◽

West African ◽

Critical Study ◽

12S Rrna ◽

Mediterranean Species ◽

New Classification ◽

African Species ◽

Dna Sequence Data

ABSTRACT The systematics of several Eastern Atlantic conoidean species, traditionally ascribed to the genus RaphitomaBellardi, 1847, are revised on the basis of DNA sequence data from three gene regions (cytochrome c oxidase subunit I, 16S rRNA and 12S rRNA). We assign genus ranking to three major lineages (Raphitoma, CyrilliaKobelt, 1905 and LeufroyiaMonterosato, 1884) and suggest that two West African species belong in the subgenus Daphnella (Paradaphne) Laseron, 1954. A new classification, based on molecular systematics and critical study of morphology, is provided for all Eastern Atlantic and Mediterranean species that are currently ascribed to Raphitoma s.l. The genus ClathromangeliaMonterosato, 1884 is confirmed as belonging to Raphitomidae. Phylogenetic relationships and genetic distances suggest that Raphitoma maculosaHøisæter, 2016 and R. obesaHøisæter, 2016 may be divergent morphotypes of R. bicolor (Risso, 1826) and Cyrillia aequalis (Jeffreys, 1867), respectively.

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A Re-analysis of the phylogeny of the genus Protobothrops (Reptilia: Viperidae), with particular reference to the systematic position of P. xiangchengensis

Amphibia-Reptilia ◽

10.1163/156853806778189954 ◽

2006 ◽

Vol 27 (3) ◽

pp. 433-439 ◽

Cited By ~ 4

Author(s):

Peng Guo ◽

Ermi Zhao ◽

Yaping Zhang ◽

Junfeng Pang

Keyword(s):

Maximum Likelihood ◽

16S Rrna ◽

Cytochrome B ◽

Phylogenetic Relationships ◽

Maximum Parsimony ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Systematic Position ◽

Valid Species ◽

12S Rrna

AbstractBased on three mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b), the phylogeny of Protobothrops is re-analyzed using Maximum-parsimony (MP), Maximum-likelihood (ML), and Bayesian (BI) approaches. All phylogenetic analyses indicate that all putative Protobothrops species examined formed a monophyletic group; however, the intrageneric relationships are still unresolved. The phylogenetic relationships further confirm that P. xiangchengensis is a valid species distinct from P. mucrosquamatus and that it is closely related to P. jerdonii.

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PSI-40 Two mitochondrial lineages revealed in North American yak

Journal of Animal Science ◽

10.1093/jas/skaa278.833 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 477-477

Author(s):

Leah K Treffer ◽

Edward S Rice ◽

Anna M Fuller ◽

Samuel Cutler ◽

Jessica L Petersen

Keyword(s):

Sequence Data ◽

Haplotype Network ◽

Ovis Aries ◽

Similar Species ◽

Nucleotide Polymorphisms ◽

Mt Dna ◽

Protein Coding ◽

Sister Clade ◽

Mtdna Sequence ◽

The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

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