Mitochondrial data are not suitable for resolving placental mammal phylogeny

Abstract McDonald/Kreitman tests performed on animal mtDNA consistently reveal significant deviations from strict neutrality in the direction of an excess number of polymorphic nonsynonymous sites, which is consistent with purifying selection acting on nonsynonymous sites. We show that under models of recurrent neutral and deleterious mutations, the mean age of segregating neutral mutations is greater than the mean age of segregating selected mutations, even in the absence of recombination. We develop a test of the hypothesis that the mean age of segregating synonymous mutations equals the mean age of segregating nonsynonymous mutations in a sample of DNA sequences. The power of this age-of-mutation test and the power of the McDonald/Kreitman test are explored by computer simulations. We apply the new test to 25 previously published mitochondrial data sets and find weak evidence for selection against nonsynonymous mutations.

Download Full-text

Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

Diversity ◽

10.3390/d13080347 ◽

2021 ◽

Vol 13 (8) ◽

pp. 347

Author(s):

Jazmín Terán-Martínez ◽

Rocío Rodiles-Hernández ◽

Marco A. A. Garduño-Sánchez ◽

Claudia Patricia Ornelas-García

Keyword(s):

Molecular Characterization ◽

Conservation Status ◽

Nuclear Data ◽

Important Species ◽

Common Snook ◽

Mitochondrial Data ◽

Haplotypic Diversity ◽

Genetic Diversity And Structure ◽

Genetic Clusters ◽

The Common

The common snook is one of the most abundant and economically important species in the Usumacinta basin in the Gulf of Mexico, which has led to overfishing, threatening their populations. The main goal of the present study was to assess the genetic diversity and structure of the common snook along the Usumacinta River in order to understand the population dynamics and conservation status of the species. We characterized two mitochondrial markers (mtCox1 and mtCytb) and 11 microsatellites in the Usumacinta basin, which was divided into three zones: rainforest, floodplain and river delta. The mitochondrial data showed very low diversity, showing some haplotypic diversity differences between the rainforest and delta zones. In contrast, we consistently recovered two genetic clusters in the Usumacinta River basin with the nuclear data in both the DAPC and STRUCTURE analyses. These results were consistent with the AMOVA analyses, which showed significant differences among the genetic clusters previously recovered by DAPC and STRUCTURE. In terms of diversity distribution, the floodplain zone corresponded to the most diverse zone according to the mitochondrial and nuclear data, suggesting that this is a transition zone in the basin. Our results support the relevance of the molecular characterization and monitoring of the fishery resources at the Usumacinta River to better understand their connectivity, which could help in their conservation and management.

Download Full-text

Cryptic lineages hybridize for worker production in the harvester ant Messor barbarus

Biology Letters ◽

10.1098/rsbl.2016.0542 ◽

2016 ◽

Vol 12 (11) ◽

pp. 20160542 ◽

Cited By ~ 6

Author(s):

Victoria Norman ◽

Hugo Darras ◽

Christopher Tranter ◽

Serge Aron ◽

William O. H. Hughes

Keyword(s):

Reproductive System ◽

Division Of Labour ◽

Insect Larvae ◽

Messor Barbarus ◽

Harvester Ant ◽

Mitochondrial Data ◽

Genetic Caste Determination ◽

Worker Castes ◽

Genetically Determined ◽

Reproductive Division

The reproductive division of labour between queen and worker castes in social insects is a defining characteristic of eusociality and a classic example of phenotypic plasticity. Whether social insect larvae develop into queens or workers has long been thought to be determined by environmental cues, i.e. larvae are developmentally totipotent. Contrary to this paradigm, several recent studies have revealed that caste is determined by genotype in some ant species, but whether this is restricted to just a few exceptional species is still unclear. Here, we show that the Mediterranean harvester ant Messor barbarus possesses an unusual reproductive system, in which the female castes are genetically determined. Using both nuclear and mitochondrial data, we show that Iberian populations have two distinct, cryptic lineages. Workers are always inter-lineage hybrids whereas queens are always produced from pure-lineage matings. The results suggest that genetic caste determination may be more widespread in ants than previously thought, and that further investigation in other species is needed to understand the frequency and evolution of this remarkable reproductive system.

Download Full-text

Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data, and a revised phylogeny for Sceloporus

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2009.09.008 ◽

2010 ◽

Vol 54 (1) ◽

pp. 150-161 ◽

Cited By ~ 81

Author(s):

John J. Wiens ◽

Caitlin A. Kuczynski ◽

Saad Arif ◽

Tod W. Reeder

Keyword(s):

Phylogenetic Relationships ◽

Mitochondrial Data

Download Full-text

Characterization of Two New preproGnRH mRNAs in the Tree Shrew: First Direct Evidence for Mesencephalic GnRH Gene Expression in a Placental Mammal

General and Comparative Endocrinology ◽

10.1006/gcen.1996.0135 ◽

1996 ◽

Vol 104 (1) ◽

pp. 7-19 ◽

Cited By ~ 90

Author(s):

Thomas L. Kasten ◽

Stephanie A. White ◽

Thomas T. Norton ◽

Chris T. Bond ◽

John P. Adelman ◽

...

Keyword(s):

Gene Expression ◽

Direct Evidence ◽

Tree Shrew ◽

Placental Mammal

Download Full-text

Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽

10.1093/auk/124.1.71 ◽

2007 ◽

Vol 124 (1) ◽

pp. 71-84 ◽

Cited By ~ 5

Author(s):

W. Andrew Cox ◽

Rebecca T. Kimball ◽

Edward L. Braun

Keyword(s):

New World ◽

Sequence Data ◽

Evolutionary Relationship ◽

Strong Support ◽

Nuclear Data ◽

Morphological Data ◽

Phylogenetic Position ◽

Data Set ◽

Mitochondrial Data ◽

Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

Download Full-text

Eutherians experienced elevated evolutionary rates in the immediate aftermath of the Cretaceous–Palaeogene mass extinction

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2015.3026 ◽

2016 ◽

Vol 283 (1833) ◽

pp. 20153026 ◽

Cited By ~ 25

Author(s):

Thomas John Dixon Halliday ◽

Paul Upchurch ◽

Anjali Goswami

Keyword(s):

Phylogenetic Analysis ◽

Adaptive Radiation ◽

Mass Extinction ◽

Fossil Record ◽

Morphological Evolution ◽

Placental Mammal ◽

Stochastic Methods ◽

Ecological Niches ◽

Evolutionary Radiation ◽

Quantitative Analyses

The effect of the Cretaceous–Palaeogene (K–Pg) mass extinction on the evolution of many groups, including placental mammals, has been hotly debated. The fossil record suggests a sudden adaptive radiation of placentals immediately after the event, but several recent quantitative analyses have reconstructed no significant increase in either clade origination rates or rates of character evolution in the Palaeocene. Here we use stochastic methods to date a recent phylogenetic analysis of Cretaceous and Palaeocene mammals and show that Placentalia likely originated in the Late Cretaceous, but that most intraordinal diversification occurred during the earliest Palaeocene. This analysis reconstructs fewer than 10 placental mammal lineages crossing the K–Pg boundary. Moreover, we show that rates of morphological evolution in the 5 Myr interval immediately after the K–Pg mass extinction are three times higher than background rates during the Cretaceous. These results suggest that the K–Pg mass extinction had a marked impact on placental mammal diversification, supporting the view that an evolutionary radiation occurred as placental lineages invaded new ecological niches during the Early Palaeocene.

Download Full-text

Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda

Genome Biology and Evolution ◽

10.1093/gbe/evz121 ◽

2019 ◽

Vol 11 (7) ◽

pp. 1797-1812 ◽

Cited By ~ 6

Author(s):

Dong Zhang ◽

Hong Zou ◽

Cong-Jie Hua ◽

Wen-Xiang Li ◽

Shahid Mahboob ◽

...

Keyword(s):

Life Histories ◽

Phylogenetic Reconstruction ◽

Mitochondrial Genomes ◽

Data Sets ◽

Long Branch Attraction ◽

Mitochondrial Data ◽

Gc Skew ◽

Limited Applicability ◽

Phylogenetic Hypotheses ◽

Almost All

Abstract The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.

Download Full-text