An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia

AbstractCambodia harbours a variety of human aboriginal populations that have scarcely been studied in terms of genetic diversity of entire mitochondrial genomes. Here we present the matrilineal gene pool of 299 Cambodian refugees from three different ethnic groups (Cham, Khmer, and Khmer Loeu) deriving from 16 Cambodian districts. After establishing a DNA-saving high-throughput strategy for mitochondrial whole-genome Sanger sequencing, a HaploGrep based workflow was used for quality control, haplogroup classification and phylogenetic reconstruction. The application of diverse phylogenetic algorithms revealed an exciting picture of the genetic diversity of Cambodia, especially in relation to populations from Southeast Asia and from the whole world. A total of 224 unique haplotypes were identified, which were mostly classified under haplogroups B5a1, F1a1, or categorized as newly defined basal haplogroups or basal sub-branches of R, N and M clades. The presence of autochthonous maternal lineages could be confirmed as reported in previous studies. The exceptional homogeneity observed between and within the three investigated Cambodian ethnic groups indicates genetic isolation of the whole population. Between ethnicities, genetic barriers were not detected. The mtDNA data presented here increases the phylogenetic resolution in Cambodia significantly, thereby highlighting the need for an update of the current human mtDNA phylogeny.

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Using mitochondrial genomes to infer phylogenetic relationships among the oldest extant winged insects (Palaeoptera)

10.1101/164459 ◽

2017 ◽

Cited By ~ 2

Author(s):

Sereina Rutschmann ◽

Ping Chen ◽

Changfa Zhou ◽

Michael T. Monaghan

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Phylogenetic Reconstruction ◽

Sister Group ◽

Data Matrix ◽

Mitochondrial Genomes ◽

Sampling Effort ◽

Reconstruction Method ◽

Marker Selection ◽

Phylogenetic Resolution

AbstractPhylogenetic relationships among the basal orders of winged insects remain unclear, in particular the relationship of the Ephemeroptera (mayflies) and the Odonata (dragonflies and damselflies) with the Neoptera. Insect evolution is thought to have followed rapid divergence in the distant past and phylogenetic reconstruction may therefore be susceptible to problems of taxon sampling, choice of outgroup, marker selection, and tree reconstruction method. Here we newly sequenced three mitochondrial genomes representing the two most diverse families of the Ephemeroptera, one of which is a basal lineage of the order. We then used an additional 90 insect mitochondrial genomes to reconstruct their phylogeny using Bayesian and maximum likelihood approaches. Bayesian analysis supported a basal Odonata hypothesis, with Ephemeroptera as sister group to the remaining insects. This was only supported when using an optimized data matrix from which rogue taxa and terminals affected by long-branch attraction were removed. None of our analyses supported a basal Ephemeroptera hypothesis or Ephemeroptera + Odonata as monophyletic clade sister to other insects (i.e., the Palaeoptera hypothesis). Our newly sequenced mitochondrial genomes of Baetis rutilocylindratus, Cloeon dipterum, and Habrophlebiodes zijinensis had a complete set of protein coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. Increased mayfly sampling, removal of problematic taxa, and a Bayesian phylogenetic framework were needed to infer phylogenetic relationships within the three ancient insect lineages of Odonata, Ephemeroptera, and Neoptera. Pruning of rogue taxa improved the number of supported nodes in all phylogenetic trees. Our results add to previous evidence for the Odonata hypothesis and indicate that the phylogenetic resolution of the basal insects can be resolved with more data and sampling effort.

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Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d221020 ◽

2021 ◽

Vol 22 (10) ◽

Author(s):

ABDUL BASITH ◽

Abinawanto Abinawanto ◽

ENI KUSRINI ◽

YASMAN YASMAN

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Phylogenetic Reconstruction ◽

Partial Sequence ◽

Diversity Analysis ◽

Epinephelus Coioides ◽

Substitution Model ◽

Genetic Diversity Analysis

Abstract. Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.

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Genetic discontinuity analysis of Collared Dove (Streptopelia decaocto)

Acta Agraria Debreceniensis ◽

10.34101/actaagrar/73/1618 ◽

2017 ◽

pp. 5-11

Author(s):

Zoltán Bagi ◽

Szilvia Kusza

Keyword(s):

Principal Component ◽

Dispersion Pattern ◽

Genetic Isolation ◽

Sample Collection ◽

Mitochondrial Coi ◽

Genetic Structure Of Populations ◽

Genetic Discontinuity ◽

Genetic Barriers ◽

Coi Sequences ◽

The Relationship

The Collared Dove conquered continent areas within a few decades. Causes and dispersion pattern of expansion has been investigated in several studies. However, the relationship between the geographic distribution and genetic structure of populations has not been researched. We used 152 individuals from 19 countries in this study. We analyze a 650 bp long mitochondrial COI sequences of each individuals. We were performed Spatial Autocorrelation Analysis, Principal Component Analysis and analysis of the genetic discontinuity in this study. Under 2500 km distance was a positive correlation between the genetic differentiation and different geographical areas. Hidden genetic barriers were found only Carpatian Basin. Could not be detected signs of genetic isolation in other regions. This will probably due to the unevenness of the sample collection, because these areas proportionally much fewer sequences were available. Therefore, is worth repeat this analysis after further sample collection, in the future.

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Multidrug-Resistant Salmonella enterica Serovar Rissen Clusters Detected in Azores Archipelago, Portugal

International Journal of Genomics ◽

10.1155/2019/1860275 ◽

2019 ◽

Vol 2019 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Leonor Silveira ◽

Miguel Pinto ◽

Joana Isidro ◽

Ângela Pista ◽

Patrícia Themudo ◽

...

Keyword(s):

Genetic Diversity ◽

Salmonella Enterica ◽

Genetic Relatedness ◽

Multidrug Resistant ◽

Reference Laboratory ◽

Multiple Sources ◽

Gastrointestinal Infections ◽

Azores Archipelago ◽

Starting Point ◽

Depth Analysis

Gastrointestinal infections caused by nontyphoidal Salmonella (NTS) remain one of the main causes of foodborne illness worldwide. Within the multiple existing Salmonella enterica serovars, the serovar Rissen is rarely reported, particularly as a cause of human salmonellosis. Between 2015 and 2017, the Portuguese National Reference Laboratory of Gastrointestinal Infections observed an increase in the number of clinical cases caused by multidrug-resistant (MDR) S. enterica serovar Rissen, particularly from the Azores archipelago. In the present study, we analyzed by whole genome sequencing (WGS) all clinical, animal, food, and environmental isolates received up to 2017 in the Portuguese Reference Laboratories. As such, through a wgMLST-based gene-by-gene analysis, we aimed to identify potential epidemiological clusters linking clinical and samples from multiple sources, while gaining insight into the genetic diversity of S. enterica serovar Rissen. We also investigated the genetic basis driving the observed multidrug resistance. By integrating 60 novel genomes with all publicly available serovar Rissen genomes, we observed a low degree of genetic diversity within this serovar. Nevertheless, the majority of Portuguese isolates showed high degree of genetic relatedness and a potential link to pork production. An in-depth analysis of these isolates revealed the existence of two major clusters from the Azores archipelago composed of MDR isolates, most of which were resistant to at least five antimicrobials. Considering the well-known spread of MDR between gastrointestinal bacteria, the identification of MDR circulating clones should constitute an alert to public health authorities. Finally, this study constitutes the starting point for the implementation of the “One Health” approach for Salmonella surveillance in Portugal.

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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.

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Rates of evolution and fossils in phylogenetic analysis: a computer simulation approach

The Paleontological Society Special Publications ◽

10.1017/s2475262200007000 ◽

1992 ◽

Vol 6 ◽

pp. 140-140

Author(s):

John P. Huelsenbeck ◽

David M. Hillis

Keyword(s):

Phylogenetic Analysis ◽

Wide Spectrum ◽

Phylogenetic Reconstruction ◽

Length Distribution ◽

Temporal Position ◽

Rate Of Evolution ◽

Rates Of Evolution ◽

Phylogenetic Resolution ◽

Main Determinants ◽

The Relationship

Whereas many studies have examined the performance of various character-data sets in phylogenetic analysis, little work has been done on the effect that various classes of taxa have on phylogenetic reconstruction. In particular, the “fossil versus living taxa” debate has concentrated mainly on the effects of fossils in reconstructing vertebrate and plant relationships. While this work has contributed to the understanding of the role that fossils play in systematics, a computer model clarifies the relationship among the main determinants of the fossil-taxa problem. In addition, simulations of phylogenies over a wide spectrum of evolutionary rates clarify the relative efficiencies of various tree-estimation procedures.In this study, computer generated phylogenies were used to examine the relationship between the temporal position and completeness of additional taxa in a phylogenetic analysis and the rate of evolution or, equivalently, the temporal scope of the phylogenetic problem. In the simulations, four fossil taxa of varying temporal position and completeness were added to an analysis that included four living taxa. Additional taxa varied in completeness (25%, 50%, 75%, and 100% completeness) and in temporal position (0%, 33%, 66%, and 100% of the distance from the ancestor to the living time plane). Fifty trees were generated each for low, low intermediate, high intermediate, and high rates of evolution or temporal scope. Because additional taxa that are 100% complete and 100% of the distance to the living time plane are equivalent to the addition of living taxa, this study directly compares the effects of addition of living versus fossil taxa in phylogenetic analysis.The importance of fossil taxa varied depending on their completeness and temporal position and on the rate of evolution under which the phylogeny was generated. In general, high completeness and temporal position near the ancestor of a clade improved phylogenetic resolution as measured by the percentage of the tree-length distribution that contains the real tree. Furthermore, the conditions of completeness and temporal position under which fossil taxa improved phylogenetic resolution over living taxa became less restrictive as the rate of evolution or the temporal scope of the tree increased.

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