DNA barcoding and species delimitation: the Stylodrilus heringianus case (Annelida : Clitellata : Lumbriculidae)

2013 ◽  
Vol 27 (1) ◽  
pp. 118 ◽  
Author(s):  
Ainara Achurra ◽  
Christer Erséus
Keyword(s):  
Nuclear Genes ◽  
Pairwise Distance ◽  
Taxonomic Resolution ◽  
Secondary Contact ◽  
Internal Transcribed Spacer Region ◽  
Distance Method ◽  
Network Analyses ◽  
Histone 3 ◽  
Allopatric Divergence ◽  
Phylogeographic History

Individuals of the aquatic oligochaete species Stylodrilus heringianus Claparède, 1862 were collected across a part of this species’ distribution range in Sweden, Estonia, Great Britain and Spain to test whether they represent a single metapopulation or several separately evolving lineages. Using sequences of the barcoding gene cytochrome c oxidase subunit I (COI) and two nuclear genes (internal transcribed spacer region and histone 3), three different approaches were conducted: pairwise distance-method, Bayesian inference and network analysis. Both the COI phylogeny and network analyses were concordant in recovering six haplotype clusters, which showed a maximum genetic distance of 7.7% (K2P) among each other. Nevertheless, nuclear genes failed to confirm any lineage separation, and we conclude that the sampled specimens all belong to the same species. A phylogeographic history with allopatric divergence and secondary contact is suggested to explain this intraspecific pattern of mitochondrial divergence and nuclear non-divergence. The study shows that a mitochondrial single-locus approach can be problematic for the accurate delimitation of species, and we emphasise the need for nuclear genes as supplementary markers, when taxonomic resolution is assessed with COI barcodes.

scholarly journals Phylogenetic and Haplotype Network Analyses of Diaporthe eres Species in China Based on Sequences of Multiple Loci

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 179
Author(s):  
Chingchai Chaisiri ◽  
Xiangyu Liu ◽  
Yang Lin ◽  
Yanping Fu ◽  
Fuxing Zhu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Elongation Factor ◽  
Haplotype Network ◽  
Population Diversity ◽  
Plant Diseases ◽  
Broad Host Range ◽  
Internal Transcribed Spacer Region ◽  
Chinese Populations ◽  
Network Analyses ◽  
Haplotype Networks

Diaporthe eres is considered one of the most important causal agents of many plant diseases, with a broad host range worldwide. In this study, multiple sequences of ribosomal internal transcribed spacer region (ITS), translation elongation factor 1-α gene (EF1-α), beta-tubulin gene (TUB2), calmodulin gene (CAL), and histone-3 gene (HIS) were used for multi-locus phylogenetic analysis. For phylogenetic analysis, maximum likelihood (ML), maximum parsimony (MP), and Bayesian inferred (BI) approaches were performed to investigate relationships of D. eres with closely related species. The results strongly support that the D. eres species falls into a monophyletic lineage, with the characteristics of a species complex. Phylogenetic informativeness (PI) analysis showed that clear boundaries could be proposed by using EF1-α, whereas ITS showed an ineffective reconstruction and, thus, was unsuitable for speciating boundaries for Diaporthe species. A combined dataset of EF1-α, CAL, TUB2, and HIS showed strong resolution for Diaporthe species, providing insights for the D. eres complex. Accordingly, besides D. biguttusis, D. camptothecicola, D. castaneae-mollissimae, D. cotoneastri, D. ellipicola, D. longicicola, D. mahothocarpus, D. momicola, D. nobilis, and Phomopsis fukushii, which have already been previously considered the synonymous species of D. eres, another three species, D. henanensis, D. lonicerae and D. rosicola, were further revealed to be synonyms of D. eres in this study. In order to demonstrate the genetic diversity of D. eres species in China, 138 D. eres isolates were randomly selected from previous studies in 16 provinces. These isolates were obtained from different major plant species from 2006 to 2020. The genetic distance was estimated with phylogenetic analysis and haplotype networks, and it was revealed that two major haplotypes existed in the Chinese populations of D. eres. The haplotype networks were widely dispersed and not uniquely correlated to specific populations. Overall, our analyses evaluated the phylogenetic identification for D. eres species and demonstrated the population diversity of D. eres in China.

Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae, Madiinae)

2008 ◽  
Vol 33 (3) ◽  
pp. 589-597 ◽  
Author(s):  
Elizabeth A. Friar ◽  
Linda M. Prince ◽  
Jennifer M. Cruse-Sanders ◽  
Mitchell E. McGlaughlin ◽  
Charles A. Butterworth ◽  
...  
Keyword(s):  
Single Copy ◽  
Nuclear Genes ◽  
Hybrid Origin ◽  
Internal Transcribed Spacer Region ◽  
Hybrid Species ◽  
Cytogenetic Data ◽  
Molecular Phylogenetic ◽  
Distinct Lineage ◽  
Phylogenetic Hypotheses ◽  
Genomic Regions

Incongruence among different estimates of species relationships in plants, from different molecules, cytogenetic data, biogeographic data, morphological/anatomical data or other sources, has been used frequently as an indication of introgression, hybrid species origin, or chloroplast (cp) capture. In plants, these incongruences are most often seen between data derived from the nuclear vs. the cp genomes and the nuclear markers used for comparison usually have been from the nuclear ribosomal (nr) internal transcribed spacer region (ITS). The amount of genomic material shared between introgressing species can be highly variable. In some of these cases, other nuclear genomic regions have moved between species without leaving a signature on the nrITS. An example of well-supported phylogenetic incongruence is the placement of Dubautia scabra (DC.) D. D. Keck in the Hawaiian silversword alliance (HSA); evolutionary hypotheses for D. scabra based on molecular as opposed to cytogenetic data are strongly discordant. In this paper, we test these two conflicting phylogenetic hypotheses regarding the evolutionary relationships of Dubautia scabra using evidence from six low-copy nuclear genes, as well as multiple chloroplast noncoding regions and nrITS. The nrITS region is also examined for the presence of multiple copy types. Incongruence between inferred relationships based on nuclear chromosomal arrangements and molecular phylogenetic data from chloroplast DNA and nrITS is resolved in favor of a hypothesis of ancient hybridization rather than cytogenetic homoplasy involving dysploidy. Most single-copy nuclear genes track histories of D. scabra compatible with cytogenetic data whereas chloroplast and nrITS data track a common, different history that appears to reflect hybridization with a chromosomally distinct lineage that also occurs on Maui Nui and Hawai'i (the Big Island).

scholarly journals Implications of intraspecific behavioral interactions on the evolution of the mbuna cichlids of Lake Malawi and the effects of a small class intervention on a group of at-‐risk undergraduate students

2017 ◽  
Author(s):  
David Thomas Mellor
Keyword(s):  
At Risk ◽  
Reproductive Success ◽  
Female Choice ◽  
Female Preference ◽  
Lake Malawi ◽  
Secondary Contact ◽  
Small Scale ◽  
Male Reproductive Success ◽  
Allopatric Divergence ◽  
Male Contests

The rock-dwelling cichlids of Lake Malawi, the mbuna, are a model system of rapid, sympatric diversification of vertebrates. Though sexual selection has often been invoked to explain their radiation, the best evidence to date suggests that female choice and male-male interactions act to reinforce incipient, allopatric divergence upon secondary contact. First, I expand on the evidence previously gathered on male-male interactions at the inter-population level, by examining within-population behavioral patterns that could explain the diversification of this lineage. Specifically, I measure female preference for conspecific males who are in social isolation and those who are in groups of interacting males. I found that females show preference for males who score higher in male-male contests. In chapter two, I measure the effect of these male-male interactions on female choice and show that these interactions do affect female preference. By controlling the outcome of each male-male interaction, I show that female preference is affected by the male-male contests themselves. In chapter three, I measure the reflectance of brightly colored, territorial males and look for a correlation between color-similarity and level of aggression between two males. Males show more aggression towards similarly colored conspecific rivals than they do towards rivals who are more differently colored. In chapter four, I measure male reproductive success and the chromatic, behavioral, and territorial traits that affect it. Male color does predict reproductive success. Given my desire to integrate scholarship into every aspect of my academic career, I undertake an investigation on students who are at risk for leaving college because of low academic performance. I describe the social and psychological issues affecting the high rate of college attrition and the effects of a small scale class intervention on student retention, GPA, locus of control, and academic self-efficacy.

scholarly journals Allopatric Divergence, Secondary Contact, and Genetic Isolation in Wild Yeast Populations

2007 ◽  
Vol 17 (5) ◽  
pp. 407-411 ◽  
Author(s):  
Heidi A. Kuehne ◽  
Helen A. Murphy ◽  
Chantal A. Francis ◽  
Paul D. Sniegowski
Keyword(s):  
Secondary Contact ◽  
Genetic Isolation ◽  
Wild Yeast ◽  
Allopatric Divergence

scholarly journals Maintenance of Fungal Pathogen Species That Are Specialized to Different Hosts: Allopatric Divergence and Introgression through Secondary Contact

2010 ◽  
Vol 28 (1) ◽  
pp. 459-471 ◽  
Author(s):  
P. Gladieux ◽  
E. Vercken ◽  
M. C. Fontaine ◽  
M. E. Hood ◽  
O. Jonot ◽  
...  
Keyword(s):  
Fungal Pathogen ◽  
Secondary Contact ◽  
Allopatric Divergence

Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation

2019 ◽  
Vol 128 (1) ◽  
pp. 149-169 ◽  
Author(s):  
Drew R Schield ◽  
Blair W Perry ◽  
Richard H Adams ◽  
Daren C Card ◽  
Tereza Jezkova ◽  
...  
Keyword(s):  
Gene Flow ◽  
Demographic History ◽  
Secondary Contact ◽  
Tree Model ◽  
Crotalus Viridis ◽  
Species Complexes ◽  
Isolating Mechanisms ◽  
Allopatric Divergence ◽  
History Of ◽  
Study Population

Abstract The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus, Crotalus viridis, Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically.

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