scholarly journals Genetic differentiation of the southern population of the fathead minnow Pimephales promelas Rafinesque (Actinopterygii: Cyprinidae)

2018 ◽  
Author(s):  
Nayarit E Ballesteros-Nova ◽  
Rodolfo Pérez-Rodríguez ◽  
Rosa G Beltrán-López ◽  
Omar Domínguez-Domínguez
Keyword(s):  
Phylogenetic Trees ◽  
Pimephales Promelas ◽  
Phylogenetic Reconstruction ◽  
Genetic Distances ◽  
Tectonic Events ◽  
Phylogenetic Studies ◽  
Haplotype Networks ◽  
Species Complexes ◽  
Well Differentiated ◽  
Cabeza De Vaca

Background. Mexico is one of the most megadiverse countries in the world, with considerable reaches and endemicity in the diversity of fishes compared to other countries and regions. Recent phylogenetic studies in co-distributed species of widespread fishes, besides revealing a subestimation of species richness in the Mesa del Norte, in Mexico, suggest phylogenetic congruence in some species complexes. Previous morphological and meristic analyses concluded that at least three subspecies of Pimephales promelas exist in United States populations, suggesting that the richness in Pimephales could be underestimated. But no studies have examined the morphologic and genetic diversity in Southern populations of Pimephales promelas. We presented analyses of the genetic variation among P. promelas populations across its Southern distributional range. Methods. Phylogenetic reconstruction and genetic distances using cytochrome b and S7 sequences were done. Results. The results based on phylogenetic trees, species tree, genetic distances and haplotype networks revealed the existence of at least four well-differentiated lineages (Yaqui Lineage, Nazas+Conchos Lineage, Santa Maria Lineage and Casas Grandes Lineage). Discussion. The four well supported lineages found confirm Pimephales promelas as a species complex. Composition and distribution of these major lineages is also consistent with previous biogeographic hypothesis for other fishes in the region, supporting the fragmentation of the ancestral Lake Cabeza de Vaca, possibly due to the combined influence of tectonic events and increasing regional aridity, as well as events of interchange between basins via stream capture.

scholarly journals Genetic differentiation of the southern population of the fathead minnow Pimephales promelas Rafinesque (Actinopterygii: Cyprinidae)

2018 ◽  
Author(s):  
Nayarit E Ballesteros-Nova ◽  
Rodolfo Pérez-Rodríguez ◽  
Rosa G Beltrán-López ◽  
Omar Domínguez-Domínguez
Keyword(s):  
Phylogenetic Trees ◽  
Pimephales Promelas ◽  
Phylogenetic Reconstruction ◽  
Genetic Distances ◽  
Tectonic Events ◽  
Phylogenetic Studies ◽  
Haplotype Networks ◽  
Species Complexes ◽  
Well Differentiated ◽  
Cabeza De Vaca

Background. Mexico is one of the most megadiverse countries in the world, with considerable reaches and endemicity in the diversity of fishes compared to other countries and regions. Recent phylogenetic studies in co-distributed species of widespread fishes, besides revealing a subestimation of species richness in the Mesa del Norte, in Mexico, suggest phylogenetic congruence in some species complexes. Previous morphological and meristic analyses concluded that at least three subspecies of Pimephales promelas exist in United States populations, suggesting that the richness in Pimephales could be underestimated. But no studies have examined the morphologic and genetic diversity in Southern populations of Pimephales promelas. We presented analyses of the genetic variation among P. promelas populations across its Southern distributional range. Methods. Phylogenetic reconstruction and genetic distances using cytochrome b and S7 sequences were done. Results. The results based on phylogenetic trees, species tree, genetic distances and haplotype networks revealed the existence of at least four well-differentiated lineages (Yaqui Lineage, Nazas+Conchos Lineage, Santa Maria Lineage and Casas Grandes Lineage). Discussion. The four well supported lineages found confirm Pimephales promelas as a species complex. Composition and distribution of these major lineages is also consistent with previous biogeographic hypothesis for other fishes in the region, supporting the fragmentation of the ancestral Lake Cabeza de Vaca, possibly due to the combined influence of tectonic events and increasing regional aridity, as well as events of interchange between basins via stream capture.

scholarly journals Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets

2021 ◽  
Author(s):  
Daniele De Luca ◽  
Roberta Piredda ◽  
Diana Sarno ◽  
Wiebe H.C.F. Kooistra
Keyword(s):  
Gene Flow ◽  
Cryptic Species ◽  
Phylogenetic Trees ◽  
Distribution Patterns ◽  
Chaetoceros Curvisetus ◽  
Haplotype Networks ◽  
Species Complexes ◽  
Biogeographic Regions ◽  
Ocean Sampling ◽  
Marine Protists

AbstractMarine protists have traditionally been assumed to be lowly diverse and cosmopolitan. Yet, several recent studies have shown that many protist species actually consist of cryptic complexes of species whose members are often restricted to particular biogeographic regions. Nonetheless, detection of cryptic species is usually hampered by sampling coverage and application of methods (e.g. phylogenetic trees) that are not well suited to identify relatively recent divergence and ongoing gene flow. In this paper, we show how these issues can be overcome by inferring phylogenetic haplotype networks from global metabarcoding datasets. We use the Chaetoceros curvisetus (Bacillariophyta) species complex as study case. Using two complementary metabarcoding datasets (Ocean Sampling Day and Tara Oceans), we equally resolve the cryptic complex in terms of number of inferred species. We detect new hypothetical species in both datasets. Gene flow between most of species is absent, but no barcoding gap exists. Some species have restricted distribution patterns whereas others are widely distributed. Closely related taxa occupy contrasting biogeographic regions, suggesting that geographic and ecological differentiation drive speciation. In conclusion, we show the potential of the analysis of metabarcoding data with evolutionary approaches for systematic and phylogeographic studies of marine protists.

scholarly journals An evaluation of genetic distances for use with microsatellite loci.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 463-471 ◽  
Author(s):  
D B Goldstein ◽  
A Ruiz Linares ◽  
L L Cavalli-Sforza ◽  
M W Feldman
Keyword(s):  
Microsatellite Loci ◽  
Phylogenetic Reconstruction ◽  
Genetic Distances ◽  
Stepwise Mutation Model ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
The Difference ◽  
Nei's Distance ◽  
Infinite Alleles Model ◽  
Overall Reliability

Abstract Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

scholarly journals Optimal markers for the identification ofColletotrichumspecies

2019 ◽  
Author(s):  
Willie Anderson dos Santos Vieira ◽  
Priscila Alves Bezerra ◽  
Anthony Carlos da Silva ◽  
Josiene Silva Veloso ◽  
Marcos Paz Saraiva Câmara ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Species Complex ◽  
Plant Pathogens ◽  
Phylogenetic Signal ◽  
Intergenic Spacer ◽  
Internal Transcribed Spacers ◽  
Type Locus ◽  
Phylogenetic Studies ◽  
Fungal Plant Pathogens ◽  
Species Complexes

ABSTRACTColletotrichumis among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection ofColletotrichumisolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locusMAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.

scholarly journals Characterization of Five New Earthworm Mitogenomes (Oligochaeta: Lumbricidae): Mitochondrial Phylogeny of Lumbricidae

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 580
Author(s):  
Hongyi Liu ◽  
Yufeng Zhang ◽  
Wei Xu ◽  
Yu Fang ◽  
Honghua Ruan
Keyword(s):  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Morphological Characteristics ◽  
Molecular Techniques ◽  
Phylogenetic Studies ◽  
Octolasion Tyrtaeum ◽  
Eisenia Nordenskioldi ◽  
Novel Strategy

Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus, Dendrobaena octaedra, Eisenia andrei, Eisenia nordenskioldi, and Octolasion tyrtaeum) with lengths ranging from 14,977 to 15,715 were presented. Each mitogenome possessed a putative control region that resided between tRNA-Arg and tRNA-His. All of the PCGs were under negative selection according to the value of Ka/Ks. The phylogenetic trees supported the classification of Eisenia and Lumbricus; however, the trees based on cox1 did not. Through various comparisons, it was determined that cox1 fragments might be more suitable for molecular identification. These results lay the foundation for further phylogenetic studies on Lumbricidae.

Can the Cambrian explosion be inferred through molecular phylogeny?

Development ◽  
1994 ◽  
Vol 1994 (Supplement) ◽  
pp. 15-25
Author(s):  
Hervé Philippe ◽  
Anne Chenuil ◽  
André Adoutte
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Phylogenetic Reconstruction ◽  
Cambrian Explosion ◽  
Bootstrap Support ◽  
Time Interval ◽  
Short Time Interval ◽  
Data Set ◽  
Molecular Phylogenetic ◽  
Animal Phyla

Most of the major invertebrate phyla appear in the fossil record during a relatively short time interval, not exceeding 20 million years (Myr), 540-520 Myr ago. This rapid diversification is known as the `Cambrian explosion'. In the present paper, we ask whether molecular phylogenetic reconstruction provides confirmation for such an evolutionary burst. The expectation is that the molecular phylogenetic trees should take the form of a large unresolved multifurcation of the various animal lineages. Complete 18S rRNA sequences of 69 extant representatives of 15 animal phyla were obtained from data banks. After eliminating a major source of artefact leading to lack of resolution in phylogenetic trees (mutational saturation of sequences), we indeed observe that the major lines of triploblast coelomates (arthropods, molluscs, echinoderms, chordates...) are very poorly resolved i.e. the nodes defining the various clades are not supported by high bootstrap values. Using a previously developed procedure consisting of calculating bootstrap proportions of each node of the tree as a function of increasing amount of nucleotides (Lecointre, G., Philippe, H. Le, H. L. V. and Le Guyader, H. (1994) Mol. Phyl. Evol., in press) we obtain a more informative indication of the robustness of each node. In addition, this procedure allows us to estimate the number of additional nucleotides that would be required to resolve confidently the currently uncertain nodes; this number turns out to be extremely high and experimentally unfeasible. We then take this approach one step further: using parameters derived from the above analysis, assuming a molecular clock and using palaeontological dates for calibration, we establish a relationship between the number of sites contained in a given data set and the time interval that this data set can confidently resolve (with 95% bootstrap support). Under these assumptions, the presently available 18S rRNA database cannot confidently resolve cladogenetic events separated by less than about 40 Myr. Thus, at the present time, the potential resolution by the palaeontological approach is higher than that by the molecular one.

Ultrastructural Analysis of Mouthparts of Adult Horn Fly (Diptera: Muscidae) From the Brazilian Midwest Region

2020 ◽  
Vol 57 (5) ◽  
pp. 1447-1458 ◽  
Author(s):  
Fernando de Freitas Fernandes ◽  
Ana Cristina Bahia ◽  
Nágila Francinete Costa Secundino ◽  
Paulo Filemon Paolucci Pimenta
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Morphological Characteristics ◽  
Sense Organs ◽  
Horn Fly ◽  
Phylogenetic Studies ◽  
Midwest Region ◽  
Well Differentiated ◽  
Maxillary Palps ◽  
Scanning Electron

Abstract The ultrastructure of the mouthparts of Haematobia irritans (L.) was investigated by scanning electron microscopy. The morphological characteristics of the maxillary palps, labium (prementum and postmentum), labrum, hypopharynx, haustellum, and labellar lobes are described, as well as of the sensilla evidenced on all the surface of the mouthparts, and the set of different positions assumed by the mouth apparatus of this fly. Based on their morphology, 12 well-differentiated sensilla were identified, among three types of cuticular sensilla: trichoidea, coeloconica, and campaniformia. A slight sexual dimorphism in the sensilla patterns found in the mouthparts of H. irritans was evidenced. These observations are discussed with reference to the current literature on the functional morphology of sense organs of Insecta. These results could facilitate the recognition of the chemosensory sensilla by electrophysiological techniques, and foment future taxonomic and phylogenetic studies to better elucidate the evolution of Diptera, Muscomorpha.

scholarly journals A51 Genetic variability of small ruminant lentiviruses in sheep and goats from single-species flocks from Poland

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
Monika Olech ◽  
Jacek Kuźmak
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variability ◽  
Phylogenetic Trees ◽  
Small Ruminant ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Genetic Distances ◽  
Sheep And Goats ◽  
Viral Recombination ◽  
Species Flocks

Abstract Previous phylogenetic analyses of small ruminant lentivirus (SRLV) sequences found in Poland revealed the circulation of subtype A1 in both sheep and goats, subtypes B1 in goats, and subtypes B2, A12, and A13 in sheep only. This study aimed to analyze the genetic nature of SRLV circulating in sheep and goats from single-species flocks. In order to analyze the degree of genetic variability, the fragments of gag and env genes of 24 SRLV strains were amplified by PCR, cloned into plasmid vectors, sequenced, and consensus sequences were aligned to each other and to reference sequences available from GenBank. Phylogenetic analysis was performed using the Geneious tree-builder tool, and phylogenetic trees were constructed using Mr Bayes (using the general time reversible substitution model) within Geneious Pro 5.3. Pairwise genetic distances were calculated in MEGA 6. Phylogenetic analysis revealed that the strains were highly heterogeneous and represented ovine strains belonging to subtypes A12 and B2 and caprine strains grouped in subtypes B1, B2, A1, and A12. In addition, two novel subtypes, A16 and A17, were found in goats. The mean pairwise genetic distances of gag and env sequences of both clusters were above 15 per cent nucleotide divergence when compared to all other subtypes within group A, which is a criterion required to distinguish a new subtype. Additionally, the existence of two separated clusters was confirmed by high bootstrap values. Co-infections with strains belonging to different subtypes within A and B groups were detected in one sheep and four goats originating from four flocks. Since the co-infection with more than one lentivirus genotype offers an opportunity for viral recombination, the possible recombination events were tested based on RDP analysis. For all co-infected animals, no evidence of recombination was found within the gag gene; however, env sequences showed some recombination patterns in three samples. In conclusion, we have demonstrated extended genetic variability of SRLV in sheep and goats from Poland with the existence of co-infection and recombination events.

scholarly journals Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 288
Author(s):  
Nuria Macías-Hernández ◽  
Marc Domènech ◽  
Pedro Cardoso ◽  
Brent C. Emerson ◽  
Paulo Alexandre Vieira Borges ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Dna Barcode ◽  
Phylogenetic Reconstruction ◽  
Local Communities ◽  
Background Information ◽  
Ecological Processes ◽  
Phylogenetic Structure ◽  
Topological Constraint ◽  
Ecosystem Research

Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.

Ammonites phylogenetic analysis: state of the art and new prospects

2004 ◽  
Vol 175 (5) ◽  
pp. 507-512 ◽  
Author(s):  
Isabelle Rouget ◽  
Pascal Neigeet ◽  
Jean-Louis Dommergues
Keyword(s):  
Phylogenetic Reconstruction ◽  
Cladistic Analysis ◽  
Relative Weight ◽  
Morphological Characters ◽  
Quality Of Data ◽  
Phylogenetic Studies ◽  
Evolutionary Concepts ◽  
Phylogenetic Hypotheses ◽  
Definition Of ◽  
Iterative Evolution

Abstract Two main types of data are available to resolve phylogenies using fossils data: (1) stratigraphic ordering of taxa, and (2) morphological characters. In most phylogenetic studies dealing with ammonites, authors have given priority to the stratigraphic distribution of taxa. This practice is classically justified by the fact that the ammonite fossil record is frequently outstandingly good. In practice, the level of integration of stratigraphic and morphologic information in a single analysis depends on the confidence that authors have in the quality of data. Besides, many evolutionary concepts, which could differ over time and between authors (e.g. anagenesis, cladogenesis, iterative evolution), are added to these data to help infer phylogenetic relationships. As a result, phylogenetic hypotheses are based on eclectic methods which depend on the relative weight given to stratigraphic and morphologic information as well as on evolutionary concepts used. The validity of relationships proposed by previous authors is not dealt with in this paper. Instead, our goal is to draw attention to problems that these eclectic methods may cause, that is to say: (1) ammonites systematics is poorly formalised and (2) phylogenetic hypotheses as they are classically constructed are not rigorously testable. During the last 10 years, cladistic analysis has been applied to ammonites but is still unpopular among ammonitologists. However, studies have consistently shown that cladistics is not as unsuited a tool for ammonites phylogenetic reconstruction as is widely believed. Moreover, classical works open new questions about ammonite phylogeny and in particular, help to reappraise our view on the definition of morphological characters and their phylogenetic significance.

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