scholarly journals Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars

2014 ◽  
Vol 5 ◽  
Author(s):  
Arwa Shahin ◽  
Marinus J. M. Smulders ◽  
Jaap M. van Tuyl ◽  
Paul Arens ◽  
Freek T. Bakker
Keyword(s):  
Genetic Divergence ◽  
Sequence Data ◽  
Allelic Sequence

The maritime shrew, Sorex maritimensis (Insectivora: Soricidae): a newly recognized Canadian endemic

2002 ◽  
Vol 80 (1) ◽  
pp. 94-99 ◽  
Author(s):  
Donald T Stewart ◽  
Neil D Perry ◽  
Luca Fumagalli
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Divergence ◽  
Common Ancestor ◽  
Sequence Data ◽  
Distinct Species ◽  
Sister Group ◽  
The Other ◽  
The Arctic ◽  
Base Pairs ◽  
Two Parameter

Previous morphological and cytological analyses have suggested that the arctic shrew (Sorex arcticus) as currently recognized may be two distinct species. Specifically, those studies demonstrated considerable differentiation between the putative subspecies S. a. maritimensis and one or both of the other two subspecies, S. a. arcticus and S. a. laricorum. Phylogenetic analysis of 546 base pairs of cytochrome b sequence data from 10 arctic shrews from across Canada indicates that maritimensis is the sister-group to arcticus + laricorum. Furthermore, there is considerable genetic divergence between maritimensis and the other two putative subspecies (~8–9%; Kimura's two-parameter distance). Given that maritimensis and arcticus + laricorum appear to be reciprocally monophyletic clades with considerable genetic divergence (i.e., greater than that between other recognized pairs of sister-species within the S. araneus–arcticus group), we propose that S. maritimensis be recognized as a distinct species. The proportion of third-position transversion substitutions between S. arcticus and S. maritimensis suggests that these two species shared a common ancestor approximately 2.4 million years ago.

scholarly journals Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

2021 ◽  
Author(s):  
Atal Saha ◽  
Anastasia Andersson ◽  
Sara Kurland ◽  
Naomi Keehnen ◽  
Verena Esther Kutschera ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Brown Trout ◽  
Genetic Divergence ◽  
Salmo Trutta ◽  
Sequence Data ◽  
Whole Genome ◽  
Similar Data ◽  
Genome Resequencing ◽  
Genome Wide ◽  
Whole Genome Resequencing

The sympatric existence of genetically distinct populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves only certain parts of the genome. We return to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (lactate dehydrogenase, LDH-A1) in brown trout in the small Lakes Bunnersjöarna, central Sweden. We use DNA from samples collected in the 1970s and a 96 SNP fluidigm array to verify the existence of the coexisting demes. We then apply whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; strong genetic divergence is observed with genome-wide FST=0.13. Nucleotide diversity is estimated to 0.0013 in Deme I but only 0.0005 in Deme II. Individual whole-genome resequencing of two individuals per deme suggests considerably higher inbreeding in Deme II vs. Deme I. Comparing with similar data from other lakes we find that the genome-wide divergence between the demes is similar to that between reproductively isolated populations. We located two genes for LDH-A and found divergence between the demes in a regulatory section of one of the genes, but we could not find a perfect fit between allozyme and sequence data. Our data demonstrate genome-wide divergence governed by genetic drift and diversifying selection, confirming reproductive isolation between the sympatric demes.

Genetic variation within the genus Macropostrongyloides (Nematoda: Strongyloidea) from Australian macropodid and vombatid marsupials

Parasitology ◽  
2019 ◽  
Vol 146 (13) ◽  
pp. 1673-1682 ◽  
Author(s):  
Tanapan Sukee ◽  
Ian Beveridge ◽  
Neil B. Chilton ◽  
Abdul Jabbar
Keyword(s):  
Genetic Variation ◽  
Genetic Divergence ◽  
Species Complex ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Rrna Gene ◽  
Similar Species ◽  
Geographical Regions

AbstractThe genetic variation and taxonomic status of the four morphologically-defined species of Macropostrongyloides in Australian macropodid and vombatid marsupials were examined using sequence data of the ITS+ region (=first and second internal transcribed spacers, and the 5.8S rRNA gene) of the nuclear ribosomal DNA. The results of the phylogenetic analyses revealed that Ma. baylisi was a species complex consisting of four genetically distinct groups, some of which are host-specific. In addition, Ma. lasiorhini in the common wombat (Vombatus ursinus) did not form a monophyletic clade with Ma. lasiorhini from the southern hairy-nosed wombat (Lasiorhinus latifrons), suggesting the possibility of cryptic (genetically distinct but morphologically similar) species. There was also some genetic divergence between Ma. dissimilis in swamp wallabies (Wallabia bicolor) from different geographical regions. In contrast, there was no genetic divergence among specimens of Ma. yamagutii across its broad geographical range or between host species (i.e. Macropus fuliginosus and M. giganteus). Macropostrongyloides dissimilis represented the sister taxon to Ma. baylisi, Ma. yamagutii and Ma. lasiorhini. Further morphological and molecular studies are required to assess the species complex of Ma. baylisi.

scholarly journals Phylogenetic Relationships of Micronesian White-Eyes Based on Mitochondrial Sequence Data

The Auk ◽  
2000 ◽  
Vol 117 (2) ◽  
pp. 355-365 ◽  
Author(s):  
Beth Slikas ◽  
Isaac B. Jones ◽  
Scott R. Derrickson ◽  
Robert C. Fleischer
Keyword(s):  
Genetic Divergence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Single Species ◽  
Additional Species ◽  
Data Set ◽  
Mitochondrial Sequence ◽  
Sister Relationships ◽  
Optimal Trees

Abstract Using mitochondrial sequence data, we estimated phylogenetic relationships and genetic divergence among selected species of white-eyes (Zosteropidae). We focused on taxa endemic to islands in Micronesia, specifically Zosterops conspicillatus, Z. semperi, Z. hypolais, Rukia oleaginea, and Cleptornis marchei. We also included in our data set five additional species of Zosterops from the Indo-Australian region and three species from Africa, as well as additional passerine outgroups. Our mitochondrial sequence data revealed substantial genetic divergence (5.7 to 7.3%) among Z. conspicillatus, Z. semperi, and Z. hypolais, three taxa that formerly were treated as a single species. In addition, a sequence divergence of 6.5 ± SE of 1.7% was found between the population of Z. conspicillatus from Rota and “conspecific” populations on Guam, Tinian, and Saipan. The distinctiveness of the Rota population suggests that this taxon should be recognized as a distinct species, a result that bears on the conservation of this population because it has been declining dramatically in recent years. All optimal trees based on analysis of the mitochondrial sequence data place Rukia oleaginea within the genus Zosterops. In all optimal trees, Cleptornis marchei positions as the sister taxon to a clade including all other zosteropids included in this study. The trees based on our data strongly contradict the traditional classification of Cleptornis as a honeyeater (family Meliphagidae). Our data cannot resolve with any confidence the sister relationships of the insular endemic white-eyes, although the optimal trees suggest multiple colonizations of Micronesia by more than one white-eye lineage.

scholarly journals Genetic divergence in Cork Oak based on cpDNA sequence data

2011 ◽  
Vol 5 (Suppl 7) ◽  
pp. P13 ◽  
Author(s):  
Joana Costa ◽  
Célia Miguel ◽  
Helena Almeida ◽  
Margarida M Oliveira ◽  
José A Matos ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
Sequence Data ◽  
Cork Oak ◽  
Cpdna Sequence

scholarly journals Molecular data suggest that Heteromys irroratus bulleri should be recognized as a species-level taxon

Therya ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 139-148
Author(s):  
Maria A. Gutiérrez-Costa ◽  
Francisco X. González-Cózatl ◽  
María Magdalena Ramírez-Martínez, ◽  
Luis Ignacio Iñiguez-Dávalos ◽  
Duke S. Rogers
Keyword(s):  
Genetic Divergence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Conservation Status ◽  
Biosphere Reserve ◽  
Genetic Distances ◽  
Species Level ◽  
Cranial Measurements ◽  
Sierra De Manantlán ◽  
Pocket Mouse

Recent collecting surveys in the Sierra de Manantlán Biosphere Reserve, Jalisco (México), uncovered the existence of a new population of the Mexican spiny pocket mouse, Heteromys irroratus.  Because the subspecies H. i. bulleri and H. i. jaliscensis occur nearby, our objective was to properly determine the taxonomic identity of the novel sample.  Also, we evaluate its distinctiveness, both in terms of genetic divergence and phylogenetic placement, relative to other members of H. irroratus.  Preliminary, we compared external and cranial measurements of recently collected individuals to those reported for representatives of the subspecies of H. irroratus occurring close by.  In addition, we examined levels of genetic differentiation and phylogenetic relationships, based on sequence data of the Cytochrome b, among this population and other members of H. irroratus, including an individual from Sierra de Juanacatlán, Jalisco, the type locality of H. i. bulleri. Phylogenetic relationships were estimated using Maximum Likelihood and Bayesian Inference methods and levels of genetic divergence were assessed employing Kimura-2-parameters genetic distances.  Samples from Sierra de Manantlán and Sierra de Juanacatlán were grouped together in a well-supported haplogroup and genetic distances between them were lower than < 1.02 %.  Our phylogenetic hypothesis shows that H. i. bulleri represents the sister group to all other samples of H. irroratus but that, genetically, is a very divergent lineage.  Distances values between H. i. bulleri to any of the other groups were > 10.05 %.  Comparison of external and cranial measurements showed that, in average, individuals from Sierra de Manantlán are larger than those of H. i. jaliscensis, but more similar in size to H. i. bulleri.  Our results show that the new population of the Mexican spiny pocket mouse from Sierra de Manantlán belongs to H. i. bulleri.  In addition, the phylogenetic separation and the high levels of genetic divergence of H. i. bulleri, relative to other members of H. irroratus, suggest that the first should be recognized as a species-level taxon.  Considering the scarce collecting records of H. i. bulleri and the known area of occurrence, that is very restricted, this taxon may warrant special conservation status.

Genetic divergence within the Drosophila mayaguana subcluster, a closely related triad of Caribbean species in the repleta species group

Hereditas ◽  
2002 ◽  
Vol 136 (3) ◽  
pp. 240-246 ◽  
Author(s):  
P. M. O'GRADY ◽  
C. M. DURANDO ◽  
W. B. HEED ◽  
M. WASSERMAN ◽  
W. ETGES ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
Species Group

GENETIC DIVERGENCE IN BABUL (ACACIA NILOTIKA)

2019 ◽  
Vol 25 (1) ◽  
Author(s):  
SUDHANSHU SHEKHAR ◽  
V.P. DWIVEDI ◽  
N.K. SRIVASTAVA
Keyword(s):  
Genetic Distance ◽  
Genetic Divergence ◽  
Acacia Nilotica ◽  
Hybridization Programme

Genetic divergence of Babul (Acacia nilotica) was assessed using Mahalanobis 0 statistics. They were grouped into eight clusters. Maximum genetic distance was recorded between III & VIII ciusters indicating greater distance between two clusters that showed maximum diversity amount the genotype and helps in hybridization programme.

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