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

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.

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Species delimitation, phylogenetic relationships, and two new species in the Cuscuta gracillima complex (Convolvulaceae)This paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽

10.1139/b08-030 ◽

2008 ◽

Vol 86 (7) ◽

pp. 670-681 ◽

Cited By ~ 9

Author(s):

Mihai Costea ◽

Fiona Aiston ◽

Saša Stefanović

Keyword(s):

New Species ◽

Phylogenetic Relationships ◽

Species Delimitation ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Conservation Status ◽

Special Issue ◽

Dna Sequence Data ◽

F Region ◽

Selection Of

Basic morphology, scanning electron microscopy, and DNA sequence data from the plastid trnL–F region and the nuclear internal transcribed spacer (ITS) regions were used to delimit the species of a recently circumscribed clade of Cuscuta (Convolvulaceae) and to investigate their phylogenetic relationships. This clade comprises the Cuscuta gracillima complex from Mexico, Central and northern South America, a group which is characterized by inflorescences that appear to emerge directly from the host stem. Eight lineages are recognized, with two of them described here as new species: Cuscuta punana Costea & Stefanović, sp. nov. from Ecuador and Cuscuta vandevenderi Costea & Stefanović, sp. nov. from Mexico. Cuscuta colombiana Yunck is redefined to include Cuscuta aristeguietae Yunck., and Cuscuta deltoidea Yunck. is broadened to encompass Cuscuta serruloba Yunck. A taxonomic treatment with an identification key, descriptions, and illustrations is provided; the biogeography and conservation status of the eight species are also discussed.

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

The Auk ◽

10.1093/auk/117.2.355 ◽

2000 ◽

Vol 117 (2) ◽

pp. 355-365 ◽

Cited By ~ 8

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.

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Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes

10.1101/440925 ◽

2018 ◽

Cited By ~ 3

Author(s):

Thomas L.P. Couvreur ◽

Andrew J. Helmstetter ◽

Erik J.M. Koenen ◽

Kevin Bethune ◽

Rita D. Brandão ◽

...

Keyword(s):

Phylogenetic Tree ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Gene Tree ◽

Nuclear Gene ◽

Species Level ◽

Molecular Dating ◽

Plant Family ◽

Two Samples ◽

Targeted Enrichment

AbstractTargeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 109 genera and ca. 2450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364 653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked eaually well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

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Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

Scientific Reports ◽

10.1038/s41598-021-84705-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bobby Lim-Ho Kong ◽

Hyun-Seung Park ◽

Tai-Wai David Lau ◽

Zhixiu Lin ◽

Tae-Jin Yang ◽

...

Keyword(s):

Hong Kong ◽

Comparative Analysis ◽

Phylogenetic Relationships ◽

Species Level ◽

The Other ◽

Trna Genes ◽

Protein Coding ◽

Chloroplast Genomes ◽

Plant Group ◽

Ilex Rotunda

AbstractIlex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.

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High Intraspecific Genetic Diversity ofNocardia brasiliensis, a Pathogen Responsible for Cutaneous Nocardiosis Found in France: Phylogenetic Relationships by Usingsodandhsp65Genes

BioMed Research International ◽

10.1155/2018/7314054 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10

Author(s):

D. Kosova-Maali ◽

E. Bergeron ◽

Y. Maali ◽

T. Durand ◽

J. Gonzalez ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Genetic Characterization ◽

Haplotype Diversity ◽

Species Level ◽

Genotype 1 ◽

Tropical Regions ◽

High Bootstrap ◽

Almost All ◽

A New Species ◽

Immunocompetent Patients

This study aims at genetic characterization and phylogenetic relationships ofNocardia brasiliensisfocusing by using housekeepingrrs,hsp65,andsodAgenes.N. brasiliensisis the species responsible for 80% of cases of actinomycetoma, one form of cutaneous nocardiosis which occurs mainly in tropical regions reaching immunocompetent patients in which the disease can lead to amputation. We analyze 36 indigenous cases ofN. brasiliensisthat happened in France. Phylogenetic analysis targetingrrsgene showed no robustness at phylogenetic nodes level. However, the use of a concatenation ofhsp65andsodAgenes showed that the tested strains surprisingly ranked in 3 well-defined genotypes. Genotypes 2 and 3 were phylogenetically closer to each other and both diverged from genotype 1 sustained by a high bootstrap of 81%. This last genotype hosts all the cases of pulmonary forms (3), the sole cerebral form, and almost all the cases of immunocompromised patients (3 out of 4). Moreover, excepting one of them, all the strains belonging to this group present a susceptibility to imipenem which is not the case in the other genotypes that rarely count among them strains being susceptible to this drug. The haplotype diversity (Hd) ofhsp65(0.927) andsodA(0.885) genes was higher than that ofrrs(0.824). For this gene, we obtained 16 polymorphic sites whereas, forhsp65andsodAgenes, up to 27 and 29 were identified, respectively. This study reveals that these two genes have an important genetic discriminatory power for the evaluation of the intraspecies genetic variability ofN. brasiliensisand they may be useful for identification purposes at species level. This study also reveals the possible existence of a new species harbored by genotype 1.

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Morphological and molecular evidence places Maronina into synonymy with Protoparmelia (Ascomycota: Lecanorales)

The Lichenologist ◽

10.1017/s0024282911000284 ◽

2011 ◽

Vol 43 (6) ◽

pp. 561-567 ◽

Cited By ~ 15

Author(s):

K. PAPONG ◽

G. KANTVILAS ◽

H. T. LUMBSCH

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Distinct Species ◽

Genetic Distances ◽

Molecular Evidence ◽

New Combinations ◽

Secondary Chemistry ◽

Phenotypic Characters ◽

Dna Sequence Data ◽

Phylogenetic Placement

AbstractThe phylogenetic placement of the genus Maronina was studied, based chiefly on phenotypic characters such as thallus colour and anatomy, secondary chemistry, the anatomy of the excipulum and the ascus-type. DNA sequence data of mitochondrial and nuclear ribosomal loci from some of the species support the hypothesis that Maronina is nested within Protoparmelia. Hence, Maronina is reduced to synonymy with Protoparmelia. Comparison of genetic distances suggests that the two varieties within M. orientalis should be regarded as distinct species. Consequently, the new combinations Protoparmelia australiensis (Hafellner & R. W. Rogers) Kantvilas et al., P. corallifera (Kantvilas & Papong) Kantvilas et al., P. hesperia (Kantvilas & Elix) Kantvilas et al., P. multifera (Nyl.) Kantvilas et al., and P. orientalis (Kantvilas & Papong) Kantvilas et al. are proposed.

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Novel Comprehensive Molecular and Ecological Study Introducing Coastal Mud Shrimp (Solenocera Crassicornis) Recorded at the Gulf of Suez, Egypt

Journal of Marine Science and Engineering ◽

10.3390/jmse9010009 ◽

2020 ◽

Vol 9 (1) ◽

pp. 9

Author(s):

Eman M. Abbas ◽

Fawzia S. Ali ◽

Mohammed G. Desouky ◽

Mohamed Ashour ◽

Ahmed El-Shafei ◽

...

Keyword(s):

Molecular Identification ◽

Phylogenetic Relationships ◽

Genetic Distances ◽

Larval Rearing ◽

Gulf Of Suez ◽

Commercial Catch ◽

Monthly Total ◽

Wet Weight ◽

Commercially Important ◽

The Relationship

Solenocera crassicornis is a commercially important shrimp of the Solenoceridae family. The current study investigated the morphology, molecular identification, phylogenetic relationships, and population dynamics of S. crassicornis in Egypt. Samples were collected monthly (total, 1722; male = 40.19%, wet weight, 0.89–10.77 g; female = 59.81%, wet weight, 1.55–19.24 g) from Al-Attaka commercial catch in the Gulf of Suez in the Red Sea. Two barcode markers, 18S rRNA and cytochrome c oxidase subunit I (COI), were used for molecular identification. COI partial sequences were used to construct the phylogenetic relationships among different species of genus Solenocera and to infer the origin of the studied Solenocera crassicornis. The applied molecular markers successfully identified the studied species to the species level. The genetic distances among S. crassicornis sequences from different countries revealed the Indo-West Pacific origin of S. crassicornis. The relationship between total length (TL) and total weight (TW) was TW = 0.035TL2.275 and r2 = 0.805 for males and TW = 0.007TL3.036 and r2 = 0.883 for females, indicating that females were heavier than males. Despite its social and economic relevance in the area, information on the hatching, larval rearing, and farming of S. crassicornis is scarce and requires future studies under Egyptian conditions.

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Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000400007 ◽

2000 ◽

Vol 23 (4) ◽

pp. 739-743 ◽

Cited By ~ 1

Author(s):

Mariana Pires de Campos Telles ◽

José Alexandre Felizola Diniz-Filho

Keyword(s):

Stochastic Process ◽

Genetic Divergence ◽

Isolation By Distance ◽

Genetic Distances ◽

Small Sample ◽

Group Method ◽

Gene Frequencies ◽

Exponential Relationship ◽

Local Populations ◽

Pair Group

An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a relatively small number of local populations, the correlogram profiles varied considerably, with Manhattan distances greater than those defined by other simulation studies. This method allows one to establish a range of correlogram profiles under the same stochastic process of spatial divergence, thereby avoiding the use of unnecessary explanations of genetic divergence based on other microevolutionary processes.

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Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽

10.1515/mammalia-2017-0081 ◽

2019 ◽

Vol 83 (2) ◽

pp. 180-189 ◽

Cited By ~ 2

Author(s):

Adam W. Ferguson ◽

Houssein R. Roble ◽

Molly M. McDonough

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Alternative Hypothesis ◽

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Sister Relationship ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Molecular Phylogenetic ◽

Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

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Paracarphalea, a new genus of the coffee family segregated from the Malagasy endemic genus Carphalea (Rubiaceae, Rubioideae, Knoxieae)

Phytotaxa ◽

10.11646/phytotaxa.263.2.2 ◽

2016 ◽

Vol 263 (2) ◽

pp. 98 ◽

Cited By ~ 1

Author(s):

JULIA FERM ◽

JESPER KÅREHED ◽

BIRGITTA BREMER ◽

SYLVAIN G. RAZAFIMANDIMBISON

Keyword(s):

Bayesian Methods ◽

Type Species ◽

New Genus ◽

Sequence Data ◽

Conservation Status ◽

Endemic Genus ◽

Phylogenetic Studies ◽

Molecular Phylogenetic ◽

Nuclear Its ◽

Iucn Criteria

The Malagasy genus Carphalea (Rubiaceae) consists of six species (C. angulata, C. cloiselii, C. kirondron, C. linearifolia, C. madagascariensis, C. pervilleana) of shrubs or small trees and is recognizable by a distinctly lobed calyx, 2(–4)-locular ovaries, each locule with several ovules on a rod-like stalk arising from the base of the locule, and indehiscent fruits. Carphalea linearifolia, rediscovered in 2010, has not previously been included in any Rubiaceae molecular phylogenetic studies. We re-investigated the monophyly of Carphalea using sequence data from chloroplast (rps16 and trnT-F) and nuclear (ITS and ETS) markers analysed with parsimony and Bayesian methods. Carphalea linearifolia forms a clade with C. cloiselii and the type species C. madagascariensis. This clade is sister to a clade consisting of the rest of the Carphalea species plus the genus Triainolepis. According to these results, the new genus Paracarphalea is here described to accommodate Carphalea angulata, C. kirondron, and C. pervilleana. The conservation status of Carphalea linearifolia is assessed as critically endangered according to IUCN criteria.

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