scholarly journals Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

2021 ◽  
pp. 1-28
Author(s):  
Yoshimasa Kumekawa ◽  
Haruka Fujimoto ◽  
Osamu Miura ◽  
Ryo Arakawa ◽  
Jun Yokoyama ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Ryukyu Archipelago ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Polymerase Chain

Abstract Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

Molecular phylogeny and divergence time estimates in pennatulaceans (Cnidaria: Octocorallia: Pennatulacea)

2020 ◽  
Vol 84 (4) ◽  
pp. 317-330
Author(s):  
Francisco J. García-Cárdenas ◽  
Mónica Núñez-Flores ◽  
Pablo J. López-González
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Nuclear Markers ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Soft Bottoms

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times.

scholarly journals Mountains as Islands: Species Delimitation and Evolutionary History of the Ant-Loving Beetle Genus Panabachia (Coleoptera, Staphylinidae) from the Northern Andes

Insects ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 64
Author(s):  
Sofía Muñoz-Tobar ◽  
Michael Caterino
Keyword(s):  
Species Delimitation ◽  
Divergence Time ◽  
Morphological Characters ◽  
Protein Coding ◽  
Widespread Species ◽  
Mitochondrial Coi ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Putative Species ◽  
History Of

The ant-loving beetle genus Panabachia Park 1942 is a poorly studied beetle lineage from the new world tropics. We recently collected Panabachia from several previously unrecorded locations in the páramo biome of the high Ecuadorian Andes, with males exhibiting great morphological variation in the distribution of the foveae and depressions in the pronotum, as well as aspects of the male genitalia. Here, we employ phylogenetic and species delimitation methods with mitochondrial (COI) and nuclear protein-coding (wingless) gene sequences to examine the concordance of morphological characters and geography with hypothesized species boundaries. Three methods of species delimitation (bPTP, GMYC and Stacey) were used to estimate the number of species, and divergence times between putative species using molecular clock calibration. Phylogenetic analysis revealed two parallel radiations, and species delimitation analyses suggest there are between 17 and 22 putative species. Based on clade support and concordance across species delimitation methods we hypothesize 17 distinct clusters, with allopatric speciation consistent with most geographic patterns. Additionally, a widespread species appears to be present in northern páramo sites, and some sister species sympatry may indicate other diversification processes have operated on certain lineages of Panabachia. Divergence time estimates suggest that Panabachia originated in the Miocene, but most species analyzed diverged during the Pliocene and Pleistocene (5.3–0.11 Mya), contemporaneous with the evolution of páramo plant species.

Evolutionary history of trypanosomes from South American caiman (Caiman yacare) and African crocodiles inferred by phylogenetic analyses using SSU rDNA and gGAPDH genes

Parasitology ◽  
2008 ◽  
Vol 136 (1) ◽  
pp. 55-65 ◽  
Author(s):  
L. B. VIOLA ◽  
R. S. ALMEIDA ◽  
R. C. FERREIRA ◽  
M. CAMPANER ◽  
C. S. A. TAKATA ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Ssu Rdna ◽  
Tsetse Flies ◽  
South American ◽  
Data Set ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
History Of ◽  
Brazilian Pantanal

SUMMARYIn this study, using a combined data set of SSU rDNA and gGAPDH gene sequences, we provide phylogenetic evidence that supports clustering of crocodilian trypanosomes from the Brazilian Caiman yacare (Alligatoridae) and Trypanosoma grayi, a species that circulates between African crocodiles (Crocodilydae) and tsetse flies. In a survey of trypanosomes in Caiman yacare from the Brazilian Pantanal, the prevalence of trypanosome infection was 35% as determined by microhaematocrit and haemoculture, and 9 cultures were obtained. The morphology of trypomastigotes from caiman blood and tissue imprints was compared with those described for other crocodilian trypanosomes. Differences in morphology and growth behaviour of caiman trypanosomes were corroborated by molecular polymorphism that revealed 2 genotypes. Eight isolates were ascribed to genotype Cay01 and 1 to genotype Cay02. Phylogenetic inferences based on concatenated SSU rDNA and gGAPDH sequences showed that caiman isolates are closely related to T. grayi, constituting a well-supported monophyletic assemblage (clade T. grayi). Divergence time estimates based on clade composition, and biogeographical and geological events were used to discuss the relationships between the evolutionary histories of crocodilian trypanosomes and their hosts.

scholarly journals Molecular phylogenetic and phylogeography of Soriculus nigrescens in southwest China

2021 ◽  
Author(s):  
Haijun Jiang ◽  
Changkun Fu ◽  
Keyi Tang ◽  
Fengjun Li ◽  
Fei Xie ◽  
...  
Keyword(s):  
Southwest China ◽  
Ecological Niche Modeling ◽  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Species Status ◽  
Putative Species ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Different Altitudes

The Himalayan Shrew belongs to the genus Soriculus, which is a monotypic genus. We investigated the phylogeographic patterns, speciation, divergence time, and demographic history of Soriculus nigrescens in southwestern China. A total of 128 samples from 29 regions were analyzed for both mitochondrial and nuclear genes. Phylogenetic analyses of the concatenated mtDNA and nuDNA data revealed three highly divergent lineages within the S. nigrescens. One group represented subspecies S. n. minors, another group represented subspecies S. n. nigrescens, which is made up of two Clades A and B. The species delimitation analyses, based on two methods, supported the species status of the two Clades of S. n. nigrescens. In addtion, it was found that individuals at different altitudes in Motuo were divided into two Clades. Bayesian skyline plotting analyses and ecological niche modeling also supported demographic and range expansions during the LGM for S. n. nigrescens. We propose that S. n. nigrescens appears to be composed of two putative species, and S. n. minor should be elevated to species status. Our study also suggested that climate change since the Miocene periods and the uplift of the QTP may have resulted in the diversification and speciation of S. nigrescens.

scholarly journals Notes, outline and divergence times of Basidiomycota

2019 ◽  
Vol 99 (1) ◽  
pp. 105-367 ◽  
Author(s):  
Mao-Qiang He ◽  
Rui-Lin Zhao ◽  
Kevin D. Hyde ◽  
Dominik Begerow ◽  
Martin Kemler ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Divergence Times ◽  
Sequence Information ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
The Family ◽  
Life Mode ◽  
Species Type ◽  
Phylogeny And Evolution

AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

scholarly journals Mitogenomic phylogeny of Callithrix with special focus on human transferred taxa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Joanna Malukiewicz ◽  
Reed A. Cartwright ◽  
Nelson H. A. Curi ◽  
Jorge A. Dergam ◽  
Claudia S. Igayara ◽  
...  
Keyword(s):  
Atlantic Forest ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Complete Sequence ◽  
Special Focus ◽  
Brazilian Atlantic Forest ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Mtdna Haplotypes ◽  
Show Evidence

Abstract Background Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed here to reconstruct a robust Callithrix phylogeny and divergence time estimates, and identify the biogeographic origins of autochthonous and allochthonous Callithrix mitogenome lineages. We sequenced 49 mitogenomes from four species (C. aurita, C. geoffroyi, C. jacchus, C. penicillata) and anthropogenic hybrids (C. aurita x Callithrix sp., C. penicillata x C. jacchus, Callithrix sp. x Callithrix sp., C. penicillata x C. geoffroyi) via Sanger and whole genome sequencing. We combined these data with previously published Callithrix mitogenomes to analyze five Callithrix species in total. Results We report the complete sequence and organization of the C. aurita mitogenome. Phylogenetic analyses showed that C. aurita was the first to diverge within Callithrix 3.54 million years ago (Ma), while C. jacchus and C. penicillata lineages diverged most recently 0.5 Ma as sister clades. MtDNA clades of C. aurita, C. geoffroyi, and C. penicillata show intraspecific geographic structure, but C. penicillata clades appear polyphyletic. Hybrids, which were identified by phenotype, possessed mainly C. penicillata or C. jacchus mtDNA haplotypes. The biogeographic origins of mtDNA haplotypes from hybrid and allochthonous Callithrix were broadly distributed across natural Callithrix ranges. Our phylogenetic results also evidence introgression of C. jacchus mtDNA into C. aurita. Conclusion Our robust Callithrix mitogenome phylogeny shows C. aurita lineages as basal and C. jacchus lineages among the most recent within Callithrix. We provide the first evidence that parental mtDNA lineages of anthropogenic hybrid and allochthonous marmosets are broadly distributed inside and outside of the Atlantic Forest. We also show evidence of cryptic hybridization between allochthonous Callithrix and autochthonous C. aurita. Our results encouragingly show that further development of genomic resources will allow to more clearly elucidate Callithrix evolutionary relationships and understand the dynamics of Callithrix anthropogenic introductions into the Brazilian Atlantic Forest.

scholarly journals Striatiguttulaceae, a new pleosporalean family to accommodate Longicorpus and Striatiguttula gen. nov. from palms

MycoKeys ◽  
2019 ◽  
Vol 49 ◽  
pp. 99-129 ◽  
Author(s):  
Sheng-Nan Zhang ◽  
Kevin D. Hyde ◽  
E.B. Gareth Jones ◽  
Rajesh Jeewon ◽  
Ratchadawan Cheewangkoon ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
New Combination ◽  
Monophyletic Clade ◽  
Vast Array ◽  
Dna Sequence Data ◽  
Divergence Time Estimates ◽  
Mucilaginous Sheath ◽  
Time Estimates

Palms represent the most morphological diverse monocotyledonous plants and support a vast array of fungi. Recent examinations of palmicolous fungi in Thailand led to the discovery of a group of morphologically similar and interesting taxa. A polyphasic approach based on morphology, multi-gene phylogenetic analyses and divergence time estimates supports the establishment of a novel pleosporalean family Striatiguttulaceae, which diversified approximately 39 (20–63) MYA (crown age) and 60 (35–91) MYA (stem age). Striatiguttulaceae is characterized by stromata or ascomata with a short to long neck, trabeculate pseudoparaphyses and fusiform to ellipsoidal, 1–3-septate ascospores, with longitudinal striations and paler end cells, surrounded by a mucilaginous sheath. Multi-gene phylogenetic analysis showed that taxa of Striatiguttulaceae form a well-supported and distinct monophyletic clade in Pleosporales, and related to Ligninsphaeriaceae and Pseudoastrosphaeriellaceae. However, these families can be morphologically demarcated by the slit-like ascomata and extremely large ascospores in Ligninsphaeriaceae and the rather narrow fusiform ascospores in Pseudoastrosphaeriellaceae. Eight strains of Striatiguttulaceae formed two monophyletic sub-clades, which can be recognized as Longicorpusgen. nov. and Striatiguttulagen. nov. Morphologically, the genus Longicorpus can be differentiated from Striatiguttula by its elongated immersed ascomata and fusiform ascospores with relatively larger middle cells and paler end cells. Two new species Striatiguttulanypae and S.phoenicis, and one new combination, Longicorpusstriataspora are introduced with morphological details, and phylogenetic relationships are discussed based on DNA sequence data.

scholarly journals Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia

2017 ◽  
Author(s):  
Shingo Hosoishi ◽  
Kazuo Ogata
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Divergence Time ◽  
Morphological Characters ◽  
Systematic Position ◽  
Species Group ◽  
Morphological Evidence ◽  
Divergence Time Estimates ◽  
Close Relationship ◽  
Molecular Phylogenetic

Two distinct new species of the ant genus Crematogaster, C. khmerensis sp. nov. and C. pfeifferi sp. nov., are described from Cambodia and Malaysia, respectively. The two species are unique among Asian Crematogaster in that they have vertically directed propodeal spines, but their systematic positions have not been determined based on morphological characters alone. Molecular phylogenetic analysis of 89 Crematogaster taxon matrices previously published plus C. khmerensis sp. nov., using nuclear genes, reveals that C. khmerensis sp. nov. is nested within the Australo-Asian Crematogaster clade. Morphological assignment of the developed pronotal shoulders implies a close relationship between C. khmerensis sp. nov. and the C. tetracantha-group. Based on molecular and morphological evidence, we erect a new species group, C. khmerensis-group, to contain C. khmerensis sp. nov. and C. pfeifferi sp. nov. Divergence time estimates using MCMCTree shows that the root node of the C. khmerensis sp. nov. terminal is estimated to be of middle Miocene age at 15 million years old. The position of the C. khmerensis-group well supports the Oriental- to Australian-region dispersal history that has been proposed for the Australo-Asian Crematogaster clade.

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