Integrating Different Lines of Evidence to Establish a Novel Ascomycete Genus and Family (Anastomitrabeculia, Anastomitrabeculiaceae) in Pleosporales

A novel genus, Anastomitrabeculia, is introduced herein for a distinct species, Anastomitrabeculia didymospora, collected as a saprobe on dead bamboo culms from a freshwater stream in Thailand. Anastomitrabeculia is distinct in its trabeculate pseudoparaphyses and ascospores with longitudinally striate wall ornamentation. A new family, Anastomitrabeculiaceae, is introduced to accommodate Anastomitrabeculia. Anastomitrabeculiaceae forms an independent lineage basal to Halojulellaceae in Pleosporales and it is closely related to Neohendersoniaceae based on phylogenetic analyses of a combined LSU, SSU and TEF1α dataset. In addition, divergence time estimates provide further support for the establishment of Anastomitrabeculiaceae. The family diverged around 84 million years ago (MYA) during the Cretaceous period, which supports the establishment of the new family. The crown and stem age of Anastomitrabeculiaceae was also compared to morphologically similar pleosporalean families.

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Notes, outline and divergence times of Basidiomycota

Fungal Diversity ◽

10.1007/s13225-019-00435-4 ◽

2019 ◽

Vol 99 (1) ◽

pp. 105-367 ◽

Cited By ~ 32

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.

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Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications

PeerJ ◽

10.7717/peerj.8033 ◽

2019 ◽

Vol 7 ◽

pp. e8033

Author(s):

Siuli Mitra ◽

Vaishnavi Kunteepuram ◽

Klaus-Peter Koepfli ◽

Neha Mehra ◽

Wajeeda Tabasum ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Mitochondrial Protein ◽

Divergence Time ◽

Protein Coding ◽

Divergence Time Estimates ◽

Time Estimates ◽

Phylogenetic Implications ◽

The Family

The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.

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Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)

Zootaxa ◽

10.11646/zootaxa.2107.1.2 ◽

2009 ◽

Vol 2107 (1) ◽

pp. 41-52 ◽

Cited By ~ 5

Author(s):

CAROLINA M VOLOCH ◽

PABLO R FREIRE ◽

CLAUDIA A M RUSSO

Keyword(s):

Fossil Record ◽

Divergence Time ◽

Penaeid Shrimp ◽

Divergence Time Estimates ◽

Time Estimates ◽

Global Clock ◽

Late Tertiary ◽

The Family ◽

Molecular Studies ◽

Triassic Period

Fossil record of penaeids indicates that the family exists since the Triassic period, but extant genera appeared only recently in Tertiary strata. Molecular based divergence time estimates on the matter of penaeid radiation were never properly addressed, due to shortcomings of the global molecular clock assumptions. Here, we studied the diversification patterns of the family, uncovering, more specifically, a correlation between fossil and extant Penaeid fauna. For this, we have used a Bayesian framework that does not assume a global clock. Our results suggest that Penaeid genera originated between 20 million years ago and 43 million years ago, much earlier than expected by previous molecular studies. Altogether, these results promptly discard late Tertiary or even Quaternary hypotheses that presumed a major glaciations influence on the diversification patterns of the family.

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

The Canadian Entomologist ◽

10.4039/tce.2021.42 ◽

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.

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Mitogenomic phylogeny of Callithrix with special focus on human transferred taxa

BMC Genomics ◽

10.1186/s12864-021-07533-1 ◽

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.

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Taxonomy, Phylogeny, Molecular Dating and Ancestral State Reconstruction of Xylariomycetidae (Sordariomycetes)

10.21203/rs.3.rs-935829/v1 ◽

2021 ◽

Author(s):

Milan C. Samarakoon ◽

Kevin D Hyde ◽

Sajeewa S. N. Maharachchikumbura ◽

Marc Stadler ◽

E. B. Gareth Jones ◽

...

Keyword(s):

Divergence Time ◽

Molecular Dating ◽

Character State ◽

Ancestral State ◽

New Host ◽

State Reconstruction ◽

Divergence Time Estimates ◽

New Family ◽

Ancestral Character State ◽

Time Estimates

Abstract Xylariomycetidae ( Ascomycota ) is a highly diversified group with variable stromatic characters. Our research focused on inconspicuous stromatic xylarialean taxa from China, Italy, Russia, Thailand and the United Kingdom. Detailed morphological descriptions, illustrations and combined ITS-LSU- rpb 2- tub 2- tef 1 phylogenies revealed 38 taxa from our collections belonging to Amphisphaeriales and Xylariales . A new family ( Appendicosporaceae ), five new genera ( Magnostiolata , Melanostictus , Neoamphisphaeria , Nigropunctata and Paravamsapriya ), 27 new species ( Acrocordiella photiniicola , Allocryptovalsa sichuanensis , Amphisphaeria parvispora , Anthostomella lamiacearum , Apiospora guiyangensis , Ap. sichuanensis , Biscogniauxia magna , Eutypa camelliae , Helicogermslita clypeata , Hypocopra zeae , Magnostiolata mucida , Melanostictus longiostiolatus , Me. thailandicus , Nemania longipedicellata , Ne. delonicis , Ne. paraphysata , Ne. thailandensis , Neoamphisphaeria hyalinospora , Neoanthostomella bambusicola , Nigropunctata bambusicola , Ni. nigrocircularis , Ni. thailandica , Occultitheca rosae , Paravamsapriya ostiolata , Peroneutypa leucaenae , Seiridium italicum and Vamsapriya mucosa ) and seven new host/geographical records are introduced and reported. Divergence time estimates indicate that Delonicicolales diverged from Amphisphaeriales + Xylariales at 161 (123–197) MYA. Amphisphaeriales and Xylariales diverged 154 (117–190) MYA with a crown age of 127 (92–165) MYA and 147 (111–184) MYA, respectively. Appendicosporaceae ( Amphisphaeriales ) has a stem age of 89 (65–117) MYA. Ancestral character state reconstruction indicates that astromatic, clypeate ascomata with aseptate, hyaline ascospores that lack germ slits may probably be ancestral Xylariomycetidae having plant-fungal endophytic associations. The Amphisphaeriales remained mostly astromatic with common septate, hyaline ascospores. Stromatic variations may have developed mostly during the Cretaceous period. Brown ascospores are common in Xylariales , but they first appeared in Amphisphaeriaceae , Melogrammataceae and Sporocadaceae during the early Cretaceous. The ascospore germ slits appeared only in Xylariales during the Cretaceous after the divergence of Lopadostomataceae . Hyaline, filiform and apiospores may have appeared as separate lineages providing the basis to Xylariaceae , which may have diverged independently. The future classification of polyphyletic xylarialean taxa will not be based on stromatic variations, but the type of ring, the colour of the ascospores, and the presence or absence of the type of germ slit.

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

MycoKeys ◽

10.3897/mycokeys.49.30886 ◽

2019 ◽

Vol 49 ◽

pp. 99-129 ◽

Cited By ~ 5

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.

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

Scientia Marina ◽

10.3989/scimar.05067.28a ◽

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.

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Divergence time analyses suggest a Miocene origin of the narrow Amazonian endemic rheophytic Ceratolejeunea temnantha (Spruce) Reiner-Drehwald (Porellales, Lejeuneaceae)

Bryophyte Diversity and Evolution ◽

10.11646/bde.40.2.4 ◽

2018 ◽

Vol 40 (2) ◽

pp. 55

Author(s):

ADRIEL M. SIERRA ◽

JULIA BECHTELER ◽

DOMINGOS CARDOSO ◽

CHARLES E. ZARTMAN ◽

JUAN CARLOS VILLARREAL

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Original Description ◽

Phylogenetic Position ◽

Ecological Niches ◽

Divergence Time Estimates ◽

Potential Habitat ◽

The North ◽

Time Estimates ◽

Rio Negro

The recent rediscovery of the rheophytic endemic Ceratolejeunea temnantha ~130 years after its original description, on the upper Rio Negro in the Brazilian Amazon, has enabled the assessment of its enigmatic phylogenetic position, estimates of its divergence time, and updates on its distribution and potential habitat threats. Phylogenetic analyses strongly supported its placement in the genus Ceratolejeunea in a geographically disparate clade including a Madagascar endemic C. saroltae and two Neotropical taxa, C. confusa and C. caducifolia. Divergence time estimates date the clade’s stem age to the late Miocene (8.92 [HPD: 12.39–6.04] Ma) offering further evidence that the evolution of rheophytes in northern South America is correlated with the expansion of cryptogams into novel ecological niches promoted by dramatic landscape changes during the Miocene. Major geomorphological and hydrological transformations contributing to such diversification are most likely the changing dynamics of the inundated mega lake system to the establishment of the Amazon River due to the Andean orogeny and the subsequent cessation of marine influences in the north-western portion of the Basin. Until recently, this rheophyte of seasonally inundated black-water forests was only known from its type collection from the Rio Negro near São Gabriel da Cachoeira (Brazil) as described by Richard Spruce in 1884. These new collections extend the distribution of this rare narrow endemic to the middle Rio Uaupés, a tributary of the upper Rio Negro near the Columbian border.

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

Parasitology ◽

10.1017/s003118200800512x ◽

2008 ◽

Vol 136 (1) ◽

pp. 55-65 ◽

Cited By ~ 16

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.

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