Generic delimitation and phylogenetic uncertainty: an example from a group that has undergone an explosive radiation

Phylogenetic trees can provide a stable basis for a higher-level classification of organisms that reflects evolutionary relationships. However, some lineages have a complex evolutionary history that involves explosive radiation or hybridisation. Such histories have become increasingly apparent with the use of DNA sequence data for phylogeny estimation and explain, in part, past difficulties in producing stable morphology-based classifications for some groups. We illustrate this situation by using the example of tribe Mirbelieae (Fabaceae), whose generic classification has been fraught for decades. In particular, we discuss a recent proposal to combine 19 of the 25 Mirbelieae genera into a single genus, Pultenaea sens. lat., and how we might find stable and consistent ways to squeeze something as complex as life into little boxes for our own convenience.

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Reconstructing the past

Evolutionary Genetics ◽

10.1093/oso/9780198830917.003.0009 ◽

2019 ◽

pp. 214-249

Author(s):

Glenn-Peter Sætre ◽

Mark Ravinet

Keyword(s):

Phylogenetic Trees ◽

Evolutionary History ◽

Sequence Data ◽

Modern Human ◽

Evolutionary Relationships ◽

Human Populations ◽

Gene Trees ◽

Exciting Field ◽

History Of ◽

Life On Earth

How can genetics and genomics be used to understand the evolutionary history of organisms? This chapter focuses on such methods. First, the field of phylogenetics is introduced, as a way to visualize and quantify the evolutionary relationships among species. The chapter outlines how we go from aligning DNA sequence data to building gene trees and we argue that “tree-thinking” is fundamentally important for understanding evolution. The chapter also goes beyond phylogenetic trees to focus on phylogeography, i.e. the understanding of evolutionary relationships in a spatial context. More recently, the explosion of genomic data from ancient and modern human populations has made this an extremely exciting field which is transforming our understanding of our own evolutionary history. Before that, though, the chapter reviews how modern phylogenetics has arisen from historical efforts to classify life on Earth.

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Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

Mycological Progress ◽

10.1007/s11557-021-01706-8 ◽

2021 ◽

Vol 20 (7) ◽

pp. 911-927

Author(s):

Lucia Muggia ◽

Yu Quan ◽

Cécile Gueidan ◽

Abdullah M. S. Al-Hatmi ◽

Martin Grube ◽

...

Keyword(s):

Sequence Data ◽

Single Species ◽

Sister Group ◽

Asexual Propagation ◽

Dna Sequence Data ◽

Wide Range ◽

The Family ◽

Rock Inhabiting Fungi ◽

Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

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Phylogenetic relationships and generic delimitation in subtribe Arctotidinae (Asteraceae: Arctotideae) inferred by DNA sequence data from ITS and five chloroplast regions

American Journal of Botany ◽

10.3732/ajb.93.8.1222 ◽

2006 ◽

Vol 93 (8) ◽

pp. 1222-1235 ◽

Cited By ~ 15

Author(s):

R. J. McKenzie ◽

E. M. Muller ◽

A. K. W. Skinner ◽

P. O. Karis ◽

N. P. Barker

Keyword(s):

Dna Sequence ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Generic Delimitation ◽

Dna Sequence Data

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Traditional Infrageneric Classification of Gymnopilus Is Not Supported by Ribosomal DNA Sequence Data

Mycologia ◽

10.2307/3761920 ◽

2003 ◽

Vol 95 (6) ◽

pp. 1204 ◽

Cited By ~ 5

Author(s):

Laura Guzman-Davalos ◽

Gregory M. Mueller ◽

Joaquin Cifuentes ◽

Andrew N. Miller ◽

Anne Santerre

Keyword(s):

Dna Sequence ◽

Ribosomal Dna ◽

Sequence Data ◽

Infrageneric Classification ◽

Dna Sequence Data ◽

Ribosomal Dna Sequence

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INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720006001709 ◽

2006 ◽

Vol 04 (01) ◽

pp. 59-74 ◽

Cited By ~ 20

Author(s):

YING-JUN HE ◽

TRINH N. D. HUYNH ◽

JESPER JANSSON ◽

WING-KIN SUNG

Keyword(s):

Approximation Algorithms ◽

Phylogenetic Tree ◽

Phylogenetic Trees ◽

Evolutionary History ◽

Phylogenetic Network ◽

Evolutionary Relationships ◽

Large Set ◽

Tree Network ◽

History Of ◽

Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

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The generic classification of the Trochilini (Aves: Trochilidae): Reconciling taxonomy with phylogeny

Zootaxa ◽

10.11646/zootaxa.4353.3.1 ◽

2017 ◽

Vol 4353 (3) ◽

pp. 401 ◽

Cited By ~ 4

Author(s):

F. GARY STILES ◽

J. V. JR. REMSEN ◽

JIMMY A. MCGUIRE

Keyword(s):

New Genus ◽

Sequence Data ◽

Historical Review ◽

Genetic Data ◽

Zoological Nomenclature ◽

Tabular Form ◽

Dna Sequence Data ◽

The Family ◽

Traditional Classification

The generic nomenclature of the hummingbirds is unusually complicated. McGuire et al.’s (2014) recent phylogeny of the Trochilidae based on DNA sequence data has greatly clarified relationships within the family but conflicts strongly with the traditional classification of the family at the genus level, especially that of the largest and most recently derived clade, the Trochilini or “emeralds”. We recently presented a historical review of this classification and the generic modifications required by the Code of the International Commission on Zoological Nomenclature. Herein we present a revised generic classification of the Trochilini based upon McGuire et al.’s genetic data, while producing diagnosable generic groupings and preserving nomenclatural stability insofar as possible. However, this generic rearrangement has necessitated the resurrection of nine generic names currently considered synonyms, the synonymization of seven currently recognized genera and the creation of one new genus. The generic changes we recommend to the classification are drastic, and we summarize these in tabular form in comparison with the three most recent classifications of the Trochilini. Where appropriate, we outline alternatives to our proposed arrangement. The classification treats 110 species in 35 genera, including two species that remain unplaced for lack of genetic samples.

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Two new Chrysomyxa rust species on the endemic plant, Picea asperata in western China, and expanded description of C. succinea

Phytotaxa ◽

10.11646/phytotaxa.292.3.2 ◽

2017 ◽

Vol 292 (3) ◽

pp. 218 ◽

Cited By ~ 7

Author(s):

JING CAO ◽

CHENGMING TIAN ◽

YINGMEI LIANG ◽

CHONGJUAN YOU

Keyword(s):

Phylogenetic Trees ◽

Sequence Data ◽

Morphological Characters ◽

Western China ◽

Endemic Plant ◽

Internal Transcribed Spacer Region ◽

Dna Sequence Data ◽

Species Cluster ◽

Picea Asperata ◽

First Time

Two new rust species, Chrysomyxa diebuensis and C. zhuoniensis, on Picea asperata are recognized by morphological characters and DNA sequence data. A detailed description, illustrations, and discussion concerning morphologically similar and phylogenetically closely related species are provided for each species. From light and scanning electron microscopy observations C. diebuensis is characterized by the nailhead to peltate aeciospores, with separated stilt-like base. C. zhuoniensis differs from other known Chrysomyxa species in the annulate aeciospores with distinct longitudinal smooth cap at ends of spores, as well as with a broken, fissured edge. Analysis based on internal transcribed spacer region (ITS) partial gene sequences reveals that the two species cluster as a highly supported group in the phylogenetic trees. Correlations between the morphological and phylogenetic features are discussed. Illustrations and a detailed description are also provided for the aecia of C. succinea in China for the first time.

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Genome-scale DNA sequence data and the evolutionary history of placental mammals

Data in Brief ◽

10.1016/j.dib.2018.04.094 ◽

2018 ◽

Vol 18 ◽

pp. 1972-1975 ◽

Cited By ~ 7

Author(s):

Shaoyuan Wu ◽

Scott Edwards ◽

Liang Liu

Keyword(s):

Dna Sequence ◽

Evolutionary History ◽

Sequence Data ◽

Dna Sequence Data ◽

History Of ◽

Genome Scale

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Status of the New Zealand cave weta (Rhaphidophoridae) genera Pachyrhamma, Gymnoplectron and Turbottoplectron

Invertebrate Systematics ◽

10.1071/is09047 ◽

2010 ◽

Vol 24 (2) ◽

pp. 131 ◽

Cited By ~ 6

Author(s):

Lorraine D. Cook ◽

Steven A. Trewick ◽

Mary Morgan-Richards ◽

Peter M. Johns

Keyword(s):

Mitochondrial Dna ◽

New Zealand ◽

Sequence Data ◽

Taxonomic Revision ◽

Spatial Diversity ◽

Species Level ◽

Dna Sequence Data ◽

Poorly Differentiated ◽

Single Genus ◽

Endemic Genera

The New Zealand Rhaphidophoridae Walker, 1869 comprise 18 endemic genera (including 8 that are monotypic). Although there are many new species to be described, rationalisation at the genus level is also required due to inconsistencies in their current systematics. Even the largest and best known taxa, including those that occupy cave systems and are the most frequently encountered by people, require taxonomic revision. These cave weta include species assigned to three poorly differentiated genera, Pachyrhamma Brunner v. Wattenwyl, 1888, Gymnoplectron Hutton, 1897 and Turbottoplectron Salmon, 1948, that are best known from North Island New Zealand. We used mitochondrial DNA sequence data to examine their relationships using representatives of each genus. The results indicate that a single genus Pachyrhamma would be appropriate for all, as Gymnoplectron and Turbottoplectron nest phylogenetically within it. There are insufficient morphological, spatial or ecological reasons to justify retention of all three. However, we also note that species level diversity does not correlate with genetic or spatial diversity; some species are genetically well partitioned and widespread while others have narrow ranges in single cave systems and are closely related to one another.

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