scholarly journals Mammal madness: is the mammal tree of life not yet resolved?

2016 ◽  
Vol 371 (1699) ◽  
pp. 20150140 ◽  
Author(s):  
Nicole M. Foley ◽  
Mark S. Springer ◽  
Emma C. Teeling
Keyword(s):  
Comparative Studies ◽  
Common Ancestor ◽  
Divergence Time ◽  
Tree Of Life ◽  
Phylogenetic Studies ◽  
Molecular Studies ◽  
Molecular Phylogenetic ◽  
High Level

Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90–110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position and divergence time of the root of placental mammals, and certain ‘hard nodes’ such as the Laurasiatheria polytomy and Paenungulata that seem impossible to resolve. Here, we explore recent consensus and conflict among mammalian phylogenetic studies and explore the reasons for the remaining conflicts. The question of whether the mammal tree of life is or can be ever resolved is also addressed.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

scholarly journals Colonization and diversification of Galápagos terrestrial fauna: a phylogenetic and biogeographical synthesis

2008 ◽  
Vol 363 (1508) ◽  
pp. 3347-3361 ◽  
Author(s):  
Christine E Parent ◽  
Adalgisa Caccone ◽  
Kenneth Petren
Keyword(s):  
Natural History ◽  
Comparative Studies ◽  
Oceanic Islands ◽  
Habitat Specialization ◽  
Geological History ◽  
Galápagos Islands ◽  
Evolutionary Processes ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Geological Formation

Remote oceanic islands have long been recognized as natural models for the study of evolutionary processes involved in diversification. Their remoteness provides opportunities for isolation and divergence of populations, which make islands remarkable settings for the study of diversification. Groups of islands may share a relatively similar geological history and comparable climate, but their inhabitants experience subtly different environments and have distinct evolutionary histories, offering the potential for comparative studies. A range of organisms have colonized the Galápagos Islands, and various lineages have radiated throughout the archipelago to form unique assemblages. This review pays particular attention to molecular phylogenetic studies of Galápagos terrestrial fauna. We find that most of the Galápagos terrestrial fauna have diversified in parallel to the geological formation of the islands. Lineages have occasionally diversified within islands, and the clearest cases occur in taxa with very low vagility and on large islands with diverse habitats. Ecology and habitat specialization appear to be critical in speciation both within and between islands. Although the number of phylogenetic studies is continuously increasing, studies of natural history, ecology, evolution and behaviour are essential to completely reveal how diversification proceeded on these islands.

scholarly journals Mapping the Tree of Life: Progress and Prospects

2009 ◽  
Vol 73 (4) ◽  
pp. 565-576 ◽  
Author(s):  
Norman R. Pace
Keyword(s):  
Tree Of Life ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Phylogenetic Structure ◽  
Microbial Identification ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Sequence Representation ◽  
Rrna Sequences ◽  
Natural Way

SUMMARY The intent of this article is to provide a critical assessment of our current understanding of life's phylogenetic diversity. Phylogenetic comparison of gene sequences is a natural way to identify microorganisms and can also be used to infer the course of evolution. Three decades of molecular phylogenetic studies with various molecular markers have provided the outlines of a universal tree of life (ToL), the three-domain pattern of archaea, bacteria, and eucarya. The sequence-based perspective on microbial identification additionally opened the way to the identification of environmental microbes without the requirement for culture, particularly through analysis of rRNA gene sequences. Environmental rRNA sequences, which now far outnumber those from cultivars, expand our knowledge of the extent of microbial diversity and contribute increasingly heavily to the emerging ToL. Although the three-domain structure of the ToL is established, the deep phylogenetic structure of each of the domains remains murky and sometimes controversial. Obstacles to accurate inference of deep phylogenetic relationships are both systematic, in molecular phylogenetic calculations, and practical, due to a paucity of sequence representation for many groups of organisms.

scholarly journals A synthesis tree of the Copepoda: integrating phylogenetic and taxonomic data reveals multiple origins of parasitism

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12034
Author(s):  
James P. Bernot ◽  
Geoffrey A. Boxshall ◽  
Keith A. Crandall
Keyword(s):  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Copepod Species ◽  
Taxon Sampling ◽  
Multiple Origins ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Parasitic Lifestyle ◽  
Freshwater Plankton ◽  
Species Taxon

The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine metazoans, mostly as parasites. Unfortunately, our understanding of copepod evolutionary relationships is relatively limited in part because of their extremely divergent morphology, sparse taxon sampling in molecular phylogenetic analyses, a reliance on only a handful of molecular markers, and little taxonomic overlap between phylogenetic studies. Here, a synthesis tree method is used to integrate published phylogenies into a more comprehensive tree of copepods by leveraging phylogenetic and taxonomic data. A literature review in this study finds fewer than 500 species of copepods have been sampled in molecular phylogenetic studies. Using the Open Tree of Life platform, those taxa that have been sampled in previous phylogenetic studies are grafted together and combined with the underlying copepod taxonomic hierarchy from the Open Tree of Life Taxonomy to make a synthesis phylogeny of all copepod species. Taxon sampling with respect to molecular phylogenetic analyses is reviewed for all orders of copepods and shows only 3% of copepod species have been sampled in phylogenetic studies. The resulting synthesis phylogeny reveals copepods have transitioned to a parasitic lifestyle on at least 14 occasions. We examine the underlying phylogenetic, taxonomic, and natural history data supporting these transitions to parasitism; review the species diversity of each parasitic clade; and identify key areas for further phylogenetic investigation.

Transfer of the Kobresia taxa of the flora of Russia and adjacent countries to the genus Carex (Cyperaceae)

2020 ◽  
pp. 125-129
Author(s):  
D. G. Melnikov ◽  
L. I. Krupkina
Keyword(s):  
International Collaboration ◽  
Morphological Characters ◽  
Published Data ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
New Nomenclatural Combinations

Based on the published data of molecular phylogenetic studies of the tribe Cariceae Dumort. genera (Cyperaceae), obtained by an international collaboration (The Global Carex Group, 2016; et al.), and morphological characters of the genera (Kukkonen, 1990; and others), new nomenclatural combinations and replacement names in the genus Carex L. are published for 11 species, one subspecies and two sections previously included in the genus Kobresia Willd.

Systematics and evolution of Lentibulariaceae: III. Utricularia

2018 ◽  
Author(s):  
Richard W. Jobson ◽  
Paulo C. Baleeiro ◽  
Cástor Guisande
Keyword(s):  
Gene Flow ◽  
Species Diversity ◽  
Population Level ◽  
Oceanic Islands ◽  
Vulnerable Species ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic

Utricularia is a morphologically and ecologically diverse genus currently comprising more than 230 species divided into three subgenera—Polypompholyx, Utricularia, and Bivalvaria—and 35 sections. The genus is distributed worldwide except on the poles and most oceanic islands. The Neotropics has the highest species diversity, followed by Australia. Compared to its sister genera, Utricularia has undergone greater rates of speciation, which are linked to its extreme morphological flexibility that has resulted in the evolution of habitat-specific forms: terrestrial, rheophytic, aquatic, lithophytic, and epiphytic. Molecular phylogenetic studies have resolved relationships for 44% of the species across 80% of the sections. Scant data are available for phylogeography or population-level processes such as gene flow, hybridization, or pollination. Because nearly 90% of the species are endemics, data are urgently needed to determine how to protect vulnerable species and their habitats.

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

Zootaxa ◽  
2009 ◽  
Vol 2107 (1) ◽  
pp. 41-52 ◽  
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.

scholarly journals Mechanisms of Dinucleotide Repeat Instability in Escherichia coli

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 533-542
Author(s):  
Marc Bichara ◽  
Isabelle Pinet ◽  
Sylvie Schumacher ◽  
Robert P P Fuchs
Keyword(s):  
Escherichia Coli ◽  
Mismatch Repair ◽  
Genetic Instability ◽  
Positional Cloning ◽  
Dinucleotide Repeats ◽  
Disease Pathogenesis ◽  
Complementary Sequence ◽  
Phylogenetic Studies ◽  
High Level

Abstract The high level of polymorphism of microsatellites has been used for a variety of purposes such as positional cloning of genes associated with diseases, forensic medicine, and phylogenetic studies. The discovery that microsatellites are associated with human diseases, not only as markers of risk but also directly in disease pathogenesis, has triggered a renewed interest in understanding the mechanism of their instability. In this work we have investigated the role of DNA replication, long patch mismatch repair, and transcription on the genetic instability of all possible combinations of dinucleotide repeats in Escherichia coli. We show that the (GpC) and (ApT) self-complementary sequence repeats are the most unstable and that the mode of replication plays an important role in their instability. We also found that long patch mismatch repair is involved in avoiding both short deletion and expansion events and also in instabilities resulting from the processing of bulges of 6 to 8 bp for the (GpT/ApC)- and (ApG/CpT)-containing repeats. For each dinucleotide sequence repeat, we propose models for instability that involve the possible participation of unusual secondary structures.

scholarly journals Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

2021 ◽  
Vol 7 (12) ◽  
pp. eabe2741
Author(s):  
Paschalia Kapli ◽  
Paschalis Natsidis ◽  
Daniel J. Leite ◽  
Maximilian Fursman ◽  
Nadia Jeffrie ◽  
...  
Keyword(s):  
Systematic Error ◽  
Tree Reconstruction ◽  
Simulation Experiments ◽  
Animal Evolution ◽  
Phylogenetic Studies ◽  
Branch Lengths ◽  
Molecular Phylogenetic ◽  
Common Ancestors

The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors—inadequate models, short internal branches, faster evolving genes, and unequal branch lengths—coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.

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

Phytotaxa ◽  
2016 ◽  
Vol 263 (2) ◽  
pp. 98 ◽  
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.

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.

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